From e0f22d615b1f1ad5d851354fae18b3e4f56e12f4 Mon Sep 17 00:00:00 2001 From: Anubhav Jain Date: Tue, 2 Apr 2019 14:31:26 -0700 Subject: [PATCH] Update to v0.8.8 --- atomate/__init__.py | 2 +- .../atomate.vasp.workflows.base.rst.txt | 8 ++ .../atomate.vasp.workflows.tests.rst.txt | 8 ++ docs/_sources/changelog.rst.txt | 6 + docs/_sources/contributors.rst.txt | 4 +- docs/_static/documentation_options.js | 2 +- docs/atomate.common.firetasks.html | 6 +- docs/atomate.common.firetasks.tests.html | 6 +- docs/atomate.common.html | 6 +- docs/atomate.feff.firetasks.html | 6 +- docs/atomate.feff.firetasks.tests.html | 6 +- docs/atomate.feff.fireworks.html | 6 +- docs/atomate.feff.fireworks.tests.html | 6 +- docs/atomate.feff.html | 6 +- docs/atomate.feff.workflows.html | 6 +- docs/atomate.feff.workflows.tests.html | 6 +- docs/atomate.html | 8 +- docs/atomate.lammps.firetasks.html | 6 +- docs/atomate.lammps.fireworks.html | 6 +- docs/atomate.lammps.html | 6 +- docs/atomate.lammps.workflows.html | 6 +- docs/atomate.qchem.firetasks.html | 6 +- docs/atomate.qchem.firetasks.tests.html | 6 +- docs/atomate.qchem.fireworks.html | 6 +- docs/atomate.qchem.html | 6 +- docs/atomate.qchem.workflows.base.html | 6 +- docs/atomate.qchem.workflows.html | 6 +- docs/atomate.qchem.workflows.tests.html | 6 +- docs/atomate.tools.html | 6 +- docs/atomate.tools.post_process.html | 6 +- docs/atomate.tools.tests.html | 6 +- docs/atomate.utils.html | 6 +- docs/atomate.utils.tests.html | 6 +- docs/atomate.vasp.analysis.html | 6 +- docs/atomate.vasp.builders.examples.html | 6 +- docs/atomate.vasp.builders.html | 6 +- docs/atomate.vasp.examples.html | 6 +- docs/atomate.vasp.firetasks.html | 120 ++++++++++++++++- docs/atomate.vasp.firetasks.tests.html | 6 +- docs/atomate.vasp.fireworks.html | 35 +++-- docs/atomate.vasp.html | 19 ++- docs/atomate.vasp.tests.html | 6 +- docs/atomate.vasp.workflows.base.html | 125 +++++++++++++++++- docs/atomate.vasp.workflows.html | 8 +- docs/atomate.vasp.workflows.presets.html | 6 +- docs/atomate.vasp.workflows.tests.html | 37 +++++- docs/builders.html | 6 +- docs/changelog.html | 12 +- docs/concepts.html | 6 +- docs/contributors.html | 10 +- docs/creating_workflows.html | 6 +- docs/customizing_workflows.html | 6 +- docs/developer_installation.html | 6 +- docs/genindex.html | 66 +++++++-- docs/gibbs_workflow_tutorial.html | 6 +- docs/index.html | 6 +- docs/installation.html | 6 +- docs/license.html | 6 +- docs/modules.html | 6 +- docs/objects.inv | Bin 7477 -> 7612 bytes docs/py-modindex.html | 16 ++- docs/running_workflows.html | 6 +- docs/search.html | 6 +- docs/searchindex.js | 2 +- docs/workflow_yaml_reference.html | 6 +- docs_rst/atomate.vasp.workflows.base.rst | 8 ++ docs_rst/atomate.vasp.workflows.tests.rst | 8 ++ docs_rst/changelog.rst | 6 + docs_rst/contributors.rst | 4 +- setup.py | 2 +- 70 files changed, 590 insertions(+), 202 deletions(-) diff --git a/atomate/__init__.py b/atomate/__init__.py index d1f5d670a..5f543798c 100644 --- a/atomate/__init__.py +++ b/atomate/__init__.py @@ -1 +1 @@ -__version__ = "0.8.7" \ No newline at end of file +__version__ = "0.8.8" \ No newline at end of file diff --git a/docs/_sources/atomate.vasp.workflows.base.rst.txt b/docs/_sources/atomate.vasp.workflows.base.rst.txt index c891174c8..b42dc89da 100644 --- a/docs/_sources/atomate.vasp.workflows.base.rst.txt +++ b/docs/_sources/atomate.vasp.workflows.base.rst.txt @@ -60,6 +60,14 @@ atomate.vasp.workflows.base.gibbs module :undoc-members: :show-inheritance: +atomate.vasp.workflows.base.magnetism module +-------------------------------------------- + +.. automodule:: atomate.vasp.workflows.base.magnetism + :members: + :undoc-members: + :show-inheritance: + atomate.vasp.workflows.base.neb module -------------------------------------- diff --git a/docs/_sources/atomate.vasp.workflows.tests.rst.txt b/docs/_sources/atomate.vasp.workflows.tests.rst.txt index 23b6261d0..48e98f18a 100644 --- a/docs/_sources/atomate.vasp.workflows.tests.rst.txt +++ b/docs/_sources/atomate.vasp.workflows.tests.rst.txt @@ -36,6 +36,14 @@ atomate.vasp.workflows.tests.test\_ferroelectric\_workflow module :undoc-members: :show-inheritance: +atomate.vasp.workflows.tests.test\_magnetism\_workflow module +------------------------------------------------------------- + +.. automodule:: atomate.vasp.workflows.tests.test_magnetism_workflow + :members: + :undoc-members: + :show-inheritance: + atomate.vasp.workflows.tests.test\_neb\_workflow module ------------------------------------------------------- diff --git a/docs/_sources/changelog.rst.txt b/docs/_sources/changelog.rst.txt index ec752b158..5258526d8 100644 --- a/docs/_sources/changelog.rst.txt +++ b/docs/_sources/changelog.rst.txt @@ -2,6 +2,12 @@ atomate Changelog ================= +**v0.8.8** + +* magnetic ordering workflows (M. Horton) +* better checks for AECAR storage (J. Shen) +* update VASP NCF set NEDOS (M. Dylla) + **v0.8.7** * store custodian data in its own key in FWAction (E. Sivonxay) diff --git a/docs/_sources/contributors.rst.txt b/docs/_sources/contributors.rst.txt index 5452e7547..f9edea431 100644 --- a/docs/_sources/contributors.rst.txt +++ b/docs/_sources/contributors.rst.txt @@ -2,7 +2,7 @@ Contributors ============ -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. +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: @@ -12,4 +12,4 @@ Contributions are provided by: * Brandon Bocklund, who led the atomate documentation effort, through the research group of Prof. Zi-Kiu Liu at Penn State. * Tess Smidt through the research group of Prof. Jeff Neaton at UC Berkeley. * Danny Broberg through the research group of Prof. Mark Asta at UC Berkeley. -* External contributors: specter119, M. Dias Costa, S. Torrisi +* External contributors: specter119, M. Dias Costa, S. 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    • diff --git a/docs/atomate.vasp.firetasks.html b/docs/atomate.vasp.firetasks.html index e107a70e7..57b51edc7 100644 --- a/docs/atomate.vasp.firetasks.html +++ b/docs/atomate.vasp.firetasks.html @@ -6,7 +6,7 @@ - atomate.vasp.firetasks package — atomate 0.8.7 documentation + atomate.vasp.firetasks package — atomate 0.8.8 documentation @@ -28,7 +28,7 @@

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    • @@ -916,6 +916,120 @@

    Submodulesatomate.vasp.firetasks.parse_outputs.JsonToDb

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

    Bases: fireworks.core.firework.FiretaskBase

    +

    Used to calculate magnetic deformation from +get_wf_magnetic_deformation workflow. See docstring +for that workflow for more information. +Required parameters:

    +
    +
    db_file (str): path to the db file that holds your tasks +collection and that you want to hold the magnetic_orderings +collection +wf_uuid (str): auto-generated from get_wf_magnetic_orderings, +used to make it easier to retrieve task docs
    +
    +
    Optional parameters:
    +
    to_db (bool): if True, the data will be inserted into +dedicated collection in database, otherwise, will be dumped +to a .json file.
    +
    +
    +
    +optional_params = ['to_db']
    +
    + +
    +
    +required_params = ['db_file', 'wf_uuid']
    +
    + +
    +
    +run_task(fw_spec)
    +

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

    +
    +
    Args:
    +
    +
    fw_spec (dict): A Firework spec. This comes from the master spec.
    +
    In addition, this spec contains a special “_fw_env” key that +contains the env settings of the FWorker calling this method. +This provides for abstracting out certain commands or +settings. For example, “foo” may be named “foo1” in resource +1 and “foo2” in resource 2. The FWorker env can specify { +“foo”: “foo1”}, which maps an abstract variable “foo” to the +relevant “foo1” or “foo2”. You can then write a task that +uses fw_spec[“_fw_env”][“foo”] that will work across all +these multiple resources.
    +
    +
    +
    Returns:
    +
    (FWAction)
    +
    +
    + +
    + +
    +
    +class atomate.vasp.firetasks.parse_outputs.MagneticOrderingsToDB(*args, **kwargs)
    +

    Bases: fireworks.core.firework.FiretaskBase

    +

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

    +
    +
    db_file (str): path to the db file that holds your tasks +collection and that you want to hold the magnetic_orderings +collection +wf_uuid (str): auto-generated from get_wf_magnetic_orderings, +used to make it easier to retrieve task docs +parent_structure: Structure of parent crystal (not magnetically +ordered)
    +
    +
    +optional_params = ['origins', 'input_index']
    +
    + +
    +
    +required_params = ['db_file', 'wf_uuid', 'parent_structure', 'perform_bader', 'scan']
    +
    + +
    +
    +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.parse_outputs.PolarizationToDb(*args, **kwargs)
    @@ -2117,7 +2231,7 @@

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    • @@ -274,17 +274,19 @@

    Submodules
    -class atomate.vasp.fireworks.core.NonSCFFW(parents=None, prev_calc_dir=None, structure=None, name='nscf', mode='uniform', vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, **kwargs)
    +class atomate.vasp.fireworks.core.NonSCFFW(parents=None, prev_calc_dir=None, structure=None, name='nscf', mode='uniform', vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, input_set_overrides=None, **kwargs)

    Bases: fireworks.core.firework.Firework

    -__init__(parents=None, prev_calc_dir=None, structure=None, name='nscf', mode='uniform', vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, **kwargs)
    -

    Standard NonSCF Calculation Firework supporting both -uniform and line modes.

    +__init__(parents=None, prev_calc_dir=None, structure=None, name='nscf', mode='uniform', vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, input_set_overrides=None, **kwargs) +

    Standard NonSCF Calculation Firework supporting uniform and line modes.

    Args:
    -

    structure (Structure): Input structure - used only to set the name of the FW. -name (str): Name for the Firework. +

    +
    structure (Structure): Input structure - used only to set the name
    +
    of the FW.
    +
    +

    name (str): Name for the Firework. mode (str): “uniform” or “line” mode. vasp_cmd (str): Command to run vasp. copy_vasp_outputs (bool): Whether to copy outputs from previous

    @@ -295,6 +297,16 @@

    Submodules +
    input_set_overrides (dict): Arguments passed to the
    +

    “from_prev_calc” method of the MPNonSCFSet. This parameter +allows a user to modify the default values of the input set. +For example, passing the key value pair

    +
    +
    {‘reciprocal_density’: 1000}
    +

    will override default k-point meshes for uniform calculations.

    +
    +

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

    @@ -400,11 +412,11 @@

    Submodules
    -class atomate.vasp.fireworks.core.StaticFW(structure=None, name='static', vasp_input_set=None, vasp_input_set_params=None, vasp_cmd='vasp', prev_calc_loc=True, prev_calc_dir=None, db_file=None, vasptodb_kwargs={}, parents=None, **kwargs)
    +class atomate.vasp.fireworks.core.StaticFW(structure=None, name='static', vasp_input_set=None, vasp_input_set_params=None, vasp_cmd='vasp', prev_calc_loc=True, prev_calc_dir=None, db_file=None, vasptodb_kwargs=None, parents=None, **kwargs)

    Bases: fireworks.core.firework.Firework

    -__init__(structure=None, name='static', vasp_input_set=None, vasp_input_set_params=None, vasp_cmd='vasp', prev_calc_loc=True, prev_calc_dir=None, db_file=None, vasptodb_kwargs={}, parents=None, **kwargs)
    +__init__(structure=None, name='static', vasp_input_set=None, vasp_input_set_params=None, vasp_cmd='vasp', prev_calc_loc=True, prev_calc_dir=None, db_file=None, vasptodb_kwargs=None, parents=None, **kwargs)

    Standard static calculation Firework - either from a previous location or from a structure.

    Args:
    @@ -426,6 +438,7 @@

    Submodulesprev_calc_dir (str): Path to a previous calculation to copy from db_file (str): Path to file specifying db credentials. parents (Firework): Parents of this particular Firework. FW or list of FWS. +vasptodb_kwargs (dict): kwargs to pass to VaspToDb **kwargs: Other kwargs that are passed to Firework.__init__.

    @@ -656,7 +669,7 @@

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    • +
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    • @@ -124,6 +124,7 @@

    Subpackagesatomate.vasp.workflows.base.elastic module
  • atomate.vasp.workflows.base.ferroelectric module
  • atomate.vasp.workflows.base.gibbs module
    • +
  • atomate.vasp.workflows.base.magnetism module
  • atomate.vasp.workflows.base.neb module
  • atomate.vasp.workflows.base.raman module
  • atomate.vasp.workflows.base.thermal_expansion module
    • @@ -143,6 +144,7 @@

    Subpackagesatomate.vasp.workflows.tests.test_bulk_modulus_workflow module
  • atomate.vasp.workflows.tests.test_elastic_workflow module
  • atomate.vasp.workflows.tests.test_ferroelectric_workflow module
    • +
  • atomate.vasp.workflows.tests.test_magnetism_workflow module
  • atomate.vasp.workflows.tests.test_neb_workflow module
  • atomate.vasp.workflows.tests.test_nmr module
  • atomate.vasp.workflows.tests.test_raman_workflow module
    • @@ -192,14 +194,15 @@

    Submodules
    -get_aeccar(task_id)
    +get_aeccar(task_id, check_valid=True)

    Read the AECCAR0 + AECCAR2 grid_fs data into a Chgcar object Args:

    -
    task_id(int or str): the task_id containing the gridfs metadata
    +
    task_id(int or str): the task_id containing the gridfs metadata +check_valid (bool): make sure that the aeccar is positive definite
    Returns:
    -
    (aeccar0, aeccar2): Chgcar objects
    +
    {“aeccar0” : Chgcar, “aeccar2” : Chgcar}: dict of Chgcar objects

    @@ -251,7 +254,9 @@

    Submodules insert_task(task_doc, use_gridfs=False)

    Inserts a task document (e.g., as returned by Drone.assimilate()) into the database. -Handles putting DOS and band structure into GridFS as needed.

    +Handles putting DOS, band structure and charge density into GridFS as needed. +During testing, a percentage of runs on some clusters had corrupted AECCAR files when even if everything else about the calculation looked OK. +So we do a quick check here and only record the AECCARs if they are valid

    Args:
    task_doc: (dict) the task document @@ -957,7 +962,7 @@

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    • @@ -239,7 +239,7 @@

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    • diff --git a/docs/atomate.vasp.workflows.base.html b/docs/atomate.vasp.workflows.base.html index 2b76105ed..faa0a449f 100644 --- a/docs/atomate.vasp.workflows.base.html +++ b/docs/atomate.vasp.workflows.base.html @@ -6,7 +6,7 @@ - atomate.vasp.workflows.base package — atomate 0.8.7 documentation + atomate.vasp.workflows.base package — atomate 0.8.8 documentation @@ -28,7 +28,7 @@

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    • @@ -402,6 +402,124 @@

    Submodules +

    atomate.vasp.workflows.base.magnetism module

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

    Bases: object

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

    This workflow will try several different collinear +magnetic orderings for a given input structure, +and output a summary to a dedicated database +collection, magnetic_orderings, in the supplied +db_file.

    +

    If the input structure has magnetic moments defined, it +is possible to use these as a hint as to which elements are +magnetic, otherwise magnetic elements will be guessed +(this can be changed using default_magmoms kwarg).

    +
    +
    A brief description on how this workflow works:
    +
      +
    1. We make a note of the input structure, and then +sanitize it (make it ferromagnetic, primitive)
      2. +
    2. We gather information on which sites are likely +magnetic, how many unique magnetic sites there +are (whether one species is in several unique +environments, e.g. tetrahedral/octahedra as Fe +in a spinel)
      3. +
    3. We generate ordered magnetic structures, first +antiferromagnetic, and then, if appropriate, +ferrimagnetic_Cr2NiO4 structures either by species or +by environment – this makes use of some new +additions to MagOrderingTransformation to allow +the spins of different species to be coupled together +(e.g. all one species spin up, all other species spin +down, with an overall order parameter of 0.5)
      4. +
    4. For each ordered structure, we perform a relaxation +and static calculation. Then an aggregation is performed +which finds which ordering is the ground state (of +those attempted in this specific workflow). For +high-throughput studies, a dedicated builder is +recommended.
      5. +
    5. For book-keeping, a record is kept of whether the +input structure is enumerated by the algorithm or +not. This is useful when supplying the workflow with +a magnetic structure obtained by experiment, to measure +the performance of the workflow.
      6. +
    +
    +
    Args:
    +
    structure: input structure +default_magmoms: (optional, defaults provided) dict of
    +
    +

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

    +
    +
    strategies: different ordering strategies to use, choose from:
    +

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

    +
    +
    automatic: if True, will automatically choose sensible strategies +truncate_by_symmetry: if True, will remove very unsymmetrical
    +
    +
    orderings that are likely physically implausible
    +
    transformation_kwargs: keyword arguments to pass to
    +
    +

    MagOrderingTransformation, to change automatic cell size limits, etc.

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

    Retrieve the FireWorks workflow.

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

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

    +
    +
    perform_bader: if True, make sure the “bader” binary is in your
    +

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

    +
    +
    num_orderings_hard_limit: will make sure total number of magnetic
    +

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

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

    Returns: FireWorks Workflow

    +
    + +
    + +
    +
    +atomate.vasp.workflows.base.magnetism.get_wf_magnetic_deformation(structure, c=None, vis=None)
    +

    Minimal workflow to obtain magnetic deformation proxy, as +defined by Bocarsly et al. 2017, doi: 10.1021/acs.chemmater.6b04729

    +
    +
    Args:
    +
    structure: input structure, must be structure with magnetic
    +
    +

    elements, such that pymatgen will initalize ferromagnetic input by +default – see MPRelaxSet.yaml for list of default elements

    +
    +
    c: Workflow config dict, in the same format
    +
    +
    as in presets/core.py and elsewhere in atomate
    +
    vis: A VaspInputSet to use for the first FW
    +
    +

    Returns: Workflow

    +
    + diff --git a/docs/atomate.vasp.workflows.html b/docs/atomate.vasp.workflows.html index f545dcd2b..05586d099 100644 --- a/docs/atomate.vasp.workflows.html +++ b/docs/atomate.vasp.workflows.html @@ -6,7 +6,7 @@ - atomate.vasp.workflows package — atomate 0.8.7 documentation + atomate.vasp.workflows package — atomate 0.8.8 documentation @@ -28,7 +28,7 @@

    Navigation

  • modules |
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  • atomate 0.8.7 documentation »
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  • atomate 0.8.8 documentation »
    • @@ -52,6 +52,7 @@

    Subpackagesatomate.vasp.workflows.base.elastic module
  • atomate.vasp.workflows.base.ferroelectric module
  • atomate.vasp.workflows.base.gibbs module
    • +
  • atomate.vasp.workflows.base.magnetism module
  • atomate.vasp.workflows.base.neb module
  • atomate.vasp.workflows.base.raman module
  • atomate.vasp.workflows.base.thermal_expansion module
    • @@ -71,6 +72,7 @@

    Subpackagesatomate.vasp.workflows.tests.test_bulk_modulus_workflow module
  • atomate.vasp.workflows.tests.test_elastic_workflow module
  • atomate.vasp.workflows.tests.test_ferroelectric_workflow module
    • +
  • atomate.vasp.workflows.tests.test_magnetism_workflow module
  • atomate.vasp.workflows.tests.test_neb_workflow module
  • atomate.vasp.workflows.tests.test_nmr module
  • atomate.vasp.workflows.tests.test_raman_workflow module
    • @@ -133,7 +135,7 @@

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    • @@ -165,6 +165,36 @@

    Submodules +

    atomate.vasp.workflows.tests.test_magnetism_workflow module

    +
    +
    +class atomate.vasp.workflows.tests.test_magnetism_workflow.TestMagneticDeformationWorkflow(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +test_analysis()
    +
    + +
    + +
    +
    +class atomate.vasp.workflows.tests.test_magnetism_workflow.TestMagneticOrderingsWorkflow(methodName='runTest')
    +

    Bases: atomate.utils.testing.AtomateTest

    +
    +
    +test_analysis()
    +
    + +
    +
    +test_ordering_enumeration()
    +
    + +
    + diff --git a/docs/builders.html b/docs/builders.html index 1b1952682..576ecb7fe 100644 --- a/docs/builders.html +++ b/docs/builders.html @@ -6,7 +6,7 @@ - Builders — atomate 0.8.7 documentation + Builders — atomate 0.8.8 documentation @@ -36,7 +36,7 @@

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    atomate Changelog

    +

    v0.8.8

    +
      +
    • magnetic ordering workflows (M. Horton)
      • +
    • better checks for AECAR storage (J. Shen)
      • +
    • update VASP NCF set NEDOS (M. Dylla)
      • +

    v0.8.7

    diff --git a/docs/concepts.html b/docs/concepts.html index e0833c041..b78ab1c0c 100644 --- a/docs/concepts.html +++ b/docs/concepts.html @@ -6,7 +6,7 @@ - Atomate concepts — atomate 0.8.7 documentation + Atomate concepts — atomate 0.8.8 documentation @@ -32,7 +32,7 @@

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    Contributors

    -

    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.

    +

    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:

    diff --git a/docs/creating_workflows.html b/docs/creating_workflows.html index c5673389e..a54db4260 100644 --- a/docs/creating_workflows.html +++ b/docs/creating_workflows.html @@ -6,7 +6,7 @@ - Creating workflows — atomate 0.8.7 documentation + Creating workflows — atomate 0.8.8 documentation @@ -36,7 +36,7 @@

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    • @@ -157,6 +157,8 @@

    _

  • (atomate.vasp.submission_filter.SubmissionFilter method)
  • (atomate.vasp.workflows.base.adsorption.MPSurfaceSet method) +
    • +
  • (atomate.vasp.workflows.base.magnetism.MagneticOrderingsWF method)
    • @@ -329,10 +331,10 @@

    A

  • atomate.qchem.workflows.base (module)
    • - - + - +
    • get_valid_paths() (atomate.common.firetasks.tests.test_parse_outputs.TestDrone method)
      • -
    • get_wf() (in module atomate.vasp.workflows.base.core) +
    • get_wf() (atomate.vasp.workflows.base.magnetism.MagneticOrderingsWF method) + +
    • get_wf_basic() (in module atomate.lammps.workflows.core)
    • get_wf_bulk_modulus() (in module atomate.vasp.workflows.base.bulk_modulus) @@ -756,6 +766,8 @@

      G

    • get_wf_from_spec_dict() (in module atomate.utils.utils)
    • get_wf_gibbs_free_energy() (in module atomate.vasp.workflows.base.gibbs) +
      • +
    • get_wf_magnetic_deformation() (in module atomate.vasp.workflows.base.magnetism)
    • get_wf_molecules() (in module atomate.vasp.workflows.base.adsorption)
      • @@ -853,16 +865,22 @@

      L

      M

      + - + + + + + +
      diff --git a/docs/gibbs_workflow_tutorial.html b/docs/gibbs_workflow_tutorial.html index f66c0bf44..3f47d74b1 100644 --- a/docs/gibbs_workflow_tutorial.html +++ b/docs/gibbs_workflow_tutorial.html @@ -6,7 +6,7 @@ - Running Gibbs workflows — atomate 0.8.7 documentation + Running Gibbs workflows — atomate 0.8.8 documentation @@ -36,7 +36,7 @@

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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 a1f98b40a..3a419aef3 100644 --- a/docs/workflow_yaml_reference.html +++ b/docs/workflow_yaml_reference.html @@ -6,7 +6,7 @@ - Workflow YAML Reference — atomate 0.8.7 documentation + Workflow YAML Reference — atomate 0.8.8 documentation @@ -36,7 +36,7 @@

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    • atomate 0.8.7 documentation »
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      • @@ -237,7 +237,7 @@

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    • atomate 0.8.7 documentation »
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      • diff --git a/docs_rst/atomate.vasp.workflows.base.rst b/docs_rst/atomate.vasp.workflows.base.rst index c891174c8..b42dc89da 100644 --- a/docs_rst/atomate.vasp.workflows.base.rst +++ b/docs_rst/atomate.vasp.workflows.base.rst @@ -60,6 +60,14 @@ atomate.vasp.workflows.base.gibbs module :undoc-members: :show-inheritance: +atomate.vasp.workflows.base.magnetism module +-------------------------------------------- + +.. automodule:: atomate.vasp.workflows.base.magnetism + :members: + :undoc-members: + :show-inheritance: + atomate.vasp.workflows.base.neb module -------------------------------------- diff --git a/docs_rst/atomate.vasp.workflows.tests.rst b/docs_rst/atomate.vasp.workflows.tests.rst index 23b6261d0..48e98f18a 100644 --- a/docs_rst/atomate.vasp.workflows.tests.rst +++ b/docs_rst/atomate.vasp.workflows.tests.rst @@ -36,6 +36,14 @@ atomate.vasp.workflows.tests.test\_ferroelectric\_workflow module :undoc-members: :show-inheritance: +atomate.vasp.workflows.tests.test\_magnetism\_workflow module +------------------------------------------------------------- + +.. automodule:: atomate.vasp.workflows.tests.test_magnetism_workflow + :members: + :undoc-members: + :show-inheritance: + atomate.vasp.workflows.tests.test\_neb\_workflow module ------------------------------------------------------- diff --git a/docs_rst/changelog.rst b/docs_rst/changelog.rst index ec752b158..5258526d8 100644 --- a/docs_rst/changelog.rst +++ b/docs_rst/changelog.rst @@ -2,6 +2,12 @@ atomate Changelog ================= +**v0.8.8** + +* magnetic ordering workflows (M. Horton) +* better checks for AECAR storage (J. Shen) +* update VASP NCF set NEDOS (M. Dylla) + **v0.8.7** * store custodian data in its own key in FWAction (E. Sivonxay) diff --git a/docs_rst/contributors.rst b/docs_rst/contributors.rst index 5452e7547..f9edea431 100644 --- a/docs_rst/contributors.rst +++ b/docs_rst/contributors.rst @@ -2,7 +2,7 @@ Contributors ============ -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. +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: @@ -12,4 +12,4 @@ Contributions are provided by: * Brandon Bocklund, who led the atomate documentation effort, through the research group of Prof. Zi-Kiu Liu at Penn State. * Tess Smidt through the research group of Prof. Jeff Neaton at UC Berkeley. * Danny Broberg through the research group of Prof. Mark Asta at UC Berkeley. -* External contributors: specter119, M. Dias Costa, S. Torrisi +* External contributors: specter119, M. Dias Costa, S. Torrisi, Max Dylla diff --git a/setup.py b/setup.py index 47461eeed..a3bfcf6c8 100644 --- a/setup.py +++ b/setup.py @@ -9,7 +9,7 @@ if __name__ == "__main__": setup( name='atomate', - version='0.8.7', + version='0.8.8', description='atomate has implementations of FireWorks workflows for ' 'Materials Science', long_description=open(os.path.join(module_dir, 'README.md')).read(),