atomate.vasp.fireworks package

Submodules

atomate.vasp.fireworks.core module

class atomate.vasp.fireworks.core.BoltztrapFW(structure, name='boltztrap', db_file=None, parents=None, scissor=0.0, soc=False, additional_fields=None, **kwargs)

Bases: fireworks.core.firework.Firework

__init__(structure, name='boltztrap', db_file=None, parents=None, scissor=0.0, soc=False, additional_fields=None, **kwargs)

Run Boltztrap (which includes writing bolztrap input files and parsing outputs). Assumes you have a previous FW with the calc_locs passed into the current FW.

Args:

structure (Structure): - only used for setting name of FW name (str): name of this FW db_file (str): path to the db file parents (Firework): Parents of this particular Firework. FW or list of FWS. scissor (float): if scissor > 0, apply scissor on the band structure so that new

band gap = scissor (in eV)

soc (bool): whether the band structure is calculated with spin-orbit coupling additional_fields (dict): fields added to the document such as user-defined tags or name, ids, etc **kwargs: Other kwargs that are passed to Firework.__init__.

class atomate.vasp.fireworks.core.HSEBSFW(structure, parents, mode='gap', name=None, vasp_cmd='vasp', db_file=None, **kwargs)

Bases: fireworks.core.firework.Firework

__init__(structure, parents, mode='gap', name=None, vasp_cmd='vasp', db_file=None, **kwargs)

For getting a more accurate band gap or a full band structure with HSE - requires previous calculation that gives VBM/CBM info or the high-symmetry kpoints.

Args:

structure (Structure): Input structure - used only to set the name of the FW. parents (Firework): Parents of this particular Firework. FW or list of FWS. mode (string): options:

“line” to get a full band structure along symmetry lines or “uniform” for uniform mesh band structure or “gap” to get the energy at the CBM and VBM

name (str): Name for the Firework. vasp_cmd (str): Command to run vasp. db_file (str): Path to file specifying db credentials. **kwargs: Other kwargs that are passed to Firework.__init__.

class atomate.vasp.fireworks.core.LepsFW(structure, name='static dielectric', vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, parents=None, phonon=False, mode=None, displacement=None, user_incar_settings=None, **kwargs)

Bases: fireworks.core.firework.Firework

__init__(structure, name='static dielectric', vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, parents=None, phonon=False, mode=None, displacement=None, user_incar_settings=None, **kwargs)

Standard static calculation Firework for dielectric constants using DFPT.

Args:
structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
name of the FW.

name (str): Name for the Firework. vasp_cmd (str): Command to run vasp. copy_vasp_outputs (bool): Whether to copy outputs from previous

run. Defaults to True.

db_file (str): Path to file specifying db credentials. parents (Firework): Parents of this particular Firework.

FW or list of FWS.
phonon (bool): Whether or not to extract normal modes and pass it. This argument along
with the mode and displacement arguments must be set for the calculation of dielectric constant in the Raman tensor workflow.

mode (int): normal mode index. displacement (float): displacement along the normal mode in Angstroms. user_incar_settings (dict): Parameters in INCAR to override **kwargs: Other kwargs that are passed to Firework.__init__.

class atomate.vasp.fireworks.core.MDFW(structure, start_temp, end_temp, nsteps, name='molecular dynamics', vasp_input_set=None, vasp_cmd='vasp', override_default_vasp_params=None, wall_time=19200, db_file=None, parents=None, copy_vasp_outputs=True, **kwargs)

Bases: fireworks.core.firework.Firework

__init__(structure, start_temp, end_temp, nsteps, name='molecular dynamics', vasp_input_set=None, vasp_cmd='vasp', override_default_vasp_params=None, wall_time=19200, db_file=None, parents=None, copy_vasp_outputs=True, **kwargs)

Standard firework for a single MD run.

Args:

structure (Structure): Input structure. start_temp (float): Start temperature of MD run. end_temp (float): End temperature of MD run. nsteps (int): Number of MD steps name (string): Name for the Firework. vasp_input_set (string): string name for the VASP input set (e.g.,

“MITMDVaspInputSet”).

vasp_cmd (string): Command to run vasp. override_default_vasp_params (dict): If this is not None,

these params are passed to the default vasp_input_set, i.e., MITMDSet. This allows one to easily override some settings, e.g., user_incar_settings, etc. Particular to MD, one can control time_step and all other settings of the input set.

wall_time (int): Total wall time in seconds before writing STOPCAR. copy_vasp_outputs (bool): Whether to copy outputs from previous run. Defaults to True. db_file (string): Path to file specifying db credentials. parents (Firework): Parents of this particular Firework. FW or list of FWS. **kwargs: Other kwargs that are passed to Firework.__init__.

class atomate.vasp.fireworks.core.NEBFW(spec, neb_label, from_images=True, user_incar_settings=None, user_kpoints_settings=None, additional_cust_args=None, **kwargs)

Bases: fireworks.core.firework.Firework

CI-NEB Firework in NEB Workflow.

Task 1) Read in image structures from spec and generates input sets.
The group of structures are labeled with neb_label (1, 2…)

Task 2) Run NEB VASP using Custodian Task 3) Update structure to spec Task 4) Pass CalcLocs named “neb_{}”.format(neb_label)

__init__(spec, neb_label, from_images=True, user_incar_settings=None, user_kpoints_settings=None, additional_cust_args=None, **kwargs)
Args:

spec (dict): Specification of the job to run. neb_label (str): “1”, “2”…, label neb run. from_images (bool): Set True to initialize from image structures, False starting

from relaxed endpoint structures.

user_incar_settings (dict): Additional INCAR settings. user_kpoints_settings (dict): Additional KPOINTS settings. additional_cust_args (dict): Other kwargs that are passed to RunVaspCustodian. **kwargs: Other kwargs that are passed to Firework.__init__.

class atomate.vasp.fireworks.core.NEBRelaxationFW(spec, label, user_incar_settings=None, user_kpoints_settings=None, additional_cust_args=None, **kwargs)

Bases: fireworks.core.firework.Firework

Relaxation Firework in NEB Workflow.

Task 1) Read in a structure with “st_label” (“rlx”, “ep0” or “ep1”) and generates input sets. Task 2) Run VASP using Custodian Task 3) Update structure to spec Task 4) Pass CalcLocs named “{}_dir”.format(st_label)

__init__(spec, label, user_incar_settings=None, user_kpoints_settings=None, additional_cust_args=None, **kwargs)
Args:
spec (dict): Specification of the job to run. label (str): “parent”, “ep0” or “ep1” vasp_input_set (VaspInputSet): Input set to use. user_kpoints_settings (dict): Additional KPOINTS settings. additional_cust_args (dict): Other kwargs that are passed to RunVaspCustodian. **kwargs: Other kwargs that are passed to Firework.__init__.
class atomate.vasp.fireworks.core.NonSCFFW(structure, name='nscf', mode='uniform', vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, parents=None, **kwargs)

Bases: fireworks.core.firework.Firework

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

Standard NonSCF Calculation Firework supporting both uniform and line modes.

Args:

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

run. Defaults to True.

db_file (str): Path to file specifying db credentials. parents (Firework): Parents of this particular Firework.

FW or list of FWS.

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

class atomate.vasp.fireworks.core.OptimizeFW(structure, name='structure optimization', vasp_input_set=None, vasp_cmd='vasp', override_default_vasp_params=None, ediffg=None, db_file=None, force_gamma=True, job_type='double_relaxation_run', max_force_threshold=0.25, auto_npar='>>auto_npar<<', parents=None, **kwargs)

Bases: fireworks.core.firework.Firework

__init__(structure, name='structure optimization', vasp_input_set=None, vasp_cmd='vasp', override_default_vasp_params=None, ediffg=None, db_file=None, force_gamma=True, job_type='double_relaxation_run', max_force_threshold=0.25, auto_npar='>>auto_npar<<', parents=None, **kwargs)

Optimize the given structure.

Args:

structure (Structure): Input structure. name (str): Name for the Firework. vasp_input_set (VaspInputSet): input set to use. Defaults to MPRelaxSet() if None. override_default_vasp_params (dict): If this is not None, these params are passed to

the default vasp_input_set, i.e., MPRelaxSet. This allows one to easily override some settings, e.g., user_incar_settings, etc.

vasp_cmd (str): Command to run vasp. ediffg (float): Shortcut to set ediffg in certain jobs db_file (str): Path to file specifying db credentials to place output parsing. force_gamma (bool): Force gamma centered kpoint generation job_type (str): custodian job type (default “double_relaxation_run”) max_force_threshold (float): max force on a site allowed at end; otherwise, reject job auto_npar (bool or str): whether to set auto_npar. defaults to env_chk: “>>auto_npar<<” parents ([Firework]): Parents of this particular Firework. **kwargs: Other kwargs that are passed to Firework.__init__.

class atomate.vasp.fireworks.core.SOCFW(structure, magmom, name='spin-orbit coupling', saxis=(0, 0, 1), vasp_cmd='vasp_ncl', copy_vasp_outputs=True, db_file=None, parents=None, **kwargs)

Bases: fireworks.core.firework.Firework

__init__(structure, magmom, name='spin-orbit coupling', saxis=(0, 0, 1), vasp_cmd='vasp_ncl', copy_vasp_outputs=True, db_file=None, parents=None, **kwargs)

Firework for spin orbit coupling calculation.

Args:
structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
name of the FW.

name (str): Name for the Firework. vasp_cmd (str): Command to run vasp. copy_vasp_outputs (bool): Whether to copy outputs from previous

run. Defaults to True.

db_file (str): Path to file specifying db credentials. parents (Firework): Parents of this particular Firework.

FW or list of FWS.

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

class atomate.vasp.fireworks.core.StaticFW(structure, name='static', vasp_input_set=None, vasp_cmd='vasp', prev_calc_loc=True, db_file=None, parents=None, **kwargs)

Bases: fireworks.core.firework.Firework

__init__(structure, name='static', vasp_input_set=None, vasp_cmd='vasp', prev_calc_loc=True, db_file=None, parents=None, **kwargs)

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

Args:
structure (Structure): Input structure. Note that for prev_calc_loc jobs, the structure
is only used to set the name of the FW and any structure with the same composition can be used.

name (str): Name for the Firework. vasp_input_set (VaspInputSet): input set to use (for jobs w/no parents)

Defaults to MPStaticSet() if None.

vasp_cmd (str): Command to run vasp. prev_calc_loc (bool or str): If true (default), copies outputs from previous calc. If

a str value, grabs a previous calculation output by name. If False/None, will create new static calculation using the provided structure.

db_file (str): Path to file specifying db credentials. parents (Firework): Parents of this particular Firework. FW or list of FWS. **kwargs: Other kwargs that are passed to Firework.__init__.

class atomate.vasp.fireworks.core.TransmuterFW(structure, transformations, transformation_params=None, vasp_input_set=None, name='structure transmuter', vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, parents=None, override_default_vasp_params=None, **kwargs)

Bases: fireworks.core.firework.Firework

__init__(structure, transformations, transformation_params=None, vasp_input_set=None, name='structure transmuter', vasp_cmd='vasp', copy_vasp_outputs=True, db_file=None, parents=None, override_default_vasp_params=None, **kwargs)

Apply the transformations to the input structure, write the input set corresponding to the transformed structure, and run vasp on them. Note that if a transformation yields many structures from one, only the last structure in the list is used.

Args:

structure (Structure): Input structure. transformations (list): list of names of transformation classes as defined in

the modules in pymatgen.transformations. eg: transformations=[‘DeformStructureTransformation’, ‘SupercellTransformation’]
transformation_params (list): list of dicts where each dict specify the input
parameters to instantiate the transformation class in the transformations list.
vasp_input_set (VaspInputSet): VASP input set, used to write the input set for the
transmuted structure.

name (string): Name for the Firework. vasp_cmd (string): Command to run vasp. copy_vasp_outputs (bool): Whether to copy outputs from previous run. Defaults to True. db_file (string): Path to file specifying db credentials. parents (Firework): Parents of this particular Firework. FW or list of FWS. override_default_vasp_params (dict): additional user input settings for vasp_input_set. **kwargs: Other kwargs that are passed to Firework.__init__.

Module contents