atomate.vasp package¶
Subpackages¶
- atomate.vasp.analysis package
- atomate.vasp.builders package
- Subpackages
- Submodules
- 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.utils module
- Module contents
- atomate.vasp.firetasks package
- Subpackages
- atomate.vasp.firetasks.tests package
- Submodules
- atomate.vasp.firetasks.tests.test_copy module
- atomate.vasp.firetasks.tests.test_get_interpolated_poscar module
- atomate.vasp.firetasks.tests.test_polarization_to_db module
- atomate.vasp.firetasks.tests.test_write_vasp module
- atomate.vasp.firetasks.tests.test_write_vasp_from_interpolated_poscar module
- Module contents
- atomate.vasp.firetasks.tests package
- Submodules
- atomate.vasp.firetasks.glue_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
- Module contents
- Subpackages
- atomate.vasp.fireworks package
- atomate.vasp.tests package
- atomate.vasp.workflows package
- Subpackages
- atomate.vasp.workflows.base package
- Submodules
- atomate.vasp.workflows.base.adsorption module
- atomate.vasp.workflows.base.bulk_modulus module
- atomate.vasp.workflows.base.core module
- atomate.vasp.workflows.base.deformations module
- atomate.vasp.workflows.base.elastic module
- atomate.vasp.workflows.base.ferroelectric module
- atomate.vasp.workflows.base.gibbs module
- atomate.vasp.workflows.base.neb module
- atomate.vasp.workflows.base.raman module
- atomate.vasp.workflows.base.thermal_expansion module
- Module contents
- atomate.vasp.workflows.presets package
- atomate.vasp.workflows.tests package
- Submodules
- atomate.vasp.workflows.tests.test_adsorbate_workflow module
- atomate.vasp.workflows.tests.test_bulk_modulus_workflow module
- atomate.vasp.workflows.tests.test_elastic_workflow module
- atomate.vasp.workflows.tests.test_ferroelectric_workflow module
- atomate.vasp.workflows.tests.test_neb_workflow module
- atomate.vasp.workflows.tests.test_raman_workflow module
- atomate.vasp.workflows.tests.test_vasp_workflows module
- Module contents
- atomate.vasp.workflows.base package
- Module contents
- Subpackages
Submodules¶
atomate.vasp.config module¶
atomate.vasp.database module¶
-
class
atomate.vasp.database.
VaspCalcDb
(host='localhost', port=27017, database='vasp', collection='tasks', user=None, password=None)¶ Bases:
atomate.utils.database.CalcDb
Class to help manage database insertions of Vasp drones
-
__init__
(host='localhost', port=27017, database='vasp', collection='tasks', user=None, password=None)¶
-
build_indexes
(indexes=None, background=True)¶ Build the indexes.
- Args:
- indexes (list): list of single field indexes to be built. background (bool): Run in the background or not.
- TODO: make sure that the index building is sensible and check for
- existing indexes.
-
get_band_structure
(task_id)¶
-
get_dos
(task_id)¶
-
insert_gridfs
(d, collection='fs', compress=True, oid=None)¶ Insert the given document into GridFS.
- Args:
- d (dict): the document collection (string): the GridFS collection name compress (bool): Whether to compress the data or not oid (ObjectId()): the _id of the file; if specified, it must not already exist in GridFS
- Returns:
- file id, the type of compression used.
-
insert_task
(task_doc, parse_dos=False, parse_bs=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.
- Args:
- task_doc: (dict) the task document parse_dos: (bool) attempt to parse dos in task_doc and insert into Gridfs parse_bs: (bool) attempt to parse bandstructure in task_doc and insert into Gridfs
- Returns:
- (int) - task_id of inserted document
-
reset
()¶
-
retrieve_task
(task_id)¶ Retrieves a task document and unpacks the band structure and DOS as dict
- Args:
- task_id: (int) task_id to retrieve
- Returns:
- (dict) complete task document with BS + DOS included
-
atomate.vasp.drones module¶
atomate.vasp.powerups 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
()¶
-
classmethod
from_dict
(d)¶
-
test
(structure)¶
-