atomate.vasp.fireworks package¶
Submodules¶
atomate.vasp.fireworks.core module¶
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class
atomate.vasp.fireworks.core.
BoltztrapFW
(structure, name=u'boltztrap', db_file=None, parents=None, scissor=0.0, soc=False, additional_fields=None, **kwargs)¶ Bases:
fireworks.core.firework.Firework
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__init__
(structure, name=u'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__.
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class
atomate.vasp.fireworks.core.
DFPTFW
(structure, name=u'static dielectric', vasp_cmd=u'vasp', copy_vasp_outputs=True, db_file=None, parents=None, user_incar_settings=None, pass_nm_results=False, **kwargs)¶ Bases:
fireworks.core.firework.Firework
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__init__
(structure, name=u'static dielectric', vasp_cmd=u'vasp', copy_vasp_outputs=True, db_file=None, parents=None, user_incar_settings=None, pass_nm_results=False, **kwargs)¶ - Static DFPT calculation Firework
- 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.user_incar_settings (dict): Parameters in INCAR to override pass_nm_results (bool): if true the normal mode eigen vals and vecs are passed so that
next firework can use it.**kwargs: Other kwargs that are passed to Firework.__init__.
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class
atomate.vasp.fireworks.core.
HSEBSFW
(structure, parents, mode=u'gap', name=None, vasp_cmd=u'vasp', db_file=None, **kwargs)¶ Bases:
fireworks.core.firework.Firework
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__init__
(structure, parents, mode=u'gap', name=None, vasp_cmd=u'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 VBMname (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__.
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class
atomate.vasp.fireworks.core.
LepsFW
(structure, name=u'static dielectric', vasp_cmd=u'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
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__init__
(structure, name=u'static dielectric', vasp_cmd=u'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__.
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class
atomate.vasp.fireworks.core.
MDFW
(structure, start_temp, end_temp, nsteps, name=u'molecular dynamics', vasp_input_set=None, vasp_cmd=u'vasp', override_default_vasp_params=None, wall_time=19200, db_file=None, parents=None, copy_vasp_outputs=True, **kwargs)¶ Bases:
fireworks.core.firework.Firework
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__init__
(structure, start_temp, end_temp, nsteps, name=u'molecular dynamics', vasp_input_set=None, vasp_cmd=u'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__.
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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)
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__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__.
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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)
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__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__.
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class
atomate.vasp.fireworks.core.
NonSCFFW
(structure, name=u'nscf', mode=u'uniform', vasp_cmd=u'vasp', copy_vasp_outputs=True, db_file=None, parents=None, **kwargs)¶ Bases:
fireworks.core.firework.Firework
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__init__
(structure, name=u'nscf', mode=u'uniform', vasp_cmd=u'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__.
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class
atomate.vasp.fireworks.core.
OptimizeFW
(structure, name=u'structure optimization', vasp_input_set=None, vasp_cmd=u'vasp', override_default_vasp_params=None, ediffg=None, db_file=None, force_gamma=True, job_type=u'double_relaxation_run', max_force_threshold=0.25, auto_npar=u'>>auto_npar<<', half_kpts_first_relax=False, parents=None, **kwargs)¶ Bases:
fireworks.core.firework.Firework
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__init__
(structure, name=u'structure optimization', vasp_input_set=None, vasp_cmd=u'vasp', override_default_vasp_params=None, ediffg=None, db_file=None, force_gamma=True, job_type=u'double_relaxation_run', max_force_threshold=0.25, auto_npar=u'>>auto_npar<<', half_kpts_first_relax=False, 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<<” half_kpts_first_relax (bool): whether to use half the kpoints for the first relaxation parents ([Firework]): Parents of this particular Firework. **kwargs: Other kwargs that are passed to Firework.__init__.
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class
atomate.vasp.fireworks.core.
RamanFW
(structure, mode, displacement, name=u'raman', vasp_cmd=u'vasp', db_file=None, parents=None, user_incar_settings=None, **kwargs)¶ Bases:
fireworks.core.firework.Firework
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__init__
(structure, mode, displacement, name=u'raman', vasp_cmd=u'vasp', db_file=None, parents=None, user_incar_settings=None, **kwargs)¶ Static calculation Firework that computes the DFPT dielectric constant for structure displaced along the given normal mode direction.
- Args:
- structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
- name of the FW.
mode (int): normal mode index. displacement (float): displacement along the normal mode in Angstroms. name (str): Name for the Firework. vasp_cmd (str): Command to run vasp. db_file (str): Path to file specifying db credentials. parents (Firework): Parents of this particular Firework.
FW or list of FWS.user_incar_settings (dict): Parameters in INCAR to override **kwargs: Other kwargs that are passed to Firework.__init__.
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class
atomate.vasp.fireworks.core.
SOCFW
(structure, magmom, name=u'spin-orbit coupling', saxis=(0, 0, 1), vasp_cmd=u'vasp_ncl', copy_vasp_outputs=True, db_file=None, parents=None, **kwargs)¶ Bases:
fireworks.core.firework.Firework
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__init__
(structure, magmom, name=u'spin-orbit coupling', saxis=(0, 0, 1), vasp_cmd=u'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__.
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class
atomate.vasp.fireworks.core.
StaticFW
(structure, name=u'static', vasp_input_set=None, vasp_cmd=u'vasp', prev_calc_loc=True, db_file=None, parents=None, **kwargs)¶ Bases:
fireworks.core.firework.Firework
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__init__
(structure, name=u'static', vasp_input_set=None, vasp_cmd=u'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__.
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class
atomate.vasp.fireworks.core.
TransmuterFW
(structure, transformations, transformation_params=None, vasp_input_set=None, name=u'structure transmuter', vasp_cmd=u'vasp', copy_vasp_outputs=True, db_file=None, parents=None, override_default_vasp_params=None, **kwargs)¶ Bases:
fireworks.core.firework.Firework
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__init__
(structure, transformations, transformation_params=None, vasp_input_set=None, name=u'structure transmuter', vasp_cmd=u'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__.
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