Merge pull request #9 from SpM-lab/spellcheck

add function of spelling check for making documentation

docs/manual/build/html/_sources/docs/inputfile.rst.txt

@@ -7,7 +7,7 @@
 
 Input files
 ===============================
-1. Paramete file (param.in)
+1. Parameter file (param.in)
 
 The variables for which default value is not given are mandatory.
 
@@ -47,7 +47,7 @@ The variables for which default value is not given are mandatory.
      :widths: 1,1,2,4
 
      Name, Type, Default value, Description
-     SVmin, Double, 1e-10, Truncation value of singlular values.
+     SVmin, Double, 1e-10, Truncation value of singular values.
 
 
 * ADMM
@@ -62,7 +62,7 @@ The variables for which default value is not given are mandatory.
      lambdalogend, Double, -1, The log value of minimum lambda. lambda_min is given by :math:`10^{\verb|lambdalogend|}`
      Nlambda, Integer, ---,  The number of lambda to be calculated.
      penalty, Double, 10.0, "The value of penalty coefficient. If negative, penalty is optimized during the iteration starting with its absolute value."
-     tolerance, Double, 1e-6, The criteria of convergience.
+     tolerance, Double, 1e-6, The criteria of convergence.
      maxiteration, Integer,1000,	The maximum number of iterations.
      printlevel, Integer,2,	"0; minimum, 1; moderate, 2; verbose."
 
@@ -71,4 +71,4 @@ The variables for which default value is not given are mandatory.
    In SPM, the values of Green's function is only used for calculation,
    i.e. tau is automatically determined by the beta and the step.
    Please indicate the column number where the values of G(tau) are
-   stored by "column" in the prameter file.
+   stored by "column" in the parameter file.

docs/manual/build/html/_sources/docs/tutorials.rst.txt

@@ -150,7 +150,7 @@ Let us look at some graphs below.
 
 - *find_lambda_opt.eps*
 
-    User should check how the regularization parameter :math:`\lambda` is determined and whether the choice is resonable.
+    User should check how the regularization parameter :math:`\lambda` is determined and whether the choice is reasonable.
     Loot at the file ``output/find_lambda_opt.eps``
 
     .. image:: figs/find_lambda_opt.jpg

docs/manual/build/html/_sources/index.rst.txt

@@ -5,7 +5,7 @@
 
 Welcome to SpM's documentation!
 ===============================
-This is a documantation of Sparse Modeling (SpM) tool for analytical continuation.
+This is a documentation of Sparse Modeling (SpM) tool for analytical continuation.
 
 What is SpM ?
 -------------

docs/manual/build/html/_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -82,9 +82,21 @@ div.sphinxsidebar input {
 }
 
 div.sphinxsidebar #searchbox input[type="text"] {
-    width: 170px;
+    float: left;
+    width: 80%;
+    padding: 0.25em;
+    box-sizing: border-box;
+}
+
+div.sphinxsidebar #searchbox input[type="submit"] {
+    float: left;
+    width: 20%;
+    border-left: none;
+    padding: 0.25em;
+    box-sizing: border-box;
 }
 
+
 img {
     border: 0;
     max-width: 100%;
@@ -199,6 +211,11 @@ table.modindextable td {
 
 /* -- general body styles --------------------------------------------------- */
 
+div.body {
+    min-width: 450px;
+    max-width: 800px;
+}
+
 div.body p, div.body dd, div.body li, div.body blockquote {
     -moz-hyphens: auto;
     -ms-hyphens: auto;
@@ -332,6 +349,11 @@ table.docutils {
     border-collapse: collapse;
 }
 
+table.align-center {
+    margin-left: auto;
+    margin-right: auto;
+}
+
 table caption span.caption-number {
     font-style: italic;
 }

docs/manual/build/html/_static/doctools.js

@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for all documentation.
  *
- * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -204,7 +204,7 @@ var Documentation = {
    * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
    */
   fixFirefoxAnchorBug : function() {
-    if (document.location.hash)
+    if (document.location.hash && $.browser.mozilla)
       window.setTimeout(function() {
         document.location.href += '';
       }, 10);

docs/manual/build/html/_static/searchtools.js

@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for the full-text search.
  *
- * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

docs/manual/build/html/_static/websupport.js

@@ -4,7 +4,7 @@
  *
  * sphinx.websupport utilities for all documentation.
  *
- * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -301,7 +301,7 @@
     li.hide();
 
     // Determine where in the parents children list to insert this comment.
-    for(i=0; i < siblings.length; i++) {
+    for(var i=0; i < siblings.length; i++) {
       if (comp(comment, siblings[i]) <= 0) {
         $('#cd' + siblings[i].id)
           .parent()

docs/manual/build/html/docs/algorithm.html

@@ -4,20 +4,12 @@
 
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
+    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     <title>3. Algorithm &#8212; SpM 1.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-    <script type="text/javascript">
-      var DOCUMENTATION_OPTIONS = {
-        URL_ROOT:    '../',
-        VERSION:     '1.0.0',
-        COLLAPSE_INDEX: false,
-        FILE_SUFFIX: '.html',
-        HAS_SOURCE:  true,
-        SOURCELINK_SUFFIX: '.txt'
-      };
-    </script>
+    <script type="text/javascript" src="../_static/documentation_options.js"></script>
     <script type="text/javascript" src="../_static/jquery.js"></script>
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
@@ -31,8 +23,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
-  </head>
-  <body>
+  </head><body>
 
 
     <div class="document">
@@ -42,15 +33,15 @@
 
   <div class="section" id="algorithm">
 <h1>3. Algorithm<a class="headerlink" href="#algorithm" title="Permalink to this headline">¶</a></h1>
-<p><code class="docutils literal"><span class="pre">SpM</span></code> program solves the linear equation <img class="math" src="../_images/math/379721c563c5940c2c493c638e2bbd7607140312.png" alt="\bm{G}=K\bm{\rho}"/> with respect to <img class="math" src="../_images/math/08ee2ced3e4c74283f24491dbb1e4612e1953b38.png" alt="\bm{\rho}"/> for given <img class="math" src="../_images/math/d3abeeec19e04fc372e23a3383efcb60678ecdb8.png" alt="\bm{G}"/>.
+<p><code class="docutils literal notranslate"><span class="pre">SpM</span></code> program solves the linear equation <img class="math" src="../_images/math/379721c563c5940c2c493c638e2bbd7607140312.png" alt="\bm{G}=K\bm{\rho}"/> with respect to <img class="math" src="../_images/math/08ee2ced3e4c74283f24491dbb1e4612e1953b38.png" alt="\bm{\rho}"/> for given <img class="math" src="../_images/math/d3abeeec19e04fc372e23a3383efcb60678ecdb8.png" alt="\bm{G}"/>.
 Because of <strong>ill-conditioned</strong> nature of the matrix <img class="math" src="../_images/math/684381a21cd73ebbf43b63a087d3f7410ee99ce8.png" alt="K"/>, a simple treatment of this equation is numerically unstable.
 For example, the solution using the <a class="reference external" href="https://en.wikipedia.org/wiki/Moore%E2%80%93Penrose_pseudoinverse">Moore-Penrose pseudo-inverse matrix</a>
 results in NaN.
 Even if one manages to derive a definite solution, it is quite sensitive to numerical noise and often breaks preconditions that any physical spectra must satisfy.
 This becomes particularly problematic when <img class="math" src="../_images/math/d3abeeec19e04fc372e23a3383efcb60678ecdb8.png" alt="\bm{G}"/> is evaluated by quantum Monte Carlo technique.</p>
-<p><code class="docutils literal"><span class="pre">SpM</span></code> provides a <strong>physical</strong> solution which fulfills the equation of concern within a certain accuracy.
+<p><code class="docutils literal notranslate"><span class="pre">SpM</span></code> provides a <strong>physical</strong> solution which fulfills the equation of concern within a certain accuracy.
 The solution satisfies the constraints such as sum rule and nonnegativity.
-The engine of <code class="docutils literal"><span class="pre">SpM</span></code> program uses the method of <strong>L1-norm regularization</strong> to separate relevant information in <img class="math" src="../_images/math/d3abeeec19e04fc372e23a3383efcb60678ecdb8.png" alt="\bm{G}"/> from irrelevant one which makes the spectrum unphysical. This process is automatically done without hand-tuning parameters.</p>
+The engine of <code class="docutils literal notranslate"><span class="pre">SpM</span></code> program uses the method of <strong>L1-norm regularization</strong> to separate relevant information in <img class="math" src="../_images/math/d3abeeec19e04fc372e23a3383efcb60678ecdb8.png" alt="\bm{G}"/> from irrelevant one which makes the spectrum unphysical. This process is automatically done without hand-tuning parameters.</p>
 <p>For details, see the original article</p>
 <blockquote>
 <div>J. Otsuki, M. Ohzeki, H. Shinaoka, K. Yoshimi,
@@ -99,12 +90,14 @@ <h3>Related Topics</h3>
 </div>
 <div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
+    <div class="searchformwrapper">
     <form class="search" action="../search.html" method="get">
-      <div><input type="text" name="q" /></div>
-      <div><input type="submit" value="Go" /></div>
+      <input type="text" name="q" />
+      <input type="submit" value="Go" />
       <input type="hidden" name="check_keywords" value="yes" />
       <input type="hidden" name="area" value="default" />
     </form>
+    </div>
 </div>
 <script type="text/javascript">$('#searchbox').show(0);</script>
         </div>
@@ -115,7 +108,7 @@ <h3>Quick search</h3>
       &copy;2017, Junya Otsuki, Kazuyoshi Yoshimi, Hiroshi Shinaoka.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.6.5</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.7.1</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.10</a>
 
       |

docs/manual/build/html/docs/function.html

@@ -4,20 +4,12 @@
 
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
+    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     <title>4. Calculation flow &#8212; SpM 1.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-    <script type="text/javascript">
-      var DOCUMENTATION_OPTIONS = {
-        URL_ROOT:    '../',
-        VERSION:     '1.0.0',
-        COLLAPSE_INDEX: false,
-        FILE_SUFFIX: '.html',
-        HAS_SOURCE:  true,
-        SOURCELINK_SUFFIX: '.txt'
-      };
-    </script>
+    <script type="text/javascript" src="../_static/documentation_options.js"></script>
     <script type="text/javascript" src="../_static/jquery.js"></script>
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
@@ -31,8 +23,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
-  </head>
-  <body>
+  </head><body>
 
 
     <div class="document">
@@ -62,11 +53,11 @@ <h2>4.1. Overview of calculation flow<a class="headerlink" href="#overview-of-ca
   <rect fill="rgb(0,0,0)" height="40" stroke="rgb(0,0,0)" style="filter:url(#filter_blur);opacity:0.7;fill-opacity:1" width="128" x="259" y="46" />
   <rect fill="rgb(0,0,0)" height="40" stroke="rgb(0,0,0)" style="filter:url(#filter_blur);opacity:0.7;fill-opacity:1" width="128" x="451" y="46" />
   <rect fill="rgb(255,255,255)" height="40" stroke="rgb(0,0,0)" width="128" x="64" y="40" />
-  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="126" x="128" y="66">Set initial condition</text>
+  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="126" x="128.0" y="66">Set initial condition</text>
   <rect fill="rgb(255,255,255)" height="40" stroke="rgb(0,0,0)" width="128" x="256" y="40" />
-  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="84" x="320" y="66">Solve equation</text>
+  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="84" x="320.0" y="66">Solve equation</text>
   <rect fill="rgb(255,255,255)" height="40" stroke="rgb(0,0,0)" width="128" x="448" y="40" />
-  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="84" x="512" y="66">Output results</text>
+  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="84" x="512.0" y="66">Output results</text>
   <path d="M 192 60 L 248 60" fill="none" stroke="rgb(0,0,0)" />
   <polygon fill="rgb(0,0,0)" points="255,60 248,56 248,64 255,60" stroke="rgb(0,0,0)" />
   <path d="M 384 60 L 440 60" fill="none" stroke="rgb(0,0,0)" />
@@ -88,11 +79,11 @@ <h2>4.1. Overview of calculation flow<a class="headerlink" href="#overview-of-ca
   <rect fill="rgb(0,0,0)" height="40" stroke="rgb(0,0,0)" style="filter:url(#filter_blur);opacity:0.7;fill-opacity:1" width="128" x="259" y="46" />
   <rect fill="rgb(0,0,0)" height="40" stroke="rgb(0,0,0)" style="filter:url(#filter_blur);opacity:0.7;fill-opacity:1" width="128" x="451" y="46" />
   <rect fill="rgb(255,255,255)" height="40" stroke="rgb(0,0,0)" width="128" x="64" y="40" />
-  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="90" x="128" y="66">Read parameters</text>
+  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="90" x="128.0" y="66">Read parameters</text>
   <rect fill="rgb(255,255,255)" height="40" stroke="rgb(0,0,0)" width="128" x="256" y="40" />
-  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="54" x="320" y="66">Read Gtau</text>
+  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="54" x="320.0" y="66">Read Gtau</text>
   <rect fill="rgb(255,255,255)" height="40" stroke="rgb(0,0,0)" width="128" x="448" y="40" />
-  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="78" x="512" y="66">Make a kernel</text>
+  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="78" x="512.0" y="66">Make a kernel</text>
   <path d="M 192 60 L 248 60" fill="none" stroke="rgb(0,0,0)" />
   <polygon fill="rgb(0,0,0)" points="255,60 248,56 248,64 255,60" stroke="rgb(0,0,0)" />
   <path d="M 384 60 L 440 60" fill="none" stroke="rgb(0,0,0)" />
@@ -119,12 +110,12 @@ <h2>4.1. Overview of calculation flow<a class="headerlink" href="#overview-of-ca
   <rect fill="rgb(0,0,0)" height="40" stroke="rgb(0,0,0)" style="filter:url(#filter_blur);opacity:0.7;fill-opacity:1" width="128" x="259" y="46" />
   <rect fill="rgb(0,0,0)" height="40" stroke="rgb(0,0,0)" style="filter:url(#filter_blur);opacity:0.7;fill-opacity:1" width="128" x="451" y="46" />
   <rect fill="rgb(255,255,255)" height="40" stroke="rgb(0,0,0)" width="128" x="64" y="40" />
-  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="84" x="128" y="66">Set parameters</text>
+  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="84" x="128.0" y="66">Set parameters</text>
   <rect fill="rgb(255,255,255)" height="40" stroke="rgb(0,0,0)" width="128" x="256" y="40" />
-  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="102" x="320" y="59">Solve equation by</text>
-  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="66" x="320" y="72">ADMM method</text>
+  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="102" x="320.0" y="59">Solve equation by</text>
+  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="66" x="320.0" y="72">ADMM method</text>
   <rect fill="rgb(255,255,255)" height="40" stroke="rgb(0,0,0)" width="128" x="448" y="40" />
-  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="66" x="512" y="66">Get results</text>
+  <text fill="rgb(0,0,0)" font-family="sans-serif" font-size="11" font-style="normal" font-weight="normal" text-anchor="middle" textLength="66" x="512.0" y="66">Get results</text>
   <path d="M 192 60 L 248 60" fill="none" stroke="rgb(0,0,0)" />
   <polygon fill="rgb(0,0,0)" points="255,60 248,56 248,64 255,60" stroke="rgb(0,0,0)" />
   <path d="M 384 60 L 440 60" fill="none" stroke="rgb(0,0,0)" />
@@ -193,12 +184,14 @@ <h3>Related Topics</h3>
 </div>
 <div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
+    <div class="searchformwrapper">
     <form class="search" action="../search.html" method="get">
-      <div><input type="text" name="q" /></div>
-      <div><input type="submit" value="Go" /></div>
+      <input type="text" name="q" />
+      <input type="submit" value="Go" />
       <input type="hidden" name="check_keywords" value="yes" />
       <input type="hidden" name="area" value="default" />
     </form>
+    </div>
 </div>
 <script type="text/javascript">$('#searchbox').show(0);</script>
         </div>
@@ -209,7 +202,7 @@ <h3>Quick search</h3>
       &copy;2017, Junya Otsuki, Kazuyoshi Yoshimi, Hiroshi Shinaoka.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.6.5</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.7.1</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.10</a>
 
       |