diff --git a/atomate/__init__.py b/atomate/__init__.py index 874fa9ae6..725c309b4 100644 --- a/atomate/__init__.py +++ b/atomate/__init__.py @@ -1 +1 @@ -__version__ = "0.9.6" \ No newline at end of file +__version__ = "0.9.8" \ No newline at end of file diff --git a/docs/_sources/contributors.rst.txt b/docs/_sources/contributors.rst.txt index 16c622f2b..b5850370b 100644 --- a/docs/_sources/contributors.rst.txt +++ b/docs/_sources/contributors.rst.txt @@ -2,7 +2,7 @@ Contributors ============ -.. caution:: Starting v0.9.6 onwards, the contributors list is no longer maintained. Please check the Github commit log for a record of changes. +.. caution:: Starting v0.9.6 onwards, the contributors list is no longer maintained. the contributors list is no longer maintained. Please check the Github contributors list instead. atomate development is led by the Hacking Materials research group led by Anubhav Jain at Lawrence Berkeley National Lab, using primarily research funding from U.S. Department of Energy Early Career program; additional support and funding is from the U.S. Department of Energy Materials Project program. diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt index 160e8a6bf..55387a1c6 100644 --- a/docs/_sources/index.rst.txt +++ b/docs/_sources/index.rst.txt @@ -109,7 +109,7 @@ The list of contributors to atomate can be found :doc:`here `. There is an `atomate Discourse forum`_ dedicated to discussion and basic support. -For specifics on how to contribute, see our `contribution guidelines. `_ +For specifics on how to contribute, see our `contribution guidelines. `_ .. _atomate Discourse forum: https://discuss.matsci.org/c/atomate diff --git a/docs/_sources/installation.rst.txt b/docs/_sources/installation.rst.txt index b3a1e1a3b..52f1fd041 100644 --- a/docs/_sources/installation.rst.txt +++ b/docs/_sources/installation.rst.txt @@ -344,7 +344,7 @@ This is not at all required, but if you want to see what the queue templates loo .. _FireWorks documentation for writing queue adapters: https://materialsproject.github.io/fireworks/qadapter_programming.html?highlight=qadapter -.. _here: https://github.com/materialsproject/fireworks/tree/master/fireworks/user_objects/queue_adapters +.. _here: https://github.com/materialsproject/fireworks/tree/main/fireworks/user_objects/queue_adapters FW_config.yaml @@ -481,7 +481,7 @@ Below are 4 different options for adding a workflow to the database. You only ne All of these function specify (i) a type of workflow and (ii) the structure to feed into that workflow. * The ``-l vasp`` option states to use the ``vasp`` library of workflows. -* The ``-s optimize_only.yaml`` sets the specification of the workflow using the ``optimize_only.yaml`` file in `this directory `_. Alternatively, the ``-p wf_structure_optimization`` sets the workflow specification using the preset Python function located in `this module `_. For now, it's probably best not to worry about the distinction but to know that both libraries of workflows are available to you. +* The ``-s optimize_only.yaml`` sets the specification of the workflow using the ``optimize_only.yaml`` file in `this directory `_. Alternatively, the ``-p wf_structure_optimization`` sets the workflow specification using the preset Python function located in `this module `_. For now, it's probably best not to worry about the distinction but to know that both libraries of workflows are available to you. * The ``-c`` option is used in file-based workflows to make sure that one uses the ``vasp_cmd`` and ``db_file`` that are specified in ``my_fworker.yaml`` that you specified earlier. In the preset workflows, it is the default behavior to take these parameters from the ``my_fworker.yaml`` so this option is not needed. Verify the workflow diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index c84f1f77e..1aa910a8c 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: '0.9.6', + VERSION: '0.9.8', LANGUAGE: 'None', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/docs/advanced_stores.html b/docs/advanced_stores.html index a810a59d9..fb9755d43 100644 --- a/docs/advanced_stores.html +++ b/docs/advanced_stores.html @@ -5,7 +5,7 @@ - Advanced Storage Stratagies — atomate 0.9.6 documentation + Advanced Storage Stratagies — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • Advanced Storage Stratagies
    • @@ -151,7 +151,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • Advanced Storage Stratagies
    • diff --git a/docs/atomate.common.firetasks.html b/docs/atomate.common.firetasks.html index 67d33f445..a8e9a1110 100644 --- a/docs/atomate.common.firetasks.html +++ b/docs/atomate.common.firetasks.html @@ -5,7 +5,7 @@ - atomate.common.firetasks package — atomate 0.9.6 documentation + atomate.common.firetasks package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.common.firetasks package
    • @@ -47,7 +47,7 @@

    Subpackagesatomate.common.firetasks.tests package @@ -57,14 +57,670 @@

    Subpackages

    Submodules

    -
    -

    atomate.common.firetasks.glue_tasks module

    +
    +

    atomate.common.firetasks.glue_tasks module

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

    Bases: fireworks.core.firework.FiretaskBase

    +

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

    +
    +
    Optional params:

    from_dir (str): path to the directory containing the files to be copied. Supports env_chk. +to_dir (str): path to the destination directory. Supports env_chk. +filesystem (str) +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.

    +
    +
    +
    +
    +
    +
    +copy_files()
    +

    Defines the copy operation. Override this to customize copying.

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

    +
    +
    +
    + +
    +
    +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): 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.

    +
    +
    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.

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

    Bases: fireworks.core.firework.FiretaskBase

    +

    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.

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

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

    +
    +

    and name_append cannot be set in this case.

    +
    +

    Accepts glob patterns.

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

    directory.

    +
    +
    +

    name_append (str): string to append to destination filenames. +exclude_files (list): list of file names to be excluded. Accepts glob

    +
    +

    patterns.

    +
    +
    +
    +
    +
    +optional_params = ['filenames', 'name_prepend', 'name_append', 'exclude_files']
    +
    + +
    +
    +required_params = ['calc_loc']
    +
    + +
    +
    +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.CreateFolder(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

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

    +
    +
    Required params:

    folder_name (str): folder name.

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

    Defaults to False.

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

    Defaults to True.

    +
    +
    +
    +
    +
    +
    +optional_params = ['change_dir', 'relative_path']
    +
    + +
    +
    +required_params = ['folder_name']
    +
    + +
    +
    +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.common.firetasks.glue_tasks.DeleteFiles(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

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

    +
    +
    Required params:

    files: list of files to remove

    +
    +
    +
    +
    +required_params = ['files']
    +
    + +
    +
    +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.DeleteFilesPrevFolder(*args, **kwargs)
    +

    Bases: atomate.common.firetasks.glue_tasks.DeleteFiles

    +

    Can delete files, also from a previous folder in the wf if one of the optional parameters are given +Required params:

    +
    +

    files: list of files to remove

    +
    +
    +
    Optional params:

    calc_dir: directory to delete the files from +calc_loc (str OR bool): if True will set most recent calc_loc. If str

    +
    +

    search for the most recent calc_loc with the matching name

    +
    +
    +
    +
    +
    +optional_params = ['calc_dir', 'calc_loc']
    +
    + +
    +
    +required_params = ['files']
    +
    + +
    +
    +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.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)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

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

    +
    +
    Required params:

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

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

    defaults to None

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

    current working directory.

    +
    +
    +
    +
    +
    +
    +optional_params = ['filesystem', 'path']
    +
    + +
    +
    +required_params = ['name']
    +
    + +
    +
    +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.common.firetasks.glue_tasks.PassResult(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

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

    +

    PassResult(pass_dict={‘stress’: “>>ionic_steps.-1.stress”})

    +
    +
    Required params:
    +
    pass_dict (dict): dictionary designating keys and values to pass

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

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

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

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

    e. g. {“filename”: “vasprun.xml”, “parse_dos”: False, +“parse_eigen”: False}

    +
    +
    +
    +
    Optional params:
    +
    calc_dir (str): path to dir that contains VASP output files, defaults

    to ‘.’, e. g. current directory

    +
    +
    mod_spec_cmd (str): command to issue for mod_spec, e. g. “_set” or “_push”,

    defaults to “_set”

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

    to “prev_calc_result”

    +
    +
    +
    +
    +
    +
    +optional_params = ['calc_dir', 'mod_spec_cmd', 'mod_spec_key']
    +
    + +
    +
    +required_params = ['pass_dict', 'parse_class', 'parse_kwargs']
    +
    + +
    +
    +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.common.firetasks.glue_tasks.get_calc_loc(target_name, calc_locs)
    +

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

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

      with matching nameget_

      +
      +
      +
      • +

    • Otherwise, return most recent calc_loc overall

      • +
    +
    +
    Args:
    +
    target_name: (bool or str) If str, will search for calc_loc with

    matching name, else use most recent calc_loc

    +
    +
    +

    calc_locs: (dict) The dictionary of all calc_locs

    +
    +
    Returns:

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

    +
    +
    +
    +
    -
    -

    atomate.common.firetasks.parse_outputs module

    +
    +

    atomate.common.firetasks.parse_outputs module

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

    Bases: fireworks.core.firework.FiretaskBase

    +

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

    +
    +
    Required params:

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

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

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

    +
    +
    +

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

    +
    +

    Default: use current working directory.

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

    recent calc_loc with the matching name

    +
    +
    +

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

    +
    +
    +
    +
    +optional_params = ['mmdb', 'db_file', 'calc_dir', 'calc_loc', 'additional_fields', 'options']
    +
    + +
    +
    +required_params = ['drone']
    +
    + +
    +
    +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.common.firetasks.run_calc module

    +
    +

    atomate.common.firetasks.run_calc module

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

    Bases: fireworks.core.firework.FiretaskBase

    +

    Execute a command directly (no custodian).

    +
    +
    Required params:

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

    +
    +
    Optional params:

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

    +
    +
    +
    +
    +optional_params = ['expand_vars']
    +
    + +
    +
    +required_params = ['cmd']
    +
    + +
    +
    +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.common.firetasks.run_calc.RunCustodianFromObjects(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

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

    +
    +
    Required params:

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

    +
    +
    Optional params:

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

    +
    +
    +
    +
    +optional_params = ['validators', 'custodian_params']
    +
    + +
    +
    +required_params = ['jobs', 'handlers']
    +
    + +
    +
    +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)

    +
    +
    +
    + +
    +
    diff --git a/docs/atomate.common.firetasks.tests.html b/docs/atomate.common.firetasks.tests.html index 73fa17691..c10548f5a 100644 --- a/docs/atomate.common.firetasks.tests.html +++ b/docs/atomate.common.firetasks.tests.html @@ -5,7 +5,7 @@ - atomate.common.firetasks.tests package — atomate 0.9.6 documentation + atomate.common.firetasks.tests package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.common.firetasks.tests package
    • @@ -46,8 +46,66 @@

    Submodules

    atomate.common.firetasks.tests.test_glue_tasks module

    -
    -

    atomate.common.firetasks.tests.test_parse_outputs module

    +
    +

    atomate.common.firetasks.tests.test_parse_outputs module

    +
    +
    +class atomate.common.firetasks.tests.test_parse_outputs.TestDrone
    +

    Bases: pymatgen.apps.borg.hive.AbstractDrone

    +
    +
    +__init__()
    +

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

    +
    + +
    +
    +assimilate(path)
    +

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

    +
    +
    Args:

    path: directory path

    +
    +
    Returns:

    An assimilated object

    +
    +
    +
    + +
    +
    +get_valid_paths(path)
    +

    Checks if path contains valid data for assimilation, and then returns +the valid paths. The paths returned can be a list of directory or file +paths, depending on what kind of data you are assimilating. For +example, if you are assimilating VASP runs, you are only interested in +directories containing vasprun.xml files. On the other hand, if you are +interested converting all POSCARs in a directory tree to cifs for +example, you will want the file paths.

    +
    +
    Args:
    +
    path: input path as a tuple generated from os.walk, i.e.,

    (parent, subdirs, files).

    +
    +
    +
    +
    Returns:

    List of valid dir/file paths for assimilation

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

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +test_ToDbTask()
    +
    + +
    +
    diff --git a/docs/atomate.common.html b/docs/atomate.common.html index 56d87b700..834ca1602 100644 --- a/docs/atomate.common.html +++ b/docs/atomate.common.html @@ -5,7 +5,7 @@ - atomate.common package — atomate 0.9.6 documentation + atomate.common package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.common package
    • @@ -49,22 +49,22 @@

    Subpackagesatomate.common.firetasks.tests package
  • Submodules
    • -
  • atomate.common.firetasks.glue_tasks module
    • -
  • atomate.common.firetasks.parse_outputs module
    • -
  • atomate.common.firetasks.run_calc module
    • +
  • atomate.common.firetasks.glue_tasks module
    • +
  • atomate.common.firetasks.parse_outputs module
    • +
  • atomate.common.firetasks.run_calc module
  • Module contents
  • atomate.common.tests package
    • @@ -74,8 +74,24 @@

    Subpackages

    Submodules

    -
    -

    atomate.common.powerups module

    +
    +

    atomate.common.powerups module

    +

    This module defines general powerups that can be used for all workflows

    +
    +
    +atomate.common.powerups.set_queue_adapter(original_wf: fireworks.core.firework.Workflow, queueadapter: dict = None, fw_name_constraint: str = None, task_name_constraint: str = None) → fireworks.core.firework.Workflow
    +

    set _queueadapter spec of Fireworker(s) of a Workflow. It can be used to change the overall queueadapter during the run.

    +
    +
    Args:

    original_wf (Workflow): workflow that will be changed +queueadapter (dict): dict to change _queueadapter +fw_name_constraint (str): name of the Fireworks to be tagged (all if None is passed) +task_name_constraint (str): name of the Firetasks to be tagged (e.g. None or ‘RunVasp’)

    +
    +
    Returns:

    Workflow: modified workflow with specified Fireworkers tagged

    +
    +
    +
    +
    diff --git a/docs/atomate.common.tests.html b/docs/atomate.common.tests.html index 8d8bcbd53..22b795334 100644 --- a/docs/atomate.common.tests.html +++ b/docs/atomate.common.tests.html @@ -5,7 +5,7 @@ - atomate.common.tests package — atomate 0.9.6 documentation + atomate.common.tests package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.common.tests package
    • @@ -43,8 +43,25 @@

    atomate.common.tests package

    Submodules

    -
    -

    atomate.common.tests.test_powerups module

    +
    +

    atomate.common.tests.test_powerups module

    +
    +
    +class atomate.common.tests.test_powerups.ModifiedScriptTask(*args, **kwargs)
    +

    Bases: fireworks.user_objects.firetasks.script_task.ScriptTask

    +
    + +
    +
    +class atomate.common.tests.test_powerups.TestPowerups(methodName='runTest')
    +

    Bases: unittest.case.TestCase

    +
    +
    +test_set_queue_adapter()
    +
    + +
    +
    diff --git a/docs/atomate.feff.firetasks.html b/docs/atomate.feff.firetasks.html index d43215da0..c4befbf90 100644 --- a/docs/atomate.feff.firetasks.html +++ b/docs/atomate.feff.firetasks.html @@ -5,7 +5,7 @@ - atomate.feff.firetasks package — atomate 0.9.6 documentation + atomate.feff.firetasks package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.feff.firetasks package
    • @@ -124,7 +124,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.feff.firetasks package
    • diff --git a/docs/atomate.feff.firetasks.tests.html b/docs/atomate.feff.firetasks.tests.html index fd015c744..33ad6a9c7 100644 --- a/docs/atomate.feff.firetasks.tests.html +++ b/docs/atomate.feff.firetasks.tests.html @@ -5,7 +5,7 @@ - atomate.feff.firetasks.tests package — atomate 0.9.6 documentation + atomate.feff.firetasks.tests package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.feff.firetasks.tests package
    • @@ -98,7 +98,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.feff.firetasks.tests package
    • diff --git a/docs/atomate.feff.fireworks.html b/docs/atomate.feff.fireworks.html index 0fdeb660a..43dfbf303 100644 --- a/docs/atomate.feff.fireworks.html +++ b/docs/atomate.feff.fireworks.html @@ -5,7 +5,7 @@ - atomate.feff.fireworks package — atomate 0.9.6 documentation + atomate.feff.fireworks package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
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  • atomate.feff.fireworks package
    • @@ -112,7 +112,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.feff.fireworks package
    • diff --git a/docs/atomate.feff.fireworks.tests.html b/docs/atomate.feff.fireworks.tests.html index 2b655875e..692eb0692 100644 --- a/docs/atomate.feff.fireworks.tests.html +++ b/docs/atomate.feff.fireworks.tests.html @@ -5,7 +5,7 @@ - atomate.feff.fireworks.tests package — atomate 0.9.6 documentation + atomate.feff.fireworks.tests package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
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  • atomate.feff.fireworks.tests package
    • @@ -98,7 +98,7 @@

    Navigation

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  • atomate 0.9.6 documentation »
    • +
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  • atomate.feff.fireworks.tests package
    • diff --git a/docs/atomate.feff.html b/docs/atomate.feff.html index c5b7ddf21..28bd5f67d 100644 --- a/docs/atomate.feff.html +++ b/docs/atomate.feff.html @@ -5,7 +5,7 @@ - atomate.feff package — atomate 0.9.6 documentation + atomate.feff package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
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  • atomate 0.9.6 documentation »
    • +
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  • atomate.feff package
    • @@ -157,7 +157,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.feff package
    • diff --git a/docs/atomate.feff.workflows.html b/docs/atomate.feff.workflows.html index c07186110..6b295df74 100644 --- a/docs/atomate.feff.workflows.html +++ b/docs/atomate.feff.workflows.html @@ -5,7 +5,7 @@ - atomate.feff.workflows package — atomate 0.9.6 documentation + atomate.feff.workflows package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
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  • atomate.feff.workflows package
    • @@ -118,7 +118,7 @@

    Navigation

  • modules |
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  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.feff.workflows package
    • diff --git a/docs/atomate.feff.workflows.tests.html b/docs/atomate.feff.workflows.tests.html index 76ce9188c..48845f461 100644 --- a/docs/atomate.feff.workflows.tests.html +++ b/docs/atomate.feff.workflows.tests.html @@ -5,7 +5,7 @@ - atomate.feff.workflows.tests package — atomate 0.9.6 documentation + atomate.feff.workflows.tests package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
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  • atomate.feff.workflows.tests package
    • @@ -106,7 +106,7 @@

    Navigation

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  • atomate 0.9.6 documentation »
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  • atomate.feff.workflows.tests package
    • diff --git a/docs/atomate.html b/docs/atomate.html index 07691cc15..eee9cbe82 100644 --- a/docs/atomate.html +++ b/docs/atomate.html @@ -5,7 +5,7 @@ - atomate package — atomate 0.9.6 documentation + atomate package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate package
    • @@ -49,22 +49,22 @@

    Subpackagesatomate.common.firetasks package
  • atomate.common.tests package
  • Submodules
    • -
  • atomate.common.powerups module
    • +
  • atomate.common.powerups module
  • Module contents
    • @@ -106,10 +106,10 @@

    SubpackagesSubpackages @@ -173,8 +173,8 @@

    Subpackagesatomate.utils.tests package @@ -183,8 +183,8 @@

    SubpackagesSubmodules
  • atomate.utils.database module
  • atomate.utils.fileio module
    • -
  • atomate.utils.testing module
    • -
  • atomate.utils.utils module
    • +
  • atomate.utils.testing module
    • +
  • atomate.utils.utils module
  • Module contents
    • @@ -199,16 +199,16 @@

    Subpackagesatomate.vasp.builders package @@ -217,9 +217,9 @@

    SubpackagesSubpackages
  • Submodules
  • atomate.vasp.firetasks.exchange module
    • -
  • atomate.vasp.firetasks.glue_tasks module
    • +
  • atomate.vasp.firetasks.glue_tasks module
  • atomate.vasp.firetasks.lobster_tasks module
    • -
  • atomate.vasp.firetasks.neb_tasks module
    • +
  • atomate.vasp.firetasks.neb_tasks module
  • atomate.vasp.firetasks.parse_outputs module
  • atomate.vasp.firetasks.run_calc module
  • atomate.vasp.firetasks.write_inputs module
    • @@ -238,8 +238,8 @@

    Subpackagesatomate.vasp.tests package @@ -254,9 +254,9 @@

    SubpackagesSubmodules
  • atomate.vasp.config module
  • atomate.vasp.database module
    • -
  • atomate.vasp.drones module
    • +
  • atomate.vasp.drones module
  • atomate.vasp.powerups module
    • -
  • atomate.vasp.submission_filter module
    • +
  • atomate.vasp.submission_filter module
  • atomate.vasp.vasp_config module
  • atomate.vasp.vasp_powerups module
  • Module contents
    • @@ -316,7 +316,7 @@

    Navigation

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    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate package
    • diff --git a/docs/atomate.lammps.firetasks.html b/docs/atomate.lammps.firetasks.html index 2636d8593..aa896ab10 100644 --- a/docs/atomate.lammps.firetasks.html +++ b/docs/atomate.lammps.firetasks.html @@ -5,7 +5,7 @@ - atomate.lammps.firetasks package — atomate 0.9.6 documentation + atomate.lammps.firetasks package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.lammps.firetasks package
    • @@ -43,17 +43,309 @@

    atomate.lammps.firetasks package

    Submodules

    -
    -

    atomate.lammps.firetasks.glue_tasks module

    +
    +

    atomate.lammps.firetasks.glue_tasks module

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

    Bases: atomate.common.firetasks.glue_tasks.CopyFiles

    +

    Copy files from a previous run directory to the current directory. +Note: must specify either “calc_loc” or “calc_dir” to indicate the directory

    +
    +

    containing the files to copy.

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

    search for the most recent calc_loc with the matching name.

    +
    +
    +

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

    +
    +

    NOte: by default nothing is excluded.

    +
    +
    +
    +
    +
    +optional_params = ['calc_loc', 'calc_dir', 'filesystem', 'exclude_files']
    +
    + +
    +
    +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.lammps.firetasks.parse_outputs module

    -
    -

    atomate.lammps.firetasks.run_calc module

    +
    +

    atomate.lammps.firetasks.run_calc module

    +

    This module defines firetasks for running lammps

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

    Bases: fireworks.core.firework.FiretaskBase

    +

    Run LAMMPS directly (no custodian).

    +
    +
    Required params:
    +
    lammsps_cmd (str): lammps command to run sans the input file name.

    e.g. ‘mpirun -n 4 lmp_mpi’

    +
    +
    +
    +
    +
    +
    +required_params = ['lammps_cmd', 'input_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.lammps.firetasks.run_calc.RunLammpsFake(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

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

    +
    +
    Required params:

    ref_dir (str): path to the reference dir

    +
    +
    +
    +
    +required_params = ['ref_dir']
    +
    + +
    +
    +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.lammps.firetasks.run_calc.RunPackmol(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Run packmol.

    +
    +
    Required params:

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

    +
    +

    molecules list. eg: config settings for a single moelcule +[{“number”: 1, “inside box”:[0,0,0,100,100,100]}]

    +
    +
    +
    Optional params:

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

    +
    +

    than structure/atoms

    +
    +

    output_file (str): output file name. The extension will be adjusted according to the filetype +site_property (str): the specified site property will be restored for the final Molecule object.

    +
    +
    +
    +
    +optional_params = ['tolerance', 'filetype', 'control_params', 'output_file', 'site_property']
    +
    + +
    +
    +required_params = ['molecules', 'packing_config', 'packmol_cmd']
    +
    + +
    +
    +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.lammps.firetasks.write_inputs module

    +
    +

    atomate.lammps.firetasks.write_inputs module

    +

    This module defines firetasks for writing LAMMPS input files (data file and the control +parameters file)

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

    Bases: fireworks.core.firework.FiretaskBase

    +
    +
    +optional_params = ['data_filename', 'user_settings', 'ff_site_property']
    +
    + +
    +
    +required_params = ['input_file', 'final_molecule', 'constituent_molecules', 'mols_number', 'box_size', 'forcefield', 'topologies', 'input_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.lammps.firetasks.write_inputs.WriteInputFromIOSet(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

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

    +
    +
    required_params:

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

    +
    +
    optional_params:

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

    +
    +
    +
    +
    +optional_params = ['data_filename']
    +
    + +
    +
    +required_params = ['lammps_input_set', 'input_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)

    +
    +
    +
    + +
    +
    diff --git a/docs/atomate.lammps.fireworks.html b/docs/atomate.lammps.fireworks.html index aac157eca..f19479d3d 100644 --- a/docs/atomate.lammps.fireworks.html +++ b/docs/atomate.lammps.fireworks.html @@ -5,7 +5,7 @@ - atomate.lammps.fireworks package — atomate 0.9.6 documentation + atomate.lammps.fireworks package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.lammps.fireworks package
    • @@ -98,7 +98,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.lammps.fireworks package
    • diff --git a/docs/atomate.lammps.html b/docs/atomate.lammps.html index b0ee79f00..5003a404b 100644 --- a/docs/atomate.lammps.html +++ b/docs/atomate.lammps.html @@ -5,7 +5,7 @@ - atomate.lammps package — atomate 0.9.6 documentation + atomate.lammps package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.lammps package
    • @@ -46,10 +46,10 @@

    Subpackagesatomate.lammps.firetasks package @@ -74,11 +74,124 @@

    Submodules

    atomate.lammps.database module

    -
    -

    atomate.lammps.drones module

    +
    +

    atomate.lammps.drones module

    +

    Lammps Drones.

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

    Bases: pymatgen.apps.borg.hive.AbstractDrone

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

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

    +
    +

    of diffusion statistics will be added.

    +
    +
    +
    +
    + +
    +
    +as_dict()
    +

    A JSON serializable dict representation of an object.

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

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

    +
    +
    Args:

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

    +
    +
    Returns:

    dict

    +
    +
    +
    + +
    +
    +classmethod from_dict(d)
    +
    +
    Parameters
    +

    d – Dict representation.

    +
    +
    Returns
    +

    MSONable class.

    +
    +
    +
    + +
    +
    +generate_doc(dir_name, lmps_input, log, dumps)
    +
    +
    Args:

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

    +
    +
    Returns:

    dict

    +
    +
    +
    + +
    +
    +get_valid_paths(path)
    +

    Checks if path contains valid data for assimilation, and then returns +the valid paths. The paths returned can be a list of directory or file +paths, depending on what kind of data you are assimilating. For +example, if you are assimilating VASP runs, you are only interested in +directories containing vasprun.xml files. On the other hand, if you are +interested converting all POSCARs in a directory tree to cifs for +example, you will want the file paths.

    +
    +
    Args:
    +
    path: input path as a tuple generated from os.walk, i.e.,

    (parent, subdirs, files).

    +
    +
    +
    +
    Returns:

    List of valid dir/file paths for assimilation

    +
    +
    +
    + +
    +
    +post_process(d, lmps_run)
    +

    Simple post processing.

    +
    +
    Args:

    d (dict) +lmps_run (LammpsRun)

    +
    +
    +
    + +
    +
    +schema = {'root': {'completed_at', 'dir_name', 'input', 'last_updated', 'output', 'schema', 'state'}}
    +
    + +
    +
    -
    -

    atomate.lammps.utils module

    +
    +

    atomate.lammps.utils module

    +
    +
    +atomate.lammps.utils.use_fake_lammps(original_wf, ref_dir)
    +
    +
    diff --git a/docs/atomate.lammps.workflows.html b/docs/atomate.lammps.workflows.html index 6321d1592..7522825ec 100644 --- a/docs/atomate.lammps.workflows.html +++ b/docs/atomate.lammps.workflows.html @@ -5,7 +5,7 @@ - atomate.lammps.workflows package — atomate 0.9.6 documentation + atomate.lammps.workflows package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.lammps.workflows package
    • @@ -98,7 +98,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.lammps.workflows package
    • diff --git a/docs/atomate.qchem.firetasks.html b/docs/atomate.qchem.firetasks.html index ce1105124..0bde32e5b 100644 --- a/docs/atomate.qchem.firetasks.html +++ b/docs/atomate.qchem.firetasks.html @@ -5,7 +5,7 @@ - atomate.qchem.firetasks package — atomate 0.9.6 documentation + atomate.qchem.firetasks package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.qchem.firetasks package
    • @@ -48,7 +48,7 @@

    SubpackagesSubmodules
  • atomate.qchem.firetasks.tests.test_critic2 module
  • atomate.qchem.firetasks.tests.test_fragmenter module
    • -
  • atomate.qchem.firetasks.tests.test_geo_transformations module
    • +
  • atomate.qchem.firetasks.tests.test_geo_transformations module
  • atomate.qchem.firetasks.tests.test_run_calc module
  • atomate.qchem.firetasks.tests.test_write_inputs module
  • Module contents
    • @@ -188,7 +188,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.qchem.firetasks package
    • diff --git a/docs/atomate.qchem.firetasks.tests.html b/docs/atomate.qchem.firetasks.tests.html index fdbfe6c22..4bae20078 100644 --- a/docs/atomate.qchem.firetasks.tests.html +++ b/docs/atomate.qchem.firetasks.tests.html @@ -5,7 +5,7 @@ - atomate.qchem.firetasks.tests package — atomate 0.9.6 documentation + atomate.qchem.firetasks.tests package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.qchem.firetasks.tests package
    • @@ -49,8 +49,38 @@

    atomate.qchem.firetasks.tests.test_critic2 module

    atomate.qchem.firetasks.tests.test_fragmenter module

    -
    -

    atomate.qchem.firetasks.tests.test_geo_transformations module

    +
    +

    atomate.qchem.firetasks.tests.test_geo_transformations module

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

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +setUp(lpad=False)
    +

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

    +
    + +
    +
    +classmethod setUpClass()
    +

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

    +
    + +
    +
    +tearDown()
    +

    Remove the scratch directory and teardown the test db.

    +
    + +
    +
    +test_rotate_torsion()
    +
    + +
    +
    diff --git a/docs/atomate.qchem.fireworks.html b/docs/atomate.qchem.fireworks.html index 98c994db1..736301ce3 100644 --- a/docs/atomate.qchem.fireworks.html +++ b/docs/atomate.qchem.fireworks.html @@ -5,7 +5,7 @@ - atomate.qchem.fireworks package — atomate 0.9.6 documentation + atomate.qchem.fireworks package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.qchem.fireworks package
    • @@ -98,7 +98,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.qchem.fireworks package
    • diff --git a/docs/atomate.qchem.html b/docs/atomate.qchem.html index 3bf5d25fb..3d587a131 100644 --- a/docs/atomate.qchem.html +++ b/docs/atomate.qchem.html @@ -5,7 +5,7 @@ - atomate.qchem package — atomate 0.9.6 documentation + atomate.qchem package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.qchem package
    • @@ -50,7 +50,7 @@

    SubpackagesSubmodules
  • atomate.qchem.firetasks.tests.test_critic2 module
  • atomate.qchem.firetasks.tests.test_fragmenter module
    • -
  • atomate.qchem.firetasks.tests.test_geo_transformations module
    • +
  • atomate.qchem.firetasks.tests.test_geo_transformations module
  • atomate.qchem.firetasks.tests.test_run_calc module
  • atomate.qchem.firetasks.tests.test_write_inputs module
  • Module contents
    • @@ -170,7 +170,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.qchem package
    • diff --git a/docs/atomate.qchem.workflows.base.html b/docs/atomate.qchem.workflows.base.html index 47ebcf69a..ce2b478f3 100644 --- a/docs/atomate.qchem.workflows.base.html +++ b/docs/atomate.qchem.workflows.base.html @@ -5,7 +5,7 @@ - atomate.qchem.workflows.base package — atomate 0.9.6 documentation + atomate.qchem.workflows.base package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.qchem.workflows.base package
    • @@ -110,7 +110,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.qchem.workflows.base package
    • diff --git a/docs/atomate.qchem.workflows.html b/docs/atomate.qchem.workflows.html index 34abf63ee..a29c7355e 100644 --- a/docs/atomate.qchem.workflows.html +++ b/docs/atomate.qchem.workflows.html @@ -5,7 +5,7 @@ - atomate.qchem.workflows package — atomate 0.9.6 documentation + atomate.qchem.workflows package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.qchem.workflows package
    • @@ -117,7 +117,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.qchem.workflows package
    • diff --git a/docs/atomate.qchem.workflows.tests.html b/docs/atomate.qchem.workflows.tests.html index 3fd6f5237..469a763e7 100644 --- a/docs/atomate.qchem.workflows.tests.html +++ b/docs/atomate.qchem.workflows.tests.html @@ -5,7 +5,7 @@ - atomate.qchem.workflows.tests package — atomate 0.9.6 documentation + atomate.qchem.workflows.tests package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.qchem.workflows.tests package
    • @@ -114,7 +114,7 @@

    Navigation

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  • atomate 0.9.8 documentation »
  • atomate.qchem.workflows.tests package
    • diff --git a/docs/atomate.tools.html b/docs/atomate.tools.html index 347648c7b..e8bcde7a4 100644 --- a/docs/atomate.tools.html +++ b/docs/atomate.tools.html @@ -5,7 +5,7 @@ - atomate.tools package — atomate 0.9.6 documentation + atomate.tools package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
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  • atomate 0.9.6 documentation »
    • +
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  • atomate.tools package
    • @@ -113,7 +113,7 @@

    Navigation

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  • atomate 0.9.8 documentation »
  • atomate.tools package
    • diff --git a/docs/atomate.tools.post_process.html b/docs/atomate.tools.post_process.html index d7b1bd600..187e6673e 100644 --- a/docs/atomate.tools.post_process.html +++ b/docs/atomate.tools.post_process.html @@ -5,7 +5,7 @@ - atomate.tools.post_process package — atomate 0.9.6 documentation + atomate.tools.post_process package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
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    • @@ -102,7 +102,7 @@

    Navigation

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  • atomate.tools.post_process package
    • diff --git a/docs/atomate.tools.tests.html b/docs/atomate.tools.tests.html index 985d17531..fda6f91c0 100644 --- a/docs/atomate.tools.tests.html +++ b/docs/atomate.tools.tests.html @@ -5,7 +5,7 @@ - atomate.tools.tests package — atomate 0.9.6 documentation + atomate.tools.tests package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
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    • @@ -98,7 +98,7 @@

    Navigation

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  • atomate.tools.tests package
    • diff --git a/docs/atomate.utils.html b/docs/atomate.utils.html index a168dcf80..6a7a0b6d5 100644 --- a/docs/atomate.utils.html +++ b/docs/atomate.utils.html @@ -5,7 +5,7 @@ - atomate.utils package — atomate 0.9.6 documentation + atomate.utils package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

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  • atomate 0.9.6 documentation »
    • +
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  • atomate.utils package
    • @@ -47,8 +47,8 @@

    Subpackagesatomate.utils.tests package @@ -155,11 +155,254 @@

    atomate.utils.database module -

    atomate.utils.testing module

    +
    +

    atomate.utils.testing module

    +
    +
    +class atomate.utils.testing.AtomateTest(methodName='runTest')
    +

    Bases: unittest.case.TestCase

    +
    +
    +get_task_collection(coll_name=None)
    +

    Returns pymongo collection

    +
    + +
    +
    +get_task_database()
    +

    Returns pymongo db connection.

    +
    + +
    +
    +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.

    +
    + +
    +
    -
    -

    atomate.utils.utils module

    +
    +

    atomate.utils.utils module

    +
    +
    +atomate.utils.utils.env_chk(val, fw_spec, strict=True, default=None)
    +

    env_chk() is a way to set different values for a property depending +on the worker machine. For example, you might have slightly different +executable names or scratch directories on different machines.

    +

    env_chk() works using the principles of the FWorker env in FireWorks.

    +

    This helper method translates string “val” that looks like this: +“>>ENV_KEY<<” +to the contents of: +fw_spec[“_fw_env”][ENV_KEY]

    +

    Otherwise, the string “val” is interpreted literally and passed-through as is.

    +

    The fw_spec[“_fw_env”] is in turn set by the FWorker. For more details, +see: https://materialsproject.github.io/fireworks/worker_tutorial.html

    +

    Since the fw_env can be set differently for each FireWorker, one can +use this method to translate a single “val” into multiple possibilities, +thus achieving different behavior on different machines.

    +
    +
    Args:

    val: any value, with “>><<” notation reserved for special env lookup values +fw_spec: (dict) fw_spec where one can find the _fw_env keys +strict (bool): if True, errors if env format (>><<) specified but cannot be found in fw_spec +default: if val is None or env cannot be found in non-strict mode,

    +
    +

    return default

    +
    +
    +
    +
    + +
    +
    +atomate.utils.utils.get_a_unique_id()
    +
    + +
    +
    +atomate.utils.utils.get_database(config_file=None, settings=None, admin=False, **kwargs)
    +
    + +
    +
    +atomate.utils.utils.get_fws_and_tasks(workflow, fw_name_constraint=None, task_name_constraint=None)
    +

    Helper method: given a workflow, returns back the fw_ids and task_ids that match name +constraints. Used in developing multiple powerups.

    +
    +
    Args:

    workflow (Workflow): Workflow +fw_name_constraint (str): a constraint on the FW name +task_name_constraint (str): a constraint on the task name

    +
    +
    Returns:

    a list of tuples of the form (fw_id, task_id) of the RunVasp-type tasks

    +
    +
    +
    + +
    +
    +atomate.utils.utils.get_logger(name, level=10, log_format='%(asctime)s %(levelname)s %(name)s %(message)s', stream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)
    +
    + +
    +
    +atomate.utils.utils.get_meta_from_structure(structure)
    +
    + +
    +
    +atomate.utils.utils.get_mongolike(d, key)
    +

    Retrieve a dict value using dot-notation like “a.b.c” from dict {“a”:{“b”:{“c”: 3}}} +Args:

    +
    +

    d (dict): the dictionary to search +key (str): the key we want to retrieve with dot notation, e.g., “a.b.c”

    +
    +
    +
    Returns:

    value from desired dict (whatever is stored at the desired key)

    +
    +
    +
    + +
    +
    +atomate.utils.utils.get_uri(dir_name)
    +

    Returns the URI path for a directory. This allows files hosted on +different file servers to have distinct locations. +Args:

    +
    +
    +
    dir_name:

    A directory name.

    +
    +
    +
    +
    +
    Returns:

    Full URI path, e.g., fileserver.host.com:/full/path/of/dir_name.

    +
    +
    +
    + +
    +
    +atomate.utils.utils.get_wf_from_spec_dict(structure, wfspec, common_param_updates=None)
    +

    Load a WF from a structure and a spec dict. This allows simple +custom workflows to be constructed quickly via a YAML file.

    +
    +
    Args:

    structure (Structure): An input structure object. +wfspec (dict): A dict specifying workflow. A sample of the dict in

    +
    +

    YAML format for the usual MP workflow is given as follows:

    +

    ``` +fireworks: +- fw: atomate.vasp.fireworks.core.OptimizeFW +- fw: atomate.vasp.fireworks.core.StaticFW

    +
    +
    +
    params:

    parents: 0

    +
    +
    +
    +
      +

    • fw: atomate.vasp.fireworks.core.NonSCFUniformFW +params:

      +
      +

      parents: 1

      +
      +
      • +

    • fw: atomate.vasp.fireworks.core.NonSCFLineFW +params:

      +
      +

      parents: 1

      +
      +
      • +
    +
    +
    common_params:

    db_file: db.json +$vasp_cmd: $HOME/opt/vasp

    +
    +
    +

    name: bandstructure +metadata:

    +
    +

    tag: testing_workflow

    +
    +

    ```

    +

    The fireworks key is a list of Fireworks; it is expected that +all such Fireworks have “structure” as the first argument and +other optional arguments following that. Each Firework is specified +via “fw”: <explicit path>.

    +

    You can pass arguments into the constructor using the special +keyword params, which is a dict. Any param starting with a $ will +be expanded using environment variables.If multiple fireworks share +the same params, you can use common_params to specify a common +set of arguments that are passed to all fireworks. Local params +take precedent over global params.

    +

    Another special keyword is parents, which provides +the indices of the parents of that particular Firework in the +list. This allows you to link the Fireworks into a logical +workflow.

    +

    Finally, name is used to set the Workflow name +(structure formula + name) which can be helpful in record keeping.

    +
    +

    common_param_updates (dict): A dict specifying any user-specified updates to common_params

    +
    +
    Returns:

    Workflow

    +
    +
    +
    + +
    +
    +atomate.utils.utils.load_class(modulepath, classname)
    +

    Load and return the class from the given module.

    +
    +
    Args:

    modulepath (str): dotted path to the module. eg: “pymatgen.io.vasp.sets” +classname (str): name of the class to be loaded.

    +
    +
    Returns:

    class

    +
    +
    +
    + +
    +
    +atomate.utils.utils.recursive_get_result(d, result)
    +

    Function that gets designated keys or values of d +(i. e. those that start with “d>>” or “a>>”) from +the corresponding entry in result_dict, similar to +FireWorks recursive_deserialize.

    +

    Note that the plain “>>” notation will get a key from +the result.as_dict() object and may use MongoDB +dot notation, while “a>>” will get an attribute +of the object.

    +

    Examples:

    +
    +
    Getting a dict key from a VaspRun instance:

    recursive_get_result({“stress”:”>>output.ionic_steps.-1.stress”}, vasprun) +–> {“stress”:[[0.2, 0, 0], [0, 0.3, 0], [0, 0, 0.3]]}

    +
    +
    Getting an attribute from a vasprun:

    recursive_get_result({“epsilon”:”a>>epsilon_static”, vasprun} +–> {“epsilon”:-3.4}

    +
    +
    +
    + +
    +
    +atomate.utils.utils.recursive_update(d, u)
    +

    Recursive updates d with values from u +Args:

    +
    +

    d (dict): dict to update +u (dict): updates to propogate

    +
    +
    +
    diff --git a/docs/atomate.utils.tests.html b/docs/atomate.utils.tests.html index 9ba5e96e7..e57064ef1 100644 --- a/docs/atomate.utils.tests.html +++ b/docs/atomate.utils.tests.html @@ -5,7 +5,7 @@ - atomate.utils.tests package — atomate 0.9.6 documentation + atomate.utils.tests package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.utils.tests package
    • @@ -46,11 +46,138 @@

    Submodules

    atomate.utils.tests.test_database module

    -
    -

    atomate.utils.tests.test_loaders module

    +
    +

    atomate.utils.tests.test_loaders module

    +
    +
    +class atomate.utils.tests.test_loaders.FuncTest(methodName='runTest')
    +

    Bases: pymatgen.util.testing.PymatgenTest

    +
    +
    +setUp()
    +

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

    +
    + +
    +
    +test_get_wf_from_spec_dict()
    +
    + +
    +
    +test_multi_parent()
    +
    + +
    +
    -
    -

    atomate.utils.tests.test_utils module

    +
    +

    atomate.utils.tests.test_utils module

    +
    +
    +class atomate.utils.tests.test_utils.Task1(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +
    +
    +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.utils.tests.test_utils.Task2(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +
    +
    +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.utils.tests.test_utils.UtilsTests(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +setUp(lpad=True)
    +

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

    +
    + +
    +
    +test_env_chk()
    +
    + +
    +
    +test_get_database()
    +
    + +
    +
    +test_get_mongolike()
    +
    + +
    +
    +test_get_uri()
    +
    + +
    +
    +test_recursive_get_result()
    +
    + +
    +
    +test_recursiveupdate()
    +
    + +
    +
    diff --git a/docs/atomate.vasp.analysis.html b/docs/atomate.vasp.analysis.html index 03b417cb0..7b1811a5a 100644 --- a/docs/atomate.vasp.analysis.html +++ b/docs/atomate.vasp.analysis.html @@ -5,7 +5,7 @@ - atomate.vasp.analysis package — atomate 0.9.6 documentation + atomate.vasp.analysis package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.analysis package
    • @@ -170,7 +170,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.analysis package
    • diff --git a/docs/atomate.vasp.builders.examples.html b/docs/atomate.vasp.builders.examples.html index b76ffc87d..39d8f63d0 100644 --- a/docs/atomate.vasp.builders.examples.html +++ b/docs/atomate.vasp.builders.examples.html @@ -5,7 +5,7 @@ - atomate.vasp.builders.examples package — atomate 0.9.6 documentation + atomate.vasp.builders.examples package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.builders.examples package
    • @@ -43,8 +43,10 @@

    atomate.vasp.builders.examples package

    Submodules

    -
    -

    atomate.vasp.builders.examples.run_builders module

    +
    +

    atomate.vasp.builders.examples.run_builders module

    +

    To use this file, first modify db.json located in this directory with details for your atomate +output database.

    diff --git a/docs/atomate.vasp.builders.html b/docs/atomate.vasp.builders.html index 376a3220c..0a207611e 100644 --- a/docs/atomate.vasp.builders.html +++ b/docs/atomate.vasp.builders.html @@ -5,7 +5,7 @@ - atomate.vasp.builders package — atomate 0.9.6 documentation + atomate.vasp.builders package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.builders package
    • @@ -46,7 +46,7 @@

    Subpackagesatomate.vasp.builders.examples package @@ -56,8 +56,50 @@

    Subpackages

    Submodules

    -
    -

    atomate.vasp.builders.bandgap_estimation module

    +
    +

    atomate.vasp.builders.bandgap_estimation module

    +
    +
    +class atomate.vasp.builders.bandgap_estimation.BandgapEstimationBuilder(materials_write)
    +

    Bases: object

    +
    +
    +__init__(materials_write)
    +

    Starting with an existing materials collection with dielectric constant data, adds +estimated band gaps that may be more accurate than typical GGA calculations.

    +

    Run the “DielectricBuilder” before running this builder.

    +
    +
    Args:

    materials_write: mongodb collection for materials (write access needed)

    +
    +
    +
    + +
    +
    +static from_file(db_file, m='materials', **kwargs)
    +

    Get builder using only a db file.

    +
    +
    Args:

    db_file: (str) path to db file +m: (str) name of “materials” collection +**kwargs: other parameters to feed into the builder, e.g. mapi_key

    +
    +
    Returns:

    BandgapEstimationBuilder

    +
    +
    +
    + +
    +
    +reset()
    +
    + +
    +
    +run()
    +
    + +
    +

    atomate.vasp.builders.base module

    @@ -87,29 +129,387 @@

    atomate.vasp.builders.bandgap_estimation module -

    atomate.vasp.builders.boltztrap_materials module

    +
    +

    atomate.vasp.builders.boltztrap_materials module

    +
    +
    +class atomate.vasp.builders.boltztrap_materials.BoltztrapMaterialsBuilder(materials_write, boltztrap_read)
    +

    Bases: atomate.vasp.builders.base.AbstractBuilder

    +
    +
    +__init__(materials_write, boltztrap_read)
    +

    Update materials collection based on boltztrap collection.

    +
    +
    Args:

    materials_write (pymongo.collection): mongodb collection for materials (write access needed) +boltztrap_read (pymongo.collection): mongodb collection for boltztrap (suggest read-only for safety)

    +
    +
    +
    + +
    +
    +classmethod from_file(db_file, m='materials', b='boltztrap', **kwargs)
    +

    Get a BoltztrapMaterialsBuilder using only a db file.

    +
    +
    Args:

    db_file (str): path to db file +m (str): name of “materials” collection +b (str): name of “boltztrap” collection +**kwargs: other params to put into BoltztrapMaterialsBuilder

    +
    +
    +
    + +
    +
    +reset()
    +

    Unset the building.

    +
    + +
    +
    +run()
    +

    Run the builder.

    +
    + +
    +
    -
    -

    atomate.vasp.builders.dielectric module

    +
    +

    atomate.vasp.builders.dielectric module

    +
    +
    +class atomate.vasp.builders.dielectric.DielectricBuilder(materials_write)
    +

    Bases: object

    +
    +
    +__init__(materials_write)
    +

    Starting with an existing materials collection, adds some averages and +eigenvalues for dielectric constants rather than just the tensor

    +
    +
    Args:

    materials_write: mongodb collection for materials (write access needed)

    +
    +
    +
    + +
    +
    +static from_file(db_file, m='materials', **kwargs)
    +

    Get a MaterialsEhullBuilder using only a db file.

    +
    +
    Args:

    db_file: (str) path to db file +m: (str) name of “materials” collection +**kwargs: other parameters to feed into the builder, e.g. mapi_key

    +
    +
    Returns:

    DielectricBuilder

    +
    +
    +
    + +
    +
    +reset()
    +
    + +
    +
    +run()
    +
    + +
    +
    -
    -

    atomate.vasp.builders.file_materials module

    +
    +

    atomate.vasp.builders.file_materials module

    +
    +
    +class atomate.vasp.builders.file_materials.FileMaterialsBuilder(materials_write, data_file, delimiter=',', header_lines=0)
    +

    Bases: atomate.vasp.builders.base.AbstractBuilder

    +
    +
    +__init__(materials_write, data_file, delimiter=',', header_lines=0)
    +

    Updates the database using a data file. Format of file must be: +<material_id or formula>, <property>, <value>

    +

    Comment lines should start with ‘#’.

    +
    +
    Args:

    materials_write: mongodb collection for materials (write access needed) +data_file (str): path to data file +delimiter (str): delimiter for file parsing +header_lines (int): number of header lines to skip in data file

    +
    +
    +
    + +
    +
    +classmethod from_file(db_file, data_file=None, m='materials', **kwargs)
    +

    Get a FileMaterialsBuilder using only a db file.

    +
    +
    Args:

    db_file (str): path to db file +data_file (str): path to data file +m (str): name of “materials” collection +**kwargs: other parameters to feed into the builder, e.g. mapi_key

    +
    +
    +
    + +
    +
    +reset()
    +

    Unset the building.

    +
    + +
    +
    +run()
    +

    Run the builder.

    +
    + +
    +
    -
    -

    atomate.vasp.builders.fix_tasks module

    +
    +

    atomate.vasp.builders.fix_tasks module

    +
    +
    +class atomate.vasp.builders.fix_tasks.FixTasksBuilder(tasks_write)
    +

    Bases: atomate.vasp.builders.base.AbstractBuilder

    +
    +
    +__init__(tasks_write)
    +

    Fix historical problems in the tasks database

    +
    +
    Args:

    tasks_write (pymongo.collection): mongodb collection for tasks (write access needed)

    +
    +
    +
    + +
    +
    +classmethod from_file(db_file, t='tasks', **kwargs)
    +

    Get a FixTasksBuilder using only a db file.

    +
    +
    Args:

    db_file (str): path to db file +t (str): name of “tasks” collection +**kwargs: other params to put into FixTasksBuilder

    +
    +
    +
    + +
    +
    +reset()
    +

    Unset the building.

    +
    + +
    +
    +run()
    +

    Run the builder.

    +
    + +
    +
    -
    -

    atomate.vasp.builders.materials_descriptor module

    +
    +

    atomate.vasp.builders.materials_descriptor module

    +
    +
    +class atomate.vasp.builders.materials_descriptor.MaterialsDescriptorBuilder(materials_write, update_all=False)
    +

    Bases: atomate.vasp.builders.base.AbstractBuilder

    +
    +
    +__init__(materials_write, update_all=False)
    +

    Starting with an existing materials collection, adds some compositional and structural +descriptors.

    +
    +
    Args:

    materials_write: mongodb collection for materials (write access needed) +update_all: (bool) - if true, updates all docs. If false, updates incrementally

    +
    +
    +
    + +
    +
    +classmethod from_file(db_file, m='materials', **kwargs)
    +

    Get a MaterialsDescriptorBuilder using only a db file.

    +
    +
    Args:

    db_file: (str) path to db file +m: (str) name of “materials” collection +**kwargs: other parameters to feed into the builder

    +
    +
    +
    + +
    +
    +reset()
    +

    Unset the building.

    +
    + +
    +
    +run()
    +

    Run the builder.

    +
    + +
    +
    -
    -

    atomate.vasp.builders.materials_ehull module

    +
    +

    atomate.vasp.builders.materials_ehull module

    +
    +
    +class atomate.vasp.builders.materials_ehull.MaterialsEhullBuilder(materials_write, mapi_key=None, update_all=False)
    +

    Bases: atomate.vasp.builders.base.AbstractBuilder

    +
    +
    +__init__(materials_write, mapi_key=None, update_all=False)
    +

    Starting with an existing materials collection, adds stability information and +The Materials Project ID. +Args:

    +
    +

    materials_write: mongodb collection for materials (write access needed) +mapi_key: (str) Materials API key (if MAPI_KEY env. var. not set) +update_all: (bool) - if true, updates all docs. If false, only updates

    +
    +

    docs w/o a stability key

    +
    +
    +
    + +
    +
    +classmethod from_file(db_file, m='materials', **kwargs)
    +

    Get a MaterialsEhullBuilder using only a db file +Args:

    +
    +

    db_file: (str) path to db file +m: (str) name of “materials” collection +**kwargs: other parameters to feed into the builder, e.g. mapi_key

    +
    +
    + +
    +
    +reset()
    +

    Unset the building.

    +
    + +
    +
    +run()
    +

    Run the builder.

    +
    + +
    +
    -
    -

    atomate.vasp.builders.tags module

    +
    +

    atomate.vasp.builders.tags module

    +
    +
    +class atomate.vasp.builders.tags.TagsBuilder(materials_write, tasks_read, tasks_prefix='t')
    +

    Bases: atomate.vasp.builders.base.AbstractBuilder

    +
    +
    +__init__(materials_write, tasks_read, tasks_prefix='t')
    +

    Starting with an existing materials collection, searches all its component tasks for +the “tags” and key in the tasks collection and copies them to the materials collection. +Thus, the “tags” for a material will be the union of all the tags for its component tasks.

    +
    +
    Args:

    materials_write (pymongo.collection): materials collection with write access. +tasks_read (pymongo.collection): read-only(for safety) tasks collection. +tasks_prefix (str): the string prefix for tasks, e.g. “t” for a task_id like “t-132”

    +
    +
    +
    + +
    +
    +classmethod from_file(db_file, m='materials', t='tasks', **kwargs)
    +

    Get a TagsCollector using only a db file.

    +
    +
    Args:

    db_file (str): path to db file +m (str): name of “materials” collection +**kwargs: other parameters to feed into the builder, e.g. update_all

    +
    +
    +
    + +
    +
    +reset()
    +

    Unset the building.

    +
    + +
    +
    +run()
    +

    Run the builder.

    +
    + +
    +
    -
    -

    atomate.vasp.builders.tasks_materials module

    +
    +

    atomate.vasp.builders.tasks_materials module

    +
    +
    +class atomate.vasp.builders.tasks_materials.TasksMaterialsBuilder(materials_write, counter_write, tasks_read, tasks_prefix='t', materials_prefix='m', query=None, settings_file=None)
    +

    Bases: atomate.vasp.builders.base.AbstractBuilder

    +
    +
    +__init__(materials_write, counter_write, tasks_read, tasks_prefix='t', materials_prefix='m', query=None, settings_file=None)
    +

    Create a materials collection from a tasks collection.

    +
    +
    Args:

    materials_write (pymongo.collection): mongodb collection for materials (write access needed) +counter_write (pymongo.collection): mongodb collection for counter (write access needed) +tasks_read (pymongo.collection): mongodb collection for tasks (suggest read-only for safety) +tasks_prefix (str): a string prefix for tasks, e.g. “t” gives a task_id like “t-132” +materials_prefix (str): a string prefix to prepend to material_ids +query (dict): a pymongo query on tasks_read for which tasks to include in the builder +settings_file (str): filepath to a custom settings path

    +
    +
    +
    + +
    +
    +classmethod from_file(db_file, m='materials', c='counter', t='tasks', **kwargs)
    +

    Get a TaskMaterialsBuilder using only a db file.

    +
    +
    Args:

    db_file (str): path to db file +m (str): name of “materials” collection +c (str): name of “counter” collection +t (str): name of “tasks” collection +**kwargs: other params to put into TasksMaterialsBuilder

    +
    +
    +
    + +
    +
    +reset()
    +

    Unset the building.

    +
    + +
    +
    +run()
    +

    Run the builder.

    +
    + +
    + +
    +
    +atomate.vasp.builders.tasks_materials.module_dir = '/Users/ajain/Documents/code_lbl/atomate/atomate/vasp/builders'
    +

    This class collects all “tasks” (individual calculations) on a single compound and produces a +summary report in a new collection (“materials”). The tasks are matched based on having the same +crystal structure, with some options for overriding this.

    +

    There is lots of config for this builder in the accompanying “tasks_materials_settings.yaml” file.

    +
    +
    diff --git a/docs/atomate.vasp.examples.html b/docs/atomate.vasp.examples.html index 884603f55..eb3b30d14 100644 --- a/docs/atomate.vasp.examples.html +++ b/docs/atomate.vasp.examples.html @@ -5,7 +5,7 @@ - atomate.vasp.examples package — atomate 0.9.6 documentation + atomate.vasp.examples package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.examples package
    • @@ -98,7 +98,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.examples package
    • diff --git a/docs/atomate.vasp.firetasks.html b/docs/atomate.vasp.firetasks.html index 7cb1c1a4e..3b6a9cc3f 100644 --- a/docs/atomate.vasp.firetasks.html +++ b/docs/atomate.vasp.firetasks.html @@ -5,7 +5,7 @@ - atomate.vasp.firetasks package — atomate 0.9.6 documentation + atomate.vasp.firetasks package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.firetasks package
    • @@ -65,14 +65,516 @@

    Submodules

    atomate.vasp.firetasks.exchange module

    -
    -

    atomate.vasp.firetasks.glue_tasks module

    +
    +

    atomate.vasp.firetasks.glue_tasks module

    +
    +
    +class atomate.vasp.firetasks.glue_tasks.CheckBandgap(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Checks the band gap of an entry. If band gap is >min_gap or <max_gap, then +the task will return a FWAction that will defuse all remaining tasks.

    +
    +
    Required params:

    (none) - but you should set either min_gap or max_gap

    +
    +
    Optional params:

    min_gap: (float) minimum gap energy in eV to proceed +max_gap: (float) maximum gap energy in eV to proceed +vasprun_path: (str) path to vasprun.xml file

    +
    +
    +
    +
    +optional_params = ['min_gap', 'max_gap', 'vasprun_path']
    +
    + +
    +
    +required_params = []
    +
    + +
    +
    +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.glue_tasks.CheckStability(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Checks the stability of the entry against the Materials Project database. +If the stability is less than the cutoff (default is 0.1 eV/atom), then +the task will return a FWAction that will defuse all remaining tasks.

    +
    +
    Required params:

    (none) - but your MAPI key must be set as an environ var in this case

    +
    +
    Optional params:
    +
    ehull_cutoff: (float) energy in eV/atom to use as ehull cutoff. Default

    is 0.05 eV/atom.

    +
    +
    +

    MAPI_KEY: (str) set MAPI key directly. Supports env_chk. +calc_dir: (str) string to path containing vasprun.xml (default currdir)

    +
    +
    +
    +
    +optional_params = ['ehull_cutoff', 'MAPI_KEY', 'calc_dir']
    +
    + +
    +
    +required_params = []
    +
    + +
    +
    +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.glue_tasks.CopyVaspOutputs(*args, **kwargs)
    +

    Bases: atomate.common.firetasks.glue_tasks.CopyFiles

    +

    Copy files from a previous VASP run directory to the current directory. +By default, copies ‘INCAR’, ‘POSCAR’ (default: via ‘CONTCAR’), ‘KPOINTS’, +‘POTCAR’, ‘OUTCAR’, and ‘vasprun.xml’. Additional files, e.g. ‘CHGCAR’, +can also be specified. Automatically handles files that have a “.gz” +extension (copies and unzips).

    +

    Note that you must specify either “calc_loc” or “calc_dir” to indicate +the directory containing the previous VASP run.

    +
    +
    Required params:

    (none) - but you must specify either “calc_loc” OR “calc_dir”

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

    search for the most recent calc_loc with the matching name

    +
    +
    +

    calc_dir (str): path to dir that contains VASP output files. +filesystem (str): remote filesystem. e.g. username@host +additional_files ([str]): additional files to copy,

    +
    +

    e.g. [“CHGCAR”, “WAVECAR”]. Use $ALL if you just want to copy +everything

    +
    +
    +
    contcar_to_poscar (bool): If True (default), will move CONTCAR to

    POSCAR (original POSCAR is not copied).

    +
    +
    potcar_spec (bool): Instead of copying the POTCAR, copy the

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

    +
    +
    +
    +
    +
    +
    +copy_files()
    +

    Defines the copy operation. Override this to customize copying.

    +
    + +
    +
    +optional_params = ['calc_loc', 'calc_dir', 'filesystem', 'additional_files', 'contcar_to_poscar', '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.glue_tasks.GetInterpolatedPOSCAR(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Grabs CONTCARS from two previous calculations to create interpolated +structure.

    +

    The code gets the CONTCAR locations using get_calc_loc of two calculations +indicated by the start and end params, creates a folder named “interpolate” +in the current FireWork directory, and copies the two CONTCARs to this folder. +The two CONTCARs are then used to create nimages interpolated structures using +pymatgen.core.structure.Structure.interpolate. Finally, the structure indicated +by this_image is written as a POSCAR file.

    +
    +
    Required params:

    start (str): name of fw for start of interpolation. +end (str): name of fw for end of interpolation. +this_image (int): which interpolation this is. +nimages (int) : number of interpolations.

    +
    +
    Optional params:
    +
    autosort_tol (float): parameter used by Structure.interpolate.

    a distance tolerance in angstrom in which to automatically +sort end_structure to match to the closest +points in this particular structure. Default is 0.0.

    +
    +
    +
    +
    +
    +
    +interpolate_poscar(fw_spec)
    +
    + +
    +
    +optional_params = ['autosort_tol']
    +
    + +
    +
    +required_params = ['start', 'end', 'this_image', 'nimages']
    +
    + +
    +
    +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.pass_vasp_result(pass_dict=None, calc_dir='.', filename='vasprun.xml.gz', parse_eigen=False, parse_dos=False, **kwargs)
    +

    Function that gets a PassResult firework corresponding to output from a Vasprun. Covers +most use cases in which user needs to pass results from a vasp run to child FWs +(e. g. analysis FWs)

    +

    pass_vasp_result(pass_dict={‘stress’: “>>ionic_steps.-1.stress”})

    +
    +
    Args:
    +
    pass_dict (dict): dictionary designating keys and values to pass

    to child fireworks. If value is a string beginning with ‘>>’, +the firework will search the parsed VASP output dictionary +for the designated property by following the sequence of keys +separated with periods, e. g. “>>ionic_steps.-1.stress” is used +to designate the stress from the last ionic_step. If the value +is not a string or does not begin with “>>” or “a>>” (for an +object attribute, rather than nested key of .as_dict() conversion), +it is passed as is. Defaults to pass the computed entry of +the Vasprun.

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

    to ‘.’, e. g. current directory

    +
    +
    filename (str): filename for vasp xml file to parse, defaults to

    “vasprun.xml.gz”

    +
    +
    parse_eigen (bool): flag on whether or not to parse eigenvalues,

    defaults to false

    +
    +
    parse_eigen (bool): flag on whether or not to parse dos,

    defaults to false

    +
    +
    **kwargs (keyword args): other keyword arguments passed to PassResult

    e.g. mod_spec_key or mod_spec_cmd

    +
    +
    +
    +
    +
    +

    atomate.vasp.firetasks.lobster_tasks module

    -
    -

    atomate.vasp.firetasks.neb_tasks module

    +
    +

    atomate.vasp.firetasks.neb_tasks module

    +
    +
    +class atomate.vasp.firetasks.neb_tasks.RunNEBVaspFake(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Vasp Emulator for NEB, which has a different file arrangement. Similar to RunVaspFake class.

    +
    +
    Required params:
    +
    ref_dir (string): Path to reference vasp run directory with input files in the folder named

    ‘inputs’ and output files in the folder named ‘outputs’.

    +
    +
    +
    +
    Optional params:

    params_to_check (list): optional list of incar parameters to check.

    +
    +
    +
    +
    +optional_params = ['params_to_check']
    +
    + +
    +
    +required_params = ['ref_dir']
    +
    + +
    +
    +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.neb_tasks.TransferNEBTask(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    This class transfers NEB outputs from current directory to destination directory. “label” is +used to determine the step of calculation and hence the final path. The corresponding structure +will be updated in fw_spec before files transferring.

    +
    +
    Required params:
    +
    label (str): Type of calculation outputs being transferred, choose from “parent”, “ep0”,

    “ep1”, “neb1”, “neb2” and etc..

    +
    +
    +
    +
    Optional params:
    +
    d_img (float): Distance between neighbouring images, used to determine the number of images

    if “IMAGES” not provided in user_incar_settings, in Angstrom.

    +
    +
    +
    +
    +
    +
    +optional_params = ['d_img']
    +
    + +
    +
    +required_params = ['label']
    +
    + +
    +
    +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.neb_tasks.WriteNEBFromEndpoints(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Generate NEB input sets using endpoint structures, default writes CI-NEB input. +MVLCINEBSet is the only vasp_input_set supported now.

    +
    +
    The number of images:
      +

    1. search in “user_incar_settings”;

      2. +

    2. otherwise, calculated using “d_img”.

      3. +
    +
    +
    Required parameters:

    user_incar_settings (dict): additional INCAR settings.

    +
    +
    Optional parameters:

    user_kpoints_settings (dict): additional KPOINTS settings. +sort_tol (float): Distance tolerance (in Angstrom) used to match the atomic indices between

    +
    +

    start and end structures. If it is set 0, then no sorting will be performed.

    +
    +
    +
    d_img (float): distance in Angstrom, used in calculating number of images. Default 0.7

    Angstrom.

    +
    +
    interpolation_type (str): method to do image interpolation from two endpoints.

    Choose from [“IDPP”, “linear”], default “IDPP”

    +
    +
    +
    +
    +
    +
    +optional_params = ['user_kpoints_settings', 'sort_tol', 'd_img', 'interpolation_type']
    +
    + +
    +
    +required_params = ['user_incar_settings']
    +
    + +
    +
    +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.neb_tasks.WriteNEBFromImages(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

    Generate CI-NEB input sets using given images and endpoints structures. The structures +correspond to structures nested in subfolders (“00”, “01”, “02”, etc.)

    +
    +
    Required parameters:

    neb_label (str): “1”, “2”, etc., labels the running sequence of NEB

    +
    +
    Optional parameters:

    user_incar_settings (dict): Additional INCAR settings. +user_kpoints_settings (dict): Additional KPOINTS settings.

    +
    +
    +
    +
    +optional_params = ['user_incar_settings', 'user_kpoints_settings']
    +
    + +
    +
    +required_params = ['neb_label']
    +
    + +
    +
    +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)

    +
    +
    +
    + +
    +
    diff --git a/docs/atomate.vasp.firetasks.tests.html b/docs/atomate.vasp.firetasks.tests.html index b43217f96..145b7a9ec 100644 --- a/docs/atomate.vasp.firetasks.tests.html +++ b/docs/atomate.vasp.firetasks.tests.html @@ -5,7 +5,7 @@ - atomate.vasp.firetasks.tests package — atomate 0.9.6 documentation + atomate.vasp.firetasks.tests package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.firetasks.tests package
    • @@ -122,7 +122,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.firetasks.tests package
    • diff --git a/docs/atomate.vasp.fireworks.html b/docs/atomate.vasp.fireworks.html index 4cbda114f..d7ec75476 100644 --- a/docs/atomate.vasp.fireworks.html +++ b/docs/atomate.vasp.fireworks.html @@ -5,7 +5,7 @@ - atomate.vasp.fireworks package — atomate 0.9.6 documentation + atomate.vasp.fireworks package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.fireworks package
    • @@ -114,7 +114,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.fireworks package
    • diff --git a/docs/atomate.vasp.html b/docs/atomate.vasp.html index 4f5e6b775..5bdbb9a9e 100644 --- a/docs/atomate.vasp.html +++ b/docs/atomate.vasp.html @@ -5,7 +5,7 @@ - atomate.vasp package — atomate 0.9.6 documentation + atomate.vasp package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp package
    • @@ -54,23 +54,23 @@

    SubpackagesSubpackages
  • Submodules
    • -
  • atomate.vasp.builders.bandgap_estimation module
    • +
  • atomate.vasp.builders.bandgap_estimation module
  • atomate.vasp.builders.base module
    • -
  • atomate.vasp.builders.boltztrap_materials module
    • -
  • atomate.vasp.builders.dielectric module
    • -
  • atomate.vasp.builders.file_materials module
    • -
  • atomate.vasp.builders.fix_tasks module
    • -
  • atomate.vasp.builders.materials_descriptor module
    • -
  • atomate.vasp.builders.materials_ehull module
    • -
  • atomate.vasp.builders.tags module
    • -
  • atomate.vasp.builders.tasks_materials module
    • +
  • atomate.vasp.builders.boltztrap_materials module
    • +
  • atomate.vasp.builders.dielectric module
    • +
  • atomate.vasp.builders.file_materials module
    • +
  • atomate.vasp.builders.fix_tasks module
    • +
  • atomate.vasp.builders.materials_descriptor module
    • +
  • atomate.vasp.builders.materials_ehull module
    • +
  • atomate.vasp.builders.tags module
    • +
  • atomate.vasp.builders.tasks_materials module
  • atomate.vasp.builders.utils module
  • Module contents
    • @@ -93,9 +93,9 @@

    SubpackagesSubmodules
  • atomate.vasp.firetasks.exchange module
    • -
  • atomate.vasp.firetasks.glue_tasks module
    • +
  • atomate.vasp.firetasks.glue_tasks module
  • atomate.vasp.firetasks.lobster_tasks module
    • -
  • atomate.vasp.firetasks.neb_tasks module
    • +
  • atomate.vasp.firetasks.neb_tasks module
  • atomate.vasp.firetasks.parse_outputs module
  • atomate.vasp.firetasks.run_calc module
  • atomate.vasp.firetasks.write_inputs module
    • @@ -114,8 +114,8 @@

    Subpackagesatomate.vasp.tests package @@ -180,14 +180,267 @@

    Submodules

    atomate.vasp.database module

    -
    -

    atomate.vasp.drones module

    +
    +

    atomate.vasp.drones module

    +

    This Drone tries to produce a more sensible task dictionary than the default VaspToDbTaskDrone. +Some of the changes are documented in this thread: +https://groups.google.com/forum/#!topic/pymatgen/pQ-emBpeV5U

    +
    +
    +class atomate.vasp.drones.VaspDrone(runs=None, parse_dos='auto', bandstructure_mode='auto', parse_locpot=True, additional_fields=None, use_full_uri=True, parse_bader=None, parse_chgcar=False, parse_aeccar=False, parse_potcar_file=True, store_volumetric_data=(), store_additional_json=False)
    +

    Bases: pymatgen.apps.borg.hive.AbstractDrone

    +

    pymatgen-db VaspToDbTaskDrone with updated schema and documents processing methods. +Please refer to matgendb.creator.VaspToDbTaskDrone documentation.

    +
    +
    +__init__(runs=None, parse_dos='auto', bandstructure_mode='auto', parse_locpot=True, additional_fields=None, use_full_uri=True, parse_bader=None, parse_chgcar=False, parse_aeccar=False, parse_potcar_file=True, store_volumetric_data=(), store_additional_json=False)
    +

    Initialize a Vasp drone to parse vasp outputs +Args:

    +
    +
    +
    runs (list): Naming scheme for multiple calcuations in on folder e.g. [“relax1”,”relax2”].

    Can be subfolder or extension

    +
    +
    +

    parse_dos (str or bool): Whether to parse the DOS. Can be “auto”, True or False. +“auto” will only parse DOS if NSW = 0, so there are no ionic steps +bandstructure_mode (str or bool): How to parse the bandstructure or not. +Can be “auto”,”line”, True or False.

    +
    +
    +
    “auto” will parse the bandstructure with projections for NSCF calcs and decide automatically

    if it’s line mode or uniform. Saves the bandstructure in the output doc.

    +
    +
    “line” will parse the bandstructure as a line mode calculation with projections.

    Saves the bandstructure in the output doc.

    +
    +
    True will parse the bandstructure with projections as a uniform calculation.

    Saves the bandstructure in the output doc.

    +
    +
    False will parse the bandstructure without projections to calculate vbm, cbm, band_gap, is_metal and efermi

    Dose not saves the bandstructure in the output doc.

    +
    +
    +
    +

    parse_locpot (bool): Parses the LOCPOT file and saves the 3 axis averages +additional_fields (dict): dictionary of additional fields to add to output document +use_full_uri (bool): converts the directory path to the full URI path +parse_bader (bool): Run and parse Bader charge data. Defaults to True if Bader is present +parse_chgcar (bool): Run and parse CHGCAR file +parse_aeccar (bool): Run and parse AECCAR0 and AECCAR2 files +store_volumetric_data (list): List of files to store, choose from (‘CHGCAR’, ‘LOCPOT’, +‘AECCAR0’, ‘AECCAR1’, ‘AECCAR2’, ‘ELFCAR’), case insensitive +store_additional_json (bool): If True, parse any .json files present and store as +sub-doc including the FW.json if present

    +
    +
    + +
    +
    +as_dict()
    +

    A JSON serializable dict representation of an object.

    +
    + +
    +
    +assimilate(path)
    +

    Adapted from matgendb.creator +Parses vasp runs(vasprun.xml file) and insert the result into the db. +Get the entire task doc from the vasprum.xml and the OUTCAR files in the path. +Also adds some post-processed info.

    +
    +
    Args:

    path (str): Path to the directory containing vasprun.xml and OUTCAR files

    +
    +
    Returns:

    (dict): a task dictionary

    +
    +
    +
    + +
    +
    +filter_files(path, file_pattern='vasprun.xml')
    +

    Find the files that match the pattern in the given path and +return them in an ordered dictionary. The searched for files are +filtered by the run types defined in self.runs. e.g. [“relax1”, “relax2”, …]. +Only 2 schemes of the file filtering is enabled: searching for run types +in the list of files and in the filenames. Modify this method if more +sophisticated filtering scheme is needed.

    +
    +
    Args:

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

    +
    +
    Returns:

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

    +
    +
    +
    + +
    +
    +classmethod from_dict(d)
    +
    +
    Parameters
    +

    d – Dict representation.

    +
    +
    Returns
    +

    MSONable class.

    +
    +
    +
    + +
    +
    +generate_doc(dir_name, vasprun_files, outcar_files)
    +

    Adapted from matgendb.creator.generate_doc

    +
    + +
    +
    +get_valid_paths(path)
    +

    There are some restrictions on the valid directory structures:

    +
      +

    1. There can be only one vasp run in each directory. Nested directories +are fine.

      2. +

    2. Directories designated “relax1”…”relax9” are considered to be +parts of a multiple-optimization run.

      3. +

    3. Directories containing vasp output with “.relax1”…”.relax9” are +also considered as parts of a multiple-optimization run.

      4. +
    +
    + +
    +
    +post_process(dir_name, d)
    +

    Post-processing for various files other than the vasprun.xml and OUTCAR. +Looks for files: transformations.json and custodian.json. Modify this if other +output files need to be processed.

    +
    +
    Args:
    +
    dir_name:

    The dir_name.

    +
    +
    d:

    Current doc generated.

    +
    +
    +
    +
    +
    + +
    +
    +process_bandstructure(vrun)
    +
    + +
    +
    +process_dos(vrun)
    +
    + +
    +
    +process_raw_data(dir_name, taskname='standard')
    +

    It is useful to store what raw data has been calculated +and exists for easier querying of the taskdoc.

    +
    +
    Parameters
    +
      +

    • dir_name – directory to search

      • +

    • taskname – taskname, e.g. “relax1”

      • +
    +
    +
    Returns
    +

    dict of files present

    +
    +
    +
    + +
    +
    +process_vasprun(dir_name, taskname, filename)
    +

    Adapted from matgendb.creator

    +

    Process a vasprun.xml file.

    +
    + +
    +
    +schema = {'analysis': {'delta_volume', 'delta_volume_as_percent', 'errors', 'max_force', 'warnings'}, 'calcs_reversed': {'completed_at', 'composition_reduced', 'composition_unit_cell', 'dir_name', 'elements', 'formula_anonymous', 'formula_pretty', 'formula_reduced_abc', 'has_vasp_completed', 'input', 'nelements', 'nsites', 'output', 'run_type', 'task', 'vasp_version'}, 'input': {'hubbards', 'is_hubbard', 'is_lasph', 'potcar_spec', 'pseudo_potential', 'structure', 'xc_override'}, 'output': {'bandgap', 'cbm', 'density', 'energy', 'energy_per_atom', 'forces', 'is_gap_direct', 'is_metal', 'spacegroup', 'stress', 'structure', 'vbm'}, 'root': {'analysis', 'calcs_reversed', 'chemsys', 'completed_at', 'composition_reduced', 'composition_unit_cell', 'dir_name', 'elements', 'formula_anonymous', 'formula_pretty', 'formula_reduced_abc', 'input', 'nelements', 'nsites', 'output', 'run_stats', 'schema', 'state'}}
    +
    + +
    +
    +static set_analysis(d, max_force_threshold=0.5, volume_change_threshold=0.2)
    +

    Adapted from matgendb.creator

    +

    set the ‘analysis’ key

    +
    + +
    +
    +validate_doc(d)
    +

    Sanity check. +Make sure all the important keys are set

    +
    + +
    +

    atomate.vasp.powerups module

    -
    -

    atomate.vasp.submission_filter module

    +
    +

    atomate.vasp.submission_filter module

    +
    +
    +class atomate.vasp.submission_filter.SubmissionFilter(is_valid=True, potcar_exists=True, max_natoms=200, is_ordered=True, not_in_MP=True, MAPI_KEY=None, require_bandstructure=False)
    +

    Bases: pymatgen.alchemy.filters.AbstractStructureFilter

    +
    +
    +NO_POTCARS = ['Po', 'At', 'Rn', 'Fr', 'Ra', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr']
    +
    + +
    +
    +__init__(is_valid=True, potcar_exists=True, max_natoms=200, is_ordered=True, not_in_MP=True, MAPI_KEY=None, require_bandstructure=False)
    +

    Initialize a submission filter for checking that structures are valid for calculations.

    +
    +
    Args:

    is_valid (bool): If true, checks structure validity +potcar_exists (bool): If true, ensures all elements have VASP PAW_PBE POTCAR +max_natoms (int): If not None, ensures structure has <=max_natoms atoms +is_ordered (bool): If true, ensures structure is ordered +not_in_MP (bool): If true, ensures structure not in MP +MAPI_KEY (str): For MP checks, your MAPI key if not previously set as config var +require_bandstructure (bool): For MP checks, require a band structure calc

    +
    +
    +
    + +
    +
    +as_dict()
    +

    A JSON serializable dict representation of an object.

    +
    + +
    +
    +classmethod from_dict(d)
    +
    +
    Parameters
    +

    d – Dict representation.

    +
    +
    Returns
    +

    MSONable class.

    +
    +
    +
    + +
    +
    +test(structure)
    +

    Method to execute the test.

    +
    +
    Args:

    structure (Structure): Input structure to test

    +
    +
    Returns:

    (bool) Structures that return true are kept in the Transmuter +object during filtering.

    +
    +
    +
    + +
    +
    diff --git a/docs/atomate.vasp.tests.html b/docs/atomate.vasp.tests.html index ca76db0b4..aa661e753 100644 --- a/docs/atomate.vasp.tests.html +++ b/docs/atomate.vasp.tests.html @@ -5,7 +5,7 @@ - atomate.vasp.tests package — atomate 0.9.6 documentation + atomate.vasp.tests package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.tests package
    • @@ -43,11 +43,92 @@

    atomate.vasp.tests package

    Submodules

    -
    -

    atomate.vasp.tests.test_drones module

    +
    +

    atomate.vasp.tests.test_drones module

    +
    +
    +class atomate.vasp.tests.test_drones.VaspToDbTaskDroneTest(methodName='runTest')
    +

    Bases: unittest.case.TestCase

    +
    +
    +classmethod setUpClass()
    +

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

    +
    + +
    +
    +test_assimilate()
    +
    + +
    +
    +test_bandstructure()
    +
    + +
    +
    +test_detect_output_file_paths()
    +
    + +
    +
    +test_parse_chrgcar()
    +
    + +
    +
    +test_parse_locpot()
    +
    + +
    +
    +test_parse_optical()
    +
    + +
    +
    +test_parse_potcar()
    +
    + +
    +
    +test_runs_assimilate()
    +
    + +
    +
    -
    -

    atomate.vasp.tests.test_setup module

    +
    +

    atomate.vasp.tests.test_setup module

    +
    +
    +class atomate.vasp.tests.test_setup.TestSetup(methodName='runTest')
    +

    Bases: unittest.case.TestCase

    +
    +
    +setUp()
    +

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

    +
    + +
    +
    +classmethod setUpClass()
    +

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

    +
    + +
    +
    +tearDown()
    +

    Hook method for deconstructing the test fixture after testing it.

    +
    + +
    +
    +test_setup()
    +
    + +
    +
    diff --git a/docs/atomate.vasp.workflows.base.html b/docs/atomate.vasp.workflows.base.html index 51de27fbc..9f86ffc02 100644 --- a/docs/atomate.vasp.workflows.base.html +++ b/docs/atomate.vasp.workflows.base.html @@ -5,7 +5,7 @@ - atomate.vasp.workflows.base package — atomate 0.9.6 documentation + atomate.vasp.workflows.base package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.workflows.base package
    • @@ -146,7 +146,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.workflows.base package
    • diff --git a/docs/atomate.vasp.workflows.html b/docs/atomate.vasp.workflows.html index 1349f5cb5..e23c26393 100644 --- a/docs/atomate.vasp.workflows.html +++ b/docs/atomate.vasp.workflows.html @@ -5,7 +5,7 @@ - atomate.vasp.workflows package — atomate 0.9.6 documentation + atomate.vasp.workflows package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.workflows package
    • @@ -139,7 +139,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.workflows package
    • diff --git a/docs/atomate.vasp.workflows.presets.html b/docs/atomate.vasp.workflows.presets.html index d40cae154..14710b9e5 100644 --- a/docs/atomate.vasp.workflows.presets.html +++ b/docs/atomate.vasp.workflows.presets.html @@ -5,7 +5,7 @@ - atomate.vasp.workflows.presets package — atomate 0.9.6 documentation + atomate.vasp.workflows.presets package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.workflows.presets package
    • @@ -102,7 +102,7 @@

    Navigation

  • modules |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.workflows.presets package
    • diff --git a/docs/atomate.vasp.workflows.tests.html b/docs/atomate.vasp.workflows.tests.html index c470ac318..4802e47c2 100644 --- a/docs/atomate.vasp.workflows.tests.html +++ b/docs/atomate.vasp.workflows.tests.html @@ -5,7 +5,7 @@ - atomate.vasp.workflows.tests package — atomate 0.9.6 documentation + atomate.vasp.workflows.tests package — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
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  • atomate 0.9.6 documentation »
    • +
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  • atomate.vasp.workflows.tests package
    • @@ -138,7 +138,7 @@

    Navigation

  • modules |
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  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate.vasp.workflows.tests package
    • diff --git a/docs/builders.html b/docs/builders.html index 260cee04a..b84a62f9f 100644 --- a/docs/builders.html +++ b/docs/builders.html @@ -5,7 +5,7 @@ - Builders — atomate 0.9.6 documentation + Builders — atomate 0.9.8 documentation @@ -36,7 +36,7 @@

    Navigation

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  • atomate 0.9.6 documentation »
    • +
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  • Builders
    • @@ -154,7 +154,7 @@

    Navigation

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  • atomate 0.9.6 documentation »
    • +
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  • Builders
    • diff --git a/docs/changelog.html b/docs/changelog.html index 00e1beb5c..39657ba98 100644 --- a/docs/changelog.html +++ b/docs/changelog.html @@ -5,7 +5,7 @@ - atomate Changelog — atomate 0.9.6 documentation + atomate Changelog — atomate 0.9.8 documentation @@ -36,7 +36,7 @@

    Navigation

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  • atomate Changelog
    • @@ -467,7 +467,7 @@

    Navigation

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  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • atomate Changelog
    • diff --git a/docs/concepts.html b/docs/concepts.html index d0ed24fe7..37c06a0a8 100644 --- a/docs/concepts.html +++ b/docs/concepts.html @@ -5,7 +5,7 @@ - Atomate concepts — atomate 0.9.6 documentation + Atomate concepts — atomate 0.9.8 documentation @@ -32,7 +32,7 @@

    Navigation

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  • Atomate concepts
    • @@ -152,7 +152,7 @@

    Navigation

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    • +
  • atomate 0.9.8 documentation »
  • Atomate concepts
    • diff --git a/docs/contributors.html b/docs/contributors.html index ea76a4c23..24f6e7f2f 100644 --- a/docs/contributors.html +++ b/docs/contributors.html @@ -5,7 +5,7 @@ - Contributors — atomate 0.9.6 documentation + Contributors — atomate 0.9.8 documentation @@ -36,7 +36,7 @@

    Navigation

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  • Contributors
    • @@ -50,7 +50,7 @@

    Navigation

    Contributors

    Caution

    -

    Starting v0.9.6 onwards, the contributors list is no longer maintained. Please check the Github commit log for a record of changes.

    +

    Starting v0.9.6 onwards, the contributors list is no longer maintained. the contributors list is no longer maintained. Please check the Github contributors list instead.

    atomate development is led by the Hacking Materials research group led by Anubhav Jain at Lawrence Berkeley National Lab, using primarily research funding from U.S. Department of Energy Early Career program; additional support and funding is from the U.S. Department of Energy Materials Project program.

    Contributions are provided by:

    @@ -114,7 +114,7 @@

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  • Contributors
    • diff --git a/docs/creating_workflows.html b/docs/creating_workflows.html index 92a13f317..edcfa9a8d 100644 --- a/docs/creating_workflows.html +++ b/docs/creating_workflows.html @@ -5,7 +5,7 @@ - Creating workflows — atomate 0.9.6 documentation + Creating workflows — atomate 0.9.8 documentation @@ -36,7 +36,7 @@

    Navigation

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    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • Creating workflows
    • @@ -373,7 +373,7 @@

    Powerups

    PassCalcLocs

    -

    In order to be able to act on and modify the initial structure as it changes throughout workflows, there needed to be a way to refer to previous calculations that without hard coding file paths or by meticululously keeping track of paths throughout Firetasks and Fireworks. PassCalcLocs (atomate.common.firetasks.glue_tasks) solves this problem by easily tracking previous calculation directories and making them available to consecutive Fireworks, even between different computing resources. PassCalcLocs enables Fireworks to be dynamically added and removed from workflows during runtime, enabling features such as branching during the calculation. Such branching could be used by having different workflow steps for handing metals and non-metals.

    +

    In order to be able to act on and modify the initial structure as it changes throughout workflows, there needed to be a way to refer to previous calculations that without hard coding file paths or by meticululously keeping track of paths throughout Firetasks and Fireworks. PassCalcLocs (atomate.common.firetasks.glue_tasks) solves this problem by easily tracking previous calculation directories and making them available to consecutive Fireworks, even between different computing resources. PassCalcLocs enables Fireworks to be dynamically added and removed from workflows during runtime, enabling features such as branching during the calculation. Such branching could be used by having different workflow steps for handing metals and non-metals.

    diff --git a/docs/customizing_workflows.html b/docs/customizing_workflows.html index 33de6d87b..089a63ac8 100644 --- a/docs/customizing_workflows.html +++ b/docs/customizing_workflows.html @@ -5,7 +5,7 @@ - Customizing workflows — atomate 0.9.6 documentation + Customizing workflows — atomate 0.9.8 documentation @@ -36,7 +36,7 @@

    Navigation

  • previous |
    • -
  • atomate 0.9.6 documentation »
    • +
  • atomate 0.9.8 documentation »
  • Customizing workflows
    • @@ -69,7 +69,7 @@

    Prerequisites
    from atomate.vasp.workflows.presets.core import wf_elastic_constant
 from atomate.vasp.powerups import add_modify_incar
-from pymatgen import Structure
+from pymatgen.core import Structure
 
 # load your structure, e.g. from a POSCAR
 struct = Structure.from_file('POSCAR')
@@ -104,7 +104,7 @@ 
    Using a different functional
    from fireworks import Workflow
 from atomate.vasp.fireworks.core import OptimizeFW
 from pymatgen.io.vasp.sets import MPRelaxSet
-from pymatgen import Structure
+from pymatgen.core import Structure
 
 def get_optimize_wf(structure, name="optimization wf", vasp_input_set=None,
                     vasp_cmd="vasp", db_file=None, user_kpoints_settings=None,
@@ -161,7 +161,7 @@ 
    Custom KPOINTS settings
    user_kpoints_settings: Override kpoints setting by supplying a dict. E.g., {"reciprocal_density": 1000}. Other options are grid_density or length.
    
 
 
    from pymatgen.io.vasp.sets import MPRelaxSet
-from pymatgen import Structure
+from pymatgen.core import Structure
 
 # load your structure, e.g. from a POSCAR
 struct = Structure.from_file('POSCAR')
@@ -176,7 +176,7 @@ 
    Custom KPOINTS settingsIf you need more control, create the Kpoints object directly with pymatgen. It is flexible and only a brief example will be shown. See the full Kpoints documentation for more
    
 
    from pymatgen.io.vasp.sets import MPRelaxSet
 from pymatgen.io.vasp.inputs import Kpoints
-from pymatgen import Structure
+from pymatgen.core import Structure
 
 # load your structure, e.g. from a POSCAR
 struct = Structure.from_file('POSCAR')
@@ -215,7 +215,7 @@ 
    Custom INCAR settingsUse a different POTCAR
    
 
    Which POTCAR file you want to use is controlled by the input set as well. The easist way to control it is by updating the config_dict dictionary of your input set.
    
 
    from pymatgen.io.vasp.sets import MPRelaxSet
-from pymatgen import Structure
+from pymatgen.core import Structure
 
 # load your structure, e.g. from a POSCAR
 struct = Structure.from_file('POSCAR')
@@ -306,7 +306,7 @@ 
    Navigation
    
         
  • 
           previous |
    • 
-        
  • atomate 0.9.6 documentation »
    • 
+        
  • atomate 0.9.8 documentation »
    • 
         
  • Customizing workflows
    •  
       
     
    
diff --git a/docs/developer_installation.html b/docs/developer_installation.html
index 05ef4ff7c..fa86ad3fb 100644
--- a/docs/developer_installation.html
+++ b/docs/developer_installation.html
@@ -5,7 +5,7 @@
   
     
     
-    Atomate developer installation — atomate 0.9.6 documentation
+    Atomate developer installation — atomate 0.9.8 documentation
     
     
     
@@ -36,7 +36,7 @@ 
    Navigation
    
         
  • 
           previous |
    • 
-        
  • atomate 0.9.6 documentation »
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+        
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    •  
       
     
      
@@ -168,7 +168,7 @@ 
    Navigation
    
         
  • 
           previous |
    • 
-        
  • atomate 0.9.6 documentation »
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+        
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    •  
       
     
    
diff --git a/docs/genindex.html b/docs/genindex.html
index 821d873c6..d7512e318 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -5,7 +5,7 @@
   
     
     
-    Index — atomate 0.9.6 documentation
+    Index — atomate 0.9.8 documentation
     
     
     
@@ -28,7 +28,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • atomate 0.9.6 documentation »
    • 
+        
  • atomate 0.9.8 documentation »
    • 
         
  • Index
    •  
       
     
      
@@ -44,22 +44,59 @@ 
    Index
    
 
    
  _
  | A
+ | B
  | C
  | D
  | E
  | F
  | G
+ | I
  | L
  | M
+ | N
  | O
+ | P
  | R
+ | S
+ | T
+ | U
+ | V
+ | W
  
 
    
 
    _
    
 
    
   
 
    
 
@@ -70,6 +107,22 @@ 
    A
    
 
       
  • AbstractBuilder (class in atomate.vasp.builders.base)
 
    • 
+      
  • as_dict() (atomate.lammps.drones.LammpsDrone method)
+
+      
    • 
+      
  • assimilate() (atomate.common.firetasks.tests.test_parse_outputs.TestDrone method)
+
+      
    • 
       
  • 
     atomate
 
@@ -89,6 +142,27 @@ 
    A
    
 
       
    • 
+      
  • 
+    atomate.common.firetasks.glue_tasks
+
+      
    • 
+      
  • 
+    atomate.common.firetasks.parse_outputs
+
+      
    • 
+      
  • 
+    atomate.common.firetasks.run_calc
+
+      
    • 
       
  • 
@@ -96,6 +170,20 @@ 
    A
    
 
       
    • 
+      
  • 
+    atomate.common.firetasks.tests.test_parse_outputs
+
+      
    • 
+      
  • 
+    atomate.common.powerups
+
+      
    • 
       
  • 
@@ -103,6 +191,13 @@ 
    A
    
 
       
    • 
+      
  • 
+    atomate.common.tests.test_powerups
+
+      
    • 
       
  • 
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    Navigation
    
         
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           modules |
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  • Index
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diff --git a/docs/gibbs_workflow_tutorial.html b/docs/gibbs_workflow_tutorial.html
index 21cea9f5f..5db1f010e 100644
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+++ b/docs/gibbs_workflow_tutorial.html
@@ -5,7 +5,7 @@
   
     
     
-    Running Gibbs workflows — atomate 0.9.6 documentation
+    Running Gibbs workflows — atomate 0.9.8 documentation
     
     
     
@@ -36,7 +36,7 @@ 
    Navigation
    
         
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  • Running Gibbs workflows
    •  
       
     
      
@@ -114,7 +114,7 @@ 
    Use Python to generate and add the workflowgibbs.py with the following contents:
    
 
    #!/usr/bin/env python
 import numpy as np
-from pymatgen import MPRester
+from pymatgen.ext.matproj import MPRester
 from fireworks import LaunchPad
 from atomate.vasp.workflows.presets.core import wf_gibbs_free_energy
 
@@ -170,7 +170,7 @@ 
    Analyzing an Equation of State Workflowgibbs-analysis.py) to your folder and run it
    
 
    from atomate.vasp.database import VaspCalcDb
-from pymatgen import Structure
+from pymatgen.core import Structure
 import numpy as np
 
 import matplotlib.pyplot as plt
@@ -297,7 +297,7 @@ 
    Navigation
    
         
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diff --git a/docs/index.html b/docs/index.html
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-    atomate (Materials Science Workflows) — atomate 0.9.6 documentation
+    atomate (Materials Science Workflows) — atomate 0.9.8 documentation
     
     
     
@@ -32,7 +32,7 @@ 
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@@ -133,7 +133,7 @@ 
    Citing atomatehere.
    
 
    There is an atomate Discourse forum dedicated to discussion and basic support.
    
-
    For specifics on how to contribute, see our contribution guidelines.
    
+
    For specifics on how to contribute, see our contribution guidelines.
    
 
    
 
diff --git a/docs/installation.html b/docs/installation.html
index abaeceb2f..6ed6d7278 100644
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-    Installing atomate — atomate 0.9.6 documentation
+    Installing atomate — atomate 0.9.8 documentation
     
     
     
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  • Installing atomate
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@@ -319,7 +319,7 @@ 
    my_qadapter.yamlFireWorks documentation for writing queue adapters. The FireWorks documentation also has tutorials on setting up your jobs to run on a queue in a way that is more interactive than the minimal details specified here.
    
 
    
 
    nodes, walltime are the default reservations made to the queue as you would expect. queue refers to the name of the queue you will submit to. Some clusters support this and appropriate values might be regular, normal, knl, etc. as defined by the compute resource you are using. The account option refers to which account to charge. Again, whether or not you need to set this depends on the resource. pre_rocket and post_rocket add lines to before and after you job launches in your queue submission script. One use of this would be to enter directives such as #SBATCH -C knl,quad,cache to configure SLURM to run on knl nodes. Any parameters left null will not be used to write the queue file.
    
-
    This is not at all required, but if you want to see what the queue templates look like, you can see them here. The values you put in your my_qadapter.yaml file above are used to fill in the unknown values of the template.
    
+
    This is not at all required, but if you want to see what the queue templates look like, you can see them here. The values you put in your my_qadapter.yaml file above are used to fill in the unknown values of the template.

    FW_config.yaml

    @@ -414,7 +414,7 @@

    Add a workflow

  • The -l vasp option states to use the vasp library of workflows.

    • -

  • The -s optimize_only.yaml sets the specification of the workflow using the optimize_only.yaml file in this directory. Alternatively, the -p wf_structure_optimization sets the workflow specification using the preset Python function located in this module. For now, it’s probably best not to worry about the distinction but to know that both libraries of workflows are available to you.

    • +

  • The -s optimize_only.yaml sets the specification of the workflow using the optimize_only.yaml file in this directory. Alternatively, the -p wf_structure_optimization sets the workflow specification using the preset Python function located in this module. For now, it’s probably best not to worry about the distinction but to know that both libraries of workflows are available to you.

  • The -c option is used in file-based workflows to make sure that one uses the vasp_cmd and db_file that are specified in my_fworker.yaml that you specified earlier. In the preset workflows, it is the default behavior to take these parameters from the my_fworker.yaml so this option is not needed.

    • @@ -642,7 +642,7 @@

    Navigation

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  • atomate 0.9.8 documentation »
  • Installing atomate
    • diff --git a/docs/license.html b/docs/license.html index 27491111f..cb274bd1a 100644 --- a/docs/license.html +++ b/docs/license.html @@ -5,7 +5,7 @@ - License — atomate 0.9.6 documentation + License — atomate 0.9.8 documentation @@ -36,7 +36,7 @@

    Navigation

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  • License
    • @@ -148,7 +148,7 @@

    Navigation

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    • diff --git a/docs/modules.html b/docs/modules.html index c39d56b37..8e9acbbe4 100644 --- a/docs/modules.html +++ b/docs/modules.html @@ -5,7 +5,7 @@ - atomate — atomate 0.9.6 documentation + atomate — atomate 0.9.8 documentation @@ -28,7 +28,7 @@

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  • atomate 0.9.6 documentation »
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  • atomate
    • @@ -47,7 +47,7 @@

    atomateatomate.common package @@ -62,8 +62,8 @@

    atomateSubpackages
  • Submodules
  • atomate.lammps.database module
    • -
  • atomate.lammps.drones module
    • -
  • atomate.lammps.utils module
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  • atomate.lammps.drones module
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  • atomate.lammps.utils module
  • Module contents
    • @@ -81,8 +81,8 @@

    atomateSubmodules
  • atomate.utils.database module
  • atomate.utils.fileio module
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  • atomate.utils.testing module
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  • atomate.utils.testing module
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    • @@ -91,9 +91,9 @@

    atomateSubmodules
  • atomate.vasp.config module
  • atomate.vasp.database module
    • -
  • atomate.vasp.drones module
    • +
  • atomate.vasp.drones module
  • atomate.vasp.powerups module
    • -
  • atomate.vasp.submission_filter module
    • +
  • atomate.vasp.submission_filter module
  • atomate.vasp.vasp_config module
  • atomate.vasp.vasp_powerups module
  • Module contents
    • @@ -145,7 +145,7 @@

    Navigation

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  • atomate
    • diff --git a/docs/objects.inv b/docs/objects.inv index 17eef7710..e7a090f87 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 245def676..1058caa63 100644 --- a/docs/py-modindex.html +++ b/docs/py-modindex.html @@ -5,7 +5,7 @@ - Python Module Index — atomate 0.9.6 documentation + Python Module Index — atomate 0.9.8 documentation @@ -31,7 +31,7 @@

    Navigation

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  • atomate 0.9.6 documentation »
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  • atomate 0.9.8 documentation »
  • Python Module Index
    • @@ -68,16 +68,46 @@

    Python Module Index

        atomate.common.firetasks + + +     + atomate.common.firetasks.glue_tasks + + + +     + atomate.common.firetasks.parse_outputs + + + +     + atomate.common.firetasks.run_calc +     atomate.common.firetasks.tests + + +     + atomate.common.firetasks.tests.test_parse_outputs + + + +     + atomate.common.powerups +     atomate.common.tests + + +     + atomate.common.tests.test_powerups +     @@ -88,16 +118,41 @@

    Python Module Index

        atomate.lammps + + +     + atomate.lammps.drones +     atomate.lammps.firetasks + + +     + atomate.lammps.firetasks.glue_tasks + + + +     + atomate.lammps.firetasks.run_calc + + + +     + atomate.lammps.firetasks.write_inputs +     atomate.lammps.fireworks + + +     + atomate.lammps.utils +     @@ -123,6 +178,11 @@

    Python Module Index

        atomate.qchem.firetasks.tests + + +     + atomate.qchem.firetasks.tests.test_geo_transformations +     @@ -153,11 +213,31 @@

    Python Module Index

        atomate.utils.fileio + + +     + atomate.utils.testing +     atomate.utils.tests + + +     + atomate.utils.tests.test_loaders + + + +     + atomate.utils.tests.test_utils + + + +     + atomate.utils.utils +     @@ -178,16 +258,66 @@

    Python Module Index

        atomate.vasp.builders + + +     + atomate.vasp.builders.bandgap_estimation +     atomate.vasp.builders.base + + +     + atomate.vasp.builders.boltztrap_materials + + + +     + atomate.vasp.builders.dielectric +     atomate.vasp.builders.examples + + +     + atomate.vasp.builders.examples.run_builders + + + +     + atomate.vasp.builders.file_materials + + + +     + atomate.vasp.builders.fix_tasks + + + +     + atomate.vasp.builders.materials_descriptor + + + +     + atomate.vasp.builders.materials_ehull + + + +     + atomate.vasp.builders.tags + + + +     + atomate.vasp.builders.tasks_materials +     @@ -198,16 +328,46 @@

    Python Module Index

        atomate.vasp.config + + +     + atomate.vasp.drones +     atomate.vasp.examples + + +     + atomate.vasp.firetasks.glue_tasks + + + +     + atomate.vasp.firetasks.neb_tasks + + + +     + atomate.vasp.submission_filter +     atomate.vasp.tests + + +     + atomate.vasp.tests.test_drones + + + +     + atomate.vasp.tests.test_setup +     @@ -250,7 +410,7 @@

    Navigation

  • modules |
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  • atomate 0.9.6 documentation »
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  • Python Module Index
    • diff --git a/docs/running_workflows.html b/docs/running_workflows.html index 1d31a76cd..0749eb08a 100644 --- a/docs/running_workflows.html +++ b/docs/running_workflows.html @@ -5,7 +5,7 @@ - Running workflows tutorial — atomate 0.9.6 documentation + Running workflows tutorial — atomate 0.9.8 documentation @@ -36,7 +36,7 @@

    Navigation

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  • Running workflows tutorial
    • @@ -151,7 +151,7 @@

    Option 3: use Python to generate and add the workflowIn 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
-from pymatgen import Structure
+from pymatgen.core import Structure
 from fireworks import LaunchPad
 from atomate.vasp.workflows.presets.core import wf_bandstructure
 from atomate.vasp.powerups import add_modify_incar
@@ -315,7 +315,7 @@ 
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    •
    diff --git a/docs/search.html b/docs/search.html index 9c2319ed1..3d0338a6c 100644 --- a/docs/search.html +++ b/docs/search.html @@ -5,7 +5,7 @@ - Search — atomate 0.9.6 documentation + Search — atomate 0.9.8 documentation @@ -33,7 +33,7 @@

    Navigation

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    • @@ -84,7 +84,7 @@

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  • Search
    • diff --git a/docs/searchindex.js b/docs/searchindex.js index 60898363c..06d783277 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 85926f9ee..f6b23b90f 100644 --- a/docs/workflow_yaml_reference.html +++ b/docs/workflow_yaml_reference.html @@ -5,7 +5,7 @@ - Workflow YAML Reference — atomate 0.9.6 documentation + Workflow YAML Reference — atomate 0.9.8 documentation @@ -36,7 +36,7 @@

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    • @@ -237,7 +237,7 @@

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    • diff --git a/setup.py b/setup.py index c2a6424ef..9f8bee4f3 100644 --- a/setup.py +++ b/setup.py @@ -9,7 +9,7 @@ if __name__ == "__main__": setup( name='atomate', - version='0.9.6', + version='0.9.8', description='atomate has implementations of FireWorks workflows for ' 'Materials Science', long_description=open(os.path.join(module_dir, 'README.md')).read(),