diff --git a/atomate/__init__.py b/atomate/__init__.py index acec196db..66c04154f 100644 --- a/atomate/__init__.py +++ b/atomate/__init__.py @@ -1 +1 @@ -__version__ = "0.9.4" \ No newline at end of file +__version__ = "0.9.5" \ No newline at end of file diff --git a/docs/_sources/atomate.vasp.firetasks.rst.txt b/docs/_sources/atomate.vasp.firetasks.rst.txt index f2e04229c..7c14ade13 100644 --- a/docs/_sources/atomate.vasp.firetasks.rst.txt +++ b/docs/_sources/atomate.vasp.firetasks.rst.txt @@ -11,6 +11,14 @@ Subpackages Submodules ---------- +atomate.vasp.firetasks.exchange module +-------------------------------------- + +.. automodule:: atomate.vasp.firetasks.exchange + :members: + :undoc-members: + :show-inheritance: + atomate.vasp.firetasks.glue\_tasks module ----------------------------------------- diff --git a/docs/_sources/atomate.vasp.firetasks.tests.rst.txt b/docs/_sources/atomate.vasp.firetasks.tests.rst.txt index a8d1755d0..3e725097c 100644 --- a/docs/_sources/atomate.vasp.firetasks.tests.rst.txt +++ b/docs/_sources/atomate.vasp.firetasks.tests.rst.txt @@ -12,6 +12,14 @@ atomate.vasp.firetasks.tests.test\_copy module :undoc-members: :show-inheritance: +atomate.vasp.firetasks.tests.test\_exchange module +-------------------------------------------------- + +.. automodule:: atomate.vasp.firetasks.tests.test_exchange + :members: + :undoc-members: + :show-inheritance: + atomate.vasp.firetasks.tests.test\_get\_interpolated\_poscar module ------------------------------------------------------------------- diff --git a/docs/_sources/atomate.vasp.fireworks.rst.txt b/docs/_sources/atomate.vasp.fireworks.rst.txt index 9490e08b0..f82e94ade 100644 --- a/docs/_sources/atomate.vasp.fireworks.rst.txt +++ b/docs/_sources/atomate.vasp.fireworks.rst.txt @@ -12,6 +12,14 @@ atomate.vasp.fireworks.core module :undoc-members: :show-inheritance: +atomate.vasp.fireworks.exchange module +-------------------------------------- + +.. automodule:: atomate.vasp.fireworks.exchange + :members: + :undoc-members: + :show-inheritance: + atomate.vasp.fireworks.nmr module --------------------------------- diff --git a/docs/_sources/atomate.vasp.workflows.base.rst.txt b/docs/_sources/atomate.vasp.workflows.base.rst.txt index 31b694d3d..2f91b0d1d 100644 --- a/docs/_sources/atomate.vasp.workflows.base.rst.txt +++ b/docs/_sources/atomate.vasp.workflows.base.rst.txt @@ -44,6 +44,14 @@ atomate.vasp.workflows.base.elastic module :undoc-members: :show-inheritance: +atomate.vasp.workflows.base.exchange module +------------------------------------------- + +.. automodule:: atomate.vasp.workflows.base.exchange + :members: + :undoc-members: + :show-inheritance: + atomate.vasp.workflows.base.ferroelectric module ------------------------------------------------ diff --git a/docs/_sources/atomate.vasp.workflows.tests.rst.txt b/docs/_sources/atomate.vasp.workflows.tests.rst.txt index 62ff4bc8a..364abd6be 100644 --- a/docs/_sources/atomate.vasp.workflows.tests.rst.txt +++ b/docs/_sources/atomate.vasp.workflows.tests.rst.txt @@ -28,6 +28,14 @@ atomate.vasp.workflows.tests.test\_elastic\_workflow module :undoc-members: :show-inheritance: +atomate.vasp.workflows.tests.test\_exchange\_workflow module +------------------------------------------------------------ + +.. automodule:: atomate.vasp.workflows.tests.test_exchange_workflow + :members: + :undoc-members: + :show-inheritance: + atomate.vasp.workflows.tests.test\_ferroelectric\_workflow module ----------------------------------------------------------------- diff --git a/docs/_sources/changelog.rst.txt b/docs/_sources/changelog.rst.txt index 929794fbe..57c42db36 100644 --- a/docs/_sources/changelog.rst.txt +++ b/docs/_sources/changelog.rst.txt @@ -2,6 +2,14 @@ atomate Changelog ================= +**v0.9.5** + +* Add magnetism workflow (M. Horton, N. Frey) +* Overhaul SCAN workflow (R. Kingsbury) +* Move help to Discourse (A. Ganose) +* add ModifyKPoints Firetask (M. Siron) +* Misc fixes, dependency updates, and improvements (M. Horton, N. Frey, A. Jain, M. Siron, A. Ganose) + **v0.9.4** * Fixes for new pymatgen (S. Blau, S.P. Ong) diff --git a/docs/_sources/contributors.rst.txt b/docs/_sources/contributors.rst.txt index e6ada5387..4a280704d 100644 --- a/docs/_sources/contributors.rst.txt +++ b/docs/_sources/contributors.rst.txt @@ -7,9 +7,9 @@ atomate development is led by the Hacking Materials research group led by Anubha Contributions are provided by: * 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. +* Kiran Mathew, Shyam Dwaraknath, Joey Montoya, Murat Aykol, Matt Horton, Patrick Huck, Brandon Wood, Sam Blau, Jimmy Shen, Ryan Kingsbury, 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, Tara Maria Boland +* External contributors: specter119, M. Dias Costa, S. Torrisi, Max Dylla, Marnik Bercx, Tara Maria Boland, Nathan Frey, Martin Siron diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index ffea9688b..126511455 100644 --- a/docs/_static/documentation_options.js +++ b/docs/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '0.9.4', + VERSION: '0.9.5', LANGUAGE: 'None', COLLAPSE_INDEX: false, FILE_SUFFIX: '.html', diff --git a/docs/atomate.common.firetasks.html b/docs/atomate.common.firetasks.html index 05e8e3936..01ff8afd3 100644 --- a/docs/atomate.common.firetasks.html +++ b/docs/atomate.common.firetasks.html @@ -4,7 +4,7 @@ - atomate.common.firetasks package — atomate 0.9.4 documentation + atomate.common.firetasks package — atomate 0.9.5 documentation @@ -27,7 +27,7 @@

Navigation

  • modules |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • @@ -63,12 +63,20 @@

    Submodulesfireworks.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. -to_dir (str): path to the destination directory +

    +
    Optional params:

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

    +files_to_copy (list): list of file names. Defaults to copying everything in from_dir. +exclude_files (list): list of file names to be excluded. +suffix (str): suffix to append to each filename when copying

    +
    +

    (e.g., rename ‘INCAR’ to ‘INCAR.precondition’)

    +
    +
    +
    continue_on_missing(bool): Whether to continue copying when a file

    in filenames is missing. Defaults to False.

    +
    +
    @@ -79,7 +87,7 @@

    Submodules
    -optional_params = ['from_dir', 'to_dir', 'filesystem', 'files_to_copy', 'exclude_files']
    +optional_params = ['from_dir', 'to_dir', 'filesystem', 'files_to_copy', 'exclude_files', 'suffix', 'continue_on_missing']

    @@ -109,18 +117,24 @@

    Submodules
    -setup_copy(from_dir, to_dir=None, filesystem=None, files_to_copy=None, exclude_files=None, from_path_dict=None)
    +setup_copy(from_dir, to_dir=None, filesystem=None, files_to_copy=None, exclude_files=None, from_path_dict=None, suffix=None, fw_spec=None, continue_on_missing=False)

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

    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

    +exclude_files (list): list of file names to be excluded. +suffix (str): suffix to append to each filename when copying

    -

    the key “path” that specifies the path to the from_dir.

    +

    (e.g., rename ‘INCAR’ to ‘INCAR.precondition’)

    +
    +
    continue_on_missing(bool): Whether to continue copying when a file

    in filenames is missing. Defaults to False.

    +
    +
    from_path_dict (dict): dict specification of the path. If specified must contain atleast

    the key “path” that specifies the path to the from_dir.

    +
    +

    @@ -131,7 +145,7 @@

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

    Bases: fireworks.core.firework.FiretaskBase

    -

    Based on CopyVaspOutputs but for general file copying. Note that “calc_locs” +

    Based on CopyVaspOutputs but for general file copying. Note “calc_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.

    @@ -141,17 +155,23 @@

    Submodules
    -optional_params = ['filenames', 'name_prepend', 'name_append']
    +optional_params = ['filenames', 'name_prepend', 'name_append', 'exclude_files']

    @@ -281,6 +301,48 @@

    Submodules +
    +class atomate.common.firetasks.glue_tasks.GzipDir(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Task to gzip the current directory.

    +
    +
    +optional_params = []
    +
    + +
    +
    +required_params = []
    +
    + +
    +
    +run_task(fw_spec=None)
    +

    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 “_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, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.

    +
    +
    +
    +
    Returns:

    (FWAction)

    +
    +
    +
    + +

    +
    class atomate.common.firetasks.glue_tasks.PassCalcLocs(*args, **kwargs)
    @@ -658,7 +720,7 @@

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    • diff --git a/docs/atomate.vasp.firetasks.html b/docs/atomate.vasp.firetasks.html index 03fec1ecf..fc4b2e5fe 100644 --- a/docs/atomate.vasp.firetasks.html +++ b/docs/atomate.vasp.firetasks.html @@ -4,7 +4,7 @@ - atomate.vasp.firetasks package — atomate 0.9.4 documentation + atomate.vasp.firetasks package — atomate 0.9.5 documentation @@ -27,7 +27,7 @@

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    • @@ -45,6 +45,7 @@

    Subpackagesatomate.vasp.firetasks.tests package
    • Submodules
    • atomate.vasp.firetasks.tests.test_copy module
      • +
    • atomate.vasp.firetasks.tests.test_exchange module
    • atomate.vasp.firetasks.tests.test_get_interpolated_poscar module
    • atomate.vasp.firetasks.tests.test_polarization_to_db module
    • atomate.vasp.firetasks.tests.test_write_vasp module
      • @@ -57,6 +58,266 @@

      Subpackages

      Submodules

      + +
      +

      atomate.vasp.firetasks.exchange module

      +
      +
      +class atomate.vasp.firetasks.exchange.HeisenbergConvergence(*args, **kwargs)
      +

      Bases: fireworks.core.firework.FiretaskBase

      +

      Quick check to see if the Heisenberg model has “converged” for any +particular nearest neighbor cutoff value in the sense that |J_ij| < |E_0| +for all i, j.

      +

      If not, it doesn’t make sense to do Monte Carlo and the system is either +1) not well described by the Heisenberg Model (perhaps the magnetic +moments are not localized) or 2) not correctly captured by the provided +low-energy magnetic orderings.

      +
      +
      Args:

      db_file (str): path to file containing the database credentials. +wf_uuid (int): Unique id for record keeping. +average (bool): <J> exchange param only.

      +
      +
      TODO:
        +

      • More robust convergence check

        • +
      +
      +
      +
      +
      +required_params = ['db_file', 'wf_uuid', 'average']
      +
      + +
      +
      +run_task(fw_spec)
      +

      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 “_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, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.

      +
      +
      +
      +
      Returns:

      (FWAction)

      +
      +
      +
      + +
      + +
      +
      +class atomate.vasp.firetasks.exchange.HeisenbergModelMapping(*args, **kwargs)
      +

      Bases: fireworks.core.firework.FiretaskBase

      +

      Map structures and energies to a Heisenberg model and compute exchange +parameters for a given NN cutoff.

      +
        +
      • +
        heisenberg_settings:

        cutoff (float): Starting point for nearest neighbor search. +tol (float): Tolerance for equivalent NN bonds.

        +
        +
        +
        • +
      +
      +
      Args:

      structures (list): Magnetic structures. +energies (list): Energies / atom (eV).

      +
      +
      Optional parameters:
      +
      heisenberg_settings (dict): A config dict for Heisenberg model

      mapping, detailed above.

      +
      +
      +
      +
      +
      +
      +optional_params = ['heisenberg_settings']
      +
      + +
      +
      +required_params = ['structures', 'energies']
      +
      + +
      +
      +run_task(fw_spec)
      +

      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 “_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, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.

      +
      +
      +
      +
      Returns:

      (FWAction)

      +
      +
      +
      + +
      + +
      +
      +class atomate.vasp.firetasks.exchange.HeisenbergModelToDb(*args, **kwargs)
      +

      Bases: fireworks.core.firework.FiretaskBase

      +

      Insert Heisenberg Model object into a DB. Assumes you are in a +directory with a model written to a .json file.

      +
      +
      Args:

      db_file (str): path to file containing the database credentials. +wf_uuid (int): Unique id for record keeping.

      +
      +
      +
      +
      +required_params = ['db_file', 'wf_uuid']
      +
      + +
      +
      +run_task(fw_spec)
      +

      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 “_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, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.

      +
      +
      +
      +
      Returns:

      (FWAction)

      +
      +
      +
      + +
      + +
      +
      +class atomate.vasp.firetasks.exchange.VampireMC(*args, **kwargs)
      +

      Bases: fireworks.core.firework.FiretaskBase

      +

      If there is a suitable Heisenberg model, run Monte Carlo to compute the +critical temperature.

      +
      +
      Args:

      db_file (str): path to file containing the database credentials. +wf_uuid (int): Unique id for record keeping.

      +
      +
      Optional args:
      +
      mc_settings (dict): A configuration dict for monte carlo.

      See pymatgen.command_line.VampireCaller for options.

      +
      +
      +
      +
      TODO:
        +

      • Include HeisenbergModel convergence check.

        • +
      +
      +
      +
      +
      +optional_params = ['mc_settings']
      +
      + +
      +
      +required_params = ['db_file', 'wf_uuid']
      +
      + +
      +
      +run_task(fw_spec)
      +

      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 “_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, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.

      +
      +
      +
      +
      Returns:

      (FWAction)

      +
      +
      +
      + +
      + +
      +
      +class atomate.vasp.firetasks.exchange.VampireToDb(*args, **kwargs)
      +

      Bases: fireworks.core.firework.FiretaskBase

      +

      Insert VAMPIRE output into DB.

      +

      Assumes you are in a directory with output written to a .json.

      +
      +
      Args:

      db_file (str): path to file containing the database credentials. +wf_uuid (int): Unique id for record keeping.

      +
      +
      +
      +
      +required_params = ['db_file', 'wf_uuid']
      +
      + +
      +
      +run_task(fw_spec)
      +

      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 “_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, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.

      +
      +
      +
      +
      Returns:

      (FWAction)

      +
      +
      +
      + +
      +

      atomate.vasp.firetasks.glue_tasks module

      @@ -893,39 +1154,41 @@

      Submodules -
      -class atomate.vasp.firetasks.parse_outputs.MagneticDeformationToDB(*args, **kwargs)
      +
      +class atomate.vasp.firetasks.parse_outputs.MagneticDeformationToDb(*args, **kwargs)

      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 -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

      -
      +for that workflow for more information.

      -
      Optional parameters:

      to_db (bool): if True, the data will be inserted into -dedicated collection in database, otherwise, will be dumped +

      Required parameters:
      +
      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

      dedicated collection in database, otherwise, will be dumped to a .json file.

      +
      +
      -
      -optional_params = ['to_db']
      +
      +optional_params = ['to_db']
      -
      -required_params = ['db_file', 'wf_uuid']
      +
      +required_params = ['db_file', 'wf_uuid']
      -
      -run_task(fw_spec)
      +
      +run_task(fw_spec)

      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.

      @@ -951,37 +1214,56 @@

      Submodules -
      -class atomate.vasp.firetasks.parse_outputs.MagneticOrderingsToDB(*args, **kwargs)
      +
      +class atomate.vasp.firetasks.parse_outputs.MagneticOrderingsToDb(*args, **kwargs)

      Bases: fireworks.core.firework.FiretaskBase

      Used to aggregate tasks docs from magnetic ordering workflow. For large-scale/high-throughput use, would recommend a specific builder, this is intended for easy, automated use for calculating magnetic orderings directly from the get_wf_magnetic_orderings -workflow. It’s unlikely you will want to call this directly. -Required parameters:

      +workflow. It’s unlikely you will want to call this directly.

      +
      +
      Required parameters:
      +
      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

      +
      +
      parent_structure (Structure): Structure of parent crystal (not

      magnetically ordered)

      +
      +
      +

      perform_bader (bool): Perform Bader charge analysis. +scan (bool): Do static calcs with SCAN functional.

      +
      +
      Optional parameters:
      +
      origins (list): str indicating transformations that generated

      orderings.

      +
      +
      +

      input_index (int): index of input structure to enumerator. +to_db (bool): if True, the data will be inserted into

      -

      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 -parent_structure: Structure of parent crystal (not magnetically -ordered)

      +

      dedicated collection in database, otherwise, will be dumped +to a .json file.

      +
      +
      additional_fields (dict): fields added to the document such as

      user-defined tags or name, ids, etc

      +
      +
      +
      +
      -
      -optional_params = ['origins', 'input_index']
      +
      +optional_params = ['origins', 'input_index', 'to_db', 'additional_fields']
      -
      -required_params = ['db_file', 'wf_uuid', 'parent_structure', 'perform_bader', 'scan']
      +
      +required_params = ['db_file', 'wf_uuid', 'parent_structure', 'perform_bader', 'scan']
      -
      -run_task(fw_spec)
      +
      +run_task(fw_spec)

      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.

      @@ -1176,6 +1458,8 @@

      Submodules
      -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']
      +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', 'parse_potcar_file', 'store_volumetric_data']

      @@ -1456,12 +1740,13 @@

      Submodules
      -optional_params = ['params_to_check', 'check_incar', 'check_kpoints', 'check_poscar', 'check_potcar']
      +optional_params = ['params_to_check', 'check_incar', 'check_kpoints', 'check_poscar', 'check_potcar', 'clear_inputs']

      @@ -1499,7 +1784,7 @@

      Submodules

      atomate.vasp.firetasks.write_inputs module

      -

      This module defines tasks for writing vasp input sets for various types of vasp calculations

      +

      This module defines tasks for writing vasp input sets.

      class atomate.vasp.firetasks.write_inputs.ModifyIncar(*args, **kwargs)
      @@ -1553,6 +1838,56 @@

      Submodules +
      +class atomate.vasp.firetasks.write_inputs.ModifyKpoints(*args, **kwargs)
      +

      Bases: fireworks.core.firework.FiretaskBase

      +

      Modify an KPOINTS file.

      +
      +
      Required params:

      (none)

      +
      +
      Optional params:
      +
      kpoints_update (dict): overwrite Kpoint dict key. Supports env_chk.

      keys can be anything property of a kpoint object (kpts, kpts_shift, +kpts_weights, labels, comment, coord_type, num_kpts, +tet_connections, tet_number, tet_weight)

      +
      +
      +

      input_filename (str): Input filename (if not “KPOINTS”) +output_filename (str): Output filename (if not “KPOINTS”)

      +
      +
      +
      +
      +optional_params = ['kpoints_update', 'input_filename', 'output_filename']
      +
      + +
      +
      +run_task(fw_spec)
      +

      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 “_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, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.

      +
      +
      +
      +
      Returns:

      (FWAction)

      +
      +
      +
      + +

      +
      class atomate.vasp.firetasks.write_inputs.ModifyPotcar(*args, **kwargs)
      @@ -1603,13 +1938,65 @@

      Submodules +
      +class atomate.vasp.firetasks.write_inputs.UpdateScanRelaxBandgap(*args, **kwargs)
      +

      Bases: fireworks.core.firework.FiretaskBase

      +

      Writes input files for a SCAN relaxation by constructing a new input set. +The purpose of this Firetask is to allow the KSPACING and smearing parameters +to be recalculated based on the bandgap from the PBE relaxation in the +SCAN relaxation workflow. Assumes that output files from a previous +(e.g., optimization) run can be accessed in current dir or prev_calc_dir.

      +
      +
      Optional params (dict):
      +
      override_default_vasp_params: Dict of any keyword arguments supported

      by MPScanRelaxSet.

      +
      +
      potcar_spec (bool): Instead of writing the POTCAR, write a

      “POTCAR.spec”. This is intended to allow testing of workflows +without requiring pseudo-potentials to be installed on the system.

      +
      +
      +
      +
      +
      +
      +optional_params = ['override_default_vasp_params', 'potcar_spec']
      +
      + +
      +
      +run_task(fw_spec)
      +

      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 “_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, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.

      +
      +
      +
      +
      Returns:

      (FWAction)

      +
      +
      +
      + +

      +
      class atomate.vasp.firetasks.write_inputs.WriteNormalmodeDisplacedPoscar(*args, **kwargs)

      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 “normalmodes” -key with “eigenvecs” sub-key that is likely produced by a previous calc.

      +

      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 “normalmodes” key with “eigenvecs” 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

      @@ -1652,28 +2039,37 @@

      Submodulesclass atomate.vasp.firetasks.write_inputs.WriteTransmutedStructureIOSet(*args, **kwargs)

      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.

      +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 -transformations (list): list of names of transformation classes as defined in

      +transformations (list): list of names of transformation classes as

      -

      the modules in pymatgen.transformations

      +

      defined in 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.

      +
      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. -prev_calc_dir: path to previous calculation if using structure from another calculation.

      +prev_calc_dir: path to previous calculation if using structure from

      +
      +

      another calculation.

      +
      +
      +
      potcar_spec (bool): Instead of writing the POTCAR, write a

      “POTCAR.spec”. This is intended to allow testing of workflows +without requiring pseudo-potentials to be installed on the system.

      +
      +
      -optional_params = ['prev_calc_dir', 'transformation_params', 'override_default_vasp_params']
      +optional_params = ['prev_calc_dir', 'transformation_params', 'override_default_vasp_params', 'potcar_spec']
      @@ -1712,27 +2108,33 @@

      Submodules class atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet(*args, **kwargs)

      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.

      +

      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 -vasp_input_set (AbstractVaspInputSet or str): Either a VaspInputSet object or a string

      +vasp_input_set (AbstractVaspInputSet or str): Either a VaspInputSet

      -

      name for the VASP input set (e.g., “MPRelaxSet”).

      +

      object or a string name for the VASP input set (e.g., “MPRelaxSet”).

      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: {“user_incar_settings”: …}. -This setting is ignored if you provide the full object representation of a VaspInputSet -rather than a String.

      +
      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: +{“user_incar_settings”: …}. This setting is ignored if you provide +the full object representation of a VaspInputSet rather than a +String.

      +
      +
      potcar_spec (bool): Instead of writing the POTCAR, write a

      “POTCAR.spec”. This is intended to allow testing of workflows +without requiring pseudo-potentials to be installed on the system.

      -optional_params = ['vasp_input_params']
      +optional_params = ['vasp_input_params', 'potcar_spec']
      @@ -1785,20 +2187,28 @@

      Submodules +
      vasp_input_set (str): a string name for the VASP input set (e.g.,

      “MPRelaxSet”).

      +
      +

      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: {“user_incar_settings”: …}. -This setting is ignored if you provide the full object representation of a VaspInputSet -rather than a String.

      +
      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: +{“user_incar_settings”: …}. This setting is ignored if you provide +the full object representation of a VaspInputSet rather than a +String.

      +
      +
      potcar_spec (bool): Instead of writing the POTCAR, write a

      “POTCAR.spec”. This is intended to allow testing of workflows +without requiring pseudo-potentials to be installed on the system.

      -optional_params = ['vasp_input_params', 'autosort_tol']
      +optional_params = ['vasp_input_params', 'autosort_tol', 'potcar_spec']
      @@ -1838,9 +2248,9 @@

      Submodulesclass atomate.vasp.firetasks.write_inputs.WriteVaspFromPMGObjects(*args, **kwargs)

      Bases: fireworks.core.firework.FiretaskBase

      Write VASP files using pymatgen objects.

      +

      Note, that although this firetask has no required params, it is +non-functional unless at least one optional param is set.

      -
      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 @@ -1883,20 +2293,24 @@

      Submodules class atomate.vasp.firetasks.write_inputs.WriteVaspHSEBSFromPrev(*args, **kwargs)

      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)

      +

      Writes input files for HSE band structure run. Assumes that output files +from 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).

      +
      +
      Optional params:
      +
      potcar_spec (bool): Instead of writing the POTCAR, write a

      “POTCAR.spec”. This is intended to allow testing of workflows +without requiring pseudo-potentials to be installed on the system.

      -
      Optional params:

      (documentation for all other optional params can be found in +

      +

      (documentation for all other optional params can be found in MPHSEBSSet)

      -optional_params = ['prev_calc_dir', 'mode', 'reciprocal_density', 'kpoints_line_density']
      +optional_params = ['prev_calc_dir', 'mode', 'reciprocal_density', 'kpoints_line_density', 'potcar_spec']
      @@ -1941,15 +2355,24 @@

      Submodules +
      reciprocal_density (int): the reciprocal density for the kpoint mesh,

      defaults to 100

      +
      +

      +

      other_params (dict) : any other params passed to MPNMRSet as a dict. +potcar_spec (bool): Instead of writing the POTCAR, write a

      +
      +

      “POTCAR.spec”. This is intended to allow testing of workflows +without requiring pseudo-potentials to be installed on the system.

      -

      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']
      +optional_params = ['prev_calc_dir', 'mode', 'isotopes', 'reciprocal_density', 'other_params', 'potcar_spec']
      @@ -1986,16 +2409,19 @@

      Submodules -
      Required params:

      (none)

      +
      +
      Optional params:
      +
      potcar_spec (bool): Instead of writing the POTCAR, write a

      “POTCAR.spec”. This is intended to allow testing of workflows +without requiring pseudo-potentials to be installed on the system.

      -
      Optional params:

      (documentation for all optional params can be found in +

      +

      (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']
      +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', 'potcar_spec']
      @@ -2035,14 +2461,21 @@

      Submodulesclass atomate.vasp.firetasks.write_inputs.WriteVaspSOCFromPrev(*args, **kwargs)

      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

      +
      Optional params:
      +
      potcar_spec (bool): Instead of writing the POTCAR, write a

      “POTCAR.spec”. This is intended to allow testing of workflows +without requiring pseudo-potentials to be installed on the system.

      +
      +
      +

      (documentation for all optional params can be found in MPSOCSet)

      +
      -optional_params = ['prev_calc_dir', 'copy_chgcar', 'nbands_factor', 'reciprocal_density', 'small_gap_multiply', 'standardize', 'sym_prec', 'international_monoclinic', 'other_params']
      +optional_params = ['prev_calc_dir', 'copy_chgcar', 'nbands_factor', 'reciprocal_density', 'small_gap_multiply', 'standardize', 'sym_prec', 'international_monoclinic', 'other_params', 'potcar_spec']
      @@ -2081,19 +2514,22 @@

      Submodules class atomate.vasp.firetasks.write_inputs.WriteVaspStaticFromPrev(*args, **kwargs)

      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)

      +

      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.

      +
      +
      Optional params:
      +
      potcar_spec (bool): Instead of writing the POTCAR, write a

      “POTCAR.spec”. This is intended to allow testing of workflows +without requiring pseudo-potentials to be installed on the system.

      -
      Optional params:

      (documentation for all other optional params can be found in +

      +

      (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']
      +optional_params = ['prev_calc_dir', 'reciprocal_density', 'small_gap_multiply', 'standardize', 'sym_prec', 'international_monoclinic', 'lepsilon', 'other_params', 'potcar_spec']
      @@ -2140,6 +2576,7 @@

      Table of Contents

    • atomate.vasp.firetasks package

      • diff --git a/docs/atomate.vasp.firetasks.tests.html b/docs/atomate.vasp.firetasks.tests.html index 7bc314fc4..dd6d68166 100644 --- a/docs/atomate.vasp.firetasks.tests.html +++ b/docs/atomate.vasp.firetasks.tests.html @@ -4,7 +4,7 @@ - atomate.vasp.firetasks.tests package — atomate 0.9.4 documentation + atomate.vasp.firetasks.tests package — atomate 0.9.5 documentation @@ -27,7 +27,7 @@

      Navigation

    • modules |
      • -
    • atomate 0.9.4 documentation »
      • +
    • atomate 0.9.5 documentation »
    @@ -80,6 +80,26 @@

    Submodules +

    atomate.vasp.firetasks.tests.test_exchange module

    +
    +
    +class atomate.vasp.firetasks.tests.test_exchange.TestExchangeTasks(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +classmethod setUpClass()
    +

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

    +
    + +
    +
    +test_heisenberg_mm()
    +
    + +
    +

    atomate.vasp.firetasks.tests.test_get_interpolated_poscar module

    @@ -160,6 +180,11 @@

    Submodulestest_modify_incar()

    +
    +
    +test_modify_kpoints()
    +
    +
    test_modify_potcar()
    @@ -170,6 +195,11 @@

    Submodulestest_pmgobjects()

    +
    +
    +test_potcar_spec()
    +
    +

    @@ -209,6 +239,7 @@

    Table of Contents

  • atomate.vasp.firetasks.tests package diff --git a/docs/atomate.vasp.fireworks.html b/docs/atomate.vasp.fireworks.html index 5310e0415..8c107f0de 100644 --- a/docs/atomate.vasp.fireworks.html +++ b/docs/atomate.vasp.fireworks.html @@ -4,7 +4,7 @@ - atomate.vasp.fireworks package — atomate 0.9.4 documentation + atomate.vasp.fireworks package — atomate 0.9.5 documentation @@ -27,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • @@ -416,6 +416,53 @@

    Submodules +
    +class atomate.vasp.fireworks.core.ScanOptimizeFW(structure, name='SCAN structure optimization', vasp_input_set=None, vasp_cmd='>>vasp_cmd<<', override_default_vasp_params=None, db_file='>>db_file<<', vdw_kernel_dir='>>vdw_kernel_dir<<', parents=None, **kwargs)
    +

    Bases: fireworks.core.firework.Firework

    +
    +
    +__init__(structure, name='SCAN structure optimization', vasp_input_set=None, vasp_cmd='>>vasp_cmd<<', override_default_vasp_params=None, db_file='>>db_file<<', vdw_kernel_dir='>>vdw_kernel_dir<<', parents=None, **kwargs)
    +

    Structure optimization using the SCAN metaGGA functional.

    +

    This workflow performs a 3-step optmization. The first step (‘relax1’) +is a conventional GGA run relaxation that initializes the geometry and +calculates the bandgap of the structure. The bandgap is used to update +the KSPACING parameter, which sets the appropriate number of k-points +for the structure. The second step (‘.relax2’) is a static GGA +calculation that computes wavefunctions using the updated number of +k-points. The third step (‘relax3’) is a SCAN relaxation.

    +

    By default, .relax1 and .relax2 are force converged with +EDIFFG = -0.05, and .relax3 is force converged with EDIFFG=-0.02.

    +
    +
    Args:

    structure (Structure): Input structure. +name (str): Name for the Firework. +vasp_input_set (VaspInputSet): input set to use. Defaults to

    +
    +

    MPScanRelaxSet() if None.

    +
    +
    +
    override_default_vasp_params (dict): If this is not None, and

    vasp_input_set is None, these params are passed to the default +vasp_input_set, i.e., MPScanRelaxSet. This allows one to easily +override some settings, e.g., bandgap, user_incar_settings, etc.

    +
    +
    +

    vasp_cmd (str): Command to run vasp. Supports env_chk. +vdw_kernel_dir (str): Directory containing the pre-compiled VdW

    +
    +

    kernel. Supports env_chk.

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

    output parsing. Supports env_chk.

    +
    +
    +

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

    +
    +
    +
    + +
    +
    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)
    @@ -523,6 +570,79 @@

    Submodules +

    atomate.vasp.fireworks.exchange module

    +
    +
    +class atomate.vasp.fireworks.exchange.HeisenbergModelFW(wf_uuid, parent_structure, parents, db_file='>>db_file<<', heisenberg_settings=None, name='heisenberg model', structures=None, energies=None)
    +

    Bases: fireworks.core.firework.Firework

    +
    +
    +__init__(wf_uuid, parent_structure, parents, db_file='>>db_file<<', heisenberg_settings=None, name='heisenberg model', structures=None, energies=None)
    +

    Takes a set of low-energy magnetic orderings and energies and maps +them to a Heisenberg Model to compute exchange params.

    +
      +
    • +
      heisenberg_settings:

      cutoff (float): Starting point for nearest neighbor search. +tol (float): Tolerance for equivalent NN bonds.

      +
      +
      +
      • +
    +
    +
    Args:

    wf_uuid (int): Unique id for record keeping. +parent_structure (Structure): Magnetic ground state. +parents (FireWorks): Parent FWs. +db_file (str): Path to file containing db credentials. +heisenberg_settings (dict): A config dict for Heisenberg model

    +
    +

    mapping, detailed above.

    +
    +

    name (str): Labels the FW. +structures (list): Magnetic structures. +energies (list): Total energies of magnetic structures.

    +
    +
    TODO:
      +

    • Test a range of nn cutoffs and add convergence check.

      • +
    +
    +
    +
    + +
    + +
    +
    +class atomate.vasp.fireworks.exchange.VampireCallerFW(wf_uuid, parent_structure, parents, db_file='>>db_file<<', mc_settings=None, name='vampire caller')
    +

    Bases: fireworks.core.firework.Firework

    +
    +
    +__init__(wf_uuid, parent_structure, parents, db_file='>>db_file<<', mc_settings=None, name='vampire caller')
    +

    Run Vampire Monte Carlo from a HeisenbergModel.

    +
      +
    • +
      mc_settings:

      mc_box_size (float): MC simulation box size in nm. +equil_timesteps (int): Number of MC equilibration moves. +mc_timesteps (int): Number of MC moves for averaging. +avg (bool): Compute only <J>.

      +
      +
      +
      • +
    +
    +
    Args:

    wf_uuid (int): Unique id for record keeping. +parent_structure (Structure): Magnetic ground state. +parents (FireWorks): Parent FWs. +db_file (str): Path to file containing db credentials. +mc_settings (dict): A configuration dict for monte carlo. +name (str): Labels the FW.

    +
    +
    +
    + +
    +

    atomate.vasp.fireworks.nmr module

    @@ -573,50 +693,78 @@

    Submodules
    __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)
    -

    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. -1. A StaticFW or StaticInterpolatFW calculation is performed to compute the band gap of the structure. -2. Because VASP cannot compute the dipole moment of metallic structures, CheckBandgap checks that the structure -has a band gap greater than gap_threshold. If the structure has a band gap less than gap_threshold, -the Firework defuses. Otherwise, -3. a polarization calculation (LCALCPOL=TRUE) is performed to calculate the dipole moment.

    -

    If interpolate is equal to True, the keywords start and end are PassCalcLoc names used to locate the output -structures (CONTCAR) of two previous calculations. These two structures must have the same number and -type of atoms given in identical order in the structures. These structures are used to create nimages structures -interpolations.

    -

    this_image specifies which of the interpolated structures to use in this Firework. For example in the -ferroelectric workflow, two structures that can be distorted into one another (a -high-symmetry nonpolar structure and a low-symmetry polar structure) are relaxed using OptimizeFW. Then the -dipole moment is calculated for nimages intermediate structures generated by interpolating between these two -relaxed structures.

    +

    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.

    +
      +

    1. A StaticFW or StaticInterpolatFW calculation is performed to compute

      2. +
    +
    +

    the band gap of the structure.

    +
    +
      +

    1. Because VASP cannot compute the dipole moment of metallic structures,

      2. +
    +
    +

    CheckBandgap checks that the structure has a band gap greater than +gap_threshold. If the structure has a band gap less than +gap_threshold, the Firework defuses. Otherwise,

    +
    +
      +

    1. a polarization calculation (LCALCPOL=TRUE) is performed to calculate

      2. +
    +
    +

    the dipole moment.

    +
    +

    If interpolate is equal to True, the keywords start and end are +PassCalcLoc names used to locate the output structures (CONTCAR) of two +previous calculations. These two structures must have the same number +and type of atoms given in identical order in the structures. These +structures are used to create nimages structures interpolations.

    +

    this_image specifies which of the interpolated structures to use in this +Firework. For example in the ferroelectric workflow, two structures that +can be distorted into one another (a high-symmetry nonpolar structure +and a low-symmetry polar structure) are relaxed using OptimizeFW. Then +the dipole moment is calculated for nimages intermediate structures +generated by interpolating between these two relaxed structures.

    Args:
    -
    structure (Structure): Input structure. For an interpolation, this is a dummy structure. See interpolate arg

    description.

    +
    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. -vasp_cmd (str): Command to run vasp. -vasp_input_set (str): string name for the VASP input set (e.g., “MITMDVaspInputSet”). -vasp_input_set_params (dict): Dict of vasp_input_set_kwargs. +static_name (str): Name for the SCF run to be used in PassCalcLoc

    +
    +

    if copy_vasp_outputs != True.

    +
    +

    vasp_cmd (str): Command to run vasp. +vasp_input_set (str): string name for the VASP input set (e.g.,

    +
    +

    “MITMDVaspInputSet”).

    +
    +

    vasp_input_set_params (dict): Dict of vasp_input_set_kwargs. db_file (str): Path to file specifying db credentials. -parents (Firework): Parents of this particular Firework. FW or list of FWS. -gap_threshold: Band gap cutoff for determining whether polarization calculation will proceed from

    +parents (Firework): Parents of this particular Firework. FW or list

    -

    SCF band gap.

    +

    of FWS.

    -
    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.

    +
    gap_threshold: Band gap cutoff for determining whether polarization

    calculation will proceed from 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.

    -

    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.

    -

    @@ -640,6 +788,7 @@

    Table of Contents

  • atomate.vasp.fireworks package diff --git a/docs/atomate.vasp.html b/docs/atomate.vasp.html index 2da9fa4da..476f472cf 100644 --- a/docs/atomate.vasp.html +++ b/docs/atomate.vasp.html @@ -4,7 +4,7 @@ - atomate.vasp package — atomate 0.9.4 documentation + atomate.vasp package — atomate 0.9.5 documentation @@ -27,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • @@ -78,6 +78,7 @@

    Subpackagesatomate.vasp.firetasks.tests package @@ -78,6 +78,11 @@

    Submodulestest_parse_locpot()
    +
    +
    +test_parse_potcar()
    +
    +
    test_runs_assimilate()
    @@ -170,11 +175,26 @@

    Submodulestest_modify_incar()

    +
    +
    +test_modify_kpoints()
    +
    +
    test_modify_potcar()
    +
    +
    +test_queue_options()
    +
    + +
    +
    +test_use_potcar_spec()
    +
    +
    test_use_scratch_dir()
    @@ -182,6 +202,11 @@

    Submodules +
    +atomate.vasp.tests.test_vasp_powerups.copy_wf(wf)
    +

    +

    Module contents

    @@ -236,7 +261,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • diff --git a/docs/atomate.vasp.workflows.base.html b/docs/atomate.vasp.workflows.base.html index 2a8e3e7a7..426d3d3ed 100644 --- a/docs/atomate.vasp.workflows.base.html +++ b/docs/atomate.vasp.workflows.base.html @@ -4,7 +4,7 @@ - atomate.vasp.workflows.base package — atomate 0.9.4 documentation + atomate.vasp.workflows.base package — atomate 0.9.5 documentation @@ -27,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • @@ -345,6 +345,87 @@

    Submodules +

    atomate.vasp.workflows.base.exchange module

    +
    +
    +class atomate.vasp.workflows.base.exchange.ExchangeWF(magnetic_structures, energies, default_magmoms=None, db_file='>>db_file<<', name='Exchange WF')
    +

    Bases: object

    +
    +
    +__init__(magnetic_structures, energies, default_magmoms=None, db_file='>>db_file<<', name='Exchange WF')
    +

    Workflow for computing exchange parameters.

    +

    This workflow takes a set of magnetic orderings and their energies +from MagneticOrderingsWF and fits to a classical Heisenberg +Hamiltonian to compute exchange parameters. The critical temperature +can then be calculated with Monte Carlo.

    +

    Optionally, only the lowest energy FM and AFM configurations can be +used to compute the average exchange interaction, <J>, without any +static calculations.

    +
    +
    Args:
    +
    magnetic_structures (list): Structure objects with the ‘magmom’

    site property.

    +
    +
    +

    energies (list): Energies per atom in eV. +default_magmoms (dict): (optional, defaults provided) dict of

    +
    +

    magnetic elements to their initial magnetic moments in µB, +generally these are chosen to be high-spin since they can +relax to a low-spin configuration during a DFT electronic +configuration.

    +
    +

    db_file (string): Path to database file. +name (string): Name of workflow.

    +
    +
    +
    + +
    +
    +get_wf(num_orderings_hard_limit=16, c=None)
    +

    Retrieve Fireworks workflow.

    +

    c is an optional dictionary that can contain: +* heisenberg_settings:

    +
    +

    cutoff (float): Starting point for nearest neighbor search. +tol (float): Tolerance for equivalent NN bonds.

    +
    +
      +
    • +
      mc_settings:

      mc_box_size (float): MC simulation box size in nm. +equil_timesteps (int): Number of MC equilibration moves. +mc_timesteps (int): Number of MC moves for averaging. +avg (bool): Compute only <J>.

      +
      +
      +
      • +
    • +
      DB_FILE:

      path to db.json.

      +
      +
      +
      • +
    +
    +
    Args:
    +
    num_orderings_hard_limit (int): will make sure total number of

    magnetic orderings does not exceed this number even if there +are extra orderings of equivalent symmetry

    +
    +
    +

    c Optional[dict]: additional config dict described above

    +
    +
    Returns:

    wf (Workflow): Heisenberg Model + Vampire Monte Carlo.

    +
    +
    TODO:
      +

    • Add static SCAN option (only optimization is available)

      • +
    +
    +
    +
    + +
    +

    atomate.vasp.workflows.base.ferroelectric module

    @@ -376,7 +457,7 @@

    Submoduleswfid_”. If None this is atomatically generated (recommended). +wfid (string): Unique worfklow id starting with “wfid_”. If None this is atomatically generated (recommended). tags (list of strings): Additional tags to add such as identifiers for structures.

    @@ -434,11 +515,11 @@

    Submodules

    atomate.vasp.workflows.base.magnetism module

    -class atomate.vasp.workflows.base.magnetism.MagneticOrderingsWF(structure, default_magmoms=None, strategies=('ferromagnetic', 'antiferromagnetic'), automatic=True, truncate_by_symmetry=True, transformation_kwargs=None)
    +class atomate.vasp.workflows.base.magnetism.MagneticOrderingsWF(structure, default_magmoms=None, strategies=('ferromagnetic', 'antiferromagnetic'), automatic=True, truncate_by_symmetry=True, transformation_kwargs=None, static=False)

    Bases: object

    -__init__(structure, default_magmoms=None, strategies=('ferromagnetic', 'antiferromagnetic'), automatic=True, truncate_by_symmetry=True, transformation_kwargs=None)
    +__init__(structure, default_magmoms=None, strategies=('ferromagnetic', 'antiferromagnetic'), automatic=True, truncate_by_symmetry=True, transformation_kwargs=None, static=False)

    This workflow will try several different collinear magnetic orderings for a given input structure, and output a summary to a dedicated database @@ -448,7 +529,7 @@

    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. @@ -479,58 +560,85 @@

      Submodules -
      orderings that are likely physically implausible

      transformation_kwargs: keyword arguments to pass to

      +
      strategies (tuple): different ordering strategies to use, choose

      from: ferromagnetic, antiferromagnetic, +antiferromagnetic_by_motif, ferrimagnetic_by_motif and +ferrimagnetic_by_species (here, “motif”, +means to use a different ordering parameter for symmetry +inequivalent sites)

      +
      +
      automatic (bool): if True, will automatically choose sensible

      strategies

      +
      +
      truncate_by_symmetry (bool): if True, will remove very

      unsymmetrical orderings that are likely physically implausible

      +
      +
      transformation_kwargs (dict): keyword arguments to pass to

      MagOrderingTransformation, to change automatic cell size +limits, etc.

      +
      +
      static (bool): Run only static calcs (no optimization) of

      different magnetic orderings in a fixed ground state +geometry.

      +
      +

    -

    MagOrderingTransformation, to change automatic cell size limits, etc.

    get_wf(scan=False, perform_bader=True, num_orderings_hard_limit=16, c=None)

    Retrieve the FireWorks workflow.

    -
    -
    Args:

    scan: if True, use the SCAN functional instead of GGA+U, since

    +
    +
    Args:
    +
    scan (bool): 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 (bool): if True, make sure the “bader” binary is in

    your path, will use Bader analysis to calculate +atom-projected magnetic moments

    +
    +
    num_orderings_hard_limit (int): will make sure total number of

    magnetic orderings does not exceed this number even if there +are extra orderings of equivalent symmetry

    +
    +
    +

    c (dict): additional config dict (as used elsewhere in atomate)

    -

    the SCAN functional has shown to have improved performance for -magnetic systems in some cases

    -
    -

    perform_bader: if True, make sure the “bader” 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

    -
    -

    orderings does not exceed this number even if there are extra orderings -of equivalent symmetry

    -
    -

    c: additional config dict (as used elsewhere in atomate)

    -

    Returns: FireWorks Workflow

    +
    +
    +atomate.vasp.workflows.base.magnetism.get_commensurate_orderings(magnetic_structures, energies)
    +

    Generate supercells for static calculations.

    +

    From the ground state magnetic ordering and first excited state, +generate supercells with magnetic orderings.

    +

    If the gs is FM, match supercells to the 1st es. +If the gs is AFM, FM is included by default, 1st es may not be. +If the gs is FiM, 1st es may not be captured.

    +
    +
    Args:

    magnetic_structures (list): Structures. +energies (list): Energies per atom.

    +
    +
    Returns:
    +
    matched_structures (list): Commensurate supercells for static

    calculations.

    +
    +
    +
    +
    TODO:
      +

    • Only consider orderings with |S_i| = ground state

      • +

    • Constrain noncollinear magmoms

      • +
    +
    +
    +
    +
    atomate.vasp.workflows.base.magnetism.get_wf_magnetic_deformation(structure, c=None, vis=None)
    @@ -761,6 +869,7 @@

    Table of Contents

  • atomate.vasp.workflows.base.core module
  • atomate.vasp.workflows.base.deformations module
  • atomate.vasp.workflows.base.elastic module
    • +
  • atomate.vasp.workflows.base.exchange module
  • atomate.vasp.workflows.base.ferroelectric module
  • atomate.vasp.workflows.base.gibbs module
  • atomate.vasp.workflows.base.magnetism module
    • @@ -802,7 +911,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »

    • diff --git a/docs/atomate.vasp.workflows.html b/docs/atomate.vasp.workflows.html index 042a9ab27..45ffe701f 100644 --- a/docs/atomate.vasp.workflows.html +++ b/docs/atomate.vasp.workflows.html @@ -4,7 +4,7 @@ - atomate.vasp.workflows package — atomate 0.9.4 documentation + atomate.vasp.workflows package — atomate 0.9.5 documentation @@ -27,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • @@ -49,6 +49,7 @@

    Subpackagesatomate.vasp.workflows.base.core module
  • atomate.vasp.workflows.base.deformations module
  • atomate.vasp.workflows.base.elastic module
    • +
  • atomate.vasp.workflows.base.exchange module
  • atomate.vasp.workflows.base.ferroelectric module
  • atomate.vasp.workflows.base.gibbs module
  • atomate.vasp.workflows.base.magnetism module
    • @@ -70,6 +71,7 @@

    Subpackagesatomate.vasp.workflows.tests.test_adsorbate_workflow module
  • atomate.vasp.workflows.tests.test_bulk_modulus_workflow module
  • atomate.vasp.workflows.tests.test_elastic_workflow module
    • +
  • atomate.vasp.workflows.tests.test_exchange_workflow module
  • atomate.vasp.workflows.tests.test_ferroelectric_workflow module
  • atomate.vasp.workflows.tests.test_magnetism_workflow module
  • atomate.vasp.workflows.tests.test_neb_workflow module
    • @@ -132,7 +134,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • diff --git a/docs/atomate.vasp.workflows.presets.html b/docs/atomate.vasp.workflows.presets.html index 3678a032d..237b34659 100644 --- a/docs/atomate.vasp.workflows.presets.html +++ b/docs/atomate.vasp.workflows.presets.html @@ -4,7 +4,7 @@ - atomate.vasp.workflows.presets package — atomate 0.9.4 documentation + atomate.vasp.workflows.presets package — atomate 0.9.5 documentation @@ -27,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • @@ -208,7 +208,13 @@

    Submodules
    atomate.vasp.workflows.presets.scan.wf_scan_opt(structure, c=None)
    -
    +

    Structure optimization using the SCAN metaGGA functional.

    +

    This workflow performs a 2-step optmization. The first step +is a conventional GGA run and serves to precondition the geometry and +wavefunctions. The second step is a SCAN structure optimization.

    +

    The first optimization is force converged with EDIFFG = -0.05, +and the second optimization is force converged with EDIFFG=-0.02.

    +
    @@ -263,7 +269,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • diff --git a/docs/atomate.vasp.workflows.tests.html b/docs/atomate.vasp.workflows.tests.html index 9f669f041..3227ff730 100644 --- a/docs/atomate.vasp.workflows.tests.html +++ b/docs/atomate.vasp.workflows.tests.html @@ -4,7 +4,7 @@ - atomate.vasp.workflows.tests package — atomate 0.9.4 documentation + atomate.vasp.workflows.tests package — atomate 0.9.5 documentation @@ -27,7 +27,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • @@ -139,6 +139,26 @@

    Submodules +

    atomate.vasp.workflows.tests.test_exchange_workflow module

    +
    +
    +class atomate.vasp.workflows.tests.test_exchange_workflow.TestExchangeWF(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +classmethod setUpClass()
    +

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

    +
    + +
    +
    +test_workflow()
    +
    + +
    +

    atomate.vasp.workflows.tests.test_ferroelectric_workflow module

    @@ -148,22 +168,38 @@

    Submodulesatomate.utils.testing.AtomateTest

    -setUp()
    +setUp(lpad=True)

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

    +
    +
    +tearDown()
    +

    Remove the scratch directory and teardown the test db.

    +
    +
    test_wf()
    -
    -
    -untarTestFiles()
    +
    + +
    +
    +atomate.vasp.workflows.tests.test_ferroelectric_workflow.delete_folder(path)
    - +
    +
    +atomate.vasp.workflows.tests.test_ferroelectric_workflow.get_simulated_wf(wf)
    +
    + +
    +
    +atomate.vasp.workflows.tests.test_ferroelectric_workflow.untar_test_files()
    +

    @@ -218,6 +254,11 @@

    Submodules +
    +atomate.vasp.workflows.tests.test_neb_workflow.get_simulated_wf(wf)
    +
    +

    atomate.vasp.workflows.tests.test_nmr module

    @@ -266,6 +307,44 @@

    Submodules

    atomate.vasp.workflows.tests.test_vasp_workflows module

    +
    +
    +class atomate.vasp.workflows.tests.test_vasp_workflows.TestScanOptimizeWorkflow(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +setUp()
    +

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

    +
    + +
    +
    +test_SCAN_incar_override()
    +
    + +
    +
    +test_SCAN_large_bandgap()
    +
    + +
    +
    +test_SCAN_no_bandgap()
    +
    + +
    +
    +test_SCAN_small_bandgap()
    +
    + +
    +
    +test_SCAN_with_vdw()
    +
    + +
    +
    class atomate.vasp.workflows.tests.test_vasp_workflows.TestVaspWorkflows(methodName='runTest')
    @@ -333,6 +412,7 @@

    Table of Contents

  • atomate.vasp.workflows.tests.test_adsorbate_workflow module
  • atomate.vasp.workflows.tests.test_bulk_modulus_workflow module
  • atomate.vasp.workflows.tests.test_elastic_workflow module
    • +
  • atomate.vasp.workflows.tests.test_exchange_workflow module
  • atomate.vasp.workflows.tests.test_ferroelectric_workflow module
  • atomate.vasp.workflows.tests.test_magnetism_workflow module
  • atomate.vasp.workflows.tests.test_neb_workflow module
    • @@ -374,7 +454,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »

    • diff --git a/docs/builders.html b/docs/builders.html index d055fbf9b..f873d800d 100644 --- a/docs/builders.html +++ b/docs/builders.html @@ -4,7 +4,7 @@ - Builders — atomate 0.9.4 documentation + Builders — atomate 0.9.5 documentation @@ -35,7 +35,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • @@ -151,7 +151,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • diff --git a/docs/changelog.html b/docs/changelog.html index edaa0eef2..ca2dedcad 100644 --- a/docs/changelog.html +++ b/docs/changelog.html @@ -4,7 +4,7 @@ - atomate Changelog — atomate 0.9.4 documentation + atomate Changelog — atomate 0.9.5 documentation @@ -35,7 +35,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • @@ -46,6 +46,14 @@

    Navigation

    atomate Changelog

    +

    v0.9.5

    +

    v0.9.4

    diff --git a/docs/concepts.html b/docs/concepts.html index ba56fa258..7570eaf0a 100644 --- a/docs/concepts.html +++ b/docs/concepts.html @@ -4,7 +4,7 @@ - Atomate concepts — atomate 0.9.4 documentation + Atomate concepts — atomate 0.9.5 documentation @@ -31,7 +31,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • @@ -149,7 +149,7 @@

    Navigation

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    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • diff --git a/docs/contributors.html b/docs/contributors.html index 8c04fb4cc..683c7e82b 100644 --- a/docs/contributors.html +++ b/docs/contributors.html @@ -4,7 +4,7 @@ - Contributors — atomate 0.9.4 documentation + Contributors — atomate 0.9.5 documentation @@ -35,7 +35,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • @@ -50,12 +50,12 @@

    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.

    • +

  • Kiran Mathew, Shyam Dwaraknath, Joey Montoya, Murat Aykol, Matt Horton, Patrick Huck, Brandon Wood, Sam Blau, Jimmy Shen, Ryan Kingsbury, 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, Tara Maria Boland

    • +

  • External contributors: specter119, M. Dias Costa, S. Torrisi, Max Dylla, Marnik Bercx, Tara Maria Boland, Nathan Frey, Martin Siron

    • @@ -107,7 +107,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • diff --git a/docs/creating_workflows.html b/docs/creating_workflows.html index eb69f7111..834b980a7 100644 --- a/docs/creating_workflows.html +++ b/docs/creating_workflows.html @@ -4,7 +4,7 @@ - Creating workflows — atomate 0.9.4 documentation + Creating workflows — atomate 0.9.5 documentation @@ -35,7 +35,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • @@ -232,8 +232,8 @@

    Creating the workflowfrom atomate.vasp.firetasks.parse_outputs import GibbsFreeEnergyTask -def wf_gibbs_free_energy(structure, deformations, vasp_input_set_relax=None, vasp_input_set_static=None, vasp_cmd="vasp", - db_file=None, user_kpoints_settings=None, t_step=10, t_min=0, t_max=1000, +def wf_gibbs_free_energy(structure, deformations, vasp_input_set_relax=None, vasp_input_set_static=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): """ @@ -264,7 +264,7 @@

    Creating the workflowtag = datetime.utcnow().strftime('%Y-%m-%d-%H-%M-%S-%f') # get the input set for the optimization and update it if we passed custom settings - vis_relax = vasp_input_set or MPRelaxSet(structure, force_gamma=True) + vis_relax = vasp_input_set or MPRelaxSet(structure, force_gamma=True) if user_kpoints_settings: v = vis_relax.as_dict() v.update({"user_kpoints_settings": user_kpoints_settings}) @@ -272,15 +272,15 @@

    Creating the workflow# Structure optimization firework fws = [OptimizeFW(structure=structure, vasp_input_set=vis_relax, vasp_cmd=vasp_cmd, - db_file=db_file, name="{} structure optimization".format(tag))] + db_file=db_file, name="{} structure optimization".format(tag))] # get the input set for the static calculations and update it if we passed custom settings uis_static = {"ISIF": 2, "ISTART":1} - lepsilon = False # use IBRION = -1; don't update the ions + lepsilon = False # use IBRION = -1; don't update the ions if qha_type not in ['debye model']: uis_static = {'ISIF'} - lepsilon = True # use IBRION = -8; DFPT - vis_static = MPStaticSet(structure, force_gamma=True, lepsilon=lepsilon, + lepsilon = True # use IBRION = -8; DFPT + vis_static = MPStaticSet(structure, force_gamma=True, lepsilon=lepsilon, user_kpoints_settings=user_kpoints_settings, user_incar_settings=uis_static) @@ -288,7 +288,7 @@

    Creating the workflowparents = fws[0] deformations = [Deformation(defo_mat) for defo_mat in deformations] for n, deformation in enumerate(deformations): - fw = TransmuterFW(name="{} {} {}".format(tag, 'gibbs deformation', n), structure=structure, + fw = TransmuterFW(name="{} {} {}".format(tag, 'gibbs deformation', n), structure=structure, transformations=['DeformStructureTransformation'], transformation_params=[{"deformation": deformation.tolist()}], vasp_input_set=vis_static, parents=parents, @@ -306,7 +306,7 @@

    Creating the workflow# finally, create the workflow wf_gibbs = Workflow(fws) - wf_gibbs.name = "{}:{}".format(structure.composition.reduced_formula, "gibbs free energy") + wf_gibbs.name = "{}:{}".format(structure.composition.reduced_formula, "gibbs free energy") return wf_gibbs @@ -454,7 +454,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • diff --git a/docs/customizing_workflows.html b/docs/customizing_workflows.html index 06121ec69..c762d6996 100644 --- a/docs/customizing_workflows.html +++ b/docs/customizing_workflows.html @@ -4,7 +4,7 @@ - Customizing workflows — atomate 0.9.4 documentation + Customizing workflows — atomate 0.9.5 documentation @@ -35,7 +35,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • @@ -104,9 +104,9 @@

    Using a different functionalfrom pymatgen.io.vasp.sets import MPRelaxSet from pymatgen import Structure -def get_optimize_wf(structure, name="optimization wf", vasp_input_set=None, - vasp_cmd="vasp", db_file=None, user_kpoints_settings=None, - tag="", metadata=None): +def get_optimize_wf(structure, name="optimization wf", vasp_input_set=None, + vasp_cmd="vasp", db_file=None, user_kpoints_settings=None, + tag="", metadata=None): """ Returns a structure optimization workflow. @@ -133,9 +133,9 @@

    Using a different functional# Structure optimization firework fws = [OptimizeFW(structure=structure, vasp_input_set=vis_relax, vasp_cmd=vasp_cmd, - db_file=db_file, name="{} structure optimization".format(tag))] + db_file=db_file, name="{} structure optimization".format(tag))] - wfname = "{}:{}".format(structure.composition.reduced_formula, name) + wfname = "{}:{}".format(structure.composition.reduced_formula, name) return Workflow(fws, name=wfname, metadata=metadata) @@ -165,7 +165,7 @@

    Custom KPOINTS settingsstruct = Structure.from_file('POSCAR') # create a custom input set -my_custom_input_set = MPRelaxSet(struct, force_gamma=True, {"grid_density": 10} ) +my_custom_input_set = MPRelaxSet(struct, force_gamma=True, {"grid_density": 10} ) # create the workflow my_wf = get_optimize_wf(struct, vasp_input_set=my_custom_input_set) @@ -198,7 +198,7 @@

    Custom KPOINTS settings# create an instance of the custom input set my_custom_input_set = MyInputSet(struct, points=(5,5,5), shift=(1,1,1)) # show that the set applied -print(my_custom_input_set.kpoints) +print(my_custom_input_set.kpoints) # create the workflow my_wf = get_optimize_wf(struct, vasp_input_set=my_custom_input_set) @@ -220,10 +220,10 @@

    Use a different POTCAR# create a custom input set my_custom_input_set = MPRelaxSet(struct) -print('Config dict example: {}\n'.format(my_custom_input_set.config_dict)) -print('Before change: {}'.format(my_custom_input_set.config_dict['POTCAR']['Mg'])) +print('Config dict example: {}\n'.format(my_custom_input_set.config_dict)) +print('Before change: {}'.format(my_custom_input_set.config_dict['POTCAR']['Mg'])) my_custom_input_set.config_dict['POTCAR']['Mg'] = 'Mg' -print('After change: {}'.format(my_custom_input_set.config_dict['POTCAR']['Mg'])) +print('After change: {}'.format(my_custom_input_set.config_dict['POTCAR']['Mg'])) # create the workflow my_wf = get_optimize_wf(struct, vasp_input_set=my_custom_input_set) @@ -303,7 +303,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • diff --git a/docs/developer_installation.html b/docs/developer_installation.html index c84c0343e..f230802ab 100644 --- a/docs/developer_installation.html +++ b/docs/developer_installation.html @@ -4,7 +4,7 @@ - Atomate developer installation — atomate 0.9.4 documentation + Atomate developer installation — atomate 0.9.5 documentation @@ -35,7 +35,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • @@ -165,7 +165,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • diff --git a/docs/genindex.html b/docs/genindex.html index bcc2417b0..1d532c81d 100644 --- a/docs/genindex.html +++ b/docs/genindex.html @@ -5,7 +5,7 @@ - Index — atomate 0.9.4 documentation + Index — atomate 0.9.5 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.4 documentation »
    • +
  • atomate 0.9.5 documentation »
    • @@ -152,12 +152,18 @@

    _

  • (atomate.vasp.fireworks.core.RamanFW method)
  • (atomate.vasp.fireworks.core.SOCFW method) +
    • +
  • (atomate.vasp.fireworks.core.ScanOptimizeFW method)
  • (atomate.vasp.fireworks.core.StaticFW method)
  • (atomate.vasp.fireworks.core.StaticInterpolateFW method)
  • (atomate.vasp.fireworks.core.TransmuterFW method) +
    • +
  • (atomate.vasp.fireworks.exchange.HeisenbergModelFW method) +
    • +
  • (atomate.vasp.fireworks.exchange.VampireCallerFW method)
  • (atomate.vasp.fireworks.nmr.NMRFW method)
    • @@ -166,6 +172,8 @@

    _

  • (atomate.vasp.submission_filter.SubmissionFilter method)
  • (atomate.vasp.workflows.base.adsorption.MPSurfaceSet method) +
    • +
  • (atomate.vasp.workflows.base.exchange.ExchangeWF method)
  • (atomate.vasp.workflows.base.magnetism.MagneticOrderingsWF method)
    • @@ -189,6 +197,8 @@

    A

  • add_modify_incar() (in module atomate.vasp.powerups)
  • add_modify_incar_envchk() (in module atomate.vasp.powerups) +
    • +
  • add_modify_kpoints() (in module atomate.vasp.powerups)
  • add_modify_potcar() (in module atomate.vasp.powerups)
    • @@ -352,12 +362,12 @@

    A

  • atomate.qchem.workflows.base.fragmentation (module)
    • - - + -
  • get_wf() (atomate.vasp.workflows.base.magnetism.MagneticOrderingsWF method) +
  • get_wf() (atomate.vasp.workflows.base.exchange.ExchangeWF method)
    • @@ -835,6 +871,8 @@

    G

  • GibbsFreeEnergyTask (class in atomate.vasp.firetasks.parse_outputs)
  • glob() (atomate.utils.fileio.FileClient method) +
    • +
  • GzipDir (class in atomate.common.firetasks.glue_tasks)
    • @@ -842,6 +880,16 @@

    G

    H

    + @@ -906,9 +954,9 @@

    L

    M

      -
    • MagneticDeformationToDB (class in atomate.vasp.firetasks.parse_outputs) +
    • MagneticDeformationToDb (class in atomate.vasp.firetasks.parse_outputs)
      • -
    • MagneticOrderingsToDB (class in atomate.vasp.firetasks.parse_outputs) +
    • MagneticOrderingsToDb (class in atomate.vasp.firetasks.parse_outputs)
    • MagneticOrderingsWF (class in atomate.vasp.workflows.base.magnetism)
      • @@ -925,6 +973,8 @@

      M

    • modify_to_soc() (in module atomate.vasp.powerups)
    • ModifyIncar (class in atomate.vasp.firetasks.write_inputs) +
      • +
    • ModifyKpoints (class in atomate.vasp.firetasks.write_inputs)
    • ModifyPotcar (class in atomate.vasp.firetasks.write_inputs)
      • @@ -968,6 +1018,8 @@

      O

    • (atomate.common.firetasks.glue_tasks.CopyFilesFromCalcLoc attribute)
    • (atomate.common.firetasks.glue_tasks.CreateFolder attribute) +
      • +
    • (atomate.common.firetasks.glue_tasks.GzipDir attribute)
    • (atomate.common.firetasks.glue_tasks.PassCalcLocs attribute)
      • @@ -1016,6 +1068,10 @@

      O

    • (atomate.qchem.firetasks.write_inputs.WriteInput attribute)
    • (atomate.qchem.firetasks.write_inputs.WriteInputFromIOSet attribute) +
      • +
    • (atomate.vasp.firetasks.exchange.HeisenbergModelMapping attribute) +
      • +
    • (atomate.vasp.firetasks.exchange.VampireMC attribute)
    • (atomate.vasp.firetasks.glue_tasks.CheckBandgap attribute)
      • @@ -1043,9 +1099,9 @@

      O

    • (atomate.vasp.firetasks.parse_outputs.JsonToDb attribute)
      • -
    • (atomate.vasp.firetasks.parse_outputs.MagneticDeformationToDB attribute) +
    • (atomate.vasp.firetasks.parse_outputs.MagneticDeformationToDb attribute)
      • -
    • (atomate.vasp.firetasks.parse_outputs.MagneticOrderingsToDB attribute) +
    • (atomate.vasp.firetasks.parse_outputs.MagneticOrderingsToDb attribute)
    • (atomate.vasp.firetasks.parse_outputs.PolarizationToDb attribute)
      • @@ -1064,8 +1120,12 @@

      O

    • (atomate.vasp.firetasks.run_calc.RunVaspFake attribute)
    • (atomate.vasp.firetasks.write_inputs.ModifyIncar attribute) +
      • +
    • (atomate.vasp.firetasks.write_inputs.ModifyKpoints attribute)
    • (atomate.vasp.firetasks.write_inputs.ModifyPotcar attribute) +
      • +
    • (atomate.vasp.firetasks.write_inputs.UpdateScanRelaxBandgap attribute)
    • (atomate.vasp.firetasks.write_inputs.WriteTransmutedStructureIOSet attribute)
      • @@ -1115,8 +1175,6 @@

      P

    • preserve_fworker() (in module atomate.vasp.powerups)
    • process_bandstructure() (atomate.vasp.drones.VaspDrone method) -
      • -
    • process_chgcar() (atomate.vasp.drones.VaspDrone class method)
    • process_dos() (atomate.vasp.drones.VaspDrone method)
      • @@ -1166,6 +1224,8 @@

      R

    • (atomate.common.firetasks.glue_tasks.CreateFolder attribute)
    • (atomate.common.firetasks.glue_tasks.DeleteFiles attribute) +
      • +
    • (atomate.common.firetasks.glue_tasks.GzipDir attribute)
    • (atomate.common.firetasks.glue_tasks.PassCalcLocs attribute)
      • @@ -1210,6 +1270,16 @@

      R

    • (atomate.qchem.firetasks.write_inputs.WriteInput attribute)
    • (atomate.qchem.firetasks.write_inputs.WriteInputFromIOSet attribute) +
      • +
    • (atomate.vasp.firetasks.exchange.HeisenbergConvergence attribute) +
      • +
    • (atomate.vasp.firetasks.exchange.HeisenbergModelMapping attribute) +
      • +
    • (atomate.vasp.firetasks.exchange.HeisenbergModelToDb attribute) +
      • +
    • (atomate.vasp.firetasks.exchange.VampireMC attribute) +
      • +
    • (atomate.vasp.firetasks.exchange.VampireToDb attribute)
    • (atomate.vasp.firetasks.glue_tasks.CheckBandgap attribute)
      • @@ -1231,9 +1301,9 @@

      R

    • (atomate.vasp.firetasks.parse_outputs.GibbsAnalysisToDb attribute)
      • -
    • (atomate.vasp.firetasks.parse_outputs.MagneticDeformationToDB attribute) +
    • (atomate.vasp.firetasks.parse_outputs.MagneticDeformationToDb attribute)
      • -
    • (atomate.vasp.firetasks.parse_outputs.MagneticOrderingsToDB attribute) +
    • (atomate.vasp.firetasks.parse_outputs.MagneticOrderingsToDb attribute)
    • (atomate.vasp.firetasks.parse_outputs.ThermalExpansionCoeffToDb attribute)
      • @@ -1326,6 +1396,8 @@

      R

    • (atomate.common.firetasks.glue_tasks.CreateFolder method)
    • (atomate.common.firetasks.glue_tasks.DeleteFiles method) +
      • +
    • (atomate.common.firetasks.glue_tasks.GzipDir method)
    • (atomate.common.firetasks.glue_tasks.PassCalcLocs method)
      • @@ -1386,6 +1458,16 @@

      R

    • (atomate.utils.tests.test_utils.Task1 method)
    • (atomate.utils.tests.test_utils.Task2 method) +
      • +
    • (atomate.vasp.firetasks.exchange.HeisenbergConvergence method) +
      • +
    • (atomate.vasp.firetasks.exchange.HeisenbergModelMapping method) +
      • +
    • (atomate.vasp.firetasks.exchange.HeisenbergModelToDb method) +
      • +
    • (atomate.vasp.firetasks.exchange.VampireMC method) +
      • +
    • (atomate.vasp.firetasks.exchange.VampireToDb method)
    • (atomate.vasp.firetasks.glue_tasks.CheckBandgap method)
      • @@ -1413,9 +1495,9 @@

      R

    • (atomate.vasp.firetasks.parse_outputs.JsonToDb method)
      • -
    • (atomate.vasp.firetasks.parse_outputs.MagneticDeformationToDB method) +
    • (atomate.vasp.firetasks.parse_outputs.MagneticDeformationToDb method)
      • -
    • (atomate.vasp.firetasks.parse_outputs.MagneticOrderingsToDB method) +
    • (atomate.vasp.firetasks.parse_outputs.MagneticOrderingsToDb method)
    • (atomate.vasp.firetasks.parse_outputs.PolarizationToDb method)
      • @@ -1436,8 +1518,12 @@

      R

    • (atomate.vasp.firetasks.run_calc.RunVaspFake method)
    • (atomate.vasp.firetasks.write_inputs.ModifyIncar method) +
      • +
    • (atomate.vasp.firetasks.write_inputs.ModifyKpoints method)
    • (atomate.vasp.firetasks.write_inputs.ModifyPotcar method) +
      • +
    • (atomate.vasp.firetasks.write_inputs.UpdateScanRelaxBandgap method)
    • (atomate.vasp.firetasks.write_inputs.WriteNormalmodeDisplacedPoscar method)
      • @@ -1500,6 +1586,8 @@

      R

      S

      - +
    • test() (atomate.vasp.submission_filter.SubmissionFilter method) @@ -1731,6 +1829,8 @@

      T

    • test_getinterpolatedposcar() (atomate.vasp.firetasks.tests.test_get_interpolated_poscar.TestGetInterpolatedPOSCAR method)
    • test_gzip_copy() (atomate.vasp.firetasks.tests.test_copy.TestCopyVaspOutputs method) +
      • +
    • test_heisenberg_mm() (atomate.vasp.firetasks.tests.test_exchange.TestExchangeTasks method)
    • test_in_database_and_EC_neg_frag() (atomate.qchem.firetasks.tests.test_fragmenter.TestFragmentMolecule method)
      • @@ -1750,6 +1850,12 @@

      T

      +
    • test_modify_kpoints() (atomate.vasp.firetasks.tests.test_write_vasp.TestWriteVasp method) + +
    • test_modify_potcar() (atomate.vasp.firetasks.tests.test_write_vasp.TestWriteVasp method) @@ -1775,6 +1881,8 @@

      T

    • test_parse_pass_rotate_write() (atomate.qchem.workflows.tests.test_parse_pass_write.TestParsePassWrite method)
    • test_parse_pass_write() (atomate.qchem.workflows.tests.test_parse_pass_write.TestParsePassWrite method) +
      • +
    • test_parse_potcar() (atomate.vasp.tests.test_drones.VaspToDbTaskDroneTest method)
    • test_passcalclocs() (atomate.common.firetasks.tests.test_glue_tasks.TestPassCalcLocs method)
      • @@ -1787,13 +1895,17 @@

      T

    • test_pmgobjects() (atomate.vasp.firetasks.tests.test_write_vasp.TestWriteVasp method)
    • test_polarizationtodb() (atomate.vasp.firetasks.tests.test_polarization_to_db.TestFerroelectricWorkflow method) +
      • +
    • test_potcar_spec() (atomate.vasp.firetasks.tests.test_write_vasp.TestWriteVasp method) +
      • +
    • test_queue_options() (atomate.vasp.tests.test_vasp_powerups.TestVaspPowerups method)
    • test_recursive_get_result() (atomate.utils.tests.test_utils.UtilsTests method)
      • -
      • test_relax2_copy() (atomate.vasp.firetasks.tests.test_copy.TestCopyVaspOutputs method)
      • test_rotate_torsion() (atomate.qchem.firetasks.tests.test_geo_transformations.TestGeoTransformations method) @@ -1821,6 +1933,16 @@

        T

      • test_RunQChemFake() (atomate.qchem.firetasks.tests.test_run_calc.TestFakeRunQChem method)
      • test_runs_assimilate() (atomate.vasp.tests.test_drones.VaspToDbTaskDroneTest method) +
        • +
      • test_SCAN_incar_override() (atomate.vasp.workflows.tests.test_vasp_workflows.TestScanOptimizeWorkflow method) +
        • +
      • test_SCAN_large_bandgap() (atomate.vasp.workflows.tests.test_vasp_workflows.TestScanOptimizeWorkflow method) +
        • +
      • test_SCAN_no_bandgap() (atomate.vasp.workflows.tests.test_vasp_workflows.TestScanOptimizeWorkflow method) +
        • +
      • test_SCAN_small_bandgap() (atomate.vasp.workflows.tests.test_vasp_workflows.TestScanOptimizeWorkflow method) +
        • +
      • test_SCAN_with_vdw() (atomate.vasp.workflows.tests.test_vasp_workflows.TestScanOptimizeWorkflow method)
      • test_setup() (atomate.vasp.tests.test_setup.TestSetup method)
        • @@ -1835,6 +1957,8 @@

        T

      • test_trackers() (atomate.vasp.workflows.tests.test_vasp_workflows.TestVaspWorkflows method)
      • test_unittestsetup() (atomate.vasp.firetasks.tests.test_copy.TestCopyVaspOutputs method) +
        • +
      • test_use_potcar_spec() (atomate.vasp.tests.test_vasp_powerups.TestVaspPowerups method)
      • test_use_scratch_dir() (atomate.vasp.tests.test_vasp_powerups.TestVaspPowerups method)
        • @@ -1857,6 +1981,8 @@

        T

      • test_wf_functions() (atomate.vasp.workflows.tests.test_adsorbate_workflow.TestAdsorptionWorkflow method)
      • test_wflow_composition() (atomate.feff.workflows.tests.test_exafs_scattering_paths.TestEXAFSPaths method) +
        • +
      • test_workflow() (atomate.vasp.workflows.tests.test_exchange_workflow.TestExchangeWF method)
      • test_write_custom_input() (atomate.qchem.firetasks.tests.test_write_inputs.TestWriteInputQChem method)
        • @@ -1903,6 +2029,10 @@

        T

      • TestElasticWorkflow (class in atomate.vasp.workflows.tests.test_elastic_workflow)
      • TestEXAFSPaths (class in atomate.feff.workflows.tests.test_exafs_scattering_paths) +
        • +
      • TestExchangeTasks (class in atomate.vasp.firetasks.tests.test_exchange) +
        • +
      • TestExchangeWF (class in atomate.vasp.workflows.tests.test_exchange_workflow)
      • TestFakeRunQChem (class in atomate.qchem.firetasks.tests.test_run_calc)
        • @@ -1937,6 +2067,8 @@

        T

      • TestRamanWorkflow (class in atomate.vasp.workflows.tests.test_raman_workflow)
      • TestRunCalcQChem (class in atomate.qchem.firetasks.tests.test_run_calc) +
        • +
      • TestScanOptimizeWorkflow (class in atomate.vasp.workflows.tests.test_vasp_workflows)
      • TestSetup (class in atomate.vasp.tests.test_setup)
        • @@ -1974,7 +2106,9 @@

        T

        U

        + + + + + + + + + + + + + + +
        -
      • VaspCalcDb (class in atomate.vasp.database) +
      • VampireCallerFW (class in atomate.vasp.fireworks.exchange) +
        • +
      • VampireMC (class in atomate.vasp.firetasks.exchange) +
        • +
      • VampireToDb (class in atomate.vasp.firetasks.exchange)
        		• diff --git a/docs/gibbs_workflow_tutorial.html b/docs/gibbs_workflow_tutorial.html index 047a12329..88e36180f 100644 --- a/docs/gibbs_workflow_tutorial.html +++ b/docs/gibbs_workflow_tutorial.html @@ -4,7 +4,7 @@ - Running Gibbs workflows — atomate 0.9.4 documentation + Running Gibbs workflows — atomate 0.9.5 documentation @@ -35,7 +35,7 @@

        Navigation

      • previous |
        • -
      • atomate 0.9.4 documentation »
        • +
      • atomate 0.9.5 documentation »
        • @@ -111,7 +111,7 @@

        Use Python to generate and add the workflowgibbs.py with the following contents:

        #!/usr/bin/env python
-import numpy as np
+import numpy as np
 from pymatgen import MPRester
 from fireworks import LaunchPad
 from atomate.vasp.workflows.presets.core import wf_gibbs_free_energy
@@ -130,7 +130,7 @@ 
        Use Python to generate and add the workflow# of anharmonic contributions, and finally the deformation matrix describing points
 # on the energy vs. volume curve.
 c = {"T_MIN": 10, "T_STEP": 10, "T_MAX": 2000,
-     "POISSON": 0.20, "ANHARMONIC_CONTRIBUTION": True,
+     "POISSON": 0.20, "ANHARMONIC_CONTRIBUTION": True,
      "DEFORMATIONS": deformations}
 
 # Create the workflow
@@ -169,9 +169,9 @@ 
        Analyzing an Equation of State Workflowgibbs-analysis.py) to your folder and run it
        
 
        from atomate.vasp.database import VaspCalcDb
 from pymatgen import Structure
-import numpy as np
+import numpy as np
 
-import matplotlib.pyplot as plt
+import matplotlib.pyplot as plt
 
 # create the atomate db from your db.json
 PATH_TO_MY_DB_JSON = '/path/to/my/db.json'
@@ -294,7 +294,7 @@ 
        Navigation
        
         
      • 
           previous |
        • 
-        
      • atomate 0.9.4 documentation »
        •  
+        
      • atomate 0.9.5 documentation »
        •  
       
     
        
 
diff --git a/docs/index.html b/docs/index.html
index 69fbc20c5..50c3e3a89 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -4,7 +4,7 @@
 
   
     
-    atomate (Materials Science Workflows) — atomate 0.9.4 documentation
+    atomate (Materials Science Workflows) — atomate 0.9.5 documentation
     
     
     
@@ -31,7 +31,7 @@ 
        Navigation
        
         
      • 
           next |
        • 
-        
      • atomate 0.9.4 documentation »
        •  
+        
      • atomate 0.9.5 documentation »
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@@ -388,7 +388,7 @@ 
        Navigation
        
         
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        diff --git a/docs/installation.html b/docs/installation.html index 54506bf0b..e6ce01933 100644 --- a/docs/installation.html +++ b/docs/installation.html @@ -4,7 +4,7 @@ - Installing atomate — atomate 0.9.4 documentation + Installing atomate — atomate 0.9.5 documentation @@ -35,7 +35,7 @@

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        • @@ -224,7 +224,7 @@

        db.json
        from atomate.vasp.database import VaspCalcDb
 x = VaspCalcDb.from_db_file("db.json")
 x.reset()
-print("SUCCESS")
+print("SUCCESS")
        @@ -637,7 +637,7 @@

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        • diff --git a/docs/license.html b/docs/license.html index a983c097d..4dc663a09 100644 --- a/docs/license.html +++ b/docs/license.html @@ -4,7 +4,7 @@ - License — atomate 0.9.4 documentation + License — atomate 0.9.5 documentation @@ -35,7 +35,7 @@

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        • @@ -145,7 +145,7 @@

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        • diff --git a/docs/modules.html b/docs/modules.html index da8406b8b..09f0bb138 100644 --- a/docs/modules.html +++ b/docs/modules.html @@ -4,7 +4,7 @@ - atomate — atomate 0.9.4 documentation + atomate — atomate 0.9.5 documentation @@ -27,7 +27,7 @@

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        • @@ -140,7 +140,7 @@

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        • diff --git a/docs/objects.inv b/docs/objects.inv index 13c0ab5b7..696e8cdf9 100644 Binary files a/docs/objects.inv and b/docs/objects.inv differ diff --git a/docs/py-modindex.html b/docs/py-modindex.html index eb5186559..87501f109 100644 --- a/docs/py-modindex.html +++ b/docs/py-modindex.html @@ -4,7 +4,7 @@ - Python Module Index — atomate 0.9.4 documentation + Python Module Index — atomate 0.9.5 documentation @@ -30,7 +30,7 @@

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        • @@ -546,6 +546,11 @@

        Python Module Index

        		    atomate.vasp.firetasks
            + atomate.vasp.firetasks.exchange +
            @@ -576,6 +581,11 @@

        Python Module Index

        		    atomate.vasp.firetasks.tests.test_copy
            + atomate.vasp.firetasks.tests.test_exchange +
            @@ -611,6 +621,11 @@

        Python Module Index

        		    atomate.vasp.fireworks.core
            + atomate.vasp.fireworks.exchange +
            @@ -696,6 +711,11 @@

        Python Module Index

        		    atomate.vasp.workflows.base.elastic
            + atomate.vasp.workflows.base.exchange +
            @@ -761,6 +781,11 @@

        Python Module Index

        		    atomate.vasp.workflows.tests.test_elastic_workflow
            + atomate.vasp.workflows.tests.test_exchange_workflow +
            @@ -822,7 +847,7 @@

        Navigation

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        • diff --git a/docs/running_workflows.html b/docs/running_workflows.html index edfe85ef1..45b7b431d 100644 --- a/docs/running_workflows.html +++ b/docs/running_workflows.html @@ -4,7 +4,7 @@ - Running workflows tutorial — atomate 0.9.4 documentation + Running workflows tutorial — atomate 0.9.5 documentation @@ -35,7 +35,7 @@

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        • @@ -148,7 +148,7 @@

        Option 3: use Python to generate and add the workflowCreate the workflow script

        In the same directory as the POSCAR, create a Python script named mgo_bandstructure.py with the following contents:

        # Create a bandstructure from the workflow from the atomate presets
-import numpy as np
+import numpy as np
 from pymatgen import Structure
 from fireworks import LaunchPad
 from atomate.vasp.workflows.presets.core import wf_bandstructure
@@ -207,8 +207,8 @@ 
        Analyzing a Bandstructure Workflow#dos_plotter.save_plot('MgO-dos.pdf', img_format='pdf', xlim=(-10, 10))
 
 # print the Fermi energy and bandgap from the DOS:
-print('Fermi energy: {} eV'.format(complete_dos.efermi))
-print('Bandgap: {} eV'.format(complete_dos.get_gap()))
+print('Fermi energy: {} eV'.format(complete_dos.efermi))
+print('Bandgap: {} eV'.format(complete_dos.get_gap()))
 
 # get the entry from the database and
 # use the get_band_structure method of the database to get the pymatgen BandStructureSymmLine for that task id
@@ -312,7 +312,7 @@ 
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        • diff --git a/docs/searchindex.js b/docs/searchindex.js index 422d0783d..4f5ef231f 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ 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\ No newline at end of file diff --git a/docs/workflow_yaml_reference.html b/docs/workflow_yaml_reference.html index c02e9c824..8a43c02a4 100644 --- a/docs/workflow_yaml_reference.html +++ b/docs/workflow_yaml_reference.html @@ -4,7 +4,7 @@ - Workflow YAML Reference — atomate 0.9.4 documentation + Workflow YAML Reference — atomate 0.9.5 documentation @@ -35,7 +35,7 @@

        Navigation

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      • atomate 0.9.4 documentation »
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      • atomate 0.9.5 documentation »
        • @@ -234,7 +234,7 @@

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      • atomate 0.9.4 documentation »
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      • atomate 0.9.5 documentation »
        • diff --git a/docs_rst/atomate.vasp.firetasks.rst b/docs_rst/atomate.vasp.firetasks.rst index f2e04229c..7c14ade13 100644 --- a/docs_rst/atomate.vasp.firetasks.rst +++ b/docs_rst/atomate.vasp.firetasks.rst @@ -11,6 +11,14 @@ Subpackages Submodules ---------- +atomate.vasp.firetasks.exchange module +-------------------------------------- + +.. automodule:: atomate.vasp.firetasks.exchange + :members: + :undoc-members: + :show-inheritance: + atomate.vasp.firetasks.glue\_tasks module ----------------------------------------- diff --git a/docs_rst/atomate.vasp.firetasks.tests.rst b/docs_rst/atomate.vasp.firetasks.tests.rst index a8d1755d0..3e725097c 100644 --- a/docs_rst/atomate.vasp.firetasks.tests.rst +++ b/docs_rst/atomate.vasp.firetasks.tests.rst @@ -12,6 +12,14 @@ atomate.vasp.firetasks.tests.test\_copy module :undoc-members: :show-inheritance: +atomate.vasp.firetasks.tests.test\_exchange module +-------------------------------------------------- + +.. automodule:: atomate.vasp.firetasks.tests.test_exchange + :members: + :undoc-members: + :show-inheritance: + atomate.vasp.firetasks.tests.test\_get\_interpolated\_poscar module ------------------------------------------------------------------- diff --git a/docs_rst/atomate.vasp.fireworks.rst b/docs_rst/atomate.vasp.fireworks.rst index 9490e08b0..f82e94ade 100644 --- a/docs_rst/atomate.vasp.fireworks.rst +++ b/docs_rst/atomate.vasp.fireworks.rst @@ -12,6 +12,14 @@ atomate.vasp.fireworks.core module :undoc-members: :show-inheritance: +atomate.vasp.fireworks.exchange module +-------------------------------------- + +.. automodule:: atomate.vasp.fireworks.exchange + :members: + :undoc-members: + :show-inheritance: + atomate.vasp.fireworks.nmr module --------------------------------- diff --git a/docs_rst/atomate.vasp.workflows.base.rst b/docs_rst/atomate.vasp.workflows.base.rst index 31b694d3d..2f91b0d1d 100644 --- a/docs_rst/atomate.vasp.workflows.base.rst +++ b/docs_rst/atomate.vasp.workflows.base.rst @@ -44,6 +44,14 @@ atomate.vasp.workflows.base.elastic module :undoc-members: :show-inheritance: +atomate.vasp.workflows.base.exchange module +------------------------------------------- + +.. automodule:: atomate.vasp.workflows.base.exchange + :members: + :undoc-members: + :show-inheritance: + atomate.vasp.workflows.base.ferroelectric module ------------------------------------------------ diff --git a/docs_rst/atomate.vasp.workflows.tests.rst b/docs_rst/atomate.vasp.workflows.tests.rst index 62ff4bc8a..364abd6be 100644 --- a/docs_rst/atomate.vasp.workflows.tests.rst +++ b/docs_rst/atomate.vasp.workflows.tests.rst @@ -28,6 +28,14 @@ atomate.vasp.workflows.tests.test\_elastic\_workflow module :undoc-members: :show-inheritance: +atomate.vasp.workflows.tests.test\_exchange\_workflow module +------------------------------------------------------------ + +.. automodule:: atomate.vasp.workflows.tests.test_exchange_workflow + :members: + :undoc-members: + :show-inheritance: + atomate.vasp.workflows.tests.test\_ferroelectric\_workflow module ----------------------------------------------------------------- diff --git a/docs_rst/changelog.rst b/docs_rst/changelog.rst index 929794fbe..57c42db36 100644 --- a/docs_rst/changelog.rst +++ b/docs_rst/changelog.rst @@ -2,6 +2,14 @@ atomate Changelog ================= +**v0.9.5** + +* Add magnetism workflow (M. Horton, N. Frey) +* Overhaul SCAN workflow (R. Kingsbury) +* Move help to Discourse (A. Ganose) +* add ModifyKPoints Firetask (M. Siron) +* Misc fixes, dependency updates, and improvements (M. Horton, N. Frey, A. Jain, M. Siron, A. Ganose) + **v0.9.4** * Fixes for new pymatgen (S. Blau, S.P. Ong) diff --git a/docs_rst/contributors.rst b/docs_rst/contributors.rst index 4e371d834..4a280704d 100644 --- a/docs_rst/contributors.rst +++ b/docs_rst/contributors.rst @@ -7,9 +7,9 @@ atomate development is led by the Hacking Materials research group led by Anubha Contributions are provided by: * 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. +* Kiran Mathew, Shyam Dwaraknath, Joey Montoya, Murat Aykol, Matt Horton, Patrick Huck, Brandon Wood, Sam Blau, Jimmy Shen, Ryan Kingsbury, 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, Tara Maria Boland, Nathan Frey. +* External contributors: specter119, M. Dias Costa, S. Torrisi, Max Dylla, Marnik Bercx, Tara Maria Boland, Nathan Frey, Martin Siron diff --git a/setup.py b/setup.py index 055c2b9f5..e0ea06e0d 100644 --- a/setup.py +++ b/setup.py @@ -9,7 +9,7 @@ if __name__ == "__main__": setup( name='atomate', - version='0.9.4', + version='0.9.5', description='atomate has implementations of FireWorks workflows for ' 'Materials Science', long_description=open(os.path.join(module_dir, 'README.md')).read(),