From 129c5dfbfb721ecb3f6f8d4610e43dba18626744 Mon Sep 17 00:00:00 2001 From: Anubhav Jain Date: Tue, 6 Aug 2019 09:47:08 -0700 Subject: [PATCH] Update to v0.9.2 --- atomate/__init__.py | 2 +- ...ec8b7a278c8facb18e2385d9c54b5ddeb93f83.png | Bin 0 -> 966 bytes ...d137cf01c787ecda732761c3f95b0f65a6c3e9.png | Bin 0 -> 221 bytes ...b155c5e8565ef9b1c7fb856be369955109eea3.png | Bin 0 -> 460 bytes ...a4fe9c81dae83d151d1e9628cbd4239f37f9ac.png | Bin 0 -> 308 bytes ...450e1cb12e1bc543af59fccc656b613329b0fd.png | Bin 0 -> 471 bytes ...3a0496747e918d1a810978ae2ba791433377fe.png | Bin 0 -> 524 bytes ...70e68f407c20515867e86ce3c7f9b1d8f74616.png | Bin 0 -> 469 bytes ...2cf818704e858252c680ccf36abe9d6e03d168.png | Bin 0 -> 303 bytes ...163183fd5bb094b5dec6090d9a92b0481732f7.png | Bin 0 -> 384 bytes ...da3e2259c23a06d98be2ee457a29a8e1b73eeb.png | Bin 0 -> 467 bytes ...df63172953a1cc84d31c5fa7d1354eddacf567.png | Bin 0 -> 395 bytes .../_sources/atomate.common.firetasks.rst.txt | 26 +- 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diff --git a/docs/_images/math/b5df63172953a1cc84d31c5fa7d1354eddacf567.png b/docs/_images/math/b5df63172953a1cc84d31c5fa7d1354eddacf567.png new file mode 100644 index 0000000000000000000000000000000000000000..bae4f32f81c92bc83d85261029bfc14f3033112f GIT binary patch literal 395 zcmeAS@N?(olHy`uVBq!ia0vp^T0kts!VDzu9|>FmqznRlLR|m<{|{sm5A^RYs0OO$ zFA4GsW{}wb`|iv09wl=V)_*qYb|}xe0+iw`@Q5sCVBk9f!i-b3`J{n@&pcfmLnJOI zCp0ixN;La7FfxiH@El_iSop`&^C>rTI^*GI{;WJT@zN4uO-~{ki(Glu@bJu$Z^&wh zif~-?hu49zt(=EPM&6M}fsM;xjd()(gM<&M2?_tt9oQhFae&XLf}dG ``vasp_input_params`` in some cases (thanks to M. Horton for pointing out) diff --git a/docs/_sources/contributors.rst.txt b/docs/_sources/contributors.rst.txt index 18c663c56..0735c88f2 100644 --- a/docs/_sources/contributors.rst.txt +++ b/docs/_sources/contributors.rst.txt @@ -12,4 +12,4 @@ Contributions are provided by: * Brandon Bocklund, who led the atomate documentation effort, through the research group of Prof. Zi-Kiu Liu at Penn State. * Tess Smidt through the research group of Prof. Jeff Neaton at UC Berkeley. * Danny Broberg through the research group of Prof. Mark Asta at UC Berkeley. -* External contributors: specter119, M. Dias Costa, S. Torrisi, Max Dylla +* External contributors: specter119, M. Dias Costa, S. Torrisi, Max Dylla, Marnik Bercx diff --git a/docs/_static/basic.css b/docs/_static/basic.css index 104f076ae..c41d718e4 100644 --- a/docs/_static/basic.css +++ b/docs/_static/basic.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- basic theme. * - * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -231,6 +231,16 @@ a.headerlink { visibility: hidden; } +a.brackets:before, +span.brackets > a:before{ + content: "["; +} + +a.brackets:after, +span.brackets > a:after { + content: "]"; +} + h1:hover > a.headerlink, h2:hover > a.headerlink, h3:hover > a.headerlink, @@ -279,6 +289,12 @@ img.align-center, .figure.align-center, object.align-center { margin-right: auto; } +img.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + .align-left { text-align: left; } @@ -287,6 +303,10 @@ img.align-center, .figure.align-center, object.align-center { text-align: center; } +.align-default { + text-align: center; +} + .align-right { text-align: right; } @@ -358,6 +378,11 @@ table.align-center { margin-right: auto; } +table.align-default { + margin-left: auto; + margin-right: auto; +} + table caption span.caption-number { font-style: italic; } @@ -391,6 +416,16 @@ table.citation td { border-bottom: none; } +th > p:first-child, +td > p:first-child { + margin-top: 0px; +} + +th > p:last-child, +td > p:last-child { + margin-bottom: 0px; +} + /* -- figures --------------------------------------------------------------- */ div.figure { @@ -460,11 +495,57 @@ ol.upperroman { list-style: upper-roman; } +li > p:first-child { + margin-top: 0px; +} + +li > p:last-child { + margin-bottom: 0px; +} + +dl.footnote > dt, +dl.citation > dt { + float: left; +} + +dl.footnote > dd, +dl.citation > dd { + margin-bottom: 0em; +} + +dl.footnote > dd:after, +dl.citation > dd:after { + content: ""; + clear: both; +} + +dl.field-list { + display: flex; + flex-wrap: wrap; +} + +dl.field-list > dt { + flex-basis: 20%; + font-weight: bold; + word-break: break-word; +} + +dl.field-list > dt:after { + content: ":"; +} + +dl.field-list > dd { + flex-basis: 70%; + padding-left: 1em; + margin-left: 0em; + margin-bottom: 0em; +} + dl { margin-bottom: 15px; } -dd p { +dd > p:first-child { margin-top: 0px; } @@ -537,6 +618,12 @@ dl.glossary dt { font-style: oblique; } +.classifier:before { + font-style: normal; + margin: 0.5em; + content: ":"; +} + abbr, acronym { border-bottom: dotted 1px; cursor: help; diff --git a/docs/_static/doctools.js b/docs/_static/doctools.js index ffadbec11..b33f87fcb 100644 --- a/docs/_static/doctools.js +++ b/docs/_static/doctools.js @@ -4,7 +4,7 @@ * * Sphinx JavaScript utilities for all documentation. * - * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -87,14 +87,13 @@ jQuery.fn.highlightText = function(text, className) { node.nextSibling)); node.nodeValue = val.substr(0, pos); if (isInSVG) { - var bbox = span.getBBox(); var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); - rect.x.baseVal.value = bbox.x; + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; rect.y.baseVal.value = bbox.y; rect.width.baseVal.value = bbox.width; rect.height.baseVal.value = bbox.height; rect.setAttribute('class', className); - var parentOfText = node.parentNode.parentNode; addItems.push({ "parent": node.parentNode, "target": rect}); diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index 9f4d02579..8870cc3f0 100644 --- a/docs/_static/documentation_options.js +++ b/docs/_static/documentation_options.js @@ -1,296 +1,10 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '0.9.1', + VERSION: '0.9.2', LANGUAGE: 'None', COLLAPSE_INDEX: false, FILE_SUFFIX: '.html', HAS_SOURCE: true, SOURCELINK_SUFFIX: '.txt', - NAVIGATION_WITH_KEYS: false, - SEARCH_LANGUAGE_STOP_WORDS: ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"] -}; - - - -/* Non-minified version JS is _stemmer.js if file is provided */ -/** - * Porter Stemmer - */ -var Stemmer = function() { - - var step2list = { - ational: 'ate', - tional: 'tion', - enci: 'ence', - anci: 'ance', - izer: 'ize', - bli: 'ble', - alli: 'al', - entli: 'ent', - eli: 'e', - ousli: 'ous', - ization: 'ize', - ation: 'ate', - ator: 'ate', - alism: 'al', - iveness: 'ive', - fulness: 'ful', - ousness: 'ous', - aliti: 'al', - iviti: 'ive', - biliti: 'ble', - logi: 'log' - }; - - var step3list = { - icate: 'ic', - ative: '', - alize: 'al', - iciti: 'ic', - ical: 'ic', - ful: '', - ness: '' - }; - - var c = "[^aeiou]"; // consonant - var v = "[aeiouy]"; // vowel - var C = c + "[^aeiouy]*"; // consonant sequence - var V = v + "[aeiou]*"; // vowel sequence - - var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 - var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 - var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 - var s_v = "^(" + C + ")?" + v; // vowel in stem - - this.stemWord = function (w) { - var stem; - var suffix; - var firstch; - var origword = w; - - if (w.length < 3) - return w; - - var re; - var re2; - var re3; - var re4; - - firstch = w.substr(0,1); - if (firstch == "y") - w = firstch.toUpperCase() + w.substr(1); - - // Step 1a - re = /^(.+?)(ss|i)es$/; - re2 = /^(.+?)([^s])s$/; - - if (re.test(w)) - w = w.replace(re,"$1$2"); - else if (re2.test(w)) - w = w.replace(re2,"$1$2"); - - // Step 1b - re = /^(.+?)eed$/; - re2 = /^(.+?)(ed|ing)$/; - if (re.test(w)) { - var fp = re.exec(w); - re = new RegExp(mgr0); - if (re.test(fp[1])) { - re = /.$/; - w = w.replace(re,""); - } - } - else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1]; - re2 = new RegExp(s_v); - if (re2.test(stem)) { - w = stem; - re2 = /(at|bl|iz)$/; - re3 = new RegExp("([^aeiouylsz])\\1$"); - re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - if (re2.test(w)) - w = w + "e"; - else if (re3.test(w)) { - re = /.$/; - w = w.replace(re,""); - } - else if (re4.test(w)) - w = w + "e"; - } - } - - // Step 1c - re = /^(.+?)y$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(s_v); - if (re.test(stem)) - w = stem + "i"; - } - - // Step 2 - re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = new RegExp(mgr0); - if (re.test(stem)) - w = stem + step2list[suffix]; - } - - // Step 3 - re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = new RegExp(mgr0); - if (re.test(stem)) - w = stem + step3list[suffix]; - } - - // Step 4 - re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; - re2 = /^(.+?)(s|t)(ion)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(mgr1); - if (re.test(stem)) - w = stem; - } - else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1] + fp[2]; - re2 = new RegExp(mgr1); - if (re2.test(stem)) - w = stem; - } - - // Step 5 - re = /^(.+?)e$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(mgr1); - re2 = new RegExp(meq1); - re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) - w = stem; - } - re = /ll$/; - re2 = new RegExp(mgr1); - if (re.test(w) && re2.test(w)) { - re = /.$/; - w = w.replace(re,""); - } - - // and turn initial Y back to y - if (firstch == "y") - w = firstch.toLowerCase() + w.substr(1); - return w; - } -} - - - - - -var splitChars = (function() { - var result = {}; - var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648, - 1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702, - 2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971, - 2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345, - 3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761, - 3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823, - 4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125, - 8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695, - 11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587, - 43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141]; - var i, j, start, end; - for (i = 0; i < singles.length; i++) { - result[singles[i]] = true; - } - var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709], - [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161], - [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568], - [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807], - [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047], - [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383], - [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450], - [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547], - [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673], - [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820], - [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946], - [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023], - [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173], - [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332], - [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481], - [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718], - [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791], - [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095], - [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205], - [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687], - [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968], - [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869], - [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102], - [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271], - [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592], - [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822], - [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167], - [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959], - [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143], - [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318], - [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483], - [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101], - [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567], - [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292], - [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444], - [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783], - [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311], - [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511], - [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774], - [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071], - [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263], - [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519], - [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647], - [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967], - [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295], - [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274], - [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007], - [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381], - [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]]; - for (i = 0; i < ranges.length; i++) { - start = ranges[i][0]; - end = ranges[i][1]; - for (j = start; j <= end; j++) { - result[j] = true; - } - } - return result; -})(); - -function splitQuery(query) { - var result = []; - var start = -1; - for (var i = 0; i < query.length; i++) { - if (splitChars[query.charCodeAt(i)]) { - if (start !== -1) { - result.push(query.slice(start, i)); - start = -1; - } - } else if (start === -1) { - start = i; - } - } - if (start !== -1) { - result.push(query.slice(start)); - } - return result; -} - - + NAVIGATION_WITH_KEYS: false +}; \ No newline at end of file diff --git a/docs/_static/language_data.js b/docs/_static/language_data.js new file mode 100644 index 000000000..5266fb19e --- /dev/null +++ b/docs/_static/language_data.js @@ -0,0 +1,297 @@ +/* + * language_data.js + * ~~~~~~~~~~~~~~~~ + * + * This script contains the language-specific data used by searchtools.js, + * namely the list of stopwords, stemmer, scorer and splitter. + * + * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"]; + + +/* Non-minified version JS is _stemmer.js if file is provided */ +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; + + var step3list = { + icate: 'ic', + ative: '', + alize: 'al', + iciti: 'ic', + ical: 'ic', + ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + + + + + +var splitChars = (function() { + var result = {}; + var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648, + 1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702, + 2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971, + 2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345, + 3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761, + 3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823, + 4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125, + 8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695, + 11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587, + 43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141]; + var i, j, start, end; + for (i = 0; i < singles.length; i++) { + result[singles[i]] = true; + } + var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709], + [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161], + [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568], + [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807], + [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047], + [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383], + [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450], + [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547], + [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673], + [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820], + [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946], + [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023], + [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173], + [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332], + [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481], + [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718], + [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791], + [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095], + [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205], + [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687], + [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968], + [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869], + [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102], + [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271], + [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592], + [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822], + [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167], + [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959], + [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143], + [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318], + [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483], + [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101], + [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567], + [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292], + [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444], + [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783], + [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311], + [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511], + [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774], + [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071], + [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263], + [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519], + [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647], + [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967], + [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295], + [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274], + [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007], + [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381], + [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]]; + for (i = 0; i < ranges.length; i++) { + start = ranges[i][0]; + end = ranges[i][1]; + for (j = start; j <= end; j++) { + result[j] = true; + } + } + return result; +})(); + +function splitQuery(query) { + var result = []; + var start = -1; + for (var i = 0; i < query.length; i++) { + if (splitChars[query.charCodeAt(i)]) { + if (start !== -1) { + result.push(query.slice(start, i)); + start = -1; + } + } else if (start === -1) { + start = i; + } + } + if (start !== -1) { + result.push(query.slice(start)); + } + return result; +} + + diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js index 7473859b2..6031f9913 100644 --- a/docs/_static/searchtools.js +++ b/docs/_static/searchtools.js @@ -4,7 +4,7 @@ * * Sphinx JavaScript utilities for the full-text search. * - * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -36,8 +36,10 @@ if (!Scorer) { // query found in title title: 15, + partialTitle: 7, // query found in terms - term: 5 + term: 5, + partialTerm: 2 }; } @@ -56,6 +58,14 @@ var Search = { _queued_query : null, _pulse_status : -1, + htmlToText : function(htmlString) { + var htmlElement = document.createElement('span'); + htmlElement.innerHTML = htmlString; + $(htmlElement).find('.headerlink').remove(); + docContent = $(htmlElement).find('[role=main]')[0]; + return docContent.textContent || docContent.innerText; + }, + init : function() { var params = $.getQueryParameters(); if (params.q) { @@ -120,7 +130,7 @@ var Search = { this.out = $('#search-results'); this.title = $('

' + _('Searching') + '

').appendTo(this.out); this.dots = $('').appendTo(this.title); - this.status = $('

').appendTo(this.out); + this.status = $('

 

').appendTo(this.out); this.output = $('
    ').appendTo(this.out); $('#search-progress').text(_('Preparing search...')); @@ -138,7 +148,6 @@ var Search = { */ query : function(query) { var i; - var stopwords = DOCUMENTATION_OPTIONS.SEARCH_LANGUAGE_STOP_WORDS; // stem the searchterms and add them to the correct list var stemmer = new Stemmer(); @@ -260,11 +269,7 @@ var Search = { displayNextItem(); }); } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) { - var suffix = DOCUMENTATION_OPTIONS.SOURCELINK_SUFFIX; - if (suffix === undefined) { - suffix = '.txt'; - } - $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[5] + (item[5].slice(-suffix.length) === suffix ? '' : suffix), + $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX, dataType: "text", complete: function(jqxhr, textstatus) { var data = jqxhr.responseText; @@ -314,12 +319,13 @@ var Search = { for (var prefix in objects) { for (var name in objects[prefix]) { var fullname = (prefix ? prefix + '.' : '') + name; - if (fullname.toLowerCase().indexOf(object) > -1) { + var fullnameLower = fullname.toLowerCase() + if (fullnameLower.indexOf(object) > -1) { var score = 0; - var parts = fullname.split('.'); + var parts = fullnameLower.split('.'); // check for different match types: exact matches of full name or // "last name" (i.e. last dotted part) - if (fullname == object || parts[parts.length - 1] == object) { + if (fullnameLower == object || parts[parts.length - 1] == object) { score += Scorer.objNameMatch; // matches in last name } else if (parts[parts.length - 1].indexOf(object) > -1) { @@ -386,6 +392,19 @@ var Search = { {files: terms[word], score: Scorer.term}, {files: titleterms[word], score: Scorer.title} ]; + // add support for partial matches + if (word.length > 2) { + for (var w in terms) { + if (w.match(word) && !terms[word]) { + _o.push({files: terms[w], score: Scorer.partialTerm}) + } + } + for (var w in titleterms) { + if (w.match(word) && !titleterms[word]) { + _o.push({files: titleterms[w], score: Scorer.partialTitle}) + } + } + } // no match but word was a required one if ($u.every(_o, function(o){return o.files === undefined;})) { @@ -425,8 +444,12 @@ var Search = { var valid = true; // check if all requirements are matched - if (fileMap[file].length != searchterms.length) - continue; + var filteredTermCount = // as search terms with length < 3 are discarded: ignore + searchterms.filter(function(term){return term.length > 2}).length + if ( + fileMap[file].length != searchterms.length && + fileMap[file].length != filteredTermCount + ) continue; // ensure that none of the excluded terms is in the search result for (i = 0; i < excluded.length; i++) { @@ -457,7 +480,8 @@ var Search = { * words. the first one is used to find the occurrence, the * latter for highlighting it. */ - makeSearchSummary : function(text, keywords, hlwords) { + makeSearchSummary : function(htmlText, keywords, hlwords) { + var text = Search.htmlToText(htmlText); var textLower = text.toLowerCase(); var start = 0; $.each(keywords, function() { diff --git a/docs/atomate.common.firetasks.html b/docs/atomate.common.firetasks.html index 4b9ed6af3..9f43d145f 100644 --- a/docs/atomate.common.firetasks.html +++ b/docs/atomate.common.firetasks.html @@ -1,18 +1,17 @@ - + - - - atomate.common.firetasks package — atomate 0.9.1 documentation + + atomate.common.firetasks package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
@@ -60,40 +59,38 @@

Submodules

atomate.common.firetasks.glue_tasks moduleΒΆ

-class atomate.common.firetasks.glue_tasks.CopyFiles(*args, **kwargs)ΒΆ
+class atomate.common.firetasks.glue_tasks.CopyFiles(*args, **kwargs)ΒΆ

Bases: fireworks.core.firework.FiretaskBase

Task to copy the given list of files from the given directory to the destination directory. To customize override the setup_copy and copy_files methods.

-
-
Optional params:
-
from_dir (str): path to the directory containing the files to be copied. +
+
Optional params:

from_dir (str): path to the directory containing the files to be copied. to_dir (str): path to the destination directory filesystem (str) files_to_copy (list): list of file names. -exclude_files (list): list of file names to be excluded.

+exclude_files (list): list of file names to be excluded.

+
-copy_files()ΒΆ
+copy_files()ΒΆ

Defines the copy operation. Override this to customize copying.

-optional_params = ['from_dir', 'to_dir', 'filesystem', 'files_to_copy', 'exclude_files']ΒΆ
+optional_params = ['from_dir', 'to_dir', 'filesystem', 'files_to_copy', 'exclude_files']ΒΆ
-run_task(fw_spec)ΒΆ
+run_task(fw_spec)ΒΆ

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

-
-
Args:
-
-
fw_spec (dict): A Firework spec. This comes from the master spec.
-
In addition, this spec contains a special β€œ_fw_env” key that +
+
Args:
+
fw_spec (dict): A Firework spec. This comes from the master spec.

In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -101,28 +98,29 @@

Submodules
-setup_copy(from_dir, to_dir=None, filesystem=None, files_to_copy=None, exclude_files=None, from_path_dict=None)ΒΆ
+setup_copy(from_dir, to_dir=None, filesystem=None, files_to_copy=None, exclude_files=None, from_path_dict=None)ΒΆ

setup the copy i.e setup the from directory, filesystem, destination directory etc.

-
-
Args:
-

from_dir (str) +

+
Args:

from_dir (str) to_dir (str) filesystem (str) files_to_copy (list): if None all the files in the from_dir will be copied exclude_files (list) from_path_dict (dict): dict specification of the path. If specified must contain atleast

-
-
the key β€œpath” that specifies the path to the from_dir.
+
+

the key β€œpath” that specifies the path to the from_dir.

+
@@ -131,48 +129,45 @@

Submodules
-class atomate.common.firetasks.glue_tasks.CopyFilesFromCalcLoc(*args, **kwargs)ΒΆ
+class atomate.common.firetasks.glue_tasks.CopyFilesFromCalcLoc(*args, **kwargs)ΒΆ

Bases: fireworks.core.firework.FiretaskBase

Based on CopyVaspOutputs but for general file copying. Note that β€œcalc_locs” must be set in the fw_spec. Files are copied to the current folder.

-
-
Required params:
-
calc_loc: name of target fw to get location for within the calc_locs.
-
Optional params:
-
-
filenames (list(str)): filenames to copy. Special behavior for:
-

None: if filenames not set, all files in calc_loc will be copied +

+
Required params:

calc_loc: name of target fw to get location for within the calc_locs.

+
+
Optional params:
+
filenames (list(str)): filenames to copy. Special behavior for:

None: if filenames not set, all files in calc_loc will be copied β€˜$ALL_NO_SUBDIRS’ in filenames: similar to filenames is None β€˜$ALL’ in filenames: all files and subfolders copied, name_prepend

-
-
and name_append cannot be set in this case
+
+

and name_append cannot be set in this case

+
-

name_prepend (str): string to prepend filenames, e.g. can be a directory. +

name_prepend (str): string to prepend filenames, e.g. can be a directory. name_append (str): string to append to destination filenames.

-optional_params = ['filenames', 'name_prepend', 'name_append']ΒΆ
+optional_params = ['filenames', 'name_prepend', 'name_append']ΒΆ
-required_params = ['calc_loc']ΒΆ
+required_params = ['calc_loc']ΒΆ
-run_task(fw_spec=None)ΒΆ
+run_task(fw_spec=None)ΒΆ

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

-
-
Args:
-
-
fw_spec (dict): A Firework spec. This comes from the master spec.
-
In addition, this spec contains a special β€œ_fw_env” key that +
+
Args:
+
fw_spec (dict): A Firework spec. This comes from the master spec.

In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -180,11 +175,12 @@

Submodules
-class atomate.common.firetasks.glue_tasks.CreateFolder(*args, **kwargs)ΒΆ
+class atomate.common.firetasks.glue_tasks.CreateFolder(*args, **kwargs)ΒΆ

Bases: fireworks.core.firework.FiretaskBase

FireTask to create new folder with the option of changing directory to the new folder.

-
-
Required params:
-
folder_name (str): folder name.
-
Optional params:
-
-
change_dir(bool): change working dir to new folder after creation.
-
Defaults to False.
-
relative_path (bool): whether folder name is relative or absolute.
-
Defaults to True.
+
+
Required params:

folder_name (str): folder name.

+
+
Optional params:
+
change_dir(bool): change working dir to new folder after creation.

Defaults to False.

+
+
relative_path (bool): whether folder name is relative or absolute.

Defaults to True.

+
-optional_params = ['change_dir', 'relative_path']ΒΆ
+optional_params = ['change_dir', 'relative_path']ΒΆ
-required_params = ['folder_name']ΒΆ
+required_params = ['folder_name']ΒΆ
-run_task(fw_spec)ΒΆ
+run_task(fw_spec)ΒΆ

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

-
-
Args:
-
-
fw_spec (dict): A Firework spec. This comes from the master spec.
-
In addition, this spec contains a special β€œ_fw_env” key that +
+
Args:
+
fw_spec (dict): A Firework spec. This comes from the master spec.

In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -235,11 +228,12 @@

Submodules
-class atomate.common.firetasks.glue_tasks.DeleteFiles(*args, **kwargs)ΒΆ
+class atomate.common.firetasks.glue_tasks.DeleteFiles(*args, **kwargs)ΒΆ

Bases: fireworks.core.firework.FiretaskBase

Delete files Uses glob to search for files so any pattern it can accept can be used

-
-
Required params:
-
files: list of files to remove
+
+
Required params:

files: list of files to remove

+
-required_params = ['files']ΒΆ
+required_params = ['files']ΒΆ
-run_task(fw_spec=None)ΒΆ
+run_task(fw_spec=None)ΒΆ

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

-
-
Args:
-
-
fw_spec (dict): A Firework spec. This comes from the master spec.
-
In addition, this spec contains a special β€œ_fw_env” key that +
+
Args:
+
fw_spec (dict): A Firework spec. This comes from the master spec.

In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -278,11 +270,12 @@

Submodules
-class atomate.common.firetasks.glue_tasks.PassCalcLocs(*args, **kwargs)ΒΆ
+class atomate.common.firetasks.glue_tasks.PassCalcLocs(*args, **kwargs)ΒΆ

Bases: fireworks.core.firework.FiretaskBase

Passes information about where the current calculation is located for the next FireWork. This is achieved by passing a key to the fw_spec called β€œcalc_locs” with this information.

-
-
Required params:
-
name (str): descriptive name for this calculation file/dir
-
Optional params:
-
-
filesystem (str or custom user format): name of filesystem. Supports env_chk.
-
defaults to None
-
path (str): The path to the directory containing the calculation. defaults to
-
current working directory.
+
+
Required params:

name (str): descriptive name for this calculation file/dir

+
+
Optional params:
+
filesystem (str or custom user format): name of filesystem. Supports env_chk.

defaults to None

+
+
path (str): The path to the directory containing the calculation. defaults to

current working directory.

+
-optional_params = ['filesystem', 'path']ΒΆ
+optional_params = ['filesystem', 'path']ΒΆ
-required_params = ['name']ΒΆ
+required_params = ['name']ΒΆ
-run_task(fw_spec)ΒΆ
+run_task(fw_spec)ΒΆ

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

-
-
Args:
-
-
fw_spec (dict): A Firework spec. This comes from the master spec.
-
In addition, this spec contains a special β€œ_fw_env” key that +
+
Args:
+
fw_spec (dict): A Firework spec. This comes from the master spec.

In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -335,11 +325,12 @@

Submodules
-class atomate.common.firetasks.glue_tasks.PassResult(*args, **kwargs)ΒΆ
+class atomate.common.firetasks.glue_tasks.PassResult(*args, **kwargs)ΒΆ

Bases: fireworks.core.firework.FiretaskBase

Passes properties and corresponding user-specified data resulting from a run from parent to child fireworks. Uses a string syntax similar to Mongo-style queries to designate values of output file dictionaries to retrieve. For example, one could specify a task to pass the stress from the current calculation using:

PassResult(pass_dict={β€˜stress’: β€œ>>ionic_steps.-1.stress”})

-
-
Required params:
-
-
pass_dict (dict): dictionary designating keys and values to pass
-
to child fireworks. If value is a string beginning with β€˜>>’, +
+
Required params:
+
pass_dict (dict): dictionary designating keys and values to pass

to child fireworks. If value is a string beginning with β€˜>>’, the firework will search the parsed VASP output dictionary for the designated property by following the sequence of keys separated with periods, e. g. β€œ>>ionic_steps.-1.stress” is used to designate the stress from the last ionic_step. If the value -is not a string or does not begin with β€œ>>”, it is passed as is.

-
parse_class (str): string representation of complete path to a class
-
with which to parse the output, e. g. pymatgen.io.vasp.Vasprun -or pymatgen.io.feff.LDos.from_file, class must be MSONable
-
parse_kwargs (str): dict of kwargs for the parse class,
-
e. g. {β€œfilename”: β€œvasprun.xml”, β€œparse_dos”: False, -β€œparse_eigen”: False}
+is not a string or does not begin with β€œ>>”, it is passed as is.

+
+
parse_class (str): string representation of complete path to a class

with which to parse the output, e. g. pymatgen.io.vasp.Vasprun +or pymatgen.io.feff.LDos.from_file, class must be MSONable

+
+
parse_kwargs (str): dict of kwargs for the parse class,

e. g. {β€œfilename”: β€œvasprun.xml”, β€œparse_dos”: False, +β€œparse_eigen”: False}

+
-
Optional params:
-
-
calc_dir (str): path to dir that contains VASP output files, defaults
-
to β€˜.’, e. g. current directory
-
mod_spec_cmd (str): command to issue for mod_spec, e. g. β€œ_set” or β€œ_push”,
-
defaults to β€œ_set”
-
mod_spec_key (str): key to pass to mod_spec _set dictmod command, defaults
-
to β€œprev_calc_result”
+
Optional params:
+
calc_dir (str): path to dir that contains VASP output files, defaults

to β€˜.’, e. g. current directory

+
+
mod_spec_cmd (str): command to issue for mod_spec, e. g. β€œ_set” or β€œ_push”,

defaults to β€œ_set”

+
+
mod_spec_key (str): key to pass to mod_spec _set dictmod command, defaults

to β€œprev_calc_result”

+
-optional_params = ['calc_dir', 'mod_spec_cmd', 'mod_spec_key']ΒΆ
+optional_params = ['calc_dir', 'mod_spec_cmd', 'mod_spec_key']ΒΆ
-required_params = ['pass_dict', 'parse_class', 'parse_kwargs']ΒΆ
+required_params = ['pass_dict', 'parse_class', 'parse_kwargs']ΒΆ
-run_task(fw_spec)ΒΆ
+run_task(fw_spec)ΒΆ

This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

-
-
Args:
-
-
fw_spec (dict): A Firework spec. This comes from the master spec.
-
In addition, this spec contains a special β€œ_fw_env” key that +
+
Args:
+
fw_spec (dict): A Firework spec. This comes from the master spec.

In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -411,11 +398,12 @@

Submodules
-atomate.common.firetasks.glue_tasks.get_calc_loc(target_name, calc_locs)ΒΆ
+atomate.common.firetasks.glue_tasks.get_calc_loc(target_name, calc_locs)ΒΆ

This is a helper method that helps you pick out a certain calculation from an array of calc_locs.

-
-
There are three modes:
-
    -
  • -
    If you set target_name to a String, search for most recent calc_loc
    -
    with matching nameget_
    +
    +
    There are three modes:
      +
    • +
      If you set target_name to a String, search for most recent calc_loc

      with matching nameget_

      +
      • -
    • Otherwise, return most recent calc_loc overall
      • +

    • Otherwise, return most recent calc_loc overall

    -
    Args:
    -
    -
    target_name: (bool or str) If str, will search for calc_loc with
    -
    matching name, else use most recent calc_loc
    +
    Args:
    +
    target_name: (bool or str) If str, will search for calc_loc with

    matching name, else use most recent calc_loc

    +
    -

    calc_locs: (dict) The dictionary of all calc_locs

    +

    calc_locs: (dict) The dictionary of all calc_locs

    +
    +
    Returns:

    (dict) dict with subkeys path, filesystem, and name

    -
    Returns:
    -
    (dict) dict with subkeys path, filesystem, and name
    @@ -454,51 +440,49 @@

    Submodules

    atomate.common.firetasks.parse_outputs moduleΒΆ

    -class atomate.common.firetasks.parse_outputs.ToDbTask(*args, **kwargs)ΒΆ
    +class atomate.common.firetasks.parse_outputs.ToDbTask(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    General task to parse output data via a Drone and either (i) write to JSON file or (ii) insert into a database.

    -
    -
    Required params:
    -
    drone (AbstractDrone): Drone to convert the data to dict
    -
    Optional params:
    -
    -
    db_file (str): path to file containing the database credentials. Supports env_chk.
    -
    Default is None, which will write data to JSON file.
    +
    +
    Required params:

    drone (AbstractDrone): Drone to convert the data to dict

    +
    +
    Optional params:
    +
    db_file (str): path to file containing the database credentials. Supports env_chk.

    Default is None, which will write data to JSON file.

    +

    mmdb (MMDb) (str): If db_file, sets the type of MMDb, e.g. β€œatomate.vasp.database.MMVaspDb” calc_dir (str): path to dir (on current filesystem) that contains calculation output files.

    -
    Default: use current working directory.
    -
    -
    calc_loc (str OR bool): if True will set most recent calc_loc. If str search for the most
    -
    recent calc_loc with the matching name
    +

    Default: use current working directory.

    +
    +
    +
    calc_loc (str OR bool): if True will set most recent calc_loc. If str search for the most

    recent calc_loc with the matching name

    +
    -

    options (dict): dict of options to pass into the Drone +

    options (dict): dict of options to pass into the Drone additional_fields (dict): dict of additional fields to add

    -optional_params = ['mmdb', 'db_file', 'calc_dir', 'calc_loc', 'additional_fields', 'options']ΒΆ
    +optional_params = ['mmdb', 'db_file', 'calc_dir', 'calc_loc', 'additional_fields', 'options']ΒΆ
    -required_params = ['drone']ΒΆ
    +required_params = ['drone']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -506,11 +490,12 @@

    Submodules

    atomate.common.firetasks.run_calc moduleΒΆ

    -class atomate.common.firetasks.run_calc.RunCommand(*args, **kwargs)ΒΆ
    +class atomate.common.firetasks.run_calc.RunCommand(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Execute a command directly (no custodian).

    -
    -
    Required params:
    -
    cmd (str): the name of the full executable to run. Supports env_chk.
    -
    Optional params:
    -
    expand_vars (str): Set to true to expand variable names in the cmd.
    +
    +
    Required params:

    cmd (str): the name of the full executable to run. Supports env_chk.

    +
    +
    Optional params:

    expand_vars (str): Set to true to expand variable names in the cmd.

    +
    -optional_params = ['expand_vars']ΒΆ
    +optional_params = ['expand_vars']ΒΆ
    -required_params = ['cmd']ΒΆ
    +required_params = ['cmd']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -558,11 +541,12 @@

    Submodules
    -class atomate.common.firetasks.run_calc.RunCustodianFromObjects(*args, **kwargs)ΒΆ
    +class atomate.common.firetasks.run_calc.RunCustodianFromObjects(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Run VASP using custodian in a generic manner using built-in custodian objects

    -
    -
    Required params:
    -
    jobs: ([Job]) - a list of custodian jobs to run -handlers: ([ErrorHandler]) - a list of error handlers
    -
    Optional params:
    -
    validators: ([Validator]) - a list of Validators -custodian_params ({}) - dict of all other custodian parameters
    +
    +
    Required params:

    jobs: ([Job]) - a list of custodian jobs to run +handlers: ([ErrorHandler]) - a list of error handlers

    +
    +
    Optional params:

    validators: ([Validator]) - a list of Validators +custodian_params ({}) - dict of all other custodian parameters

    +
    -optional_params = ['validators', 'custodian_params']ΒΆ
    +optional_params = ['validators', 'custodian_params']ΒΆ
    -required_params = ['jobs', 'handlers']ΒΆ
    +required_params = ['jobs', 'handlers']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -610,11 +592,12 @@

    Submodules
  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »

diff --git a/docs/atomate.common.firetasks.tests.html b/docs/atomate.common.firetasks.tests.html index ef1ce8476..1212b3790 100644 --- a/docs/atomate.common.firetasks.tests.html +++ b/docs/atomate.common.firetasks.tests.html @@ -1,18 +1,17 @@ - + - - - atomate.common.firetasks.tests package — atomate 0.9.1 documentation + + atomate.common.firetasks.tests package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -46,50 +45,50 @@

    Submodules

    atomate.common.firetasks.tests.test_glue_tasks moduleΒΆ

    -class atomate.common.firetasks.tests.test_glue_tasks.TestCopyFilesFromCalcLoc(methodName='runTest')ΒΆ
    +class atomate.common.firetasks.tests.test_glue_tasks.TestCopyFilesFromCalcLoc(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -
    +
    -classmethod setUpClass()ΒΆ
    +classmethod setUpClass()ΒΆ

    Hook method for setting up class fixture before running tests in the class.

    -test_copyfilesfromcalcloc()ΒΆ
    +test_copyfilesfromcalcloc()ΒΆ
    -class atomate.common.firetasks.tests.test_glue_tasks.TestCreateFolder(methodName='runTest')ΒΆ
    +class atomate.common.firetasks.tests.test_glue_tasks.TestCreateFolder(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -test_createfolder()ΒΆ
    +test_createfolder()ΒΆ
    -class atomate.common.firetasks.tests.test_glue_tasks.TestDeleteFiles(methodName='runTest')ΒΆ
    +class atomate.common.firetasks.tests.test_glue_tasks.TestDeleteFiles(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -test_cleanupfiles()ΒΆ
    +test_cleanupfiles()ΒΆ
    -class atomate.common.firetasks.tests.test_glue_tasks.TestPassCalcLocs(methodName='runTest')ΒΆ
    +class atomate.common.firetasks.tests.test_glue_tasks.TestPassCalcLocs(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -test_passcalclocs()ΒΆ
    +test_passcalclocs()ΒΆ
    @@ -99,31 +98,31 @@

    Submodules

    atomate.common.firetasks.tests.test_parse_outputs moduleΒΆ

    -class atomate.common.firetasks.tests.test_parse_outputs.TestDroneΒΆ
    +class atomate.common.firetasks.tests.test_parse_outputs.TestDroneΒΆ

    Bases: pymatgen.apps.borg.hive.AbstractDrone

    -__init__()ΒΆ
    +__init__()ΒΆ

    Initialize self. See help(type(self)) for accurate signature.

    -assimilate(path)ΒΆ
    +assimilate(path)ΒΆ

    Assimilate data in a directory path into a pymatgen object. Because of the quirky nature of Python”s multiprocessing, the object must support pymatgen’s as_dict() for parallel processing.

    -
    -
    Args:
    -
    path: directory path
    -
    Returns:
    -
    An assimilated object
    +
    +
    Args:

    path: directory path

    +
    +
    Returns:

    An assimilated object

    +
    -get_valid_paths(path)ΒΆ
    +get_valid_paths(path)ΒΆ

    Checks if path contains valid data for assimilation, and then returns the valid paths. The paths returned can be a list of directory or file paths, depending on what kind of data you are assimilating. For @@ -131,15 +130,14 @@

    Submodules -
    Args:
    -
    -
    path: input path as a tuple generated from os.walk, i.e.,
    -
    (parent, subdirs, files).
    +
    +
    Args:
    +
    path: input path as a tuple generated from os.walk, i.e.,

    (parent, subdirs, files).

    +
    -
    Returns:
    -
    List of valid dir/file paths for assimilation
    +
    Returns:

    List of valid dir/file paths for assimilation

    +

    @@ -147,11 +145,11 @@

    Submodules
    -class atomate.common.firetasks.tests.test_parse_outputs.TestToDbTask(methodName='runTest')ΒΆ
    +class atomate.common.firetasks.tests.test_parse_outputs.TestToDbTask(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -test_ToDbTask()ΒΆ
    +test_ToDbTask()ΒΆ

    @@ -187,13 +185,11 @@

    This Page

    @@ -211,13 +207,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.common.html b/docs/atomate.common.html index 9de5584f8..5a4c688f6 100644 --- a/docs/atomate.common.html +++ b/docs/atomate.common.html @@ -1,18 +1,17 @@ - + - - - atomate.common package — atomate 0.9.1 documentation + + atomate.common package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -92,13 +91,11 @@

    This Page

    @@ -116,13 +113,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.feff.firetasks.html b/docs/atomate.feff.firetasks.html index 2bc07a043..832e3604b 100644 --- a/docs/atomate.feff.firetasks.html +++ b/docs/atomate.feff.firetasks.html @@ -1,18 +1,17 @@ - + - - - atomate.feff.firetasks package — atomate 0.9.1 documentation + + atomate.feff.firetasks package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -59,39 +58,37 @@

    Submodules

    atomate.feff.firetasks.glue_tasks moduleΒΆ

    -class atomate.feff.firetasks.glue_tasks.CopyFeffOutputs(*args, **kwargs)ΒΆ
    +class atomate.feff.firetasks.glue_tasks.CopyFeffOutputs(*args, **kwargs)ΒΆ

    Bases: atomate.common.firetasks.glue_tasks.CopyFiles

    Copy files from a previous run directory to the current directory. Note: must specify either β€œcalc_loc” or β€œcalc_dir” to indicate the directory

    -
    containing the files to copy.
    -
    -
    Optional params:
    -
    -
    calc_loc (str OR bool): if True will set most recent calc_loc. If str
    -
    search for the most recent calc_loc with the matching name.
    +

    containing the files to copy.

    +
    +
    +
    Optional params:
    +
    calc_loc (str OR bool): if True will set most recent calc_loc. If str

    search for the most recent calc_loc with the matching name.

    +
    -

    calc_dir (str): path to dir that contains VASP output files. +

    calc_dir (str): path to dir that contains VASP output files. filesystem (str): remote filesystem. e.g. username@host exclude_files (list): list fo filenames to be excluded when copying.

    -optional_params = ['calc_loc', 'calc_dir', 'filesystem', 'exclude_files']ΒΆ
    +optional_params = ['calc_loc', 'calc_dir', 'filesystem', 'exclude_files']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -99,11 +96,12 @@

    Submodules

    atomate.feff.firetasks.parse_outputs moduleΒΆ

    -class atomate.feff.firetasks.parse_outputs.AddPathsToFilepadTask(*args, **kwargs)ΒΆ
    +class atomate.feff.firetasks.parse_outputs.AddPathsToFilepadTask(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Insert the scattering amplitude outputs(all feffNNNN.dat files) to gridfs using filepad.

    -
    -
    Optional_params:
    -
    labels (list): list of labels to tag the inserted files. Useful for querying later. +
    +
    Optional_params:

    labels (list): list of labels to tag the inserted files. Useful for querying later. filepad_file (str): path to the filepad connection settings file. compress (bool): wether or not to compress the file contents before insertion. -metadata (dict): metadata.

    +metadata (dict): metadata.

    +
    -optional_params = ['labels', 'filepad_file', 'compress', 'metadata']ΒΆ
    +optional_params = ['labels', 'filepad_file', 'compress', 'metadata']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -147,11 +143,12 @@

    Submodules
    -class atomate.feff.firetasks.parse_outputs.SpectrumToDbTask(*args, **kwargs)ΒΆ
    +class atomate.feff.firetasks.parse_outputs.SpectrumToDbTask(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Parse the output of absorption/core-loss spectrum calculations(xmu.dat, eels.dat) and insert it into the database.

    -
    -
    Required_params:
    -
    absorbing_atom (str): absorbing atom symbol +
    +
    Required_params:

    absorbing_atom (str): absorbing atom symbol structure (Structure): input structure spectrum_type (str): XANES, EXAFS, ELNES, EXELFS -output_file (str): the output file name. xmu.dat or eels.dat

    -
    Optional_params:
    -

    input_file (str): path to the feff input file. +output_file (str): the output file name. xmu.dat or eels.dat

    +
    +
    Optional_params:

    input_file (str): path to the feff input file. calc_dir (str): path to dir (on current filesystem) that contains FEFF output files.

    -
    Default: use current working directory.
    -
    -
    calc_loc (str OR bool): if True will set most recent calc_loc. If str search for the most
    -
    recent calc_loc with the matching name
    +

    Default: use current working directory.

    +
    +
    +
    calc_loc (str OR bool): if True will set most recent calc_loc. If str search for the most

    recent calc_loc with the matching name

    +
    -

    db_file (str): path to the db file. +

    db_file (str): path to the db file. edge (str): absorption edge metadata (dict): meta data

    -optional_params = ['input_file', 'calc_dir', 'calc_loc', 'db_file', 'edge', 'metadata']ΒΆ
    +optional_params = ['input_file', 'calc_dir', 'calc_loc', 'db_file', 'edge', 'metadata']ΒΆ
    -required_params = ['absorbing_atom', 'structure', 'spectrum_type', 'output_file']ΒΆ
    +required_params = ['absorbing_atom', 'structure', 'spectrum_type', 'output_file']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -211,11 +206,12 @@

    Submodules

    atomate.feff.firetasks.run_calc moduleΒΆ

    -class atomate.feff.firetasks.run_calc.RunFeffDirect(*args, **kwargs)ΒΆ
    +class atomate.feff.firetasks.run_calc.RunFeffDirect(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Run FEFF.

    -
    -
    Required params:
    -
    feff_cmd (str): the name of the full executable for running FEFF (supports env_chk)
    +
    +
    Required params:

    feff_cmd (str): the name of the full executable for running FEFF (supports env_chk)

    +
    -required_params = ['feff_cmd']ΒΆ
    +required_params = ['feff_cmd']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -256,11 +250,12 @@

    Submodules

    atomate.feff.firetasks.write_inputs moduleΒΆ

    -class atomate.feff.firetasks.write_inputs.WriteEXAFSPaths(*args, **kwargs)ΒΆ
    +class atomate.feff.firetasks.write_inputs.WriteEXAFSPaths(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Write the scattering paths to paths.dat file.

    -
    -
    Required_params:
    -
    feff_input_set: (FeffDictSet subclass) -paths (list): list of paths. A path = list of site indices.
    -
    Optional_params:
    -
    degeneracies (list): list of path degeneracies.
    +
    +
    Required_params:

    feff_input_set: (FeffDictSet subclass) +paths (list): list of paths. A path = list of site indices.

    +
    +
    Optional_params:

    degeneracies (list): list of path degeneracies.

    +
    -optional_params = ['degeneracies']ΒΆ
    +optional_params = ['degeneracies']ΒΆ
    -required_params = ['feff_input_set', 'paths']ΒΆ
    +required_params = ['feff_input_set', 'paths']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -309,11 +302,12 @@

    Submodules
    -class atomate.feff.firetasks.write_inputs.WriteFeffFromIOSet(*args, **kwargs)ΒΆ
    +class atomate.feff.firetasks.write_inputs.WriteFeffFromIOSet(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Generate FEFF input (feff.inp) from the given InputSet object or InputSet name

    -
    -
    Required_params:
    -

    absorbing_atom (str): absorbing atom symbol +

    +
    Required_params:

    absorbing_atom (str): absorbing atom symbol structure (Structure): input structure feff_input_set (str or FeffDictSet subclass): The inputset for setting params. If string

    -
    -
    then either the entire path to the class or the spectrum type must be provided -e.g. β€œpymatgen.io.feff.sets.MPXANESSet” or β€œXANES”
    +
    +

    then either the entire path to the class or the spectrum type must be provided +e.g. β€œpymatgen.io.feff.sets.MPXANESSet” or β€œXANES”

    +
    +
    +
    Optional_params:

    radius (float): cluster radius in angstroms +other_params (dict): **kwargs to pass into the desired InputSet if using str feff_input_set

    -
    Optional_params:
    -
    radius (float): cluster radius in angstroms -other_params (dict): **kwargs to pass into the desired InputSet if using str feff_input_set
    -optional_params = ['radius', 'other_params']ΒΆ
    +optional_params = ['radius', 'other_params']ΒΆ
    -required_params = ['absorbing_atom', 'structure', 'feff_input_set']ΒΆ
    +required_params = ['absorbing_atom', 'structure', 'feff_input_set']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -365,11 +357,12 @@

    Submodules
    -atomate.feff.firetasks.write_inputs.get_feff_input_set_obj(fis, *args, **kwargs)ΒΆ
    +atomate.feff.firetasks.write_inputs.get_feff_input_set_obj(fis, *args, **kwargs)ΒΆ

    returns feff input set object.

    -
    -
    Args:
    -
    -
    fis (str or FeffDictSet subclass): The inputset for setting params. If string then
    -
    the entire path to the class or the spectrum type must be provided -e.g. β€œpymatgen.io.feff.sets.MPXANESSet” or β€œXANES”
    +
    +
    Args:
    +
    fis (str or FeffDictSet subclass): The inputset for setting params. If string then

    the entire path to the class or the spectrum type must be provided +e.g. β€œpymatgen.io.feff.sets.MPXANESSet” or β€œXANES”

    +
    -

    args (tuple): feff input set args +

    args (tuple): feff input set args kwargs (dict): feff input set kwargs

    -
    Returns:
    -
    FeffDictSet object
    +
    Returns:

    FeffDictSet object

    +
    @@ -428,13 +420,11 @@

    This Page

    @@ -452,13 +442,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.feff.firetasks.tests.html b/docs/atomate.feff.firetasks.tests.html index afc625d94..25e6fd2d2 100644 --- a/docs/atomate.feff.firetasks.tests.html +++ b/docs/atomate.feff.firetasks.tests.html @@ -1,18 +1,17 @@ - + - - - atomate.feff.firetasks.tests package — atomate 0.9.1 documentation + + atomate.feff.firetasks.tests package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -46,23 +45,23 @@

    Submodules

    atomate.feff.firetasks.tests.test_tasks moduleΒΆ

    -class atomate.feff.firetasks.tests.test_tasks.TestTasks(methodName='runTest')ΒΆ
    +class atomate.feff.firetasks.tests.test_tasks.TestTasks(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -setUp()ΒΆ
    +setUp()ΒΆ

    Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

    -test_copy_feff_outputs_task()ΒΆ
    +test_copy_feff_outputs_task()ΒΆ
    -test_write_paths_task()ΒΆ
    +test_write_paths_task()ΒΆ
    @@ -97,13 +96,11 @@

    This Page

    @@ -121,13 +118,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.feff.fireworks.html b/docs/atomate.feff.fireworks.html index 5f80c839d..0a6ac026c 100644 --- a/docs/atomate.feff.fireworks.html +++ b/docs/atomate.feff.fireworks.html @@ -1,18 +1,17 @@ - + - - - atomate.feff.fireworks package — atomate 0.9.1 documentation + + atomate.feff.fireworks package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -59,22 +58,22 @@

    Submodules

    atomate.feff.fireworks.core moduleΒΆ

    -class atomate.feff.fireworks.core.EELSFW(absorbing_atom, structure, feff_input_set='ELNES', edge='K', radius=10.0, name='EELS spectroscopy', beam_energy=100, beam_direction=None, collection_angle=1, convergence_angle=1, user_eels_settings=None, feff_cmd='feff', override_default_feff_params=None, db_file=None, parents=None, metadata=None, **kwargs)ΒΆ
    +class atomate.feff.fireworks.core.EELSFW(absorbing_atom, structure, feff_input_set='ELNES', edge='K', radius=10.0, name='EELS spectroscopy', beam_energy=100, beam_direction=None, collection_angle=1, convergence_angle=1, user_eels_settings=None, feff_cmd='feff', override_default_feff_params=None, db_file=None, parents=None, metadata=None, **kwargs)ΒΆ

    Bases: fireworks.core.firework.Firework

    -__init__(absorbing_atom, structure, feff_input_set='ELNES', edge='K', radius=10.0, name='EELS spectroscopy', beam_energy=100, beam_direction=None, collection_angle=1, convergence_angle=1, user_eels_settings=None, feff_cmd='feff', override_default_feff_params=None, db_file=None, parents=None, metadata=None, **kwargs)ΒΆ
    +__init__(absorbing_atom, structure, feff_input_set='ELNES', edge='K', radius=10.0, name='EELS spectroscopy', beam_energy=100, beam_direction=None, collection_angle=1, convergence_angle=1, user_eels_settings=None, feff_cmd='feff', override_default_feff_params=None, db_file=None, parents=None, metadata=None, **kwargs)ΒΆ

    Write the input set for FEFF-EELSS spectroscopy, run feff and insert the core-loss spectrum to the database(or dump to a json file if db_file=None).

    -
    -
    Args:
    -

    absorbing_atom (str): absorbing atom symbol +

    +
    Args:

    absorbing_atom (str): absorbing atom symbol structure (Structure): input structure feff_input_set (str or FeffDictSet subclass): The inputset for setting params. If string

    -
    then the entire path to the class or the spectrum type must be provide -e.g. β€œpymatgen.io.feff.sets.MPELNESSet” or β€œELNES”
    -

    edge (str): absorption edge +

    then the entire path to the class or the spectrum type must be provide +e.g. β€œpymatgen.io.feff.sets.MPELNESSet” or β€œELNES”

    +
    +

    edge (str): absorption edge radius (float): cluster radius in angstroms name (str) beam_energy (float): Incident beam energy in keV @@ -96,16 +95,15 @@

    Submodules
    -class atomate.feff.fireworks.core.EXAFSPathsFW(absorbing_atom, structure, paths, degeneracies=None, edge='K', radius=10.0, name='EXAFS Paths', feff_input_set='pymatgen.io.feff.sets.MPEXAFSSet', feff_cmd='feff', override_default_feff_params=None, parents=None, filepad_file=None, labels=None, metadata=None, **kwargs)ΒΆ
    +class atomate.feff.fireworks.core.EXAFSPathsFW(absorbing_atom, structure, paths, degeneracies=None, edge='K', radius=10.0, name='EXAFS Paths', feff_input_set='pymatgen.io.feff.sets.MPEXAFSSet', feff_cmd='feff', override_default_feff_params=None, parents=None, filepad_file=None, labels=None, metadata=None, **kwargs)ΒΆ

    Bases: fireworks.core.firework.Firework

    -__init__(absorbing_atom, structure, paths, degeneracies=None, edge='K', radius=10.0, name='EXAFS Paths', feff_input_set='pymatgen.io.feff.sets.MPEXAFSSet', feff_cmd='feff', override_default_feff_params=None, parents=None, filepad_file=None, labels=None, metadata=None, **kwargs)ΒΆ
    +__init__(absorbing_atom, structure, paths, degeneracies=None, edge='K', radius=10.0, name='EXAFS Paths', feff_input_set='pymatgen.io.feff.sets.MPEXAFSSet', feff_cmd='feff', override_default_feff_params=None, parents=None, filepad_file=None, labels=None, metadata=None, **kwargs)ΒΆ

    Write the input set for FEFF-EXAFS spectroscopy with customized scattering paths, run feff, and insert the scattering amplitude output files(feffNNNN.dat files) to filepad.

    -
    -
    Args:
    -
    absorbing_atom (str): absorbing atom symbol +
    +
    Args:

    absorbing_atom (str): absorbing atom symbol structure (Structure): input structure paths (list): list of paths. A path = list of site indices that defines the path legs. degeneracies (list): degeneracy of each path. @@ -119,7 +117,8 @@

    Submodules**kwargs: Other kwargs that are passed to Firework.__init__.

    +**kwargs: Other kwargs that are passed to Firework.__init__.

    +
    @@ -127,22 +126,22 @@

    Submodules
    -class atomate.feff.fireworks.core.XASFW(absorbing_atom, structure, feff_input_set='XANES', edge='K', radius=10.0, name='XAS spectroscopy', feff_cmd='feff', override_default_feff_params=None, db_file=None, parents=None, metadata=None, **kwargs)ΒΆ
    +class atomate.feff.fireworks.core.XASFW(absorbing_atom, structure, feff_input_set='XANES', edge='K', radius=10.0, name='XAS spectroscopy', feff_cmd='feff', override_default_feff_params=None, db_file=None, parents=None, metadata=None, **kwargs)ΒΆ

    Bases: fireworks.core.firework.Firework

    -__init__(absorbing_atom, structure, feff_input_set='XANES', edge='K', radius=10.0, name='XAS spectroscopy', feff_cmd='feff', override_default_feff_params=None, db_file=None, parents=None, metadata=None, **kwargs)ΒΆ
    +__init__(absorbing_atom, structure, feff_input_set='XANES', edge='K', radius=10.0, name='XAS spectroscopy', feff_cmd='feff', override_default_feff_params=None, db_file=None, parents=None, metadata=None, **kwargs)ΒΆ

    Write the input set for FEFF-XAS spectroscopy, run FEFF and insert the absorption coefficient to the database (or dump to a json file if db_file=None).

    -
    -
    Args:
    -

    absorbing_atom (str): absorbing atom symbol +

    +
    Args:

    absorbing_atom (str): absorbing atom symbol structure (Structure): input structure feff_input_set (str or FeffDictSet subclass): The inputset for setting params. If string

    -
    then either the entire path to the class or spectrum type must be provided -e.g. β€œpymatgen.io.feff.sets.MPXANESSet” or β€œXANES”
    -

    edge (str): absorption edge +

    then either the entire path to the class or spectrum type must be provided +e.g. β€œpymatgen.io.feff.sets.MPXANESSet” or β€œXANES”

    +
    +

    edge (str): absorption edge radius (float): cluster radius in angstroms name (str) feff_cmd (str): path to the feff binary @@ -188,13 +187,11 @@

    This Page

    @@ -212,13 +209,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.feff.fireworks.tests.html b/docs/atomate.feff.fireworks.tests.html index d218e42e2..9bda83d40 100644 --- a/docs/atomate.feff.fireworks.tests.html +++ b/docs/atomate.feff.fireworks.tests.html @@ -1,18 +1,17 @@ - + - - - atomate.feff.fireworks.tests package — atomate 0.9.1 documentation + + atomate.feff.fireworks.tests package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -46,18 +45,18 @@

    Submodules

    atomate.feff.fireworks.tests.test_fireworks moduleΒΆ

    -class atomate.feff.fireworks.tests.test_fireworks.TestFireworks(methodName='runTest')ΒΆ
    +class atomate.feff.fireworks.tests.test_fireworks.TestFireworks(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -setUp()ΒΆ
    +setUp()ΒΆ

    Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

    -test_exafs_paths_fw()ΒΆ
    +test_exafs_paths_fw()ΒΆ
    @@ -92,13 +91,11 @@

    This Page

    @@ -116,13 +113,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.feff.html b/docs/atomate.feff.html index de8dbcea7..b5e8d514f 100644 --- a/docs/atomate.feff.html +++ b/docs/atomate.feff.html @@ -1,18 +1,17 @@ - + - - - atomate.feff package — atomate 0.9.1 documentation + + atomate.feff package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -104,28 +103,28 @@

    Submodules

    atomate.feff.database moduleΒΆ

    -class atomate.feff.database.FeffCalcDb(host='localhost', port=27017, database='feff', collection='tasks', user=None, password=None, **kwargs)ΒΆ
    +class atomate.feff.database.FeffCalcDb(host='localhost', port=27017, database='feff', collection='tasks', user=None, password=None, **kwargs)ΒΆ

    Bases: atomate.utils.database.CalcDb

    -__init__(host='localhost', port=27017, database='feff', collection='tasks', user=None, password=None, **kwargs)ΒΆ
    +__init__(host='localhost', port=27017, database='feff', collection='tasks', user=None, password=None, **kwargs)ΒΆ

    Initialize self. See help(type(self)) for accurate signature.

    -build_indexes(indexes=None, background=True)ΒΆ
    +build_indexes(indexes=None, background=True)ΒΆ

    Build the indexes.

    -
    -
    Args:
    -
    indexes (list): list of single field indexes to be built. -background (bool): Run in the background or not.
    +
    +
    Args:

    indexes (list): list of single field indexes to be built. +background (bool): Run in the background or not.

    +
    -reset()ΒΆ
    +reset()ΒΆ
    @@ -161,13 +160,11 @@

    This Page

    @@ -185,13 +182,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.feff.workflows.html b/docs/atomate.feff.workflows.html index 7e4ab3fd5..4fc90b9bb 100644 --- a/docs/atomate.feff.workflows.html +++ b/docs/atomate.feff.workflows.html @@ -1,18 +1,17 @@ - + - - - atomate.feff.workflows package — atomate 0.9.1 documentation + + atomate.feff.workflows package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -61,42 +60,43 @@

    Submodules

    atomate.feff.workflows.core moduleΒΆ

    -atomate.feff.workflows.core.get_absorbing_atom_indices(structure, absorbing_atom)ΒΆ
    -
    -
    Args:
    -
    structure (Structure): -absorbing_atom (int/str):
    -
    Returns:
    -
    list of site ids
    +atomate.feff.workflows.core.get_absorbing_atom_indices(structure, absorbing_atom)ΒΆ +
    +
    Args:

    structure (Structure): +absorbing_atom (int/str):

    +
    +
    Returns:

    list of site ids

    +
    -atomate.feff.workflows.core.get_unique_site_indices(structure)ΒΆ
    +atomate.feff.workflows.core.get_unique_site_indices(structure)ΒΆ
    -atomate.feff.workflows.core.get_wf_eels(absorbing_atom, structure=None, feff_input_set='pymatgen.io.feff.sets.MPELNESSet', edge='K', radius=10.0, beam_energy=100, beam_direction=None, collection_angle=1, convergence_angle=1, user_eels_settings=None, user_tag_settings=None, feff_cmd='feff', db_file=None, metadata=None, use_primitive=False)ΒΆ
    +atomate.feff.workflows.core.get_wf_eels(absorbing_atom, structure=None, feff_input_set='pymatgen.io.feff.sets.MPELNESSet', edge='K', radius=10.0, beam_energy=100, beam_direction=None, collection_angle=1, convergence_angle=1, user_eels_settings=None, user_tag_settings=None, feff_cmd='feff', db_file=None, metadata=None, use_primitive=False)ΒΆ

    Returns FEFF ELNES/EXELFS spectroscopy workflow.

    -
    -
    Args:
    -

    absorbing_atom (str): absorbing atom symbol +

    +
    Args:

    absorbing_atom (str): absorbing atom symbol structure (Structure): input structure. If None and mp_id is provided, the corresponding

    -
    structure will be fetched from the Materials Project db.
    -
    -
    feff_input_set (str or FeffDictSet subclass): The inputset for setting params. If string
    -
    then either the entire path to the class or spectrum type must be provided -e.g. β€œpymatgen.io.feff.sets.MPELNESSet” or β€œELNES”
    +

    structure will be fetched from the Materials Project db.

    +
    +
    +
    feff_input_set (str or FeffDictSet subclass): The inputset for setting params. If string

    then either the entire path to the class or spectrum type must be provided +e.g. β€œpymatgen.io.feff.sets.MPELNESSet” or β€œELNES”

    +

    edge (str): absorption edge. K, L1, L2, L3 radius (float): cluster radius in angstroms. Ignored for reciprocal space calculations beam_energy (float): the incident beam energy in keV beam_direction (list): incident beam direction. Default is none ==> the spectrum will be

    -
    averaged over all directions.
    +

    averaged over all directions.

    +

    collection_angle (float): collection angle in mrad convergence_angle (float): convergence angle in mrad user_eels_settings (dict): override default eels settings. @@ -105,27 +105,27 @@

    Submodules -
    reduce the number of fireworks in the workflow if the absorbing atoms is -specified by its atomic symbol.
    +
    +

    reduce the number of fireworks in the workflow if the absorbing atoms is +specified by its atomic symbol.

    +
    +

    +
    Returns:

    Workflow

    -
    Returns:
    -
    Workflow
    -atomate.feff.workflows.core.get_wf_exafs_paths(absorbing_atom, structure, paths, degeneracies=None, edge='K', radius=10.0, feff_input_set='pymatgen.io.feff.sets.MPEXAFSSet', feff_cmd='feff', db_file=None, metadata=None, user_tag_settings=None, use_primitive=False, labels=None, filepad_file=None)ΒΆ
    +atomate.feff.workflows.core.get_wf_exafs_paths(absorbing_atom, structure, paths, degeneracies=None, edge='K', radius=10.0, feff_input_set='pymatgen.io.feff.sets.MPEXAFSSet', feff_cmd='feff', db_file=None, metadata=None, user_tag_settings=None, use_primitive=False, labels=None, filepad_file=None)ΒΆ

    Returns FEFF EXAFS spectroscopy workflow that generates the scattering amplitudes for the given list of scattering paths. The scattering amplitude output files(feffNNNN.dat files) are inserted to filepad(see fireworks.utilities.filepad.py) on completion.

    -
    -
    Args:
    -
    -
    absorbing_atom (str/int): absorbing atom symbol or site index. If the symbol is given,
    -
    then the returned workflow will have fireworks for each absorbing site with the -same symbol.
    +
    +
    Args:
    +
    absorbing_atom (str/int): absorbing atom symbol or site index. If the symbol is given,

    then the returned workflow will have fireworks for each absorbing site with the +same symbol.

    +

    structure (Structure): input structure paths (list): list of paths. path = list of site indices. @@ -134,43 +134,45 @@

    Submodules -
    labels ([str]): list of labels for the scattering amplitudes file contents inserted into
    -
    filepad. Useful for fetching the data from filepad later.
    +

    reduce the number of fireworks in the workflow if the absorbing atom is +specified by its atomic symbol.

    +
    +
    +
    labels ([str]): list of labels for the scattering amplitudes file contents inserted into

    filepad. Useful for fetching the data from filepad later.

    +
    -

    filepad_file (str): path to filepad connection settings file.

    +

    filepad_file (str): path to filepad connection settings file.

    +

    +
    Returns:

    Workflow

    -
    Returns:
    -
    Workflow
    -atomate.feff.workflows.core.get_wf_xas(absorbing_atom, structure, feff_input_set='pymatgen.io.feff.sets.MPXANESSet', edge='K', radius=10.0, feff_cmd='feff', db_file=None, metadata=None, user_tag_settings=None, use_primitive=False)ΒΆ
    +atomate.feff.workflows.core.get_wf_xas(absorbing_atom, structure, feff_input_set='pymatgen.io.feff.sets.MPXANESSet', edge='K', radius=10.0, feff_cmd='feff', db_file=None, metadata=None, user_tag_settings=None, use_primitive=False)ΒΆ

    Returns FEFF XANES/EXAFS spectroscopy workflow.

    -
    -
    Args:
    -
    -
    absorbing_atom (str/int): absorbing atom symbol or site index. If the symbol is given,
    -
    then the returned workflow will have fireworks for each absorbing site with the -same symbol.
    +
    +
    Args:
    +
    absorbing_atom (str/int): absorbing atom symbol or site index. If the symbol is given,

    then the returned workflow will have fireworks for each absorbing site with the +same symbol.

    +

    structure (Structure): input structure feff_input_set (str or FeffDictSet subclass): The inputset for setting params. If string

    -
    then either the entire path to the class or spectrum type must be provided -e.g. β€œpymatgen.io.feff.sets.MPXANESSet” or β€œXANES”
    +

    then either the entire path to the class or spectrum type must be provided +e.g. β€œpymatgen.io.feff.sets.MPXANESSet” or β€œXANES”

    +

    edge (str): absorption edge. Example: K, L1, L2, L3 radius (float): cluster radius in angstroms. Ignored for K space calculations feff_cmd (str): path to the feff binary @@ -178,12 +180,13 @@

    Submodules -
    reduce the number of fireworks in the workflow if the absorbing atom is -specified by its atomic symbol.
    +
    +

    reduce the number of fireworks in the workflow if the absorbing atom is +specified by its atomic symbol.

    +
    +

    +
    Returns:

    Workflow

    -
    Returns:
    -
    Workflow
    @@ -192,7 +195,7 @@

    Submodules

    atomate.feff.workflows.presets moduleΒΆ

    -atomate.feff.workflows.presets.wf_Xanes_K_edge(structure, c=None)ΒΆ
    +atomate.feff.workflows.presets.wf_Xanes_K_edge(structure, c=None)ΒΆ
    @@ -227,13 +230,11 @@

    This Page

    @@ -251,13 +252,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.feff.workflows.tests.html b/docs/atomate.feff.workflows.tests.html index 52623dc7b..0303292e2 100644 --- a/docs/atomate.feff.workflows.tests.html +++ b/docs/atomate.feff.workflows.tests.html @@ -1,18 +1,17 @@ - + - - - atomate.feff.workflows.tests package — atomate 0.9.1 documentation + + atomate.feff.workflows.tests package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -46,28 +45,28 @@

    Submodules

    atomate.feff.workflows.tests.test_eels_workflows moduleΒΆ

    -class atomate.feff.workflows.tests.test_eels_workflows.TestEELSWorkflow(methodName='runTest')ΒΆ
    +class atomate.feff.workflows.tests.test_eels_workflows.TestEELSWorkflow(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -setUp()ΒΆ
    +setUp()ΒΆ

    Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

    -test_eels_wflow_abatom_by_idx()ΒΆ
    +test_eels_wflow_abatom_by_idx()ΒΆ
    -test_eels_wflow_abatom_by_symbol()ΒΆ
    +test_eels_wflow_abatom_by_symbol()ΒΆ
    -test_elnes_vs_exelfs()ΒΆ
    +test_elnes_vs_exelfs()ΒΆ
    @@ -77,27 +76,27 @@

    Submodules

    atomate.feff.workflows.tests.test_exafs_scattering_paths moduleΒΆ

    -class atomate.feff.workflows.tests.test_exafs_scattering_paths.TestEXAFSPaths(methodName='runTest')ΒΆ
    +class atomate.feff.workflows.tests.test_exafs_scattering_paths.TestEXAFSPaths(methodName='runTest')ΒΆ

    Bases: unittest.case.TestCase

    -setUp()ΒΆ
    +setUp()ΒΆ

    Hook method for setting up the test fixture before exercising it.

    -test_feff_input_sets()ΒΆ
    +test_feff_input_sets()ΒΆ
    -test_paths()ΒΆ
    +test_paths()ΒΆ
    -test_wflow_composition()ΒΆ
    +test_wflow_composition()ΒΆ
    @@ -107,28 +106,28 @@

    Submodules

    atomate.feff.workflows.tests.test_xas_workflows moduleΒΆ

    -class atomate.feff.workflows.tests.test_xas_workflows.TestXASWorkflow(methodName='runTest')ΒΆ
    +class atomate.feff.workflows.tests.test_xas_workflows.TestXASWorkflow(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -setUp()ΒΆ
    +setUp()ΒΆ

    Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

    -test_xanes_vs_exafs()ΒΆ
    +test_xanes_vs_exafs()ΒΆ
    -test_xas_wflow_abatom_by_idx()ΒΆ
    +test_xas_wflow_abatom_by_idx()ΒΆ
    -test_xas_wflow_abatom_by_symbol()ΒΆ
    +test_xas_wflow_abatom_by_symbol()ΒΆ
    @@ -165,13 +164,11 @@

    This Page

    @@ -189,13 +186,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.html b/docs/atomate.html index 72249d79a..ab5c41bc3 100644 --- a/docs/atomate.html +++ b/docs/atomate.html @@ -1,18 +1,17 @@ - + - - - atomate package — atomate 0.9.1 documentation + + atomate package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -402,13 +401,11 @@

    This Page

    @@ -426,13 +423,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.lammps.firetasks.html b/docs/atomate.lammps.firetasks.html index 7b67c7837..92b1b3005 100644 --- a/docs/atomate.lammps.firetasks.html +++ b/docs/atomate.lammps.firetasks.html @@ -1,18 +1,17 @@ - + - - - atomate.lammps.firetasks package — atomate 0.9.1 documentation + + atomate.lammps.firetasks package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -46,41 +45,40 @@

    Submodules

    atomate.lammps.firetasks.glue_tasks moduleΒΆ

    -class atomate.lammps.firetasks.glue_tasks.CopyPackmolOutputs(*args, **kwargs)ΒΆ
    +class atomate.lammps.firetasks.glue_tasks.CopyPackmolOutputs(*args, **kwargs)ΒΆ

    Bases: atomate.common.firetasks.glue_tasks.CopyFiles

    Copy files from a previous run directory to the current directory. Note: must specify either β€œcalc_loc” or β€œcalc_dir” to indicate the directory

    -
    containing the files to copy.
    -
    -
    Optional params:
    -
    -
    calc_loc (str OR bool): if True will set most recent calc_loc. If str
    -
    search for the most recent calc_loc with the matching name.
    +

    containing the files to copy.

    +
    +
    +
    Optional params:
    +
    calc_loc (str OR bool): if True will set most recent calc_loc. If str

    search for the most recent calc_loc with the matching name.

    +

    calc_dir (str): path to dir that contains VASP output files. filesystem (str): remote filesystem. e.g. username@host exclude_files (list): list fo filenames to be excluded when copying.

    -
    -
    NOte: by default nothing is excluded.
    +
    +

    NOte: by default nothing is excluded.

    +
    -optional_params = ['calc_loc', 'calc_dir', 'filesystem', 'exclude_files']ΒΆ
    +optional_params = ['calc_loc', 'calc_dir', 'filesystem', 'exclude_files']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -88,11 +86,12 @@

    Submodules

    atomate.lammps.firetasks.parse_outputs moduleΒΆ

    -class atomate.lammps.firetasks.parse_outputs.LammpsToDB(*args, **kwargs)ΒΆ
    +class atomate.lammps.firetasks.parse_outputs.LammpsToDB(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Enter a LAMMPS calculation into the database.

    -
    -
    required_params:
    -
    input_filename (str)
    -
    optional_params:
    -
    -
    calc_dir (str): path to dir (on current filesystem) that contains LAMMPS
    -
    output files. Default: use current working directory.
    -
    calc_loc (str OR bool): if True will set most recent calc_loc. If str
    -
    search for the most recent calc_loc with the matching name
    -
    db_file (str): path to file containing the database credentials.
    -
    Supports env_chk. Default: write data to JSON file.
    +
    +
    required_params:

    input_filename (str)

    +
    +
    optional_params:
    +
    calc_dir (str): path to dir (on current filesystem) that contains LAMMPS

    output files. Default: use current working directory.

    +
    +
    calc_loc (str OR bool): if True will set most recent calc_loc. If str

    search for the most recent calc_loc with the matching name

    +
    +
    db_file (str): path to file containing the database credentials.

    Supports env_chk. Default: write data to JSON file.

    +
    -

    fw_spec_field: +

    fw_spec_field: data_filename: log_filename: dump_filenames: @@ -128,25 +126,23 @@

    Submodules
    -optional_params = ['calc_dir', 'calc_loc', 'db_file', 'fw_spec_field', 'data_filename', 'log_filename', 'dump_filenames', 'diffusion_params', 'additional_fields']ΒΆ
    +optional_params = ['calc_dir', 'calc_loc', 'db_file', 'fw_spec_field', 'data_filename', 'log_filename', 'dump_filenames', 'diffusion_params', 'additional_fields']ΒΆ

    -required_params = ['input_filename']ΒΆ
    +required_params = ['input_filename']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -154,11 +150,12 @@

    Submodules

    atomate.lammps.firetasks.run_calc moduleΒΆ

    -class atomate.lammps.firetasks.run_calc.RunLammpsDirect(*args, **kwargs)ΒΆ
    +class atomate.lammps.firetasks.run_calc.RunLammpsDirect(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Run LAMMPS directly (no custodian).

    -
    -
    Required params:
    -
    -
    lammsps_cmd (str): lammps command to run sans the input file name.
    -
    e.g. β€˜mpirun -n 4 lmp_mpi’
    +
    +
    Required params:
    +
    lammsps_cmd (str): lammps command to run sans the input file name.

    e.g. β€˜mpirun -n 4 lmp_mpi’

    +
    -required_params = ['lammps_cmd', 'input_filename']ΒΆ
    +required_params = ['lammps_cmd', 'input_filename']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -203,11 +197,12 @@

    Submodules
    -class atomate.lammps.firetasks.run_calc.RunLammpsFake(*args, **kwargs)ΒΆ
    +class atomate.lammps.firetasks.run_calc.RunLammpsFake(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Pretend run i.e just copy files from existing run dir.

    -
    -
    Required params:
    -
    ref_dir (str): path to the reference dir
    +
    +
    Required params:

    ref_dir (str): path to the reference dir

    +
    -required_params = ['ref_dir']ΒΆ
    +required_params = ['ref_dir']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -245,11 +238,12 @@

    Submodules
    -class atomate.lammps.firetasks.run_calc.RunPackmol(*args, **kwargs)ΒΆ
    +class atomate.lammps.firetasks.run_calc.RunPackmol(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Run packmol.

    -
    -
    Required params:
    -

    molecules (list): list of constituent molecules(Molecule objects) +

    +
    Required params:

    molecules (list): list of constituent molecules(Molecule objects) packing_config (list): list of dict config settings for each molecule in the

    -
    -
    molecules list. eg: config settings for a single moelcule -[{β€œnumber”: 1, β€œinside box”:[0,0,0,100,100,100]}]
    +
    +

    molecules list. eg: config settings for a single moelcule +[{β€œnumber”: 1, β€œinside box”:[0,0,0,100,100,100]}]

    +
    -
    Optional params:
    -

    tolerance (float): packmol tolerance +

    Optional params:

    tolerance (float): packmol tolerance filetype (string): input/output structure file type control_params (dict): packmol control parameters dictionary. Basically all parameters other

    -
    than structure/atoms
    +

    than structure/atoms

    +

    output_file (str): output file name. The extension will be adjusted according to the filetype copy_to_current_on_exit (bool): whether or not to copy the packed molecule output file to

    -
    the current directory.
    -

    site_property (str): the specified site property will be restored for the final Molecule object.

    +

    the current directory.

    +
    +

    site_property (str): the specified site property will be restored for the final Molecule object.

    -optional_params = ['tolerance', 'filetype', 'control_params', 'output_file', 'copy_to_current_on_exit', 'site_property']ΒΆ
    +optional_params = ['tolerance', 'filetype', 'control_params', 'output_file', 'copy_to_current_on_exit', 'site_property']ΒΆ
    -required_params = ['molecules', 'packing_config', 'packmol_cmd']ΒΆ
    +required_params = ['molecules', 'packing_config', 'packmol_cmd']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -309,11 +302,12 @@

    Submodules

    atomate.lammps.firetasks.write_inputs moduleΒΆ

    -class atomate.lammps.firetasks.write_inputs.WriteInputFromForceFieldAndTopology(*args, **kwargs)ΒΆ
    +class atomate.lammps.firetasks.write_inputs.WriteInputFromForceFieldAndTopology(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    -optional_params = ['data_filename', 'user_settings', 'ff_site_property']ΒΆ
    +optional_params = ['data_filename', 'user_settings', 'ff_site_property']ΒΆ
    -required_params = ['input_file', 'final_molecule', 'constituent_molecules', 'mols_number', 'box_size', 'forcefield', 'topologies', 'input_filename']ΒΆ
    +required_params = ['input_file', 'final_molecule', 'constituent_molecules', 'mols_number', 'box_size', 'forcefield', 'topologies', 'input_filename']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -354,11 +346,12 @@

    Submodules
    -class atomate.lammps.firetasks.write_inputs.WriteInputFromIOSet(*args, **kwargs)ΒΆ
    +class atomate.lammps.firetasks.write_inputs.WriteInputFromIOSet(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Writes LAMMPS Input files(data file and the control parameters file) from DictLammpsInput.

    -
    -
    required_params:
    -
    lammps_input_set (LammpsInputSet) -input_file (string): name of the file to which the input params will be written
    -
    optional_params:
    -
    data_filename (string): if specified the data file will be renamed
    +
    +
    required_params:

    lammps_input_set (LammpsInputSet) +input_file (string): name of the file to which the input params will be written

    +
    +
    optional_params:

    data_filename (string): if specified the data file will be renamed

    +
    -optional_params = ['data_filename']ΒΆ
    +optional_params = ['data_filename']ΒΆ
    -required_params = ['lammps_input_set', 'input_filename']ΒΆ
    +required_params = ['lammps_input_set', 'input_filename']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -404,11 +395,12 @@

    Submodules
  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.lammps.fireworks.html b/docs/atomate.lammps.fireworks.html index fac368f0f..35f8e1b04 100644 --- a/docs/atomate.lammps.fireworks.html +++ b/docs/atomate.lammps.fireworks.html @@ -1,18 +1,17 @@ - + - - - atomate.lammps.fireworks package — atomate 0.9.1 documentation + + atomate.lammps.fireworks package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -46,21 +45,21 @@

    Submodules

    atomate.lammps.fireworks.core moduleΒΆ

    -class atomate.lammps.fireworks.core.LammpsFW(lammps_input_set, input_filename='lammps.in', data_filename='lammps.data', lammps_cmd='lammps', db_file=None, parents=None, name='LammpsFW', log_filename='log.lammps', dump_filename=None, **kwargs)ΒΆ
    +class atomate.lammps.fireworks.core.LammpsFW(lammps_input_set, input_filename='lammps.in', data_filename='lammps.data', lammps_cmd='lammps', db_file=None, parents=None, name='LammpsFW', log_filename='log.lammps', dump_filename=None, **kwargs)ΒΆ

    Bases: fireworks.core.firework.Firework

    -__init__(lammps_input_set, input_filename='lammps.in', data_filename='lammps.data', lammps_cmd='lammps', db_file=None, parents=None, name='LammpsFW', log_filename='log.lammps', dump_filename=None, **kwargs)ΒΆ
    +__init__(lammps_input_set, input_filename='lammps.in', data_filename='lammps.data', lammps_cmd='lammps', db_file=None, parents=None, name='LammpsFW', log_filename='log.lammps', dump_filename=None, **kwargs)ΒΆ

    write lammps inputset, run, and store the output.

    -
    -
    Args:
    -

    lammps_input_set (DictLammpsInput): lammps input set +

    +
    Args:

    lammps_input_set (DictLammpsInput): lammps input set input_filename (str): input file name data_filename (str): data file name lammps_cmd (str): command to run lammps (skip the input file).

    -
    e.g. β€˜mpirun -n 8 lmp_mpi’
    -

    db_file (str): path to file specifying db credentials to place output parsing. +

    e.g. β€˜mpirun -n 8 lmp_mpi’

    +
    +

    db_file (str): path to file specifying db credentials to place output parsing. parents ([Fireworks)]: parents of this particular Firework. name (str): descriptive name for lammps simulation log_filename (str) @@ -74,23 +73,23 @@

    Submodules
    -class atomate.lammps.fireworks.core.LammpsForceFieldFW(input_file, final_molecule, forcefield, box_size, topologies=None, constituent_molecules=None, mols_number=None, user_settings=None, ff_site_property=None, input_filename='lammps.in', data_filename='lammps.data', lammps_cmd='lammps', db_file=None, parents=None, log_filename='log.lammps', dump_filenames=None, name='LammpsFFFW', **kwargs)ΒΆ
    +class atomate.lammps.fireworks.core.LammpsForceFieldFW(input_file, final_molecule, forcefield, box_size, topologies=None, constituent_molecules=None, mols_number=None, user_settings=None, ff_site_property=None, input_filename='lammps.in', data_filename='lammps.data', lammps_cmd='lammps', db_file=None, parents=None, log_filename='log.lammps', dump_filenames=None, name='LammpsFFFW', **kwargs)ΒΆ

    Bases: fireworks.core.firework.Firework

    -__init__(input_file, final_molecule, forcefield, box_size, topologies=None, constituent_molecules=None, mols_number=None, user_settings=None, ff_site_property=None, input_filename='lammps.in', data_filename='lammps.data', lammps_cmd='lammps', db_file=None, parents=None, log_filename='log.lammps', dump_filenames=None, name='LammpsFFFW', **kwargs)ΒΆ
    +__init__(input_file, final_molecule, forcefield, box_size, topologies=None, constituent_molecules=None, mols_number=None, user_settings=None, ff_site_property=None, input_filename='lammps.in', data_filename='lammps.data', lammps_cmd='lammps', db_file=None, parents=None, log_filename='log.lammps', dump_filenames=None, name='LammpsFFFW', **kwargs)ΒΆ

    Write lammps input from forcefield and topology, run lammps, store results. Can be used with RunPackmol firework.

    -
    -
    Args:
    -

    input_file (str): path to lammps input(or template) file. +

    +
    Args:

    input_file (str): path to lammps input(or template) file. final_molecule (str/Molecule): either path to the moelcule of Molecule object. forcefield (ForceField): pymatgen.io.lammps.force_field.ForceField object box_size (list): list of list of low and high values for each dimension [[xlow, xhigh], …] topologies ([Topology]): list of pymatgen.io.lammps.topology.Topology objects, one for

    -
    each constituent molecule.
    -

    constituent_molecules ([Molecule]): list of Molecule objects that make up the final_molecule +

    each constituent molecule.

    +
    +

    constituent_molecules ([Molecule]): list of Molecule objects that make up the final_molecule mols_number (list): list of number of each constituent moelcule. user_settings (dict): ff_site_property (str): the site property used for forcefiled mapping @@ -111,28 +110,30 @@

    Submodules
    -class atomate.lammps.fireworks.core.PackmolFW(molecules, packing_config, tolerance=2.0, filetype='xyz', control_params=None, output_file='packed.xyz', copy_to_current_on_exit=False, site_property=None, parents=None, name='PackmolFW', packmol_cmd='packmol', **kwargs)ΒΆ
    +class atomate.lammps.fireworks.core.PackmolFW(molecules, packing_config, tolerance=2.0, filetype='xyz', control_params=None, output_file='packed.xyz', copy_to_current_on_exit=False, site_property=None, parents=None, name='PackmolFW', packmol_cmd='packmol', **kwargs)ΒΆ

    Bases: fireworks.core.firework.Firework

    -__init__(molecules, packing_config, tolerance=2.0, filetype='xyz', control_params=None, output_file='packed.xyz', copy_to_current_on_exit=False, site_property=None, parents=None, name='PackmolFW', packmol_cmd='packmol', **kwargs)ΒΆ
    -
    -
    Args:
    -

    molecules (list): list of constituent molecules(Molecule objects) +__init__(molecules, packing_config, tolerance=2.0, filetype='xyz', control_params=None, output_file='packed.xyz', copy_to_current_on_exit=False, site_property=None, parents=None, name='PackmolFW', packmol_cmd='packmol', **kwargs)ΒΆ +

    +
    Args:

    molecules (list): list of constituent molecules(Molecule objects) packing_config (list): list of dict config settings for each molecule in the

    -
    molecules list. eg: config settings for a single molecule -[{β€œnumber”: 1, β€œinside box”:[0,0,0,100,100,100]}]
    +

    molecules list. eg: config settings for a single molecule +[{β€œnumber”: 1, β€œinside box”:[0,0,0,100,100,100]}]

    +

    tolerance (float): packmol tolerance filetype (string): input/output structure file type control_params (dict): packmol control parameters dictionary. Basically all parameters

    -
    other than structure/atoms.
    +

    other than structure/atoms.

    +

    output_file (str): output file name. The extension will be adjusted according to the filetype. copy_to_current_on_exit (bool): whether or not to copy the packed molecule output file

    -
    to the current directory.
    -

    site_property (str): the specified site property will be restored for the final Molecule object. +

    to the current directory.

    +
    +

    site_property (str): the specified site property will be restored for the final Molecule object. parents ([Firework]): parent fireworks name (str): firework name packmol_cmd (str): path to packmol bin @@ -173,13 +174,11 @@

    This Page

    @@ -197,13 +196,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.lammps.html b/docs/atomate.lammps.html index 6caaca151..5991ebc27 100644 --- a/docs/atomate.lammps.html +++ b/docs/atomate.lammps.html @@ -1,18 +1,17 @@ - + - - - atomate.lammps package — atomate 0.9.1 documentation + + atomate.lammps package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -74,28 +73,28 @@

    Submodules

    atomate.lammps.database moduleΒΆ

    -class atomate.lammps.database.LammpsCalcDb(host='localhost', port=27017, database='lammps', collection='tasks', user=None, password=None, **kwargs)ΒΆ
    +class atomate.lammps.database.LammpsCalcDb(host='localhost', port=27017, database='lammps', collection='tasks', user=None, password=None, **kwargs)ΒΆ

    Bases: atomate.utils.database.CalcDb

    -__init__(host='localhost', port=27017, database='lammps', collection='tasks', user=None, password=None, **kwargs)ΒΆ
    +__init__(host='localhost', port=27017, database='lammps', collection='tasks', user=None, password=None, **kwargs)ΒΆ

    Initialize self. See help(type(self)) for accurate signature.

    -build_indexes(indexes=None, background=True)ΒΆ
    +build_indexes(indexes=None, background=True)ΒΆ

    Build the indexes.

    -
    -
    Args:
    -
    indexes (list): list of single field indexes to be built. -background (bool): Run in the background or not.
    +
    +
    Args:

    indexes (list): list of single field indexes to be built. +background (bool): Run in the background or not.

    +
    -reset()ΒΆ
    +reset()ΒΆ
    @@ -105,67 +104,67 @@

    Submodules

    atomate.lammps.drones moduleΒΆ

    -class atomate.lammps.drones.LammpsDrone(additional_fields=None, use_full_uri=True, diffusion_params=None)ΒΆ
    +class atomate.lammps.drones.LammpsDrone(additional_fields=None, use_full_uri=True, diffusion_params=None)ΒΆ

    Bases: pymatgen.apps.borg.hive.AbstractDrone

    -__init__(additional_fields=None, use_full_uri=True, diffusion_params=None)ΒΆ
    -
    -
    Args:
    -

    additional_fields (dict): +__init__(additional_fields=None, use_full_uri=True, diffusion_params=None)ΒΆ +

    +
    Args:

    additional_fields (dict): use_full_uri (bool): diffusion_params (dict): parameters to the diffusion_analyzer. If specified a summary

    -
    -
    of diffusion statistics will be added.
    +
    +

    of diffusion statistics will be added.

    +
    -as_dict()ΒΆ
    +as_dict()ΒΆ

    A JSON serializable dict representation of an object.

    -assimilate(path, input_filename, log_filename='log.lammps', is_forcefield=False, data_filename=None, dump_files=None)ΒΆ
    +assimilate(path, input_filename, log_filename='log.lammps', is_forcefield=False, data_filename=None, dump_files=None)ΒΆ

    Parses lammps input, data and log files and insert the result into the db.

    -
    -
    Args:
    -
    path (str): path to the run folder +
    +
    Args:

    path (str): path to the run folder input_filename (str): just the name of the input file log_filename (str): lammps log file name is_forcefield (bool): whether or not ot parse forcefield info data_filename (str): name of the data file -dump_files ([str]): list of dump file names

    -
    Returns:
    -
    dict
    +dump_files ([str]): list of dump file names

    +
    +
    Returns:

    dict

    +
    -
    +
    -classmethod from_dict(d)ΒΆ
    +classmethod from_dict(d)ΒΆ
    -generate_doc(dir_name, lmps_input, log, dumps)ΒΆ
    -
    -
    Args:
    -
    dir_name (str): path to the run dir. +generate_doc(dir_name, lmps_input, log, dumps)ΒΆ +
    +
    Args:

    dir_name (str): path to the run dir. lmps_input (LammpsInput/LammpsInputSet): log (LammpsLog): -dumps ([(filename, LammpsDump)]): list of (dump filename, dump) tuples

    -
    Returns:
    -
    dict
    +dumps ([(filename, LammpsDump)]): list of (dump filename, dump) tuples

    +
    +
    Returns:

    dict

    +
    -get_valid_paths(path)ΒΆ
    +get_valid_paths(path)ΒΆ

    Checks if path contains valid data for assimilation, and then returns the valid paths. The paths returned can be a list of directory or file paths, depending on what kind of data you are assimilating. For @@ -173,32 +172,31 @@

    Submodules -
    Args:
    -
    -
    path: input path as a tuple generated from os.walk, i.e.,
    -
    (parent, subdirs, files).
    +
    +
    Args:
    +
    path: input path as a tuple generated from os.walk, i.e.,

    (parent, subdirs, files).

    +
    -
    Returns:
    -
    List of valid dir/file paths for assimilation
    +
    Returns:

    List of valid dir/file paths for assimilation

    +

    -post_process(d, lmps_run)ΒΆ
    +post_process(d, lmps_run)ΒΆ

    Simple post processing.

    -
    -
    Args:
    -
    d (dict) -lmps_run (LammpsRun)
    +
    +
    Args:

    d (dict) +lmps_run (LammpsRun)

    +
    -schema = {'root': {'completed_at', 'dir_name', 'input', 'last_updated', 'output', 'schema', 'state'}}ΒΆ
    +schema = {'root': {'completed_at', 'dir_name', 'input', 'last_updated', 'output', 'schema', 'state'}}ΒΆ
    @@ -208,7 +206,7 @@

    Submodules

    atomate.lammps.utils moduleΒΆ

    -atomate.lammps.utils.use_fake_lammps(original_wf, ref_dir)ΒΆ
    +atomate.lammps.utils.use_fake_lammps(original_wf, ref_dir)ΒΆ
    @@ -244,13 +242,11 @@

    This Page

    @@ -268,13 +264,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.lammps.workflows.html b/docs/atomate.lammps.workflows.html index a721be041..e833292f7 100644 --- a/docs/atomate.lammps.workflows.html +++ b/docs/atomate.lammps.workflows.html @@ -1,18 +1,17 @@ - + - - - atomate.lammps.workflows package — atomate 0.9.1 documentation + + atomate.lammps.workflows package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -46,24 +45,25 @@

    Submodules

    atomate.lammps.workflows.core moduleΒΆ

    -atomate.lammps.workflows.core.get_packmol_wf(input_file, user_settings, constituent_molecules, packing_config, forcefield, final_box_size, topologies=None, ff_site_property=None, tolerance=2.0, filetype='xyz', control_params=None, lammps_cmd='lmp_serial', packmol_cmd='packmol', dump_filenames=None, db_file=None, name='Packmol Lammps Wflow')ΒΆ
    +atomate.lammps.workflows.core.get_packmol_wf(input_file, user_settings, constituent_molecules, packing_config, forcefield, final_box_size, topologies=None, ff_site_property=None, tolerance=2.0, filetype='xyz', control_params=None, lammps_cmd='lmp_serial', packmol_cmd='packmol', dump_filenames=None, db_file=None, name='Packmol Lammps Wflow')ΒΆ

    Returns workflow that uses Packmol to pack the constituent molecules into the given configuration and then run lammps on the final packed molecule for the given list of user_settings.

    -
    -
    Args:
    -

    input_file (str): path to lammps input(or template) file. +

    +
    Args:

    input_file (str): path to lammps input(or template) file. user_settings ([dict] or dict): list of settings dict. if the input_file is a tempalte file

    -
    then each dict contains the key value pairs for the template file.
    +

    then each dict contains the key value pairs for the template file.

    +

    constituent_molecules ([Molecules]): list of pymatgen Molecule objects packing_config ([dict]): list of configuration dictionaries, one for each constituent molecule. forcefield (ForceField): pymatgen.io.lammps.forcefield.ForceField object final_box_size ([list]): list of list of low and high values for each dimension [[xlow, xhigh], …] topologies ([Topology]): list of Topology objects. If not given, will be set from the

    -
    topology of the constituent molecules.
    -

    ff_site_property (str): the name of the site property used for forcefield mapping +

    topology of the constituent molecules.

    +
    +

    ff_site_property (str): the name of the site property used for forcefield mapping tolerance (float): packmol tolerance filetype (str): packmol i/o file type. control_params (dict): packmol control params @@ -73,37 +73,36 @@

    Submodules
    -atomate.lammps.workflows.core.get_wf_basic(input_file, user_settings, lammps_data=None, input_filename='lammps.in', is_forcefield=False, lammps_cmd='lmp_serial', dump_filenames=None, db_file=None, name='LAMMPS Wflow')ΒΆ
    +atomate.lammps.workflows.core.get_wf_basic(input_file, user_settings, lammps_data=None, input_filename='lammps.in', is_forcefield=False, lammps_cmd='lmp_serial', dump_filenames=None, db_file=None, name='LAMMPS Wflow')ΒΆ

    Returns basic lammps workflow. This is more useful if the input_file is template file with the corresponding settings defined in user_settings

    -
    -
    Args:
    -
    -
    input_file (str): path to lammps input file.
    -
    Note: It could be a template file too, then the user_settings must be set.
    -
    user_settings ([dict] or dict): list of settings dict. if the input_file is a tempalte file
    -
    then each dict contains the key value pairs for the template file.
    -
    lammps_data (string/LammpsData/LammpsForceFieldData): path to the data file or
    -
    an appropriate object.
    -
    input_filename (string): input file name. This is the name of the input file passed to the
    -
    lammps binary.
    -
    is_forcefield (bool): whether the data file has forcefield and topology info in it.
    -
    This is required only if lammps_data is a path to the data file instead of a data object.
    +
    +
    Args:
    +
    input_file (str): path to lammps input file.

    Note: It could be a template file too, then the user_settings must be set.

    +
    +
    user_settings ([dict] or dict): list of settings dict. if the input_file is a tempalte file

    then each dict contains the key value pairs for the template file.

    +
    +
    lammps_data (string/LammpsData/LammpsForceFieldData): path to the data file or

    an appropriate object.

    +
    +
    input_filename (string): input file name. This is the name of the input file passed to the

    lammps binary.

    +
    +
    is_forcefield (bool): whether the data file has forcefield and topology info in it.

    This is required only if lammps_data is a path to the data file instead of a data object.

    +
    -

    lammps_cmd (string): lammps command to run (skip the input file). +

    lammps_cmd (string): lammps command to run (skip the input file). dump_filenames ([str]): list of dump file names db_file (string): path to the db file. name (str): workflow name

    -
    Returns:
    -
    Workflow
    +
    Returns:

    Workflow

    +
    @@ -137,13 +136,11 @@

    This Page

    @@ -161,13 +158,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.qchem.firetasks.html b/docs/atomate.qchem.firetasks.html index 50113d76d..a20ef5e56 100644 --- a/docs/atomate.qchem.firetasks.html +++ b/docs/atomate.qchem.firetasks.html @@ -1,18 +1,17 @@ - + - - - atomate.qchem.firetasks package — atomate 0.9.1 documentation + + atomate.qchem.firetasks package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -62,66 +61,68 @@

    Submodules

    atomate.qchem.firetasks.fragmenter moduleΒΆ

    -class atomate.qchem.firetasks.fragmenter.FragmentMolecule(*args, **kwargs)ΒΆ
    +class atomate.qchem.firetasks.fragmenter.FragmentMolecule(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Simulate all unique fragments of a molecule relevant for realistic fragmentation of the molecule itself or of its subfragments.

    -
    -
    Realistic fragmentation of a neutral molecule will almost always be one of the following:
    -
    molecule(charge=0) -> fragment1(charge=0) + fragment2(charge=0) +
    +
    Realistic fragmentation of a neutral molecule will almost always be one of the following:

    molecule(charge=0) -> fragment1(charge=0) + fragment2(charge=0) molecule(charge=0) -> fragment1(charge=1) + fragment2(charge=-1) -molecule(charge=0) -> fragment1(charge=-1) + fragment2(charge=1)

    +molecule(charge=0) -> fragment1(charge=-1) + fragment2(charge=1)

    +

    Thus, we want to simulate charges -1, 0, and 1 of each fragment.

    Realistic fragmentation of a positively charged molecule (using charge=1 as an example here) will almost always be one of the following:

    -
    molecule(charge=1) -> fragment1(charge=0) + fragment2(charge=1) -molecule(charge=1) -> fragment1(charge=1) + fragment2(charge=0)
    +

    molecule(charge=1) -> fragment1(charge=0) + fragment2(charge=1) +molecule(charge=1) -> fragment1(charge=1) + fragment2(charge=0)

    +

    Thus, we want to simulate charges 0 and 1 of each fragment, given charge=1. Generalizing to any positively charged principle with charge P, we simulate P and P-1.

    Realistic fragmentation of a negatively charged molecule (using charge=-1 as an example here) will almost always be one of the following:

    -
    molecule(charge=-1) -> fragment1(charge=0) + fragment2(charge=-1) -molecule(charge=-1) -> fragment1(charge=-1) + fragment2(charge=0)
    +

    molecule(charge=-1) -> fragment1(charge=0) + fragment2(charge=-1) +molecule(charge=-1) -> fragment1(charge=-1) + fragment2(charge=0)

    +

    Thus, we want to simulate charges -1 and 0 of each fragment, given charge=-1. Generalizing to any positively charged principle with charge P, we simulate P and P+1.

    If additional charges are desired by the user, they can be specified with the additional_charges input parameter as described below.

    -
    -
    Optional params:
    -

    molecule (Molecule): The molecule to fragment +

    +
    Optional params:

    molecule (Molecule): The molecule to fragment edges (list): List of index pairs that define graph edges, aka molecule bonds. If not

    -
    set, edges will be determined with OpenBabel.
    -
    -
    depth (int): The number of levels of iterative fragmentation to perform, where each
    -
    level will include fragments obtained by breaking one bond of a fragment +

    set, edges will be determined with OpenBabel.

    +
    +
    +
    depth (int): The number of levels of iterative fragmentation to perform, where each

    level will include fragments obtained by breaking one bond of a fragment one level up. Defaults to 1. However, if set to 0, instead all possible -fragments are generated using an alternative, non-iterative scheme.

    -
    open_rings (bool): Whether or not to open any rings encountered during fragmentation.
    -
    Defaults to True. If true, any bond that fails to yield disconnected +fragments are generated using an alternative, non-iterative scheme.

    +
    +
    open_rings (bool): Whether or not to open any rings encountered during fragmentation.

    Defaults to True. If true, any bond that fails to yield disconnected graphs when broken is instead removed and the entire structure is optimized with OpenBabel in order to obtain a good initial guess for an opened geometry that can then be put back into QChem to be -optimized without the ring just reforming.

    +optimized without the ring just reforming.

    +

    opt_steps (int): Number of optimization steps when opening rings. Defaults to 10000. additional_charges (list): List of additional charges besides the defaults described

    -
    above. For example, if a principle molecule with a +2 charge +

    above. For example, if a principle molecule with a +2 charge is provided, by default all fragments will be calculated with +1 and +2 charges as explained above. If the user includes additional_charges=[0] then all fragments will be calculated with 0, +1, and +2 charges. Additional charge values of 1 or 2 would not cause any new charges to be calculated as they are -already done. Defaults to [].

    -
    -
    do_triplets (bool): Whether to simulate triplets as well as singlets for molecules with
    -
    an even number of electrons. Defaults to True.
    -
    qchem_input_params (dict): Specify kwargs for instantiating the input set parameters.
    -
    Basic uses would be to modify the default inputs of the set, +already done. Defaults to [].

    + +
    +
    do_triplets (bool): Whether to simulate triplets as well as singlets for molecules with

    an even number of electrons. Defaults to True.

    +
    +
    qchem_input_params (dict): Specify kwargs for instantiating the input set parameters.

    Basic uses would be to modify the default inputs of the set, such as dft_rung, basis_set, pcm_dielectric, scf_algorithm, or max_scf_cycles. See pymatgen/io/qchem/sets.py for default values of all input parameters. For instance, if a user wanted @@ -137,31 +138,31 @@

    Submodules -
    Defaults to bool(db_file), aka true if a db_file is present and -false if db_file is None.
    +
    +

    Defaults to bool(db_file), aka true if a db_file is present and +false if db_file is None.

    +

    -optional_params = ['molecule', 'edges', 'depth', 'open_rings', 'opt_steps', 'additional_charges', 'do_triplets', 'qchem_input_params', 'db_file', 'check_db']ΒΆ
    +optional_params = ['molecule', 'edges', 'depth', 'open_rings', 'opt_steps', 'additional_charges', 'do_triplets', 'qchem_input_params', 'db_file', 'check_db']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -169,11 +170,12 @@

    Submodules

    atomate.qchem.firetasks.geo_transformations moduleΒΆ

    -class atomate.qchem.firetasks.geo_transformations.RotateTorsion(*args, **kwargs)ΒΆ
    +class atomate.qchem.firetasks.geo_transformations.RotateTorsion(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Writes QChem Input files from input sets. A dictionary is passed to WriteInputFromIOSet where parameters are given as keys in the dictionary.

    -
    -
    required_params:
    -
    atom_indexes (list): This should be a list of the pymatgen molecule indexes of the four atoms +
    +
    required_params:

    atom_indexes (list): This should be a list of the pymatgen molecule indexes of the four atoms in torsion angle to be rotated -angle (float): This is the desired torsion angle in degrees (the value should be between -180 and 180)

    -
    optional_params:
    -
    molecule (Molecule): Specify a pymatgen molecule to be rotated. A molecule is optional because molecules can -be inherited from previous fireworks
    +angle (float): This is the desired torsion angle in degrees (the value should be between -180 and 180)

    +
    +
    optional_params:

    molecule (Molecule): Specify a pymatgen molecule to be rotated. A molecule is optional because molecules can +be inherited from previous fireworks

    +
    -optional_params = ['molecule']ΒΆ
    +optional_params = ['molecule']ΒΆ
    -required_params = ['atom_indexes', 'angle']ΒΆ
    +required_params = ['atom_indexes', 'angle']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -225,11 +225,12 @@

    Submodules

    atomate.qchem.firetasks.parse_outputs moduleΒΆ

    -class atomate.qchem.firetasks.parse_outputs.QChemToDb(*args, **kwargs)ΒΆ
    +class atomate.qchem.firetasks.parse_outputs.QChemToDb(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Enter a QChem run into the database. Uses current directory unless you specify calc_dir or calc_loc.

    -
    -
    Optional params:
    -
    -
    calc_dir (str): path to dir (on current filesystem) that contains QChem
    -
    input and output files. Default: use current working directory.
    -
    calc_loc (str OR bool): if True will set most recent calc_loc. If str
    -
    search for the most recent calc_loc with the matching name
    +
    +
    Optional params:
    +
    calc_dir (str): path to dir (on current filesystem) that contains QChem

    input and output files. Default: use current working directory.

    +
    +
    calc_loc (str OR bool): if True will set most recent calc_loc. If str

    search for the most recent calc_loc with the matching name

    +

    input_file (str): name of the QChem input file output_file (str): name of the QChem output file additional_fields (dict): dict of additional fields to add db_file (str): path to file containing the database credentials.

    -
    Supports env_chk. Default: write data to JSON file.
    -
    -
    fw_spec_field (str): if set, will update the task doc with the contents
    -
    of this key in the fw_spec.
    -
    multirun (bool): Whether the job to parse includes multiple
    -
    calculations in one input / output pair.
    +

    Supports env_chk. Default: write data to JSON file.

    +
    +
    +
    fw_spec_field (str): if set, will update the task doc with the contents

    of this key in the fw_spec.

    +
    +
    multirun (bool): Whether the job to parse includes multiple

    calculations in one input / output pair.

    +
    -optional_params = ['calc_dir', 'calc_loc', 'input_file', 'output_file', 'additional_fields', 'db_file', 'fw_spec_field', 'multirun']ΒΆ
    +optional_params = ['calc_dir', 'calc_loc', 'input_file', 'output_file', 'additional_fields', 'db_file', 'fw_spec_field', 'multirun']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -289,11 +288,12 @@

    Submodules

    atomate.qchem.firetasks.run_calc moduleΒΆ

    -class atomate.qchem.firetasks.run_calc.RunNoQChem(*args, **kwargs)ΒΆ
    +class atomate.qchem.firetasks.run_calc.RunNoQChem(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Do NOT run QChem. Do nothing.

    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -325,11 +323,12 @@

    Submodules
    -class atomate.qchem.firetasks.run_calc.RunQChemCustodian(*args, **kwargs)ΒΆ
    +class atomate.qchem.firetasks.run_calc.RunQChemCustodian(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Run QChem using custodian β€œon rails”, i.e. in a simple way that supports most common options.

    -
    -
    Required params:
    -
    -
    qchem_cmd (str): The name of the full executable for running QChem. Note that this is
    -
    explicitly different from qchem_cmd in RunQChemDirect because it does +
    +
    Required params:
    +
    qchem_cmd (str): The name of the full executable for running QChem. Note that this is

    explicitly different from qchem_cmd in RunQChemDirect because it does not include any flags and should only be the call to the executable. -Supports env_chk.

    +Supports env_chk.

    +
    -
    Optional params:
    -
    -
    multimode (str): Parallelization scheme, either openmp or mpi. Defaults to openmp.
    -
    Supports env_chk.
    +
    Optional params:
    +
    multimode (str): Parallelization scheme, either openmp or mpi. Defaults to openmp.

    Supports env_chk.

    +

    input_file (str): Name of the QChem input file. Defaults to β€œmol.qin”. output_file (str): Name of the QChem output file. Defaults to β€œmol.qout” max_cores (int): Maximum number of cores to parallelize over. Supports env_chk. qclog_file (str): Name of the file to redirect the standard output to. None means

    -
    not to record the standard output. Defaults to None.
    +

    not to record the standard output. Defaults to None.

    +

    suffix (str): String to append to the file in postprocess. scratch_dir (str): QCSCRATCH directory. Defaults to β€œ/dev/shm/qcscratch/”.

    -
    Supports env_chk.
    +

    Supports env_chk.

    +

    save_scratch (bool): Whether to save scratch directory contents. Defaults to False. save_name (str): Name of the saved scratch directory. Defaults to β€œdefault_save_name”. max_errors (int): Maximum # of errors to fix before giving up (default=5) job_type (str): Choose from β€œnormal” (default) and β€œopt_with_frequency_flattener” handler_group (str): Group of handlers to use. See handler_groups dict in the code

    -
    for the groups and complete list of handlers in each group.
    +

    for the groups and complete list of handlers in each group.

    +

    gzip_output (bool): gzip output (default=T)

    * Just for opt_with_frequency_flattener * max_iterations (int): Number of perturbation -> optimization -> frequency iterations

    -
    to perform. Defaults to 10.
    -
    -
    max_molecule_perturb_scale (float): The maximum scaled perturbation that can be
    -
    applied to the molecule. Defaults to 0.3.
    -
    reversed_direction (bool): Whether to reverse the direction of the vibrational
    -
    frequency vectors. Defaults to False.
    +

    to perform. Defaults to 10.

    +
    +
    +
    max_molecule_perturb_scale (float): The maximum scaled perturbation that can be

    applied to the molecule. Defaults to 0.3.

    +
    +
    reversed_direction (bool): Whether to reverse the direction of the vibrational

    frequency vectors. Defaults to False.

    +
    -optional_params = ['multimode', 'input_file', 'output_file', 'max_cores', 'qclog_file', 'suffix', 'scratch_dir', 'save_scratch', 'save_name', 'max_errors', 'max_iterations', 'max_molecule_perturb_scale', 'reversed_direction', 'job_type', 'handler_group', 'gzipped_output']ΒΆ
    +optional_params = ['multimode', 'input_file', 'output_file', 'max_cores', 'qclog_file', 'suffix', 'scratch_dir', 'save_scratch', 'save_name', 'max_errors', 'max_iterations', 'max_molecule_perturb_scale', 'reversed_direction', 'job_type', 'handler_group', 'gzipped_output']ΒΆ
    -required_params = ['qchem_cmd']ΒΆ
    +required_params = ['qchem_cmd']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -412,11 +411,12 @@

    Submodules
    -class atomate.qchem.firetasks.run_calc.RunQChemDirect(*args, **kwargs)ΒΆ
    +class atomate.qchem.firetasks.run_calc.RunQChemDirect(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Execute a command directly (no custodian).

    -
    -
    Required params:
    -
    -
    qchem_cmd (str): The name of the full command line call to run. This should include any
    -
    flags for parallelization, saving scratch, and input / output files. -Does NOT support env_chk.
    +
    +
    Required params:
    +
    qchem_cmd (str): The name of the full command line call to run. This should include any

    flags for parallelization, saving scratch, and input / output files. +Does NOT support env_chk.

    +
    -
    Optional params:
    -
    -
    scratch_dir (str): Path to the scratch directory. Defaults to β€œ/dev/shm/qcscratch/”.
    -
    Supports env_chk.
    +
    Optional params:
    +
    scratch_dir (str): Path to the scratch directory. Defaults to β€œ/dev/shm/qcscratch/”.

    Supports env_chk.

    +
    -optional_params = ['scratch_dir']ΒΆ
    +optional_params = ['scratch_dir']ΒΆ
    -required_params = ['qchem_cmd']ΒΆ
    +required_params = ['qchem_cmd']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -470,11 +466,12 @@

    Submodules
    -class atomate.qchem.firetasks.run_calc.RunQChemFake(*args, **kwargs)ΒΆ
    +class atomate.qchem.firetasks.run_calc.RunQChemFake(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    QChem Emulator

    -
    -
    Required params:
    -
    -
    ref_dir (string): Path to reference qchem run directory with input file in the folder
    -
    named β€œmol.qin” and output file in the folder named β€œmol.qout”.
    +
    +
    Required params:
    +
    ref_dir (string): Path to reference qchem run directory with input file in the folder

    named β€œmol.qin” and output file in the folder named β€œmol.qout”.

    +
    -required_params = ['ref_dir']ΒΆ
    +required_params = ['ref_dir']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -516,11 +510,12 @@

    Submodules

    atomate.qchem.firetasks.write_inputs moduleΒΆ

    -class atomate.qchem.firetasks.write_inputs.WriteCustomInput(*args, **kwargs)ΒΆ
    +class atomate.qchem.firetasks.write_inputs.WriteCustomInput(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Writes QChem Input files from custom input sets. This firetask gives the maximum flexibility when trying to define custom input parameters.

    -
    -
    required_params:
    -
    qchem_input_custom (dict): Define custom input parameters to generate a qchem input file. +
    +
    required_params:

    qchem_input_custom (dict): Define custom input parameters to generate a qchem input file. This should be a dictionary of dictionaries (i.e. {{β€œrem”: {β€œmethod”: β€œb3lyp”, basis”: β€œ6-31*G++”, …} Each QChem section should be a key with its own dictionary as the value. For more details on how the input should be structured look at pymatgen.io.qchem.inputs -* *

    -
    optional_params:
    -
    molecule (Molecule): +* *

    +
    +
    optional_params:

    molecule (Molecule): input_file (str): Name of the QChem input file. Defaults to mol.qin write_to_dir (str): Path of the directory where the QChem input file will be written, -the default is to write to the current working directory

    +the default is to write to the current working directory

    +
    -optional_params = ['molecule', 'opt', 'pcm', 'solvent', 'input_file', 'write_to_dir']ΒΆ
    +optional_params = ['molecule', 'opt', 'pcm', 'solvent', 'input_file', 'write_to_dir']ΒΆ
    -required_params = ['rem']ΒΆ
    +required_params = ['rem']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -576,11 +569,12 @@

    Submodules
    -class atomate.qchem.firetasks.write_inputs.WriteInput(*args, **kwargs)ΒΆ
    +class atomate.qchem.firetasks.write_inputs.WriteInput(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Writes QChem input file from QCInput object.

    -
    -
    required_params:
    -
    qc_input (QCInput): QCInput object
    -
    optional_params:
    -
    input_file (str): Name of the QChem input file. Defaults to mol.qin +
    +
    required_params:

    qc_input (QCInput): QCInput object

    +
    +
    optional_params:

    input_file (str): Name of the QChem input file. Defaults to mol.qin write_to_dir (str): Path of the directory where the QChem input file will be written, -the default is to write to the current working directory

    +the default is to write to the current working directory

    +
    -optional_params = ['input_file', 'write_to_dir']ΒΆ
    +optional_params = ['input_file', 'write_to_dir']ΒΆ
    -required_params = ['qc_input']ΒΆ
    +required_params = ['qc_input']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -627,11 +619,12 @@

    Submodules
    -class atomate.qchem.firetasks.write_inputs.WriteInputFromIOSet(*args, **kwargs)ΒΆ
    +class atomate.qchem.firetasks.write_inputs.WriteInputFromIOSet(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Writes QChem Input files from input sets. A dictionary is passed to WriteInputFromIOSet where parameters are given as keys in the dictionary.

    -
    -
    required_params:
    -
    qc_input_set (QChemDictSet or str): Either a QChemDictSet object or a string +
    +
    required_params:

    qc_input_set (QChemDictSet or str): Either a QChemDictSet object or a string name for the QChem input set (e.g., β€œOptSet”). * Note that if the molecule is to be inherited through -fw_spec qc_input_set must be a string name for the QChem input set. *

    -
    optional_params:
    -
    -
    qchem_input_params (dict): When using a string name for QChem input set, use this as a dict
    -
    to specify kwargs for instantiating the input set parameters. This +fw_spec qc_input_set must be a string name for the QChem input set. *

    +
    +
    optional_params:
    +
    qchem_input_params (dict): When using a string name for QChem input set, use this as a dict

    to specify kwargs for instantiating the input set parameters. This setting is ignored if you provide the full object representation of a QChemDictSet. Basic uses would be to modify the default inputs of the set, such as dft_rung, basis_set, pcm_dielectric, scf_algorithm, @@ -668,9 +659,10 @@

    Submodulesmolecule (Molecule): +

    molecule (Molecule): input_file (str): Name of the QChem input file. Defaults to mol.qin write_to_dir (str): Path of the directory where the QChem input file will be written, the default is to write to the current working directory

    @@ -678,25 +670,23 @@

    Submodules
    -optional_params = ['molecule', 'qchem_input_params', 'input_file', 'write_to_dir']ΒΆ
    +optional_params = ['molecule', 'qchem_input_params', 'input_file', 'write_to_dir']ΒΆ

    -required_params = ['qchem_input_set']ΒΆ
    +required_params = ['qchem_input_set']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -704,11 +694,12 @@

    Submodules
  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.qchem.firetasks.tests.html b/docs/atomate.qchem.firetasks.tests.html index b8301a69b..6f08a798d 100644 --- a/docs/atomate.qchem.firetasks.tests.html +++ b/docs/atomate.qchem.firetasks.tests.html @@ -1,18 +1,17 @@ - + - - - atomate.qchem.firetasks.tests package — atomate 0.9.1 documentation + + atomate.qchem.firetasks.tests package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -46,105 +45,105 @@

    Submodules

    atomate.qchem.firetasks.tests.test_fragmenter moduleΒΆ

    -class atomate.qchem.firetasks.tests.test_fragmenter.TestFragmentMolecule(methodName='runTest')ΒΆ
    +class atomate.qchem.firetasks.tests.test_fragmenter.TestFragmentMolecule(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -setUp(lpad=False)ΒΆ
    +setUp(lpad=False)ΒΆ

    Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

    -
    +
    -classmethod setUpClass()ΒΆ
    +classmethod setUpClass()ΒΆ

    Hook method for setting up class fixture before running tests in the class.

    -tearDown()ΒΆ
    +tearDown()ΒΆ

    Remove the scratch directory and teardown the test db.

    -test_EC_neg()ΒΆ
    +test_EC_neg()ΒΆ
    -test_babel_PC_depth_0_vs_depth_10()ΒΆ
    +test_babel_PC_depth_0_vs_depth_10()ΒΆ
    -test_babel_PC_frag1()ΒΆ
    +test_babel_PC_frag1()ΒΆ
    -test_babel_PC_with_RO_depth_0_vs_depth_10()ΒΆ
    +test_babel_PC_with_RO_depth_0_vs_depth_10()ΒΆ
    -test_babel_TFSI()ΒΆ
    +test_babel_TFSI()ΒΆ
    -test_build_new_FWs()ΒΆ
    +test_build_new_FWs()ΒΆ
    -test_build_unique_relevant_molecules()ΒΆ
    +test_build_unique_relevant_molecules()ΒΆ
    -test_build_unique_relevant_molecules_with_triplets()ΒΆ
    +test_build_unique_relevant_molecules_with_triplets()ΒΆ
    -test_edges_given_PC()ΒΆ
    +test_edges_given_PC()ΒΆ
    -test_edges_given_PC_frag1()ΒΆ
    +test_edges_given_PC_frag1()ΒΆ
    -test_edges_given_TFSI()ΒΆ
    +test_edges_given_TFSI()ΒΆ
    -test_in_database_and_EC_neg_frag()ΒΆ
    +test_in_database_and_EC_neg_frag()ΒΆ
    -test_in_database_through_build_new_FWs()ΒΆ
    +test_in_database_through_build_new_FWs()ΒΆ
    -test_in_database_with_actual_database()ΒΆ
    +test_in_database_with_actual_database()ΒΆ
    -test_neg_TFSI()ΒΆ
    +test_neg_TFSI()ΒΆ
    -test_neg_TFSI_with_additional_charges()ΒΆ
    +test_neg_TFSI_with_additional_charges()ΒΆ
    @@ -154,30 +153,30 @@

    Submodules

    atomate.qchem.firetasks.tests.test_geo_transformations moduleΒΆ

    -class atomate.qchem.firetasks.tests.test_geo_transformations.TestGeoTransformations(methodName='runTest')ΒΆ
    +class atomate.qchem.firetasks.tests.test_geo_transformations.TestGeoTransformations(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -setUp(lpad=False)ΒΆ
    +setUp(lpad=False)ΒΆ

    Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

    -
    +
    -classmethod setUpClass()ΒΆ
    +classmethod setUpClass()ΒΆ

    Hook method for setting up class fixture before running tests in the class.

    -tearDown()ΒΆ
    +tearDown()ΒΆ

    Remove the scratch directory and teardown the test db.

    -test_rotate_torsion()ΒΆ
    +test_rotate_torsion()ΒΆ
    @@ -187,93 +186,93 @@

    Submodules

    atomate.qchem.firetasks.tests.test_run_calc moduleΒΆ

    -class atomate.qchem.firetasks.tests.test_run_calc.TestFakeRunQChem(methodName='runTest')ΒΆ
    +class atomate.qchem.firetasks.tests.test_run_calc.TestFakeRunQChem(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -setUp(lpad=False)ΒΆ
    +setUp(lpad=False)ΒΆ

    Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

    -tearDown()ΒΆ
    +tearDown()ΒΆ

    Remove the scratch directory and teardown the test db.

    -test_RunQChemFake()ΒΆ
    +test_RunQChemFake()ΒΆ
    -class atomate.qchem.firetasks.tests.test_run_calc.TestRunCalcQChem(methodName='runTest')ΒΆ
    +class atomate.qchem.firetasks.tests.test_run_calc.TestRunCalcQChem(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -setUp(lpad=False)ΒΆ
    +setUp(lpad=False)ΒΆ

    Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

    -tearDown()ΒΆ
    +tearDown()ΒΆ

    Remove the scratch directory and teardown the test db.

    -test_RunQChemCustodian_FF_basic_defaults()ΒΆ
    +test_RunQChemCustodian_FF_basic_defaults()ΒΆ
    -test_RunQChemCustodian_FF_basic_not_defaults()ΒΆ
    +test_RunQChemCustodian_FF_basic_not_defaults()ΒΆ
    -test_RunQChemCustodian_FF_using_fw_spec_defaults()ΒΆ
    +test_RunQChemCustodian_FF_using_fw_spec_defaults()ΒΆ
    -test_RunQChemCustodian_FF_using_fw_spec_not_defaults()ΒΆ
    +test_RunQChemCustodian_FF_using_fw_spec_not_defaults()ΒΆ
    -test_RunQChemCustodian_basic_defaults()ΒΆ
    +test_RunQChemCustodian_basic_defaults()ΒΆ
    -test_RunQChemCustodian_basic_not_defaults()ΒΆ
    +test_RunQChemCustodian_basic_not_defaults()ΒΆ
    -test_RunQChemCustodian_using_fw_spec_defaults()ΒΆ
    +test_RunQChemCustodian_using_fw_spec_defaults()ΒΆ
    -test_RunQChemCustodian_using_fw_spec_not_defaults()ΒΆ
    +test_RunQChemCustodian_using_fw_spec_not_defaults()ΒΆ
    -test_RunQChemDirect_basic()ΒΆ
    +test_RunQChemDirect_basic()ΒΆ
    -test_RunQChemDirect_with_fw_spec()ΒΆ
    +test_RunQChemDirect_with_fw_spec()ΒΆ
    @@ -283,55 +282,55 @@

    Submodules

    atomate.qchem.firetasks.tests.test_write_inputs moduleΒΆ

    -class atomate.qchem.firetasks.tests.test_write_inputs.TestWriteInputQChem(methodName='runTest')ΒΆ
    +class atomate.qchem.firetasks.tests.test_write_inputs.TestWriteInputQChem(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -setUp(lpad=False)ΒΆ
    +setUp(lpad=False)ΒΆ

    Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

    -
    +
    -classmethod setUpClass()ΒΆ
    +classmethod setUpClass()ΒΆ

    Hook method for setting up class fixture before running tests in the class.

    -tearDown()ΒΆ
    +tearDown()ΒΆ

    Remove the scratch directory and teardown the test db.

    -test_write_custom_input()ΒΆ
    +test_write_custom_input()ΒΆ
    -test_write_input()ΒΆ
    +test_write_input()ΒΆ
    -test_write_input_from_io_set()ΒΆ
    +test_write_input_from_io_set()ΒΆ
    -test_write_input_from_io_set_diff_mol()ΒΆ
    +test_write_input_from_io_set_diff_mol()ΒΆ
    -test_write_input_from_io_set_diff_mol_pcm()ΒΆ
    +test_write_input_from_io_set_diff_mol_pcm()ΒΆ
    -test_write_input_from_io_set_write_dir()ΒΆ
    +test_write_input_from_io_set_write_dir()ΒΆ
    @@ -369,13 +368,11 @@

    This Page

    @@ -393,13 +390,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.qchem.fireworks.html b/docs/atomate.qchem.fireworks.html index d8efda65d..cab77fb8e 100644 --- a/docs/atomate.qchem.fireworks.html +++ b/docs/atomate.qchem.fireworks.html @@ -1,18 +1,17 @@ - + - - - atomate.qchem.fireworks package — atomate 0.9.1 documentation + + atomate.qchem.fireworks package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -46,24 +45,24 @@

    Submodules

    atomate.qchem.fireworks.core moduleΒΆ

    -class atomate.qchem.fireworks.core.FragmentFW(molecule=None, depth=1, open_rings=True, additional_charges=None, do_triplets=True, name='fragment and optimize', qchem_cmd='>>qchem_cmd<<', multimode='>>multimode<<', max_cores='>>max_cores<<', qchem_input_params=None, db_file=None, check_db=True, parents=None, **kwargs)ΒΆ
    +class atomate.qchem.fireworks.core.FragmentFW(molecule=None, depth=1, open_rings=True, additional_charges=None, do_triplets=True, name='fragment and optimize', qchem_cmd='>>qchem_cmd<<', multimode='>>multimode<<', max_cores='>>max_cores<<', qchem_input_params=None, db_file=None, check_db=True, parents=None, **kwargs)ΒΆ

    Bases: fireworks.core.firework.Firework

    -__init__(molecule=None, depth=1, open_rings=True, additional_charges=None, do_triplets=True, name='fragment and optimize', qchem_cmd='>>qchem_cmd<<', multimode='>>multimode<<', max_cores='>>max_cores<<', qchem_input_params=None, db_file=None, check_db=True, parents=None, **kwargs)ΒΆ
    +__init__(molecule=None, depth=1, open_rings=True, additional_charges=None, do_triplets=True, name='fragment and optimize', qchem_cmd='>>qchem_cmd<<', multimode='>>multimode<<', max_cores='>>max_cores<<', qchem_input_params=None, db_file=None, check_db=True, parents=None, **kwargs)ΒΆ

    Fragment the given structure and optimize all unique fragments

    -
    -
    Args:
    -

    molecule (Molecule): Input molecule. +

    +
    Args:

    molecule (Molecule): Input molecule. depth (int): Fragmentation depth. Defaults to 1. See fragmenter firetask for more details. open_rings (bool): Whether or not to open any rings encountered during fragmentation.

    -
    Defaults to True. See fragmenter firetask for more details.
    -
    -
    additional_charges (list): List of additional charges besides the defaults. See fragmenter
    -
    firetask for more details.
    -
    do_triplets (bool): Whether to simulate triplets as well as singlets for molecules with an
    -
    even number of electrons. Defaults to True.
    +

    Defaults to True. See fragmenter firetask for more details.

    +
    +
    +
    additional_charges (list): List of additional charges besides the defaults. See fragmenter

    firetask for more details.

    +
    +
    do_triplets (bool): Whether to simulate triplets as well as singlets for molecules with an

    even number of electrons. Defaults to True.

    +

    name (str): Name for the Firework. qchem_cmd (str): Command to run QChem. Supports env_chk. @@ -71,7 +70,7 @@

    Submodulesparents ([Firework]): Parents of this particular Firework. +

    before adding new fragment fireworks. Defaults to True.

    +
    +

    parents ([Firework]): Parents of this particular Firework. **kwargs: Other kwargs that are passed to Firework.__init__.

    @@ -102,23 +103,22 @@

    Submodules
    -class atomate.qchem.fireworks.core.FrequencyFlatteningOptimizeFW(molecule=None, name='frequency flattening structure optimization', qchem_cmd='>>qchem_cmd<<', multimode='>>multimode<<', max_cores='>>max_cores<<', qchem_input_params=None, max_iterations=10, max_molecule_perturb_scale=0.3, reversed_direction=False, db_file=None, parents=None, **kwargs)ΒΆ
    +class atomate.qchem.fireworks.core.FrequencyFlatteningOptimizeFW(molecule=None, name='frequency flattening structure optimization', qchem_cmd='>>qchem_cmd<<', multimode='>>multimode<<', max_cores='>>max_cores<<', qchem_input_params=None, max_iterations=10, max_molecule_perturb_scale=0.3, reversed_direction=False, db_file=None, parents=None, **kwargs)ΒΆ

    Bases: fireworks.core.firework.Firework

    -__init__(molecule=None, name='frequency flattening structure optimization', qchem_cmd='>>qchem_cmd<<', multimode='>>multimode<<', max_cores='>>max_cores<<', qchem_input_params=None, max_iterations=10, max_molecule_perturb_scale=0.3, reversed_direction=False, db_file=None, parents=None, **kwargs)ΒΆ
    +__init__(molecule=None, name='frequency flattening structure optimization', qchem_cmd='>>qchem_cmd<<', multimode='>>multimode<<', max_cores='>>max_cores<<', qchem_input_params=None, max_iterations=10, max_molecule_perturb_scale=0.3, reversed_direction=False, db_file=None, parents=None, **kwargs)ΒΆ

    Iteratively optimize the given structure and flatten imaginary frequencies to ensure that the resulting structure is a true minima and not a saddle point.

    -
    -
    Args:
    -

    molecule (Molecule): Input molecule. +

    +
    Args:

    molecule (Molecule): Input molecule. name (str): Name for the Firework. qchem_cmd (str): Command to run QChem. Supports env_chk. multimode (str): Parallelization scheme, either openmp or mpi. Supports env_chk. max_cores (int): Maximum number of cores to parallelize over. Supports env_chk. qchem_input_params (dict): Specify kwargs for instantiating the input set parameters.

    -
    Basic uses would be to modify the default inputs of the set, +

    Basic uses would be to modify the default inputs of the set, such as dft_rung, basis_set, pcm_dielectric, scf_algorithm, or max_scf_cycles. See pymatgen/io/qchem/sets.py for default values of all input parameters. For instance, if a user wanted @@ -134,16 +134,17 @@

    Submodules -
    max_iterations (int): Number of perturbation -> optimization -> frequency
    -
    iterations to perform. Defaults to 10.
    -
    max_molecule_perturb_scale (float): The maximum scaled perturbation that can be
    -
    applied to the molecule. Defaults to 0.3.
    -
    reversed_direction (bool): Whether to reverse the direction of the vibrational
    -
    frequency vectors. Defaults to False.
    +as seen in the test_double_FF_opt workflow test.

    +

    +
    +
    max_iterations (int): Number of perturbation -> optimization -> frequency

    iterations to perform. Defaults to 10.

    +
    +
    max_molecule_perturb_scale (float): The maximum scaled perturbation that can be

    applied to the molecule. Defaults to 0.3.

    +
    +
    reversed_direction (bool): Whether to reverse the direction of the vibrational

    frequency vectors. Defaults to False.

    +
    -

    db_file (str): Path to file specifying db credentials to place output parsing. +

    db_file (str): Path to file specifying db credentials to place output parsing. parents ([Firework]): Parents of this particular Firework. **kwargs: Other kwargs that are passed to Firework.__init__.

    @@ -154,22 +155,21 @@

    Submodules
    -class atomate.qchem.fireworks.core.OptimizeFW(molecule=None, name='structure optimization', qchem_cmd='>>qchem_cmd<<', multimode='>>multimode<<', max_cores='>>max_cores<<', qchem_input_params=None, db_file=None, parents=None, **kwargs)ΒΆ
    +class atomate.qchem.fireworks.core.OptimizeFW(molecule=None, name='structure optimization', qchem_cmd='>>qchem_cmd<<', multimode='>>multimode<<', max_cores='>>max_cores<<', qchem_input_params=None, db_file=None, parents=None, **kwargs)ΒΆ

    Bases: fireworks.core.firework.Firework

    -__init__(molecule=None, name='structure optimization', qchem_cmd='>>qchem_cmd<<', multimode='>>multimode<<', max_cores='>>max_cores<<', qchem_input_params=None, db_file=None, parents=None, **kwargs)ΒΆ
    +__init__(molecule=None, name='structure optimization', qchem_cmd='>>qchem_cmd<<', multimode='>>multimode<<', max_cores='>>max_cores<<', qchem_input_params=None, db_file=None, parents=None, **kwargs)ΒΆ

    Optimize the given structure.

    -
    -
    Args:
    -

    molecule (Molecule): Input molecule. +

    +
    Args:

    molecule (Molecule): Input molecule. name (str): Name for the Firework. qchem_cmd (str): Command to run QChem. Supports env_chk. multimode (str): Parallelization scheme, either openmp or mpi. Defaults to openmp. max_cores (int): Maximum number of cores to parallelize over. Supports env_chk. qchem_input_params (dict): Specify kwargs for instantiating the input set parameters.

    -
    Basic uses would be to modify the default inputs of the set, +

    Basic uses would be to modify the default inputs of the set, such as dft_rung, basis_set, pcm_dielectric, scf_algorithm, or max_scf_cycles. See pymatgen/io/qchem/sets.py for default values of all input parameters. For instance, if a user wanted @@ -185,8 +185,9 @@

    Submodulesdb_file (str): Path to file specifying db credentials to place output parsing. +as seen in the test_double_FF_opt workflow test.

    +

    +

    db_file (str): Path to file specifying db credentials to place output parsing. parents ([Firework]): Parents of this particular Firework. **kwargs: Other kwargs that are passed to Firework.__init__.

    @@ -197,21 +198,20 @@

    Submodules
    -class atomate.qchem.fireworks.core.SinglePointFW(molecule=None, name='single point', qchem_cmd='>>qchem_cmd<<', multimode='>>multimode<<', max_cores='>>max_cores<<', qchem_input_params=None, db_file=None, parents=None, **kwargs)ΒΆ
    +class atomate.qchem.fireworks.core.SinglePointFW(molecule=None, name='single point', qchem_cmd='>>qchem_cmd<<', multimode='>>multimode<<', max_cores='>>max_cores<<', qchem_input_params=None, db_file=None, parents=None, **kwargs)ΒΆ

    Bases: fireworks.core.firework.Firework

    -__init__(molecule=None, name='single point', qchem_cmd='>>qchem_cmd<<', multimode='>>multimode<<', max_cores='>>max_cores<<', qchem_input_params=None, db_file=None, parents=None, **kwargs)ΒΆ
    -
    -
    Args:
    -

    molecule (Molecule): Input molecule. +__init__(molecule=None, name='single point', qchem_cmd='>>qchem_cmd<<', multimode='>>multimode<<', max_cores='>>max_cores<<', qchem_input_params=None, db_file=None, parents=None, **kwargs)ΒΆ +

    +
    Args:

    molecule (Molecule): Input molecule. name (str): Name for the Firework. qchem_cmd (str): Command to run QChem. Supports env_chk. multimode (str): Parallelization scheme, either openmp or mpi. Supports env_chk. max_cores (int): Maximum number of cores to parallelize over. Supports env_chk. qchem_input_params (dict): Specify kwargs for instantiating the input set parameters.

    -
    Basic uses would be to modify the default inputs of the set, +

    Basic uses would be to modify the default inputs of the set, such as dft_rung, basis_set, pcm_dielectric, scf_algorithm, or max_scf_cycles. See pymatgen/io/qchem/sets.py for default values of all input parameters. For instance, if a user wanted @@ -227,8 +227,9 @@

    Submodulesdb_file (str): Path to file specifying db credentials to place output parsing. +as seen in the test_double_FF_opt workflow test.

    +

    +

    db_file (str): Path to file specifying db credentials to place output parsing. parents ([Firework]): Parents of this particular Firework. **kwargs: Other kwargs that are passed to Firework.__init__.

    @@ -267,13 +268,11 @@

    This Page

    @@ -291,13 +290,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.qchem.html b/docs/atomate.qchem.html index f752f2fd6..3b79a961f 100644 --- a/docs/atomate.qchem.html +++ b/docs/atomate.qchem.html @@ -1,18 +1,17 @@ - + - - - atomate.qchem package — atomate 0.9.1 documentation + + atomate.qchem package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -105,31 +104,31 @@

    Submodules

    atomate.qchem.database moduleΒΆ

    -class atomate.qchem.database.QChemCalcDb(host='localhost', port=27017, database='qchem', collection='tasks', user=None, password=None, **kwargs)ΒΆ
    +class atomate.qchem.database.QChemCalcDb(host='localhost', port=27017, database='qchem', collection='tasks', user=None, password=None, **kwargs)ΒΆ

    Bases: atomate.utils.database.CalcDb

    Class to help manage database insertions of QChem drones

    -__init__(host='localhost', port=27017, database='qchem', collection='tasks', user=None, password=None, **kwargs)ΒΆ
    +__init__(host='localhost', port=27017, database='qchem', collection='tasks', user=None, password=None, **kwargs)ΒΆ

    Initialize self. See help(type(self)) for accurate signature.

    -build_indexes(indexes=None, background=True)ΒΆ
    +build_indexes(indexes=None, background=True)ΒΆ

    Build the indexes.

    -
    -
    Args:
    -
    indexes (list): list of single field indexes to be built. -background (bool): Run in the background or not.
    -
    TODO: make sure that the index building is sensible and check for
    -
    existing indexes.
    +
    +
    Args:

    indexes (list): list of single field indexes to be built. +background (bool): Run in the background or not.

    +
    +
    TODO: make sure that the index building is sensible and check for

    existing indexes.

    +
    -reset()ΒΆ
    +reset()ΒΆ
    @@ -139,61 +138,62 @@

    Submodules

    atomate.qchem.drones moduleΒΆ

    -class atomate.qchem.drones.QChemDrone(runs=None, additional_fields=None)ΒΆ
    +class atomate.qchem.drones.QChemDrone(runs=None, additional_fields=None)ΒΆ

    Bases: pymatgen.apps.borg.hive.AbstractDrone

    A QChem drone to parse QChem calculations and insert an organized, searchable entry into the database.

    -__init__(runs=None, additional_fields=None)ΒΆ
    +__init__(runs=None, additional_fields=None)ΒΆ

    Initialize a QChem drone to parse qchem calculations Args:

    -
    runs (list): Naming scheme for multiple calcuations in one folder -additional_fields (dict): dictionary of additional fields to add to output document
    +

    runs (list): Naming scheme for multiple calcuations in one folder +additional_fields (dict): dictionary of additional fields to add to output document

    +
    -assimilate(path, input_file, output_file, multirun)ΒΆ
    +assimilate(path, input_file, output_file, multirun)ΒΆ

    Parses qchem input and output files and insert the result into the db.

    -
    -
    Args:
    -

    path (str): Path to the directory containing output file +

    +
    Args:

    path (str): Path to the directory containing output file input_file (str): base name of the input file(s) output_file (str): base name of the output file(s) multirun (bool): Whether the job to parse includes multiple

    -
    -
    calculations in one input / output pair.
    +
    +

    calculations in one input / output pair.

    +
    +
    +
    Returns:

    d (dict): a task dictionary

    -
    Returns:
    -
    d (dict): a task dictionary
    -filter_files(path, file_pattern)ΒΆ
    +filter_files(path, file_pattern)ΒΆ

    Find the files that match the pattern in the given path and return them in an ordered dictionary. The searched for files are filtered by the run types defined in self.runs.

    -
    -
    Args:
    -
    path (string): path to the folder -file_pattern (string): base files to be searched for
    -
    Returns:
    -
    OrderedDict of the names of the files to be processed further. -The key is set from list of run types: self.runs
    +
    +
    Args:

    path (string): path to the folder +file_pattern (string): base files to be searched for

    +
    +
    Returns:

    OrderedDict of the names of the files to be processed further. +The key is set from list of run types: self.runs

    +
    -generate_doc(dir_name, qcinput_files, qcoutput_files, multirun)ΒΆ
    +generate_doc(dir_name, qcinput_files, qcoutput_files, multirun)ΒΆ
    -
    +
    -static get_valid_paths(self, path)ΒΆ
    +static get_valid_paths(self, path)ΒΆ

    Checks if path contains valid data for assimilation, and then returns the valid paths. The paths returned can be a list of directory or file paths, depending on what kind of data you are assimilating. For @@ -201,46 +201,45 @@

    Submodules -
    Args:
    -
    -
    path: input path as a tuple generated from os.walk, i.e.,
    -
    (parent, subdirs, files).
    +
    +
    Args:
    +
    path: input path as a tuple generated from os.walk, i.e.,

    (parent, subdirs, files).

    +
    -
    Returns:
    -
    List of valid dir/file paths for assimilation
    +
    Returns:

    List of valid dir/file paths for assimilation

    +

    -
    +
    -static post_process(dir_name, d)ΒΆ
    +static post_process(dir_name, d)ΒΆ

    Post-processing for various files other than the QChem input and output files. Currently only looks for custodian.json. Modify this if other files need to be processed.

    -
    +
    -static process_qchem_multirun(dir_name, input_files, output_files)ΒΆ
    +static process_qchem_multirun(dir_name, input_files, output_files)ΒΆ

    Process a QChem run which is known to include multiple calculations in a single input/output pair.

    -
    +
    -static process_qchemrun(dir_name, taskname, input_file, output_file)ΒΆ
    +static process_qchemrun(dir_name, taskname, input_file, output_file)ΒΆ

    Process a QChem calculation, aka an input/output pair.

    -schema = {'input': {'initial_molecule', 'job_type'}, 'output': {'initial_molecule', 'job_type'}, 'root': {'calcs_reversed', 'chemsys', 'cputime', 'dir_name', 'formula_anonymous', 'formula_pretty', 'input', 'output', 'pointgroup', 'smiles', 'walltime'}}ΒΆ
    +schema = {'input': {'initial_molecule', 'job_type'}, 'output': {'initial_molecule', 'job_type'}, 'root': {'calcs_reversed', 'chemsys', 'cputime', 'dir_name', 'formula_anonymous', 'formula_pretty', 'input', 'output', 'pointgroup', 'smiles', 'walltime'}}ΒΆ
    -validate_doc(d)ΒΆ
    +validate_doc(d)ΒΆ

    Sanity check, aka make sure all the important keys are set. Note that a failure to pass validation is unfortunately unlikely to be noticed by a user.

    @@ -252,15 +251,15 @@

    Submodules

    atomate.qchem.powerups moduleΒΆ

    -atomate.qchem.powerups.use_fake_qchem(original_wf, ref_dirs)ΒΆ
    +atomate.qchem.powerups.use_fake_qchem(original_wf, ref_dirs)ΒΆ

    Replaces all RunQChem commands (i.e. RunQChemDirect, RunQChemCustodian) with RunQChemFake. This allows for testing without actually running QChem

    -
    -
    Args:
    -
    original_wf (Workflow) -ref_dirs (dict): key=firework name, value=path to the reference QChem calculation directory
    -
    Returns:
    -
    Workflow
    +
    +
    Args:

    original_wf (Workflow) +ref_dirs (dict): key=firework name, value=path to the reference QChem calculation directory

    +
    +
    Returns:

    Workflow

    +
    @@ -297,13 +296,11 @@

    This Page

    @@ -321,13 +318,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.qchem.workflows.base.html b/docs/atomate.qchem.workflows.base.html index 9dd4584c6..20512b88b 100644 --- a/docs/atomate.qchem.workflows.base.html +++ b/docs/atomate.qchem.workflows.base.html @@ -1,18 +1,17 @@ - + - - - atomate.qchem.workflows.base package — atomate 0.9.1 documentation + + atomate.qchem.workflows.base package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -46,28 +45,27 @@

    Submodules

    atomate.qchem.workflows.base.double_FF_opt moduleΒΆ

    -atomate.qchem.workflows.base.double_FF_opt.get_wf_double_FF_opt(molecule, pcm_dielectric, max_cores='>>max_cores<<', qchem_input_params=None, name='douple_FF_opt', qchem_cmd='>>qchem_cmd<<', db_file='>>db_file<<', **kwargs)ΒΆ
    -
    -
    Firework 1 : write QChem input for an FF optimization,
    -
    run FF_opt QCJob, +atomate.qchem.workflows.base.double_FF_opt.get_wf_double_FF_opt(molecule, pcm_dielectric, max_cores='>>max_cores<<', qchem_input_params=None, name='douple_FF_opt', qchem_cmd='>>qchem_cmd<<', db_file='>>db_file<<', **kwargs)ΒΆ +
    +
    Firework 1write QChem input for an FF optimization,

    run FF_opt QCJob, parse directory and insert into db, -pass relaxed molecule to fw_spec and on to fw2,

    -
    Firework 2 : write QChem input for an optimization in the
    -
    -
    presence of a PCM, using the molecule passed -from fw1,
    -

    run FF_opt QCJob, +pass relaxed molecule to fw_spec and on to fw2,

    +
    +
    Firework 2write QChem input for an optimization in the
    +

    presence of a PCM, using the molecule passed +from fw1,

    +
    +

    run FF_opt QCJob, parse directory and insert into db

    -
    Args:
    -

    molecule (Molecule): input molecule to be optimized and run. +

    Args:

    molecule (Molecule): input molecule to be optimized and run. pcm_dielectric (float): The PCM dielectric constant. max_cores (int): Maximum number of cores to parallelize over.

    -
    Defaults to 32.
    -
    -
    qchem_input_params (dict): Specify kwargs for instantiating the input set parameters.
    -
    Basic uses would be to modify the default inputs of the set, +

    Defaults to 32.

    +
    +
    +
    qchem_input_params (dict): Specify kwargs for instantiating the input set parameters.

    Basic uses would be to modify the default inputs of the set, such as dft_rung, basis_set, pcm_dielectric, scf_algorithm, or max_scf_cycles. See pymatgen/io/qchem/sets.py for default values of all input parameters. For instance, if a user wanted @@ -83,14 +81,15 @@

    Submodulesqchem_cmd (str): Command to run QChem. +

    qchem_cmd (str): Command to run QChem. db_file (str): path to file containing the database credentials. kwargs (keyword arguments): additional kwargs to be passed to Workflow

    -
    Returns:
    -
    Workflow
    +
    Returns:

    Workflow

    +
    @@ -99,42 +98,42 @@

    Submodules

    atomate.qchem.workflows.base.fragmentation moduleΒΆ

    -atomate.qchem.workflows.base.fragmentation.get_fragmentation_wf(molecule, depth=1, open_rings=True, additional_charges=None, do_triplets=True, pcm_dielectric=None, do_optimization=True, max_cores='>>max_cores<<', qchem_input_params=None, name='FF then fragment', qchem_cmd='>>qchem_cmd<<', db_file='>>db_file<<', check_db=True, **kwargs)ΒΆ
    -
    -
    Args:
    -

    molecule (Molecule): input molecule to be fragmented. +atomate.qchem.workflows.base.fragmentation.get_fragmentation_wf(molecule, depth=1, open_rings=True, additional_charges=None, do_triplets=True, pcm_dielectric=None, do_optimization=True, max_cores='>>max_cores<<', qchem_input_params=None, name='FF then fragment', qchem_cmd='>>qchem_cmd<<', db_file='>>db_file<<', check_db=True, **kwargs)ΒΆ +

    +
    Args:

    molecule (Molecule): input molecule to be fragmented. depth (int): The number of levels of iterative fragmentation to perform,

    -
    where each evel will include fragments obtained by breaking +

    where each evel will include fragments obtained by breaking one bond of a fragment one level up. If set to 0, instead all possible fragments are generated using an alternative, -non-iterative scheme. Defaults to 1.

    -
    -
    open_rings (bool): Whether or not to open any rings encountered during fragmentation.
    -
    Defaults to True. If true, any bond that fails to yield disconnected +non-iterative scheme. Defaults to 1.

    + +
    +
    open_rings (bool): Whether or not to open any rings encountered during fragmentation.

    Defaults to True. If true, any bond that fails to yield disconnected graphs when broken is instead removed and the entire structure is optimized with OpenBabel in order to obtain a good initial guess for an opened geometry that can then be put back into QChem to be -optimized without the ring just reforming.

    -
    additional_charges (list): List of additional charges besides the defaults described in the
    -
    firetask. For example, if a principle molecule with a +2 charge +optimized without the ring just reforming.

    +
    +
    additional_charges (list): List of additional charges besides the defaults described in the

    firetask. For example, if a principle molecule with a +2 charge is provided, by default all fragments will be calculated with +1 and +2 charges. If the user includes additional_charges=[0] then all fragments will be calculated with 0, +1, and +2 charges. Additional charge values of 1 or 2 would not cause any new charges -to be calculated as they are already done. Defaults to [].

    -
    do_triplets (bool): Whether to simulate triplets as well as singlets for molecules with
    -
    an even number of electrons. Defaults to True.
    +to be calculated as they are already done. Defaults to [].

    +
    +
    do_triplets (bool): Whether to simulate triplets as well as singlets for molecules with

    an even number of electrons. Defaults to True.

    +

    pcm_dielectric (float): The PCM dielectric constant. do_optimization (bool): Whether or not to optimize the given molecule

    -
    before fragmentation. Defaults to True.
    -
    -
    max_cores (int): Maximum number of cores to parallelize over.
    -
    Value obtained from the environment by default.
    -
    qchem_input_params (dict): Specify kwargs for instantiating the input set parameters.
    -
    Basic uses would be to modify the default inputs of the set, +

    before fragmentation. Defaults to True.

    +
    +
    +
    max_cores (int): Maximum number of cores to parallelize over.

    Value obtained from the environment by default.

    +
    +
    qchem_input_params (dict): Specify kwargs for instantiating the input set parameters.

    Basic uses would be to modify the default inputs of the set, such as dft_rung, basis_set, pcm_dielectric, scf_algorithm, or max_scf_cycles. See pymatgen/io/qchem/sets.py for default values of all input parameters. For instance, if a user wanted @@ -150,28 +149,29 @@

    Submoduleskwargs (keyword arguments): additional kwargs to be passed to Workflow

    +

    structures before adding new fragment fireworks. +Defaults to True.

    +
    +

    kwargs (keyword arguments): additional kwargs to be passed to Workflow

    -
    Returns:
    -

    Workflow with the following fireworks:

    -
    -
    Firework 1 : write QChem input for an FF optimization,
    -
    run FF_opt QCJob, +
    Returns:

    Workflow with the following fireworks:

    +
    +
    Firework 1write QChem input for an FF optimization,

    run FF_opt QCJob, parse directory and insert into db, -pass relaxed molecule to fw_spec and on to fw2,

    -
    Firework 2 : find all unique fragments of the optimized molecule
    -
    and add a frequency flattening optimize FW to the -workflow for each one
    +pass relaxed molecule to fw_spec and on to fw2,

    +
    +
    Firework 2find all unique fragments of the optimized molecule

    and add a frequency flattening optimize FW to the +workflow for each one

    +
    -

    Note that Firework 1 is only present if do_optimization=True.

    +

    Note that Firework 1 is only present if do_optimization=True.

    @@ -181,23 +181,22 @@

    Submodules

    atomate.qchem.workflows.base.torsion_potential moduleΒΆ

    -atomate.qchem.workflows.base.torsion_potential.get_wf_torsion_potential(molecule, atom_indexes, angles, rem, name='torsion_potential', qchem_cmd='>>qchem_cmd<<', multimode='>>multimode<<', max_cores='>>max_cores<<', db_file=None, **kwargs)ΒΆ
    +atomate.qchem.workflows.base.torsion_potential.get_wf_torsion_potential(molecule, atom_indexes, angles, rem, name='torsion_potential', qchem_cmd='>>qchem_cmd<<', multimode='>>multimode<<', max_cores='>>max_cores<<', db_file=None, **kwargs)ΒΆ

    Returns a workflow to the torsion potential for a molecule.

    -
    -
    Firework 1 : write QChem input for an optimization,
    -
    run Qchem, +
    +
    Firework 1write QChem input for an optimization,

    run Qchem, parse output and insert into db, -pass relaxed molecule to fw_spec and on to fw2,

    -
    Firework 2 : rotate molecule torsion to a particular angle,
    -
    write QChem input for an optimization, +pass relaxed molecule to fw_spec and on to fw2,

    +
    +
    Firework 2rotate molecule torsion to a particular angle,

    write QChem input for an optimization, run Qchem, -parse output and insert into db

    +parse output and insert into db

    +

    last Firework : add analysis code at some point

    -
    -
    Args:
    -

    molecule (Molecule): Input molecule (needs to be a pymatgen molecule object) +

    +
    Args:

    molecule (Molecule): Input molecule (needs to be a pymatgen molecule object) atom_indexes (list of ints): list of atom indexes in the torsion angle to be rotated (i.e. [6, 8, 9, 10]) angles (list of floats): list of all the torsion angles to run rem (list of two rem dictionaries): a list with two rem dictionaries, one for the first optimization and @@ -210,9 +209,10 @@

    Submodulesdb_file (str): Path to file specifying db credentials to place output parsing. +

    For example, if you want to change the DFT_rung, you should +provide: {β€œDFT_rung”: …}. Defaults to None.

    +

    +

    db_file (str): Path to file specifying db credentials to place output parsing. **kwargs: Other kwargs that are passed to Firework.__init__.

    @@ -252,13 +252,11 @@

    This Page

    @@ -276,13 +274,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.qchem.workflows.html b/docs/atomate.qchem.workflows.html index 6f4b86c05..3fa1e16ae 100644 --- a/docs/atomate.qchem.workflows.html +++ b/docs/atomate.qchem.workflows.html @@ -1,18 +1,17 @@ - + - - - atomate.qchem.workflows package — atomate 0.9.1 documentation + + atomate.qchem.workflows package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -91,13 +90,11 @@

    This Page

    @@ -115,13 +112,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.qchem.workflows.tests.html b/docs/atomate.qchem.workflows.tests.html index 8099c953e..27288a46f 100644 --- a/docs/atomate.qchem.workflows.tests.html +++ b/docs/atomate.qchem.workflows.tests.html @@ -1,18 +1,17 @@ - + - - - atomate.qchem.workflows.tests package — atomate 0.9.1 documentation + + atomate.qchem.workflows.tests package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -46,11 +45,11 @@

    Submodules

    atomate.qchem.workflows.tests.test_double_FF_opt moduleΒΆ

    -class atomate.qchem.workflows.tests.test_double_FF_opt.TestDoubleFFOpt(methodName='runTest')ΒΆ
    +class atomate.qchem.workflows.tests.test_double_FF_opt.TestDoubleFFOpt(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -test_double_FF_opt()ΒΆ
    +test_double_FF_opt()ΒΆ
    @@ -60,16 +59,16 @@

    Submodules

    atomate.qchem.workflows.tests.test_fragmentation moduleΒΆ

    -class atomate.qchem.workflows.tests.test_fragmentation.TestFragmentation(methodName='runTest')ΒΆ
    +class atomate.qchem.workflows.tests.test_fragmentation.TestFragmentation(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -test_Fragmentation()ΒΆ
    +test_Fragmentation()ΒΆ
    -test_no_opt_Fragmentation()ΒΆ
    +test_no_opt_Fragmentation()ΒΆ
    @@ -79,28 +78,28 @@

    Submodules

    atomate.qchem.workflows.tests.test_parse_pass_write moduleΒΆ

    -class atomate.qchem.workflows.tests.test_parse_pass_write.TestParsePassWrite(methodName='runTest')ΒΆ
    +class atomate.qchem.workflows.tests.test_parse_pass_write.TestParsePassWrite(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -
    +
    -classmethod setUpClass()ΒΆ
    +classmethod setUpClass()ΒΆ

    Hook method for setting up class fixture before running tests in the class.

    -tearDown()ΒΆ
    +tearDown()ΒΆ

    Remove the scratch directory and teardown the test db.

    -test_parse_pass_rotate_write()ΒΆ
    +test_parse_pass_rotate_write()ΒΆ
    -test_parse_pass_write()ΒΆ
    +test_parse_pass_write()ΒΆ
    @@ -110,11 +109,11 @@

    Submodules

    atomate.qchem.workflows.tests.test_torsion_potential moduleΒΆ

    -class atomate.qchem.workflows.tests.test_torsion_potential.TestTorsionPotential(methodName='runTest')ΒΆ
    +class atomate.qchem.workflows.tests.test_torsion_potential.TestTorsionPotential(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -test_torsion_potential()ΒΆ
    +test_torsion_potential()ΒΆ
    @@ -152,13 +151,11 @@

    This Page

    @@ -176,13 +173,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.tools.html b/docs/atomate.tools.html index 35349cf1b..4568ec304 100644 --- a/docs/atomate.tools.html +++ b/docs/atomate.tools.html @@ -1,18 +1,17 @@ - + - - - atomate.tools package — atomate 0.9.1 documentation + + atomate.tools package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -89,13 +88,11 @@

    This Page

    @@ -113,13 +110,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.tools.post_process.html b/docs/atomate.tools.post_process.html index 84995c8c2..304b11448 100644 --- a/docs/atomate.tools.post_process.html +++ b/docs/atomate.tools.post_process.html @@ -1,18 +1,17 @@ - + - - - atomate.tools.post_process package — atomate 0.9.1 documentation + + atomate.tools.post_process package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -78,13 +77,11 @@

    This Page

    @@ -102,13 +99,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.tools.tests.html b/docs/atomate.tools.tests.html index ad8a115c5..417f89cb3 100644 --- a/docs/atomate.tools.tests.html +++ b/docs/atomate.tools.tests.html @@ -1,18 +1,17 @@ - + - - - atomate.tools.tests package — atomate 0.9.1 documentation + + atomate.tools.tests package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -74,13 +73,11 @@

    This Page

    @@ -98,13 +95,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.utils.html b/docs/atomate.utils.html index ab6151100..8ead0bd1a 100644 --- a/docs/atomate.utils.html +++ b/docs/atomate.utils.html @@ -1,18 +1,17 @@ - + - - - atomate.utils package — atomate 0.9.1 documentation + + atomate.utils package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -60,54 +59,54 @@

    Submodules

    atomate.utils.database moduleΒΆ

    -class atomate.utils.database.CalcDb(host, port, database, collection, user, password, **kwargs)ΒΆ
    +class atomate.utils.database.CalcDb(host, port, database, collection, user, password, **kwargs)ΒΆ

    Bases: object

    -__init__(host, port, database, collection, user, password, **kwargs)ΒΆ
    +__init__(host, port, database, collection, user, password, **kwargs)ΒΆ

    Initialize self. See help(type(self)) for accurate signature.

    -build_indexes(indexes=None, background=True)ΒΆ
    +abstract build_indexes(indexes=None, background=True)ΒΆ

    Build the indexes.

    -
    -
    Args:
    -
    indexes (list): list of single field indexes to be built. -background (bool): Run in the background or not.
    +
    +
    Args:

    indexes (list): list of single field indexes to be built. +background (bool): Run in the background or not.

    +
    -
    +
    -classmethod from_db_file(db_file, admin=True)ΒΆ
    +classmethod from_db_file(db_file, admin=True)ΒΆ

    Create MMDB from database file. File requires host, port, database, collection, and optionally admin_user/readonly_user and admin_password/readonly_password

    -
    -
    Args:
    -
    db_file (str): path to the file containing the credentials -admin (bool): whether to use the admin user
    -
    Returns:
    -
    MMDb object
    +
    +
    Args:

    db_file (str): path to the file containing the credentials +admin (bool): whether to use the admin user

    +
    +
    Returns:

    MMDb object

    +
    -insert(d, update_duplicates=True)ΒΆ
    +insert(d, update_duplicates=True)ΒΆ

    Insert the task document ot the database collection.

    -
    -
    Args:
    -
    d (dict): task document -update_duplicates (bool): whether to update the duplicates
    +
    +
    Args:

    d (dict): task document +update_duplicates (bool): whether to update the duplicates

    +
    -reset()ΒΆ
    +abstract reset()ΒΆ
    @@ -117,20 +116,19 @@

    Submodules

    atomate.utils.fileio moduleΒΆ

    -class atomate.utils.fileio.FileClient(filesystem=None, private_key='~/.ssh/id_rsa')ΒΆ
    +class atomate.utils.fileio.FileClient(filesystem=None, private_key='~/.ssh/id_rsa')ΒΆ

    Bases: object

    A client for performing many file operations while being agnostic of whether those operations are happening locally or via SSH

    -__init__(filesystem=None, private_key='~/.ssh/id_rsa')ΒΆ
    -
    -
    Args:
    -
    -
    filesystem (str): remote filesystem, e.g. username@remote_host.
    -
    If None, use local
    -
    private_key (str): path to the private key file (for remote
    -
    connections only). Note: passwordless ssh login must be setup
    +__init__(filesystem=None, private_key='~/.ssh/id_rsa')ΒΆ +
    +
    Args:
    +
    filesystem (str): remote filesystem, e.g. username@remote_host.

    If None, use local

    +
    +
    private_key (str): path to the private key file (for remote

    connections only). Note: passwordless ssh login must be setup

    +
    @@ -138,71 +136,70 @@

    Submodules
    -abspath(path)ΒΆ
    +abspath(path)ΒΆ

    return the absolute path

    -
    -
    Args:
    -
    path (str): path to get absolute string of
    +
    +
    Args:

    path (str): path to get absolute string of

    +

    -copy(src, dest)ΒΆ
    +copy(src, dest)ΒΆ

    Copy from source to destination.

    -
    -
    Args:
    -
    src (str): source full path -dest (str): destination file full path
    +
    +
    Args:

    src (str): source full path +dest (str): destination file full path

    +
    -
    +
    -static exists(sftp, path)ΒΆ
    +static exists(sftp, path)ΒΆ

    os.path.exists() for paramiko’s SCP object

    -
    -
    Args:
    -
    sftp (SFTPClient): -path (str): path to check existence of
    +
    +
    Args:

    sftp (SFTPClient): +path (str): path to check existence of

    +
    -
    +
    -static get_ssh_connection(username, host, private_key)ΒΆ
    +static get_ssh_connection(username, host, private_key)ΒΆ

    Connect to the remote host via paramiko using the private key. If the host key is not present it will be added automatically.

    -
    -
    Args:
    -

    username (str): +

    +
    Args:

    username (str): host (str):

    -

    private_key (str): path to private key file

    +

    private_key (str): path to private key file

    +
    +
    Returns:

    SSHClient

    -
    Returns:
    -
    SSHClient
    -glob(path)ΒΆ
    +glob(path)ΒΆ

    return the glob

    -
    -
    Args:
    -
    path (str): path to glob
    +
    +
    Args:

    path (str): path to glob

    +
    -listdir(ldir)ΒΆ
    +listdir(ldir)ΒΆ

    Get the directory listing from either the local or remote filesystem.

    -
    -
    Args:
    -
    ldir (str): full path to the directory
    -
    Returns:
    -
    iterator of filenames
    +
    +
    Args:

    ldir (str): full path to the directory

    +
    +
    Returns:

    iterator of filenames

    +
    @@ -213,30 +210,30 @@

    Submodules

    atomate.utils.testing moduleΒΆ

    -class atomate.utils.testing.AtomateTest(methodName='runTest')ΒΆ
    +class atomate.utils.testing.AtomateTest(methodName='runTest')ΒΆ

    Bases: unittest.case.TestCase

    -get_task_collection(coll_name=None)ΒΆ
    +get_task_collection(coll_name=None)ΒΆ

    Returns pymongo collection

    -get_task_database()ΒΆ
    +get_task_database()ΒΆ

    Returns pymongo db connection.

    -setUp(lpad=True)ΒΆ
    +setUp(lpad=True)ΒΆ

    Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

    -tearDown()ΒΆ
    +tearDown()ΒΆ

    Remove the scratch directory and teardown the test db.

    @@ -247,7 +244,7 @@

    Submodules

    atomate.utils.utils moduleΒΆ

    -atomate.utils.utils.env_chk(val, fw_spec, strict=True, default=None)ΒΆ
    +atomate.utils.utils.env_chk(val, fw_spec, strict=True, default=None)ΒΆ

    env_chk() is a way to set different values for a property depending on the worker machine. For example, you might have slightly different executable names or scratch directories on different machines.

    @@ -262,93 +259,93 @@

    Submodules -
    Args:
    -

    val: any value, with β€œ>><<” notation reserved for special env lookup values +

    +
    Args:

    val: any value, with β€œ>><<” notation reserved for special env lookup values fw_spec: (dict) fw_spec where one can find the _fw_env keys strict (bool): if True, errors if env format (>><<) specified but cannot be found in fw_spec default: if val is None or env cannot be found in non-strict mode,

    -
    -
    return default
    +
    +

    return default

    +

    -atomate.utils.utils.get_a_unique_id()ΒΆ
    +atomate.utils.utils.get_a_unique_id()ΒΆ
    -atomate.utils.utils.get_database(config_file=None, settings=None, admin=False, **kwargs)ΒΆ
    +atomate.utils.utils.get_database(config_file=None, settings=None, admin=False, **kwargs)ΒΆ
    -atomate.utils.utils.get_fws_and_tasks(workflow, fw_name_constraint=None, task_name_constraint=None)ΒΆ
    +atomate.utils.utils.get_fws_and_tasks(workflow, fw_name_constraint=None, task_name_constraint=None)ΒΆ

    Helper method: given a workflow, returns back the fw_ids and task_ids that match name constraints. Used in developing multiple powerups.

    -
    -
    Args:
    -
    workflow (Workflow): Workflow +
    +
    Args:

    workflow (Workflow): Workflow fw_name_constraint (str): a constraint on the FW name -task_name_constraint (str): a constraint on the task name

    -
    Returns:
    -
    a list of tuples of the form (fw_id, task_id) of the RunVasp-type tasks
    +task_name_constraint (str): a constraint on the task name

    +
    +
    Returns:

    a list of tuples of the form (fw_id, task_id) of the RunVasp-type tasks

    +
    -atomate.utils.utils.get_logger(name, level=10, log_format='%(asctime)s %(levelname)s %(name)s %(message)s', stream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)ΒΆ
    +atomate.utils.utils.get_logger(name, level=10, log_format='%(asctime)s %(levelname)s %(name)s %(message)s', stream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)ΒΆ
    -atomate.utils.utils.get_meta_from_structure(structure)ΒΆ
    +atomate.utils.utils.get_meta_from_structure(structure)ΒΆ
    -atomate.utils.utils.get_mongolike(d, key)ΒΆ
    +atomate.utils.utils.get_mongolike(d, key)ΒΆ

    Retrieve a dict value using dot-notation like β€œa.b.c” from dict {β€œa”:{β€œb”:{β€œc”: 3}}} Args:

    -
    d (dict): the dictionary to search -key (str): the key we want to retrieve with dot notation, e.g., β€œa.b.c”
    -
    -
    Returns:
    -
    value from desired dict (whatever is stored at the desired key)
    +

    d (dict): the dictionary to search +key (str): the key we want to retrieve with dot notation, e.g., β€œa.b.c”

    +
    +
    +
    Returns:

    value from desired dict (whatever is stored at the desired key)

    +
    -atomate.utils.utils.get_uri(dir_name)ΒΆ
    +atomate.utils.utils.get_uri(dir_name)ΒΆ

    Returns the URI path for a directory. This allows files hosted on different file servers to have distinct locations. Args:

    -
    -
    dir_name:
    -
    A directory name.
    +
    +
    dir_name:

    A directory name.

    +
    -
    -
    Returns:
    -
    Full URI path, e.g., fileserver.host.com:/full/path/of/dir_name.
    +
    +
    Returns:

    Full URI path, e.g., fileserver.host.com:/full/path/of/dir_name.

    +
    -atomate.utils.utils.get_wf_from_spec_dict(structure, wfspec, common_param_updates=None)ΒΆ
    +atomate.utils.utils.get_wf_from_spec_dict(structure, wfspec, common_param_updates=None)ΒΆ

    Load a WF from a structure and a spec dict. This allows simple custom workflows to be constructed quickly via a YAML file.

    -
    -
    Args:
    -

    structure (Structure): An input structure object. +

    +
    Args:

    structure (Structure): An input structure object. wfspec (dict): A dict specifying workflow. A sample of the dict in

    YAML format for the usual MP workflow is given as follows:

    @@ -357,34 +354,35 @@

    Submodules -
    params:
    -
    parents: 0
    +
    +
    params:

    parents: 0

    +

      -

    • fw: atomate.vasp.fireworks.core.NonSCFUniformFW +

    • fw: atomate.vasp.fireworks.core.NonSCFUniformFW params:

      parents: 1

      • -

    • fw: atomate.vasp.fireworks.core.NonSCFLineFW +

    • fw: atomate.vasp.fireworks.core.NonSCFLineFW params:

      parents: 1

    -
    -
    common_params:
    -
    db_file: db.json -$vasp_cmd: $HOME/opt/vasp
    +
    +
    common_params:

    db_file: db.json +$vasp_cmd: $HOME/opt/vasp

    +

    name: bandstructure metadata:

    -
    tag: testing_workflow
    +

    tag: testing_workflow

    +

    ```

    The fireworks key is a list of Fireworks; it is expected that all such Fireworks have β€œstructure” as the first argument and @@ -403,29 +401,29 @@

    Submodulescommon_param_updates (dict): A dict specifying any user-specified updates to common_params

    +

    common_param_updates (dict): A dict specifying any user-specified updates to common_params

    +

    +
    Returns:

    Workflow

    -
    Returns:
    -
    Workflow
    -atomate.utils.utils.load_class(modulepath, classname)ΒΆ
    +atomate.utils.utils.load_class(modulepath, classname)ΒΆ

    Load and return the class from the given module.

    -
    -
    Args:
    -
    modulepath (str): dotted path to the module. eg: β€œpymatgen.io.vasp.sets” -classname (str): name of the class to be loaded.
    -
    Returns:
    -
    class
    +
    +
    Args:

    modulepath (str): dotted path to the module. eg: β€œpymatgen.io.vasp.sets” +classname (str): name of the class to be loaded.

    +
    +
    Returns:

    class

    +
    -atomate.utils.utils.recursive_get_result(d, result)ΒΆ
    +atomate.utils.utils.recursive_get_result(d, result)ΒΆ

    Function that gets designated keys or values of d (i. e. those that start with β€œd>>” or β€œa>>”) from the corresponding entry in result_dict, similar to @@ -435,24 +433,25 @@

    Submodules -
    Getting a dict key from a VaspRun instance:
    -
    recursive_get_result({β€œstress”:”>>output.ionic_steps.-1.stress”}, vasprun) -–> {β€œstress”:[[0.2, 0, 0], [0, 0.3, 0], [0, 0, 0.3]]}
    -
    Getting an attribute from a vasprun:
    -
    recursive_get_result({β€œepsilon”:”a>>epsilon_static”, vasprun} -–> {β€œepsilon”:-3.4}
    +
    +
    Getting a dict key from a VaspRun instance:

    recursive_get_result({β€œstress”:”>>output.ionic_steps.-1.stress”}, vasprun) +–> {β€œstress”:[[0.2, 0, 0], [0, 0.3, 0], [0, 0, 0.3]]}

    +
    +
    Getting an attribute from a vasprun:

    recursive_get_result({β€œepsilon”:”a>>epsilon_static”, vasprun} +–> {β€œepsilon”:-3.4}

    +

    -atomate.utils.utils.recursive_update(d, u)ΒΆ
    +atomate.utils.utils.recursive_update(d, u)ΒΆ

    Recursive updates d with values from u Args:

    -
    d (dict): dict to update -u (dict): updates to propogate
    +

    d (dict): dict to update +u (dict): updates to propogate

    +
    @@ -489,13 +488,11 @@

    This Page

    @@ -513,13 +510,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.utils.tests.html b/docs/atomate.utils.tests.html index dc8fe71ac..a92648df3 100644 --- a/docs/atomate.utils.tests.html +++ b/docs/atomate.utils.tests.html @@ -1,18 +1,17 @@ - + - - - atomate.utils.tests package — atomate 0.9.1 documentation + + atomate.utils.tests package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -46,22 +45,22 @@

    Submodules

    atomate.utils.tests.test_loaders moduleΒΆ

    -class atomate.utils.tests.test_loaders.FuncTest(methodName='runTest')ΒΆ
    +class atomate.utils.tests.test_loaders.FuncTest(methodName='runTest')ΒΆ

    Bases: pymatgen.util.testing.PymatgenTest

    -setUp()ΒΆ
    +setUp()ΒΆ

    Hook method for setting up the test fixture before exercising it.

    -test_get_wf_from_spec_dict()ΒΆ
    +test_get_wf_from_spec_dict()ΒΆ
    -test_multi_parent()ΒΆ
    +test_multi_parent()ΒΆ
    @@ -71,19 +70,17 @@

    Submodules

    atomate.utils.tests.test_utils moduleΒΆ

    -class atomate.utils.tests.test_utils.Task1(*args, **kwargs)ΒΆ
    +class atomate.utils.tests.test_utils.Task1(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -91,11 +88,12 @@

    Submodules
    -class atomate.utils.tests.test_utils.Task2(*args, **kwargs)ΒΆ
    +class atomate.utils.tests.test_utils.Task2(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -123,11 +119,12 @@

    Submodules
    -class atomate.utils.tests.test_utils.UtilsTests(methodName='runTest')ΒΆ
    +class atomate.utils.tests.test_utils.UtilsTests(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -setUp(lpad=True)ΒΆ
    +setUp(lpad=True)ΒΆ

    Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

    -test_env_chk()ΒΆ
    +test_env_chk()ΒΆ
    -test_get_database()ΒΆ
    +test_get_database()ΒΆ
    -test_get_mongolike()ΒΆ
    +test_get_mongolike()ΒΆ
    -test_get_uri()ΒΆ
    +test_get_uri()ΒΆ
    -test_recursive_get_result()ΒΆ
    +test_recursive_get_result()ΒΆ
    -test_recursiveupdate()ΒΆ
    +test_recursiveupdate()ΒΆ

    @@ -207,13 +204,11 @@

    This Page

    @@ -231,13 +226,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.vasp.analysis.html b/docs/atomate.vasp.analysis.html index be88cacc2..8cc109a3f 100644 --- a/docs/atomate.vasp.analysis.html +++ b/docs/atomate.vasp.analysis.html @@ -1,18 +1,17 @@ - + - - - atomate.vasp.analysis package — atomate 0.9.1 documentation + + atomate.vasp.analysis package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -46,11 +45,10 @@

    Submodules

    atomate.vasp.analysis.phonopy moduleΒΆ

    -atomate.vasp.analysis.phonopy.get_phonopy_gibbs(energies, volumes, force_constants, structure, t_min, t_step, t_max, mesh, eos, pressure=0)ΒΆ
    +atomate.vasp.analysis.phonopy.get_phonopy_gibbs(energies, volumes, force_constants, structure, t_min, t_step, t_max, mesh, eos, pressure=0)ΒΆ

    Compute QHA gibbs free energy using the phonopy interface.

    -
    -
    Args:
    -

    energies (list): +

    +
    Args:

    energies (list): volumes (list): force_constants (list): structure (Structure): @@ -60,21 +58,21 @@

    Submodulespressure (float): in GPa, optional.

    +

    options supported by phonopy: vinet, murnaghan, birch_murnaghan

    +
    +

    pressure (float): in GPa, optional.

    +

    +
    Returns:

    (numpy.ndarray, numpy.ndarray): Gibbs free energy, Temperature

    -
    Returns:
    -
    (numpy.ndarray, numpy.ndarray): Gibbs free energy, Temperature
    -atomate.vasp.analysis.phonopy.get_phonopy_qha(energies, volumes, force_constants, structure, t_min, t_step, t_max, mesh, eos, pressure=0)ΒΆ
    +atomate.vasp.analysis.phonopy.get_phonopy_qha(energies, volumes, force_constants, structure, t_min, t_step, t_max, mesh, eos, pressure=0)ΒΆ

    Return phonopy QHA interface.

    -
    -
    Args:
    -

    energies (list): +

    +
    Args:

    energies (list): volumes (list): force_constants (list): structure (Structure): @@ -84,21 +82,21 @@

    Submodulespressure (float): in GPa, optional.

    +

    options supported by phonopy: vinet, murnaghan, birch_murnaghan

    +
    +

    pressure (float): in GPa, optional.

    +

    +
    Returns:

    PhonopyQHA

    -
    Returns:
    -
    PhonopyQHA
    -atomate.vasp.analysis.phonopy.get_phonopy_thermal_expansion(energies, volumes, force_constants, structure, t_min, t_step, t_max, mesh, eos, pressure=0)ΒΆ
    +atomate.vasp.analysis.phonopy.get_phonopy_thermal_expansion(energies, volumes, force_constants, structure, t_min, t_step, t_max, mesh, eos, pressure=0)ΒΆ

    Compute QHA thermal expansion coefficient using the phonopy interface.

    -
    -
    Args:
    -

    energies (list): +

    +
    Args:

    energies (list): volumes (list): force_constants (list): structure (Structure): @@ -108,11 +106,12 @@

    Submodulespressure (float): in GPa, optional.

    +

    options supported by phonopy: vinet, murnaghan, birch_murnaghan

    +
    +

    pressure (float): in GPa, optional.

    +

    +
    Returns:

    (numpy.ndarray, numpy.ndarray): thermal expansion coefficient, Temperature

    -
    Returns:
    -
    (numpy.ndarray, numpy.ndarray): thermal expansion coefficient, Temperature
    @@ -146,13 +145,11 @@

    This Page

    @@ -170,13 +167,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.vasp.builders.examples.html b/docs/atomate.vasp.builders.examples.html index 3b65b9371..2c648d2bb 100644 --- a/docs/atomate.vasp.builders.examples.html +++ b/docs/atomate.vasp.builders.examples.html @@ -1,18 +1,17 @@ - + - - - atomate.vasp.builders.examples package — atomate 0.9.1 documentation + + atomate.vasp.builders.examples package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -76,13 +75,11 @@

    This Page

    @@ -100,13 +97,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.vasp.builders.html b/docs/atomate.vasp.builders.html index aeb2cfa2a..b6117ddbf 100644 --- a/docs/atomate.vasp.builders.html +++ b/docs/atomate.vasp.builders.html @@ -1,18 +1,17 @@ - + - - - atomate.vasp.builders package — atomate 0.9.1 documentation + + atomate.vasp.builders package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -59,42 +58,42 @@

    Submodules

    atomate.vasp.builders.bandgap_estimation moduleΒΆ

    -class atomate.vasp.builders.bandgap_estimation.BandgapEstimationBuilder(materials_write)ΒΆ
    +class atomate.vasp.builders.bandgap_estimation.BandgapEstimationBuilder(materials_write)ΒΆ

    Bases: object

    -__init__(materials_write)ΒΆ
    +__init__(materials_write)ΒΆ

    Starting with an existing materials collection with dielectric constant data, adds estimated band gaps that may be more accurate than typical GGA calculations.

    Run the β€œDielectricBuilder” before running this builder.

    -
    -
    Args:
    -
    materials_write: mongodb collection for materials (write access needed)
    +
    +
    Args:

    materials_write: mongodb collection for materials (write access needed)

    +
    -
    +
    -static from_file(db_file, m='materials', **kwargs)ΒΆ
    +static from_file(db_file, m='materials', **kwargs)ΒΆ

    Get builder using only a db file.

    -
    -
    Args:
    -
    db_file: (str) path to db file +
    +
    Args:

    db_file: (str) path to db file m: (str) name of β€œmaterials” collection -**kwargs: other parameters to feed into the builder, e.g. mapi_key

    -
    Returns:
    -
    BandgapEstimationBuilder
    +**kwargs: other parameters to feed into the builder, e.g. mapi_key

    +
    +
    Returns:

    BandgapEstimationBuilder

    +
    -reset()ΒΆ
    +reset()ΒΆ
    -run()ΒΆ
    +run()ΒΆ
    @@ -104,24 +103,24 @@

    Submodules

    atomate.vasp.builders.base moduleΒΆ

    -class atomate.vasp.builders.base.AbstractBuilderΒΆ
    +class atomate.vasp.builders.base.AbstractBuilderΒΆ

    Bases: object

    Abstract builder class. Defines the contract and must be subclassed by all builders.

    -
    +
    -classmethod from_file(filename)ΒΆ
    +abstract classmethod from_file(filename)ΒΆ

    Set the builder from a config file, e.g., a db file

    -reset()ΒΆ
    +abstract reset()ΒΆ

    Unset the building.

    -run()ΒΆ
    +abstract run()ΒΆ

    Run the builder.

    @@ -132,41 +131,41 @@

    Submodules

    atomate.vasp.builders.boltztrap_materials moduleΒΆ

    -class atomate.vasp.builders.boltztrap_materials.BoltztrapMaterialsBuilder(materials_write, boltztrap_read)ΒΆ
    +class atomate.vasp.builders.boltztrap_materials.BoltztrapMaterialsBuilder(materials_write, boltztrap_read)ΒΆ

    Bases: atomate.vasp.builders.base.AbstractBuilder

    -__init__(materials_write, boltztrap_read)ΒΆ
    +__init__(materials_write, boltztrap_read)ΒΆ

    Update materials collection based on boltztrap collection.

    -
    -
    Args:
    -
    materials_write (pymongo.collection): mongodb collection for materials (write access needed) -boltztrap_read (pymongo.collection): mongodb collection for boltztrap (suggest read-only for safety)
    +
    +
    Args:

    materials_write (pymongo.collection): mongodb collection for materials (write access needed) +boltztrap_read (pymongo.collection): mongodb collection for boltztrap (suggest read-only for safety)

    +
    -
    +
    -classmethod from_file(db_file, m='materials', b='boltztrap', **kwargs)ΒΆ
    +classmethod from_file(db_file, m='materials', b='boltztrap', **kwargs)ΒΆ

    Get a BoltztrapMaterialsBuilder using only a db file.

    -
    -
    Args:
    -
    db_file (str): path to db file +
    +
    Args:

    db_file (str): path to db file m (str): name of β€œmaterials” collection b (str): name of β€œboltztrap” collection -**kwargs: other params to put into BoltztrapMaterialsBuilder

    +**kwargs: other params to put into BoltztrapMaterialsBuilder

    +
    -reset()ΒΆ
    +reset()ΒΆ

    Unset the building.

    -run()ΒΆ
    +run()ΒΆ

    Run the builder.

    @@ -177,41 +176,41 @@

    Submodules

    atomate.vasp.builders.dielectric moduleΒΆ

    -class atomate.vasp.builders.dielectric.DielectricBuilder(materials_write)ΒΆ
    +class atomate.vasp.builders.dielectric.DielectricBuilder(materials_write)ΒΆ

    Bases: object

    -__init__(materials_write)ΒΆ
    +__init__(materials_write)ΒΆ

    Starting with an existing materials collection, adds some averages and eigenvalues for dielectric constants rather than just the tensor

    -
    -
    Args:
    -
    materials_write: mongodb collection for materials (write access needed)
    +
    +
    Args:

    materials_write: mongodb collection for materials (write access needed)

    +
    -
    +
    -static from_file(db_file, m='materials', **kwargs)ΒΆ
    +static from_file(db_file, m='materials', **kwargs)ΒΆ

    Get a MaterialsEhullBuilder using only a db file.

    -
    -
    Args:
    -
    db_file: (str) path to db file +
    +
    Args:

    db_file: (str) path to db file m: (str) name of β€œmaterials” collection -**kwargs: other parameters to feed into the builder, e.g. mapi_key

    -
    Returns:
    -
    DielectricBuilder
    +**kwargs: other parameters to feed into the builder, e.g. mapi_key

    +
    +
    Returns:

    DielectricBuilder

    +
    -reset()ΒΆ
    +reset()ΒΆ
    -run()ΒΆ
    +run()ΒΆ
    @@ -221,45 +220,45 @@

    Submodules

    atomate.vasp.builders.file_materials moduleΒΆ

    -class atomate.vasp.builders.file_materials.FileMaterialsBuilder(materials_write, data_file, delimiter=', ', header_lines=0)ΒΆ
    +class atomate.vasp.builders.file_materials.FileMaterialsBuilder(materials_write, data_file, delimiter=', ', header_lines=0)ΒΆ

    Bases: atomate.vasp.builders.base.AbstractBuilder

    -__init__(materials_write, data_file, delimiter=', ', header_lines=0)ΒΆ
    +__init__(materials_write, data_file, delimiter=', ', header_lines=0)ΒΆ

    Updates the database using a data file. Format of file must be: <material_id or formula>, <property>, <value>

    Comment lines should start with β€˜#’.

    -
    -
    Args:
    -
    materials_write: mongodb collection for materials (write access needed) +
    +
    Args:

    materials_write: mongodb collection for materials (write access needed) data_file (str): path to data file delimiter (str): delimiter for file parsing -header_lines (int): number of header lines to skip in data file

    +header_lines (int): number of header lines to skip in data file

    +
    -
    +
    -classmethod from_file(db_file, data_file=None, m='materials', **kwargs)ΒΆ
    +classmethod from_file(db_file, data_file=None, m='materials', **kwargs)ΒΆ

    Get a FileMaterialsBuilder using only a db file.

    -
    -
    Args:
    -
    db_file (str): path to db file +
    +
    Args:

    db_file (str): path to db file data_file (str): path to data file m (str): name of β€œmaterials” collection -**kwargs: other parameters to feed into the builder, e.g. mapi_key

    +**kwargs: other parameters to feed into the builder, e.g. mapi_key

    +
    -reset()ΒΆ
    +reset()ΒΆ

    Unset the building.

    -run()ΒΆ
    +run()ΒΆ

    Run the builder.

    @@ -270,39 +269,39 @@

    Submodules

    atomate.vasp.builders.fix_tasks moduleΒΆ

    -class atomate.vasp.builders.fix_tasks.FixTasksBuilder(tasks_write)ΒΆ
    +class atomate.vasp.builders.fix_tasks.FixTasksBuilder(tasks_write)ΒΆ

    Bases: atomate.vasp.builders.base.AbstractBuilder

    -__init__(tasks_write)ΒΆ
    +__init__(tasks_write)ΒΆ

    Fix historical problems in the tasks database

    -
    -
    Args:
    -
    tasks_write (pymongo.collection): mongodb collection for tasks (write access needed)
    +
    +
    Args:

    tasks_write (pymongo.collection): mongodb collection for tasks (write access needed)

    +
    -
    +
    -classmethod from_file(db_file, t='tasks', **kwargs)ΒΆ
    +classmethod from_file(db_file, t='tasks', **kwargs)ΒΆ

    Get a FixTasksBuilder using only a db file.

    -
    -
    Args:
    -
    db_file (str): path to db file +
    +
    Args:

    db_file (str): path to db file t (str): name of β€œtasks” collection -**kwargs: other params to put into FixTasksBuilder

    +**kwargs: other params to put into FixTasksBuilder

    +
    -reset()ΒΆ
    +reset()ΒΆ

    Unset the building.

    -run()ΒΆ
    +run()ΒΆ

    Run the builder.

    @@ -313,41 +312,41 @@

    Submodules

    atomate.vasp.builders.materials_descriptor moduleΒΆ

    -class atomate.vasp.builders.materials_descriptor.MaterialsDescriptorBuilder(materials_write, update_all=False)ΒΆ
    +class atomate.vasp.builders.materials_descriptor.MaterialsDescriptorBuilder(materials_write, update_all=False)ΒΆ

    Bases: atomate.vasp.builders.base.AbstractBuilder

    -__init__(materials_write, update_all=False)ΒΆ
    +__init__(materials_write, update_all=False)ΒΆ

    Starting with an existing materials collection, adds some compositional and structural descriptors.

    -
    -
    Args:
    -
    materials_write: mongodb collection for materials (write access needed) -update_all: (bool) - if true, updates all docs. If false, updates incrementally
    +
    +
    Args:

    materials_write: mongodb collection for materials (write access needed) +update_all: (bool) - if true, updates all docs. If false, updates incrementally

    +
    -
    +
    -classmethod from_file(db_file, m='materials', **kwargs)ΒΆ
    +classmethod from_file(db_file, m='materials', **kwargs)ΒΆ

    Get a MaterialsDescriptorBuilder using only a db file.

    -
    -
    Args:
    -
    db_file: (str) path to db file +
    +
    Args:

    db_file: (str) path to db file m: (str) name of β€œmaterials” collection -**kwargs: other parameters to feed into the builder

    +**kwargs: other parameters to feed into the builder

    +
    -reset()ΒΆ
    +reset()ΒΆ

    Unset the building.

    -run()ΒΆ
    +run()ΒΆ

    Run the builder.

    @@ -358,11 +357,11 @@

    Submodules

    atomate.vasp.builders.materials_ehull moduleΒΆ

    -class atomate.vasp.builders.materials_ehull.MaterialsEhullBuilder(materials_write, mapi_key=None, update_all=False)ΒΆ
    +class atomate.vasp.builders.materials_ehull.MaterialsEhullBuilder(materials_write, mapi_key=None, update_all=False)ΒΆ

    Bases: atomate.vasp.builders.base.AbstractBuilder

    -__init__(materials_write, mapi_key=None, update_all=False)ΒΆ
    +__init__(materials_write, mapi_key=None, update_all=False)ΒΆ

    Starting with an existing materials collection, adds stability information and The Materials Project ID. Args:

    @@ -371,30 +370,32 @@

    Submodules +
    -classmethod from_file(db_file, m='materials', **kwargs)ΒΆ
    +classmethod from_file(db_file, m='materials', **kwargs)ΒΆ

    Get a MaterialsEhullBuilder using only a db file Args:

    -
    db_file: (str) path to db file +

    db_file: (str) path to db file m: (str) name of β€œmaterials” collection -**kwargs: other parameters to feed into the builder, e.g. mapi_key

    +**kwargs: other parameters to feed into the builder, e.g. mapi_key

    +
    -reset()ΒΆ
    +reset()ΒΆ

    Unset the building.

    -run()ΒΆ
    +run()ΒΆ

    Run the builder.

    @@ -405,43 +406,43 @@

    Submodules

    atomate.vasp.builders.tags moduleΒΆ

    -class atomate.vasp.builders.tags.TagsBuilder(materials_write, tasks_read, tasks_prefix='t')ΒΆ
    +class atomate.vasp.builders.tags.TagsBuilder(materials_write, tasks_read, tasks_prefix='t')ΒΆ

    Bases: atomate.vasp.builders.base.AbstractBuilder

    -__init__(materials_write, tasks_read, tasks_prefix='t')ΒΆ
    +__init__(materials_write, tasks_read, tasks_prefix='t')ΒΆ

    Starting with an existing materials collection, searches all its component tasks for the β€œtags” and key in the tasks collection and copies them to the materials collection. Thus, the β€œtags” for a material will be the union of all the tags for its component tasks.

    -
    -
    Args:
    -
    materials_write (pymongo.collection): materials collection with write access. +
    +
    Args:

    materials_write (pymongo.collection): materials collection with write access. tasks_read (pymongo.collection): read-only(for safety) tasks collection. -tasks_prefix (str): the string prefix for tasks, e.g. β€œt” for a task_id like β€œt-132”

    +tasks_prefix (str): the string prefix for tasks, e.g. β€œt” for a task_id like β€œt-132”

    +
    -
    +
    -classmethod from_file(db_file, m='materials', t='tasks', **kwargs)ΒΆ
    +classmethod from_file(db_file, m='materials', t='tasks', **kwargs)ΒΆ

    Get a TagsCollector using only a db file.

    -
    -
    Args:
    -
    db_file (str): path to db file +
    +
    Args:

    db_file (str): path to db file m (str): name of β€œmaterials” collection -**kwargs: other parameters to feed into the builder, e.g. update_all

    +**kwargs: other parameters to feed into the builder, e.g. update_all

    +
    -reset()ΒΆ
    +reset()ΒΆ

    Unset the building.

    -run()ΒΆ
    +run()ΒΆ

    Run the builder.

    @@ -452,47 +453,47 @@

    Submodules

    atomate.vasp.builders.tasks_materials moduleΒΆ

    -class atomate.vasp.builders.tasks_materials.TasksMaterialsBuilder(materials_write, counter_write, tasks_read, tasks_prefix='t', materials_prefix='m', query=None, settings_file=None)ΒΆ
    +class atomate.vasp.builders.tasks_materials.TasksMaterialsBuilder(materials_write, counter_write, tasks_read, tasks_prefix='t', materials_prefix='m', query=None, settings_file=None)ΒΆ

    Bases: atomate.vasp.builders.base.AbstractBuilder

    -__init__(materials_write, counter_write, tasks_read, tasks_prefix='t', materials_prefix='m', query=None, settings_file=None)ΒΆ
    +__init__(materials_write, counter_write, tasks_read, tasks_prefix='t', materials_prefix='m', query=None, settings_file=None)ΒΆ

    Create a materials collection from a tasks collection.

    -
    -
    Args:
    -
    materials_write (pymongo.collection): mongodb collection for materials (write access needed) +
    +
    Args:

    materials_write (pymongo.collection): mongodb collection for materials (write access needed) counter_write (pymongo.collection): mongodb collection for counter (write access needed) tasks_read (pymongo.collection): mongodb collection for tasks (suggest read-only for safety) tasks_prefix (str): a string prefix for tasks, e.g. β€œt” gives a task_id like β€œt-132” materials_prefix (str): a string prefix to prepend to material_ids query (dict): a pymongo query on tasks_read for which tasks to include in the builder -settings_file (str): filepath to a custom settings path

    +settings_file (str): filepath to a custom settings path

    +
    -
    +
    -classmethod from_file(db_file, m='materials', c='counter', t='tasks', **kwargs)ΒΆ
    +classmethod from_file(db_file, m='materials', c='counter', t='tasks', **kwargs)ΒΆ

    Get a TaskMaterialsBuilder using only a db file.

    -
    -
    Args:
    -
    db_file (str): path to db file +
    +
    Args:

    db_file (str): path to db file m (str): name of β€œmaterials” collection c (str): name of β€œcounter” collection t (str): name of β€œtasks” collection -**kwargs: other params to put into TasksMaterialsBuilder

    +**kwargs: other params to put into TasksMaterialsBuilder

    +
    -reset()ΒΆ
    +reset()ΒΆ

    Unset the building.

    -run()ΒΆ
    +run()ΒΆ

    Run the builder.

    @@ -500,7 +501,7 @@

    Submodules
    -atomate.vasp.builders.tasks_materials.module_dir = '/Users/ajain/Documents/code_matgen/atomate/atomate/vasp/builders'ΒΆ
    +atomate.vasp.builders.tasks_materials.module_dir = '/Users/ajain/Documents/code_matgen/atomate/atomate/vasp/builders'ΒΆ

    This class collects all β€œtasks” (individual calculations) on a single compound and produces a summary report in a new collection (β€œmaterials”). The tasks are matched based on having the same crystal structure, with some options for overriding this.

    @@ -513,12 +514,12 @@

    Submodules
    -atomate.vasp.builders.utils.dbid_to_int(dbid)ΒΆ
    +atomate.vasp.builders.utils.dbid_to_int(dbid)ΒΆ

    -atomate.vasp.builders.utils.dbid_to_str(prefix, dbid)ΒΆ
    +atomate.vasp.builders.utils.dbid_to_str(prefix, dbid)ΒΆ
    @@ -562,13 +563,11 @@

    This Page

    @@ -586,13 +585,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.vasp.examples.html b/docs/atomate.vasp.examples.html index 2ed52db28..54fee4cc3 100644 --- a/docs/atomate.vasp.examples.html +++ b/docs/atomate.vasp.examples.html @@ -1,18 +1,17 @@ - + - - - atomate.vasp.examples package — atomate 0.9.1 documentation + + atomate.vasp.examples package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -74,13 +73,11 @@

    This Page

    @@ -98,13 +95,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/atomate.vasp.firetasks.html b/docs/atomate.vasp.firetasks.html index 7aa6a34c8..69f650614 100644 --- a/docs/atomate.vasp.firetasks.html +++ b/docs/atomate.vasp.firetasks.html @@ -1,18 +1,17 @@ - + - - - atomate.vasp.firetasks package — atomate 0.9.1 documentation + + atomate.vasp.firetasks package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -63,39 +62,37 @@

    Submodules

    atomate.vasp.firetasks.glue_tasks moduleΒΆ

    -class atomate.vasp.firetasks.glue_tasks.CheckBandgap(*args, **kwargs)ΒΆ
    +class atomate.vasp.firetasks.glue_tasks.CheckBandgap(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Checks the band gap of an entry. If band gap is >min_gap or <max_gap, then the task will return a FWAction that will defuse all remaining tasks.

    -
    -
    Required params:
    -
    (none) - but you should set either min_gap or max_gap
    -
    Optional params:
    -
    min_gap: (float) minimum gap energy in eV to proceed +
    +
    Required params:

    (none) - but you should set either min_gap or max_gap

    +
    +
    Optional params:

    min_gap: (float) minimum gap energy in eV to proceed max_gap: (float) maximum gap energy in eV to proceed -vasprun_path: (str) path to vasprun.xml file

    +vasprun_path: (str) path to vasprun.xml file

    +
    -optional_params = ['min_gap', 'max_gap', 'vasprun_path']ΒΆ
    +optional_params = ['min_gap', 'max_gap', 'vasprun_path']ΒΆ
    -required_params = []ΒΆ
    +required_params = []ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -103,11 +100,12 @@

    Submodules
    -class atomate.vasp.firetasks.glue_tasks.CheckStability(*args, **kwargs)ΒΆ
    +class atomate.vasp.firetasks.glue_tasks.CheckStability(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Checks the stability of the entry against the Materials Project database. If the stability is less than the cutoff (default is 0.1 eV/atom), then the task will return a FWAction that will defuse all remaining tasks.

    -
    -
    Required params:
    -
    (none) - but your MAPI key must be set as an environ var in this case
    -
    Optional params:
    -
    -
    ehull_cutoff: (float) energy in eV/atom to use as ehull cutoff. Default
    -
    is 0.05 eV/atom.
    -
    -

    MAPI_KEY: (str) set MAPI key directly. Supports env_chk. +

    +
    Required params:

    (none) - but your MAPI key must be set as an environ var in this case

    +
    +
    Optional params:
    +
    ehull_cutoff: (float) energy in eV/atom to use as ehull cutoff. Default

    is 0.05 eV/atom.

    +
    +
    +

    MAPI_KEY: (str) set MAPI key directly. Supports env_chk. calc_dir: (str) string to path containing vasprun.xml (default currdir)

    -optional_params = ['ehull_cutoff', 'MAPI_KEY', 'calc_dir']ΒΆ
    +optional_params = ['ehull_cutoff', 'MAPI_KEY', 'calc_dir']ΒΆ
    -required_params = []ΒΆ
    +required_params = []ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -160,11 +155,12 @@

    Submodules
    -class atomate.vasp.firetasks.glue_tasks.CopyVaspOutputs(*args, **kwargs)ΒΆ
    +class atomate.vasp.firetasks.glue_tasks.CopyVaspOutputs(*args, **kwargs)ΒΆ

    Bases: atomate.common.firetasks.glue_tasks.CopyFiles

    Copy files from a previous VASP run directory to the current directory. By default, copies β€˜INCAR’, β€˜POSCAR’ (default: via β€˜CONTCAR’), β€˜KPOINTS’, @@ -181,48 +177,46 @@

    Submodules -
    Required params:
    -
    (none) - but you must specify either β€œcalc_loc” OR β€œcalc_dir”
    -
    Optional params:
    -
    -
    calc_loc (str OR bool): if True will set most recent calc_loc. If str
    -
    search for the most recent calc_loc with the matching name
    +
    +
    Required params:

    (none) - but you must specify either β€œcalc_loc” OR β€œcalc_dir”

    +
    +
    Optional params:
    +
    calc_loc (str OR bool): if True will set most recent calc_loc. If str

    search for the most recent calc_loc with the matching name

    +

    calc_dir (str): path to dir that contains VASP output files. filesystem (str): remote filesystem. e.g. username@host additional_files ([str]): additional files to copy,

    -
    e.g. [β€œCHGCAR”, β€œWAVECAR”]. Use $ALL if you just want to copy -everything
    -
    -
    contcar_to_poscar(bool): If True (default), will move CONTCAR to
    -
    POSCAR (original POSCAR is not copied).
    +

    e.g. [β€œCHGCAR”, β€œWAVECAR”]. Use $ALL if you just want to copy +everything

    +
    +
    +
    contcar_to_poscar(bool): If True (default), will move CONTCAR to

    POSCAR (original POSCAR is not copied).

    +
    -copy_files()ΒΆ
    +copy_files()ΒΆ

    Defines the copy operation. Override this to customize copying.

    -optional_params = ['calc_loc', 'calc_dir', 'filesystem', 'additional_files', 'contcar_to_poscar']ΒΆ
    +optional_params = ['calc_loc', 'calc_dir', 'filesystem', 'additional_files', 'contcar_to_poscar']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -230,11 +224,12 @@

    Submodules
    -class atomate.vasp.firetasks.glue_tasks.GetInterpolatedPOSCAR(*args, **kwargs)ΒΆ
    +class atomate.vasp.firetasks.glue_tasks.GetInterpolatedPOSCAR(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Grabs CONTCARS from two previous calculations to create interpolated structure.

    @@ -252,47 +247,44 @@

    Submodules -
    Required params:
    -
    start (str): name of fw for start of interpolation. +
    +
    Required params:

    start (str): name of fw for start of interpolation. end (str): name of fw for end of interpolation. this_image (int): which interpolation this is. -nimages (int) : number of interpolations.

    -
    Optional params:
    -
    -
    autosort_tol (float): parameter used by Structure.interpolate.
    -
    a distance tolerance in angstrom in which to automatically +nimages (int) : number of interpolations.

    +
    +
    Optional params:
    +
    autosort_tol (float): parameter used by Structure.interpolate.

    a distance tolerance in angstrom in which to automatically sort end_structure to match to the closest -points in this particular structure. Default is 0.0.

    +points in this particular structure. Default is 0.0.

    +
    -interpolate_poscar(fw_spec)ΒΆ
    +interpolate_poscar(fw_spec)ΒΆ
    -optional_params = ['autosort_tol']ΒΆ
    +optional_params = ['autosort_tol']ΒΆ
    -required_params = ['start', 'end', 'this_image', 'nimages']ΒΆ
    +required_params = ['start', 'end', 'this_image', 'nimages']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -300,11 +292,12 @@

    Submodules
    -atomate.vasp.firetasks.glue_tasks.pass_vasp_result(pass_dict=None, calc_dir='.', filename='vasprun.xml.gz', parse_eigen=False, parse_dos=False, **kwargs)ΒΆ
    +atomate.vasp.firetasks.glue_tasks.pass_vasp_result(pass_dict=None, calc_dir='.', filename='vasprun.xml.gz', parse_eigen=False, parse_dos=False, **kwargs)ΒΆ

    Function that gets a PassResult firework corresponding to output from a Vasprun. Covers most use cases in which user needs to pass results from a vasp run to child FWs (e. g. analysis FWs)

    pass_vasp_result(pass_dict={β€˜stress’: β€œ>>ionic_steps.-1.stress”})

    -
    -
    Args:
    -
    -
    pass_dict (dict): dictionary designating keys and values to pass
    -
    to child fireworks. If value is a string beginning with β€˜>>’, +
    +
    Args:
    +
    pass_dict (dict): dictionary designating keys and values to pass

    to child fireworks. If value is a string beginning with β€˜>>’, the firework will search the parsed VASP output dictionary for the designated property by following the sequence of keys separated with periods, e. g. β€œ>>ionic_steps.-1.stress” is used @@ -329,17 +320,18 @@

    Submodules**kwargs (keyword args): other keyword arguments passed to PassResult -
    e.g. mod_spec_key or mod_spec_cmd
    +the Vasprun.

    +

    +
    calc_dir (str): path to dir that contains VASP output files, defaults

    to β€˜.’, e. g. current directory

    +
    +
    filename (str): filename for vasp xml file to parse, defaults to

    β€œvasprun.xml.gz”

    +
    +
    parse_eigen (bool): flag on whether or not to parse eigenvalues,

    defaults to false

    +
    +
    parse_eigen (bool): flag on whether or not to parse dos,

    defaults to false

    +
    +
    **kwargs (keyword args): other keyword arguments passed to PassResult

    e.g. mod_spec_key or mod_spec_cmd

    +
    @@ -350,40 +342,37 @@

    Submodules

    atomate.vasp.firetasks.neb_tasks moduleΒΆ

    -class atomate.vasp.firetasks.neb_tasks.RunNEBVaspFake(*args, **kwargs)ΒΆ
    +class atomate.vasp.firetasks.neb_tasks.RunNEBVaspFake(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Vasp Emulator for NEB, which has a different file arrangement. Similar to RunVaspFake class.

    -
    -
    Required params:
    -
    -
    ref_dir (string): Path to reference vasp run directory with input files in the folder named
    -
    β€˜inputs’ and output files in the folder named β€˜outputs’.
    +
    +
    Required params:
    +
    ref_dir (string): Path to reference vasp run directory with input files in the folder named

    β€˜inputs’ and output files in the folder named β€˜outputs’.

    +
    -
    Optional params:
    -
    params_to_check (list): optional list of incar parameters to check.
    +
    Optional params:

    params_to_check (list): optional list of incar parameters to check.

    +
    -optional_params = ['params_to_check']ΒΆ
    +optional_params = ['params_to_check']ΒΆ
    -required_params = ['ref_dir']ΒΆ
    +required_params = ['ref_dir']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -391,11 +380,12 @@

    Submodules
    -class atomate.vasp.firetasks.neb_tasks.TransferNEBTask(*args, **kwargs)ΒΆ
    +class atomate.vasp.firetasks.neb_tasks.TransferNEBTask(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    This class transfers NEB outputs from current directory to destination directory. β€œlabel” is used to determine the step of calculation and hence the final path. The corresponding structure will be updated in fw_spec before files transferring.

    -
    -
    Required params:
    -
    -
    label (str): Type of calculation outputs being transferred, choose from β€œparent”, β€œep0”,
    -
    β€œep1”, β€œneb1”, β€œneb2” and etc..
    +
    +
    Required params:
    +
    label (str): Type of calculation outputs being transferred, choose from β€œparent”, β€œep0”,

    β€œep1”, β€œneb1”, β€œneb2” and etc..

    +
    -
    Optional params:
    -
    -
    d_img (float): Distance between neighbouring images, used to determine the number of images
    -
    if β€œIMAGES” not provided in user_incar_settings, in Angstrom.
    +
    Optional params:
    +
    d_img (float): Distance between neighbouring images, used to determine the number of images

    if β€œIMAGES” not provided in user_incar_settings, in Angstrom.

    +
    -optional_params = ['d_img']ΒΆ
    +optional_params = ['d_img']ΒΆ
    -required_params = ['label']ΒΆ
    +required_params = ['label']ΒΆ
    -run_task(fw_spec)ΒΆ
    +run_task(fw_spec)ΒΆ

    This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

    -
    -
    Args:
    -
    -
    fw_spec (dict): A Firework spec. This comes from the master spec.
    -
    In addition, this spec contains a special β€œ_fw_env” key that +
    +
    Args:
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.

    In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -450,11 +436,12 @@

    Submodules
    -class atomate.vasp.firetasks.neb_tasks.WriteNEBFromEndpoints(*args, **kwargs)ΒΆ
    +class atomate.vasp.firetasks.neb_tasks.WriteNEBFromEndpoints(*args, **kwargs)ΒΆ

    Bases: fireworks.core.firework.FiretaskBase

    Generate NEB input sets using endpoint structures, default writes CI-NEB input. MVLCINEBSet is the only vasp_input_set supported now.

    -
    -
    The number of images:
    -
      -
    1. search in β€œuser_incar_settings”;
      2. -
    2. otherwise, calculated using β€œd_img”.
      3. +
      +
      The number of images:
        +

      1. search in β€œuser_incar_settings”;

        2. +

      2. otherwise, calculated using β€œd_img”.

      -
      Required parameters:
      -
      user_incar_settings (dict): additional INCAR settings.
      -
      Optional parameters:
      -

      user_kpoints_settings (dict): additional KPOINTS settings. +

      Required parameters:

      user_incar_settings (dict): additional INCAR settings.

      +
      +
      Optional parameters:

      user_kpoints_settings (dict): additional KPOINTS settings. sort_tol (float): Distance tolerance (in Angstrom) used to match the atomic indices between

      -
      start and end structures. If it is set 0, then no sorting will be performed.
      -
      -
      d_img (float): distance in Angstrom, used in calculating number of images. Default 0.7
      -
      Angstrom.
      -
      interpolation_type (str): method to do image interpolation from two endpoints.
      -
      Choose from [β€œIDPP”, β€œlinear”], default β€œIDPP”
      +

      start and end structures. If it is set 0, then no sorting will be performed.

      +
      +
      +
      d_img (float): distance in Angstrom, used in calculating number of images. Default 0.7

      Angstrom.

      +
      +
      interpolation_type (str): method to do image interpolation from two endpoints.

      Choose from [β€œIDPP”, β€œlinear”], default β€œIDPP”

      +
      -optional_params = ['user_kpoints_settings', 'sort_tol', 'd_img', 'interpolation_type']ΒΆ
      +optional_params = ['user_kpoints_settings', 'sort_tol', 'd_img', 'interpolation_type']ΒΆ
      -required_params = ['user_incar_settings']ΒΆ
      +required_params = ['user_incar_settings']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -516,11 +500,12 @@

      Submodules
      -class atomate.vasp.firetasks.neb_tasks.WriteNEBFromImages(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.neb_tasks.WriteNEBFromImages(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Generate CI-NEB input sets using given images and endpoints structures. The structures correspond to structures nested in subfolders (β€œ00”, β€œ01”, β€œ02”, etc.)

      -
      -
      Required parameters:
      -
      neb_label (str): β€œ1”, β€œ2”, etc., labels the running sequence of NEB
      -
      Optional parameters:
      -
      user_incar_settings (dict): Additional INCAR settings. -user_kpoints_settings (dict): Additional KPOINTS settings.
      +
      +
      Required parameters:

      neb_label (str): β€œ1”, β€œ2”, etc., labels the running sequence of NEB

      +
      +
      Optional parameters:

      user_incar_settings (dict): Additional INCAR settings. +user_kpoints_settings (dict): Additional KPOINTS settings.

      +
      -optional_params = ['user_incar_settings', 'user_kpoints_settings']ΒΆ
      +optional_params = ['user_incar_settings', 'user_kpoints_settings']ΒΆ
      -required_params = ['neb_label']ΒΆ
      +required_params = ['neb_label']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -567,11 +550,12 @@

      Submodules

      atomate.vasp.firetasks.parse_outputs moduleΒΆ

      -class atomate.vasp.firetasks.parse_outputs.BoltztrapToDBTask(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.BoltztrapToDBTask(*args, **kwargs)ΒΆ

      Bases: atomate.vasp.firetasks.parse_outputs.BoltztrapToDb

      -class atomate.vasp.firetasks.parse_outputs.BoltztrapToDb(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.BoltztrapToDb(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Enter a BoltzTraP run into the database. Note that this assumes you are in a current dir that has the uniform band structure data with a sub-directory called β€œboltztrap” containing the BoltzTraP information.

      -
      -
      Optional params:
      -
      -
      db_file (str): path to file containing the database credentials.
      -
      Supports env_chk. Default: write data to JSON file.
      +
      +
      Optional params:
      +
      db_file (str): path to file containing the database credentials.

      Supports env_chk. Default: write data to JSON file.

      +
      -

      hall_doping (bool): set True to retain hall_doping in dict +

      hall_doping (bool): set True to retain hall_doping in dict additional_fields (dict): fields added to the document such as user-defined tags or name, ids, etc

      -optional_params = ['db_file', 'hall_doping', 'additional_fields']ΒΆ
      +optional_params = ['db_file', 'hall_doping', 'additional_fields']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -626,11 +607,12 @@

      Submodules
      -class atomate.vasp.firetasks.parse_outputs.ElasticTensorToDb(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.ElasticTensorToDb(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Analyzes the stress/strain data of an elastic workflow to produce an elastic tensor and various other quantities.

      -
      -
      Required params:
      -
      -
      structure (Structure): structure to use for symmetrization,
      -
      input structure. If an optimization was used, will -look for relaxed structure in calc locs
      +
      +
      Required params:
      +
      structure (Structure): structure to use for symmetrization,

      input structure. If an optimization was used, will +look for relaxed structure in calc locs

      +
      -
      Optional params:
      -
      -
      db_file (str): path to file containing the database credentials.
      -
      Supports env_chk. Default: write data to JSON file.
      +
      Optional params:
      +
      db_file (str): path to file containing the database credentials.

      Supports env_chk. Default: write data to JSON file.

      +

      order (int): order of fit to perform fw_spec_field (str): if set, will update the task doc with the contents

      -
      of this key in the fw_spec.
      -
      -
      fitting_method (str): if set, will use one of the specified
      -
      fitting methods from pymatgen. Supported methods are +

      of this key in the fw_spec.

      +
      +
      +
      fitting_method (str): if set, will use one of the specified

      fitting methods from pymatgen. Supported methods are β€œindependent”, β€œpseudoinverse”, and β€œfinite_difference.” Note that order 3 and higher required finite difference -fitting, and will override.

      +fitting, and will override.

      +
      -optional_params = ['db_file', 'order', 'fw_spec_field', 'fitting_method']ΒΆ
      +optional_params = ['db_file', 'order', 'fw_spec_field', 'fitting_method']ΒΆ
      -required_params = ['structure']ΒΆ
      +required_params = ['structure']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -696,11 +675,12 @@

      Submodules
      -class atomate.vasp.firetasks.parse_outputs.ElasticTensorToDbTask(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.ElasticTensorToDbTask(*args, **kwargs)ΒΆ

      Bases: atomate.vasp.firetasks.parse_outputs.ElasticTensorToDb

      -class atomate.vasp.firetasks.parse_outputs.FitEOSToDb(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.FitEOSToDb(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Retrieve the energy and volume data and fit it to the given equation of state. The summary dict is written to β€˜bulk_modulus.json’ file.

      -
      -
      Required parameters:
      -
      -
      tag (str): unique tag appended to the task labels in other fireworks so that all the
      -
      required data can be queried directly from the database.
      +
      +
      Required parameters:
      +
      tag (str): unique tag appended to the task labels in other fireworks so that all the

      required data can be queried directly from the database.

      +
      -

      db_file (str): path to the db file

      +

      db_file (str): path to the db file

      -
      Optional parameters:
      -

      to_db (bool): if True, the data will be inserted to β€œeos” collection; otherwise, dumped to a .json file. +

      Optional parameters:

      to_db (bool): if True, the data will be inserted to β€œeos” collection; otherwise, dumped to a .json file. eos (str): equation of state used for fitting the energies and the volumes.

      -
      -
      options supported by pymatgen: β€œquadratic”, β€œmurnaghan”, β€œbirch”, β€œbirch_murnaghan”, -β€œpourier_tarantola”, β€œvinet”, β€œdeltafactor”. Default: β€œvinet”
      +
      +

      options supported by pymatgen: β€œquadratic”, β€œmurnaghan”, β€œbirch”, β€œbirch_murnaghan”, +β€œpourier_tarantola”, β€œvinet”, β€œdeltafactor”. Default: β€œvinet”

      +
      -optional_params = ['to_db', 'eos']ΒΆ
      +optional_params = ['to_db', 'eos']ΒΆ
      -required_params = ['tag', 'db_file']ΒΆ
      +required_params = ['tag', 'db_file']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -762,11 +739,12 @@

      Submodules
      -class atomate.vasp.firetasks.parse_outputs.FitEquationOfStateTask(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.FitEquationOfStateTask(*args, **kwargs)ΒΆ

      Bases: atomate.vasp.firetasks.parse_outputs.FitEOSToDb

      -class atomate.vasp.firetasks.parse_outputs.GibbsAnalysisToDb(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.GibbsAnalysisToDb(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Compute the quasi-harmonic gibbs free energy. There are 2 options available for the quasi-harmonic approximation (set via β€˜qha_type’ parameter): @@ -788,18 +766,16 @@

      Submodules -
      required_params:
      -
      -
      tag (str): unique tag appended to the task labels in other fireworks so that all the
      -
      required data can be queried directly from the database.
      +
      +
      required_params:
      +
      tag (str): unique tag appended to the task labels in other fireworks so that all the

      required data can be queried directly from the database.

      +
      -

      db_file (str): path to the db file

      +

      db_file (str): path to the db file

      +
      +
      optional_params:
      +
      qha_type(str): quasi-harmonic approximation type: β€œdebye_model” or β€œphonopy”,

      default is β€œdebye_model”

      -
      optional_params:
      -
      -
      qha_type(str): quasi-harmonic approximation type: β€œdebye_model” or β€œphonopy”,
      -
      default is β€œdebye_model”

      t_min (float): min temperature t_step (float): temperature step @@ -807,37 +783,37 @@

      Submodulespressure (float): in GPa, optional. +

      Gibbs energy from the Debye model. Defaults to False.

      +
      +

      pressure (float): in GPa, optional. metadata (dict): meta data

      -optional_params = ['qha_type', 't_min', 't_step', 't_max', 'mesh', 'eos', 'pressure', 'poisson', 'anharmonic_contribution', 'metadata']ΒΆ
      +optional_params = ['qha_type', 't_min', 't_step', 't_max', 'mesh', 'eos', 'pressure', 'poisson', 'anharmonic_contribution', 'metadata']ΒΆ
      -required_params = ['tag', 'db_file']ΒΆ
      +required_params = ['tag', 'db_file']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -845,11 +821,12 @@

      Submodules
      -class atomate.vasp.firetasks.parse_outputs.GibbsFreeEnergyTask(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.GibbsFreeEnergyTask(*args, **kwargs)ΒΆ

      Bases: atomate.vasp.firetasks.parse_outputs.GibbsAnalysisToDb

      -class atomate.vasp.firetasks.parse_outputs.JsonToDb(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.JsonToDb(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Insert the a JSON file (default: task.json) directly into the tasks database. Note that if the JSON file contains a β€œtask_id” key, that task_id must not already be present in the tasks collection.

      -
      -
      Optional params:
      -

      json_filename (str): name of the JSON file to insert (default: β€œtask.json”) +

      +
      Optional params:

      json_filename (str): name of the JSON file to insert (default: β€œtask.json”) db_file (str): path to file containing the database credentials. Supports env_chk. calc_dir (str): path to dir (on current filesystem) that contains VASP output files.

      -
      -
      Default: use current working directory.
      +
      +

      Default: use current working directory.

      +
      -optional_params = ['json_filename', 'db_file', 'calc_dir']ΒΆ
      +optional_params = ['json_filename', 'db_file', 'calc_dir']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -900,11 +875,12 @@

      Submodules
      -class atomate.vasp.firetasks.parse_outputs.JsonToDbTask(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.JsonToDbTask(*args, **kwargs)ΒΆ

      Bases: atomate.vasp.firetasks.parse_outputs.JsonToDb

      -class atomate.vasp.firetasks.parse_outputs.MagneticDeformationToDB(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.MagneticDeformationToDB(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Used to calculate magnetic deformation from get_wf_magnetic_deformation workflow. See docstring for that workflow for more information. Required parameters:

      -
      db_file (str): path to the db file that holds your tasks +

      db_file (str): path to the db file that holds your tasks collection and that you want to hold the magnetic_orderings collection wf_uuid (str): auto-generated from get_wf_magnetic_orderings, -used to make it easier to retrieve task docs

      -
      -
      Optional parameters:
      -
      to_db (bool): if True, the data will be inserted into +used to make it easier to retrieve task docs

      + +
      +
      Optional parameters:

      to_db (bool): if True, the data will be inserted into dedicated collection in database, otherwise, will be dumped -to a .json file.

      +to a .json file.

      +
      -optional_params = ['to_db']ΒΆ
      +optional_params = ['to_db']ΒΆ
      -required_params = ['db_file', 'wf_uuid']ΒΆ
      +required_params = ['db_file', 'wf_uuid']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -964,11 +939,12 @@

      Submodules
      -class atomate.vasp.firetasks.parse_outputs.MagneticOrderingsToDB(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.MagneticOrderingsToDB(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Used to aggregate tasks docs from magnetic ordering workflow. For large-scale/high-throughput use, would recommend a specific @@ -985,34 +961,33 @@

      Submodules
      -optional_params = ['origins', 'input_index']ΒΆ
      +optional_params = ['origins', 'input_index']ΒΆ

      -required_params = ['db_file', 'wf_uuid', 'parent_structure', 'perform_bader', 'scan']ΒΆ
      +required_params = ['db_file', 'wf_uuid', 'parent_structure', 'perform_bader', 'scan']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -1020,11 +995,12 @@

      Submodules
      -class atomate.vasp.firetasks.parse_outputs.PolarizationToDb(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.PolarizationToDb(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Recovers the same branch polarization and spontaneous polarization for a ferroelectric workflow.

      -optional_params = ['db_file']ΒΆ
      +optional_params = ['db_file']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -1059,11 +1033,12 @@

      Submodules
      -class atomate.vasp.firetasks.parse_outputs.RamanSusceptibilityTensorToDbTask(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.RamanSusceptibilityTensorToDbTask(*args, **kwargs)ΒΆ

      Bases: atomate.vasp.firetasks.parse_outputs.RamanTensorToDb

      -class atomate.vasp.firetasks.parse_outputs.RamanTensorToDb(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.RamanTensorToDb(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      -
      -
      Raman susceptibility tensor for each mode = Finite difference derivative of the dielectric
      -
      tensor wrt the displacement along that mode.
      +
      +
      Raman susceptibility tensor for each mode = Finite difference derivative of the dielectric

      tensor wrt the displacement along that mode.

      +

      See: 10.1103/PhysRevB.73.104304. The frequencies are in the units of cm^-1. To convert the frequency to THz: multiply by 0.1884.

      -
      -
      optional_params:
      -
      db_file (str): path to the db file
      +
      +
      optional_params:

      db_file (str): path to the db file

      +
      -optional_params = ['db_file']ΒΆ
      +optional_params = ['db_file']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -1112,11 +1085,12 @@

      Submodules
      -class atomate.vasp.firetasks.parse_outputs.ThermalExpansionCoeffTask(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.ThermalExpansionCoeffTask(*args, **kwargs)ΒΆ

      Bases: atomate.vasp.firetasks.parse_outputs.ThermalExpansionCoeffToDb

      -class atomate.vasp.firetasks.parse_outputs.ThermalExpansionCoeffToDb(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.ThermalExpansionCoeffToDb(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Compute the quasi-harmonic thermal expansion coefficient using phonopy.

      -
      -
      required_params:
      -
      -
      tag (str): unique tag appended to the task labels in other fireworks so that all the
      -
      required data can be queried directly from the database.
      +
      +
      required_params:
      +
      tag (str): unique tag appended to the task labels in other fireworks so that all the

      required data can be queried directly from the database.

      +
      -

      db_file (str): path to the db file

      +

      db_file (str): path to the db file

      -
      optional_params:
      -

      t_min (float): min temperature +

      optional_params:

      t_min (float): min temperature t_step (float): temperature step t_max (float): max temperature mesh (list/tuple): reciprocal space density eos (str): equation of state used for fitting the energies and the volumes.

      -
      options supported by phonopy: β€œvinet” (default), β€œmurnaghan”, β€œbirch_murnaghan”.
      -

      pressure (float): in GPa, optional.

      +

      options supported by phonopy: β€œvinet” (default), β€œmurnaghan”, β€œbirch_murnaghan”.

      +
      +

      pressure (float): in GPa, optional.

      -optional_params = ['t_min', 't_step', 't_max', 'mesh', 'eos', 'pressure']ΒΆ
      +optional_params = ['t_min', 't_step', 't_max', 'mesh', 'eos', 'pressure']ΒΆ
      -required_params = ['tag', 'db_file']ΒΆ
      +required_params = ['tag', 'db_file']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -1180,11 +1151,12 @@

      Submodules
      -class atomate.vasp.firetasks.parse_outputs.VaspToDb(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.VaspToDb(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Enter a VASP run into the database. Uses current directory unless you specify calc_dir or calc_loc.

      -
      -
      Optional params:
      -
      -
      calc_dir (str): path to dir (on current filesystem) that contains VASP
      -
      output files. Default: use current working directory.
      -
      calc_loc (str OR bool): if True will set most recent calc_loc. If str
      -
      search for the most recent calc_loc with the matching name
      -
      parse_dos (bool): whether to parse the DOS and store in GridFS.
      -
      Defaults to False.
      -
      bandstructure_mode (str): Set to β€œuniform” for uniform band structure.
      -
      Set to β€œline” for line mode. If not set, band structure will not -be parsed.
      +
      +
      Optional params:
      +
      calc_dir (str): path to dir (on current filesystem) that contains VASP

      output files. Default: use current working directory.

      +
      +
      calc_loc (str OR bool): if True will set most recent calc_loc. If str

      search for the most recent calc_loc with the matching name

      +
      +
      parse_dos (bool): whether to parse the DOS and store in GridFS.

      Defaults to False.

      +
      +
      bandstructure_mode (str): Set to β€œuniform” for uniform band structure.

      Set to β€œline” for line mode. If not set, band structure will not +be parsed.

      +

      additional_fields (dict): dict of additional fields to add db_file (str): path to file containing the database credentials.

      -
      Supports env_chk. Default: write data to JSON file.
      -
      -
      fw_spec_field (str): if set, will update the task doc with the contents
      -
      of this key in the fw_spec.
      -
      defuse_unsuccessful (bool): this is a three-way toggle on what to do if
      -
      your job looks OK, but is actually unconverged (either electronic or +

      Supports env_chk. Default: write data to JSON file.

      +
      +
      +
      fw_spec_field (str): if set, will update the task doc with the contents

      of this key in the fw_spec.

      +
      +
      defuse_unsuccessful (bool): this is a three-way toggle on what to do if

      your job looks OK, but is actually unconverged (either electronic or ionic). True -> mark job as COMPLETED, but defuse children. False –> do nothing, continue with workflow as normal. β€œfizzle” -–> throw an error (mark this job as FIZZLED)

      -
      task_fields_to_push (dict): if set, will update the next Firework/Firetask
      -
      spec using fields from the task document. +–> throw an error (mark this job as FIZZLED)

      +
      +
      task_fields_to_push (dict): if set, will update the next Firework/Firetask

      spec using fields from the task document. Format: {key : path} -> fw.spec[key] = task_doc[path] The path is a full mongo-style path so subdocuments can be referneced using dot notation and array keys can be referenced using the index. -E.g β€œcalcs_reversed.0.output.outar.run_stats”

      +E.g β€œcalcs_reversed.0.output.outar.run_stats”

      +
      -optional_params = ['calc_dir', 'calc_loc', 'parse_dos', 'bandstructure_mode', 'additional_fields', 'db_file', 'fw_spec_field', 'defuse_unsuccessful', 'task_fields_to_push', 'parse_chgcar', 'parse_aeccar']ΒΆ
      +optional_params = ['calc_dir', 'calc_loc', 'parse_dos', 'bandstructure_mode', 'additional_fields', 'db_file', 'fw_spec_field', 'defuse_unsuccessful', 'task_fields_to_push', 'parse_chgcar', 'parse_aeccar']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -1253,11 +1223,12 @@

      Submodules
      -class atomate.vasp.firetasks.parse_outputs.VaspToDbTask(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.parse_outputs.VaspToDbTask(*args, **kwargs)ΒΆ

      Bases: atomate.vasp.firetasks.parse_outputs.VaspToDb

      @@ -1274,35 +1245,33 @@

      Submodules

      atomate.vasp.firetasks.run_calc moduleΒΆ

      -class atomate.vasp.firetasks.run_calc.RunBoltztrap(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.run_calc.RunBoltztrap(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Run Boltztrap directly. Requires vasprun.xml and OUTCAR to be in current dir.

      -
      -
      Required params:
      -
      (none)
      -
      Optional params:
      -
      scissor: (float) scissor band gap amount in eV (i.e. new gap == scissor) +
      +
      Required params:

      (none)

      +
      +
      Optional params:

      scissor: (float) scissor band gap amount in eV (i.e. new gap == scissor) tmax: (float) max temperature to evaluate (default = 1300K) tgrid: (float) temperature interval (default = 50K) doping: ([float]) doping levels you want to compute -soc: (bool) whether the band structure is calculated with spin-orbit coupling or not

      +soc: (bool) whether the band structure is calculated with spin-orbit coupling or not

      +
      -optional_params = ['scissor', 'tmax', 'tgrid', 'doping', 'soc']ΒΆ
      +optional_params = ['scissor', 'tmax', 'tgrid', 'doping', 'soc']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -1310,11 +1279,12 @@

      Submodules
      -class atomate.vasp.firetasks.run_calc.RunNoVasp(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.run_calc.RunNoVasp(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Do NOT run vasp. Do nothing.

      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -1343,11 +1311,12 @@

      Submodules
      -class atomate.vasp.firetasks.run_calc.RunVaspCustodian(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.run_calc.RunVaspCustodian(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Run VASP using custodian β€œon rails”, i.e. in a simple way that supports most common options.

      -
      -
      Required params:
      -
      vasp_cmd (str): the name of the full executable for running VASP. Supports env_chk.
      -
      Optional params:
      -
      -
      job_type: (str) - choose from β€œnormal” (default), β€œdouble_relaxation_run” (two consecutive
      -
      jobs), β€œfull_opt_run” (multiple optimizations), and β€œneb”
      -
      handler_group: (str or [ErrorHandler]) - group of handlers to use. See handler_groups dict in the code for
      -
      the groups and complete list of handlers in each group. Alternatively, you can -specify a list of ErrorHandler objects.
      -
      max_force_threshold: (float) - if >0, adds MaxForceErrorHandler. Not recommended for
      -
      nscf runs.
      -
      scratch_dir: (str) - if specified, uses this directory as the root scratch dir.
      -
      Supports env_chk.
      +
      +
      Required params:

      vasp_cmd (str): the name of the full executable for running VASP. Supports env_chk.

      +
      +
      Optional params:
      +
      job_type: (str) - choose from β€œnormal” (default), β€œdouble_relaxation_run” (two consecutive

      jobs), β€œfull_opt_run” (multiple optimizations), and β€œneb”

      +
      +
      handler_group: (str or [ErrorHandler]) - group of handlers to use. See handler_groups dict in the code for

      the groups and complete list of handlers in each group. Alternatively, you can +specify a list of ErrorHandler objects.

      +
      +
      max_force_threshold: (float) - if >0, adds MaxForceErrorHandler. Not recommended for

      nscf runs.

      +
      +
      scratch_dir: (str) - if specified, uses this directory as the root scratch dir.

      Supports env_chk.

      +

      gzip_output: (bool) - gzip output (default=T) max_errors: (int) - maximum # of errors to fix before giving up (default=5) ediffg: (float) shortcut for setting EDIFFG in special custodian jobs auto_npar: (bool) - use auto_npar (default=F). Recommended set to T

      -
      for single-node jobs only. Supports env_chk.
      -
      -
      gamma_vasp_cmd: (str) - cmd for Gamma-optimized VASP compilation.
      -
      Supports env_chk.
      +

      for single-node jobs only. Supports env_chk.

      +
      +
      +
      gamma_vasp_cmd: (str) - cmd for Gamma-optimized VASP compilation.

      Supports env_chk.

      +
      -

      wall_time (int): Total wall time in seconds. Activates WalltimeHandler if set. +

      wall_time (int): Total wall time in seconds. Activates WalltimeHandler if set. half_kpts_first_relax (bool): Use half the k-points for the first relaxation

      -optional_params = ['job_type', 'handler_group', 'max_force_threshold', 'scratch_dir', 'gzip_output', 'max_errors', 'ediffg', 'auto_npar', 'gamma_vasp_cmd', 'wall_time', 'half_kpts_first_relax']ΒΆ
      +optional_params = ['job_type', 'handler_group', 'max_force_threshold', 'scratch_dir', 'gzip_output', 'max_errors', 'ediffg', 'auto_npar', 'gamma_vasp_cmd', 'wall_time', 'half_kpts_first_relax']ΒΆ
      -required_params = ['vasp_cmd']ΒΆ
      +required_params = ['vasp_cmd']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -1415,11 +1382,12 @@

      Submodules
      -class atomate.vasp.firetasks.run_calc.RunVaspDirect(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.run_calc.RunVaspDirect(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Execute a command directly (no custodian).

      -
      -
      Required params:
      -
      cmd (str): the name of the full executable to run. Supports env_chk.
      -
      Optional params:
      -
      expand_vars (str): Set to true to expand variable names in the cmd.
      +
      +
      Required params:

      cmd (str): the name of the full executable to run. Supports env_chk.

      +
      +
      Optional params:

      expand_vars (str): Set to true to expand variable names in the cmd.

      +
      -optional_params = ['expand_vars']ΒΆ
      +optional_params = ['expand_vars']ΒΆ
      -required_params = ['vasp_cmd']ΒΆ
      +required_params = ['vasp_cmd']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -1464,11 +1430,12 @@

      Submodules
      -class atomate.vasp.firetasks.run_calc.RunVaspFake(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.run_calc.RunVaspFake(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Vasp Emulator

      -
      -
      Required params:
      -
      -
      ref_dir (string): Path to reference vasp run directory with input files in the folder
      -
      named β€˜inputs’ and output files in the folder named β€˜outputs’.
      +
      +
      Required params:
      +
      ref_dir (string): Path to reference vasp run directory with input files in the folder

      named β€˜inputs’ and output files in the folder named β€˜outputs’.

      +
      -
      Optional params:
      -
      params_to_check (list): optional list of incar parameters to check. +
      Optional params:

      params_to_check (list): optional list of incar parameters to check. check_incar (bool): whether to confirm the INCAR params (default: True) check_kpoints (bool): whether to confirm the KPOINTS params (default: True) check_poscar (bool): whether to confirm the POSCAR params (default: True) -check_potcar (bool): whether to confirm the POTCAR params (default: True)

      +check_potcar (bool): whether to confirm the POTCAR params (default: True)

      +
      -optional_params = ['params_to_check', 'check_incar', 'check_kpoints', 'check_poscar', 'check_potcar']ΒΆ
      +optional_params = ['params_to_check', 'check_incar', 'check_kpoints', 'check_poscar', 'check_potcar']ΒΆ
      -required_params = ['ref_dir']ΒΆ
      +required_params = ['ref_dir']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -1521,11 +1485,12 @@

      Submodules

      atomate.vasp.firetasks.write_inputs moduleΒΆ

      -class atomate.vasp.firetasks.write_inputs.ModifyIncar(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.write_inputs.ModifyIncar(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Modify an INCAR file.

      -
      -
      Required params:
      -
      (none)
      -
      Optional params:
      -

      incar_update (dict): overwrite Incar dict key. Supports env_chk. +

      +
      Required params:

      (none)

      +
      +
      Optional params:

      incar_update (dict): overwrite Incar dict key. Supports env_chk. incar_multiply ([{<str>:<float>}]) - multiply Incar key by a constant

      -
      factor. Supports env_chk.
      -
      -
      incar_dictmod ([{}]): use DictMod language to change Incar.
      -
      Supports env_chk.
      +

      factor. Supports env_chk.

      +
      +
      +
      incar_dictmod ([{}]): use DictMod language to change Incar.

      Supports env_chk.

      +
      -

      input_filename (str): Input filename (if not β€œINCAR”) +

      input_filename (str): Input filename (if not β€œINCAR”) output_filename (str): Output filename (if not β€œINCAR”)

      -optional_params = ['incar_update', 'incar_multiply', 'incar_dictmod', 'input_filename', 'output_filename']ΒΆ
      +optional_params = ['incar_update', 'incar_multiply', 'incar_dictmod', 'input_filename', 'output_filename']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -1578,11 +1541,12 @@

      Submodules
      -class atomate.vasp.firetasks.write_inputs.ModifyPotcar(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.write_inputs.ModifyPotcar(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Modify Potcar file.

      -
      -
      Required params:
      -
      potcar_symbols (dict): overwrite potcar with symbol. Supports env_chk.
      -
      Optional params:
      -
      functional (dict): functional to use, e.g. PBE, PBE_52, LDA_US, PW91 +
      +
      Required params:

      potcar_symbols (dict): overwrite potcar with symbol. Supports env_chk.

      +
      +
      Optional params:

      functional (dict): functional to use, e.g. PBE, PBE_52, LDA_US, PW91 input_filename (str): Input filename (if not β€œINCAR”) -output_filename (str): Output filename (if not β€œINCAR”)

      +output_filename (str): Output filename (if not β€œINCAR”)

      +
      -optional_params = ['functional', 'input_filename', 'output_filename']ΒΆ
      +optional_params = ['functional', 'input_filename', 'output_filename']ΒΆ
      -required_params = ['potcar_symbols']ΒΆ
      +required_params = ['potcar_symbols']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -1629,11 +1591,12 @@

      Submodules
      -class atomate.vasp.firetasks.write_inputs.WriteNormalmodeDisplacedPoscar(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.write_inputs.WriteNormalmodeDisplacedPoscar(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Displace the structure from the previous calculation along the provided normal mode by the given amount and write the corresponding Poscar file. The fw_spec must contain a β€œnormalmodes” key with β€œeigenvecs” sub-key that is likely produced by a previous calc.

      -
      -
      Required params:
      -
      mode (int): normal mode index -displacement (float): displacement along the normal mode in Angstroms
      +
      +
      Required params:

      mode (int): normal mode index +displacement (float): displacement along the normal mode in Angstroms

      +
      -required_params = ['mode', 'displacement']ΒΆ
      +required_params = ['mode', 'displacement']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -1674,11 +1635,12 @@

      Submodules
      -class atomate.vasp.firetasks.write_inputs.WriteTransmutedStructureIOSet(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.write_inputs.WriteTransmutedStructureIOSet(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Apply the provided transformations to the input structure and write the input set for that structure. Reads structure from POSCAR if no structure provided. Note that if a transformation yields many structures from one, only the last structure in the list is used.

      -
      -
      Required params:
      -

      structure (Structure): input structure +

      +
      Required params:

      structure (Structure): input structure transformations (list): list of names of transformation classes as defined in

      -
      the modules in pymatgen.transformations
      -

      vasp_input_set (VaspInputSet): VASP input set.

      +

      the modules in pymatgen.transformations

      +
      +

      vasp_input_set (VaspInputSet): VASP input set.

      +
      +
      Optional params:
      +
      transformation_params (list): list of dicts where each dict specifies the input parameters

      to instantiate the transformation class in the transformations list.

      -
      Optional params:
      -
      -
      transformation_params (list): list of dicts where each dict specifies the input parameters
      -
      to instantiate the transformation class in the transformations list.
      -

      override_default_vasp_params (dict): additional user input settings. +

      override_default_vasp_params (dict): additional user input settings. prev_calc_dir: path to previous calculation if using structure from another calculation.

      -optional_params = ['prev_calc_dir', 'transformation_params', 'override_default_vasp_params']ΒΆ
      +optional_params = ['prev_calc_dir', 'transformation_params', 'override_default_vasp_params']ΒΆ
      -required_params = ['structure', 'transformations', 'vasp_input_set']ΒΆ
      +required_params = ['structure', 'transformations', 'vasp_input_set']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -1737,11 +1696,12 @@

      Submodules
      -class atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Create VASP input files using implementations of pymatgen’s AbstractVaspInputSet. An input set can be provided as an object or as a String/parameter combo.

      -
      -
      Required params:
      -

      structure (Structure): structure +

      +
      Required params:

      structure (Structure): structure vasp_input_set (AbstractVaspInputSet or str): Either a VaspInputSet object or a string

      -
      -
      name for the VASP input set (e.g., β€œMPRelaxSet”).
      +
      +

      name for the VASP input set (e.g., β€œMPRelaxSet”).

      +
      -
      Optional params:
      -
      -
      vasp_input_params (dict): When using a string name for VASP input set, use this as a dict
      -
      to specify kwargs for instantiating the input set parameters. For example, if you want +
      Optional params:
      +
      vasp_input_params (dict): When using a string name for VASP input set, use this as a dict

      to specify kwargs for instantiating the input set parameters. For example, if you want to change the user_incar_settings, you should provide: {β€œuser_incar_settings”: …}. This setting is ignored if you provide the full object representation of a VaspInputSet -rather than a String.

      +rather than a String.

      +
      -optional_params = ['vasp_input_params']ΒΆ
      +optional_params = ['vasp_input_params']ΒΆ
      -required_params = ['structure', 'vasp_input_set']ΒΆ
      +required_params = ['structure', 'vasp_input_set']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -1798,11 +1755,12 @@

      Submodules
      -class atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSetFromInterpolatedPOSCAR(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSetFromInterpolatedPOSCAR(*args, **kwargs)ΒΆ

      Bases: atomate.vasp.firetasks.glue_tasks.GetInterpolatedPOSCAR

      Grabs CONTCARS from two previous calculations to create interpolated structure. Create VASP input files using implementations of pymatgen’s AbstractVaspInputSet. An input set can be provided as String/parameter combo.

      -
      -
      Required params:
      -

      start (str): name of fw for start of interpolation. +

      +
      Required params:

      start (str): name of fw for start of interpolation. end (str): name of fw for end of interpolation. this_image (int): which interpolation this is. nimages (int) : number of interpolations. autosort_tol (float): a distance tolerance in angstrom in which

      -
      to automatically sort end_structure to match to the closest -points in this particular structure.
      -

      vasp_input_set (str): a string name for the VASP input set (e.g., β€œMPRelaxSet”).

      -
      -
      Optional params:
      -
      -
      vasp_input_params (dict): When using a string name for VASP input set, use this as a dict
      -
      to specify kwargs for instantiating the input set parameters. For example, if you want +

      to automatically sort end_structure to match to the closest +points in this particular structure.

      +
      +

      vasp_input_set (str): a string name for the VASP input set (e.g., β€œMPRelaxSet”).

      +
      +
      Optional params:
      +
      vasp_input_params (dict): When using a string name for VASP input set, use this as a dict

      to specify kwargs for instantiating the input set parameters. For example, if you want to change the user_incar_settings, you should provide: {β€œuser_incar_settings”: …}. This setting is ignored if you provide the full object representation of a VaspInputSet -rather than a String.

      +rather than a String.

      +
      -optional_params = ['vasp_input_params', 'autosort_tol']ΒΆ
      +optional_params = ['vasp_input_params', 'autosort_tol']ΒΆ
      -required_params = ['start', 'end', 'this_image', 'nimages', 'vasp_input_set']ΒΆ
      +required_params = ['start', 'end', 'this_image', 'nimages', 'vasp_input_set']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -1866,11 +1821,12 @@

      Submodules
      -class atomate.vasp.firetasks.write_inputs.WriteVaspFromPMGObjects(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.write_inputs.WriteVaspFromPMGObjects(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Write VASP files using pymatgen objects.

      -
      -
      Required params:
      -
      (none) - although non-functional unless you set one or more optional params
      -
      Optional params:
      -
      incar (Incar): pymatgen Incar object +
      +
      Required params:

      (none) - although non-functional unless you set one or more optional params

      +
      +
      Optional params:

      incar (Incar): pymatgen Incar object poscar (Poscar): pymatgen Poscar object kpoints (Kpoints): pymatgen Kpoints object -potcar (Potcar): pymatgen Potcar object

      +potcar (Potcar): pymatgen Potcar object

      +
      -optional_params = ['incar', 'poscar', 'kpoints', 'potcar']ΒΆ
      +optional_params = ['incar', 'poscar', 'kpoints', 'potcar']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -1913,11 +1867,12 @@

      Submodules
      -class atomate.vasp.firetasks.write_inputs.WriteVaspHSEBSFromPrev(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.write_inputs.WriteVaspHSEBSFromPrev(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Writes input files for HSE band structure run. Assumes that output files from a a previous job can be accessed. Since HSE always re-optimizes the charge density (no nSCF mode), the previous job is used to get the location of VBM/CBM for mode=”gap” (otherwise just used to get the structure / starting charge density).

      -
      -
      Required params:
      -
      (none)
      -
      Optional params:
      -
      (documentation for all other optional params can be found in -MPHSEBSSet)
      +
      +
      Required params:

      (none)

      +
      +
      Optional params:

      (documentation for all other optional params can be found in +MPHSEBSSet)

      +
      -optional_params = ['prev_calc_dir', 'mode', 'reciprocal_density', 'kpoints_line_density']ΒΆ
      +optional_params = ['prev_calc_dir', 'mode', 'reciprocal_density', 'kpoints_line_density']ΒΆ
      -required_params = []ΒΆ
      +required_params = []ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -1966,11 +1919,12 @@

      Submodules
      -class atomate.vasp.firetasks.write_inputs.WriteVaspNMRFromPrev(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.write_inputs.WriteVaspNMRFromPrev(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Writes input files for a NMR calculation

      -
      -
      Optional params::
      -

      prev_calc_dir: path to previous calculation, else current directory +

      +
      Optional params::

      prev_calc_dir: path to previous calculation, else current directory mode (str): the NMR calculation type: cs or efg, default is cs isotopes (list): list of isotopes to include, default is to include the

      -
      lowest mass quadrupolar isotope for all applicable elements
      -

      reciprocol_density (int): the reciprocol density for the kpoint mesh, defaults to 100 +

      lowest mass quadrupolar isotope for all applicable elements

      +
      +

      reciprocol_density (int): the reciprocol density for the kpoint mesh, defaults to 100 other_aprams (dict) : any other params passsed to MPNMRSet as a dictionary

      -optional_params = ['mode', 'isotopes', 'reciprocal_density', 'other_params']ΒΆ
      +optional_params = ['mode', 'isotopes', 'reciprocal_density', 'other_params']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -2015,11 +1967,12 @@

      Submodules
      -class atomate.vasp.firetasks.write_inputs.WriteVaspNSCFFromPrev(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.write_inputs.WriteVaspNSCFFromPrev(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Writes input files for an NSCF static run. Assumes that output files from an scf job can be accessed. There are many options, e.g. uniform mode, line mode, adding the optical properties, etc.

      -
      -
      Required params:
      -
      (none)
      -
      Optional params:
      -
      (documentation for all optional params can be found in -NonSCFVaspInputSet)
      +
      +
      Required params:

      (none)

      +
      +
      Optional params:

      (documentation for all optional params can be found in +NonSCFVaspInputSet)

      +
      -optional_params = ['prev_calc_dir', 'copy_chgcar', 'nbands_factor', 'reciprocal_density', 'kpoints_line_density', 'small_gap_multiply', 'standardize', 'sym_prec', 'international_monoclinic', 'mode', 'nedos', 'optics', 'other_params']ΒΆ
      +optional_params = ['prev_calc_dir', 'copy_chgcar', 'nbands_factor', 'reciprocal_density', 'kpoints_line_density', 'small_gap_multiply', 'standardize', 'sym_prec', 'international_monoclinic', 'mode', 'nedos', 'optics', 'other_params']ΒΆ
      -required_params = []ΒΆ
      +required_params = []ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -2067,11 +2018,12 @@

      Submodules
      -class atomate.vasp.firetasks.write_inputs.WriteVaspSOCFromPrev(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.write_inputs.WriteVaspSOCFromPrev(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Writes input files for a spinorbit coupling calculation.

      -
      -
      Required params:
      -
      magmom (list): magnetic moment values for each site in the structure. -saxis (list): magnetic field direction
      +
      +
      Required params:

      magmom (list): magnetic moment values for each site in the structure. +saxis (list): magnetic field direction

      +
      -optional_params = ['prev_calc_dir', 'copy_chgcar', 'nbands_factor', 'reciprocal_density', 'small_gap_multiply', 'standardize', 'sym_prec', 'international_monoclinic', 'other_params']ΒΆ
      +optional_params = ['prev_calc_dir', 'copy_chgcar', 'nbands_factor', 'reciprocal_density', 'small_gap_multiply', 'standardize', 'sym_prec', 'international_monoclinic', 'other_params']ΒΆ
      -required_params = ['magmom', 'saxis']ΒΆ
      +required_params = ['magmom', 'saxis']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -2115,11 +2065,12 @@

      Submodules
      -class atomate.vasp.firetasks.write_inputs.WriteVaspStaticFromPrev(*args, **kwargs)ΒΆ
      +class atomate.vasp.firetasks.write_inputs.WriteVaspStaticFromPrev(*args, **kwargs)ΒΆ

      Bases: fireworks.core.firework.FiretaskBase

      Writes input files for a static run. Assumes that output files from a previous (e.g., optimization) run can be accessed in current dir or prev_calc_dir. Also allows lepsilon (dielectric constant) calcs.

      -
      -
      Required params:
      -
      (none)
      -
      Optional params:
      -
      (documentation for all other optional params can be found in -MPStaticSet)
      +
      +
      Required params:

      (none)

      +
      +
      Optional params:

      (documentation for all other optional params can be found in +MPStaticSet)

      +
      -optional_params = ['prev_calc_dir', 'reciprocal_density', 'small_gap_multiply', 'standardize', 'sym_prec', 'international_monoclinic', 'lepsilon', 'other_params']ΒΆ
      +optional_params = ['prev_calc_dir', 'reciprocal_density', 'small_gap_multiply', 'standardize', 'sym_prec', 'international_monoclinic', 'lepsilon', 'other_params']ΒΆ
      -run_task(fw_spec)ΒΆ
      +run_task(fw_spec)ΒΆ

      This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.

      -
      -
      Args:
      -
      -
      fw_spec (dict): A Firework spec. This comes from the master spec.
      -
      In addition, this spec contains a special β€œ_fw_env” key that +
      +
      Args:
      +
      fw_spec (dict): A Firework spec. This comes from the master spec.

      In addition, this spec contains a special β€œ_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, β€œfoo” may be named β€œfoo1” in resource @@ -2162,11 +2111,12 @@

      Submodules
    3. modules |
      4. -
    4. atomate 0.9.1 documentation »
      5. +
    5. atomate 0.9.2 documentation »
      6. diff --git a/docs/atomate.vasp.firetasks.tests.html b/docs/atomate.vasp.firetasks.tests.html index 8fbb5b30a..1853b372f 100644 --- a/docs/atomate.vasp.firetasks.tests.html +++ b/docs/atomate.vasp.firetasks.tests.html @@ -1,18 +1,17 @@ - + - - - atomate.vasp.firetasks.tests package — atomate 0.9.1 documentation + + atomate.vasp.firetasks.tests package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

      Navigation

    6. modules |
      7. -
    7. atomate 0.9.1 documentation »
      8. +
    8. atomate 0.9.2 documentation »
      9. @@ -46,37 +45,37 @@

      Submodules

      atomate.vasp.firetasks.tests.test_copy moduleΒΆ

      -class atomate.vasp.firetasks.tests.test_copy.TestCopyVaspOutputs(methodName='runTest')ΒΆ
      +class atomate.vasp.firetasks.tests.test_copy.TestCopyVaspOutputs(methodName='runTest')ΒΆ

      Bases: atomate.utils.testing.AtomateTest

      -
      +
      -classmethod setUpClass()ΒΆ
      +classmethod setUpClass()ΒΆ

      Hook method for setting up class fixture before running tests in the class.

      -test_gzip_copy()ΒΆ
      +test_gzip_copy()ΒΆ
      -test_plain_copy()ΒΆ
      +test_plain_copy()ΒΆ
      -test_plain_copy_more()ΒΆ
      +test_plain_copy_more()ΒΆ
      -test_relax2_copy()ΒΆ
      +test_relax2_copy()ΒΆ
      -test_unittestsetup()ΒΆ
      +test_unittestsetup()ΒΆ
      @@ -86,17 +85,17 @@

      Submodules

      atomate.vasp.firetasks.tests.test_get_interpolated_poscar moduleΒΆ

      -class atomate.vasp.firetasks.tests.test_get_interpolated_poscar.TestGetInterpolatedPOSCAR(methodName='runTest')ΒΆ
      +class atomate.vasp.firetasks.tests.test_get_interpolated_poscar.TestGetInterpolatedPOSCAR(methodName='runTest')ΒΆ

      Bases: atomate.utils.testing.AtomateTest

      -
      +
      -classmethod setUpClass()ΒΆ
      +classmethod setUpClass()ΒΆ

      Hook method for setting up class fixture before running tests in the class.

      -test_getinterpolatedposcar()ΒΆ
      +test_getinterpolatedposcar()ΒΆ
      @@ -106,11 +105,11 @@

      Submodules

      atomate.vasp.firetasks.tests.test_polarization_to_db moduleΒΆ

      -class atomate.vasp.firetasks.tests.test_polarization_to_db.TestFerroelectricWorkflow(methodName='runTest')ΒΆ
      +class atomate.vasp.firetasks.tests.test_polarization_to_db.TestFerroelectricWorkflow(methodName='runTest')ΒΆ

      Bases: atomate.utils.testing.AtomateTest

      -test_polarizationtodb()ΒΆ
      +test_polarizationtodb()ΒΆ
      @@ -120,55 +119,55 @@

      Submodules

      atomate.vasp.firetasks.tests.test_write_vasp moduleΒΆ

      -class atomate.vasp.firetasks.tests.test_write_vasp.TestWriteVasp(methodName='runTest')ΒΆ
      +class atomate.vasp.firetasks.tests.test_write_vasp.TestWriteVasp(methodName='runTest')ΒΆ

      Bases: atomate.utils.testing.AtomateTest

      -setUp()ΒΆ
      +setUp()ΒΆ

      Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

      -
      +
      -classmethod setUpClass()ΒΆ
      +classmethod setUpClass()ΒΆ

      Hook method for setting up class fixture before running tests in the class.

      -tearDown()ΒΆ
      +tearDown()ΒΆ

      Remove the scratch directory and teardown the test db.

      -test_ioset_explicit()ΒΆ
      +test_ioset_explicit()ΒΆ
      -test_ioset_implicit()ΒΆ
      +test_ioset_implicit()ΒΆ
      -test_ioset_params()ΒΆ
      +test_ioset_params()ΒΆ
      -test_modify_incar()ΒΆ
      +test_modify_incar()ΒΆ
      -test_modify_potcar()ΒΆ
      +test_modify_potcar()ΒΆ
      -test_pmgobjects()ΒΆ
      +test_pmgobjects()ΒΆ
      @@ -178,17 +177,17 @@

      Submodules

      atomate.vasp.firetasks.tests.test_write_vasp_from_interpolated_poscar moduleΒΆ

      -class atomate.vasp.firetasks.tests.test_write_vasp_from_interpolated_poscar.TestWriteVaspFromInterpolatedPOSCAR(methodName='runTest')ΒΆ
      +class atomate.vasp.firetasks.tests.test_write_vasp_from_interpolated_poscar.TestWriteVaspFromInterpolatedPOSCAR(methodName='runTest')ΒΆ

      Bases: atomate.utils.testing.AtomateTest

      -
      +
      -classmethod setUpClass()ΒΆ
      +classmethod setUpClass()ΒΆ

      Hook method for setting up class fixture before running tests in the class.

      -test_writevaspfrominterpolatedposcar()ΒΆ
      +test_writevaspfrominterpolatedposcar()ΒΆ
      @@ -227,13 +226,11 @@

      This Page

      @@ -251,13 +248,13 @@

      Navigation

    9. modules |
      10. -
    10. atomate 0.9.1 documentation »
      11. +
    11. atomate 0.9.2 documentation »
      12. diff --git a/docs/atomate.vasp.fireworks.html b/docs/atomate.vasp.fireworks.html index b993bdb9a..c9ea6032e 100644 --- a/docs/atomate.vasp.fireworks.html +++ b/docs/atomate.vasp.fireworks.html @@ -1,18 +1,17 @@ - + - - - atomate.vasp.fireworks package — atomate 0.9.1 documentation + + atomate.vasp.fireworks package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

      Navigation

    12. modules |
      13. -
    13. atomate 0.9.1 documentation »
      14. +
    14. atomate 0.9.2 documentation »
      15. @@ -46,24 +45,24 @@

      Submodules

      atomate.vasp.fireworks.core moduleΒΆ

      -class atomate.vasp.fireworks.core.BoltztrapFW(parents=None, structure=None, name='boltztrap', db_file=None, scissor=0.0, doping=None, tmax=1300, tgrid=50, prev_calc_dir=None, soc=False, additional_fields=None, **kwargs)ΒΆ
      +class atomate.vasp.fireworks.core.BoltztrapFW(parents=None, structure=None, name='boltztrap', db_file=None, scissor=0.0, doping=None, tmax=1300, tgrid=50, prev_calc_dir=None, soc=False, additional_fields=None, **kwargs)ΒΆ

      Bases: fireworks.core.firework.Firework

      -__init__(parents=None, structure=None, name='boltztrap', db_file=None, scissor=0.0, doping=None, tmax=1300, tgrid=50, prev_calc_dir=None, soc=False, additional_fields=None, **kwargs)ΒΆ
      +__init__(parents=None, structure=None, name='boltztrap', db_file=None, scissor=0.0, doping=None, tmax=1300, tgrid=50, prev_calc_dir=None, soc=False, additional_fields=None, **kwargs)ΒΆ

      Run Boltztrap (which includes writing bolztrap input files and parsing outputs). Assumes you have a previous FW with the calc_locs passed into the current FW.

      -
      -
      Args:
      -

      structure (Structure): - only used for setting name of FW +

      +
      Args:

      structure (Structure): - only used for setting name of FW name (str): name of this FW db_file (str): path to the db file parents (Firework): Parents of this particular Firework. FW or list of FWS. prev_calc_dir (str): Path to a previous calculation to copy from scissor (float): if scissor > 0, apply scissor on the band structure so that new

      -
      band gap = scissor (in eV)
      -

      doping: ([float]) doping levels you want to compute +

      band gap = scissor (in eV)

      +
      +

      doping: ([float]) doping levels you want to compute tmax: (float) max temperature to evaluate tgrid: (float) temperature interval soc (bool): whether the band structure is calculated with spin-orbit coupling @@ -77,35 +76,38 @@

      Submodules
      -class atomate.vasp.fireworks.core.DFPTFW(structure=None, prev_calc_dir=None, name='static dielectric', vasp_cmd='>>vasp_cmd<<', copy_vasp_outputs=True, lepsilon=True, db_file='>>db_file<<', parents=None, user_incar_settings=None, pass_nm_results=False, **kwargs)ΒΆ
      +class atomate.vasp.fireworks.core.DFPTFW(structure=None, prev_calc_dir=None, name='static dielectric', vasp_cmd='>>vasp_cmd<<', copy_vasp_outputs=True, lepsilon=True, db_file='>>db_file<<', parents=None, user_incar_settings=None, pass_nm_results=False, **kwargs)ΒΆ

      Bases: fireworks.core.firework.Firework

      -__init__(structure=None, prev_calc_dir=None, name='static dielectric', vasp_cmd='>>vasp_cmd<<', copy_vasp_outputs=True, lepsilon=True, db_file='>>db_file<<', parents=None, user_incar_settings=None, pass_nm_results=False, **kwargs)ΒΆ
      +__init__(structure=None, prev_calc_dir=None, name='static dielectric', vasp_cmd='>>vasp_cmd<<', copy_vasp_outputs=True, lepsilon=True, db_file='>>db_file<<', parents=None, user_incar_settings=None, pass_nm_results=False, **kwargs)ΒΆ
      -
      Static DFPT calculation Firework
      -
      -
      Args:
      -
      -
      structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
      -
      name of the FW.
      +

      Static DFPT calculation Firework

      +
      +
      +
      Args:
      +
      structure (Structure): Input structure. If copy_vasp_outputs, used only to set the

      name of the FW.

      +

      name (str): Name for the Firework. lepsilon (bool): Turn on LEPSILON to calculate polar properties vasp_cmd (str): Command to run vasp. copy_vasp_outputs (str or bool): Whether to copy outputs from previous

      -
      run. Defaults to True.
      +

      run. Defaults to True.

      +

      prev_calc_dir (str): Path to a previous calculation to copy from db_file (str): Path to file specifying db credentials. parents (Firework): Parents of this particular Firework.

      -
      FW or list of FWS.
      +

      FW or list of FWS.

      +

      user_incar_settings (dict): Parameters in INCAR to override pass_nm_results (bool): if true the normal mode eigen vals and vecs are passed so that

      -
      next firework can use it.
      -

      **kwargs: Other kwargs that are passed to Firework.__init__.

      +

      next firework can use it.

      +
      +

      **kwargs: Other kwargs that are passed to Firework.__init__.

      @@ -114,24 +116,24 @@

      Submodules
      -class atomate.vasp.fireworks.core.HSEBSFW(parents=None, prev_calc_dir=None, structure=None, mode='gap', name=None, vasp_cmd='>>vasp_cmd<<', db_file='>>db_file<<', **kwargs)ΒΆ
      +class atomate.vasp.fireworks.core.HSEBSFW(parents=None, prev_calc_dir=None, structure=None, mode='gap', name=None, vasp_cmd='>>vasp_cmd<<', db_file='>>db_file<<', **kwargs)ΒΆ

      Bases: fireworks.core.firework.Firework

      -__init__(parents=None, prev_calc_dir=None, structure=None, mode='gap', name=None, vasp_cmd='>>vasp_cmd<<', db_file='>>db_file<<', **kwargs)ΒΆ
      +__init__(parents=None, prev_calc_dir=None, structure=None, mode='gap', name=None, vasp_cmd='>>vasp_cmd<<', db_file='>>db_file<<', **kwargs)ΒΆ

      For getting a more accurate band gap or a full band structure with HSE - requires previous calculation that gives VBM/CBM info or the high-symmetry kpoints.

      -
      -
      Args:
      -

      parents (Firework): Parents of this particular Firework. FW or list of FWS. +

      +
      Args:

      parents (Firework): Parents of this particular Firework. FW or list of FWS. prev_calc_dir (str): Path to a previous calculation to copy from structure (Structure): Input structure - used only to set the name of the FW. mode (string): options:

      -
      β€œline” to get a full band structure along symmetry lines or +

      β€œline” to get a full band structure along symmetry lines or β€œuniform” for uniform mesh band structure or -β€œgap” to get the energy at the CBM and VBM

      -

      name (str): Name for the Firework. +β€œgap” to get the energy at the CBM and VBM

      + +

      name (str): Name for the Firework. vasp_cmd (str): Command to run vasp. db_file (str): Path to file specifying db credentials. **kwargs: Other kwargs that are passed to Firework.__init__.

      @@ -143,33 +145,34 @@

      Submodules
      -class atomate.vasp.fireworks.core.LepsFW(structure, name='static dielectric', vasp_cmd='>>vasp_cmd<<', copy_vasp_outputs=True, db_file='>>db_file<<', parents=None, phonon=False, mode=None, displacement=None, user_incar_settings=None, **kwargs)ΒΆ
      +class atomate.vasp.fireworks.core.LepsFW(structure, name='static dielectric', vasp_cmd='>>vasp_cmd<<', copy_vasp_outputs=True, db_file='>>db_file<<', parents=None, phonon=False, mode=None, displacement=None, user_incar_settings=None, **kwargs)ΒΆ

      Bases: fireworks.core.firework.Firework

      -__init__(structure, name='static dielectric', vasp_cmd='>>vasp_cmd<<', copy_vasp_outputs=True, db_file='>>db_file<<', parents=None, phonon=False, mode=None, displacement=None, user_incar_settings=None, **kwargs)ΒΆ
      +__init__(structure, name='static dielectric', vasp_cmd='>>vasp_cmd<<', copy_vasp_outputs=True, db_file='>>db_file<<', parents=None, phonon=False, mode=None, displacement=None, user_incar_settings=None, **kwargs)ΒΆ

      Standard static calculation Firework for dielectric constants using DFPT.

      -
      -
      Args:
      -
      -
      structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
      -
      name of the FW.
      +
      +
      Args:
      +
      structure (Structure): Input structure. If copy_vasp_outputs, used only to set the

      name of the FW.

      +

      name (str): Name for the Firework. vasp_cmd (str): Command to run vasp. copy_vasp_outputs (bool): Whether to copy outputs from previous

      -
      run. Defaults to True.
      +

      run. Defaults to True.

      +

      db_file (str): Path to file specifying db credentials. parents (Firework): Parents of this particular Firework.

      -
      FW or list of FWS.
      -
      -
      phonon (bool): Whether or not to extract normal modes and pass it. This argument along
      -
      with the mode and displacement arguments must be set for the calculation of -dielectric constant in the Raman tensor workflow.
      +

      FW or list of FWS.

      +
      +
      +
      phonon (bool): Whether or not to extract normal modes and pass it. This argument along

      with the mode and displacement arguments must be set for the calculation of +dielectric constant in the Raman tensor workflow.

      +
      -

      mode (int): normal mode index. +

      mode (int): normal mode index. displacement (float): displacement along the normal mode in Angstroms. user_incar_settings (dict): Parameters in INCAR to override **kwargs: Other kwargs that are passed to Firework.__init__.

      @@ -181,30 +184,31 @@

      Submodules
      -class atomate.vasp.fireworks.core.MDFW(structure, start_temp, end_temp, nsteps, name='molecular dynamics', vasp_input_set=None, vasp_cmd='>>vasp_cmd<<', override_default_vasp_params=None, wall_time=19200, db_file='>>db_file<<', parents=None, copy_vasp_outputs=True, **kwargs)ΒΆ
      +class atomate.vasp.fireworks.core.MDFW(structure, start_temp, end_temp, nsteps, name='molecular dynamics', vasp_input_set=None, vasp_cmd='>>vasp_cmd<<', override_default_vasp_params=None, wall_time=19200, db_file='>>db_file<<', parents=None, copy_vasp_outputs=True, **kwargs)ΒΆ

      Bases: fireworks.core.firework.Firework

      -__init__(structure, start_temp, end_temp, nsteps, name='molecular dynamics', vasp_input_set=None, vasp_cmd='>>vasp_cmd<<', override_default_vasp_params=None, wall_time=19200, db_file='>>db_file<<', parents=None, copy_vasp_outputs=True, **kwargs)ΒΆ
      +__init__(structure, start_temp, end_temp, nsteps, name='molecular dynamics', vasp_input_set=None, vasp_cmd='>>vasp_cmd<<', override_default_vasp_params=None, wall_time=19200, db_file='>>db_file<<', parents=None, copy_vasp_outputs=True, **kwargs)ΒΆ

      Standard firework for a single MD run.

      -
      -
      Args:
      -

      structure (Structure): Input structure. +

      +
      Args:

      structure (Structure): Input structure. start_temp (float): Start temperature of MD run. end_temp (float): End temperature of MD run. nsteps (int): Number of MD steps name (string): Name for the Firework. vasp_input_set (string): string name for the VASP input set (e.g.,

      -
      β€œMITMDVaspInputSet”).
      +

      β€œMITMDVaspInputSet”).

      +

      vasp_cmd (string): Command to run vasp. override_default_vasp_params (dict): If this is not None,

      -
      these params are passed to the default vasp_input_set, i.e., +

      these params are passed to the default vasp_input_set, i.e., MITMDSet. This allows one to easily override some settings, e.g., user_incar_settings, etc. Particular to MD, -one can control time_step and all other settings of the input set.

      -

      wall_time (int): Total wall time in seconds before writing STOPCAR. +one can control time_step and all other settings of the input set.

      + +

      wall_time (int): Total wall time in seconds before writing STOPCAR. copy_vasp_outputs (bool): Whether to copy outputs from previous run. Defaults to True. db_file (string): Path to file specifying db credentials. parents (Firework): Parents of this particular Firework. FW or list of FWS. @@ -217,27 +221,27 @@

      Submodules
      -class atomate.vasp.fireworks.core.NEBFW(spec, neb_label, from_images=True, user_incar_settings=None, user_kpoints_settings=None, additional_cust_args=None, **kwargs)ΒΆ
      +class atomate.vasp.fireworks.core.NEBFW(spec, neb_label, from_images=True, user_incar_settings=None, user_kpoints_settings=None, additional_cust_args=None, **kwargs)ΒΆ

      Bases: fireworks.core.firework.Firework

      CI-NEB Firework in NEB Workflow.

      -
      -
      Task 1) Read in image structures from spec and generates input sets.
      -
      The group of structures are labeled with neb_label (1, 2…)
      +
      +
      Task 1) Read in image structures from spec and generates input sets.

      The group of structures are labeled with neb_label (1, 2…)

      +

      Task 2) Run NEB VASP using Custodian Task 3) Update structure to spec Task 4) Pass CalcLocs named β€œneb_{}”.format(neb_label)

      -__init__(spec, neb_label, from_images=True, user_incar_settings=None, user_kpoints_settings=None, additional_cust_args=None, **kwargs)ΒΆ
      -
      -
      Args:
      -

      spec (dict): Specification of the job to run. +__init__(spec, neb_label, from_images=True, user_incar_settings=None, user_kpoints_settings=None, additional_cust_args=None, **kwargs)ΒΆ +

      +
      Args:

      spec (dict): Specification of the job to run. neb_label (str): β€œ1”, β€œ2”…, label neb run. from_images (bool): Set True to initialize from image structures, False starting

      -
      from relaxed endpoint structures.
      -

      user_incar_settings (dict): Additional INCAR settings. +

      from relaxed endpoint structures.

      +
      +

      user_incar_settings (dict): Additional INCAR settings. user_kpoints_settings (dict): Additional KPOINTS settings. additional_cust_args (dict): Other kwargs that are passed to RunVaspCustodian. **kwargs: Other kwargs that are passed to Firework.__init__.

      @@ -249,7 +253,7 @@

      Submodules
      -class atomate.vasp.fireworks.core.NEBRelaxationFW(spec, label, user_incar_settings=None, user_kpoints_settings=None, additional_cust_args=None, **kwargs)ΒΆ
      +class atomate.vasp.fireworks.core.NEBRelaxationFW(spec, label, user_incar_settings=None, user_kpoints_settings=None, additional_cust_args=None, **kwargs)ΒΆ

      Bases: fireworks.core.firework.Firework

      Relaxation Firework in NEB Workflow.

      Task 1) Read in a structure with β€œst_label” (β€œrlx”, β€œep0” or β€œep1”) and generates input sets. @@ -258,15 +262,15 @@

      Submodules
      -__init__(spec, label, user_incar_settings=None, user_kpoints_settings=None, additional_cust_args=None, **kwargs)ΒΆ
      -
      -
      Args:
      -
      spec (dict): Specification of the job to run. +__init__(spec, label, user_incar_settings=None, user_kpoints_settings=None, additional_cust_args=None, **kwargs)ΒΆ +
      +
      Args:

      spec (dict): Specification of the job to run. label (str): β€œparent”, β€œep0” or β€œep1” vasp_input_set (VaspInputSet): Input set to use. user_kpoints_settings (dict): Additional KPOINTS settings. additional_cust_args (dict): Other kwargs that are passed to RunVaspCustodian. -**kwargs: Other kwargs that are passed to Firework.__init__.

      +**kwargs: Other kwargs that are passed to Firework.__init__.

      +

      @@ -274,40 +278,41 @@

      Submodules
      -class atomate.vasp.fireworks.core.NonSCFFW(parents=None, prev_calc_dir=None, structure=None, name='nscf', mode='uniform', vasp_cmd='>>vasp_cmd<<', copy_vasp_outputs=True, db_file='>>db_file<<', input_set_overrides=None, **kwargs)ΒΆ
      +class atomate.vasp.fireworks.core.NonSCFFW(parents=None, prev_calc_dir=None, structure=None, name='nscf', mode='uniform', vasp_cmd='>>vasp_cmd<<', copy_vasp_outputs=True, db_file='>>db_file<<', input_set_overrides=None, **kwargs)ΒΆ

      Bases: fireworks.core.firework.Firework

      -__init__(parents=None, prev_calc_dir=None, structure=None, name='nscf', mode='uniform', vasp_cmd='>>vasp_cmd<<', copy_vasp_outputs=True, db_file='>>db_file<<', input_set_overrides=None, **kwargs)ΒΆ
      +__init__(parents=None, prev_calc_dir=None, structure=None, name='nscf', mode='uniform', vasp_cmd='>>vasp_cmd<<', copy_vasp_outputs=True, db_file='>>db_file<<', input_set_overrides=None, **kwargs)ΒΆ

      Standard NonSCF Calculation Firework supporting uniform and line modes.

      -
      -
      Args:
      -
      -
      structure (Structure): Input structure - used only to set the name
      -
      of the FW.
      +
      +
      Args:
      +
      structure (Structure): Input structure - used only to set the name

      of the FW.

      +

      name (str): Name for the Firework. mode (str): β€œuniform” or β€œline” mode. vasp_cmd (str): Command to run vasp. copy_vasp_outputs (bool): Whether to copy outputs from previous

      -
      run. Defaults to True.
      +

      run. Defaults to True.

      +

      prev_calc_dir (str): Path to a previous calculation to copy from db_file (str): Path to file specifying db credentials. parents (Firework): Parents of this particular Firework.

      -
      FW or list of FWS.
      -
      -
      input_set_overrides (dict): Arguments passed to the
      -

      β€œfrom_prev_calc” method of the MPNonSCFSet. This parameter +

      FW or list of FWS.

      +
      +
      +
      input_set_overrides (dict): Arguments passed to the

      β€œfrom_prev_calc” method of the MPNonSCFSet. This parameter allows a user to modify the default values of the input set. For example, passing the key value pair

      -
      {β€˜reciprocal_density’: 1000}
      -

      will override default k-point meshes for uniform calculations.

      +

      {β€˜reciprocal_density’: 1000}

      +
      +

      will override default k-point meshes for uniform calculations.

      -

      **kwargs: Other kwargs that are passed to Firework.__init__.

      +

      **kwargs: Other kwargs that are passed to Firework.__init__.

      @@ -316,22 +321,22 @@

      Submodules
      -class atomate.vasp.fireworks.core.OptimizeFW(structure, name='structure optimization', vasp_input_set=None, vasp_cmd='>>vasp_cmd<<', override_default_vasp_params=None, ediffg=None, db_file='>>db_file<<', force_gamma=True, job_type='double_relaxation_run', max_force_threshold=0.25, auto_npar='>>auto_npar<<', half_kpts_first_relax=False, parents=None, **kwargs)ΒΆ
      +class atomate.vasp.fireworks.core.OptimizeFW(structure, name='structure optimization', vasp_input_set=None, vasp_cmd='>>vasp_cmd<<', override_default_vasp_params=None, ediffg=None, db_file='>>db_file<<', force_gamma=True, job_type='double_relaxation_run', max_force_threshold=0.25, auto_npar='>>auto_npar<<', half_kpts_first_relax=False, parents=None, **kwargs)ΒΆ

      Bases: fireworks.core.firework.Firework

      -__init__(structure, name='structure optimization', vasp_input_set=None, vasp_cmd='>>vasp_cmd<<', override_default_vasp_params=None, ediffg=None, db_file='>>db_file<<', force_gamma=True, job_type='double_relaxation_run', max_force_threshold=0.25, auto_npar='>>auto_npar<<', half_kpts_first_relax=False, parents=None, **kwargs)ΒΆ
      +__init__(structure, name='structure optimization', vasp_input_set=None, vasp_cmd='>>vasp_cmd<<', override_default_vasp_params=None, ediffg=None, db_file='>>db_file<<', force_gamma=True, job_type='double_relaxation_run', max_force_threshold=0.25, auto_npar='>>auto_npar<<', half_kpts_first_relax=False, parents=None, **kwargs)ΒΆ

      Optimize the given structure.

      -
      -
      Args:
      -

      structure (Structure): Input structure. +

      +
      Args:

      structure (Structure): Input structure. name (str): Name for the Firework. vasp_input_set (VaspInputSet): input set to use. Defaults to MPRelaxSet() if None. override_default_vasp_params (dict): If this is not None, these params are passed to

      -
      the default vasp_input_set, i.e., MPRelaxSet. This allows one to easily override -some settings, e.g., user_incar_settings, etc.
      -

      vasp_cmd (str): Command to run vasp. +

      the default vasp_input_set, i.e., MPRelaxSet. This allows one to easily override +some settings, e.g., user_incar_settings, etc.

      +
      +

      vasp_cmd (str): Command to run vasp. ediffg (float): Shortcut to set ediffg in certain jobs db_file (str): Path to file specifying db credentials to place output parsing. force_gamma (bool): Force gamma centered kpoint generation @@ -349,18 +354,17 @@

      Submodules
      -class atomate.vasp.fireworks.core.RamanFW(mode, displacement, prev_calc_dir=None, structure=None, name='raman', vasp_cmd='>>vasp_cmd<<', db_file='>>db_file<<', parents=None, user_incar_settings=None, **kwargs)ΒΆ
      +class atomate.vasp.fireworks.core.RamanFW(mode, displacement, prev_calc_dir=None, structure=None, name='raman', vasp_cmd='>>vasp_cmd<<', db_file='>>db_file<<', parents=None, user_incar_settings=None, **kwargs)ΒΆ

      Bases: fireworks.core.firework.Firework

      -__init__(mode, displacement, prev_calc_dir=None, structure=None, name='raman', vasp_cmd='>>vasp_cmd<<', db_file='>>db_file<<', parents=None, user_incar_settings=None, **kwargs)ΒΆ
      +__init__(mode, displacement, prev_calc_dir=None, structure=None, name='raman', vasp_cmd='>>vasp_cmd<<', db_file='>>db_file<<', parents=None, user_incar_settings=None, **kwargs)ΒΆ

      Static calculation Firework that computes the DFPT dielectric constant for structure displaced along the given normal mode direction.

      -
      -
      Args:
      -
      -
      structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
      -
      name of the FW.
      +
      +
      Args:
      +
      structure (Structure): Input structure. If copy_vasp_outputs, used only to set the

      name of the FW.

      +

      mode (int): normal mode index. displacement (float): displacement along the normal mode in Angstroms. @@ -370,8 +374,9 @@

      Submodulesuser_incar_settings (dict): Parameters in INCAR to override +

      FW or list of FWS.

      +
      +

      user_incar_settings (dict): Parameters in INCAR to override **kwargs: Other kwargs that are passed to Firework.__init__.

      @@ -381,29 +386,30 @@

      Submodules
      -class atomate.vasp.fireworks.core.SOCFW(magmom, structure=None, name='spin-orbit coupling', saxis=(0, 0, 1), prev_calc_dir=None, vasp_cmd='vasp_ncl', copy_vasp_outputs=True, db_file=None, parents=None, **kwargs)ΒΆ
      +class atomate.vasp.fireworks.core.SOCFW(magmom, structure=None, name='spin-orbit coupling', saxis=(0, 0, 1), prev_calc_dir=None, vasp_cmd='vasp_ncl', copy_vasp_outputs=True, db_file=None, parents=None, **kwargs)ΒΆ

      Bases: fireworks.core.firework.Firework

      -__init__(magmom, structure=None, name='spin-orbit coupling', saxis=(0, 0, 1), prev_calc_dir=None, vasp_cmd='vasp_ncl', copy_vasp_outputs=True, db_file=None, parents=None, **kwargs)ΒΆ
      +__init__(magmom, structure=None, name='spin-orbit coupling', saxis=(0, 0, 1), prev_calc_dir=None, vasp_cmd='vasp_ncl', copy_vasp_outputs=True, db_file=None, parents=None, **kwargs)ΒΆ

      Firework for spin orbit coupling calculation.

      -
      -
      Args:
      -
      -
      structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
      -
      name of the FW.
      +
      +
      Args:
      +
      structure (Structure): Input structure. If copy_vasp_outputs, used only to set the

      name of the FW.

      +

      name (str): Name for the Firework. prev_calc_dir (str): Path to a previous calculation to copy from vasp_cmd (str): Command to run vasp. copy_vasp_outputs (bool): Whether to copy outputs from previous

      -
      run. Defaults to True.
      +

      run. Defaults to True.

      +

      db_file (str): Path to file specifying db credentials. parents (Firework): Parents of this particular Firework.

      -
      FW or list of FWS.
      -

      **kwargs: Other kwargs that are passed to Firework.__init__.

      +

      FW or list of FWS.

      +
      +

      **kwargs: Other kwargs that are passed to Firework.__init__.

      @@ -412,30 +418,31 @@

      Submodules
      -class atomate.vasp.fireworks.core.StaticFW(structure=None, name='static', vasp_input_set=None, vasp_input_set_params=None, vasp_cmd='>>vasp_cmd<<', prev_calc_loc=True, prev_calc_dir=None, db_file='>>db_file<<', vasptodb_kwargs=None, parents=None, **kwargs)ΒΆ
      +class atomate.vasp.fireworks.core.StaticFW(structure=None, name='static', vasp_input_set=None, vasp_input_set_params=None, vasp_cmd='>>vasp_cmd<<', prev_calc_loc=True, prev_calc_dir=None, db_file='>>db_file<<', vasptodb_kwargs=None, parents=None, **kwargs)ΒΆ

      Bases: fireworks.core.firework.Firework

      -__init__(structure=None, name='static', vasp_input_set=None, vasp_input_set_params=None, vasp_cmd='>>vasp_cmd<<', prev_calc_loc=True, prev_calc_dir=None, db_file='>>db_file<<', vasptodb_kwargs=None, parents=None, **kwargs)ΒΆ
      +__init__(structure=None, name='static', vasp_input_set=None, vasp_input_set_params=None, vasp_cmd='>>vasp_cmd<<', prev_calc_loc=True, prev_calc_dir=None, db_file='>>db_file<<', vasptodb_kwargs=None, parents=None, **kwargs)ΒΆ

      Standard static calculation Firework - either from a previous location or from a structure.

      -
      -
      Args:
      -
      -
      structure (Structure): Input structure. Note that for prev_calc_loc jobs, the structure
      -
      is only used to set the name of the FW and any structure with the same composition -can be used.
      +
      +
      Args:
      +
      structure (Structure): Input structure. Note that for prev_calc_loc jobs, the structure

      is only used to set the name of the FW and any structure with the same composition +can be used.

      +

      name (str): Name for the Firework. vasp_input_set (VaspInputSet): input set to use (for jobs w/no parents)

      -
      Defaults to MPStaticSet() if None.
      +

      Defaults to MPStaticSet() if None.

      +

      vasp_input_set_params (dict): Dict of vasp_input_set kwargs. vasp_cmd (str): Command to run vasp. prev_calc_loc (bool or str): If true (default), copies outputs from previous calc. If

      -
      a str value, retrieves a previous calculation output by name. If False/None, will create -new static calculation using the provided structure.
      -

      prev_calc_dir (str): Path to a previous calculation to copy from +

      a str value, retrieves a previous calculation output by name. If False/None, will create +new static calculation using the provided structure.

      +
      +

      prev_calc_dir (str): Path to a previous calculation to copy from db_file (str): Path to file specifying db credentials. parents (Firework): Parents of this particular Firework. FW or list of FWS. vasptodb_kwargs (dict): kwargs to pass to VaspToDb @@ -448,15 +455,14 @@

      Submodules
      -class atomate.vasp.fireworks.core.StaticInterpolateFW(structure, start, end, name='static', vasp_input_set='MPStaticSet', vasp_input_set_params=None, vasp_cmd='>>vasp_cmd<<', db_file='>>db_file<<', parents=None, this_image=None, nimages=None, autosort_tol=0, **kwargs)ΒΆ
      +class atomate.vasp.fireworks.core.StaticInterpolateFW(structure, start, end, name='static', vasp_input_set='MPStaticSet', vasp_input_set_params=None, vasp_cmd='>>vasp_cmd<<', db_file='>>db_file<<', parents=None, this_image=None, nimages=None, autosort_tol=0, **kwargs)ΒΆ

      Bases: fireworks.core.firework.Firework

      -__init__(structure, start, end, name='static', vasp_input_set='MPStaticSet', vasp_input_set_params=None, vasp_cmd='>>vasp_cmd<<', db_file='>>db_file<<', parents=None, this_image=None, nimages=None, autosort_tol=0, **kwargs)ΒΆ
      +__init__(structure, start, end, name='static', vasp_input_set='MPStaticSet', vasp_input_set_params=None, vasp_cmd='>>vasp_cmd<<', db_file='>>db_file<<', parents=None, this_image=None, nimages=None, autosort_tol=0, **kwargs)ΒΆ

      Standard static calculation Firework that interpolates structures from two previous calculations.

      -
      -
      Args:
      -

      structure (Structure): Input structure used to name FireWork. +

      +
      Args:

      structure (Structure): Input structure used to name FireWork. start (str): PassCalcLoc name of StaticFW or RelaxFW run of starting structure. end (str): PassCalcLoc name of StaticFW or RelaxFW run of ending structure. name (str): Name for the Firework. @@ -470,9 +476,10 @@

      Submodules**kwargs: Other kwargs that are passed to Firework.__init__.

      +

      to automatically sort end_structure to match to the closest +points in this particular structure.

      +
      +

      **kwargs: Other kwargs that are passed to Firework.__init__.

      @@ -481,28 +488,28 @@

      Submodules
      -class atomate.vasp.fireworks.core.TransmuterFW(structure, transformations, transformation_params=None, vasp_input_set=None, prev_calc_dir=None, name='structure transmuter', vasp_cmd='>>vasp_cmd<<', copy_vasp_outputs=True, db_file='>>db_file<<', parents=None, override_default_vasp_params=None, **kwargs)ΒΆ
      +class atomate.vasp.fireworks.core.TransmuterFW(structure, transformations, transformation_params=None, vasp_input_set=None, prev_calc_dir=None, name='structure transmuter', vasp_cmd='>>vasp_cmd<<', copy_vasp_outputs=True, db_file='>>db_file<<', parents=None, override_default_vasp_params=None, **kwargs)ΒΆ

      Bases: fireworks.core.firework.Firework

      -__init__(structure, transformations, transformation_params=None, vasp_input_set=None, prev_calc_dir=None, name='structure transmuter', vasp_cmd='>>vasp_cmd<<', copy_vasp_outputs=True, db_file='>>db_file<<', parents=None, override_default_vasp_params=None, **kwargs)ΒΆ
      +__init__(structure, transformations, transformation_params=None, vasp_input_set=None, prev_calc_dir=None, name='structure transmuter', vasp_cmd='>>vasp_cmd<<', copy_vasp_outputs=True, db_file='>>db_file<<', parents=None, override_default_vasp_params=None, **kwargs)ΒΆ

      Apply the transformations to the input structure, write the input set corresponding to the transformed structure, and run vasp on them. Note that if a transformation yields many structures from one, only the last structure in the list is used.

      -
      -
      Args:
      -

      structure (Structure): Input structure. +

      +
      Args:

      structure (Structure): Input structure. transformations (list): list of names of transformation classes as defined in

      -
      the modules in pymatgen.transformations. -eg: transformations=[β€˜DeformStructureTransformation’, β€˜SupercellTransformation’]
      -
      -
      transformation_params (list): list of dicts where each dict specify the input
      -
      parameters to instantiate the transformation class in the transformations list.
      -
      vasp_input_set (VaspInputSet): VASP input set, used to write the input set for the
      -
      transmuted structure.
      +

      the modules in pymatgen.transformations. +eg: transformations=[β€˜DeformStructureTransformation’, β€˜SupercellTransformation’]

      +
      +
      +
      transformation_params (list): list of dicts where each dict specify the input

      parameters to instantiate the transformation class in the transformations list.

      +
      +
      vasp_input_set (VaspInputSet): VASP input set, used to write the input set for the

      transmuted structure.

      +
      -

      name (string): Name for the Firework. +

      name (string): Name for the Firework. vasp_cmd (string): Command to run vasp. copy_vasp_outputs (bool): Whether to copy outputs from previous run. Defaults to True. prev_calc_dir (str): Path to a previous calculation to copy from @@ -521,33 +528,35 @@

      Submodules

      atomate.vasp.fireworks.nmr moduleΒΆ

      -class atomate.vasp.fireworks.nmr.NMRFW(structure=None, mode='cs', isotopes=None, name='nmr tensor', prev_calc_dir=None, vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, parents=None, **kwargs)ΒΆ
      +class atomate.vasp.fireworks.nmr.NMRFW(structure=None, mode='cs', isotopes=None, name='nmr tensor', prev_calc_dir=None, vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, parents=None, **kwargs)ΒΆ

      Bases: fireworks.core.firework.Firework

      -__init__(structure=None, mode='cs', isotopes=None, name='nmr tensor', prev_calc_dir=None, vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, parents=None, **kwargs)ΒΆ
      +__init__(structure=None, mode='cs', isotopes=None, name='nmr tensor', prev_calc_dir=None, vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, parents=None, **kwargs)ΒΆ

      Firework for NMR tensor calculations

      -
      -
      Args:
      -
      -
      structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
      -
      name of the FW.
      +
      +
      Args:
      +
      structure (Structure): Input structure. If copy_vasp_outputs, used only to set the

      name of the FW.

      +

      mode (str): the NMR calculation type: cs or efg, default is cs isotopes (list): list of isotopes to include, default is to include the

      -
      lowest mass quadrupolar isotope for all applicable elements
      +

      lowest mass quadrupolar isotope for all applicable elements

      +

      name (str): Name for the Firework. prev_calc_dir (str): Path to a previous calculation to copy from vasp_cmd (str): Command to run vasp. copy_vasp_outputs (bool): Whether to copy outputs from previous

      -
      run. Defaults to True.
      +

      run. Defaults to True.

      +

      db_file (str): Path to file specifying db credentials. parents (Firework): Parents of this particular Firework.

      -
      FW or list of FWS.
      -

      kwargs: Other kwargs that are passed to Firework.__init__.

      +

      FW or list of FWS.

      +
      +

      kwargs: Other kwargs that are passed to Firework.__init__.

      @@ -559,11 +568,11 @@

      Submodules

      atomate.vasp.fireworks.polarization moduleΒΆ

      -class atomate.vasp.fireworks.polarization.LcalcpolFW(structure, name='static dipole moment', static_name='static', vasp_cmd='vasp', vasp_input_set=None, vasp_input_set_params=None, db_file=None, parents=None, gap_threshold=0.01, interpolate=False, start=None, end=None, this_image=0, nimages=5, **kwargs)ΒΆ
      +class atomate.vasp.fireworks.polarization.LcalcpolFW(structure, name='static dipole moment', static_name='static', vasp_cmd='vasp', vasp_input_set=None, vasp_input_set_params=None, db_file=None, parents=None, gap_threshold=0.01, interpolate=False, start=None, end=None, this_image=0, nimages=5, **kwargs)ΒΆ

      Bases: fireworks.core.firework.Firework

      -__init__(structure, name='static dipole moment', static_name='static', vasp_cmd='vasp', vasp_input_set=None, vasp_input_set_params=None, db_file=None, parents=None, gap_threshold=0.01, interpolate=False, start=None, end=None, this_image=0, nimages=5, **kwargs)ΒΆ
      +__init__(structure, name='static dipole moment', static_name='static', vasp_cmd='vasp', vasp_input_set=None, vasp_input_set_params=None, db_file=None, parents=None, gap_threshold=0.01, interpolate=False, start=None, end=None, this_image=0, nimages=5, **kwargs)ΒΆ

      Static Firework that calculates the dipole moment of structure or a single interpolated image of structures output by two calculations specified by PassCalcLoc names start and end.

      This Firework uses three steps to calculate the dipole moment. @@ -581,11 +590,10 @@

      Submodules -
      Args:
      -
      -
      structure (Structure): Input structure. For an interpolation, this is a dummy structure. See interpolate arg
      -
      description.
      +
      +
      Args:
      +
      structure (Structure): Input structure. For an interpolation, this is a dummy structure. See interpolate arg

      description.

      +

      name (str): Name for the polarization FireWork. static_name (str): Name for the SCF run to be used in PassCalcLoc if copy_vasp_outputs != True. @@ -596,17 +604,19 @@

      Submodules -
      interpolate (bool): use structure created by interpolating CONTCAR structure from calculations indicated by
      -
      start and end PassCalcLoc names. If interpolate is False, start and end do not need to be set.
      +

      SCF band gap.

      +
      +
      +
      interpolate (bool): use structure created by interpolating CONTCAR structure from calculations indicated by

      start and end PassCalcLoc names. If interpolate is False, start and end do not need to be set.

      +

      start (str): PassCalcLoc name of StaticFW or RelaxFW run of starting structure end (str): PassCalcLoc name of StaticFW or RelaxFW run of ending structure this_image (int): which interpolation to use for this run of the nimage interpolations. nimages (int): number of interpolations between CONTCAR structures from calculations indicated by start and

      -
      -
      end args.
      +
      +

      end args.

      +

      @@ -645,13 +655,11 @@

      This Page

      @@ -669,13 +677,13 @@

      Navigation

    15. modules |
      16. -
    16. atomate 0.9.1 documentation »
      17. +
    17. atomate 0.9.2 documentation »
      18. diff --git a/docs/atomate.vasp.html b/docs/atomate.vasp.html index 08b9c0dbc..7ce3838de 100644 --- a/docs/atomate.vasp.html +++ b/docs/atomate.vasp.html @@ -1,18 +1,17 @@ - + - - - atomate.vasp package — atomate 0.9.1 documentation + + atomate.vasp package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

      Navigation

    18. modules |
      19. -
    19. atomate 0.9.1 documentation »
      20. +
    20. atomate 0.9.2 documentation »
      21. @@ -170,116 +169,118 @@

      Submodules

      atomate.vasp.database moduleΒΆ

      -class atomate.vasp.database.VaspCalcDb(host='localhost', port=27017, database='vasp', collection='tasks', user=None, password=None, **kwargs)ΒΆ
      +class atomate.vasp.database.VaspCalcDb(host='localhost', port=27017, database='vasp', collection='tasks', user=None, password=None, **kwargs)ΒΆ

      Bases: atomate.utils.database.CalcDb

      Class to help manage database insertions of Vasp drones

      -__init__(host='localhost', port=27017, database='vasp', collection='tasks', user=None, password=None, **kwargs)ΒΆ
      +__init__(host='localhost', port=27017, database='vasp', collection='tasks', user=None, password=None, **kwargs)ΒΆ

      Initialize self. See help(type(self)) for accurate signature.

      -build_indexes(indexes=None, background=True)ΒΆ
      +build_indexes(indexes=None, background=True)ΒΆ

      Build the indexes.

      -
      -
      Args:
      -
      indexes (list): list of single field indexes to be built. -background (bool): Run in the background or not.
      -
      TODO: make sure that the index building is sensible and check for
      -
      existing indexes.
      +
      +
      Args:

      indexes (list): list of single field indexes to be built. +background (bool): Run in the background or not.

      +
      +
      TODO: make sure that the index building is sensible and check for

      existing indexes.

      +
      -get_aeccar(task_id, check_valid=True)ΒΆ
      +get_aeccar(task_id, check_valid=True)ΒΆ

      Read the AECCAR0 + AECCAR2 grid_fs data into a Chgcar object Args:

      -
      task_id(int or str): the task_id containing the gridfs metadata -check_valid (bool): make sure that the aeccar is positive definite
      -
      -
      Returns:
      -
      {β€œaeccar0” : Chgcar, β€œaeccar2” : Chgcar}: dict of Chgcar objects
      +

      task_id(int or str): the task_id containing the gridfs metadata +check_valid (bool): make sure that the aeccar is positive definite

      +
      +
      +
      Returns:

      {β€œaeccar0” : Chgcar, β€œaeccar2” : Chgcar}: dict of Chgcar objects

      +
      -get_band_structure(task_id)ΒΆ
      +get_band_structure(task_id)ΒΆ
      -get_chgcar(task_id)ΒΆ
      +get_chgcar(task_id)ΒΆ

      Read the CHGCAR grid_fs data into a Chgcar object Args:

      -
      task_id(int or str): the task_id containing the gridfs metadata
      -
      -
      Returns:
      -
      chgcar: Chgcar object
      +

      task_id(int or str): the task_id containing the gridfs metadata

      +
      +
      +
      Returns:

      chgcar: Chgcar object

      +
      -get_chgcar_string(task_id)ΒΆ
      +get_chgcar_string(task_id)ΒΆ
      -get_dos(task_id)ΒΆ
      +get_dos(task_id)ΒΆ
      -insert_gridfs(d, collection='fs', compress=True, oid=None, task_id=None)ΒΆ
      +insert_gridfs(d, collection='fs', compress=True, oid=None, task_id=None)ΒΆ

      Insert the given document into GridFS.

      -
      -
      Args:
      -
      d (dict): the document +
      +
      Args:

      d (dict): the document collection (string): the GridFS collection name compress (bool): Whether to compress the data or not oid (ObjectId()): the _id of the file; if specified, it must not already exist in GridFS -task_id(int or str): the task_id to store into the gridfs metadata

      -
      Returns:
      -
      file id, the type of compression used.
      +task_id(int or str): the task_id to store into the gridfs metadata

      +
      +
      Returns:

      file id, the type of compression used.

      +
      -insert_task(task_doc, use_gridfs=False)ΒΆ
      +insert_task(task_doc, use_gridfs=False)ΒΆ

      Inserts a task document (e.g., as returned by Drone.assimilate()) into the database. Handles putting DOS, band structure and charge density into GridFS as needed. During testing, a percentage of runs on some clusters had corrupted AECCAR files when even if everything else about the calculation looked OK. So we do a quick check here and only record the AECCARs if they are valid

      -
      -
      Args:
      -
      task_doc: (dict) the task document -use_gridfs (bool) use gridfs for bandstructures and DOS
      -
      Returns:
      -
      (int) - task_id of inserted document
      +
      +
      Args:

      task_doc: (dict) the task document +use_gridfs (bool) use gridfs for bandstructures and DOS

      +
      +
      Returns:

      (int) - task_id of inserted document

      +
      -reset()ΒΆ
      +reset()ΒΆ
      -retrieve_task(task_id)ΒΆ
      +retrieve_task(task_id)ΒΆ

      Retrieves a task document and unpacks the band structure and DOS as dict

      -
      -
      Args:
      -
      task_id: (int) task_id to retrieve
      -
      Returns:
      -
      (dict) complete task document with BS + DOS included
      +
      +
      Args:

      task_id: (int) task_id to retrieve

      +
      +
      Returns:

      (dict) complete task document with BS + DOS included

      +
      @@ -290,33 +291,33 @@

      Submodules

      atomate.vasp.drones moduleΒΆ

      -class atomate.vasp.drones.VaspDrone(runs=None, parse_dos='auto', bandstructure_mode='auto', parse_locpot=True, additional_fields=None, use_full_uri=True, parse_bader=None, parse_chgcar=False, parse_aeccar=False)ΒΆ
      +class atomate.vasp.drones.VaspDrone(runs=None, parse_dos='auto', bandstructure_mode='auto', parse_locpot=True, additional_fields=None, use_full_uri=True, parse_bader=None, parse_chgcar=False, parse_aeccar=False)ΒΆ

      Bases: pymatgen.apps.borg.hive.AbstractDrone

      pymatgen-db VaspToDbTaskDrone with updated schema and documents processing methods. Please refer to matgendb.creator.VaspToDbTaskDrone documentation.

      -__init__(runs=None, parse_dos='auto', bandstructure_mode='auto', parse_locpot=True, additional_fields=None, use_full_uri=True, parse_bader=None, parse_chgcar=False, parse_aeccar=False)ΒΆ
      +__init__(runs=None, parse_dos='auto', bandstructure_mode='auto', parse_locpot=True, additional_fields=None, use_full_uri=True, parse_bader=None, parse_chgcar=False, parse_aeccar=False)ΒΆ

      Initialize a Vasp drone to parse vasp outputs Args:

      -
      -
      runs (list): Naming scheme for multiple calcuations in on folder e.g. [β€œrelax1”,”relax2”].
      -
      Can be subfolder or extension
      +
      +
      runs (list): Naming scheme for multiple calcuations in on folder e.g. [β€œrelax1”,”relax2”].

      Can be subfolder or extension

      +

      parse_dos (str or bool): Whether to parse the DOS. Can be β€œauto”, True or False. β€œauto” will only parse DOS if NSW = 0, so there are no ionic steps bandstructure_mode (str or bool): How to parse the bandstructure or not. Can be β€œauto”,”line”, True or False.

      -
      -
      β€œauto” will parse the bandstructure with projections for NSCF calcs and decide automatically
      -
      if it’s line mode or uniform. Saves the bandstructure in the output doc.
      -
      β€œline” will parse the bandstructure as a line mode calculation with projections.
      -
      Saves the bandstructure in the output doc.
      -
      True will parse the bandstructure with projections as a uniform calculation.
      -
      Saves the bandstructure in the output doc.
      -
      False will parse the bandstructure without projections to calculate vbm, cbm, band_gap, is_metal and efermi
      -
      Dose not saves the bandstructure in the output doc.
      +
      +
      β€œauto” will parse the bandstructure with projections for NSCF calcs and decide automatically

      if it’s line mode or uniform. Saves the bandstructure in the output doc.

      +
      +
      β€œline” will parse the bandstructure as a line mode calculation with projections.

      Saves the bandstructure in the output doc.

      +
      +
      True will parse the bandstructure with projections as a uniform calculation.

      Saves the bandstructure in the output doc.

      +
      +
      False will parse the bandstructure without projections to calculate vbm, cbm, band_gap, is_metal and efermi

      Dose not saves the bandstructure in the output doc.

      +

      parse_locpot (bool): Parses the LOCPOT file and saves the 3 axis averages @@ -330,82 +331,81 @@

      Submodules
      -as_dict()ΒΆ
      +as_dict()ΒΆ

      A JSON serializable dict representation of an object.

      -assimilate(path)ΒΆ
      +assimilate(path)ΒΆ

      Adapted from matgendb.creator Parses vasp runs(vasprun.xml file) and insert the result into the db. Get the entire task doc from the vasprum.xml and the OUTCAR files in the path. Also adds some post-processed info.

      -
      -
      Args:
      -
      path (str): Path to the directory containing vasprun.xml and OUTCAR files
      -
      Returns:
      -
      (dict): a task dictionary
      +
      +
      Args:

      path (str): Path to the directory containing vasprun.xml and OUTCAR files

      +
      +
      Returns:

      (dict): a task dictionary

      +
      -filter_files(path, file_pattern='vasprun.xml')ΒΆ
      +filter_files(path, file_pattern='vasprun.xml')ΒΆ

      Find the files that match the pattern in the given path and return them in an ordered dictionary. The searched for files are filtered by the run types defined in self.runs. e.g. [β€œrelax1”, β€œrelax2”, …]. Only 2 schemes of the file filtering is enabled: searching for run types in the list of files and in the filenames. Modify this method if more sophisticated filtering scheme is needed.

      -
      -
      Args:
      -
      path (string): path to the folder -file_pattern (string): files to be searched for
      -
      Returns:
      -
      OrderedDict of the names of the files to be processed further. -The key is set from list of run types: self.runs
      +
      +
      Args:

      path (string): path to the folder +file_pattern (string): files to be searched for

      +
      +
      Returns:

      OrderedDict of the names of the files to be processed further. +The key is set from list of run types: self.runs

      +
      -
      +
      -classmethod from_dict(d)ΒΆ
      +classmethod from_dict(d)ΒΆ
      -generate_doc(dir_name, vasprun_files, outcar_files)ΒΆ
      +generate_doc(dir_name, vasprun_files, outcar_files)ΒΆ

      Adapted from matgendb.creator.generate_doc

      -get_valid_paths(path)ΒΆ
      +get_valid_paths(path)ΒΆ

      There are some restrictions on the valid directory structures:

        -
      1. There can be only one vasp run in each directory. Nested directories -are fine.
        2. -
      2. Directories designated β€œrelax1”…”relax9” are considered to be -parts of a multiple-optimization run.
        3. -
      3. Directories containing vasp output with β€œ.relax1”…”.relax9” are -also considered as parts of a multiple-optimization run.
        4. +

      4. There can be only one vasp run in each directory. Nested directories +are fine.

        5. +

      5. Directories designated β€œrelax1”…”relax9” are considered to be +parts of a multiple-optimization run.

        6. +

      6. Directories containing vasp output with β€œ.relax1”…”.relax9” are +also considered as parts of a multiple-optimization run.

      -post_process(dir_name, d)ΒΆ
      +post_process(dir_name, d)ΒΆ

      Post-processing for various files other than the vasprun.xml and OUTCAR. Looks for files: transformations.json and custodian.json. Modify this if other output files need to be processed.

      -
      -
      Args:
      -
      -
      dir_name:
      -
      The dir_name.
      -
      d:
      -
      Current doc generated.
      +
      +
      Args:
      +
      dir_name:

      The dir_name.

      +
      +
      d:

      Current doc generated.

      +
      @@ -413,63 +413,59 @@

      Submodules
      -process_bandstructure(vrun)ΒΆ
      +process_bandstructure(vrun)ΒΆ

      -
      +
      -classmethod process_chgcar(chg_file)ΒΆ
      +classmethod process_chgcar(chg_file)ΒΆ
      -process_dos(vrun)ΒΆ
      +process_dos(vrun)ΒΆ
      -process_raw_data(dir_name, taskname='standard')ΒΆ
      +process_raw_data(dir_name, taskname='standard')ΒΆ

      It is useful to store what raw data has been calculated and exists for easier querying of the taskdoc.

      - --- - - - - - -
      Parameters:
        -
      • dir_name – directory to search
        • -
      • taskname – taskname, e.g. β€œrelax1”
        • +
        +
        Parameters
        +
          +

        • dir_name – directory to search

          • +

        • taskname – taskname, e.g. β€œrelax1”

        -
      Returns:

      dict of files present

      -
      +
      +
      Returns
      +

      dict of files present

      +
      +
      -process_vasprun(dir_name, taskname, filename)ΒΆ
      +process_vasprun(dir_name, taskname, filename)ΒΆ

      Adapted from matgendb.creator

      Process a vasprun.xml file.

      -schema = {'analysis': {'delta_volume', 'delta_volume_as_percent', 'errors', 'max_force', 'warnings'}, 'calcs_reversed': {'completed_at', 'composition_reduced', 'composition_unit_cell', 'dir_name', 'elements', 'formula_anonymous', 'formula_pretty', 'formula_reduced_abc', 'has_vasp_completed', 'input', 'nelements', 'nsites', 'output', 'run_type', 'task', 'vasp_version'}, 'input': {'hubbards', 'is_hubbard', 'is_lasph', 'potcar_spec', 'pseudo_potential', 'structure', 'xc_override'}, 'output': {'bandgap', 'cbm', 'density', 'energy', 'energy_per_atom', 'forces', 'is_gap_direct', 'is_metal', 'spacegroup', 'stress', 'structure', 'vbm'}, 'root': {'analysis', 'calcs_reversed', 'chemsys', 'completed_at', 'composition_reduced', 'composition_unit_cell', 'dir_name', 'elements', 'formula_anonymous', 'formula_pretty', 'formula_reduced_abc', 'input', 'nelements', 'nsites', 'output', 'run_stats', 'schema', 'state'}}ΒΆ
      +schema = {'analysis': {'delta_volume', 'delta_volume_as_percent', 'errors', 'max_force', 'warnings'}, 'calcs_reversed': {'completed_at', 'composition_reduced', 'composition_unit_cell', 'dir_name', 'elements', 'formula_anonymous', 'formula_pretty', 'formula_reduced_abc', 'has_vasp_completed', 'input', 'nelements', 'nsites', 'output', 'run_type', 'task', 'vasp_version'}, 'input': {'hubbards', 'is_hubbard', 'is_lasph', 'potcar_spec', 'pseudo_potential', 'structure', 'xc_override'}, 'output': {'bandgap', 'cbm', 'density', 'energy', 'energy_per_atom', 'forces', 'is_gap_direct', 'is_metal', 'spacegroup', 'stress', 'structure', 'vbm'}, 'root': {'analysis', 'calcs_reversed', 'chemsys', 'completed_at', 'composition_reduced', 'composition_unit_cell', 'dir_name', 'elements', 'formula_anonymous', 'formula_pretty', 'formula_reduced_abc', 'input', 'nelements', 'nsites', 'output', 'run_stats', 'schema', 'state'}}ΒΆ
      -
      +
      -static set_analysis(d, max_force_threshold=0.5, volume_change_threshold=0.2)ΒΆ
      +static set_analysis(d, max_force_threshold=0.5, volume_change_threshold=0.2)ΒΆ

      Adapted from matgendb.creator

      set the β€˜analysis’ key

      -validate_doc(d)ΒΆ
      +validate_doc(d)ΒΆ

      Sanity check. Make sure all the important keys are set

      @@ -481,218 +477,217 @@

      Submodules

      atomate.vasp.powerups moduleΒΆ

      -atomate.vasp.powerups.add_additional_fields_to_taskdocs(original_wf, update_dict=None, task_name_constraint='VaspToDb')ΒΆ
      +atomate.vasp.powerups.add_additional_fields_to_taskdocs(original_wf, update_dict=None, task_name_constraint='VaspToDb')ΒΆ

      For all VaspToDbTasks in a given workflow, add information to β€œadditional_fields” to be placed in the task doc.

      -
      -
      Args:
      -
      original_wf (Workflow) -update_dict (Dict): dictionary to add additional_fields
      -
      Returns:
      -
      Workflow
      +
      +
      Args:

      original_wf (Workflow) +update_dict (Dict): dictionary to add additional_fields

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.add_bandgap_check(original_wf, check_bandgap_params=None, fw_name_constraint=None)ΒΆ
      +atomate.vasp.powerups.add_bandgap_check(original_wf, check_bandgap_params=None, fw_name_constraint=None)ΒΆ

      Every FireWork that enters into the Db has a band gap check afterwards, e.g. min_gap and max_gap

      -
      -
      Args:
      -
      original_wf (Workflow) +
      +
      Args:

      original_wf (Workflow) check_bandgap_params (dict): a kwargs style dict of params, e.g. min_gap or max_gap -fw_name_constraint (str) - Only apply changes to FWs where fw_name contains this substring.

      -
      Returns:
      -
      Workflow
      +fw_name_constraint (str) - Only apply changes to FWs where fw_name contains this substring.

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.add_common_powerups(wf, c=None)ΒΆ
      +atomate.vasp.powerups.add_common_powerups(wf, c=None)ΒΆ

      Apply the common powerups such as add_namefile, use_scratch_dir etc. from the given config dict.

      -
      -
      Args:
      -
      wf (Workflow) -c (dict): Config dict
      -
      Returns:
      -
      Workflow
      +
      +
      Args:

      wf (Workflow) +c (dict): Config dict

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.add_modify_incar(original_wf, modify_incar_params=None, fw_name_constraint=None)ΒΆ
      +atomate.vasp.powerups.add_modify_incar(original_wf, modify_incar_params=None, fw_name_constraint=None)ΒΆ

      Every FireWork that runs VASP has a ModifyIncar task just beforehand. For example, allows you to modify the INCAR based on the Worker using env_chk or using hard-coded changes.

      -
      -
      Args:
      -
      original_wf (Workflow) +
      +
      Args:

      original_wf (Workflow) modify_incar_params (dict) - dict of parameters for ModifyIncar. -fw_name_constraint (str) - Only apply changes to FWs where fw_name contains this substring.

      -
      Returns:
      -
      Workflow
      +fw_name_constraint (str) - Only apply changes to FWs where fw_name contains this substring.

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.add_modify_incar_envchk(original_wf, fw_name_constraint=None)ΒΆ
      +atomate.vasp.powerups.add_modify_incar_envchk(original_wf, fw_name_constraint=None)ΒΆ

      If you set the β€œincar_update” parameter in the Worker env, the INCAR will update this parameter for all matching VASP runs

      -
      -
      Args:
      -
      original_wf (Workflow) -fw_name_constraint (str) - Only apply changes to FWs where fw_name contains this substring.
      -
      Returns:
      -
      Workflow
      +
      +
      Args:

      original_wf (Workflow) +fw_name_constraint (str) - Only apply changes to FWs where fw_name contains this substring.

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.add_modify_potcar(original_wf, modify_potcar_params=None, fw_name_constraint=None)ΒΆ
      +atomate.vasp.powerups.add_modify_potcar(original_wf, modify_potcar_params=None, fw_name_constraint=None)ΒΆ

      Every FireWork that runs VASP has a ModifyIncar task just beforehand. For example, allows you to modify the INCAR based on the Worker using env_chk or using hard-coded changes.

      -
      -
      Args:
      -
      original_wf (Workflow) +
      +
      Args:

      original_wf (Workflow) modify_incar_params (dict) - dict of parameters for ModifyIncar. -fw_name_constraint (str) - Only apply changes to FWs where fw_name contains this substring.

      -
      Returns:
      -
      Workflow
      +fw_name_constraint (str) - Only apply changes to FWs where fw_name contains this substring.

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.add_namefile(original_wf, use_slug=True)ΒΆ
      +atomate.vasp.powerups.add_namefile(original_wf, use_slug=True)ΒΆ

      Every FireWork begins by writing an empty file with the name β€œFW–<fw.name>”. This makes it easy to figure out what jobs are in what launcher directories, e.g. β€œls -l launch*/FW–*” from within a β€œblock” dir.

      -
      -
      Args:
      -
      original_wf (Workflow) -use_slug (bool): whether to replace whitespace-type chars with a slug
      -
      Returns:
      -
      Workflow
      +
      +
      Args:

      original_wf (Workflow) +use_slug (bool): whether to replace whitespace-type chars with a slug

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.add_priority(original_wf, root_priority, child_priority=None)ΒΆ
      +atomate.vasp.powerups.add_priority(original_wf, root_priority, child_priority=None)ΒΆ

      Adds priority to a workflow

      -
      -
      Args:
      -
      original_wf (Workflow): original WF +
      +
      Args:

      original_wf (Workflow): original WF root_priority (int): priority of first (root) job(s) -child_priority(int): priority of all child jobs. Defaults to root_priority

      -
      Returns:
      -
      Workflow: priority-decorated workflow
      +child_priority(int): priority of all child jobs. Defaults to root_priority

      +
      +
      Returns:

      Workflow: priority-decorated workflow

      +
      -atomate.vasp.powerups.add_small_gap_multiply(original_wf, gap_cutoff, density_multiplier, fw_name_constraint=None)ΒΆ
      +atomate.vasp.powerups.add_small_gap_multiply(original_wf, gap_cutoff, density_multiplier, fw_name_constraint=None)ΒΆ

      In all FWs with specified name constraints, add a β€˜small_gap_multiply’ parameter that multiplies the k-mesh density of compounds with gap < gap_cutoff by density multiplier. Useful for increasing the k-point mesh for metallic or small gap systems. Note that this powerup only works on FireWorks with the appropriate WriteVasp* tasks that accept the small_gap_multiply argument…

      -
      -
      Args:
      -
      original_wf (Workflow) +
      +
      Args:

      original_wf (Workflow) gap_cutoff (float): Only multiply k-points for materials with gap < gap_cutoff (eV) density_multiplier (float): Multiply k-point density by this amount -fw_name_constraint (str): Only apply changes to FWs where fw_name contains this substring.

      -
      Returns:
      -
      Workflow
      +fw_name_constraint (str): Only apply changes to FWs where fw_name contains this substring.

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.add_stability_check(original_wf, check_stability_params=None, fw_name_constraint=None)ΒΆ
      +atomate.vasp.powerups.add_stability_check(original_wf, check_stability_params=None, fw_name_constraint=None)ΒΆ

      Every FireWork that enters into the Db has a CheckStability task afterward. This allows defusing jobs that are not stable. In practice, you might want to set the fw_name_constraint so that the stability is only checked at the beginning of the workflow

      -
      -
      Args:
      -
      original_wf (Workflow) +
      +
      Args:

      original_wf (Workflow) check_stability_params (dict): a kwargs style dict of params -fw_name_constraint (str) - Only apply changes to FWs where fw_name contains this substring.

      -
      Returns:
      -
      Workflow
      +fw_name_constraint (str) - Only apply changes to FWs where fw_name contains this substring.

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.add_tags(original_wf, tags_list)ΒΆ
      +atomate.vasp.powerups.add_tags(original_wf, tags_list)ΒΆ

      Adds tags to all Fireworks in the Workflow, WF metadata, as well as additional_fields for the VaspDrone to track them later (e.g. all fireworks and vasp tasks related to a research project)

      -
      -
      Args:
      -
      original_wf (Workflow) -tags_list: list of tags parameters (list of strings)
      -
      Returns:
      -
      Workflow
      +
      +
      Args:

      original_wf (Workflow) +tags_list: list of tags parameters (list of strings)

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.add_trackers(original_wf, tracked_files=None, nlines=25)ΒΆ
      +atomate.vasp.powerups.add_trackers(original_wf, tracked_files=None, nlines=25)ΒΆ

      Every FireWork that runs VASP also tracks the OUTCAR, OSZICAR, etc using FWS Trackers.

      -
      -
      Args:
      -
      original_wf (Workflow) +
      +
      Args:

      original_wf (Workflow) tracked_files (list) : list of files to be tracked -nlines (int): number of lines at the end of files to be tracked

      -
      Returns:
      -
      Workflow
      +nlines (int): number of lines at the end of files to be tracked

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.add_wf_metadata(original_wf, structure)ΒΆ
      +atomate.vasp.powerups.add_wf_metadata(original_wf, structure)ΒΆ

      Adds structure metadata to a workflow

      -
      -
      Args:
      -
      original_wf: (Workflow) -structure: (Structure) the structure being run by this workflow
      -
      Returns:
      -
      Workflow
      +
      +
      Args:

      original_wf: (Workflow) +structure: (Structure) the structure being run by this workflow

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.clean_up_files(original_wf, files=('WAVECAR*', ), fw_name_constraint=None, task_name_constraint='RunVasp')ΒΆ
      +atomate.vasp.powerups.clean_up_files(original_wf, files=('WAVECAR*', ), fw_name_constraint=None, task_name_constraint='RunVasp')ΒΆ

      Cleans up files after another fireworks. Default behavior is to remove WAVECAR after running VASP

      -
      -
      Args:
      -
      original_wf (Workflow) +
      +
      Args:

      original_wf (Workflow) files (list): list of patterns to match for files to clean up -fw_name_constraint (str): pattern for firetask to clean up files after

      -
      Returns:
      -
      Workflow
      +fw_name_constraint (str): pattern for firetask to clean up files after

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.clear_modify(original_wf, fw_name_constraint=None)ΒΆ
      +atomate.vasp.powerups.clear_modify(original_wf, fw_name_constraint=None)ΒΆ

      Simple powerup that clears the modifications to a workflow.

      -
      -
      Args:
      -
      -
      fw_name_constraint (str): name constraint for fireworks to
      -
      have their modification tasks removed
      +
      +
      Args:
      +
      fw_name_constraint (str): name constraint for fireworks to

      have their modification tasks removed

      +
      @@ -700,160 +695,161 @@

      Submodules
      -atomate.vasp.powerups.modify_gzip_vasp(original_wf, gzip_output)ΒΆ
      +atomate.vasp.powerups.modify_gzip_vasp(original_wf, gzip_output)ΒΆ

      For all RunVaspCustodian tasks, modify gzip_output boolean Args:

      -
      original_wf (Workflow) -gzip_output (bool): Value to set gzip_output to for RunVaspCustodian
      -
      -
      Returns:
      -
      Workflow
      +

      original_wf (Workflow) +gzip_output (bool): Value to set gzip_output to for RunVaspCustodian

      +

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.modify_to_soc(original_wf, nbands, structure=None, modify_incar_params=None, fw_name_constraint=None)ΒΆ
      +atomate.vasp.powerups.modify_to_soc(original_wf, nbands, structure=None, modify_incar_params=None, fw_name_constraint=None)ΒΆ

      Takes a regular workflow and transforms its VASP fireworkers that are specified with fw_name_constraints to non-collinear calculations taking spin orbit coupling into account.

      -
      -
      Args:
      -
      original_wf (Workflow) +
      +
      Args:

      original_wf (Workflow) nbands (int): number of bands selected by the user (for now) structure (Structure) modify_incar_params ({}): a dictionary containing the setting for modyfining the INCAR (e.g. {β€œICHARG”: 11}) -fw_name_constraint (string): name of the fireworks to be modified (all if None is passed)

      -
      Returns:
      -
      Workflow: modified with SOC
      +fw_name_constraint (string): name of the fireworks to be modified (all if None is passed)

      +
      +
      Returns:

      Workflow: modified with SOC

      +
      -atomate.vasp.powerups.preserve_fworker(original_wf, fw_name_constraint=None)ΒΆ
      +atomate.vasp.powerups.preserve_fworker(original_wf, fw_name_constraint=None)ΒΆ

      set _preserve_fworker spec of Fireworker(s) of a Workflow. Can be used to pin a workflow to the first fworker it is run with. Very useful when running on multiple machines that can’t share files. fw_name_constraint can be used to only preserve fworker after a certain point where file passing becomes important

      -
      -
      Args:
      -
      original_wf (Workflow): -fw_name_constraint (str): name of the Fireworks to be tagged (all if None is passed)
      -
      Returns:
      -
      Workflow: modified workflow with specified Fireworkers tagged
      +
      +
      Args:

      original_wf (Workflow): +fw_name_constraint (str): name of the Fireworks to be tagged (all if None is passed)

      +
      +
      Returns:

      Workflow: modified workflow with specified Fireworkers tagged

      +
      -atomate.vasp.powerups.remove_custodian(original_wf, fw_name_constraint=None)ΒΆ
      +atomate.vasp.powerups.remove_custodian(original_wf, fw_name_constraint=None)ΒΆ

      Replaces all tasks with β€œRunVasp*” (e.g. RunVaspCustodian) to be RunVaspDirect.

      -
      -
      Args:
      -
      original_wf (Workflow): original workflow -fw_name_constraint (str): Only apply changes to FWs where fw_name contains this substring.
      -
      Returns:
      -
      Workflow
      +
      +
      Args:

      original_wf (Workflow): original workflow +fw_name_constraint (str): Only apply changes to FWs where fw_name contains this substring.

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.set_execution_options(original_wf, fworker_name=None, category=None, fw_name_constraint=None, task_name_constraint=None)ΒΆ
      +atomate.vasp.powerups.set_execution_options(original_wf, fworker_name=None, category=None, fw_name_constraint=None, task_name_constraint=None)ΒΆ

      set _fworker spec of Fireworker(s) of a Workflow. It can be used to specify a queue; e.g. run large-memory jobs on a separate queue.

      -
      -
      Args:
      -

      original_wf (Workflow): +

      +
      Args:

      original_wf (Workflow): fworker_name (str): user-defined tag to be added under fw.spec._fworker

      -
      e.g. β€œlarge memory”, β€œbig”, etc
      -

      category (str): category of FWorker that should pul job +

      e.g. β€œlarge memory”, β€œbig”, etc

      +
      +

      category (str): category of FWorker that should pul job fw_name_constraint (str): name of the Fireworks to be tagged (all if None is passed) task_name_constraint (str): name of the Firetasks to be tagged (e.g. None or β€˜RunVasp’)

      -
      Returns:
      -
      Workflow: modified workflow with specified Fireworkers tagged
      +
      Returns:

      Workflow: modified workflow with specified Fireworkers tagged

      +
      -atomate.vasp.powerups.use_custodian(original_wf, fw_name_constraint=None, custodian_params=None)ΒΆ
      +atomate.vasp.powerups.use_custodian(original_wf, fw_name_constraint=None, custodian_params=None)ΒΆ

      Replaces all tasks with β€œRunVasp*” (e.g. RunVaspDirect) to be RunVaspCustodian. Thus, this powerup adds error correction into VASP runs if not originally present and/or modifies the correction behavior.

      -
      -
      Args:
      -

      original_wf (Workflow): original workflow +

      +
      Args:

      original_wf (Workflow): original workflow fw_name_constraint (str): Only apply changes to FWs where fw_name contains this substring.

      -
      For example, use custodian only for certain runs, or set job_type to +

      For example, use custodian only for certain runs, or set job_type to β€œdouble_relaxation_run” only for structure optimization run, or set different -handler_group for different runs.

      -
      -
      custodian_params (dict): A dict of parameters for RunVaspCustodian. e.g., use it to set
      -
      a β€œscratch_dir” or β€œhandler_group”.
      +handler_group for different runs.

      + +
      +
      custodian_params (dict): A dict of parameters for RunVaspCustodian. e.g., use it to set

      a β€œscratch_dir” or β€œhandler_group”.

      +
      -
      Returns:
      -
      Workflow
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.use_fake_vasp(original_wf, ref_dirs, params_to_check=None)ΒΆ
      +atomate.vasp.powerups.use_fake_vasp(original_wf, ref_dirs, params_to_check=None)ΒΆ

      Replaces all tasks with β€œRunVasp” (e.g. RunVaspDirect) to be RunVaspFake. Thus, we do not actually run VASP but copy pre-determined inputs and outputs.

      -
      -
      Args:
      -
      original_wf (Workflow) +
      +
      Args:

      original_wf (Workflow) ref_dirs (dict): key=firework name, value=path to the reference vasp calculation directory -params_to_check (list): optional list of incar parameters to check.

      -
      Returns:
      -
      Workflow
      +params_to_check (list): optional list of incar parameters to check.

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.use_gamma_vasp(original_wf, gamma_vasp_cmd)ΒΆ
      +atomate.vasp.powerups.use_gamma_vasp(original_wf, gamma_vasp_cmd)ΒΆ

      For all RunVaspCustodian tasks, add the desired scratch dir.

      -
      -
      Args:
      -
      original_wf (Workflow) -gamma_vasp_cmd (str): path to gamma_vasp_cmd. Supports env_chk
      -
      Returns:
      -
      Workflow
      +
      +
      Args:

      original_wf (Workflow) +gamma_vasp_cmd (str): path to gamma_vasp_cmd. Supports env_chk

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.use_no_vasp(original_wf, ref_dirs)ΒΆ
      +atomate.vasp.powerups.use_no_vasp(original_wf, ref_dirs)ΒΆ

      Instead of running VASP, does nothing and pass task documents from task.json files in ref_dirs to task database.

      -
      -
      Args:
      -
      original_wf (Workflow) -ref_dirs(dict): key=firework name, value=path to the reference vasp calculation directory
      -
      Returns:
      -
      Workflow
      +
      +
      Args:

      original_wf (Workflow) +ref_dirs(dict): key=firework name, value=path to the reference vasp calculation directory

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.powerups.use_scratch_dir(original_wf, scratch_dir)ΒΆ
      +atomate.vasp.powerups.use_scratch_dir(original_wf, scratch_dir)ΒΆ

      For all RunVaspCustodian tasks, add the desired scratch dir.

      -
      -
      Args:
      -
      original_wf (Workflow) -scratch_dir (path): Path to the scratch dir to use. Supports env_chk
      -
      Returns:
      -
      Workflow
      +
      +
      Args:

      original_wf (Workflow) +scratch_dir (path): Path to the scratch dir to use. Supports env_chk

      +
      +
      Returns:

      Workflow

      +
      @@ -862,48 +858,48 @@

      Submodules

      atomate.vasp.submission_filter moduleΒΆ

      -class atomate.vasp.submission_filter.SubmissionFilter(is_valid=True, potcar_exists=True, max_natoms=200, is_ordered=True, not_in_MP=True, MAPI_KEY=None, require_bandstructure=False)ΒΆ
      +class atomate.vasp.submission_filter.SubmissionFilter(is_valid=True, potcar_exists=True, max_natoms=200, is_ordered=True, not_in_MP=True, MAPI_KEY=None, require_bandstructure=False)ΒΆ

      Bases: pymatgen.alchemy.filters.AbstractStructureFilter

      -NO_POTCARS = ['Po', 'At', 'Rn', 'Fr', 'Ra', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr']ΒΆ
      +NO_POTCARS = ['Po', 'At', 'Rn', 'Fr', 'Ra', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr']ΒΆ
      -__init__(is_valid=True, potcar_exists=True, max_natoms=200, is_ordered=True, not_in_MP=True, MAPI_KEY=None, require_bandstructure=False)ΒΆ
      +__init__(is_valid=True, potcar_exists=True, max_natoms=200, is_ordered=True, not_in_MP=True, MAPI_KEY=None, require_bandstructure=False)ΒΆ

      Initialize a submission filter for checking that structures are valid for calculations.

      -
      -
      Args:
      -
      is_valid (bool): If true, checks structure validity +
      +
      Args:

      is_valid (bool): If true, checks structure validity potcar_exists (bool): If true, ensures all elements have VASP PAW_PBE POTCAR max_natoms (int): If not None, ensures structure has <=max_natoms atoms is_ordered (bool): If true, ensures structure is ordered not_in_MP (bool): If true, ensures structure not in MP MAPI_KEY (str): For MP checks, your MAPI key if not previously set as config var -require_bandstructure (bool): For MP checks, require a band structure calc

      +require_bandstructure (bool): For MP checks, require a band structure calc

      +
      -as_dict()ΒΆ
      +as_dict()ΒΆ

      A JSON serializable dict representation of an object.

      -
      +
      -classmethod from_dict(d)ΒΆ
      +classmethod from_dict(d)ΒΆ
      -test(structure)ΒΆ
      +test(structure)ΒΆ

      Method to execute the test.

      -
      -
      Returns:
      -
      (bool) Structures that return true are kept in the Transmuter -object during filtering.
      +
      +
      Returns:

      (bool) Structures that return true are kept in the Transmuter +object during filtering.

      +
      @@ -952,13 +948,11 @@

      This Page

      @@ -976,13 +970,13 @@

      Navigation

    21. modules |
      22. -
    22. atomate 0.9.1 documentation »
      23. +
    23. atomate 0.9.2 documentation »
      24. diff --git a/docs/atomate.vasp.tests.html b/docs/atomate.vasp.tests.html index df4167bf4..aca8df341 100644 --- a/docs/atomate.vasp.tests.html +++ b/docs/atomate.vasp.tests.html @@ -1,18 +1,17 @@ - + - - - atomate.vasp.tests package — atomate 0.9.1 documentation + + atomate.vasp.tests package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

      Navigation

    24. modules |
      25. -
    25. atomate 0.9.1 documentation »
      26. +
    26. atomate 0.9.2 documentation »
      27. @@ -46,42 +45,42 @@

      Submodules

      atomate.vasp.tests.test_drones moduleΒΆ

      -class atomate.vasp.tests.test_drones.VaspToDbTaskDroneTest(methodName='runTest')ΒΆ
      +class atomate.vasp.tests.test_drones.VaspToDbTaskDroneTest(methodName='runTest')ΒΆ

      Bases: unittest.case.TestCase

      -
      +
      -classmethod setUpClass()ΒΆ
      +classmethod setUpClass()ΒΆ

      Hook method for setting up class fixture before running tests in the class.

      -test_assimilate()ΒΆ
      +test_assimilate()ΒΆ
      -test_bandstructure()ΒΆ
      +test_bandstructure()ΒΆ
      -test_detect_output_file_paths()ΒΆ
      +test_detect_output_file_paths()ΒΆ
      -test_parse_chrgcar()ΒΆ
      +test_parse_chrgcar()ΒΆ
      -test_parse_locpot()ΒΆ
      +test_parse_locpot()ΒΆ
      -test_runs_assimilate()ΒΆ
      +test_runs_assimilate()ΒΆ
      @@ -91,29 +90,29 @@

      Submodules

      atomate.vasp.tests.test_setup moduleΒΆ

      -class atomate.vasp.tests.test_setup.TestSetup(methodName='runTest')ΒΆ
      +class atomate.vasp.tests.test_setup.TestSetup(methodName='runTest')ΒΆ

      Bases: unittest.case.TestCase

      -setUp()ΒΆ
      +setUp()ΒΆ

      Hook method for setting up the test fixture before exercising it.

      -
      +
      -classmethod setUpClass()ΒΆ
      +classmethod setUpClass()ΒΆ

      Hook method for setting up class fixture before running tests in the class.

      -tearDown()ΒΆ
      +tearDown()ΒΆ

      Hook method for deconstructing the test fixture after testing it.

      -test_setup()ΒΆ
      +test_setup()ΒΆ
      @@ -123,62 +122,62 @@

      Submodules

      atomate.vasp.tests.test_vasp_powerups moduleΒΆ

      -class atomate.vasp.tests.test_vasp_powerups.TestVaspPowerups(methodName='runTest')ΒΆ
      +class atomate.vasp.tests.test_vasp_powerups.TestVaspPowerups(methodName='runTest')ΒΆ

      Bases: unittest.case.TestCase

      -
      +
      -classmethod setUpClass()ΒΆ
      +classmethod setUpClass()ΒΆ

      Hook method for setting up class fixture before running tests in the class.

      -test_add_clean_up()ΒΆ
      +test_add_clean_up()ΒΆ
      -test_add_priority()ΒΆ
      +test_add_priority()ΒΆ
      -test_add_small_gap_multiply()ΒΆ
      +test_add_small_gap_multiply()ΒΆ
      -test_add_tags()ΒΆ
      +test_add_tags()ΒΆ
      -test_add_trackers()ΒΆ
      +test_add_trackers()ΒΆ
      -test_add_wf_metadata()ΒΆ
      +test_add_wf_metadata()ΒΆ
      -test_custodian_powerups()ΒΆ
      +test_custodian_powerups()ΒΆ
      -test_modify_incar()ΒΆ
      +test_modify_incar()ΒΆ
      -test_modify_potcar()ΒΆ
      +test_modify_potcar()ΒΆ
      -test_use_scratch_dir()ΒΆ
      +test_use_scratch_dir()ΒΆ
      @@ -215,13 +214,11 @@

      This Page

      @@ -239,13 +236,13 @@

      Navigation

    27. modules |
      28. -
    28. atomate 0.9.1 documentation »
      29. +
    29. atomate 0.9.2 documentation »
      30. diff --git a/docs/atomate.vasp.workflows.base.html b/docs/atomate.vasp.workflows.base.html index 3b78863d1..c874a8370 100644 --- a/docs/atomate.vasp.workflows.base.html +++ b/docs/atomate.vasp.workflows.base.html @@ -1,18 +1,17 @@ - + - - - atomate.vasp.workflows.base package — atomate 0.9.1 documentation + + atomate.vasp.workflows.base package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

      Navigation

    30. modules |
      31. -
    31. atomate 0.9.1 documentation »
      32. +
    32. atomate 0.9.2 documentation »
      33. @@ -46,19 +45,19 @@

      Submodules

      atomate.vasp.workflows.base.adsorption moduleΒΆ

      -class atomate.vasp.workflows.base.adsorption.MPSurfaceSet(structure, bulk=False, auto_dipole=None, **kwargs)ΒΆ
      +class atomate.vasp.workflows.base.adsorption.MPSurfaceSet(structure, bulk=False, auto_dipole=None, **kwargs)ΒΆ

      Bases: pymatgen.io.vasp.sets.MVLSlabSet

      Input class for MP slab calcs, mostly to change parameters and defaults slightly

      -__init__(structure, bulk=False, auto_dipole=None, **kwargs)ΒΆ
      +__init__(structure, bulk=False, auto_dipole=None, **kwargs)ΒΆ

      Initialize self. See help(type(self)) for accurate signature.

      -
      +
      -incarΒΆ
      +property incarΒΆ

      Incar object

      @@ -66,115 +65,117 @@

      Submodules
      -atomate.vasp.workflows.base.adsorption.get_slab_fw(slab, transmuter=False, db_file=None, vasp_input_set=None, parents=None, vasp_cmd='vasp', name='', add_slab_metadata=True)ΒΆ
      +atomate.vasp.workflows.base.adsorption.get_slab_fw(slab, transmuter=False, db_file=None, vasp_input_set=None, parents=None, vasp_cmd='vasp', name='', add_slab_metadata=True)ΒΆ

      Function to generate a a slab firework. Returns a TransmuterFW if bulk_structure is specified, constructing the necessary transformations from the slab and slab generator parameters, or an OptimizeFW if only a slab is specified.

      -
      -
      Args:
      -
      -
      slab (Slab or Structure): structure or slab corresponding
      -
      to the slab to be calculated
      -
      transmuter (bool): whether or not to use a TransmuterFW based
      -
      on slab params, if this option is selected, input slab must -be a Slab object (as opposed to Structure)
      -
      vasp_input_set (VaspInputSet): vasp_input_set corresponding to
      -
      the slab calculation
      -
      -

      parents (Fireworks or list of ints): parent FWs +

      +
      Args:
      +
      slab (Slab or Structure): structure or slab corresponding

      to the slab to be calculated

      +
      +
      transmuter (bool): whether or not to use a TransmuterFW based

      on slab params, if this option is selected, input slab must +be a Slab object (as opposed to Structure)

      +
      +
      vasp_input_set (VaspInputSet): vasp_input_set corresponding to

      the slab calculation

      +
      +
      +

      parents (Fireworks or list of ints): parent FWs db_file (string): path to database file vasp_cmd (string): vasp command name (string): name of firework add_slab_metadata (bool): whether to add slab metadata to task doc

      -
      Returns:
      -
      Firework corresponding to slab calculation
      +
      Returns:

      Firework corresponding to slab calculation

      +
      -atomate.vasp.workflows.base.adsorption.get_slab_trans_params(slab)ΒΆ
      +atomate.vasp.workflows.base.adsorption.get_slab_trans_params(slab)ΒΆ

      Gets a set of slab transformation params

      -
      -
      Args:
      -
      slab (Slab): slab to find transformation params from
      -
      Returns (SlabTransformation):
      -
      Transformation for a transformation that will transform -the oriented unit cell to the slab
      +
      +
      Args:

      slab (Slab): slab to find transformation params from

      +
      +
      Returns (SlabTransformation):

      Transformation for a transformation that will transform +the oriented unit cell to the slab

      +
      -atomate.vasp.workflows.base.adsorption.get_wf_molecules(molecules, vasp_input_set=None, db_file=None, vasp_cmd='vasp', name='')ΒΆ
      -
      -
      Args:
      -
      molecules (Molecules): list of molecules to calculate +atomate.vasp.workflows.base.adsorption.get_wf_molecules(molecules, vasp_input_set=None, db_file=None, vasp_cmd='vasp', name='')ΒΆ +
      +
      Args:

      molecules (Molecules): list of molecules to calculate vasp_input_set (DictSet): VaspInputSet for molecules db_file (string): database file path vasp_cmd (string): VASP command -name (string): name for workflow

      -
      Returns:
      -
      workflow consisting of molecule calculations
      +name (string): name for workflow

      +
      +
      Returns:

      workflow consisting of molecule calculations

      +
      -atomate.vasp.workflows.base.adsorption.get_wf_slab(slab, include_bulk_opt=False, adsorbates=None, ads_structures_params=None, vasp_cmd='vasp', db_file=None, add_molecules_in_box=False)ΒΆ
      +atomate.vasp.workflows.base.adsorption.get_wf_slab(slab, include_bulk_opt=False, adsorbates=None, ads_structures_params=None, vasp_cmd='vasp', db_file=None, add_molecules_in_box=False)ΒΆ

      Gets a workflow corresponding to a slab calculation along with optional adsorbate calcs and precursor oriented unit cell optimization

      -
      -
      Args:
      -

      slabs (list of Slabs or Structures): slabs to calculate +

      +
      Args:

      slabs (list of Slabs or Structures): slabs to calculate include_bulk_opt (bool): whether to include bulk optimization,

      -
      this flag sets the slab fireworks to be TransmuterFWs based -on bulk optimization of oriented unit cells
      +

      this flag sets the slab fireworks to be TransmuterFWs based +on bulk optimization of oriented unit cells

      +

      adsorbates ([Molecule]): list of molecules to place as adsorbates ads_structures_params (dict): parameters to be supplied as

      -
      kwargs to AdsorbateSiteFinder.generate_adsorption_structures
      -
      -
      add_molecules_in_box (boolean): flag to add calculation of
      -
      adsorbate molecule energies to the workflow
      +

      kwargs to AdsorbateSiteFinder.generate_adsorption_structures

      +
      +
      +
      add_molecules_in_box (boolean): flag to add calculation of

      adsorbate molecule energies to the workflow

      +
      -

      db_file (string): path to database file +

      db_file (string): path to database file vasp_cmd (string): vasp command

      -
      Returns:
      -
      Workflow
      +
      Returns:

      Workflow

      +
      -atomate.vasp.workflows.base.adsorption.get_wfs_all_slabs(bulk_structure, include_bulk_opt=False, adsorbates=None, max_index=1, slab_gen_params=None, ads_structures_params=None, vasp_cmd='vasp', db_file=None, add_molecules_in_box=False)ΒΆ
      +atomate.vasp.workflows.base.adsorption.get_wfs_all_slabs(bulk_structure, include_bulk_opt=False, adsorbates=None, max_index=1, slab_gen_params=None, ads_structures_params=None, vasp_cmd='vasp', db_file=None, add_molecules_in_box=False)ΒΆ

      Convenience constructor that allows a user to construct a workflow that finds all adsorption configurations (or slabs) for a given max miller index.

      -
      -
      Args:
      -

      bulk_structure (Structure): bulk structure from which to construct slabs +

      +
      Args:

      bulk_structure (Structure): bulk structure from which to construct slabs include_bulk_opt (bool): whether to include bulk optimization

      -
      of oriented unit cells
      +

      of oriented unit cells

      +

      adsorbates ([Molecule]): adsorbates to place on surfaces max_index (int): max miller index slab_gen_params (dict): dictionary of kwargs for generate_all_slabs ads_structures_params (dict): dictionary of kwargs for generating

      -
      of adsorption structures via AdsorptionSiteFinder
      +

      of adsorption structures via AdsorptionSiteFinder

      +

      vasp_cmd (str): vasp command db_file (str): location of db file add_molecules_in_box (bool): whether to add molecules in a box

      -
      -
      for the entire workflow
      +
      +

      for the entire workflow

      +
      +
      +
      Returns:

      list of slab-specific Workflows

      -
      Returns:
      -
      list of slab-specific Workflows
      @@ -183,11 +184,10 @@

      Submodules

      atomate.vasp.workflows.base.bulk_modulus moduleΒΆ

      -atomate.vasp.workflows.base.bulk_modulus.get_wf_bulk_modulus(structure, deformations, vasp_input_set=None, vasp_cmd='vasp', db_file=None, user_kpoints_settings=None, eos='vinet', tag=None, user_incar_settings=None)ΒΆ
      +atomate.vasp.workflows.base.bulk_modulus.get_wf_bulk_modulus(structure, deformations, vasp_input_set=None, vasp_cmd='vasp', db_file=None, user_kpoints_settings=None, eos='vinet', tag=None, user_incar_settings=None)ΒΆ

      Returns the workflow that computes the bulk modulus by fitting to the given equation of state.

      -
      -
      Args:
      -

      structure (Structure): input structure. +

      +
      Args:

      structure (Structure): input structure. deformations (list): list of deformation matrices(list of lists). vasp_input_set (VaspInputSet): for the static deformation calculations vasp_cmd (str): vasp command to run. @@ -195,16 +195,17 @@

      Submodules -
      tag (str): something unique to identify the tasks in this workflow. If None a random uuid
      -
      will be assigned.
      +

      supported equation of states: β€œquadratic”, β€œmurnaghan”, β€œbirch”, β€œbirch_murnaghan”, +β€œpourier_tarantola”, β€œvinet”, β€œdeltafactor”. See pymatgen.analysis.eos.py

      +
      +
      +
      tag (str): something unique to identify the tasks in this workflow. If None a random uuid

      will be assigned.

      +
      -

      user_incar_settings (dict):

      +

      user_incar_settings (dict):

      +

      +
      Returns:

      Workflow

      -
      Returns:
      -
      Workflow
      @@ -213,24 +214,24 @@

      Submodules

      atomate.vasp.workflows.base.core moduleΒΆ

      -atomate.vasp.workflows.base.core.get_wf(structure, wf_filename, params=None, common_params=None, vis=None, wf_metadata=None)ΒΆ
      +atomate.vasp.workflows.base.core.get_wf(structure, wf_filename, params=None, common_params=None, vis=None, wf_metadata=None)ΒΆ

      Get a workflow given a structure and a name of file from the workflow library.

      Possible options for wf_filename are listed in: atomate.vasp.workflows.base.library and include band structure, dielectric constant, NEB, and more.

      You can also override some of the parameters via the function arguments.

      -
      -
      Args:
      -

      structure: (Structure) structure to run +

      +
      Args:

      structure: (Structure) structure to run wf_filename: filename in library subdir, e.g. β€œband_structure.yaml” params: (list of dicts) set params for each Firework; format is list

      -
      that is same length as # of fws in the workflow
      -

      common_params: (dict) set common params +

      that is same length as # of fws in the workflow

      +
      +

      common_params: (dict) set common params vis: (VaspInputSet) A VaspInputSet to use for the first FW wf_metadata: (dict) workflow metadata

      -
      Returns:
      -
      A Workflow
      +
      Returns:

      A Workflow

      +
      @@ -239,13 +240,12 @@

      Submodules

      atomate.vasp.workflows.base.deformations moduleΒΆ

      -atomate.vasp.workflows.base.deformations.get_wf_deformations(structure, deformations, name='deformation', vasp_input_set=None, vasp_cmd='vasp', db_file=None, tag='', copy_vasp_outputs=True, metadata=None)ΒΆ
      +atomate.vasp.workflows.base.deformations.get_wf_deformations(structure, deformations, name='deformation', vasp_input_set=None, vasp_cmd='vasp', db_file=None, tag='', copy_vasp_outputs=True, metadata=None)ΒΆ

      Returns a structure deformation workflow.

      Firework 1 : structural relaxation Firework 2 - len(deformations): Deform the optimized structure and run static calculations.

      -
      -
      Args:
      -

      structure (Structure): input structure to be optimized and run +

      +
      Args:

      structure (Structure): input structure to be optimized and run deformations (list of 3x3 array-likes): list of deformations name (str): some appropriate name for the transmuter fireworks. vasp_input_set (DictVaspInputSet): vasp input set for static deformed structure calculation. @@ -253,15 +253,16 @@

      Submodules -
      copy_vasp_outputs (bool): whether or not copy the outputs from the previous calc(usually
      -
      structure optimization) before the transmuter fireworks.
      +

      the data from those tagged fireworks can be queried later during the analysis.

      +
      +
      +
      copy_vasp_outputs (bool): whether or not copy the outputs from the previous calc(usually

      structure optimization) before the transmuter fireworks.

      +
      -

      metadata (dict): meta data

      +

      metadata (dict): meta data

      +

      +
      Returns:

      Workflow

      -
      Returns:
      -
      Workflow
      @@ -270,55 +271,56 @@

      Submodules

      atomate.vasp.workflows.base.elastic moduleΒΆ

      -atomate.vasp.workflows.base.elastic.get_default_strain_states(order=2)ΒΆ
      +atomate.vasp.workflows.base.elastic.get_default_strain_states(order=2)ΒΆ

      Generates a list of β€œstrain-states”

      -atomate.vasp.workflows.base.elastic.get_wf_elastic_constant(structure, strain_states=None, stencils=None, db_file=None, conventional=False, order=2, vasp_input_set=None, analysis=True, sym_reduce=False, tag='elastic', copy_vasp_outputs=False, **kwargs)ΒΆ
      +atomate.vasp.workflows.base.elastic.get_wf_elastic_constant(structure, strain_states=None, stencils=None, db_file=None, conventional=False, order=2, vasp_input_set=None, analysis=True, sym_reduce=False, tag='elastic', copy_vasp_outputs=False, **kwargs)ΒΆ

      Returns a workflow to calculate elastic constants.

      -
      -
      Firework 1 : write vasp input set for structural relaxation,
      -
      run vasp, +
      +
      Firework 1write vasp input set for structural relaxation,

      run vasp, pass run location, -database insertion.

      +database insertion.

      +

      Firework 2 - number of total deformations: Static runs on the deformed structures

      last Firework : Analyze Stress/Strain data and fit the elastic tensor

      -
      -
      Args:
      -

      structure (Structure): input structure to be optimized and run. +

      +
      Args:

      structure (Structure): input structure to be optimized and run. strain_states (list of Voigt-notation strains): list of ratios of nonzero elements

      -
      of Voigt-notation strain, e. g. [(1, 0, 0, 0, 0, 0), (0, 1, 0, 0, 0, 0), etc.].
      -
      -
      stencils (list of floats, or list of list of floats): values of strain to multiply
      -
      by for each strain state, i. e. stencil for the perturbation along the strain +

      of Voigt-notation strain, e. g. [(1, 0, 0, 0, 0, 0), (0, 1, 0, 0, 0, 0), etc.].

      +
      +
      +
      stencils (list of floats, or list of list of floats): values of strain to multiply

      by for each strain state, i. e. stencil for the perturbation along the strain state direction, e. g. [-0.01, -0.005, 0.005, 0.01]. If a list of lists, -stencils must correspond to each strain state provided.

      +stencils must correspond to each strain state provided.

      +

      db_file (str): path to file containing the database credentials. conventional (bool): flag to convert input structure to conventional structure,

      -
      defaults to False.
      -
      -
      order (int): order of the tensor expansion to be determined. Defaults to 2 and
      -
      currently supports up to 3.
      -
      vasp_input_set (VaspInputSet): vasp input set to be used. Defaults to static
      -
      set with ionic relaxation parameters set. Take care if replacing this, +

      defaults to False.

      +
      +
      +
      order (int): order of the tensor expansion to be determined. Defaults to 2 and

      currently supports up to 3.

      +
      +
      vasp_input_set (VaspInputSet): vasp input set to be used. Defaults to static

      set with ionic relaxation parameters set. Take care if replacing this, default ensures that ionic relaxation is done and that stress is calculated -for each vasp run.

      -
      analysis (bool): flag to indicate whether analysis task should be added
      -
      and stresses and strains passed to that task
      +for each vasp run.

      +
      +
      analysis (bool): flag to indicate whether analysis task should be added

      and stresses and strains passed to that task

      +
      -

      sym_reduce (bool): Whether or not to apply symmetry reductions +

      sym_reduce (bool): Whether or not to apply symmetry reductions tag (str): copy_vasp_outputs (bool): whether or not to copy previous vasp outputs. kwargs (keyword arguments): additional kwargs to be passed to get_wf_deformations

      -
      Returns:
      -
      Workflow
      +
      Returns:

      Workflow

      +
      @@ -327,7 +329,7 @@

      Submodules

      atomate.vasp.workflows.base.ferroelectric moduleΒΆ

      -atomate.vasp.workflows.base.ferroelectric.get_wf_ferroelectric(polar_structure, nonpolar_structure, vasp_cmd='vasp', db_file=None, vasp_input_set_polar='MPStaticSet', vasp_input_set_nonpolar='MPStaticSet', relax=False, vasp_relax_input_set_polar=None, vasp_relax_input_set_nonpolar=None, nimages=9, hse=False, add_analysis_task=False, wfid=None, tags=None)ΒΆ
      +atomate.vasp.workflows.base.ferroelectric.get_wf_ferroelectric(polar_structure, nonpolar_structure, vasp_cmd='vasp', db_file=None, vasp_input_set_polar='MPStaticSet', vasp_input_set_nonpolar='MPStaticSet', relax=False, vasp_relax_input_set_polar=None, vasp_relax_input_set_nonpolar=None, nimages=9, hse=False, add_analysis_task=False, wfid=None, tags=None)ΒΆ

      Returns a workflow to calculate the spontaneous polarization of polar_structure using a nonpolar reference phase structure and linear interpolations between the polar and nonpolar structure.

      @@ -338,9 +340,8 @@

      Submoduleshttp://www.cryst.ehu.es/cryst/rel.html)

      -
      -
      Args:
      -

      polar_structure (Structure): polar structure of candidate ferroelectric +

      +
      Args:

      polar_structure (Structure): polar structure of candidate ferroelectric nonpolar_structure (Structure): nonpolar reference structure in polar setting vasp_input_set_polar (DictVaspInputSet): VASP polar input set. Defaults to MPStaticSet. vasp_input_set_nonpolar (DictVaspInputSet): VASP nonpolar input set. Defaults to MPStaticSet. @@ -350,8 +351,9 @@

      Submodulesadd_analysis_task: Analyze polarization and energy trends as part of workflow. Default False. +

      For example, nimages = 9 will calculate 8 interpolated structures. 8 interpolations + nonpolar = 9.

      +
      +

      add_analysis_task: Analyze polarization and energy trends as part of workflow. Default False. wfid (string): Unique worfklow id starting with β€œwfid_”. If None this is atomatically generated (recommended). tags (list of strings): Additional tags to add such as identifiers for structures.

      @@ -364,12 +366,11 @@

      Submodules

      atomate.vasp.workflows.base.gibbs moduleΒΆ

      -atomate.vasp.workflows.base.gibbs.get_wf_gibbs_free_energy(structure, deformations, vasp_input_set=None, vasp_cmd='vasp', db_file=None, user_kpoints_settings=None, t_step=10, t_min=0, t_max=1000, mesh=(20, 20, 20), eos='vinet', qha_type='debye_model', pressure=0.0, poisson=0.25, anharmonic_contribution=False, metadata=None, tag=None)ΒΆ
      +atomate.vasp.workflows.base.gibbs.get_wf_gibbs_free_energy(structure, deformations, vasp_input_set=None, vasp_cmd='vasp', db_file=None, user_kpoints_settings=None, t_step=10, t_min=0, t_max=1000, mesh=(20, 20, 20), eos='vinet', qha_type='debye_model', pressure=0.0, poisson=0.25, anharmonic_contribution=False, metadata=None, tag=None)ΒΆ

      Returns quasi-harmonic gibbs free energy workflow. Note: phonopy package is required for the final analysis step if qha_type=”phonopy”

      -
      -
      Args:
      -

      structure (Structure): input structure. +

      +
      Args:

      structure (Structure): input structure. deformations (list): list of deformation matrices(list of lists). vasp_input_set (VaspInputSet) vasp_cmd (str): vasp command to run. @@ -381,24 +382,27 @@

      Submodules -
      qha_type(str): quasi-harmonic approximation type: β€œdebye_model” or β€œphonopy”,
      -
      default is β€œdebye_model”
      +

      options supported by phonopy: β€œvinet”, β€œmurnaghan”, β€œbirch_murnaghan”. +Note: pymatgen supports more options than phonopy. see pymatgen.analysis.eos.py

      +
      +
      +
      qha_type(str): quasi-harmonic approximation type: β€œdebye_model” or β€œphonopy”,

      default is β€œdebye_model”

      +

      pressure (float): in GPa poisson (float): poisson ratio anharmonic_contribution (bool): consider anharmonic contributions to

      -
      Gibbs energy from the Debye model. Defaults to False.
      +

      Gibbs energy from the Debye model. Defaults to False.

      +

      metadata (dict): meta data tag (str): something unique to identify the tasks in this workflow. If None a random uuid

      -
      -
      will be assigned.
      +
      +

      will be assigned.

      +
      +

      +
      Returns:

      Workflow

      -
      Returns:
      -
      Workflow
      @@ -407,11 +411,11 @@

      Submodules

      atomate.vasp.workflows.base.magnetism moduleΒΆ

      -class atomate.vasp.workflows.base.magnetism.MagneticOrderingsWF(structure, default_magmoms=None, strategies=('ferromagnetic', 'antiferromagnetic'), automatic=True, truncate_by_symmetry=True, transformation_kwargs=None)ΒΆ
      +class atomate.vasp.workflows.base.magnetism.MagneticOrderingsWF(structure, default_magmoms=None, strategies=('ferromagnetic', 'antiferromagnetic'), automatic=True, truncate_by_symmetry=True, transformation_kwargs=None)ΒΆ

      Bases: object

      -__init__(structure, default_magmoms=None, strategies=('ferromagnetic', 'antiferromagnetic'), automatic=True, truncate_by_symmetry=True, transformation_kwargs=None)ΒΆ
      +__init__(structure, default_magmoms=None, strategies=('ferromagnetic', 'antiferromagnetic'), automatic=True, truncate_by_symmetry=True, transformation_kwargs=None)ΒΆ

      This workflow will try several different collinear magnetic orderings for a given input structure, and output a summary to a dedicated database @@ -421,80 +425,84 @@

      Submodules -
      A brief description on how this workflow works:
      -
        -
      1. We make a note of the input structure, and then -sanitize it (make it ferromagnetic, primitive)
        2. -
      2. We gather information on which sites are likely +
        +
        A brief description on how this workflow works:
          +

        1. We make a note of the input structure, and then +sanitize it (make it ferromagnetic, primitive)

          2. +

        2. We gather information on which sites are likely magnetic, how many unique magnetic sites there are (whether one species is in several unique environments, e.g. tetrahedral/octahedra as Fe -in a spinel)

          3. -
        3. We generate ordered magnetic structures, first +in a spinel)

          4. +

        4. We generate ordered magnetic structures, first antiferromagnetic, and then, if appropriate, ferrimagnetic_Cr2NiO4 structures either by species or by environment – this makes use of some new additions to MagOrderingTransformation to allow the spins of different species to be coupled together (e.g. all one species spin up, all other species spin -down, with an overall order parameter of 0.5)

          5. -
        5. For each ordered structure, we perform a relaxation +down, with an overall order parameter of 0.5)

          6. +

        6. For each ordered structure, we perform a relaxation and static calculation. Then an aggregation is performed which finds which ordering is the ground state (of those attempted in this specific workflow). For high-throughput studies, a dedicated builder is -recommended.

          7. -
        7. For book-keeping, a record is kept of whether the +recommended.

          8. +

        8. For book-keeping, a record is kept of whether the input structure is enumerated by the algorithm or not. This is useful when supplying the workflow with a magnetic structure obtained by experiment, to measure -the performance of the workflow.

          9. +the performance of the workflow.

        -
        Args:
        -
        structure: input structure -default_magmoms: (optional, defaults provided) dict of
        +
        Args:

        structure: input structure +default_magmoms: (optional, defaults provided) dict of

        +

        magnetic elements to their initial magnetic moments in Β΅B, generally these are chosen to be high-spin since they can relax to a low-spin configuration during a DFT electronic configuration

        -
        strategies: different ordering strategies to use, choose from:
        +

        strategies: different ordering strategies to use, choose from:

        +

        ferromagnetic, antiferromagnetic, antiferromagnetic_by_motif, ferrimagnetic_by_motif and ferrimagnetic_by_species (here, β€œmotif”, means to use a different ordering parameter for symmetry inequivalent sites)

        -
        automatic: if True, will automatically choose sensible strategies -truncate_by_symmetry: if True, will remove very unsymmetrical
        -
        -
        orderings that are likely physically implausible
        -
        transformation_kwargs: keyword arguments to pass to
        +

        automatic: if True, will automatically choose sensible strategies +truncate_by_symmetry: if True, will remove very unsymmetrical

        +
        +
        +
        orderings that are likely physically implausible

        transformation_kwargs: keyword arguments to pass to

        +

        MagOrderingTransformation, to change automatic cell size limits, etc.

      -get_wf(scan=False, perform_bader=True, num_orderings_hard_limit=16, c=None)ΒΆ
      +get_wf(scan=False, perform_bader=True, num_orderings_hard_limit=16, c=None)ΒΆ

      Retrieve the FireWorks workflow.

      -
      -
      Args:
      -
      scan: if True, use the SCAN functional instead of GGA+U, since
      +
      +
      Args:

      scan: if True, use the SCAN functional instead of GGA+U, since

      +

      the SCAN functional has shown to have improved performance for magnetic systems in some cases

      -
      perform_bader: if True, make sure the β€œbader” binary is in your
      +

      perform_bader: if True, make sure the β€œbader” binary is in your

      +

      path, will use Bader analysis to calculate atom-projected magnetic moments

      -
      num_orderings_hard_limit: will make sure total number of magnetic
      +

      num_orderings_hard_limit: will make sure total number of magnetic

      +

      orderings does not exceed this number even if there are extra orderings of equivalent symmetry

      -
      c: additional config dict (as used elsewhere in atomate)
      +

      c: additional config dict (as used elsewhere in atomate)

      +

      Returns: FireWorks Workflow

      @@ -502,20 +510,21 @@

      Submodules
      -atomate.vasp.workflows.base.magnetism.get_wf_magnetic_deformation(structure, c=None, vis=None)ΒΆ
      +atomate.vasp.workflows.base.magnetism.get_wf_magnetic_deformation(structure, c=None, vis=None)ΒΆ

      Minimal workflow to obtain magnetic deformation proxy, as defined by Bocarsly et al. 2017, doi: 10.1021/acs.chemmater.6b04729

      -
      -
      Args:
      -
      structure: input structure, must be structure with magnetic
      +
      +
      Args:

      structure: input structure, must be structure with magnetic

      +

      elements, such that pymatgen will initalize ferromagnetic input by default – see MPRelaxSet.yaml for list of default elements

      -
      c: Workflow config dict, in the same format
      -
      -
      as in presets/core.py and elsewhere in atomate
      -
      vis: A VaspInputSet to use for the first FW
      +

      c: Workflow config dict, in the same format

      +
      +
      +
      as in presets/core.py and elsewhere in atomate

      vis: A VaspInputSet to use for the first FW

      +

      Returns: Workflow

      @@ -526,115 +535,118 @@

      Submodules
      -atomate.vasp.workflows.base.neb.get_wf_neb_from_endpoints(parent, endpoints, user_incar_settings=None, additional_spec=None, user_kpoints_settings=None, additional_cust_args=None)ΒΆ
      +atomate.vasp.workflows.base.neb.get_wf_neb_from_endpoints(parent, endpoints, user_incar_settings=None, additional_spec=None, user_kpoints_settings=None, additional_cust_args=None)ΒΆ

      Get a CI-NEB workflow from given endpoints. Workflow: (Endpoints relax – ) NEB_1 – NEB_2 - … - NEB_r

      -
      endpoints not optimized: ep–neb(r) -endpoints are optimized: neb(r)
      -
      -
      Args:
      -

      parent (Structure): parent structure. +

      endpoints not optimized: ep–neb(r) +endpoints are optimized: neb(r)

      +
      +
      +
      Args:

      parent (Structure): parent structure. endpoints (list[Structure]): The endpoint structures. user_incar_settings([dict]): Additional user_incar_settings. Note that the order of the

      -
      list is set as: β€œparent”, β€œep_relax”, β€œneb1”, β€œneb2” etc., which contains +

      list is set as: β€œparent”, β€œep_relax”, β€œneb1”, β€œneb2” etc., which contains at least three elements. The first dict is for parent structure relaxation, the second dict is for endpoints relaxation, and the rest are for NEB calculations. For example, [{}, {}, {β€œIOPT”: 7}, {β€œIOPT”: 1}]. Besides, user_incar_settings is used to determine how many NEB rounds will be. Default -is [{}, {}, {}].

      +is [{}, {}, {}].

      +

      additional_spec (dict): User spec settings to overwrite default_spec. user_kpoints_settings ([dict]): Additional user_kpoints_settings, which contains at at

      -
      least three elements, which is similar to user_incar_settings. For example, +

      least three elements, which is similar to user_incar_settings. For example, [{}, {}, {β€œgrid_density”: 100}] for the workflow from the parent structure relaxation, then the endpoint relaxation followed by one-round NEB simulation. -Default values depend on the selected VaspInputSet.

      -
      -
      additional_cust_args ([dict]): Optional parameters for RunVaspCustodian, same structure
      -
      with user_incar_settings and user_kpoints_settings.
      +Default values depend on the selected VaspInputSet.

      + +
      +
      additional_cust_args ([dict]): Optional parameters for RunVaspCustodian, same structure

      with user_incar_settings and user_kpoints_settings.

      +
      -
      Returns:
      -
      Workflow
      +
      Returns:

      Workflow

      +
      -atomate.vasp.workflows.base.neb.get_wf_neb_from_images(parent, images, user_incar_settings, additional_spec=None, user_kpoints_settings=None, additional_cust_args=None)ΒΆ
      +atomate.vasp.workflows.base.neb.get_wf_neb_from_images(parent, images, user_incar_settings, additional_spec=None, user_kpoints_settings=None, additional_cust_args=None)ΒΆ

      Get a CI-NEB workflow from given images. Workflow: NEB_1 – NEB_2 - … - NEB_n

      -
      -
      Args:
      -

      parent (Structure): parent structure. +

      +
      Args:

      parent (Structure): parent structure. images ([Structure]): All images and two endpoints. user_incar_settings([dict]): Additional user_incar_settings. Note that the order of the

      -
      list is set as: β€œparent”, β€œep_relax”, β€œneb1”, β€œneb2” etc., which contains +

      list is set as: β€œparent”, β€œep_relax”, β€œneb1”, β€œneb2” etc., which contains at least three elements. The first dict is for parent structure relaxation, the second dict is for endpoints relaxation, and the rest are for NEB calculations. For example, [{}, {}, {β€œIOPT”: 7}, {β€œIOPT”: 1}]. Besides, user_incar_settings is used to determine how many NEB rounds will be. Default -is [{}, {}, {}].

      +is [{}, {}, {}].

      +

      additional_spec (dict): User spec settings to overwrite default_spec. user_kpoints_settings ([dict]): Additional user_kpoints_settings, which contains at at

      -
      least three elements, which is similar to user_incar_settings. For example, +

      least three elements, which is similar to user_incar_settings. For example, [{}, {}, {β€œgrid_density”: 100}] for the workflow from the parent structure relaxation, then the endpoint relaxation followed by one-round NEB simulation. -Default values depend on the selected VaspInputSet.

      -
      -
      additional_cust_args ([dict]): Optional parameters for RunVaspCustodian, same structure
      -
      with user_incar_settings and user_kpoints_settings.
      +Default values depend on the selected VaspInputSet.

      + +
      +
      additional_cust_args ([dict]): Optional parameters for RunVaspCustodian, same structure

      with user_incar_settings and user_kpoints_settings.

      +
      -
      Returns:
      -
      Workflow
      +
      Returns:

      Workflow

      +
      -atomate.vasp.workflows.base.neb.get_wf_neb_from_structure(structure, user_incar_settings=None, additional_spec=None, user_kpoints_settings=None, additional_cust_args=None)ΒΆ
      +atomate.vasp.workflows.base.neb.get_wf_neb_from_structure(structure, user_incar_settings=None, additional_spec=None, user_kpoints_settings=None, additional_cust_args=None)ΒΆ

      Obtain the CI-NEB workflow staring with a parent structure. This works only under the single vacancy diffusion mechanism.

      -
      -
      Workflow: (parent relaxation) –> Endpoints relaxation –> NEB_1 –> NEB_2 –> … –> NEB_r
      -
        -
      1. -
        If parent is not relaxed: then parent relaxation–ep–neb(r)
        -
        (r rounds of NEB)
        +
        +
        Workflow: (parent relaxation) –> Endpoints relaxation –> NEB_1 –> NEB_2 –> … –> NEB_r
          +
        1. +
          If parent is not relaxed: then parent relaxation–ep–neb(r)

          (r rounds of NEB)

          +
          2. -
        2. If parent is relaxed: ep–neb(r) (r rounds of NEB)
          3. +

        3. If parent is relaxed: ep–neb(r) (r rounds of NEB)

        -
        Args:
        -

        structure (Structure): The parent structure. +

        Args:

        structure (Structure): The parent structure. user_incar_settings([dict]): Additional user_incar_settings. Note that the order of the

        -
        list is set as: β€œparent”, β€œep_relax”, β€œneb1”, β€œneb2” etc., which contains +

        list is set as: β€œparent”, β€œep_relax”, β€œneb1”, β€œneb2” etc., which contains at least three elements. The first dict is for parent structure relaxation, the second dict is for endpoints relaxation, and the rest are for NEB calculations. For example, [{}, {}, {β€œIOPT”: 7}, {β€œIOPT”: 1}]. Besides, user_incar_settings is used to determine how many NEB rounds will be. Default -is [{}, {}, {}].

        +is [{}, {}, {}].

        +

        additional_spec (dict): User spec settings to overwrite default_spec. user_kpoints_settings ([dict]): Additional user_kpoints_settings, which contains at at

        -
        least three elements, which is similar to user_incar_settings. For example, +

        least three elements, which is similar to user_incar_settings. For example, [{}, {}, {β€œgrid_density”: 100}] for the workflow from the parent structure relaxation, then the endpoint relaxation followed by one-round NEB simulation. -Default values depend on the selected VaspInputSet.

        -
        -
        additional_cust_args ([dict]): Optional parameters for RunVaspCustodian, same structure
        -
        with user_incar_settings and user_kpoints_settings.
        +Default values depend on the selected VaspInputSet.

        + +
        +
        additional_cust_args ([dict]): Optional parameters for RunVaspCustodian, same structure

        with user_incar_settings and user_kpoints_settings.

        +
        -
        Returns:
        -
        Workflow
        +
        Returns:

        Workflow

        +
      @@ -643,28 +655,28 @@

      Submodules

      atomate.vasp.workflows.base.raman moduleΒΆ

      -atomate.vasp.workflows.base.raman.get_wf_raman_spectra(structure, modes=None, step_size=0.005, vasp_cmd='vasp', db_file=None)ΒΆ
      -
      -
      Raman susceptibility tensor workflow:
      -
      Calculation of phonon normal modes followed by the computation of dielectric tensor for +atomate.vasp.workflows.base.raman.get_wf_raman_spectra(structure, modes=None, step_size=0.005, vasp_cmd='vasp', db_file=None)ΒΆ +
      +
      Raman susceptibility tensor workflow:

      Calculation of phonon normal modes followed by the computation of dielectric tensor for structures displaced along the normal modes. Finally the dielectric tensors corresponding to each mode are used to compute the Raman susceptibility tensor using finite difference -(central difference scheme).

      -
      Args:
      -

      structure (Structure): Input structure. +(central difference scheme).

      +
      +
      Args:

      structure (Structure): Input structure. modes (tuple/list): list of modes for which the Raman spectra need to be calculated.

      -
      The default is to use all the 3N modes.
      -
      -
      step_size (float): site displacement along the normal mode in Angstroms. Used to compute
      -
      the finite difference(central difference scheme) first derivative of the dielectric -constant along the normal modes.
      +

      The default is to use all the 3N modes.

      +
      +
      +
      step_size (float): site displacement along the normal mode in Angstroms. Used to compute

      the finite difference(central difference scheme) first derivative of the dielectric +constant along the normal modes.

      +
      -

      vasp_cmd (str): vasp command to run. +

      vasp_cmd (str): vasp command to run. db_file (str): path to file containing the database credentials.

      -
      Returns:
      -
      Workflow
      +
      Returns:

      Workflow

      +
      @@ -673,12 +685,11 @@

      Submodules

      atomate.vasp.workflows.base.thermal_expansion moduleΒΆ

      -atomate.vasp.workflows.base.thermal_expansion.get_wf_thermal_expansion(structure, deformations, vasp_input_set=None, vasp_cmd='vasp', db_file=None, user_kpoints_settings=None, t_step=10, t_min=0, t_max=1000, mesh=(20, 20, 20), eos='vinet', pressure=0.0, tag=None)ΒΆ
      +atomate.vasp.workflows.base.thermal_expansion.get_wf_thermal_expansion(structure, deformations, vasp_input_set=None, vasp_cmd='vasp', db_file=None, user_kpoints_settings=None, t_step=10, t_min=0, t_max=1000, mesh=(20, 20, 20), eos='vinet', pressure=0.0, tag=None)ΒΆ

      Returns quasi-harmonic thermal expansion workflow. Note: phonopy package is required for the final analysis step.

      -
      -
      Args:
      -

      structure (Structure): input structure. +

      +
      Args:

      structure (Structure): input structure. deformations (list): list of deformation matrices(list of lists). vasp_input_set (VaspInputSet) vasp_cmd (str): vasp command to run. @@ -690,15 +701,17 @@

      Submodules -
      will be assigned.
      +
      +

      will be assigned.

      +
      +

      +
      Returns:

      Workflow

      -
      Returns:
      -
      Workflow
      @@ -742,13 +755,11 @@

      This Page

      @@ -766,13 +777,13 @@

      Navigation

    33. modules |
      34. -
    34. atomate 0.9.1 documentation »
      35. +
    35. atomate 0.9.2 documentation »
      36. diff --git a/docs/atomate.vasp.workflows.html b/docs/atomate.vasp.workflows.html index ddd63178c..61b728b9b 100644 --- a/docs/atomate.vasp.workflows.html +++ b/docs/atomate.vasp.workflows.html @@ -1,18 +1,17 @@ - + - - - atomate.vasp.workflows package — atomate 0.9.1 documentation + + atomate.vasp.workflows package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

      Navigation

    36. modules |
      37. -
    37. atomate 0.9.1 documentation »
      38. +
    38. atomate 0.9.2 documentation »
      39. @@ -111,13 +110,11 @@

      This Page

      @@ -135,13 +132,13 @@

      Navigation

    39. modules |
      40. -
    40. atomate 0.9.1 documentation »
      41. +
    41. atomate 0.9.2 documentation »
      42. diff --git a/docs/atomate.vasp.workflows.presets.html b/docs/atomate.vasp.workflows.presets.html index bc9714756..e786733df 100644 --- a/docs/atomate.vasp.workflows.presets.html +++ b/docs/atomate.vasp.workflows.presets.html @@ -1,18 +1,17 @@ - + - - - atomate.vasp.workflows.presets package — atomate 0.9.1 documentation + + atomate.vasp.workflows.presets package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

      Navigation

    42. modules |
      43. -
    43. atomate 0.9.1 documentation »
      44. +
    44. atomate 0.9.2 documentation »
      45. @@ -46,162 +45,160 @@

      Submodules

      atomate.vasp.workflows.presets.core moduleΒΆ

      -atomate.vasp.workflows.presets.core.wf_bandstructure(structure, c=None)ΒΆ
      +atomate.vasp.workflows.presets.core.wf_bandstructure(structure, c=None)ΒΆ
      -atomate.vasp.workflows.presets.core.wf_bandstructure_hse(structure, c=None)ΒΆ
      +atomate.vasp.workflows.presets.core.wf_bandstructure_hse(structure, c=None)ΒΆ
      -atomate.vasp.workflows.presets.core.wf_bandstructure_no_opt(structure, c=None)ΒΆ
      +atomate.vasp.workflows.presets.core.wf_bandstructure_no_opt(structure, c=None)ΒΆ
      -atomate.vasp.workflows.presets.core.wf_bandstructure_plus_boltztrap(structure, c=None)ΒΆ
      +atomate.vasp.workflows.presets.core.wf_bandstructure_plus_boltztrap(structure, c=None)ΒΆ
      -atomate.vasp.workflows.presets.core.wf_bandstructure_plus_hse(structure, gap_only=True, c=None)ΒΆ
      +atomate.vasp.workflows.presets.core.wf_bandstructure_plus_hse(structure, gap_only=True, c=None)ΒΆ
      -atomate.vasp.workflows.presets.core.wf_bulk_modulus(structure, c=None)ΒΆ
      +atomate.vasp.workflows.presets.core.wf_bulk_modulus(structure, c=None)ΒΆ

      Bulk modulus workflow from the given structure and config dict.

      -
      -
      Args:
      -
      structure (Structure): input structure -c (dict): workflow config dict
      -
      Returns:
      -
      Workflow
      +
      +
      Args:

      structure (Structure): input structure +c (dict): workflow config dict

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.workflows.presets.core.wf_dielectric_constant(structure, c=None)ΒΆ
      +atomate.vasp.workflows.presets.core.wf_dielectric_constant(structure, c=None)ΒΆ
      -atomate.vasp.workflows.presets.core.wf_dielectric_constant_no_opt(structure, c=None)ΒΆ
      +atomate.vasp.workflows.presets.core.wf_dielectric_constant_no_opt(structure, c=None)ΒΆ
      -atomate.vasp.workflows.presets.core.wf_elastic_constant(structure, c=None, order=2, sym_reduce=False)ΒΆ
      +atomate.vasp.workflows.presets.core.wf_elastic_constant(structure, c=None, order=2, sym_reduce=False)ΒΆ
      -atomate.vasp.workflows.presets.core.wf_elastic_constant_minimal(structure, c=None, order=2, sym_reduce=True)ΒΆ
      +atomate.vasp.workflows.presets.core.wf_elastic_constant_minimal(structure, c=None, order=2, sym_reduce=True)ΒΆ
      -atomate.vasp.workflows.presets.core.wf_gibbs_free_energy(structure, c=None)ΒΆ
      +atomate.vasp.workflows.presets.core.wf_gibbs_free_energy(structure, c=None)ΒΆ

      Gibbs free energy workflow from the given structure and config dict.

      -
      -
      Args:
      -
      structure (Structure): input structure -c (dict): workflow config dict
      -
      Returns:
      -
      Workflow
      +
      +
      Args:

      structure (Structure): input structure +c (dict): workflow config dict

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.workflows.presets.core.wf_nmr(structure, c=None)ΒΆ
      +atomate.vasp.workflows.presets.core.wf_nmr(structure, c=None)ΒΆ
      -atomate.vasp.workflows.presets.core.wf_nudged_elastic_band(structures, parent, c=None)ΒΆ
      +atomate.vasp.workflows.presets.core.wf_nudged_elastic_band(structures, parent, c=None)ΒΆ

      Nudged elastic band (NEB) workflow from the given structures and config dict.

      β€˜is_optimized’ default False β€˜neb_round’ default 1

      -
      -
      Notes:
      -

      Length of Structure list and β€œis_optimized” are used to determine the workflow: +

      +
      Notes:

      Length of Structure list and β€œis_optimized” are used to determine the workflow: 1 structure # The parent structure & two endpoint indexes provided; need relaxation.

      -
      # The parent structure & two endpoint indexes provided; no need to relax.
      -
      -
      2 structures # Two endpoints provided; need to relax two endpoints.
      -
      # Two relaxed endpoints provided; no need to relax two endpoints.
      +

      # The parent structure & two endpoint indexes provided; no need to relax.

      +
      +
      +
      2 structures # Two endpoints provided; need to relax two endpoints.

      # Two relaxed endpoints provided; no need to relax two endpoints.

      +
      -

      >=3 structures # All images including two endpoints are provided.

      +

      >=3 structures # All images including two endpoints are provided.

      -
      Args:
      -
      -
      structures ([Structure]):
      -
        -
      1. The parent structure
        2. -
      2. Two endpoint structures
        3. -
      3. An initial NEB path that comprises both images and endpoints
        4. +
        Args:
        +
        structures ([Structure]):
          +

        1. The parent structure

          2. +

        2. Two endpoint structures

          3. +

        3. An initial NEB path that comprises both images and endpoints

        parent (Structure): parent structure used to get two endpoints. c (dict): workflow config dict, basic format:

        -
        -
        -
        {β€œfireworks”: [], β€œcommon_params”: {}, β€œadditional_ep_params”: {},
        -
        β€œadditional_neb_params”: {}}. When the length of structures is 1, β€œsite_indices” key +
        +
        +
        {β€œfireworks”: [], β€œcommon_params”: {}, β€œadditional_ep_params”: {},

        β€œadditional_neb_params”: {}}. When the length of structures is 1, β€œsite_indices” key must be included in c. Note that β€œfireworks” is a list corresponding to the order of -execution.

        +execution.

        +
        -
        Returns:
        -
        Workflow
        +
        Returns:

        Workflow

        +
      -atomate.vasp.workflows.presets.core.wf_piezoelectric_constant(structure, c=None)ΒΆ
      +atomate.vasp.workflows.presets.core.wf_piezoelectric_constant(structure, c=None)ΒΆ
      -atomate.vasp.workflows.presets.core.wf_raman_spectra(structure, c=None)ΒΆ
      +atomate.vasp.workflows.presets.core.wf_raman_spectra(structure, c=None)ΒΆ

      Raman spectra workflow from the given structure and config dict

      -
      -
      Args:
      -
      structure (Structure): input structure -c (dict): workflow config dict
      -
      Returns:
      -
      Workflow
      +
      +
      Args:

      structure (Structure): input structure +c (dict): workflow config dict

      +
      +
      Returns:

      Workflow

      +
      -atomate.vasp.workflows.presets.core.wf_static(structure, c=None)ΒΆ
      +atomate.vasp.workflows.presets.core.wf_static(structure, c=None)ΒΆ
      -atomate.vasp.workflows.presets.core.wf_structure_optimization(structure, c=None)ΒΆ
      +atomate.vasp.workflows.presets.core.wf_structure_optimization(structure, c=None)ΒΆ
      -atomate.vasp.workflows.presets.core.wf_thermal_expansion(structure, c=None)ΒΆ
      +atomate.vasp.workflows.presets.core.wf_thermal_expansion(structure, c=None)ΒΆ

      Thermal expansion coefficient workflow from the given structure and config dict.

      -
      -
      Args:
      -
      structure (Structure): input structure -c (dict): workflow config dict
      -
      Returns:
      -
      Workflow
      +
      +
      Args:

      structure (Structure): input structure +c (dict): workflow config dict

      +
      +
      Returns:

      Workflow

      +
      @@ -210,7 +207,7 @@

      Submodules

      atomate.vasp.workflows.presets.scan moduleΒΆ

      -atomate.vasp.workflows.presets.scan.wf_scan_opt(structure, c=None)ΒΆ
      +atomate.vasp.workflows.presets.scan.wf_scan_opt(structure, c=None)ΒΆ
      @@ -244,13 +241,11 @@

      This Page

      @@ -268,13 +263,13 @@

      Navigation

    45. modules |
      46. -
    46. atomate 0.9.1 documentation »
      47. +
    47. atomate 0.9.2 documentation »
      48. diff --git a/docs/atomate.vasp.workflows.tests.html b/docs/atomate.vasp.workflows.tests.html index d6b2b0628..458b04307 100644 --- a/docs/atomate.vasp.workflows.tests.html +++ b/docs/atomate.vasp.workflows.tests.html @@ -1,18 +1,17 @@ - + - - - atomate.vasp.workflows.tests package — atomate 0.9.1 documentation + + atomate.vasp.workflows.tests package — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

      Navigation

    48. modules |
      49. -
    49. atomate 0.9.1 documentation »
      50. +
    50. atomate 0.9.2 documentation »
      51. @@ -46,28 +45,28 @@

      Submodules

      atomate.vasp.workflows.tests.test_adsorbate_workflow moduleΒΆ

      -class atomate.vasp.workflows.tests.test_adsorbate_workflow.TestAdsorptionWorkflow(methodName='runTest')ΒΆ
      +class atomate.vasp.workflows.tests.test_adsorbate_workflow.TestAdsorptionWorkflow(methodName='runTest')ΒΆ

      Bases: atomate.utils.testing.AtomateTest

      -setUp()ΒΆ
      +setUp()ΒΆ

      Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

      -test_input_sets()ΒΆ
      +test_input_sets()ΒΆ
      -test_wf()ΒΆ
      +test_wf()ΒΆ
      -test_wf_functions()ΒΆ
      +test_wf_functions()ΒΆ
      @@ -77,7 +76,7 @@

      Submodules

      atomate.vasp.workflows.tests.test_bulk_modulus_workflow moduleΒΆ

      -class atomate.vasp.workflows.tests.test_bulk_modulus_workflow.TestBulkModulusWorkflow(methodName='runTest')ΒΆ
      +class atomate.vasp.workflows.tests.test_bulk_modulus_workflow.TestBulkModulusWorkflow(methodName='runTest')ΒΆ

      Bases: atomate.utils.testing.AtomateTest

      This test will either actually run VASP (if VASP_CMD is set) or artificially pass on outputs (if not VASP_CMD) and test the whole bulk modulus workflow and its implementation and outputs @@ -86,34 +85,35 @@

      Submodules -
    51. -
      once task.json is present, VaspRun can be skipped where task.json is
      -
      available and their β€œinputs” and β€œoutputs” folders can be removed
      +
    52. +
      once task.json is present, VaspRun can be skipped where task.json is

      available and their β€œinputs” and β€œoutputs” folders can be removed

      +

    -setUp()ΒΆ
    +setUp()ΒΆ

    Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

    -setup_task_docs()ΒΆ
    +setup_task_docs()ΒΆ
    -test_wf()ΒΆ
    +test_wf()ΒΆ
    -write_task_docs()ΒΆ
    +write_task_docs()ΒΆ
    @@ -123,18 +123,18 @@

    Submodules

    atomate.vasp.workflows.tests.test_elastic_workflow moduleΒΆ

    -class atomate.vasp.workflows.tests.test_elastic_workflow.TestElasticWorkflow(methodName='runTest')ΒΆ
    +class atomate.vasp.workflows.tests.test_elastic_workflow.TestElasticWorkflow(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -setUp()ΒΆ
    +setUp()ΒΆ

    Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

    -test_wf()ΒΆ
    +test_wf()ΒΆ
    @@ -144,23 +144,23 @@

    Submodules

    atomate.vasp.workflows.tests.test_ferroelectric_workflow moduleΒΆ

    -class atomate.vasp.workflows.tests.test_ferroelectric_workflow.TestFerroelectricWorkflow(methodName='runTest')ΒΆ
    +class atomate.vasp.workflows.tests.test_ferroelectric_workflow.TestFerroelectricWorkflow(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -setUp()ΒΆ
    +setUp()ΒΆ

    Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

    -test_wf()ΒΆ
    +test_wf()ΒΆ
    -untarTestFiles()ΒΆ
    +untarTestFiles()ΒΆ
    @@ -170,27 +170,27 @@

    Submodules

    atomate.vasp.workflows.tests.test_magnetism_workflow moduleΒΆ

    -class atomate.vasp.workflows.tests.test_magnetism_workflow.TestMagneticDeformationWorkflow(methodName='runTest')ΒΆ
    +class atomate.vasp.workflows.tests.test_magnetism_workflow.TestMagneticDeformationWorkflow(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -test_analysis()ΒΆ
    +test_analysis()ΒΆ
    -class atomate.vasp.workflows.tests.test_magnetism_workflow.TestMagneticOrderingsWorkflow(methodName='runTest')ΒΆ
    +class atomate.vasp.workflows.tests.test_magnetism_workflow.TestMagneticOrderingsWorkflow(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -test_analysis()ΒΆ
    +test_analysis()ΒΆ
    -test_ordering_enumeration()ΒΆ
    +test_ordering_enumeration()ΒΆ
    @@ -200,20 +200,20 @@

    Submodules

    atomate.vasp.workflows.tests.test_neb_workflow moduleΒΆ

    -class atomate.vasp.workflows.tests.test_neb_workflow.TestNudgedElasticBandWorkflow(methodName='runTest')ΒΆ
    +class atomate.vasp.workflows.tests.test_neb_workflow.TestNudgedElasticBandWorkflow(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -setUp()ΒΆ
    +setUp()ΒΆ
      -
    1. Basic check for pymatgen configurations.
      2. -
    2. Setup all test workflow.
      3. +

    3. Basic check for pymatgen configurations.

      4. +

    4. Setup all test workflow.

    -test_wf()ΒΆ
    +test_wf()ΒΆ
    @@ -223,21 +223,21 @@

    Submodules

    atomate.vasp.workflows.tests.test_nmr moduleΒΆ

    -class atomate.vasp.workflows.tests.test_nmr.TestNMRWorkflow(methodName='runTest')ΒΆ
    +class atomate.vasp.workflows.tests.test_nmr.TestNMRWorkflow(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    This test will either actually run VASP (if VASP_CMD is set) or artificially pass on outputs (if not VASP_CMD) and test the NMR workflow and its implementation and outputs for an example calculation for LiAlSiO4.

    -setUp()ΒΆ
    +setUp()ΒΆ

    Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

    -test_wf()ΒΆ
    +test_wf()ΒΆ
    @@ -247,18 +247,18 @@

    Submodules

    atomate.vasp.workflows.tests.test_raman_workflow moduleΒΆ

    -class atomate.vasp.workflows.tests.test_raman_workflow.TestRamanWorkflow(methodName='runTest')ΒΆ
    +class atomate.vasp.workflows.tests.test_raman_workflow.TestRamanWorkflow(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -setUp()ΒΆ
    +setUp()ΒΆ

    Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

    -test_wf()ΒΆ
    +test_wf()ΒΆ
    @@ -268,48 +268,48 @@

    Submodules

    atomate.vasp.workflows.tests.test_vasp_workflows moduleΒΆ

    -class atomate.vasp.workflows.tests.test_vasp_workflows.TestVaspWorkflows(methodName='runTest')ΒΆ
    +class atomate.vasp.workflows.tests.test_vasp_workflows.TestVaspWorkflows(methodName='runTest')ΒΆ

    Bases: atomate.utils.testing.AtomateTest

    -setUp()ΒΆ
    +setUp()ΒΆ

    Create scratch directory(removes the old one if there is one) and change to it. Also initialize launchpad.

    -test_bandgap_check_Vasp()ΒΆ
    +test_bandgap_check_Vasp()ΒΆ
    -test_bandstructure_Vasp()ΒΆ
    +test_bandstructure_Vasp()ΒΆ
    -test_chgcar_db_read()ΒΆ
    +test_chgcar_db_read()ΒΆ
    -test_chgcar_db_read_write()ΒΆ
    +test_chgcar_db_read_write()ΒΆ
    -test_single_Vasp()ΒΆ
    +test_single_Vasp()ΒΆ
    -test_single_Vasp_dbinsertion()ΒΆ
    +test_single_Vasp_dbinsertion()ΒΆ
    -test_trackers()ΒΆ
    +test_trackers()ΒΆ
    @@ -352,13 +352,11 @@

    This Page

    @@ -376,13 +374,13 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/builders.html b/docs/builders.html index be5cb48f9..a37524652 100644 --- a/docs/builders.html +++ b/docs/builders.html @@ -1,18 +1,17 @@ - + - - - Builders — atomate 0.9.1 documentation + + Builders — atomate 0.9.2 documentation + @@ -36,7 +35,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -59,22 +58,22 @@

    Introduction +
    Build process -

    Diagram of the build process, which collects lower-level information such as tasks and organizes it into higher-level collections like materials.

    +

    Diagram of the build process, which collects lower-level information such as tasks and organizes it into higher-level collections like materials.ΒΆ

    The core builder: TasksMaterialsBuilderΒΆ

    The core builder of atomate is TasksMaterialsBuilder. This builder will:

      -
    • automatically determine which tasks are on the same material using pymatgen’s StructureMatcher
      • -
    • collect together basic data from all those tasks into a single document that is stored in a new collection called β€œmaterials”.
      • +

    • automatically determine which tasks are on the same material using pymatgen’s StructureMatcher

      • +

    • collect together basic data from all those tasks into a single document that is stored in a new collection called β€œmaterials”.

    This core builder is one of the more complex builders because it needs to decide things like:

      -
    • what kinds of calculations should be considered as possible new materials? (for example, in general one would not like to consider a small deformation calculation performed for the purpose of elastic tensor calculation to be different β€œmaterial” than its parent)
      • -
    • if there are multiple calculation types that give different values of the same property for a single material, which calculation should be trusted?
      • -
    • how can we decide if two calculations are on the same material?
      • +

    • what kinds of calculations should be considered as possible new materials? (for example, in general one would not like to consider a small deformation calculation performed for the purpose of elastic tensor calculation to be different β€œmaterial” than its parent)

      • +

    • if there are multiple calculation types that give different values of the same property for a single material, which calculation should be trusted?

      • +

    • how can we decide if two calculations are on the same material?

    However, this is the β€œcore” builder because it begins the process of collecting together data from individual calculations and creating a single materials-centric report.

    @@ -124,13 +123,11 @@

    This Page

    @@ -154,13 +151,13 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/changelog.html b/docs/changelog.html index 7c116d02e..5f610a1e6 100644 --- a/docs/changelog.html +++ b/docs/changelog.html @@ -1,18 +1,17 @@ - + - - - atomate Changelog — atomate 0.9.1 documentation + + atomate Changelog — atomate 0.9.2 documentation + @@ -36,7 +35,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -47,293 +46,297 @@

    Navigation

    atomate ChangelogΒΆ

    +

    v0.9.2

    +
      +

    • fix CalcDB authentication issue (M. Bercx)

      • +

    v0.9.1

      -
    • bugfix: vasp_input_set_params –> vasp_input_params in some cases (thanks to M. Horton for pointing out)
      • -
    • add ability to put mongoclient_kwargs in CalcDB creds file (thanks to S. Torissi for pointing out the feature request)
      • +

    • bugfix: vasp_input_set_params –> vasp_input_params in some cases (thanks to M. Horton for pointing out)

      • +

    • add ability to put mongoclient_kwargs in CalcDB creds file (thanks to S. Torissi for pointing out the feature request)

    v0.9.0

      -
    • better error message (L. Ward)
      • -
    • Fix db authentication issue in v0.8.9 (M. Siron)
      • -
    • Change default vasp_cmd and db_file to those in config.py (M. Horton)
      • -
    • update plots in docs (A. Ganose)
      • +

    • better error message (L. Ward)

      • +

    • Fix db authentication issue in v0.8.9 (M. Siron)

      • +

    • Change default vasp_cmd and db_file to those in config.py (M. Horton)

      • +

    • update plots in docs (A. Ganose)

    v0.8.9

    -

    Caution

    -

    this version introduced a quirk in the db authentication scheme, you might need to set authsource manually or update to v0.9.0

    +

    Caution

    +

    this version introduced a quirk in the db authentication scheme, you might need to set authsource manually or update to v0.9.0

      -
    • fix NSCF run kpoint mesh and Boltztrap workflow to reflect pymatgen updates (A. Ganose)
      • -
    • allow β€œauthsource” parameter in db.json files (A. Jain)
      • -
    • add powerup for turning off gzip (D. Broberg)
      • +

    • fix NSCF run kpoint mesh and Boltztrap workflow to reflect pymatgen updates (A. Ganose)

      • +

    • allow β€œauthsource” parameter in db.json files (A. Jain)

      • +

    • add powerup for turning off gzip (D. Broberg)

    v0.8.8

      -
    • magnetic ordering workflows (M. Horton)
      • -
    • better checks for AECAR storage (J. Shen)
      • -
    • update VASP NCF set NEDOS (M. Dylla)
      • +

    • magnetic ordering workflows (M. Horton)

      • +

    • better checks for AECAR storage (J. Shen)

      • +

    • update VASP NCF set NEDOS (M. Dylla)

    v0.8.7

      -
    • store custodian data in its own key in FWAction (E. Sivonxay)
      • +

    • store custodian data in its own key in FWAction (E. Sivonxay)

    v0.8.6

      -
    • add bandstructure no-opt workflow preset (A. Ganose)
      • +

    • add bandstructure no-opt workflow preset (A. Ganose)

    v0.8.5

      -
    • add NMR workflow (S. Dwaraknath)
      • -
    • surface workflow refactor (J. Montoya)
      • -
    • update elasticity package for latest pymatgen (J. Montoya)
      • +

    • add NMR workflow (S. Dwaraknath)

      • +

    • surface workflow refactor (J. Montoya)

      • +

    • update elasticity package for latest pymatgen (J. Montoya)

    v0.8.4

      -
    • add some QChem functionality! (S. Blau, E. Spotte-Smith)
      • -
    • better credential parsing in CalcDB (A. Rutt)
      • -
    • update paramiko for better security (A. Jain)
      • -
    • add tasks_settings.yaml to site-packages (A. Jain)
      • +

    • add some QChem functionality! (S. Blau, E. Spotte-Smith)

      • +

    • better credential parsing in CalcDB (A. Rutt)

      • +

    • update paramiko for better security (A. Jain)

      • +

    • add tasks_settings.yaml to site-packages (A. Jain)

    v0.8.3

      -
    • add CHGCAR and AECAR storage options (J. Shen)
      • +

    • add CHGCAR and AECAR storage options (J. Shen)

    v0.8.2

      -
    • various requirement updates, code refactorings, and bug fixes especially in Qchem and LAMMPs packages (S. Blau)
      • +

    • various requirement updates, code refactorings, and bug fixes especially in Qchem and LAMMPs packages (S. Blau)

    v0.8.1

      -
    • add Bader charge parsing (S. Dwaraknath)
      • -
    • parse_outputs can push fields to new FWS (S. Dwaraknath)
      • -
    • minor bug fix (S. Torrisi)
      • -
    • some testing updates (A. Faghaninia, S. Blau)
      • +

    • add Bader charge parsing (S. Dwaraknath)

      • +

    • parse_outputs can push fields to new FWS (S. Dwaraknath)

      • +

    • minor bug fix (S. Torrisi)

      • +

    • some testing updates (A. Faghaninia, S. Blau)

    v0.7.9

      -
    • Overhaul and update of QChem in atomate (B. Wood, S. Blau)
      • -
    • Fix integration tests (A. Dunn)
      • -
    • Stop officially supporting Py2
      • +

    • Overhaul and update of QChem in atomate (B. Wood, S. Blau)

      • +

    • Fix integration tests (A. Dunn)

      • +

    • Stop officially supporting Py2

    v0.7.8

      -
    • some QChem tasks and workflows (B. Wood)
      • -
    • add full HSE band structure workflow (A. Jain)
      • +

    • some QChem tasks and workflows (B. Wood)

      • +

    • add full HSE band structure workflow (A. Jain)

    v0.7.7

      -
    • allow list of ErrorHandler in RunVaspCustodian (A. Jain)
      • -
    • fix adsorption unit test (J. Montoya)
      • +

    • allow list of ErrorHandler in RunVaspCustodian (A. Jain)

      • +

    • fix adsorption unit test (J. Montoya)

    v0.7.6

      -
    • remove force checking in drone (S. Dwaraknath)
      • -
    • cleanups to DOS + BS parsing and insertion in GridFS (S. Dwaraknath)
      • -
    • code cleanup and bugfixes (S. Dwaraknath, specter119)
      • -
    • some more docs on offline mode (A. Jain)
      • +

    • remove force checking in drone (S. Dwaraknath)

      • +

    • cleanups to DOS + BS parsing and insertion in GridFS (S. Dwaraknath)

      • +

    • code cleanup and bugfixes (S. Dwaraknath, specter119)

      • +

    • some more docs on offline mode (A. Jain)

    v0.7.5

      -
    • standardize drones to datetime.utcnow() (J. Montoya)
      • -
    • fixed additional field serialization issue (J. Montoya)
      • -
    • fix defuse_unsuccessful logic, hat tip to @specter119 for pointing it out (A. Jain)
      • -
    • some doc updates (A. Jain)
      • +

    • standardize drones to datetime.utcnow() (J. Montoya)

      • +

    • fixed additional field serialization issue (J. Montoya)

      • +

    • fix defuse_unsuccessful logic, hat tip to @specter119 for pointing it out (A. Jain)

      • +

    • some doc updates (A. Jain)

    v0.7.4

      -
    • fix pymatgen dep (A. Jain)
      • +

    • fix pymatgen dep (A. Jain)

    v0.7.3

      -
    • minor drones updates (S. Dwaraknath)
      • -
    • installation fix (P. Huck)
      • +

    • minor drones updates (S. Dwaraknath)

      • +

    • installation fix (P. Huck)

    v0.7.2

      -
    • Bugfix database getter in builders (S. Dwaraknath)
      • +

    • Bugfix database getter in builders (S. Dwaraknath)

    v0.7.1

      -
    • update atwf to find the path to workflows better (M. Dias Costa)
      • -
    • better surface workflow naming (A. Jain)
      • +

    • update atwf to find the path to workflows better (M. Dias Costa)

      • +

    • better surface workflow naming (A. Jain)

    v0.7.0

      -
    • change default behavior when a run looks OK but is unconverged (A. Jain)
      • -
    • Some test and code cleanups (S. Dwaraknath, J. Montoya)
      • -
    • update to FW names when no structure provided (S. Dwaraknath)
      • -
    • remove boltons dependency (A. Faghaninia)
      • -
    • fix max_force check for selective dynamics (J. Montoya)
      • +

    • change default behavior when a run looks OK but is unconverged (A. Jain)

      • +

    • Some test and code cleanups (S. Dwaraknath, J. Montoya)

      • +

    • update to FW names when no structure provided (S. Dwaraknath)

      • +

    • remove boltons dependency (A. Faghaninia)

      • +

    • fix max_force check for selective dynamics (J. Montoya)

    v0.6.9

      -
    • update requirements to include boltons
      • -
    • bugfix for atwf (S. Dwaraknath)
      • +

    • update requirements to include boltons

      • +

    • bugfix for atwf (S. Dwaraknath)

    v0.6.8

      -
    • New SCAN functional workflow (S. Dwaraknath)
      • -
    • remove dependence on pymatgen-db (S. Dwaraknath)
      • -
    • more bandgap properties parsed by drone (transition and is-direct) (S. Dwaraknath)
      • -
    • option to clean up large output files like WAVECAR (S. Dwaraknath)
      • -
    • option to recursively copy file tree in CopyFilesFromCalcLoc (A. Faghaninia)
      • -
    • bugfix: apply vasp_input_set_params when StaticFW have parents (specter119)
      • -
    • misc bugfixes (S. Dwaraknath, A. Jain)
      • +

    • New SCAN functional workflow (S. Dwaraknath)

      • +

    • remove dependence on pymatgen-db (S. Dwaraknath)

      • +

    • more bandgap properties parsed by drone (transition and is-direct) (S. Dwaraknath)

      • +

    • option to clean up large output files like WAVECAR (S. Dwaraknath)

      • +

    • option to recursively copy file tree in CopyFilesFromCalcLoc (A. Faghaninia)

      • +

    • bugfix: apply vasp_input_set_params when StaticFW have parents (specter119)

      • +

    • misc bugfixes (S. Dwaraknath, A. Jain)

    v0.6.7

      -
    • New ferroelectrics workflow! (T. Smidt)
      • -
    • option to parse LOCPOT in VaspDrone (S. Dwaraknath)
      • -
    • rename set_fworker -> set_execution_option
      • -
    • more options for BoltztrapFW (A. Faghaninia)
      • -
    • misc. bugfixes (D. Broberg, K. Mathew, P. Huck)
      • +

    • New ferroelectrics workflow! (T. Smidt)

      • +

    • option to parse LOCPOT in VaspDrone (S. Dwaraknath)

      • +

    • rename set_fworker -> set_execution_option

      • +

    • more options for BoltztrapFW (A. Faghaninia)

      • +

    • misc. bugfixes (D. Broberg, K. Mathew, P. Huck)

    v0.6.6

      -
    • powerup to preserve the same FWorker for all jobs in workflow (S. Dwaraknath)
      • -
    • DriftErrorHandler in VASP custodian jobs (S. Dwaraknath)
      • -
    • some FireTasks in anticipation of ferroelectrics workflow (T. Schmidt, A. Jain)
      • +

    • powerup to preserve the same FWorker for all jobs in workflow (S. Dwaraknath)

      • +

    • DriftErrorHandler in VASP custodian jobs (S. Dwaraknath)

      • +

    • some FireTasks in anticipation of ferroelectrics workflow (T. Schmidt, A. Jain)

    v0.6.5

      -
    • fix delta_volume_percent, set as new key and update FixTasksBuilder (B. Bocklund, A. Jain)
      • -
    • drone schema version reflects atomate version (M. Horton)
      • -
    • unit test fix (J. Montoya)
      • +

    • fix delta_volume_percent, set as new key and update FixTasksBuilder (B. Bocklund, A. Jain)

      • +

    • drone schema version reflects atomate version (M. Horton)

      • +

    • unit test fix (J. Montoya)

    v0.6.4

      -
    • add config option for half_kpts_first and max force (A. Jain, S. Dwaraknath)
      • -
    • better logic for band structure parsing (S. Dwaraknath)
      • -
    • misc bugfix (P. Huck)
      • +

    • add config option for half_kpts_first and max force (A. Jain, S. Dwaraknath)

      • +

    • better logic for band structure parsing (S. Dwaraknath)

      • +

    • misc bugfix (P. Huck)

    v0.6.3

      -
    • fix Gibbs wf db insertion (A. Dunn, K. Mathew)
      • -
    • minor doc updates & fixes (A. Jain)
      • +

    • fix Gibbs wf db insertion (A. Dunn, K. Mathew)

      • +

    • minor doc updates & fixes (A. Jain)

    v0.6.2

      -
    • Fix LepsFW after prev refactor (A. Jain)
      • -
    • Doc improvements (A. Jain, B. Bocklund)
      • +

    • Fix LepsFW after prev refactor (A. Jain)

      • +

    • Doc improvements (A. Jain, B. Bocklund)

    v0.6.1

      -
    • many improvements to documentation (A. Jain, B. Bocklund)
      • -
    • add DFPTFW (K. Mathew)
      • -
    • simplify LepsFW - move Raman into RamanFW (K. Mathew)
      • -
    • copy piezo tensor to output (S. Dwaraknath)
      • +

    • many improvements to documentation (A. Jain, B. Bocklund)

      • +

    • add DFPTFW (K. Mathew)

      • +

    • simplify LepsFW - move Raman into RamanFW (K. Mathew)

      • +

    • copy piezo tensor to output (S. Dwaraknath)

    v0.6.0

      -
    • Gibbs preset workflow and anharmonic contributions (B. Bocklund)
      • -
    • improvements to packmol workflow (K. Mathew)
      • -
    • modify_potcar powerup (J. Montoya)
      • -
    • more metadata in some analysis collections (B. Bocklund)
      • -
    • ability to specify common params in atwf (A. Jain)
      • -
    • allow powerups in atwf (J. Montoya)
      • -
    • many improvements to builders performance (A. Jain)
      • -
    • updates and fixes to installation tutorial (A. Jain, B. Bocklund)
      • -
    • unit testing updates (J. Montoya)
      • -
    • misc fixes …
      • +

    • Gibbs preset workflow and anharmonic contributions (B. Bocklund)

      • +

    • improvements to packmol workflow (K. Mathew)

      • +

    • modify_potcar powerup (J. Montoya)

      • +

    • more metadata in some analysis collections (B. Bocklund)

      • +

    • ability to specify common params in atwf (A. Jain)

      • +

    • allow powerups in atwf (J. Montoya)

      • +

    • many improvements to builders performance (A. Jain)

      • +

    • updates and fixes to installation tutorial (A. Jain, B. Bocklund)

      • +

    • unit testing updates (J. Montoya)

      • +

    • misc fixes …

    v0.5.8

      -
    • major improvements to LAMMPS workflow (B. Wood, K. Mathew)
      • -
    • doc updates (B. Bocklund)
      • -
    • minor cleanups (K. Mathew)
      • +

    • major improvements to LAMMPS workflow (B. Wood, K. Mathew)

      • +

    • doc updates (B. Bocklund)

      • +

    • minor cleanups (K. Mathew)

    v0.5.7

      -
    • VASP drone stores original inputs (S. Dwaraknath)
      • -
    • updates to EELS workflow (K. Mathew)
      • -
    • misc cleanups (A. Jain, S.P. Ong, K. Mathew)
      • +

    • VASP drone stores original inputs (S. Dwaraknath)

      • +

    • updates to EELS workflow (K. Mathew)

      • +

    • misc cleanups (A. Jain, S.P. Ong, K. Mathew)

    v0.5.6

      -
    • major improvements to elastic tensor calculations and compatibility with latest pymatgen (J. Montoya, K. Mathew)
      • +

    • major improvements to elastic tensor calculations and compatibility with latest pymatgen (J. Montoya, K. Mathew)

    v0.5.5

      -
    • remove PyPI download size by an order of magnitude
      • +

    • remove PyPI download size by an order of magnitude

    v0.5.4

      -
    • re-attempt to fix packaging of YAML workflow library in pip
      • +

    • re-attempt to fix packaging of YAML workflow library in pip

    v0.5.3

      -
    • attempt to fix packaging of YAML workflow library in pip
      • -
    • update doc links
      • +

    • attempt to fix packaging of YAML workflow library in pip

      • +

    • update doc links

    v0.5.2

      -
    • band gap estimation builder based on dielectric constants
      • -
    • clean up pypi packaging (S.P. Ong)
      • -
    • link to new doc links
      • -
    • misc bugfixes and workflow settings update/fixes (K. Mathew, A. Jain)
      • +

    • band gap estimation builder based on dielectric constants

      • +

    • clean up pypi packaging (S.P. Ong)

      • +

    • link to new doc links

      • +

    • misc bugfixes and workflow settings update/fixes (K. Mathew, A. Jain)

    v0.5.1

      -
    • use ruamel instead of pyyaml (S.P. Ong)
      • -
    • add magnetic moment parsing of output (M.K. Horton)
      • -
    • misc cleanups, bug fixes, doc improvements (K. Matthew, S. Dwaraknath, A. Jain)
      • +

    • use ruamel instead of pyyaml (S.P. Ong)

      • +

    • add magnetic moment parsing of output (M.K. Horton)

      • +

    • misc cleanups, bug fixes, doc improvements (K. Matthew, S. Dwaraknath, A. Jain)

    v0.5.0

    -

    Caution

    -

    pymatgen has updated its default kpoint scheme! Kpoint settings will change.

    +

    Caution

    +

    pymatgen has updated its default kpoint scheme! Kpoint settings will change.

      -
    • migration to new pymatgen and new kpoint settings
      • -
    • much improved docs (B. Bocklund, A. Jain)
      • -
    • major code cleanup (J. Montoya, K. Mathew, A. Jain)
      • -
    • many unit test updates (A. Faghaninia, H. Tang, S.P. Ong, A. Jain)
      • -
    • fix automated testing on pull requests (K. Mathew)
      • -
    • misc fixes
      • +

    • migration to new pymatgen and new kpoint settings

      • +

    • much improved docs (B. Bocklund, A. Jain)

      • +

    • major code cleanup (J. Montoya, K. Mathew, A. Jain)

      • +

    • many unit test updates (A. Faghaninia, H. Tang, S.P. Ong, A. Jain)

      • +

    • fix automated testing on pull requests (K. Mathew)

      • +

    • misc fixes

    v0.4.5

      -
    • extensive code review, code cleanup, and improved code docs - with some minor name refactoring
      • -
    • new builders: dielectric, structureanalysis (currently gives dimensionality of structure)
      • -
    • rewrite powerups as in-place with cleaner syntax
      • -
    • improved installation tutorial (B. Bocklund)
      • -
    • improve/fix/reorganize some unit tests
      • -
    • bug fixes (A. Jain, H. Tang, K. Mathew, B. Bocklund)
      • +

    • extensive code review, code cleanup, and improved code docs - with some minor name refactoring

      • +

    • new builders: dielectric, structureanalysis (currently gives dimensionality of structure)

      • +

    • rewrite powerups as in-place with cleaner syntax

      • +

    • improved installation tutorial (B. Bocklund)

      • +

    • improve/fix/reorganize some unit tests

      • +

    • bug fixes (A. Jain, H. Tang, K. Mathew, B. Bocklund)

    v0.4.4

      -
    • NEB workflow (H. Tang)
      • -
    • adsorption workflow (J. Montoya)
      • -
    • improvements to Gibbs workflow (K. Mathew)
      • -
    • misc bugfixes, improvements (A. Faghaninia, A. Jain)
      • +

    • NEB workflow (H. Tang)

      • +

    • adsorption workflow (J. Montoya)

      • +

    • improvements to Gibbs workflow (K. Mathew)

      • +

    • misc bugfixes, improvements (A. Faghaninia, A. Jain)

    v0.4.3

      -
    • Add Gibbs energy w/volume (K. Mathew)
      • -
    • Draft EXAFS workflow (K. Matthew)
      • -
    • Add slater-gamma formulation to compute the Gruneisen parameter (K. Matthew)
      • -
    • gamma vasp powerup (S. Dwaraknath)
      • -
    • More options for elasticity WF (J. Dagdalen)
      • -
    • Add StdErrorHandler to handlers (A. Jain)
      • -
    • Auto-detect and remove line_mode parameter in MMVaspDB (A. Jain)
      • -
    • added unit tests
      • -
    • misc cleanup, refactoring, and doc udpates
      • -
    • misc bugfixes
      • +

    • Add Gibbs energy w/volume (K. Mathew)

      • +

    • Draft EXAFS workflow (K. Matthew)

      • +

    • Add slater-gamma formulation to compute the Gruneisen parameter (K. Matthew)

      • +

    • gamma vasp powerup (S. Dwaraknath)

      • +

    • More options for elasticity WF (J. Dagdalen)

      • +

    • Add StdErrorHandler to handlers (A. Jain)

      • +

    • Auto-detect and remove line_mode parameter in MMVaspDB (A. Jain)

      • +

    • added unit tests

      • +

    • misc cleanup, refactoring, and doc udpates

      • +

    • misc bugfixes

    v0.4.2

    -

    Caution

    -

    The tags_fws powerup now has different default parameters!

    +

    Caution

    +

    The tags_fws powerup now has different default parameters!

      -
    • updates to piezo workflow (S. Dwaraknath)
      • -
    • formation energy to Ehull builder (A. Faghaninia)
      • -
    • tag_fws is more general (A. Faghaninia)
      • -
    • updates for PMG naming schemes for vars (A. Jain)
      • -
    • boltztrap runs can add tags (A. Faghaninia)
      • -
    • can filter which tasks are used in materials builder (A. Faghaninia, A. Jain)
      • +

    • updates to piezo workflow (S. Dwaraknath)

      • +

    • formation energy to Ehull builder (A. Faghaninia)

      • +

    • tag_fws is more general (A. Faghaninia)

      • +

    • updates for PMG naming schemes for vars (A. Jain)

      • +

    • boltztrap runs can add tags (A. Faghaninia)

      • +

    • can filter which tasks are used in materials builder (A. Faghaninia, A. Jain)

    v0.4.1 * more fixes for elastic workflow (J. Montoya) @@ -352,43 +355,43 @@

    atomate Changelog -
  • Raman workflow (K. Mathew)
    • -
  • Gibbs workflow (K. Mathew)
    • -
  • More efficient task builder (S. Ong)
    • -
  • tag workflows and add_trackers powerups (A. Jain, A. Faghaninia)
    • -
  • refactor elastic workflow (K. Mathew)
    • -
  • bugfixes and tools package (K. Mathew)
    • +

  • Raman workflow (K. Mathew)

    • +

  • Gibbs workflow (K. Mathew)

    • +

  • More efficient task builder (S. Ong)

    • +

  • tag workflows and add_trackers powerups (A. Jain, A. Faghaninia)

    • +

  • refactor elastic workflow (K. Mathew)

    • +

  • bugfixes and tools package (K. Mathew)

    • v0.21

      -
    • Lammps workflows and packmol support (K. Mathew)
      • -
    • Rework some of the RunVaspFake code (K. Mathew)
      • -
    • Fixes to elastic workflow (J. Montoya)
      • -
    • Minor refactoring (K. Mathew)
      • -
    • Minor MD workflow updates (M. Aykol)
      • -
    • Fix builder for HSE gap and add chemsys (A. Jain)
      • -
    • WF metadata powerup (A. Jain)
      • -
    • Minor bug fixes and misc. improvements (K. Mathew, J. Montoya, A. Faghaninia)
      • +

    • Lammps workflows and packmol support (K. Mathew)

      • +

    • Rework some of the RunVaspFake code (K. Mathew)

      • +

    • Fixes to elastic workflow (J. Montoya)

      • +

    • Minor refactoring (K. Mathew)

      • +

    • Minor MD workflow updates (M. Aykol)

      • +

    • Fix builder for HSE gap and add chemsys (A. Jain)

      • +

    • WF metadata powerup (A. Jain)

      • +

    • Minor bug fixes and misc. improvements (K. Mathew, J. Montoya, A. Faghaninia)

    v0.2

      -
    • BoltzTraP transport workflows (A. Jain)
      • -
    • major builder improvements (merge multiple collections, progressbar, config, more…)
      • -
    • use FrozenJobErrorHandler by default (A. Jain)
      • -
    • add basic configuration overrides for preset workflows (A. Jain)
      • -
    • misc improvements and bugfixes (A. Jain, K. Mathew)
      • -
    • py3 compatibility fixes (K. Mathew)
      • +

    • BoltzTraP transport workflows (A. Jain)

      • +

    • major builder improvements (merge multiple collections, progressbar, config, more…)

      • +

    • use FrozenJobErrorHandler by default (A. Jain)

      • +

    • add basic configuration overrides for preset workflows (A. Jain)

      • +

    • misc improvements and bugfixes (A. Jain, K. Mathew)

      • +

    • py3 compatibility fixes (K. Mathew)

    v0.1

      -
    • add some builders
      • -
    • elastic + piezo workflows (J. Montoya + S. Dwaraknath)
      • -
    • minor doc improvements (A. Faghaninia)
      • -
    • misc code improvements and bug fixes, plus upgrades for new pymatgen (A. Jain)
      • +

    • add some builders

      • +

    • elastic + piezo workflows (J. Montoya + S. Dwaraknath)

      • +

    • minor doc improvements (A. Faghaninia)

      • +

    • misc code improvements and bug fixes, plus upgrades for new pymatgen (A. Jain)

    v0.0.3

      -
    • initial release (A. Jain, S.P. Ong, K. Mathew, M. Aykol)
      • +

    • initial release (A. Jain, S.P. Ong, K. Mathew, M. Aykol)

    @@ -412,13 +415,11 @@

    This Page

    @@ -442,13 +443,13 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/concepts.html b/docs/concepts.html index b541fc890..e068d6448 100644 --- a/docs/concepts.html +++ b/docs/concepts.html @@ -1,18 +1,17 @@ - + - - - Atomate concepts — atomate 0.9.1 documentation + + Atomate concepts — atomate 0.9.2 documentation + @@ -32,7 +31,7 @@

    Navigation

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    • @@ -57,9 +56,9 @@

    The β€œenv_chk”, e.g. >>db_file<< syntaxCalcLocsΒΆ

    If you are running multiple VASP jobs that depend on copying the outputs of previous jobs, one issue is how to pass the directory information of previous VASP jobs from Firework to Firework. It is possible to do this manually (as was done in the MPWorks codebase), or using the pass_job_info keyword built into Fireworks, but the standard way to do this in atomate is CalcLocs. Procedurally, all you need to do is add the `PassCalcLocs FireTask to every Firework that contains a VASP job (see atomate.vasp.fireworks.core for examples). Downstream jobs like CopyVaspOutput will have a calc_loc variable that can be set to True, and will automatically get the previous VASP dir parsed from before. Similar with VaspToDbTask. Note that a couple of advantages of this system are:

      -
    • It is a general way of passing VASP directories that works with any Firework, and doesn’t require you to code the logic of passing VASP directories inside of other functions (e.g., database insertion tasks as was done previously in MPWorks). Thus, the task of reporting and passing the VASP job location is well-separated from the other functions and can just be added in very easily. The only downside is that you have to remember to add in this FireTask.
      • -
    • The CalcLocs maintains a running dictionary of job type to job location. If you need to grab outputs from multiple jobs (or say, from two jobs back), it is all supported within the framework. Just read the docs, e.g., of CopyVaspOutput.
      • -
    • Job directories are located across different machines and require scp or some other complex transfer mechanism are automatically handled by this infrastructure. You don’t have to lift a finger! Just tell the parent Firework to pass the calcloc and the child firework to copy the vasp output (which supports the calcloc framework).
      • +

    • It is a general way of passing VASP directories that works with any Firework, and doesn’t require you to code the logic of passing VASP directories inside of other functions (e.g., database insertion tasks as was done previously in MPWorks). Thus, the task of reporting and passing the VASP job location is well-separated from the other functions and can just be added in very easily. The only downside is that you have to remember to add in this FireTask.

      • +

    • The CalcLocs maintains a running dictionary of job type to job location. If you need to grab outputs from multiple jobs (or say, from two jobs back), it is all supported within the framework. Just read the docs, e.g., of CopyVaspOutput.

      • +

    • Job directories are located across different machines and require scp or some other complex transfer mechanism are automatically handled by this infrastructure. You don’t have to lift a finger! Just tell the parent Firework to pass the calcloc and the child firework to copy the vasp output (which supports the calcloc framework).

    @@ -50,13 +49,13 @@

    Contributors -
  • Alireza Faghaninia, Alex Dunn, Alex Ganose, and Evan Spotte-Smith through the research group of A. Jain at LBNL.
    • -
  • Kiran Mathew, Shyam Dwaraknath, Joey Montoya, Murat Aykol, Patrick Huck, Brandon Wood, Sam Blau, Jimmy Shen, Anne Rutt, Eric Sivonxay, and Martin Siron through the research group of Prof. Kristin Persson at UC Berkeley.
    • -
  • Hanmei Tang, Prof. Shyue Ping Ong, and the Materials Virtual Lab research group at UC San Diego.
    • -
  • Brandon Bocklund, who led the atomate documentation effort, through the research group of Prof. Zi-Kiu Liu at Penn State.
    • -
  • Tess Smidt through the research group of Prof. Jeff Neaton at UC Berkeley.
    • -
  • Danny Broberg through the research group of Prof. Mark Asta at UC Berkeley.
    • -
  • External contributors: specter119, M. Dias Costa, S. Torrisi, Max Dylla
    • +

  • Alireza Faghaninia, Alex Dunn, Alex Ganose, and Evan Spotte-Smith through the research group of A. Jain at LBNL.

    • +

  • Kiran Mathew, Shyam Dwaraknath, Joey Montoya, Murat Aykol, Patrick Huck, Brandon Wood, Sam Blau, Jimmy Shen, Anne Rutt, Eric Sivonxay, and Martin Siron through the research group of Prof. Kristin Persson at UC Berkeley.

    • +

  • Hanmei Tang, Prof. Shyue Ping Ong, and the Materials Virtual Lab research group at UC San Diego.

    • +

  • Brandon Bocklund, who led the atomate documentation effort, through the research group of Prof. Zi-Kiu Liu at Penn State.

    • +

  • Tess Smidt through the research group of Prof. Jeff Neaton at UC Berkeley.

    • +

  • Danny Broberg through the research group of Prof. Mark Asta at UC Berkeley.

    • +

  • External contributors: specter119, M. Dias Costa, S. Torrisi, Max Dylla, Marnik Bercx

    • @@ -80,13 +79,11 @@

    This Page

    @@ -110,13 +107,13 @@

    Navigation

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  • atomate 0.9.1 documentation »
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    • diff --git a/docs/creating_workflows.html b/docs/creating_workflows.html index 9568e8baa..b6e440c97 100644 --- a/docs/creating_workflows.html +++ b/docs/creating_workflows.html @@ -1,18 +1,17 @@ - + - - - Creating workflows — atomate 0.9.1 documentation + + Creating workflows — atomate 0.9.2 documentation + @@ -36,7 +35,7 @@

    Navigation

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    • @@ -56,10 +55,10 @@

    Introduction

    ObjectivesΒΆ

      -
    • Get familiar with the internal structure of Workflows, Fireworks, and Firetasks
      • -
    • Learn to compose atomate Workflows in Python from existing Fireworks
      • -
    • Understand what powerups are and how to use them
      • -
    • Learn how the FireWorker environment can control behavior
      • +

    • Get familiar with the internal structure of Workflows, Fireworks, and Firetasks

      • +

    • Learn to compose atomate Workflows in Python from existing Fireworks

      • +

    • Understand what powerups are and how to use them

      • +

    • Learn how the FireWorker environment can control behavior

    @@ -79,16 +78,16 @@

    FireWorks BackgroundA FireWorks Workflow is made up of Fireworks, which are made up of Firetasks. The description of each of these is best described by the FireWorks documentation itself:

      -
    • A Workflow is a set of FireWorks with dependencies between them. For example, you might need a parent Firework to finish and generate some output files before running two child FireWorks.
      • -
    • A Firework contains the JSON spec that includes all the information needed to bootstrap your job. For example, the spec contains an array of Firetasks to execute in sequence. The spec also includes any input parameters to pass to your Firetasks. You can easily perform the same function over different input data by creating Fireworks with identical Firetasks but different input parameters in the spec. You can design your spec however you’d like, as long as it’s valid JSON. The JSON format used for Firework specs is extremely flexible, very easy to learn (Python users familiar with dicts and arrays essentially already know JSON), and immediately makes rich searches over the input data available to end users through MongoDB’s JSON document search capabilities.
      • -
    • A Firetask is an atomic computing job. It can call a single shell script or execute a single Python function that you define (either within FireWorks, or in an external package).
      • +

    • A Workflow is a set of FireWorks with dependencies between them. For example, you might need a parent Firework to finish and generate some output files before running two child FireWorks.

      • +

    • A Firework contains the JSON spec that includes all the information needed to bootstrap your job. For example, the spec contains an array of Firetasks to execute in sequence. The spec also includes any input parameters to pass to your Firetasks. You can easily perform the same function over different input data by creating Fireworks with identical Firetasks but different input parameters in the spec. You can design your spec however you’d like, as long as it’s valid JSON. The JSON format used for Firework specs is extremely flexible, very easy to learn (Python users familiar with dicts and arrays essentially already know JSON), and immediately makes rich searches over the input data available to end users through MongoDB’s JSON document search capabilities.

      • +

    • A Firetask is an atomic computing job. It can call a single shell script or execute a single Python function that you define (either within FireWorks, or in an external package).

    In atomate, we typically design each Firework to represent one calculation or analysis step. In the example below, a typical bandstructure calculation first optimizes a crystal structure, then performs a static calculation, and finally non-SCF calculations on the band path and uniformly though the structure (which can be executed in parallel since they are not dependent on one another). Each of these calculations (each time you would run VASP) corresponds to a Firework and thus this bandstructure workflow contains 4 Fireworks. One could design this workflow with more or less Fireworks, but in our opinion this is the most natural and useful mapping. For example, note that one Firework most typically corresponds to one queue submission on a supercomputing center (although this can vary depending on the chosen execution mode).

    The Firetasks of each Firework are all of the individual steps that are performed for each calculation step. In the example, the structure optimization Firework has tasks to write the VASP input files based on the input structure, run VASP, parse the VASP outputs, and pass the output structure on to the static calculation. For the purposes of this tutorial, you don’t need to worry much about the details of Firetasks, but it helps to appreciate that Fireworks are simply composed of a few of these tasks performed in sequence that allow one to abstract out tedious calculation details like file IO. In the same way, Workflows exist to abstract out the details of different calculation and analysis steps contained in FireWorks.

    -
    +
    Bandstructure workflow. -

    Bandstructure workflow. The Optimize bulk structure Firework is a parent with one child: a Static SCF Firework. The Static SCF Firework has two children: a Static Non-SCF (line) Firework and a Static Non-SCF (uniform) Firework to get the DOS on a path and uniformly, respectively. In terms of execution, the Optimize bulk structure Firework will run the four Firetasks in sequential order with data as described by the spec. Once the Optimize bulk structure Firework and Static SCF Firework complete, the line and uniform SCF Fireworks can be launched and executed in parallel or in series. Since these Fireworks do not depend on each other, the execution order does not matter. Similar to the Optimize structure Firework, all of these Fireworks will run their respective Firetasks in series.

    +

    Bandstructure workflow. The Optimize bulk structure Firework is a parent with one child: a Static SCF Firework. The Static SCF Firework has two children: a Static Non-SCF (line) Firework and a Static Non-SCF (uniform) Firework to get the DOS on a path and uniformly, respectively. In terms of execution, the Optimize bulk structure Firework will run the four Firetasks in sequential order with data as described by the spec. Once the Optimize bulk structure Firework and Static SCF Firework complete, the line and uniform SCF Fireworks can be launched and executed in parallel or in series. Since these Fireworks do not depend on each other, the execution order does not matter. Similar to the Optimize structure Firework, all of these Fireworks will run their respective Firetasks in series.ΒΆ

    @@ -97,47 +96,47 @@

    Creating atomate WorkflowsΒΆ

    The first step when you go to write any workflow is to sketch a graph of the workflow. In particular, you want to sketch a directed acyclic graph, which for atomate just means that each calculation step is a node in the graph and parents only point to their children such that there are no loops (cycles) in the graph. Again, you should think of each large single invocation of the scientific code (VASP, LAMMPS, etc.) as corresponding to one Firework. Analysis tasks that aggregate results from several Fireworks, e.g. tasks that analyze volume deformations, also need their own Fireworks that have the calculations as parents. All of the workflow examples in the docs and the atomate paper (submitted) are valid workflow graphs.

    -

    Note

    -

    An advanced method of workflow programming in the FireWorks package allows the workflow to change depending on the results of execution. For example, a Firework can add more Fireworks to the workflow based on results that it obtained. If you need some kind of looping or branching at a high level, you’ll have to write a custom Firetask that creates new Fireworks on the fly. Writing custom Firetasks in atomate may be covered more in depth in a future workflow, but it is beyond the scope of this guide. Fireworks documentation for dynamic workflows discusses this from an abstract perspective.

    +

    Note

    +

    An advanced method of workflow programming in the FireWorks package allows the workflow to change depending on the results of execution. For example, a Firework can add more Fireworks to the workflow based on results that it obtained. If you need some kind of looping or branching at a high level, you’ll have to write a custom Firetask that creates new Fireworks on the fly. Writing custom Firetasks in atomate may be covered more in depth in a future workflow, but it is beyond the scope of this guide. Fireworks documentation for dynamic workflows discusses this from an abstract perspective.

    Finding FireworksΒΆ

    Once you have identified each calculation or analysis step as a Firework in our graph, we must determine which Fireworks correspond to each node in our graph. The full Python documentation for each of the atomate Fireworks can be found in the atomate.vasp.fireworks module documentation or the corresponding documentation page for the software you want to use. Currently FEFF, LAMMPS, and VASP are supported. Some available VASP Fireworks are

      -
    • OptimizeFW
      • -
    • StaticFW
      • -
    • TransmuterFW
      • -
    • HSEBSFW
      • -
    • NonSCFFW
      • -
    • LepsFW
      • -
    • SOCFW
      • -
    • MDFW
      • -
    • BoltztrapFW
      • -
    • NEBRelaxationFW
      • -
    • NEBFW
      • +

    • OptimizeFW

      • +

    • StaticFW

      • +

    • TransmuterFW

      • +

    • HSEBSFW

      • +

    • NonSCFFW

      • +

    • LepsFW

      • +

    • SOCFW

      • +

    • MDFW

      • +

    • BoltztrapFW

      • +

    • NEBRelaxationFW

      • +

    • NEBFW

    -

    Warning

    -

    The majority of these Fireworks are not complicated to run and you can use them directly. Some are less obvious and you should refer to the documentation for the specifics of each of these and how to use them before you do. For example, the HSEBSFW requires a previous calculation that gives VBM/CBM information or the high-symmetry kpoints.

    +

    Warning

    +

    The majority of these Fireworks are not complicated to run and you can use them directly. Some are less obvious and you should refer to the documentation for the specifics of each of these and how to use them before you do. For example, the HSEBSFW requires a previous calculation that gives VBM/CBM information or the high-symmetry kpoints.

    -

    Note

    -

    Some of these Fireworks only differ in VASP settings or options. For example, a simple OptimizeFW could in principle be customized to achieve the same functionality as several other VASP Fireworks in the same way that two types of burgers at a fast-food restaurant might become equivalent if you customized each order enough.

    +

    Note

    +

    Some of these Fireworks only differ in VASP settings or options. For example, a simple OptimizeFW could in principle be customized to achieve the same functionality as several other VASP Fireworks in the same way that two types of burgers at a fast-food restaurant might become equivalent if you customized each order enough.

    One of the main settings to pay attention to, particularly in VASP, is the input set used which determines things like functional, pseudopotential, and convergence settings. The input sets are all defined in pymatgen, such as pymatgen.io.vasp.sets or pymatgen.io.feff.sets. Most of these are fairly straightforward, but one Firework to pay specific attention to is the TransmuterFW. The TransmuterFW is very powerful because it supports transforming structures by any of the transformations supported in pymatgen.transformations. There are many supported transformations in pymatgen, some of the more common transformations include

      -
    • SupercellTransformation: Create supercells from a scaling matrix
      • -
    • SubstitutionTransformation: Substitute one species for another
      • -
    • PerturbStructureTransformation: Applies a perturbation of a specified amplitude to each site
      • -
    • DeformStructureTransformation: Apply a deformation matrix to the lattice matrix of the structure
      • +

    • SupercellTransformation: Create supercells from a scaling matrix

      • +

    • SubstitutionTransformation: Substitute one species for another

      • +

    • PerturbStructureTransformation: Applies a perturbation of a specified amplitude to each site

      • +

    • DeformStructureTransformation: Apply a deformation matrix to the lattice matrix of the structure

    You’ll notice that more generic Fireworks and Fireworks for analysis tasks are not in this list. Because they are intended to be simple and modular, these Fireworks are actually written as plain Firetasks that will get wrapped into a Firework when the Workflow is constructed. We’ll cover how to use them as Fireworks in the next section, but know that they can be found at places like atomate.common.firetasks module for software-agnostic tasks such as PassCalcLocs or atomate.vasp.firetasks package <atomate.vasp.firetasks for some VASP specific ones, including the analysis tasks usually found in atomate.vasp.firetasks.parse_outputs.

    Creating the workflowΒΆ

    With each of the Fireworks identified for our sketched workflow, they can assemble them into a complete atomate Workflow in Python. In order to understand what’s going on here, you should be comfortable with creating instances of classes and using functions. To demonstrate how to assemble and use a workflow, we will use a slightly modified version of the Gibbs Free Energy Workflow and step through each line of code to explain what is going on.

    -

    For context, the Gibbs Free Energy Workflow calculates G(P,T) for a structure. Two methods for doing this are using the Debye model (see Blanco et al. Comput. Phys. Commun., 158, (2004)) or through vibration frequencies of atoms (see Togo and Tanaka, Scr. Mater., 108 (2015). It does this by first optimizing the desired structure. Next, that optimized structure has its volume scaled and a VASP calculation that is either a static calculation or calculation with density functional perturbation theory (the IBRION = 7 or 8 INCAR setting) is performed depending on what type of analysis is used. In the analysis, the Debye model or a phonon calculation is used to extrapolate the from 0K to finite temperatures using the harmonic approximation, giving each structure an F(T) dependence. Then each of these structures are considered together and fit to an equation of state which allows us express F(V,T) for this structure, which we can transform to G(P,T) to get the Gibbs free energy of that structure. The phonopy website has a good visualization for Helmholtz energies and volumes with increasing temperature.

    +

    For context, the Gibbs Free Energy Workflow calculates G(P,T) for a structure. Two methods for doing this are using the Debye model (see Blanco et al. Comput. Phys. Commun., 158, (2004)) or through vibration frequencies of atoms (see Togo and Tanaka, Scr. Mater., 108 (2015). It does this by first optimizing the desired structure. Next, that optimized structure has its volume scaled and a VASP calculation that is either a static calculation or calculation with density functional perturbation theory (the IBRION = 7 or 8 INCAR setting) is performed depending on what type of analysis is used. In the analysis, the Debye model or a phonon calculation is used to extrapolate the from 0K to finite temperatures using the harmonic approximation, giving each structure an F(T) dependence. Then each of these structures are considered together and fit to an equation of state which allows us express F(V,T) for this structure, which we can transform to G(P,T) to get the Gibbs free energy of that structure. The phonopy website has a good visualization for Helmholtz energies and volumes with increasing temperature.

    The Python implementation of the modified Gibbs Free Energy Workflow is:

     1
  2
@@ -313,8 +312,8 @@ 
    Creating the workflow
    -

    Note

    -

    The documentation and source for the actual Gibbs Free Energy Workflow is found at atomate.vasp.workflows.base.gibbs. Here we have simplified some of the options and explicitly added each Firework.

    +

    Note

    +

    The documentation and source for the actual Gibbs Free Energy Workflow is found at atomate.vasp.workflows.base.gibbs. Here we have simplified some of the options and explicitly added each Firework.

    In the above code example, we start by importing the classes and functions we’ll be using and defining our wf_gibbs_free_energy function with all of the parameters we’d like to control from a workflow level and the documentation for those parameters. Running the function will return a FireWorks Workflow to add to the LaunchPad.

    Lines 41-51 is where we define the optimization Firework. First we check if a vasp_input_set_relax parameter was passed, if not we default to MPRelaxSet and update that set if the user_kpoints_settings parameter was passed. It’s common to see a similar parameter for user_incar_settings. On line 49 we create our list of Fireworks (fws) with the OptimizeFW that we imported. Take note that this is the only Firework we pass our structure to, which allows for more flexibility. More on this later.

    @@ -325,8 +324,8 @@

    Creating the workflow

    More helpΒΆ

      -
    • Reading the source the base Workflows (atomate.vasp.workflows.base) would be a good place to find functional examples with reasonable parameters
      • -
    • Creating workflows can also be done to some extent in YAML files. You can adapt the example along with a short explanation of the Workflow YAML Reference.
      • +

    • Reading the source the base Workflows (atomate.vasp.workflows.base) would be a good place to find functional examples with reasonable parameters

      • +

    • Creating workflows can also be done to some extent in YAML files. You can adapt the example along with a short explanation of the Workflow YAML Reference.

    @@ -338,35 +337,35 @@

    Powerupsatomate.vasp.powerups) enable modifications to be made to workflows after they have been created. The benefit of these is that you can apply powerups conditionally in code or to a large list of Workflows that you’ll later add to your LaunchPad. Some powerups affect the behavior of your calculations, others simply add metadata or change how the individual Fireworks interact with the database under the hood.

    Some useful powerups that affect the behavior of VASP are

      -
    • add_modify_incar: Update the INCAR of Fireworks specifed by (partially matched) name at runtime
      • -
    • set_fworker: specify certain FireWorkers for workflows. Useful for FireWorkers tuned for high-memory or high-precision jobs
      • -
    • modify_to_soc: makes all of the VASP calculations that match the constraints take spin orbit coupling into account
      • -
    • remove_custodian, use_custodian, run_fake_vasp: Choose to run VASP with or without custodian (or not at all, useful for debugging)
      • +

    • add_modify_incar: Update the INCAR of Fireworks specifed by (partially matched) name at runtime

      • +

    • set_fworker: specify certain FireWorkers for workflows. Useful for FireWorkers tuned for high-memory or high-precision jobs

      • +

    • modify_to_soc: makes all of the VASP calculations that match the constraints take spin orbit coupling into account

      • +

    • remove_custodian, use_custodian, run_fake_vasp: Choose to run VASP with or without custodian (or not at all, useful for debugging)

    Powerups that modify how FireWorks runs and can interact with workflows as they run

      -
    • add_priority: adds priority to root and child jobs to ensure that calculations that start have priority to finish over unstarted Fireworks
      • -
    • add_namefile: put a FW-->>fw.name<< file in the launch directory so searching filesystems for particular Fireworks is easy.
      • -
    • add_trackers: Fireworks will report the last few lines of OUTCAR and OSZICAR files that can be used to track jobs as they are still running
      • -
    • add_wf_metadata and add_tags: add metadata to workflows for easier querying
      • -
    • add_stability_check and add_bandgap_check: end workflows if the calculated structure has much lower energy than a materialsproject.org structure or if the bandgap is above or below a certain threshold
      • +

    • add_priority: adds priority to root and child jobs to ensure that calculations that start have priority to finish over unstarted Fireworks

      • +

    • add_namefile: put a FW-->>fw.name<< file in the launch directory so searching filesystems for particular Fireworks is easy.

      • +

    • add_trackers: Fireworks will report the last few lines of OUTCAR and OSZICAR files that can be used to track jobs as they are still running

      • +

    • add_wf_metadata and add_tags: add metadata to workflows for easier querying

      • +

    • add_stability_check and add_bandgap_check: end workflows if the calculated structure has much lower energy than a materialsproject.org structure or if the bandgap is above or below a certain threshold

    env_chkΒΆ

    Workflows in atomate are powerful for getting science done quickly because they are designed to be easily run heterogenously on different computing resources. env_chk enables this functionality by letting the user specify parameters that support env_chk, such as db_file, vasp_cmd, and incar_update. These allow different resources (or simply different my_fworker.yaml files on the same compute resource) to have settings specific to workflows that they run. Some ideas for using env_chk like this are

      -
    • Be able to quickly switch between different database files that are associated with different research projects
      • -
    • Ensure more consistent and easier usage of INCAR parameters you use often, such as setting a high NEDOS INCAR parameter
      • -
    • Set FireWorkers up for low and high precision jobs, or normal and high-memory jobs on the same computing resource.
      • +

    • Be able to quickly switch between different database files that are associated with different research projects

      • +

    • Ensure more consistent and easier usage of INCAR parameters you use often, such as setting a high NEDOS INCAR parameter

      • +

    • Set FireWorkers up for low and high precision jobs, or normal and high-memory jobs on the same computing resource.

    To use env_chk, you don’t have to do anything explicity, just pass '>>db_file<<', '>>vasp_cmd<<', '>>incar_update<<' to any parameter that supports env_chk.

    Currently supported env_chk variables are:

      -
    • >>scratch_dir<<
      • -
    • >>gamma_vasp_cmd<<
      • -
    • >>vasp_cmd<<
      • -
    • >>db_file<<
      • +

    • >>scratch_dir<<

      • +

    • >>gamma_vasp_cmd<<

      • +

    • >>vasp_cmd<<

      • +

    • >>db_file<<

    If you think there are other potentially useful variables that should support env_chk, please propose your idea in the atomate Google Group (or better, submit a pull request)!

    @@ -427,13 +426,11 @@

    This Page

    @@ -457,13 +454,13 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/customizing_workflows.html b/docs/customizing_workflows.html index bc207c99e..b3c49e2df 100644 --- a/docs/customizing_workflows.html +++ b/docs/customizing_workflows.html @@ -1,18 +1,17 @@ - + - - - Customizing workflows — atomate 0.9.1 documentation + + Customizing workflows — atomate 0.9.2 documentation + @@ -36,7 +35,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.1 documentation »
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    • @@ -55,7 +54,7 @@

    Introduction

    ObjectivesΒΆ

      -
    • Provide examples for customizating workflows
      • +

    • Provide examples for customizating workflows

    @@ -94,8 +93,8 @@

    PrerequisitesΒΆ

    Most VASP calculation-specific settings (e.g. those from INCAR, KPOINTS, and POTCAR files) are controlled by pymatgen’s vasp sets . VASP workflows take vasp_input_set options and you can directly import and use them or customize them before using them in atomate workflows.

    -

    Note

    -

    Using the vasp_input_set or vis keywords in workflow constructors usually only controls the first Firework that uses that set. If you want to have multiple Fireworks use custom input sets (or just not the first one, e.g. in a bandstructure workflow) then you have to make a custom workflow yourself.

    +

    Note

    +

    Using the vasp_input_set or vis keywords in workflow constructors usually only controls the first Firework that uses that set. If you want to have multiple Fireworks use custom input sets (or just not the first one, e.g. in a bandstructure workflow) then you have to make a custom workflow yourself.

    Using a different functionalΒΆ

    @@ -156,8 +155,8 @@

    Using a different functionalΒΆ

    KPOINTS settings can also be similarly customized using the above example. You can control them with the following keywords (from pymatgen’s vasp sets):

      -
    • force_gamma: always use gamma centered kpoint generation. Default (False) is to use Automatic Density kpoint scheme, which will use the Gamma centered generation scheme for hexagonal cells, and Monkhorst-Pack otherwise.
      • -
    • user_kpoints_settings: Override kpoints setting by supplying a dict. E.g., {"reciprocal_density": 1000}. Other options are grid_density or length.
      • +

    • force_gamma: always use gamma centered kpoint generation. Default (False) is to use Automatic Density kpoint scheme, which will use the Gamma centered generation scheme for hexagonal cells, and Monkhorst-Pack otherwise.

      • +

    • user_kpoints_settings: Override kpoints setting by supplying a dict. E.g., {"reciprocal_density": 1000}. Other options are grid_density or length.

    from pymatgen.io.vasp.sets import MPRelaxSet
 from pymatgen import Structure
@@ -231,8 +230,8 @@ 
    Use a different POTCAR
    -

    Warning

    -

    Make sure not to try a nested dictionary update (e.g. my_custom_input_set.config_dict.update({'POTCAR': {'Mg': 'Mg'}}) )! It will wipe out all of the other POTCAR entries in the dict.

    +

    Warning

    +

    Make sure not to try a nested dictionary update (e.g. my_custom_input_set.config_dict.update({'POTCAR': {'Mg': 'Mg'}}) )! It will wipe out all of the other POTCAR entries in the dict.

    @@ -276,13 +275,11 @@

    This Page

    @@ -306,13 +303,13 @@

    Navigation

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    • -
  • atomate 0.9.1 documentation »
    • +
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    • diff --git a/docs/developer_installation.html b/docs/developer_installation.html index 9188d10a6..016b04215 100644 --- a/docs/developer_installation.html +++ b/docs/developer_installation.html @@ -1,18 +1,17 @@ - + - - - Atomate developer installation — atomate 0.9.1 documentation + + Atomate developer installation — atomate 0.9.2 documentation + @@ -36,7 +35,7 @@

    Navigation

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    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -60,23 +59,18 @@

    Installation -

  • Note: you should have activated your virtual environment or conda environment before proceeding.

    -
    • -

  • Create a codes directory in <<INSTALL_DIR>>

    -
    • -

  • cd to your newly created <<INSTALL_DIR>>/codes directory.

    -
    • -

  • Clone each of the packages you want to install in development mode using git. You don’t have to know the details of how to use git for the installation, but if you are going to be developing code in Python, you should take a look at this simple git introduction. Most Linux distributions include git, so you shouldn’t have to install it on the cluster. To download the codes, use the following commands (one command per line):

    +

  • Note: you should have activated your virtual environment or conda environment before proceeding.

    • +

  • Create a codes directory in <<INSTALL_DIR>>

    • +

  • cd to your newly created <<INSTALL_DIR>>/codes directory.

    • +

  • Clone each of the packages you want to install in development mode using git. You don’t have to know the details of how to use git for the installation, but if you are going to be developing code in Python, you should take a look at this simple git introduction. Most Linux distributions include git, so you shouldn’t have to install it on the cluster. To download the codes, use the following commands (one command per line):

    git clone https://github.com/materialsproject/pymatgen.git
 git clone https://github.com/hackingmaterials/atomate.git

    Now you should have atomate and pymatgen directories in your codes directory.

    • -

  • For each of these folders, you cd into the folders and pip install -e . (the -e flag installs as editable, and the . simply means to install from the setup.py in the current directory) or use the conda equivalent. If you run into problems during this procedure, you may need manually install or load certain dependencies (e.g., use module load numpy on your system or pip install numpy or conda install numpy). Note that once installed, if you make changes to the code in these directories, the changes will take effect immediately without needing to reinstall. Thus, you can both view and modify the code installed in these directories.

    -
    • -

  • If you want to update these codes later on, execute git pull followed by pip install -e . (or again, the conda equivalent) in the relevant directory. Note that you should update codes in the same order as installation as listed above.

    -
    • +

  • For each of these folders, you cd into the folders and pip install -e . (the -e flag installs as editable, and the . simply means to install from the setup.py in the current directory) or use the conda equivalent. If you run into problems during this procedure, you may need manually install or load certain dependencies (e.g., use module load numpy on your system or pip install numpy or conda install numpy). Note that once installed, if you make changes to the code in these directories, the changes will take effect immediately without needing to reinstall. Thus, you can both view and modify the code installed in these directories.

    • +

  • If you want to update these codes later on, execute git pull followed by pip install -e . (or again, the conda equivalent) in the relevant directory. Note that you should update codes in the same order as installation as listed above.

    • @@ -91,8 +85,8 @@

    (optional) Run unit testsdb.json and my_launchpad.yaml in the <<INSTALL_DIR>>/codes/atomate/atomate/common/test_files directory control the database to use for the unit tests. The default is to use a MongoDB running on localhost. You can update these to whatever you like, e.g. a MongoDB instance in the cloud that you use for tests.

    -

    Warning

    -

    Although you can re-use the same Mongo host and port as your production installation for tests, do not also use the same database as your production runs! This is why the default configuration uses a database name with _unittest - so that it won’t conflict with any production database. The database and LaunchPad you use in the unit tests WILL be reset frequently. DO NOT USE YOUR PRODUCTION DATABASES FOR TESTING or you will lose everything!

    +

    Warning

    +

    Although you can re-use the same Mongo host and port as your production installation for tests, do not also use the same database as your production runs! This is why the default configuration uses a database name with _unittest - so that it won’t conflict with any production database. The database and LaunchPad you use in the unit tests WILL be reset frequently. DO NOT USE YOUR PRODUCTION DATABASES FOR TESTING or you will lose everything!

    These unit tests are designed to run without installing VASP or other codes so you can run these on your local machine. Some of them start with a VASP workflow but apply the use_fake_vasp method to replace calling the VASP executable with a β€œFaker” that verifies basic properties of the inputs and copies pre-stored output files to the current directory, thus simulating the execution of VASP.

    @@ -143,13 +137,11 @@

    This Page

    @@ -173,13 +165,13 @@

    Navigation

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  • atomate 0.9.1 documentation »
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    • diff --git a/docs/genindex.html b/docs/genindex.html index ffaaa8bd2..9ef5d1b35 100644 --- a/docs/genindex.html +++ b/docs/genindex.html @@ -1,19 +1,18 @@ - + - - - Index — atomate 0.9.1 documentation + + Index — atomate 0.9.2 documentation + @@ -29,7 +28,7 @@

    Navigation

  • modules |
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  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • @@ -847,7 +846,7 @@

    H

    I

    diff --git a/docs/gibbs_workflow_tutorial.html b/docs/gibbs_workflow_tutorial.html index f5e8e52e3..5d9d13e99 100644 --- a/docs/gibbs_workflow_tutorial.html +++ b/docs/gibbs_workflow_tutorial.html @@ -1,18 +1,17 @@ - + - - - Running Gibbs workflows — atomate 0.9.1 documentation + + Running Gibbs workflows — atomate 0.9.2 documentation + @@ -36,7 +35,7 @@

    Navigation

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    • @@ -50,7 +49,7 @@

    Navigation

    IntroductionΒΆ

    Standard density functional theory calculations are 0 K ground state calculations, but most materials are used and modeled at room temperature and above. -The Debye model and phonon calculations are two commonly used methods to obtain Gibbs free energies (G(p,T)) of structures as a function of temperature. +The Debye model and phonon calculations are two commonly used methods to obtain Gibbs free energies (G(p,T)) of structures as a function of temperature. Both the Debye model and phonon calculations are supported in atomate, where the Debye model analysis is based on the quasiharmonic technique presented in Moruzzi et al. (Phys. Rev. B 37, 790–799 (1988).) and implemented similar to Toher et al. (Phys. Rev. B 90, 1–14 (2014).. Phonon calculation analysis is performed using phonopy (Togo & Tanaka Scr. Mater. 108, 1–5 (2015).).

    @@ -60,28 +59,28 @@

    Introduction

    ObjectivesΒΆ

      -
    • Run an atomate preset workflow for the Gibbs free energy using Python
      • -
    • Query for the calculation result in the Gibbs collection of the database
      • -
    • Visualize the results with matplotlib
      • +

    • Run an atomate preset workflow for the Gibbs free energy using Python

      • +

    • Query for the calculation result in the Gibbs collection of the database

      • +

    • Visualize the results with matplotlib

    Gibbs Free Energy WorkflowsΒΆ

    Gibbs free energies are calculated in DFT based on the following relation:

    -

    G(p,T) = E(V) + pV + F_{\textrm{vib}}(V,T)

    -

    where E(V) are the total energies calculated with DFT as a function of volume and F_{\textrm{vib}}(V,T) is the vibrational contribution to the Helmholz energy. +

    G(p,T) = E(V) + pV + F_{\textrm{vib}}(V,T)

    +

    where E(V) are the total energies calculated with DFT as a function of volume and F_{\textrm{vib}}(V,T) is the vibrational contribution to the Helmholz energy. This vibrational energy is calculated using a harmonic approximation, here via the Debye model.

    -

    To calculate the Gibbs free energy, total energies are calculated for several volumes, then vibrational contributions are added for each volume over a range of temperatures to give F(V,T). +

    To calculate the Gibbs free energy, total energies are calculated for several volumes, then vibrational contributions are added for each volume over a range of temperatures to give F(V,T). Then an equation of state is fit for each set of energies and volumes at each temperature. Several different equations of state are implemented in pymatgen and several of those are discussed in terms of the Debye model by Shang et al. (Comput. Mater. Sci. 47, 1040–1048 (2010).). -Using the fit equation of state, the volume that minimized the energy at a fixed pressure (usually, but not always p=0) is found. -Finding the minimum volume at each temperature and fixed pressure yields the conversion from F_{\textrm{vib}}(V,T) to G(V,T)

    +Using the fit equation of state, the volume that minimized the energy at a fixed pressure (usually, but not always p=0) is found. +Finding the minimum volume at each temperature and fixed pressure yields the conversion from F_{\textrm{vib}}(V,T) to G(V,T)

    From the perspective of a workflow, the Gibbs free energy workflow is procedurally similar to the elastic tensor workflow. First the input structure is optimized, then volume of the optimize structure is deformed and energies calculated to yield the points for an E-V curve (or phonon calculations), finally the analysis workflow corresponding to the Debye model or phonon formalism is performed.

    -
    +
    Elastic Tensor Workflow -

    Atomate elastic tensor workflow. This uses the same pattern as the Gibbs free energy workflow, but the analysis step (final Firework) calculates the elastic tensor instead of Gibbs free energies.

    +

    Atomate elastic tensor workflow. This uses the same pattern as the Gibbs free energy workflow, but the analysis step (final Firework) calculates the elastic tensor instead of Gibbs free energies.ΒΆ

    @@ -97,8 +96,8 @@

    Setup

    -

    Warning

    -

    This will reset all of your previous Fireworks and Workflows in your LaunchPad. Do not do this if you have actual results that you want to keep!

    +

    Warning

    +

    This will reset all of your previous Fireworks and Workflows in your LaunchPad. Do not do this if you have actual results that you want to keep!

    If you do not or want to reset your LaunchPad, you can set up a different database to use for tutorials or simply accept mixing your previous results and workflows with the contents of this tutorial in your database.

    @@ -146,7 +145,7 @@

    Use Python to generate and add the workflowTrue, so that we can properly deviate from the high-temperature limit of the Debye model of 3R based on the Gruneisen parameter, \gamma.

    +

    Since we are potentially interested in the high-temperature thermodynamic behavior of Si, we set the anharmonic contribution to True, so that we can properly deviate from the high-temperature limit of the Debye model of 3R based on the Gruneisen parameter, \gamma.

    Create and add the workflow to LaunchPad

    python gibbs.py
    @@ -212,9 +211,9 @@

    Analyzing an Equation of State WorkflowSi-heat-capacity.png, it should match the one below!

    -
    @@ -223,8 +222,8 @@

    Conclusionatomate.vasp.workflows.presets. They can be set up and run in exactly the same way as this tutorial, by passing in a structure and an optional configuration dictionary.

    At this point, you might:

    @@ -267,13 +266,11 @@

    This Page

    @@ -297,13 +294,13 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.1 documentation »
    • +
  • atomate 0.9.2 documentation »
    • diff --git a/docs/index.html b/docs/index.html index b7ba92111..2dacce93f 100644 --- a/docs/index.html +++ b/docs/index.html @@ -1,18 +1,17 @@ - + - - - atomate (Materials Science Workflows) — atomate 0.9.1 documentation + + atomate (Materials Science Workflows) — atomate 0.9.2 documentation + @@ -32,7 +31,7 @@

    Navigation

  • next |
    • -
  • atomate 0.9.1 documentation »
    • +
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    • @@ -57,43 +56,43 @@

    atomate -
  • It is built on top of state-of-the-art open-source libraries: pymatgen, custodian, and FireWorks. Building off these libraries means that atomate can not only serve as a simple and friendly introduction to computational materials science, but that it is powerful enough for even the most demanding of theory users that require precise control and massive execution.
    • -
  • It is easy to get β€œstandard” workflows for a wide variety of desired materials properties - optimized structures, band structures, electronic transport properties, dielectric constants, and much more. Just provide a crystal structure (that’s it!) and let atomate set up a complete workflow that provides the property you are interested in. You can do this for a single material, 100 materials, or 100,000 materials.
    • -
  • One can easily change β€œstandard workflows” - whether that is changing some of the default calculation parameters or recomposing the workflow (adding new calculations, removing steps, etc.) - using a very expressive syntax. One can compose very complex new workflows simply by chaining together pre-built calculation steps.
    • -
  • A system of β€œpowerups” that let you quickly decorate a bare workflow with useful special properties. Just feed the workflow through the powerup and your workflow will have the feature enabled. A config file allows you to automatically set the powerups you want to apply most often.
    • -
  • It can build large databases of output properties that you can query, analyze, and share in a systematic way.
    • -
  • It automatically keeps meticulous records of jobs, their directories, runtime parameters, etc.
    • -
  • Jobs can be run on a variety of computing systems, queue systems, and architectures.
    • -
  • atomate uses a standard interface for adding new types of calculations and workflows such that it is possible for users to contribute new features and grow the capabilities of the software over time.
    • +

  • It is built on top of state-of-the-art open-source libraries: pymatgen, custodian, and FireWorks. Building off these libraries means that atomate can not only serve as a simple and friendly introduction to computational materials science, but that it is powerful enough for even the most demanding of theory users that require precise control and massive execution.

    • +

  • It is easy to get β€œstandard” workflows for a wide variety of desired materials properties - optimized structures, band structures, electronic transport properties, dielectric constants, and much more. Just provide a crystal structure (that’s it!) and let atomate set up a complete workflow that provides the property you are interested in. You can do this for a single material, 100 materials, or 100,000 materials.

    • +

  • One can easily change β€œstandard workflows” - whether that is changing some of the default calculation parameters or recomposing the workflow (adding new calculations, removing steps, etc.) - using a very expressive syntax. One can compose very complex new workflows simply by chaining together pre-built calculation steps.

    • +

  • A system of β€œpowerups” that let you quickly decorate a bare workflow with useful special properties. Just feed the workflow through the powerup and your workflow will have the feature enabled. A config file allows you to automatically set the powerups you want to apply most often.

    • +

  • It can build large databases of output properties that you can query, analyze, and share in a systematic way.

    • +

  • It automatically keeps meticulous records of jobs, their directories, runtime parameters, etc.

    • +

  • Jobs can be run on a variety of computing systems, queue systems, and architectures.

    • +

  • atomate uses a standard interface for adding new types of calculations and workflows such that it is possible for users to contribute new features and grow the capabilities of the software over time.

    • Note: Atomate is primarily built to work with the VASP electronic structure software, but it is the intention of atomate to support a variety of software. For example, FEFF software integration has been recently added and other calculation packages are also under development.

    WorkflowsΒΆ

    -
    +
    Example outputs -

    Example of GaP band structure (left) computed via atomate/VASP and La0.7Sr0.3MnO3 ELNES spectra (right) computed via atomate/FEFF.

    +

    Example of GaP band structure (left) computed via atomate/VASP and La0.7Sr0.3MnO3 ELNES spectra (right) computed via atomate/FEFF.ΒΆ

    Some of the workflows available as of June 2017 are:

      -
    • electronic band structures
      • -
    • BoltzTraP
      • -
    • full elastic tensor
      • -
    • equation of state
      • -
    • piezoelectric tensor
      • -
    • dielectric tensor
      • -
    • ferroelectricity
      • -
    • nudged elastic band
      • -
    • Raman spectroscopy
      • -
    • XAS and EELS spectra (FEFF package)
      • +

    • electronic band structures

      • +

    • BoltzTraP

      • +

    • full elastic tensor

      • +

    • equation of state

      • +

    • piezoelectric tensor

      • +

    • dielectric tensor

      • +

    • ferroelectricity

      • +

    • nudged elastic band

      • +

    • Raman spectroscopy

      • +

    • XAS and EELS spectra (FEFF package)

    One can customize any of the above workflows. Also, one can create new workflows - either from scratch, or by reusing components from the above workflows (atomate’s infrastructure makes this simple). For the VASP package, raw workflows (more parameter settings) are in atomate/vasp/workflows/base and preset workflows (generally only require a crystal structure) are in atomate/vasp/workflows/presets. Other packages should have corresponding directories.

    The basicsΒΆ

    -
    +
    Band structure workflow -

    Anatomy of a band structure workflow consisting of 4 separate calculations (Fireworks) and for which each calculation has multiple steps (Firetasks). The anatomy of this workflow is covered in more detail in the atomate tutorials.

    +

    Anatomy of a band structure workflow consisting of 4 separate calculations (Fireworks) and for which each calculation has multiple steps (Firetasks). The anatomy of this workflow is covered in more detail in the atomate tutorials.ΒΆ

    The basics of setting up and running calculationsΒΆ

    @@ -125,10 +124,10 @@

    Citing atomate

    Contributing / Contact / SupportΒΆ

    Want to see something added or changed? There are many ways to make that a reality! Some ways to get involved are:

      -
    • Help us improve the documentation - tell us where you got β€˜stuck’ and improve the install process for everyone.
      • -
    • Let us know if you need support for a queueing system or certain features.
      • -
    • Point us to areas of the code that are difficult to understand or use.
      • -
    • Contribute code! You can do this by forking atomate on Github and submitting a pull request.
      • +

    • Help us improve the documentation - tell us where you got β€˜stuck’ and improve the install process for everyone.

      • +

    • Let us know if you need support for a queueing system or certain features.

      • +

    • Point us to areas of the code that are difficult to understand or use.

      • +

    • Contribute code! You can do this by forking atomate on Github and submitting a pull request.

    The list of contributors to atomate can be found here.

    There is an atomate Google Group dedicated to discussion and basic support.

    @@ -317,9 +316,9 @@

    ReferenceΒΆ

    Autogenerated code documentation below:

    @@ -364,13 +363,11 @@

    This Page

    @@ -391,13 +388,13 @@

    Navigation

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    • -
  • atomate 0.9.1 documentation »
    • +
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    • diff --git a/docs/installation.html b/docs/installation.html index 67ed6a453..9e5123c4d 100644 --- a/docs/installation.html +++ b/docs/installation.html @@ -1,18 +1,17 @@ - + - - - Installing atomate — atomate 0.9.1 documentation + + Installing atomate — atomate 0.9.2 documentation + @@ -36,7 +35,7 @@

    Navigation

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  • atomate 0.9.1 documentation »
    • +
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    • @@ -51,9 +50,9 @@

    Navigation

    IntroductionΒΆ

    This guide will get you up and running in an environment for running high-throughput workflows with atomate. atomate is built on pymatgen, custodian, and FireWorks libraries to run materials science workflows. Briefly:

      -
    • pymatgen is used to create input files and analyze the output of materials science codes
      • -
    • custodian runs your simulation code (e.g., VASP) and performs error checking/handling and checkpointing
      • -
    • FireWorks is used to design, manage and execute workflows.
      • +

    • pymatgen is used to create input files and analyze the output of materials science codes

      • +

    • custodian runs your simulation code (e.g., VASP) and performs error checking/handling and checkpointing

      • +

    • FireWorks is used to design, manage and execute workflows.

    Details about how atomate is designed can be found in the atomate paper and an overview of how these different pieces interact are in a Slideshare presentation. Running and writing your own workflows are covered in later tutorials. For now, these topics will be covered in enough depth to get you set up and to help you know where to troubleshoot if you are having problems.

    It is assumed that you are comfortable with basic Linux shell commands and navigation. If not, Linux Journey and Linux Command breifly cover enough to get you started. It will also be helpful if you are familiar with Python, but it is not strictly required for installation.

    @@ -62,21 +61,21 @@

    Introduction

    ObjectivesΒΆ

      -
    • Install and configure atomate on your computing cluster
      • -
    • Validate the installation with a test workflow that computes a band structure
      • +

    • Install and configure atomate on your computing cluster

      • +

    • Validate the installation with a test workflow that computes a band structure

    Installation checklistΒΆ

    Completing everything on this checklist should result in a fully functioning environment. Each item will be covered in depth, but this can be used to keep track of the big picture and help reinstall on other systems.

      -
    1. Prerequisites
      2. -
    2. Create a directory scaffold for atomate
      3. -
    3. Create a Python virtual environment
      4. -
    4. Install Python packages
      5. -
    5. Configure FireWorks
      6. -
    6. Configure pymatgen
      7. -
    7. Run a test workflow
      8. +

    8. Prerequisites

      9. +

    9. Create a directory scaffold for atomate

      10. +

    10. Create a Python virtual environment

      11. +

    11. Install Python packages

      12. +

    12. Configure FireWorks

      13. +

    13. Configure pymatgen

      14. +

    14. Run a test workflow

    @@ -90,32 +89,32 @@

    VASPΒΆ

    MongoDBΒΆ

    MongoDB is a NoSQL database that stores each database entry as a document, which is represented in the JSON format (the formatting is similar to a dictionary in Python). Atomate uses MongoDB to:

      -
    • store the workflows that you want to run as well as their state details (through FireWorks - required)
      • -
    • to parse output files and create database of calculation results (strongly recommended and assumed by most default settings of workflows, but technically optional)
      • +

    • store the workflows that you want to run as well as their state details (through FireWorks - required)

      • +

    • to parse output files and create database of calculation results (strongly recommended and assumed by most default settings of workflows, but technically optional)

    Note that there are various tools to query this information later, ranging from highly useful tools that work on all MongoDB databases (e.g., MongoDB command line, MongoDB GUI programs) as well as analysis tools built into pymatgen-db, FireWorks, and atomate that are generally more specific to the information generated by these codebases.

    MongoDB must be running and available to accept connections whenever you are running workflows. Thus, it is strongly recommended that you have a server to run MongoDB or (simpler) use a hosting service. Your options are:

      -
    • use a commercial service to host your MongoDB instance. These are typically the easiest to use and offer high quality service but require payment for larger databases. mLab and MongoDB Atlas offer free 500 MB databases with payment required for larger databases; the free tier is certainly enough to get started for small to medium size projects, and it is easy to upgrade or migrate your database if you do exceed the free allocation.
      • -
    • contact your supercomputing center to see if they offer MongoDB hosting (e.g., NERSC has this, Google β€œrequest NERSC MongoDB database”)
      • -
    • self-host a MongoDB server
      • +

    • use a commercial service to host your MongoDB instance. These are typically the easiest to use and offer high quality service but require payment for larger databases. mLab and MongoDB Atlas offer free 500 MB databases with payment required for larger databases; the free tier is certainly enough to get started for small to medium size projects, and it is easy to upgrade or migrate your database if you do exceed the free allocation.

      • +

    • contact your supercomputing center to see if they offer MongoDB hosting (e.g., NERSC has this, Google β€œrequest NERSC MongoDB database”)

      • +

    • self-host a MongoDB server

    If you are just starting, we suggest the first (with a free plan) or second option (if available to you). The third option will require you to open up network settings to accept outside connections properly which can sometimes be tricky.

    Next, create a new database and set up two new username/password combinations:

      -
    • an admin user
      • -
    • a read-only user
      • +

    • an admin user

      • +

    • a read-only user

    You might choose to have two separate databases - one for the workflows and another for the results. We suggest that new users keep both sets of results in a single database and only consider using two databases if they run into specific problems.

    Keep a record of your credentials - we will configure FireWorks to connect to them in a later step. Also make sure you note down the hostname and port for the MongoDB instance.

    -

    Note

    +

    Note

    The computers that perform the calculations must have access to your MongoDB server. Some computing resources have firewalls blocking connections. Although this is not a problem for most computing centers that allow such connections (particularly from MOM-style nodes, e.g. at NERSC, SDSC, etc.), but some of the more security-sensitive centers (e.g., LLNL, PNNL, ARCHER) will run into issues. If you run into connection issues later in this tutorial, some options are:

    -
      -
    • contact your computing center to review their security policy to allow connections from your MongoDB server (best resolution)
      • -
    • host your Mongo database on a machine that you are able to securely connect to, e.g. on the supercomputing network itself (ask a system administrator for help)
      • -
    • use a proxy service to forward connections from the MongoDB –> login node –> compute node (you might try, for example, the mongo-proxy tool).
      • -
    • set up an ssh tunnel to forward connections from allowed machines (the tunnel must be kept alive at all times you are running workflows)
      • +
        +

      • contact your computing center to review their security policy to allow connections from your MongoDB server (best resolution)

        • +

      • host your Mongo database on a machine that you are able to securely connect to, e.g. on the supercomputing network itself (ask a system administrator for help)

        • +

      • use a proxy service to forward connections from the MongoDB –> login node –> compute node (you might try, for example, the mongo-proxy tool).

        • +

      • set up an ssh tunnel to forward connections from allowed machines (the tunnel must be kept alive at all times you are running workflows)

    @@ -124,11 +123,9 @@

    MongoDB

    Create a directory scaffold for atomateΒΆ

    Installing atomate includes installation of codes, configuration files, and various binaries and libraries. Thus, it is useful to create a directory structure that organizes all these items.

      -

    1. Log in to the compute cluster and make sure the Python module you want to use is loaded. We highly recommend to make sure Python is loaded upon login, e.g. through an rc file (e.g. ~/.bashrc at most centers or ~/.bashrc.ext at NERSC)

      -
      2. -

    2. Create a directory in a spot on disk that has relatively fast access from compute nodes and that is only accessible by yourself or your collaborators. Your environment and configuration files will go here, including database credentials. We will call this place <<INSTALL_DIR>>. A good name might simply be atomate, but you could also use a project-specific name (e.g., atomate-solar).

      -
      3. -

    3. Now you should scaffold the rest of your <<INSTALL_DIR>> for the things we are going to do next. Create a directories named logs, and config so your directory structure looks like:

      +

    4. Log in to the compute cluster and make sure the Python module you want to use is loaded. We highly recommend to make sure Python is loaded upon login, e.g. through an rc file (e.g. ~/.bashrc at most centers or ~/.bashrc.ext at NERSC)

      5. +

    5. Create a directory in a spot on disk that has relatively fast access from compute nodes and that is only accessible by yourself or your collaborators. Your environment and configuration files will go here, including database credentials. We will call this place <<INSTALL_DIR>>. A good name might simply be atomate, but you could also use a project-specific name (e.g., atomate-solar).

      6. +

    6. Now you should scaffold the rest of your <<INSTALL_DIR>> for the things we are going to do next. Create a directories named logs, and config so your directory structure looks like:

      atomate
 β”œβ”€β”€ config
@@ -142,8 +139,8 @@ 
      MongoDB
 
      Create a Python 3 virtual environmentΒΆ
      
 
      
-
      Note
      
-
      Make sure to create Python 3.6+ environment as recent versions of atomate only support Python 3.6 and higher.
      
+
      Note
      
+
      Make sure to create Python 3.6+ environment as recent versions of atomate only support Python 3.6 and higher.
      
 
      
 
      We highly recommended that you organize your installation of the atomate and the other Python codes using a virtual environment (e.g. virtualenv or similar tool such as anaconda).
 Ultimately, whether you want to use a virtual environment is optional and you don’t have to use one if you know what you are doing.
@@ -151,9 +148,9 @@ 
      MongoDB
-
    7. Different Python projects that have conflicting packages can coexist on the same machine.
      8. 
-
    8. Different versions of Python can exist on the same machine and be managed more easily (e.g. Python 2 and Python 3).
      9. 
-
    9. You have full rights and control over the environment. If it breaks, you can just delete the folder containing the environment and recreate it. On computing resources, this solves permissions issues with installing and modifying packages.
      10. 
+
    10. Different Python projects that have conflicting packages can coexist on the same machine.
      11. 
+
    11. Different versions of Python can exist on the same machine and be managed more easily (e.g. Python 2 and Python 3).
      12. 
+
    12. You have full rights and control over the environment. If it breaks, you can just delete the folder containing the environment and recreate it. On computing resources, this solves permissions issues with installing and modifying packages.
      13.

      The easiest way to get a Python virtual environment is to use the virtualenv tool. @@ -162,9 +159,8 @@

      MongoDBdocumentation for the conda command line tool here as well as a conversion between virtualenv and conda commands. To set up your virtual environment:

        -

      1. Go to your install directory (<<INSTALL_DIR>>) and create a virtual environment there. A good name might be atomate_env. The default command to create the environment would be virtualenv atomate_env, which creates a folder atomate_env in the directory you are in.

        -
        2. -

      2. You can ls this directory and see that you have the following structure:

        +

      3. Go to your install directory (<<INSTALL_DIR>>) and create a virtual environment there. A good name might be atomate_env. The default command to create the environment would be virtualenv atomate_env, which creates a folder atomate_env in the directory you are in.

        4. +

      4. You can ls this directory and see that you have the following structure:

        5. -

      5. Activate your environment by running source <<INSTALL_DIR>>/atomate_env/bin/activate. This makes it so when you use the command python, the version of python that you use will be the one in the bin directory rather than the system-wide Python. You can read the activation script if you are interested. It’s just does a little magic to adjust your path to point towards the bin and other directories you created.

        -
        6. -

      6. Consider adding source <<INSTALL_DIR>>/atomate_env/bin/activate to your .rc or .bash_profile file so that it is run whenever you log in. Otherwise, note that you must call this command after every log in before you can do work on your atomate project.

        -
        7. +

      7. If you look in the bin directory, you will see several programs, such as activate, pip, and Python itself. lib will be where all of your installed packages will be kept, etc. Again, if anything goes wrong in installing Python codes, you can just delete the virtual environment directory (atomate_env) and start again.

        8. +

      8. Activate your environment by running source <<INSTALL_DIR>>/atomate_env/bin/activate. This makes it so when you use the command python, the version of python that you use will be the one in the bin directory rather than the system-wide Python. You can read the activation script if you are interested. It’s just does a little magic to adjust your path to point towards the bin and other directories you created.

        9. +

      9. Consider adding source <<INSTALL_DIR>>/atomate_env/bin/activate to your .rc or .bash_profile file so that it is run whenever you log in. Otherwise, note that you must call this command after every log in before you can do work on your atomate project.

      @@ -203,12 +196,12 @@

      MongoDBinstallation guide.

      -

      Note

      -

      All of the paths here must be absolute paths. For example, the absolute path that refers to <<INSTALL_DIR>> might be /global/homes/u/username/atomate (don’t use the relative directory ~/atomate).

      +

      Note

      +

      All of the paths here must be absolute paths. For example, the absolute path that refers to <<INSTALL_DIR>> might be /global/homes/u/username/atomate (don’t use the relative directory ~/atomate).

      -

      Warning

      -

      Passwords will be stored in plain text! These files should be stored in a place that is not accessible by unauthorized users. Also, you should make random passwords that are unique only to these databases.

      +

      Warning

      +

      Passwords will be stored in plain text! These files should be stored in a place that is not accessible by unauthorized users. Also, you should make random passwords that are unique only to these databases.

      Create the following files in <<INSTALL_DIR>>/config.

      @@ -232,18 +225,18 @@

      db.jsonΒΆ

      In FireWorks’ distributed server-worker model, each computing resource where you run jobs is a FireWorker (Worker). Each worker (like NERSC or SDSC or your local cluster) needs some configuration:

        -
      • A name to help record-keeping of what calculation ran where
        • -
      • Two parameters (category and query) that can be used to control which calculations are executed on this Worker. Our default settings will just allow all calculations to be run.
        • -
      • An env that controls the environment and settings unique to the cluster, such as the path to VASP executable or location of a scratch directory which is dependent on your computing system
        • +

      • A name to help record-keeping of what calculation ran where

        • +

      • Two parameters (category and query) that can be used to control which calculations are executed on this Worker. Our default settings will just allow all calculations to be run.

        • +

      • An env that controls the environment and settings unique to the cluster, such as the path to VASP executable or location of a scratch directory which is dependent on your computing system

      If this is the only cluster you plan on using just one Worker for all of your calculations a minimal setup for the my_fworker.yaml file is

      -
      name: <<WORKER_NAME>>
-category: ''
-query: '{}'
-env:
-    db_file: <<INSTALL_DIR>>/config/db.json
-    vasp_cmd: <<VASP_CMD>>
-    scratch_dir: null
+
      name: <<WORKER_NAME>>
+category: ''
+query: '{}'
+env:
+    db_file: <<INSTALL_DIR>>/config/db.json
+    vasp_cmd: <<VASP_CMD>>
+    scratch_dir: null
 
      
 
      
 
      Where the <<WORKER_NAME>> is arbitrary and is useful for keeping track of which Worker is running your jobs (an example might be Edison if you are running on NERSC’s Edison resource). db_file points to the db.json file that you just configured and contains credentials to connect to the calculation output database. The <<VASP_CMD>> is the command that you would use to run VASP with parallelization (srun -n 16 vasp, ibrun -n 16 vasp, mpirun -n 16 vasp, …). If you don’t know which of these to use or which VASP executable is correct, check the documentation for the computing resource you are running on or try to find them interactively by checking the output of which srun, which vasp_std, etc. Optionally, you can set the scratch_dir to something other than null if there is a particular location where you have fast disk access. This key sets the β€œroot” scratch dir; a temporary directory will be created in this root directory for each calculation. Scratch directories are only temporarily while the calculation is executing.
      
@@ -253,24 +246,24 @@ 
      my_fworker.yamlΒΆ
      
 
      The db.json file contained the information to connect to MongoDB for the calculation output database. We must also configure the database for storing and managing workflows within FireWorks using my_launchpad.yaml as in FireWorks’ server-worker model. Technically, these can be different databases but we’ll configure them as the same database.
      
 
      The LaunchPad is where all of the FireWorks and Workflows are stored. Each Worker can query this database for the status of Fireworks and pull down Fireworks to reserve them in the queue and run them. A my_launchpad.yaml file with fairly verbose logging (strm_lvl: INFO) is below:
      
-
      host: <<HOSTNAME>>
-port: <<PORT>>
-name: <<DB_NAME>>
-username: <<ADMIN_USERNAME>>
-password: <<ADMIN_PASSWORD>>
-ssl_ca_file: null
-logdir: null
-strm_lvl: INFO
-user_indices: []
-wf_user_indices: []
+
      host: <<HOSTNAME>>
+port: <<PORT>>
+name: <<DB_NAME>>
+username: <<ADMIN_USERNAME>>
+password: <<ADMIN_PASSWORD>>
+ssl_ca_file: null
+logdir: null
+strm_lvl: INFO
+user_indices: []
+wf_user_indices: []
 
      
 
      
 
      Here’s what you’ll need to fill out:
      
 
        
-
      • <<HOSTNAME>> - the host of your MongoDB db server
        • 
-
      • <<PORT>> - the port of your MongoDB db server
        • 
-
      • <<DB_NAME>> - the name of the MongoDB database
        • 
-
      • <<ADMIN_USERNAME>> and <<ADMIN_PASSWORD>> - the (write) credentials to access your DB. Delete these lines if you do not have password protection in your DB (although you should).
        • 
+
      • <<HOSTNAME>> - the host of your MongoDB db server
        • 
+
      • <<PORT>> - the port of your MongoDB db server
        • 
+
      • <<DB_NAME>> - the name of the MongoDB database
        • 
+
      • <<ADMIN_USERNAME>> and <<ADMIN_PASSWORD>> - the (write) credentials to access your DB. Delete these lines if you do not have password protection in your DB (although you should).
        • 
 
      
 
      You can optionally set logdir to your <<INSTALL_DIR>>/logs directory, although you shouldn’t need them. The strm_lvl sets the verbosity of the log and user_indices and wf_user_indices can be used to speed up targeted database queries if your project grows very large and queries are slow.
      
 
      Note: If you prefer to use the same database for FireWorks and calculation outputs, these values will largely be duplicated with db.json (this is what our tutorial is assuming). If you prefer to use different databases for workflows and calculation outputs, the information here will be different than db.json.
      
@@ -286,29 +279,29 @@ 
      my_qadapter.yamlmy_qadapter.yaml file for SLURM machines might look like
      
-
      _fw_name: CommonAdapter
-_fw_q_type: SLURM
-rocket_launch: rlaunch -c <<INSTALL_DIR>>/config rapidfire
-nodes: 2
-walltime: 24:00:00
-queue: null
-account: null
-job_name: null
-pre_rocket: null
-post_rocket: null
-logdir: <<INSTALL_DIR>>/logs
+
      _fw_name: CommonAdapter
+_fw_q_type: SLURM
+rocket_launch: rlaunch -c <<INSTALL_DIR>>/config rapidfire
+nodes: 2
+walltime: 24:00:00
+queue: null
+account: null
+job_name: null
+pre_rocket: null
+post_rocket: null
+logdir: <<INSTALL_DIR>>/logs
 
      
 
      
 
      The _fw_name: CommonAdapter means that the queue is one of the built in queue systems and _fw_q_type: SLURM indicates that the SLURM system will be used. FireWorks supports the following queue systems out of the box:
      
 
        
-
      • PBS/Torque
        • 
-
      • SLURM
        • 
-
      • SGE
        • 
-
      • IBM LoadLeveler
        • 
+
      • PBS/Torque
        • 
+
      • SLURM
        • 
+
      • SGE
        • 
+
      • IBM LoadLeveler
        • 
 
      
 
      
-
      Note
      
-
      If you aren’t sure what queue system the cluster you are setting up uses, consult the documentation for that resource. If the queue system isn’t one of these preconfigured ones, consult the FireWorks documentation for writing queue adapters. The FireWorks documentation also has tutorials on setting up your jobs to run on a queue in a way that is more interactive than the minimal details specified here.
      
+
      Note
      
+
      If you aren’t sure what queue system the cluster you are setting up uses, consult the documentation for that resource. If the queue system isn’t one of these preconfigured ones, consult the FireWorks documentation for writing queue adapters. The FireWorks documentation also has tutorials on setting up your jobs to run on a queue in a way that is more interactive than the minimal details specified here.
      
 
      
 
      nodes, walltime are the default reservations made to the queue as you would expect. queue refers to the name of the queue you will submit to. Some clusters support this and appropriate values might be regular, normal, knl, etc. as defined by the compute resource you are using. The account option refers to which account to charge. Again, whether or not you need to set this depends on the resource. pre_rocket and post_rocket add lines to before and after you job launches in your queue submission script. One use of this would be to enter directives such as #SBATCH -C knl,quad,cache to configure SLURM to run on knl nodes. Any parameters left null will not be used to write the queue file.
      
 
      This is not at all required, but if you want to see what the queue templates look like, you can see them here. The values you put in your my_qadapter.yaml file above are used to fill in the unknown values of the template.
      
@@ -317,7 +310,7 @@ 
      my_qadapter.yamlΒΆ
      
 
      As you may have noticed, there are lots of config files for controlling various aspects of FireWorks. The master config file is called FW_config.yaml, which controls different FireWorks settings and also can point to the location of other configuration files. For a more complete reference to the FireWorks parameters you can control see the FireWorks documentation for modifying the FW config. Here you simply need to accomplish telling FireWorks the location of the my_launchpad.yaml, my_qadapter.yaml and my_fworker.yaml configuration files so that you can simply tell FireWorks the location of the master config file and don’t need to always specify the location of those other files.
      
 
      Create a file called FW_config.yaml in <<INSTALL_DIR>>/config with the following contents:
      
-
      CONFIG_FILE_DIR: <<INSTALL_DIR>>/config
+
      CONFIG_FILE_DIR: <<INSTALL_DIR>>/config
 
      
 
      
 
      The CONFIG_FILE_DIR is expected to contain all your other FireWorks config files.
      
@@ -375,7 +368,7 @@ 
      Pseudopotentials.pmgrc.yaml in your home folder (i.e., ~/.pmgrc.yaml) with the following contents
      
-
      PMG_VASP_PSP_DIR: <<INSTALL_DIR>>/pps
+
      PMG_VASP_PSP_DIR: <<INSTALL_DIR>>/pps
 
      
 
      
 
      If you’d like to use a non-default functional in all of your calculations, you can set the DEFAULT_FUNCTIONAL key to a functional that is supported by VASP, e.g. PS to use PBESol.
      
@@ -383,8 +376,8 @@ 
      Pseudopotentials
 
      Materials Project API keyΒΆ
      
 
      You can get an API key from the Materials Project by logging in and going to your Dashboard. Add this also to your .pmgrc.yaml so that it looks like the following
      
-
      PMG_VASP_PSP_DIR: <<INSTALL_DIR>>/pps
-PMG_MAPI_KEY: <<YOUR_API_KEY>>
+
      PMG_VASP_PSP_DIR: <<INSTALL_DIR>>/pps
+PMG_MAPI_KEY: <<YOUR_API_KEY>>
 
      
 
      
 
      
@@ -398,16 +391,16 @@ 
      Materials Project API keyΒΆ
      
 
      Below are 4 different options for adding a workflow to the database. You only need to execute one of the below commands; note that it doesn’t matter at this point whether you are loading the workflow from a file or from a Python function.
      
 
        
-
      • Option 1 (you set up a Materials Project API key, and want to load the workflow using a file): atwf add -l vasp -s optimize_only.yaml -m mp-149 -c '{"vasp_cmd": ">>vasp_cmd<<", "db_file": ">>db_file<<"}'
        • 
-
      • Option 2 (you set up a Materials Project API key, and want to load the workflow using a Python function): atwf add -l vasp -p wf_structure_optimization -m mp-149
        • 
-
      • Option 3 (you will load the structure from a POSCAR file, and want to load the workflow using a file): atwf add -l vasp -s optimize_only.yaml POSCAR -c '{"vasp_cmd": ">>vasp_cmd<<", "db_file": ">>db_file<<"}'
        • 
-
      • Option 4 (you will load the structure from a POSCAR file, and want to load the workflow using a Python function): atwf add -l vasp -p wf_structure_optimization POSCAR
        • 
+
      • Option 1 (you set up a Materials Project API key, and want to load the workflow using a file): atwf add -l vasp -s optimize_only.yaml -m mp-149 -c '{"vasp_cmd": ">>vasp_cmd<<", "db_file": ">>db_file<<"}'
        • 
+
      • Option 2 (you set up a Materials Project API key, and want to load the workflow using a Python function): atwf add -l vasp -p wf_structure_optimization -m mp-149
        • 
+
      • Option 3 (you will load the structure from a POSCAR file, and want to load the workflow using a file): atwf add -l vasp -s optimize_only.yaml POSCAR -c '{"vasp_cmd": ">>vasp_cmd<<", "db_file": ">>db_file<<"}'
        • 
+
      • Option 4 (you will load the structure from a POSCAR file, and want to load the workflow using a Python function): atwf add -l vasp -p wf_structure_optimization POSCAR
        • 
 
      
 
      All of these function specify (i) a type of workflow and (ii) the structure to feed into that workflow.
      
 
        
-
      • The -l vasp option states to use the vasp library of workflows.
        • 
-
      • The -s optimize_only.yaml sets the specification of the workflow using the optimize_only.yaml file in this directory. Alternatively, the -p wf_structure_optimization sets the workflow specification using the preset Python function located in this module. For now, it’s probably best not to worry about the distinction but to know that both libraries of workflows are available to you.
        • 
-
      • The -c option is used in file-based workflows to make sure that one uses the vasp_cmd and db_file that are specified in my_fworker.yaml that you specified earlier. In the preset workflows, it is the default behavior to take these parameters from the my_fworker.yaml so this option is not needed.
        • 
+
      • The -l vasp option states to use the vasp library of workflows.
        • 
+
      • The -s optimize_only.yaml sets the specification of the workflow using the optimize_only.yaml file in this directory. Alternatively, the -p wf_structure_optimization sets the workflow specification using the preset Python function located in this module. For now, it’s probably best not to worry about the distinction but to know that both libraries of workflows are available to you.
        • 
+
      • The -c option is used in file-based workflows to make sure that one uses the vasp_cmd and db_file that are specified in my_fworker.yaml that you specified earlier. In the preset workflows, it is the default behavior to take these parameters from the my_fworker.yaml so this option is not needed.
        • 
 
      
 
      
 
      
@@ -438,10 +431,10 @@ 
      Submit the workflow
-
    13. The -m 1 means to keep a maximum of 1 job in the queue to prevent submitting too many jobs. As with all FireWorks commands, you can get more options using qlaunch rapidfire -h or simply qlaunch -h.
      14. 
-
    14. The qlaunch mode specified above is the simplest and most general way to get started. It will end up creating a somewhat nested directory structure, but this will make more sense when there are many calculations to run.
      15. 
-
    15. One other option for qlaunch is β€œreservation mode”, i.e., qlaunch -r rapidfire. There are many nice things about this mode - you’ll get pretty queue job names that represent your calculated composition and task type (these are really nice to see specifically which calculations are queued) and you’ll have more options for tailoring specific queue parameters to specific jobs. In addition, reservation mode will automatically stop submitting jobs to the queue depending on how many jobs you have in the database so you don’t need to use the -m 1 parameter (this is usually desirable and nice, although in some cases it’s better to submit to the queue first and add jobs to the database later which reservation mode doesn’t support). However, reservation mode does add its own complications and we do not recommend starting with it (in many if not most cases, it’s not worth switching at all). If you are interested by this option, consult the FireWorks documentation for more details.
      16. 
-
    16. If you want to run directly on your computing platform rather than through a queue, use rlaunch rapidfire instead of the qlaunch command (go through the FireWorks documentation to understand the details).
      17. 
+
    17. The -m 1 means to keep a maximum of 1 job in the queue to prevent submitting too many jobs. As with all FireWorks commands, you can get more options using qlaunch rapidfire -h or simply qlaunch -h.
      18. 
+
    18. The qlaunch mode specified above is the simplest and most general way to get started. It will end up creating a somewhat nested directory structure, but this will make more sense when there are many calculations to run.
      19. 
+
    19. One other option for qlaunch is β€œreservation mode”, i.e., qlaunch -r rapidfire. There are many nice things about this mode - you’ll get pretty queue job names that represent your calculated composition and task type (these are really nice to see specifically which calculations are queued) and you’ll have more options for tailoring specific queue parameters to specific jobs. In addition, reservation mode will automatically stop submitting jobs to the queue depending on how many jobs you have in the database so you don’t need to use the -m 1 parameter (this is usually desirable and nice, although in some cases it’s better to submit to the queue first and add jobs to the database later which reservation mode doesn’t support). However, reservation mode does add its own complications and we do not recommend starting with it (in many if not most cases, it’s not worth switching at all). If you are interested by this option, consult the FireWorks documentation for more details.
      20. 
+
    20. If you want to run directly on your computing platform rather than through a queue, use rlaunch rapidfire instead of the qlaunch command (go through the FireWorks documentation to understand the details).
      21. 
 
 
      If all went well, you can check that the FireWork is in the queue by using the commands for your queue system (e.g. squeue or qstat). When the job finally starts running, you will see the state of the workflow as running using the command lpad get_wflows -d more.
      
 
      
@@ -464,9 +457,9 @@ 
      Next steps
-
    21. To see how to run and customize the existing Workflows and FireWorks try the Running Workflows Tutorial (suggested next step)
      22. 
-
    22. For submitting jobs to the queue in reservation mode see the FireWorks advanced queue submission tutorial
      23. 
-
    23. For using pymatgen-db to query your database see the pymatgen-db documentation
      24. 
+
    24. To see how to run and customize the existing Workflows and FireWorks try the Running Workflows Tutorial (suggested next step)
      25. 
+
    25. For submitting jobs to the queue in reservation mode see the FireWorks advanced queue submission tutorial
      26. 
+
    26. For using pymatgen-db to query your database see the pymatgen-db documentation
      27. 
 
 
      
 
      
@@ -474,11 +467,9 @@ 
      Next stepsΒΆ
      
 
      
 
      Q: I can’t connect to my LaunchPad databaseΒΆ
      
-
---
-
-
-
-
-
-
-
-
-
-
      


      A:
      Make sure the right LaunchPad file is getting selected
      
+
      
+
      A
      
+
      Make sure the right LaunchPad file is getting selected
      
 
      Adding the following line to your FW_config.yaml will cause the line to be printed every time that configuration is selected
      
 
      ECHO_TEST: Database at <<INSTALL_DIR>>/config/FW_config.yaml is getting selected.
 
      
@@ -492,38 +483,31 @@ 
      Q: I can’t connect to my LaunchPad databaseecho $FW_CONFIG_FILE returns the location of that file (you could use cat $FW_CONFIG_FILE to check the contents)
      
-
      A:
      Double check all of the configuration settings in my_launchpad.yaml
      
-
      A:
      Have you had success connecting before? Is there a firewall blocking your connection?
      
-
      A:
      You can try following the tutorials of FireWorks which will go through this process in a little more detail.
      
-
      
+
+
      A
      
+
      Double check all of the configuration settings in my_launchpad.yaml
      
+
      
+
      A
      
+
      Have you had success connecting before? Is there a firewall blocking your connection?
      
+
      
+
      A
      
+
      You can try following the tutorials of FireWorks which will go through this process in a little more detail.
      
+
      
+
 
      
 
      
 
      Q: My job fizzled!ΒΆ
      
-
---
-
-
-
-
      


      A:Check the *_structure_optimization.out and *_structure_optimization.error in the launch directory for any errors. Also check the FW.json to check for a Python traceback.
      
+
      
+
      A
      
+
      Check the *_structure_optimization.out and *_structure_optimization.error in the launch directory for any errors. Also check the FW.json to check for a Python traceback.
      
+
      
+
      
 
      
 
      
 
      Q: I made a mistake using reservation mode, how do I cancel my job?ΒΆ
      
-
---
-
-
-
-
      


      A:
      One drawback of using the reservation mode (the -r in qlaunch -r rapidfire) is that you have to cancel your job in two places: the queue and the LaunchPad. To cancel the job in the queue, use whatever command you usually would (e.g. scancel or qdel). To cancel or rerun the FireWork, run
      
+
      
+
      A
      
+
      One drawback of using the reservation mode (the -r in qlaunch -r rapidfire) is that you have to cancel your job in two places: the queue and the LaunchPad. To cancel the job in the queue, use whatever command you usually would (e.g. scancel or qdel). To cancel or rerun the FireWork, run
      
 
      lpad defuse_fws -i 1
 
      
 
      
@@ -531,23 +515,18 @@ 
      Q: I made a mistake using reservation mode, how do I cancel my job?
      lpad rerun_fws -i 1
 
      
 
-
      where -i 1 means to make perfom the operations on the FireWork at index 1. Run lpad -h to see all of the options.
      
-
      
+
      where -i 1 means to make perfom the operations on the FireWork at index 1. Run lpad -h to see all of the options.
      
+
+
 
      The non-reservation mode for qlaunching requires a little less maintenance with certain tradeoffs, which are detailed in the FireWorks documentation.
      
 
      
 
      
 
      Q: I honestly tried everything I can to solve my problem. I still need help!ΒΆ
      
-
---
-
-
-
-
      


      A:There is a Google group for atomate: https://groups.google.com/forum/#!forum/atomate
      
+
      
+
      A
      
+
      There is a Google group for atomate: https://groups.google.com/forum/#!forum/atomate
      
+
      
+
      
 
      
 
      
 
      
@@ -619,13 +598,11 @@ 
      This Page
      
     
    
      
 
@@ -649,13 +626,13 @@ 
      Navigation
      
         
    27. 
           previous |
      28. 
-        
    28. atomate 0.9.1 documentation »
      29.  
+        
    29. atomate 0.9.2 documentation »
      30.  
       
     
      
 
     
 
   
diff --git a/docs/license.html b/docs/license.html
index 7187e9d2a..cd66aa692 100644
--- a/docs/license.html
+++ b/docs/license.html
@@ -1,18 +1,17 @@
 
-
+
 
 
   
-    
-    
-    License — atomate 0.9.1 documentation
+    
+    License — atomate 0.9.2 documentation
     
     
     
     
     
     
+    
     
     
     
@@ -36,7 +35,7 @@ 
      Navigation
      
         
    30. 
           previous |
      31. 
-        
    31. atomate 0.9.1 documentation »
      32.  
+        
    32. atomate 0.9.2 documentation »
      33.  
       
     
        
 
@@ -118,13 +117,11 @@ 
      This Page
      
     
    
      
 
@@ -148,13 +145,13 @@ 
      Navigation
      
         
    33. 
           previous |
      34. 
-        
    34. atomate 0.9.1 documentation »
      35.  
+        
    35. atomate 0.9.2 documentation »
      36.
      diff --git a/docs/modules.html b/docs/modules.html index ac304be2f..b26009f3b 100644 --- a/docs/modules.html +++ b/docs/modules.html @@ -1,18 +1,17 @@ - + - - - atomate — atomate 0.9.1 documentation + + atomate — atomate 0.9.2 documentation + @@ -28,7 +27,7 @@

      Navigation

    36. modules |
      37. -
    37. atomate 0.9.1 documentation »
      38. +
    38. atomate 0.9.2 documentation »
      39. @@ -119,13 +118,11 @@

      This Page

      @@ -143,13 +140,13 @@

      Navigation

    39. modules |
      40. -
    40. atomate 0.9.1 documentation »
      41. +
    41. atomate 0.9.2 documentation »
      42. diff --git a/docs/objects.inv b/docs/objects.inv index 7ea11d61c25f6b58b55f568af5f93ada41044072..9cc4518c6c3bdd8e34fe27b64e1a8debe06a78ae 100644 GIT binary patch delta 7822 zcmV;99&zDPPVg0=}VGN0^(RRnQB>^t* z?z$-7?vj*niYN{1`tsKW24`rRs(cF$JxfNK=ORX+Das}(@-Pj`unK=O&J{LImF!z; z5%6?XoAYO=d8$d%mH{h3Oq#o@$gaaQ`dmbab|A5M)|Jd$k-u7+I6eb2qQO*zCb=up zm{bTFl+ZnCPGmXt!_&}_G(kiyAxK4Ie`xcF73MYqS}rvSinb}+2D-aC z!QMR;H~XiqXaMX>4UTAF8bUk^(-8uj7{gHmv_= zdCkeK^oJw{Psk=0_~guizF{`kbqu^n6bVZDq_cCpjIZbrulIJdE*{f%Re$6JtAsUlyC6vNqzM8)g(?x#EGAi! z_A~!Jso8MqB}^062WXyakNi#pAy7u~Uglq&!Abw@DgPyqNsZcxXq!iqL+CE0B40YnsGd;?^r$TS3M2JAHdU zx_@7#UJV^&YjE4~2OOcX>+eXj+)S-g#?*Oyh~o$59iIx;|0u&)=eM>ZulVZ0KZJQGbYe37gX2%rs0r1nir>I$CQVhX1un8X`LG zz{~2?a(ZS$ga3U?FE!o!i1Oj-yZ;rm4kuGXwh|&653jn)EGP2|7H^2>fgzf z3&p2O~c)jr9O z0ZYl|&XP#Xo#|ZljLU|k&6B@c5>M2kiNIiZJp_cL7^tIVz=Qt?fj~<>Q3+{p9pa8k z`R_0%b?`p{iH`(E+y!?zOK2;yRN0v=1WwfuhKc(Y)@pz2o@jlik{N_@$%i5`OOxRQ zEq})qH>~QQWE4fPJnjb1>Wmn(YFP1$p2%cmRG(WM{VJ?SAw=zrimWVXFCpo6mq80e 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-1,18 +1,17 @@ - + - - - Python Module Index — atomate 0.9.1 documentation + + Python Module Index — atomate 0.9.2 documentation + @@ -31,7 +30,7 @@

      Navigation

    42. modules |
      43. -
    43. atomate 0.9.1 documentation »
      44. +
    44. atomate 0.9.2 documentation »
      45. @@ -801,13 +800,11 @@

      Python Module Index

      @@ -56,8 +55,8 @@

      Introduction

      ObjectivesΒΆ

        -
      • Run an atomate preset workflow using Python
        • -
      • Analyze the results using pymatgen
        • +

      • Run an atomate preset workflow using Python

        • +

      • Analyze the results using pymatgen

      @@ -77,9 +76,9 @@

      Bandstructure Workflows -
      +
      Electronic Bandstructure Workflow -

      Atomate bandstructure workflow. An optimization and static calculation followed by uniform and line non-selfconsistent calculations.

      +

      Atomate bandstructure workflow. An optimization and static calculation followed by uniform and line non-selfconsistent calculations.ΒΆ

      @@ -92,8 +91,8 @@

      Setup

      -

      Warning

      -

      This will reset all of your previous Fireworks and Workflows in your LaunchPad. Do not do this if you have actual results that you want to keep!

      +

      Warning

      +

      This will reset all of your previous Fireworks and Workflows in your LaunchPad. Do not do this if you have actual results that you want to keep!

      If you do not or want to reset your LaunchPad, you can set up a different database to use for tutorials or simply accept mixing your previous results and workflows with the contents of this tutorial in your database.

      @@ -223,10 +222,10 @@

      Analyzing a Bandstructure Workflow +
      MgO density of states
      -
      +
      MgO bandstructure
      @@ -236,9 +235,9 @@

      Conclusionatomate.vasp.workflows.presets. They can be set up the same way as in this tutorial.

      At this point, you might:

      @@ -285,13 +284,11 @@

      This Page

      @@ -315,13 +312,13 @@

      Navigation

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    46. atomate 0.9.1 documentation »
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      48. diff --git a/docs/search.html b/docs/search.html index 1911a3fa9..41e30deb8 100644 --- a/docs/search.html +++ b/docs/search.html @@ -1,12 +1,10 @@ - + - - - Search — atomate 0.9.1 documentation + + Search — atomate 0.9.2 documentation @@ -14,14 +12,11 @@ + - - - + @@ -37,7 +32,7 @@

      Navigation

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      51. @@ -88,13 +83,13 @@

      Navigation

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    53. atomate 0.9.2 documentation »
      54. diff --git a/docs/searchindex.js b/docs/searchindex.js index 683cd138a..1c4b68372 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ 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Reference"],titleterms:{"function":45,"new":48,EOS:53,The:[40,42,48],Use:[45,47,52],Using:45,add:[47,49,52],adsorpt:37,analysi:[22,28,40],analyz:[47,49,52],api:49,atom:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,41,42,44,46,48,49,51,52,53],background:44,bandgap_estim:29,bandstructur:52,base:[20,29,37],basic:[46,48],boltztrap_materi:29,builder:[29,30,40],builders_exampl:31,bulk_modulu:37,calcloc:42,calcul:[40,45,48],can:49,cancel:49,center:49,changelog:[41,48],checklist:49,cite:48,code:[46,48],common:[1,2,3],comput:49,concept:42,conclus:[44,47,52],config:27,configur:49,confirm:46,connect:49,contact:48,content:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],contribut:48,contributor:[43,48],core:[7,9,13,14,18,34,37,38,40],creat:[40,44,48,49,52],custom:[45,48],data:40,databas:[4,11,15,25,27,49],db_file:42,defin:52,deform:37,develop:46,dielectr:29,differ:[42,45],directori:49,document:48,double_ff_opt:20,drone:[11,15,27],elast:37,energi:47,env_chk:[42,44],environ:49,equat:47,everyth:49,exampl:[30,31,53],faq:49,feff:[4,5,6,7,8,9,10],ferroelectr:37,file:[52,53],file_materi:29,fileio:25,find:44,finish:49,firetask:[2,3,5,6,12,16,17,32,33],firework:[7,8,13,18,34,44],fix_task:29,fizzl:49,fragment:[16,20],free:47,fw_config:49,gener:[47,52],geo_transform:16,gibb:[23,37,47],glue_task:[2,5,12,32],help:[44,49],honestli:49,how:49,incar:45,instal:[46,48,49],introduct:[40,44,45,46,47,49,52,53],job:49,json:49,kei:49,kpoint:45,lammp:[11,12,13,14],launchpad:49,licens:[48,50],machin:42,made:49,magnet:37,materi:49,materials_descriptor:29,materials_ehul:29,mistak:49,mode:[46,49],modifi:44,modul:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],mongodb:49,more:44,my_fwork:49,my_launchpad:49,my_qadapt:49,neb:37,neb_task:32,need:49,next:49,nmr:34,object:[44,45,47,49,52],option:[46,52],other:40,own:52,packag:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,49],paramet:49,pars:48,parse_output:[2,5,12,16,32],passcalcloc:44,perform:42,phonopi:28,plot_raman:23,polar:34,post:46,post_process:23,potcar:45,powerup:[15,27,42,44,45],pre:52,prerequisit:[44,45,49,52],preset:[9,38],problem:49,project:49,pseudopotenti:49,pymatgen:49,python:[46,47,49,52],qchem:[15,16,17,18,19,20,21],raman:37,refer:[48,53],report:40,reserv:49,result:[48,49],run:[40,46,47,48,49,52],run_build:30,run_calc:[2,5,12,16,32],scaffold:49,scan:38,set:[45,48],setup:[47,52],sketch:44,solv:49,state:47,step:49,still:49,structur:52,submission_filt:27,submit:49,submodul:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,37,38,39],subpackag:[0,1,2,4,5,7,9,11,15,16,19,22,25,27,29,32,36],support:48,syntax:42,tag:29,tasks_materi:29,tasksmaterialsbuild:40,test:[3,6,8,10,17,21,24,25,26,33,35,39,46,49],test_adsorbate_workflow:39,test_bulk_modulus_workflow:39,test_copi:33,test_double_ff_opt:21,test_dron:35,test_eels_workflow:10,test_elastic_workflow:39,test_exafs_scattering_path:10,test_ferroelectric_workflow:39,test_firework:8,test_fragment:[17,21],test_geo_transform:17,test_get_interpolated_poscar:33,test_glue_task:3,test_load:26,test_magnetism_workflow:39,test_neb_workflow:39,test_nmr:39,test_parse_output:3,test_parse_pass_writ:21,test_polarization_to_db:33,test_quasiharmonic_debye_approx:24,test_raman_workflow:39,test_run_calc:17,test_setup:35,test_task:6,test_torsion_potenti:21,test_util:26,test_vasp_powerup:35,test_vasp_workflow:39,test_write_input:17,test_write_vasp:33,test_write_vasp_from_interpolated_poscar:33,test_xas_workflow:10,thermal_expans:37,tool:[22,23,24],torsion_potenti:20,tri:49,troubleshoot:49,tune:42,tutori:[48,52],unit:46,use:52,using:49,util:[11,25,26,29],vasp:[27,28,29,30,31,32,33,34,35,36,37,38,39,45,49],vasp_config:27,vasp_powerup:27,verifi:49,virtual:49,what:48,workflow:[9,10,14,19,20,21,36,37,38,39,42,44,45,47,48,49,52,53],write_input:[5,12,16,32],yaml:[49,53],your:52}}) \ No newline at end of file diff --git a/docs/workflow_yaml_reference.html b/docs/workflow_yaml_reference.html index aa37c2cae..20f7cffbe 100644 --- a/docs/workflow_yaml_reference.html +++ b/docs/workflow_yaml_reference.html @@ -1,18 +1,17 @@ - + - - - Workflow YAML Reference — atomate 0.9.1 documentation + + Workflow YAML Reference — atomate 0.9.2 documentation + @@ -36,7 +35,7 @@

      Navigation

    54. previous |
      55. -
    55. atomate 0.9.1 documentation »
      56. +
    56. atomate 0.9.2 documentation »
      57. @@ -56,23 +55,23 @@

      IntroductionΒΆ

      The following illustrates an example of a YAML file that can be used in atwf to run a workflow. Unless there is an existing YAML Workflow for the workflow you are trying to create, you will have to determine which required and optional parameters to set. Every Workflow in atomate is required to have a structure as the first parameter. This is implied in all of the YAML files and does not need to be included.

      YAML format for the usual MP bandstructure workflow is given as follows:

      -
      fireworks:
-- fw: atomate.vasp.fireworks.core.OptimizeFW
-- fw: atomate.vasp.fireworks.core.StaticFW
-  params:
-    parents: 0
-- fw: atomate.vasp.fireworks.core.NonSCFUniformFW
-  params:
-    parents: 1
-- fw: atomate.vasp.fireworks.core.NonSCFLineFW
-  params:
-    parents: 1
-common_params:
-  db_file: db.json
-  $vasp_cmd: $HOME/opt/vasp
-name: bandstructure
-metadata:
-  tag: testing_workflow
+
      fireworks:
+- fw: atomate.vasp.fireworks.core.OptimizeFW
+- fw: atomate.vasp.fireworks.core.StaticFW
+  params:
+    parents: 0
+- fw: atomate.vasp.fireworks.core.NonSCFUniformFW
+  params:
+    parents: 1
+- fw: atomate.vasp.fireworks.core.NonSCFLineFW
+  params:
+    parents: 1
+common_params:
+  db_file: db.json
+  $vasp_cmd: $HOME/opt/vasp
+name: bandstructure
+metadata:
+  tag: testing_workflow
 
      
 
      
 
      At the top there is often a comment (hashtag) describing the workflow (not shown here).
      
@@ -207,13 +206,11 @@ 
      This Page
      @@ -237,13 +234,13 @@

      Navigation

    57. previous |
      58. -
    58. atomate 0.9.1 documentation »
      59. +
    59. atomate 0.9.2 documentation »
      60. diff --git a/docs_rst/atomate.common.firetasks.rst b/docs_rst/atomate.common.firetasks.rst index 8fe439dc3..9a46b2f66 100644 --- a/docs_rst/atomate.common.firetasks.rst +++ b/docs_rst/atomate.common.firetasks.rst @@ -6,7 +6,7 @@ Subpackages .. toctree:: - atomate.common.firetasks.tests + atomate.common.firetasks.tests Submodules ---------- @@ -15,31 +15,31 @@ atomate.common.firetasks.glue\_tasks module ------------------------------------------- .. automodule:: atomate.common.firetasks.glue_tasks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.common.firetasks.parse\_outputs module ---------------------------------------------- .. automodule:: atomate.common.firetasks.parse_outputs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.common.firetasks.run\_calc module ----------------------------------------- .. automodule:: atomate.common.firetasks.run_calc - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.common.firetasks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.common.firetasks.tests.rst b/docs_rst/atomate.common.firetasks.tests.rst index c3864c09c..3618d7479 100644 --- a/docs_rst/atomate.common.firetasks.tests.rst +++ b/docs_rst/atomate.common.firetasks.tests.rst @@ -8,23 +8,23 @@ atomate.common.firetasks.tests.test\_glue\_tasks module ------------------------------------------------------- .. automodule:: atomate.common.firetasks.tests.test_glue_tasks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.common.firetasks.tests.test\_parse\_outputs module ---------------------------------------------------------- .. automodule:: atomate.common.firetasks.tests.test_parse_outputs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.common.firetasks.tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.common.rst b/docs_rst/atomate.common.rst index e2b336dc6..1dc9aa13d 100644 --- a/docs_rst/atomate.common.rst +++ b/docs_rst/atomate.common.rst @@ -6,12 +6,12 @@ Subpackages .. toctree:: - atomate.common.firetasks + atomate.common.firetasks Module contents --------------- .. automodule:: atomate.common - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.feff.firetasks.rst b/docs_rst/atomate.feff.firetasks.rst index d4e6406f4..1c87f92f8 100644 --- a/docs_rst/atomate.feff.firetasks.rst +++ b/docs_rst/atomate.feff.firetasks.rst @@ -6,7 +6,7 @@ Subpackages .. toctree:: - atomate.feff.firetasks.tests + atomate.feff.firetasks.tests Submodules ---------- @@ -15,39 +15,39 @@ atomate.feff.firetasks.glue\_tasks module ----------------------------------------- .. automodule:: atomate.feff.firetasks.glue_tasks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.feff.firetasks.parse\_outputs module -------------------------------------------- .. automodule:: atomate.feff.firetasks.parse_outputs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.feff.firetasks.run\_calc module --------------------------------------- .. automodule:: atomate.feff.firetasks.run_calc - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.feff.firetasks.write\_inputs module ------------------------------------------- .. automodule:: atomate.feff.firetasks.write_inputs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.feff.firetasks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.feff.firetasks.tests.rst b/docs_rst/atomate.feff.firetasks.tests.rst index e5ba81350..87f03e252 100644 --- a/docs_rst/atomate.feff.firetasks.tests.rst +++ b/docs_rst/atomate.feff.firetasks.tests.rst @@ -8,15 +8,15 @@ atomate.feff.firetasks.tests.test\_tasks module ----------------------------------------------- .. automodule:: atomate.feff.firetasks.tests.test_tasks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.feff.firetasks.tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.feff.fireworks.rst b/docs_rst/atomate.feff.fireworks.rst index a4030b53d..d03996d42 100644 --- a/docs_rst/atomate.feff.fireworks.rst +++ b/docs_rst/atomate.feff.fireworks.rst @@ -6,7 +6,7 @@ Subpackages .. toctree:: - atomate.feff.fireworks.tests + atomate.feff.fireworks.tests Submodules ---------- @@ -15,15 +15,15 @@ atomate.feff.fireworks.core module ---------------------------------- .. automodule:: atomate.feff.fireworks.core - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.feff.fireworks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.feff.fireworks.tests.rst b/docs_rst/atomate.feff.fireworks.tests.rst index a650fcc44..f062c8223 100644 --- a/docs_rst/atomate.feff.fireworks.tests.rst +++ b/docs_rst/atomate.feff.fireworks.tests.rst @@ -8,15 +8,15 @@ atomate.feff.fireworks.tests.test\_fireworks module --------------------------------------------------- .. automodule:: atomate.feff.fireworks.tests.test_fireworks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.feff.fireworks.tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.feff.rst b/docs_rst/atomate.feff.rst index 5c5a16fbe..4f320b8aa 100644 --- a/docs_rst/atomate.feff.rst +++ b/docs_rst/atomate.feff.rst @@ -6,9 +6,9 @@ Subpackages .. toctree:: - atomate.feff.firetasks - atomate.feff.fireworks - atomate.feff.workflows + atomate.feff.firetasks + atomate.feff.fireworks + atomate.feff.workflows Submodules ---------- @@ -17,15 +17,15 @@ atomate.feff.database module ---------------------------- .. automodule:: atomate.feff.database - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.feff - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.feff.workflows.rst b/docs_rst/atomate.feff.workflows.rst index c0b556cbf..f0f3a89c5 100644 --- a/docs_rst/atomate.feff.workflows.rst +++ b/docs_rst/atomate.feff.workflows.rst @@ -6,7 +6,7 @@ Subpackages .. toctree:: - atomate.feff.workflows.tests + atomate.feff.workflows.tests Submodules ---------- @@ -15,23 +15,23 @@ atomate.feff.workflows.core module ---------------------------------- .. automodule:: atomate.feff.workflows.core - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.feff.workflows.presets module ------------------------------------- .. automodule:: atomate.feff.workflows.presets - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.feff.workflows - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.feff.workflows.tests.rst b/docs_rst/atomate.feff.workflows.tests.rst index 5f530fddf..c4208075a 100644 --- a/docs_rst/atomate.feff.workflows.tests.rst +++ b/docs_rst/atomate.feff.workflows.tests.rst @@ -8,31 +8,31 @@ atomate.feff.workflows.tests.test\_eels\_workflows module --------------------------------------------------------- .. automodule:: atomate.feff.workflows.tests.test_eels_workflows - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.feff.workflows.tests.test\_exafs\_scattering\_paths module ------------------------------------------------------------------ .. automodule:: atomate.feff.workflows.tests.test_exafs_scattering_paths - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.feff.workflows.tests.test\_xas\_workflows module -------------------------------------------------------- .. automodule:: atomate.feff.workflows.tests.test_xas_workflows - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.feff.workflows.tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.lammps.firetasks.rst b/docs_rst/atomate.lammps.firetasks.rst index 831eed402..a51a9ec0a 100644 --- a/docs_rst/atomate.lammps.firetasks.rst +++ b/docs_rst/atomate.lammps.firetasks.rst @@ -8,39 +8,39 @@ atomate.lammps.firetasks.glue\_tasks module ------------------------------------------- .. automodule:: atomate.lammps.firetasks.glue_tasks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.lammps.firetasks.parse\_outputs module ---------------------------------------------- .. automodule:: atomate.lammps.firetasks.parse_outputs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.lammps.firetasks.run\_calc module ----------------------------------------- .. automodule:: atomate.lammps.firetasks.run_calc - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.lammps.firetasks.write\_inputs module --------------------------------------------- .. automodule:: atomate.lammps.firetasks.write_inputs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.lammps.firetasks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.lammps.fireworks.rst b/docs_rst/atomate.lammps.fireworks.rst index 56f292f55..69c699cbb 100644 --- a/docs_rst/atomate.lammps.fireworks.rst +++ b/docs_rst/atomate.lammps.fireworks.rst @@ -8,15 +8,15 @@ atomate.lammps.fireworks.core module ------------------------------------ .. automodule:: atomate.lammps.fireworks.core - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.lammps.fireworks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.lammps.rst b/docs_rst/atomate.lammps.rst index a4cfa696d..267a7e4d8 100644 --- a/docs_rst/atomate.lammps.rst +++ b/docs_rst/atomate.lammps.rst @@ -6,9 +6,9 @@ Subpackages .. toctree:: - atomate.lammps.firetasks - atomate.lammps.fireworks - atomate.lammps.workflows + atomate.lammps.firetasks + atomate.lammps.fireworks + atomate.lammps.workflows Submodules ---------- @@ -17,31 +17,31 @@ atomate.lammps.database module ------------------------------ .. automodule:: atomate.lammps.database - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.lammps.drones module ---------------------------- .. automodule:: atomate.lammps.drones - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.lammps.utils module --------------------------- .. automodule:: atomate.lammps.utils - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.lammps - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.lammps.workflows.rst b/docs_rst/atomate.lammps.workflows.rst index b1696325d..cd2f9ee0d 100644 --- a/docs_rst/atomate.lammps.workflows.rst +++ b/docs_rst/atomate.lammps.workflows.rst @@ -8,15 +8,15 @@ atomate.lammps.workflows.core module ------------------------------------ .. automodule:: atomate.lammps.workflows.core - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.lammps.workflows - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.qchem.firetasks.rst b/docs_rst/atomate.qchem.firetasks.rst index c0891fbd5..67b339cee 100644 --- a/docs_rst/atomate.qchem.firetasks.rst +++ b/docs_rst/atomate.qchem.firetasks.rst @@ -6,7 +6,7 @@ Subpackages .. toctree:: - atomate.qchem.firetasks.tests + atomate.qchem.firetasks.tests Submodules ---------- @@ -15,47 +15,47 @@ atomate.qchem.firetasks.fragmenter module ----------------------------------------- .. automodule:: atomate.qchem.firetasks.fragmenter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.qchem.firetasks.geo\_transformations module --------------------------------------------------- .. automodule:: atomate.qchem.firetasks.geo_transformations - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.qchem.firetasks.parse\_outputs module --------------------------------------------- .. automodule:: atomate.qchem.firetasks.parse_outputs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.qchem.firetasks.run\_calc module ---------------------------------------- .. automodule:: atomate.qchem.firetasks.run_calc - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.qchem.firetasks.write\_inputs module -------------------------------------------- .. automodule:: atomate.qchem.firetasks.write_inputs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.qchem.firetasks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.qchem.firetasks.tests.rst b/docs_rst/atomate.qchem.firetasks.tests.rst index ee76f60cd..d1e1f88b4 100644 --- a/docs_rst/atomate.qchem.firetasks.tests.rst +++ b/docs_rst/atomate.qchem.firetasks.tests.rst @@ -8,39 +8,39 @@ atomate.qchem.firetasks.tests.test\_fragmenter module ----------------------------------------------------- .. automodule:: atomate.qchem.firetasks.tests.test_fragmenter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.qchem.firetasks.tests.test\_geo\_transformations module --------------------------------------------------------------- .. automodule:: atomate.qchem.firetasks.tests.test_geo_transformations - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.qchem.firetasks.tests.test\_run\_calc module ---------------------------------------------------- .. automodule:: atomate.qchem.firetasks.tests.test_run_calc - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.qchem.firetasks.tests.test\_write\_inputs module -------------------------------------------------------- .. automodule:: atomate.qchem.firetasks.tests.test_write_inputs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.qchem.firetasks.tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.qchem.fireworks.rst b/docs_rst/atomate.qchem.fireworks.rst index fa2bf9b1a..daf315c94 100644 --- a/docs_rst/atomate.qchem.fireworks.rst +++ b/docs_rst/atomate.qchem.fireworks.rst @@ -8,15 +8,15 @@ atomate.qchem.fireworks.core module ----------------------------------- .. automodule:: atomate.qchem.fireworks.core - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.qchem.fireworks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.qchem.rst b/docs_rst/atomate.qchem.rst index ccd529d7e..fcc9bc660 100644 --- a/docs_rst/atomate.qchem.rst +++ b/docs_rst/atomate.qchem.rst @@ -6,9 +6,9 @@ Subpackages .. toctree:: - atomate.qchem.firetasks - atomate.qchem.fireworks - atomate.qchem.workflows + atomate.qchem.firetasks + atomate.qchem.fireworks + atomate.qchem.workflows Submodules ---------- @@ -17,31 +17,31 @@ atomate.qchem.database module ----------------------------- .. automodule:: atomate.qchem.database - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.qchem.drones module --------------------------- .. automodule:: atomate.qchem.drones - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.qchem.powerups module ----------------------------- .. automodule:: atomate.qchem.powerups - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.qchem - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.qchem.workflows.base.rst b/docs_rst/atomate.qchem.workflows.base.rst index 1c34ecb74..aec9b27ab 100644 --- a/docs_rst/atomate.qchem.workflows.base.rst +++ b/docs_rst/atomate.qchem.workflows.base.rst @@ -8,31 +8,31 @@ atomate.qchem.workflows.base.double\_FF\_opt module --------------------------------------------------- .. automodule:: atomate.qchem.workflows.base.double_FF_opt - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.qchem.workflows.base.fragmentation module ------------------------------------------------- .. automodule:: atomate.qchem.workflows.base.fragmentation - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.qchem.workflows.base.torsion\_potential module ------------------------------------------------------ .. automodule:: atomate.qchem.workflows.base.torsion_potential - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.qchem.workflows.base - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.qchem.workflows.rst b/docs_rst/atomate.qchem.workflows.rst index cabb11e36..fb13d4b71 100644 --- a/docs_rst/atomate.qchem.workflows.rst +++ b/docs_rst/atomate.qchem.workflows.rst @@ -6,13 +6,13 @@ Subpackages .. toctree:: - atomate.qchem.workflows.base - atomate.qchem.workflows.tests + atomate.qchem.workflows.base + atomate.qchem.workflows.tests Module contents --------------- .. automodule:: atomate.qchem.workflows - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.qchem.workflows.tests.rst b/docs_rst/atomate.qchem.workflows.tests.rst index 417d98d0a..2f885743d 100644 --- a/docs_rst/atomate.qchem.workflows.tests.rst +++ b/docs_rst/atomate.qchem.workflows.tests.rst @@ -8,39 +8,39 @@ atomate.qchem.workflows.tests.test\_double\_FF\_opt module ---------------------------------------------------------- .. automodule:: atomate.qchem.workflows.tests.test_double_FF_opt - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.qchem.workflows.tests.test\_fragmentation module -------------------------------------------------------- .. automodule:: atomate.qchem.workflows.tests.test_fragmentation - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.qchem.workflows.tests.test\_parse\_pass\_write module ------------------------------------------------------------- .. automodule:: atomate.qchem.workflows.tests.test_parse_pass_write - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.qchem.workflows.tests.test\_torsion\_potential module ------------------------------------------------------------- .. automodule:: atomate.qchem.workflows.tests.test_torsion_potential - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.qchem.workflows.tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.rst b/docs_rst/atomate.rst index 329a5e3f3..24c3f1a76 100644 --- a/docs_rst/atomate.rst +++ b/docs_rst/atomate.rst @@ -6,17 +6,17 @@ Subpackages .. toctree:: - atomate.common - atomate.feff - atomate.lammps - atomate.qchem - atomate.utils - atomate.vasp + atomate.common + atomate.feff + atomate.lammps + atomate.qchem + atomate.utils + atomate.vasp Module contents --------------- .. automodule:: atomate - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.utils.rst b/docs_rst/atomate.utils.rst index 54694c2f8..aa4ead052 100644 --- a/docs_rst/atomate.utils.rst +++ b/docs_rst/atomate.utils.rst @@ -6,7 +6,7 @@ Subpackages .. toctree:: - atomate.utils.tests + atomate.utils.tests Submodules ---------- @@ -15,39 +15,39 @@ atomate.utils.database module ----------------------------- .. automodule:: atomate.utils.database - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.utils.fileio module --------------------------- .. automodule:: atomate.utils.fileio - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.utils.testing module ---------------------------- .. automodule:: atomate.utils.testing - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.utils.utils module -------------------------- .. automodule:: atomate.utils.utils - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.utils - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.utils.tests.rst b/docs_rst/atomate.utils.tests.rst index ee47601b7..ba30a5ae5 100644 --- a/docs_rst/atomate.utils.tests.rst +++ b/docs_rst/atomate.utils.tests.rst @@ -8,23 +8,23 @@ atomate.utils.tests.test\_loaders module ---------------------------------------- .. automodule:: atomate.utils.tests.test_loaders - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.utils.tests.test\_utils module -------------------------------------- .. automodule:: atomate.utils.tests.test_utils - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.utils.tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.vasp.analysis.rst b/docs_rst/atomate.vasp.analysis.rst index e5e879c58..ced41e6ce 100644 --- a/docs_rst/atomate.vasp.analysis.rst +++ b/docs_rst/atomate.vasp.analysis.rst @@ -8,15 +8,15 @@ atomate.vasp.analysis.phonopy module ------------------------------------ .. automodule:: atomate.vasp.analysis.phonopy - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.vasp.analysis - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.vasp.builders.examples.rst b/docs_rst/atomate.vasp.builders.examples.rst index 51a8b2cc6..3154f1c0d 100644 --- a/docs_rst/atomate.vasp.builders.examples.rst +++ b/docs_rst/atomate.vasp.builders.examples.rst @@ -8,15 +8,15 @@ atomate.vasp.builders.examples.run\_builders module --------------------------------------------------- .. automodule:: atomate.vasp.builders.examples.run_builders - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.vasp.builders.examples - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.vasp.builders.rst b/docs_rst/atomate.vasp.builders.rst index 81577e68b..7f07a3253 100644 --- a/docs_rst/atomate.vasp.builders.rst +++ b/docs_rst/atomate.vasp.builders.rst @@ -6,7 +6,7 @@ Subpackages .. toctree:: - atomate.vasp.builders.examples + atomate.vasp.builders.examples Submodules ---------- @@ -15,95 +15,95 @@ atomate.vasp.builders.bandgap\_estimation module ------------------------------------------------ .. automodule:: atomate.vasp.builders.bandgap_estimation - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.builders.base module --------------------------------- .. automodule:: atomate.vasp.builders.base - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.builders.boltztrap\_materials module ------------------------------------------------- .. automodule:: atomate.vasp.builders.boltztrap_materials - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.builders.dielectric module --------------------------------------- .. automodule:: atomate.vasp.builders.dielectric - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.builders.file\_materials module -------------------------------------------- .. automodule:: atomate.vasp.builders.file_materials - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.builders.fix\_tasks module --------------------------------------- .. automodule:: atomate.vasp.builders.fix_tasks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.builders.materials\_descriptor module -------------------------------------------------- .. automodule:: atomate.vasp.builders.materials_descriptor - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.builders.materials\_ehull module --------------------------------------------- .. automodule:: atomate.vasp.builders.materials_ehull - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.builders.tags module --------------------------------- .. automodule:: atomate.vasp.builders.tags - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.builders.tasks\_materials module --------------------------------------------- .. automodule:: atomate.vasp.builders.tasks_materials - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.builders.utils module ---------------------------------- .. automodule:: atomate.vasp.builders.utils - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.vasp.builders - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.vasp.firetasks.rst b/docs_rst/atomate.vasp.firetasks.rst index a53af1367..f2e04229c 100644 --- a/docs_rst/atomate.vasp.firetasks.rst +++ b/docs_rst/atomate.vasp.firetasks.rst @@ -6,7 +6,7 @@ Subpackages .. toctree:: - atomate.vasp.firetasks.tests + atomate.vasp.firetasks.tests Submodules ---------- @@ -15,47 +15,47 @@ atomate.vasp.firetasks.glue\_tasks module ----------------------------------------- .. automodule:: atomate.vasp.firetasks.glue_tasks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.firetasks.neb\_tasks module ---------------------------------------- .. automodule:: atomate.vasp.firetasks.neb_tasks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.firetasks.parse\_outputs module -------------------------------------------- .. automodule:: atomate.vasp.firetasks.parse_outputs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.firetasks.run\_calc module --------------------------------------- .. automodule:: atomate.vasp.firetasks.run_calc - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.firetasks.write\_inputs module ------------------------------------------- .. automodule:: atomate.vasp.firetasks.write_inputs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.vasp.firetasks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.vasp.firetasks.tests.rst b/docs_rst/atomate.vasp.firetasks.tests.rst index 962cee330..a8d1755d0 100644 --- a/docs_rst/atomate.vasp.firetasks.tests.rst +++ b/docs_rst/atomate.vasp.firetasks.tests.rst @@ -8,47 +8,47 @@ atomate.vasp.firetasks.tests.test\_copy module ---------------------------------------------- .. automodule:: atomate.vasp.firetasks.tests.test_copy - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.firetasks.tests.test\_get\_interpolated\_poscar module ------------------------------------------------------------------- .. automodule:: atomate.vasp.firetasks.tests.test_get_interpolated_poscar - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.firetasks.tests.test\_polarization\_to\_db module -------------------------------------------------------------- .. automodule:: atomate.vasp.firetasks.tests.test_polarization_to_db - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.firetasks.tests.test\_write\_vasp module ----------------------------------------------------- .. automodule:: atomate.vasp.firetasks.tests.test_write_vasp - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.firetasks.tests.test\_write\_vasp\_from\_interpolated\_poscar module --------------------------------------------------------------------------------- .. automodule:: atomate.vasp.firetasks.tests.test_write_vasp_from_interpolated_poscar - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.vasp.firetasks.tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.vasp.fireworks.rst b/docs_rst/atomate.vasp.fireworks.rst index 82ffec4c8..9490e08b0 100644 --- a/docs_rst/atomate.vasp.fireworks.rst +++ b/docs_rst/atomate.vasp.fireworks.rst @@ -8,31 +8,31 @@ atomate.vasp.fireworks.core module ---------------------------------- .. automodule:: atomate.vasp.fireworks.core - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.fireworks.nmr module --------------------------------- .. automodule:: atomate.vasp.fireworks.nmr - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.fireworks.polarization module ------------------------------------------ .. automodule:: atomate.vasp.fireworks.polarization - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.vasp.fireworks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.vasp.rst b/docs_rst/atomate.vasp.rst index 17b396afd..006b0e2c8 100644 --- a/docs_rst/atomate.vasp.rst +++ b/docs_rst/atomate.vasp.rst @@ -6,12 +6,12 @@ Subpackages .. toctree:: - atomate.vasp.analysis - atomate.vasp.builders - atomate.vasp.firetasks - atomate.vasp.fireworks - atomate.vasp.tests - atomate.vasp.workflows + atomate.vasp.analysis + atomate.vasp.builders + atomate.vasp.firetasks + atomate.vasp.fireworks + atomate.vasp.tests + atomate.vasp.workflows Submodules ---------- @@ -20,63 +20,63 @@ atomate.vasp.config module -------------------------- .. automodule:: atomate.vasp.config - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.database module ---------------------------- .. automodule:: atomate.vasp.database - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.drones module -------------------------- .. automodule:: atomate.vasp.drones - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.powerups module ---------------------------- .. automodule:: atomate.vasp.powerups - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.submission\_filter module -------------------------------------- .. automodule:: atomate.vasp.submission_filter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.vasp\_config module -------------------------------- .. automodule:: atomate.vasp.vasp_config - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.vasp\_powerups module ---------------------------------- .. automodule:: atomate.vasp.vasp_powerups - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.vasp - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.vasp.tests.rst b/docs_rst/atomate.vasp.tests.rst index 81d0eb2db..56d3d965f 100644 --- a/docs_rst/atomate.vasp.tests.rst +++ b/docs_rst/atomate.vasp.tests.rst @@ -8,31 +8,31 @@ atomate.vasp.tests.test\_drones module -------------------------------------- .. automodule:: atomate.vasp.tests.test_drones - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.tests.test\_setup module ------------------------------------- .. automodule:: atomate.vasp.tests.test_setup - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.tests.test\_vasp\_powerups module ---------------------------------------------- .. automodule:: atomate.vasp.tests.test_vasp_powerups - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.vasp.tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.vasp.workflows.base.rst b/docs_rst/atomate.vasp.workflows.base.rst index b42dc89da..31b694d3d 100644 --- a/docs_rst/atomate.vasp.workflows.base.rst +++ b/docs_rst/atomate.vasp.workflows.base.rst @@ -8,95 +8,95 @@ atomate.vasp.workflows.base.adsorption module --------------------------------------------- .. automodule:: atomate.vasp.workflows.base.adsorption - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.base.bulk\_modulus module ------------------------------------------------ .. automodule:: atomate.vasp.workflows.base.bulk_modulus - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.base.core module --------------------------------------- .. automodule:: atomate.vasp.workflows.base.core - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.base.deformations module ----------------------------------------------- .. automodule:: atomate.vasp.workflows.base.deformations - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.base.elastic module ------------------------------------------ .. automodule:: atomate.vasp.workflows.base.elastic - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.base.ferroelectric module ------------------------------------------------ .. automodule:: atomate.vasp.workflows.base.ferroelectric - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.base.gibbs module ---------------------------------------- .. automodule:: atomate.vasp.workflows.base.gibbs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.base.magnetism module -------------------------------------------- .. automodule:: atomate.vasp.workflows.base.magnetism - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.base.neb module -------------------------------------- .. automodule:: atomate.vasp.workflows.base.neb - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.base.raman module ---------------------------------------- .. automodule:: atomate.vasp.workflows.base.raman - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.base.thermal\_expansion module ----------------------------------------------------- .. automodule:: atomate.vasp.workflows.base.thermal_expansion - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.vasp.workflows.base - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.vasp.workflows.presets.rst b/docs_rst/atomate.vasp.workflows.presets.rst index 9ebf30ba7..09e7551b2 100644 --- a/docs_rst/atomate.vasp.workflows.presets.rst +++ b/docs_rst/atomate.vasp.workflows.presets.rst @@ -8,23 +8,23 @@ atomate.vasp.workflows.presets.core module ------------------------------------------ .. automodule:: atomate.vasp.workflows.presets.core - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.presets.scan module ------------------------------------------ .. automodule:: atomate.vasp.workflows.presets.scan - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.vasp.workflows.presets - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.vasp.workflows.rst b/docs_rst/atomate.vasp.workflows.rst index 08f5cdf19..e474f791d 100644 --- a/docs_rst/atomate.vasp.workflows.rst +++ b/docs_rst/atomate.vasp.workflows.rst @@ -6,14 +6,14 @@ Subpackages .. toctree:: - atomate.vasp.workflows.base - atomate.vasp.workflows.presets - atomate.vasp.workflows.tests + atomate.vasp.workflows.base + atomate.vasp.workflows.presets + atomate.vasp.workflows.tests Module contents --------------- .. automodule:: atomate.vasp.workflows - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/atomate.vasp.workflows.tests.rst b/docs_rst/atomate.vasp.workflows.tests.rst index 48e98f18a..62ff4bc8a 100644 --- a/docs_rst/atomate.vasp.workflows.tests.rst +++ b/docs_rst/atomate.vasp.workflows.tests.rst @@ -8,79 +8,79 @@ atomate.vasp.workflows.tests.test\_adsorbate\_workflow module ------------------------------------------------------------- .. automodule:: atomate.vasp.workflows.tests.test_adsorbate_workflow - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.tests.test\_bulk\_modulus\_workflow module ----------------------------------------------------------------- .. automodule:: atomate.vasp.workflows.tests.test_bulk_modulus_workflow - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.tests.test\_elastic\_workflow module ----------------------------------------------------------- .. automodule:: atomate.vasp.workflows.tests.test_elastic_workflow - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.tests.test\_ferroelectric\_workflow module ----------------------------------------------------------------- .. automodule:: atomate.vasp.workflows.tests.test_ferroelectric_workflow - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.tests.test\_magnetism\_workflow module ------------------------------------------------------------- .. automodule:: atomate.vasp.workflows.tests.test_magnetism_workflow - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.tests.test\_neb\_workflow module ------------------------------------------------------- .. automodule:: atomate.vasp.workflows.tests.test_neb_workflow - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.tests.test\_nmr module --------------------------------------------- .. automodule:: atomate.vasp.workflows.tests.test_nmr - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.tests.test\_raman\_workflow module --------------------------------------------------------- .. automodule:: atomate.vasp.workflows.tests.test_raman_workflow - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: atomate.vasp.workflows.tests.test\_vasp\_workflows module --------------------------------------------------------- .. automodule:: atomate.vasp.workflows.tests.test_vasp_workflows - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Module contents --------------- .. automodule:: atomate.vasp.workflows.tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/docs_rst/changelog.rst b/docs_rst/changelog.rst index bc264a6ad..946bfa0a8 100644 --- a/docs_rst/changelog.rst +++ b/docs_rst/changelog.rst @@ -2,6 +2,10 @@ atomate Changelog ================= +**v0.9.2** + +* fix CalcDB authentication issue (M. Bercx) + **v0.9.1** * bugfix: ``vasp_input_set_params`` --> ``vasp_input_params`` in some cases (thanks to M. Horton for pointing out) diff --git a/docs_rst/contributors.rst b/docs_rst/contributors.rst index 18c663c56..0735c88f2 100644 --- a/docs_rst/contributors.rst +++ b/docs_rst/contributors.rst @@ -12,4 +12,4 @@ Contributions are provided by: * Brandon Bocklund, who led the atomate documentation effort, through the research group of Prof. Zi-Kiu Liu at Penn State. * Tess Smidt through the research group of Prof. Jeff Neaton at UC Berkeley. * Danny Broberg through the research group of Prof. Mark Asta at UC Berkeley. -* External contributors: specter119, M. Dias Costa, S. Torrisi, Max Dylla +* External contributors: specter119, M. Dias Costa, S. Torrisi, Max Dylla, Marnik Bercx diff --git a/setup.py b/setup.py index 3f31a5395..5708ec249 100644 --- a/setup.py +++ b/setup.py @@ -9,7 +9,7 @@ if __name__ == "__main__": setup( name='atomate', - version='0.9.1', + version='0.9.2', description='atomate has implementations of FireWorks workflows for ' 'Materials Science', long_description=open(os.path.join(module_dir, 'README.md')).read(),