def get_wf_bulk_modulus(structure,
deformations,
vasp_input_set=None,
vasp_cmd="vasp",
db_file=None,
user_kpoints_settings=None,
eos="vinet",
tag=None,
user_incar_settings=None):
"""
Returns the workflow that computes the bulk modulus by fitting to the given equation of state.
Args:
structure (Structure): input structure.
deformations (list): list of deformation matrices(list of lists).
vasp_input_set (VaspInputSet): for the static deformation calculations
vasp_cmd (str): vasp command to run.
db_file (str): path to the db file.
user_kpoints_settings (dict): example: {"grid_density": 7000}
eos (str): equation of state used for fitting the energies and the volumes.
supported equation of states: "quadratic", "murnaghan", "birch", "birch_murnaghan",
"pourier_tarantola", "vinet", "deltafactor". See pymatgen.analysis.eos.py
tag (str): something unique to identify the tasks in this workflow. If None a random uuid
will be assigned.
user_incar_settings (dict):
Returns:
Workflow
"""
tag = tag or "bulk_modulus group: >>{}<<".format(str(uuid4()))
deformations = [Deformation(defo_mat) for defo_mat in deformations]
vis_static = vasp_input_set or MPStaticSet(
structure=structure,
force_gamma=True,
lepsilon=False,
user_kpoints_settings=user_kpoints_settings,
user_incar_settings=user_incar_settings)
wf_bulk_modulus = get_wf_deformations(structure,
deformations,
name="bulk_modulus deformation",
vasp_input_set=vis_static,
vasp_cmd=vasp_cmd,
db_file=db_file,
tag=tag)
fw_analysis = Firework(FitEOSToDb(tag=tag, db_file=db_file, eos=eos),
name="fit equation of state")
wf_bulk_modulus.append_wf(Workflow.from_Firework(fw_analysis),
wf_bulk_modulus.leaf_fw_ids)
wf_bulk_modulus.name = "{}:{}".format(
structure.composition.reduced_formula, "Bulk modulus")
return wf_bulk_modulus
def get_wf_thermal_expansion(structure, deformations, vasp_input_set=None, vasp_cmd="vasp",
db_file=None, user_kpoints_settings=None, t_step=10, t_min=0,
t_max=1000, mesh=(20, 20, 20), eos="vinet", pressure=0.0,
copy_vasp_outputs=False,
tag=None):
"""
Returns quasi-harmonic thermal expansion workflow.
Note: phonopy package is required for the final analysis step.
Args:
structure (Structure): input structure.
deformations (list): list of deformation matrices(list of lists).
vasp_input_set (VaspInputSet)
vasp_cmd (str): vasp command to run.
db_file (str): path to the db file.
user_kpoints_settings (dict): example: {"grid_density": 7000}
t_step (float): temperature step (in K)
t_min (float): min temperature (in K)
t_max (float): max temperature (in K)
mesh (list/tuple): reciprocal space density
eos (str): equation of state used for fitting the energies and the volumes.
options supported by phonopy: "vinet", "murnaghan", "birch_murnaghan".
Note: pymatgen supports more options than phonopy. see pymatgen.analysis.eos.py
copy_vasp_outputs (bool): whether or not copy the outputs from the previous calc
(usually structure optimization) before the deformations are performed.
pressure (float): in GPa
tag (str): something unique to identify the tasks in this workflow. If None a random uuid
will be assigned.
Returns:
Workflow
"""
try:
from phonopy import Phonopy
except ImportError:
logger.warning("'phonopy' package NOT installed. Required for the final analysis step.")
tag = tag or "thermal_expansion group: >>{}<<".format(str(uuid4()))
deformations = [Deformation(defo_mat) for defo_mat in deformations]
vis_static = vasp_input_set or MPStaticSet(structure, force_gamma=True, lepsilon=True,
user_kpoints_settings=user_kpoints_settings)
wf_alpha = get_wf_deformations(structure, deformations, name="thermal_expansion deformation",
vasp_cmd=vasp_cmd, db_file=db_file, tag=tag,
copy_vasp_outputs=copy_vasp_outputs,
vasp_input_set=vis_static)
fw_analysis = Firework(ThermalExpansionCoeffToDb(tag=tag, db_file=db_file, t_step=t_step,
t_min=t_min, t_max=t_max, mesh=mesh, eos=eos,
pressure=pressure),
name="Thermal expansion")
wf_alpha.append_wf(Workflow.from_Firework(fw_analysis), wf_alpha.leaf_fw_ids)
wf_alpha.name = "{}:{}".format(structure.composition.reduced_formula, "thermal expansion")
return wf_alpha
def get_wf_gibbs_free_energy(structure, deformations, vasp_input_set=None, vasp_cmd="vasp",
db_file=None, user_kpoints_settings=None, t_step=10, t_min=0, t_max=1000,
mesh=(20, 20, 20), eos="vinet", qha_type="debye_model", pressure=0.0):
"""
Returns quasi-harmonic gibbs free energy workflow.
Note: phonopy package is required for the final analysis step if qha_type="phonopy"
Args:
structure (Structure): input structure.
deformations (list): list of deformation matrices(list of lists).
vasp_input_set (VaspInputSet)
vasp_cmd (str): vasp command to run.
db_file (str): path to the db file.
user_kpoints_settings (dict): example: {"grid_density": 7000}
t_step (float): temperature step (in K)
t_min (float): min temperature (in K)
t_max (float): max temperature (in K)
mesh (list/tuple): reciprocal space density
eos (str): equation of state used for fitting the energies and the volumes.
options supported by phonopy: "vinet", "murnaghan", "birch_murnaghan".
Note: pymatgen supports more options than phonopy. see pymatgen.analysis.eos.py
qha_type(str): quasi-harmonic approximation type: "debye_model" or "phonopy",
default is "debye_model"
pressure (float): in GPa
Returns:
Workflow
"""
lepsilon = False
if qha_type not in ["debye_model"]:
lepsilon = True
try:
from phonopy import Phonopy
except ImportError:
logger.warn("'phonopy' package NOT installed. Required for the final analysis step."
"The debye model for the quasi harmonic approximation will be used.")
qha_type = "debye_model"
lepsilon = False
tag = datetime.utcnow().strftime('%Y-%m-%d-%H-%M-%S-%f')
deformations = [Deformation(defo_mat) for defo_mat in deformations]
wf_gibbs = get_wf_deformations(structure, deformations, name="gibbs deformation",
vasp_input_set=vasp_input_set, lepsilon=lepsilon, vasp_cmd=vasp_cmd,
db_file=db_file, user_kpoints_settings=user_kpoints_settings,
tag=tag)
fw_analysis = Firework(GibbsFreeEnergyTask(tag=tag, db_file=db_file, t_step=t_step, t_min=t_min,
t_max=t_max, mesh=mesh, eos=eos, qha_type=qha_type,
pressure=pressure),
name="Gibbs Free Energy")
append_fw_wf(wf_gibbs, fw_analysis)
wf_gibbs.name = "{}:{}".format(structure.composition.reduced_formula, "gibbs free energy")
return wf_gibbs
def get_wf_thermal_expansion(structure, deformations, vasp_input_set=None, vasp_cmd="vasp",
db_file=None, user_kpoints_settings=None, t_step=10, t_min=0, t_max=1000,
mesh=(20, 20, 20), eos="vinet", pressure=0.0):
"""
Returns quasi-harmonic thermal expansion workflow.
Note: phonopy package is required for the final analysis step.
Args:
structure (Structure): input structure.
deformations (list): list of deformation matrices(list of lists).
vasp_input_set (VaspInputSet)
vasp_cmd (str): vasp command to run.
db_file (str): path to the db file.
user_kpoints_settings (dict): example: {"grid_density": 7000}
t_step (float): temperature step (in K)
t_min (float): min temperature (in K)
t_max (float): max temperature (in K)
mesh (list/tuple): reciprocal space density
eos (str): equation of state used for fitting the energies and the volumes.
options supported by phonopy: "vinet", "murnaghan", "birch_murnaghan".
Note: pymatgen supports more options than phonopy. see pymatgen.analysis.eos.py
pressure (float): in GPa
Returns:
Workflow
"""
try:
from phonopy import Phonopy
except ImportError:
logger.warn("'phonopy' package NOT installed. Required for the final analysis step.")
tag = datetime.utcnow().strftime('%Y-%m-%d-%H-%M-%S-%f')
deformations = [Deformation(defo_mat) for defo_mat in deformations]
wf_alpha = get_wf_deformations(structure, deformations, name="thermal_expansion deformation",
vasp_input_set=vasp_input_set, lepsilon=True, vasp_cmd=vasp_cmd,
db_file=db_file, user_kpoints_settings=user_kpoints_settings,
tag=tag)
fw_analysis = Firework(ThermalExpansionCoeffTask(tag=tag, db_file=db_file, t_step=t_step,
t_min=t_min, t_max=t_max, mesh=mesh, eos=eos,
pressure=pressure),
name="Thermal expansion")
append_fw_wf(wf_alpha, fw_analysis)
wf_alpha.name = "{}:{}".format(structure.composition.reduced_formula, "thermal expansion")
return wf_alpha
def get_wf_bulk_modulus(structure, deformations, vasp_input_set=None, vasp_cmd="vasp", db_file=None,
user_kpoints_settings=None, eos="vinet", tag=None, user_incar_settings=None):
"""
Returns the workflow that computes the bulk modulus by fitting to the given equation of state.
Args:
structure (Structure): input structure.
deformations (list): list of deformation matrices(list of lists).
vasp_input_set (VaspInputSet): for the static deformation calculations
vasp_cmd (str): vasp command to run.
db_file (str): path to the db file.
user_kpoints_settings (dict): example: {"grid_density": 7000}
eos (str): equation of state used for fitting the energies and the volumes.
supported equation of states: "quadratic", "murnaghan", "birch", "birch_murnaghan",
"pourier_tarantola", "vinet", "deltafactor". See pymatgen.analysis.eos.py
tag (str): something unique to identify the tasks in this workflow. If None a random uuid
will be assigned.
user_incar_settings (dict):
Returns:
Workflow
"""
tag = tag or "bulk_modulus group: >>{}<<".format(str(uuid4()))
deformations = [Deformation(defo_mat) for defo_mat in deformations]
vis_static = vasp_input_set or MPStaticSet(structure=structure, force_gamma=True, lepsilon=False,
user_kpoints_settings=user_kpoints_settings,
user_incar_settings=user_incar_settings)
wf_bulk_modulus = get_wf_deformations(structure, deformations, name="bulk_modulus deformation",
vasp_input_set=vis_static, vasp_cmd=vasp_cmd,
db_file=db_file, tag=tag)
fw_analysis = Firework(FitEOSToDb(tag=tag, db_file=db_file, eos=eos), name="fit equation of state")
wf_bulk_modulus.append_wf(Workflow.from_Firework(fw_analysis), wf_bulk_modulus.leaf_fw_ids)
wf_bulk_modulus.name = "{}:{}".format(structure.composition.reduced_formula, "Bulk modulus")
return wf_bulk_modulus
def get_wf_bulk_modulus(structure, deformations, vasp_input_set=None, vasp_cmd="vasp", db_file=None,
user_kpoints_settings=None, eos="vinet"):
"""
Returns the workflow that computes the bulk modulus by fitting to the given equation of state.
Args:
structure (Structure): input structure.
deformations (list): list of deformation matrices(list of lists).
vasp_input_set (VaspInputSet)
vasp_cmd (str): vasp command to run.
db_file (str): path to the db file.
user_kpoints_settings (dict): example: {"grid_density": 7000}
eos (str): equation of state used for fitting the energies and the volumes.
supported equation of states: "quadratic", "murnaghan", "birch", "birch_murnaghan",
"pourier_tarantola", "vinet", "deltafactor". See pymatgen.analysis.eos.py
Returns:
Workflow
"""
tag = datetime.utcnow().strftime('%Y-%m-%d-%H-%M-%S-%f')
deformations = [Deformation(defo_mat) for defo_mat in deformations]
wf_bulk_modulus = get_wf_deformations(structure, deformations, name="bulk_modulus deformation",
vasp_input_set=vasp_input_set, lepsilon=False,
vasp_cmd=vasp_cmd, db_file=db_file,
user_kpoints_settings=user_kpoints_settings, tag=tag)
fw_analysis = Firework(FitEquationOfStateTask(tag=tag, db_file=db_file, eos=eos),
name="fit equation of state")
append_fw_wf(wf_bulk_modulus, fw_analysis)
wf_bulk_modulus.name = "{}:{}".format(structure.composition.reduced_formula, "Bulk modulus")
return wf_bulk_modulus
def get_wf_gibbs_free_energy(structure, deformations, vasp_input_set=None, vasp_cmd="vasp",
db_file=None, user_kpoints_settings=None, t_step=10, t_min=0,
t_max=1000, mesh=(20, 20, 20), eos="vinet", qha_type="debye_model",
pressure=0.0, poisson=0.25, anharmonic_contribution=False,
metadata=None, tag=None):
"""
Returns quasi-harmonic gibbs free energy workflow.
Note: phonopy package is required for the final analysis step if qha_type="phonopy"
Args:
structure (Structure): input structure.
deformations (list): list of deformation matrices(list of lists).
vasp_input_set (VaspInputSet)
vasp_cmd (str): vasp command to run.
db_file (str): path to the db file.
user_kpoints_settings (dict): example: {"grid_density": 7000}
t_step (float): temperature step (in K)
t_min (float): min temperature (in K)
t_max (float): max temperature (in K)
mesh (list/tuple): reciprocal space density
eos (str): equation of state used for fitting the energies and the volumes.
options supported by phonopy: "vinet", "murnaghan", "birch_murnaghan".
Note: pymatgen supports more options than phonopy. see pymatgen.analysis.eos.py
qha_type(str): quasi-harmonic approximation type: "debye_model" or "phonopy",
default is "debye_model"
pressure (float): in GPa
poisson (float): poisson ratio
anharmonic_contribution (bool): consider anharmonic contributions to
Gibbs energy from the Debye model. Defaults to False.
metadata (dict): meta data
tag (str): something unique to identify the tasks in this workflow. If None a random uuid
will be assigned.
Returns:
Workflow
"""
tag = tag or "gibbs group: >>{}<<".format(str(uuid4()))
deformations = [Deformation(defo_mat) for defo_mat in deformations]
# static input set for the transmuter fireworks
vis_static = vasp_input_set
if vis_static is None:
lepsilon = False
if qha_type not in ["debye_model"]:
lepsilon = True
try:
from phonopy import Phonopy
except ImportError:
raise RuntimeError("'phonopy' package is NOT installed but is required for the final "
"analysis step; you can alternatively switch to the qha_type to "
"'debye_model' which does not require 'phonopy'.")
vis_static = MPStaticSet(structure, force_gamma=True, lepsilon=lepsilon,
user_kpoints_settings=user_kpoints_settings)
wf_gibbs = get_wf_deformations(structure, deformations, name="gibbs deformation",
vasp_cmd=vasp_cmd, db_file=db_file, tag=tag, metadata=metadata,
vasp_input_set=vis_static)
fw_analysis = Firework(GibbsAnalysisToDb(tag=tag, db_file=db_file, t_step=t_step, t_min=t_min,
t_max=t_max, mesh=mesh, eos=eos, qha_type=qha_type,
pressure=pressure, poisson=poisson, metadata=metadata,
anharmonic_contribution=anharmonic_contribution,),
name="Gibbs Free Energy")
wf_gibbs.append_wf(Workflow.from_Firework(fw_analysis), wf_gibbs.leaf_fw_ids)
wf_gibbs.name = "{}:{}".format(structure.composition.reduced_formula, "gibbs free energy")
return wf_gibbs
def get_wf_elastic_constant(structure,
metadata,
strain_states=None,
stencils=None,
db_file=None,
conventional=False,
order=2,
vasp_input_set=None,
analysis=True,
sym_reduce=False,
tag='elastic',
copy_vasp_outputs=False,
**kwargs):
"""
Returns a workflow to calculate elastic constants.
Firework 1 : write vasp input set for structural relaxation,
run vasp,
pass run location,
database insertion.
Firework 2 - number of total deformations: Static runs on the deformed structures
last Firework : Analyze Stress/Strain data and fit the elastic tensor
Args:
structure (Structure): input structure to be optimized and run.
strain_states (list of Voigt-notation strains): list of ratios of nonzero elements
of Voigt-notation strain, e. g. [(1, 0, 0, 0, 0, 0), (0, 1, 0, 0, 0, 0), etc.].
stencils (list of floats, or list of list of floats): values of strain to multiply
by for each strain state, i. e. stencil for the perturbation along the strain
state direction, e. g. [-0.01, -0.005, 0.005, 0.01]. If a list of lists,
stencils must correspond to each strain state provided.
db_file (str): path to file containing the database credentials.
conventional (bool): flag to convert input structure to conventional structure,
defaults to False.
order (int): order of the tensor expansion to be determined. Defaults to 2 and
currently supports up to 3.
vasp_input_set (VaspInputSet): vasp input set to be used. Defaults to static
set with ionic relaxation parameters set. Take care if replacing this,
default ensures that ionic relaxation is done and that stress is calculated
for each vasp run.
analysis (bool): flag to indicate whether analysis task should be added
and stresses and strains passed to that task
sym_reduce (bool): Whether or not to apply symmetry reductions
tag (str):
copy_vasp_outputs (bool): whether or not to copy previous vasp outputs.
kwargs (keyword arguments): additional kwargs to be passed to get_wf_deformations
Returns:
Workflow
"""
# Convert to conventional if specified
if conventional:
structure = SpacegroupAnalyzer(
structure).get_conventional_standard_structure()
uis_elastic = {
"IBRION": 2,
"NSW": 99,
"ISIF": 2,
"ISTART": 1,
"PREC": "High"
}
vis = vasp_input_set or MPStaticSet(structure,
user_incar_settings=uis_elastic)
strains = []
if strain_states is None:
strain_states = get_default_strain_states(order)
if stencils is None:
stencils = [np.linspace(-0.01, 0.01, 5 +
(order - 2) * 2)] * len(strain_states)
if np.array(stencils).ndim == 1:
stencils = [stencils] * len(strain_states)
for state, stencil in zip(strain_states, stencils):
strains.extend(
[Strain.from_voigt(s * np.array(state)) for s in stencil])
# Remove zero strains
strains = [strain for strain in strains if not (abs(strain) < 1e-10).all()]
# Adding the zero strains for the purpose of calculating at finite pressure or thermal expansion
_strains = [Strain.from_deformation([[1, 0, 0], [0, 1, 0], [0, 0, 1]])]
strains.extend(_strains)
"""
"""
vstrains = [strain.voigt for strain in strains]
if np.linalg.matrix_rank(vstrains) < 6:
# TODO: check for sufficiency of input for nth order
raise ValueError(
"Strain list is insufficient to fit an elastic tensor")
deformations = [s.get_deformation_matrix() for s in strains]
"""
print(strains)
print(deformations)
"""
if sym_reduce:
# Note this casts deformations to a TensorMapping
# with unique deformations as keys to symmops
deformations = symmetry_reduce(deformations, structure)
wf_elastic = get_wf_deformations(structure,
deformations,
tag=tag,
db_file=db_file,
vasp_input_set=vis,
copy_vasp_outputs=copy_vasp_outputs,
**kwargs)
if analysis:
defo_fws_and_tasks = get_fws_and_tasks(
wf_elastic,
fw_name_constraint="deformation",
task_name_constraint="Transmuted")
for idx_fw, idx_t in defo_fws_and_tasks:
defo = \
wf_elastic.fws[idx_fw].tasks[idx_t]['transformation_params'][0][
'deformation']
pass_dict = {
'strain': Deformation(defo).green_lagrange_strain.tolist(),
'stress': '>>output.ionic_steps.-1.stress',
'deformation_matrix': defo
}
if sym_reduce:
pass_dict.update({'symmops': deformations[defo]})
mod_spec_key = "deformation_tasks->{}".format(idx_fw)
pass_task = pass_vasp_result(pass_dict=pass_dict,
mod_spec_key=mod_spec_key)
wf_elastic.fws[idx_fw].tasks.append(pass_task)
fw_analysis = Firework(ElasticTensorToDb(structure=structure,
db_file=db_file,
order=order,
fw_spec_field='tags',
metadata=metadata,
vasp_input_set=vis),
name="Analyze Elastic Data",
spec={"_allow_fizzled_parents": True})
wf_elastic.append_wf(Workflow.from_Firework(fw_analysis),
wf_elastic.leaf_fw_ids)
wf_elastic.name = "{}:{}".format(structure.composition.reduced_formula,
"elastic constants")
return wf_elastic
def get_wf_elastic_constant(structure, strain_states=None, stencils=None,
db_file=None,
conventional=False, order=2, vasp_input_set=None,
analysis=True,
sym_reduce=False, tag='elastic',
copy_vasp_outputs=False, **kwargs):
"""
Returns a workflow to calculate elastic constants.
Firework 1 : write vasp input set for structural relaxation,
run vasp,
pass run location,
database insertion.
Firework 2 - number of total deformations: Static runs on the deformed structures
last Firework : Analyze Stress/Strain data and fit the elastic tensor
Args:
structure (Structure): input structure to be optimized and run.
strain_states (list of Voigt-notation strains): list of ratios of nonzero elements
of Voigt-notation strain, e. g. [(1, 0, 0, 0, 0, 0), (0, 1, 0, 0, 0, 0), etc.].
stencils (list of floats, or list of list of floats): values of strain to multiply
by for each strain state, i. e. stencil for the perturbation along the strain
state direction, e. g. [-0.01, -0.005, 0.005, 0.01]. If a list of lists,
stencils must correspond to each strain state provided.
db_file (str): path to file containing the database credentials.
conventional (bool): flag to convert input structure to conventional structure,
defaults to False.
order (int): order of the tensor expansion to be determined. Defaults to 2 and
currently supports up to 3.
vasp_input_set (VaspInputSet): vasp input set to be used. Defaults to static
set with ionic relaxation parameters set. Take care if replacing this,
default ensures that ionic relaxation is done and that stress is calculated
for each vasp run.
analysis (bool): flag to indicate whether analysis task should be added
and stresses and strains passed to that task
sym_reduce (bool): Whether or not to apply symmetry reductions
tag (str):
copy_vasp_outputs (bool): whether or not to copy previous vasp outputs.
kwargs (keyword arguments): additional kwargs to be passed to get_wf_deformations
Returns:
Workflow
"""
# Convert to conventional if specified
if conventional:
structure = SpacegroupAnalyzer(
structure).get_conventional_standard_structure()
uis_elastic = {"IBRION": 2, "NSW": 99, "ISIF": 2, "ISTART": 1,
"PREC": "High"}
vis = vasp_input_set or MPStaticSet(structure,
user_incar_settings=uis_elastic)
strains = []
if strain_states is None:
strain_states = get_default_strain_states(order)
if stencils is None:
stencils = [np.linspace(-0.01, 0.01, 5 + (order - 2) * 2)] * len(
strain_states)
if np.array(stencils).ndim == 1:
stencils = [stencils] * len(strain_states)
for state, stencil in zip(strain_states, stencils):
strains.extend(
[Strain.from_voigt(s * np.array(state)) for s in stencil])
# Remove zero strains
strains = [strain for strain in strains if not (abs(strain) < 1e-10).all()]
vstrains = [strain.voigt for strain in strains]
if np.linalg.matrix_rank(vstrains) < 6:
# TODO: check for sufficiency of input for nth order
raise ValueError("Strain list is insufficient to fit an elastic tensor")
deformations = [s.get_deformation_matrix() for s in strains]
if sym_reduce:
# Note this casts deformations to a TensorMapping
# with unique deformations as keys to symmops
deformations = symmetry_reduce(deformations, structure)
wf_elastic = get_wf_deformations(structure, deformations, tag=tag,
db_file=db_file,
vasp_input_set=vis,
copy_vasp_outputs=copy_vasp_outputs,
**kwargs)
if analysis:
defo_fws_and_tasks = get_fws_and_tasks(wf_elastic,
fw_name_constraint="deformation",
task_name_constraint="Transmuted")
for idx_fw, idx_t in defo_fws_and_tasks:
defo = \
wf_elastic.fws[idx_fw].tasks[idx_t]['transformation_params'][0][
'deformation']
pass_dict = {
'strain': Deformation(defo).green_lagrange_strain.tolist(),
'stress': '>>output.ionic_steps.-1.stress',
'deformation_matrix': defo}
if sym_reduce:
pass_dict.update({'symmops': deformations[defo]})
mod_spec_key = "deformation_tasks->{}".format(idx_fw)
pass_task = pass_vasp_result(pass_dict=pass_dict,
mod_spec_key=mod_spec_key)
wf_elastic.fws[idx_fw].tasks.append(pass_task)
fw_analysis = Firework(
ElasticTensorToDb(structure=structure, db_file=db_file,
order=order, fw_spec_field='tags'),
name="Analyze Elastic Data", spec={"_allow_fizzled_parents": True})
wf_elastic.append_wf(Workflow.from_Firework(fw_analysis),
wf_elastic.leaf_fw_ids)
wf_elastic.name = "{}:{}".format(structure.composition.reduced_formula,
"elastic constants")
return wf_elastic
def get_wf_gibbs_free_energy(structure, deformations, vasp_input_set=None, vasp_cmd="vasp",
db_file=None, user_kpoints_settings=None, t_step=10, t_min=0,
t_max=1000, mesh=(20, 20, 20), eos="vinet", qha_type="debye_model",
pressure=0.0, poisson=0.25, anharmonic_contribution=False,
metadata=None, tag=None):
"""
Returns quasi-harmonic gibbs free energy workflow.
Note: phonopy package is required for the final analysis step if qha_type="phonopy"
Args:
structure (Structure): input structure.
deformations (list): list of deformation matrices(list of lists).
vasp_input_set (VaspInputSet)
vasp_cmd (str): vasp command to run.
db_file (str): path to the db file.
user_kpoints_settings (dict): example: {"grid_density": 7000}
t_step (float): temperature step (in K)
t_min (float): min temperature (in K)
t_max (float): max temperature (in K)
mesh (list/tuple): reciprocal space density
eos (str): equation of state used for fitting the energies and the volumes.
options supported by phonopy: "vinet", "murnaghan", "birch_murnaghan".
Note: pymatgen supports more options than phonopy. see pymatgen.analysis.eos.py
qha_type(str): quasi-harmonic approximation type: "debye_model" or "phonopy",
default is "debye_model"
pressure (float): in GPa
poisson (float): poisson ratio
anharmonic_contribution (bool): consider anharmonic contributions to
Gibbs energy from the Debye model. Defaults to False.
metadata (dict): meta data
tag (str): something unique to identify the tasks in this workflow. If None a random uuid
will be assigned.
Returns:
Workflow
"""
tag = tag or "gibbs group: >>{}<<".format(str(uuid4()))
deformations = [Deformation(defo_mat) for defo_mat in deformations]
# static input set for the transmuter fireworks
vis_static = vasp_input_set
if vis_static is None:
lepsilon = False
if qha_type not in ["debye_model"]:
lepsilon = True
try:
from phonopy import Phonopy
except ImportError:
raise RuntimeError("'phonopy' package is NOT installed but is required for the final "
"analysis step; you can alternatively switch to the qha_type to "
"'debye_model' which does not require 'phonopy'.")
vis_static = MPStaticSet(structure, force_gamma=True, lepsilon=lepsilon,
user_kpoints_settings=user_kpoints_settings)
wf_gibbs = get_wf_deformations(structure, deformations, name="gibbs deformation",
vasp_cmd=vasp_cmd, db_file=db_file, tag=tag, metadata=metadata,
vasp_input_set=vis_static)
fw_analysis = Firework(GibbsAnalysisToDb(tag=tag, db_file=db_file, t_step=t_step, t_min=t_min,
t_max=t_max, mesh=mesh, eos=eos, qha_type=qha_type,
pressure=pressure, poisson=poisson, metadata=metadata,
anharmonic_contribution=anharmonic_contribution,),
name="Gibbs Free Energy")
wf_gibbs.append_wf(Workflow.from_Firework(fw_analysis), wf_gibbs.leaf_fw_ids)
wf_gibbs.name = "{}:{}".format(structure.composition.reduced_formula, "gibbs free energy")
return wf_gibbs
def get_wf_elastic_constant(
structure,
vasp_input_set=None,
vasp_cmd="vasp",
norm_deformations=None,
shear_deformations=None,
additional_deformations=None,
db_file=None,
user_kpoints_settings=None,
add_analysis_task=True,
conventional=True,
):
"""
Returns a workflow to calculate elastic constants.
Firework 1 : write vasp input set for structural relaxation,
run vasp,
pass run location,
database insertion.
Firework 2 - number of total deformations: Static runs on the deformed structures
last Firework : Analyze Stress/Strain data and fit the elastic tensor
Args:
structure (Structure): input structure to be optimized and run.
norm_deformations (list): list of values to for normal deformations.
shear_deformations (list): list of values to for shear deformations.
additional_deformations (list of 3x3 array-likes): list of additional deformations.
vasp_input_set (DictVaspInputSet): vasp input set.
vasp_cmd (str): command to run.
db_file (str): path to file containing the database credentials.
user_kpoints_settings (dict): example: {"grid_density": 7000}
add_analysis_task (bool): boolean indicating whether to add analysis
Returns:
Workflow
"""
# Convert to conventional
if conventional:
structure = SpacegroupAnalyzer(structure).get_conventional_standard_structure()
# Generate deformations
deformations = []
if norm_deformations is not None:
deformations.extend(
[
Deformation.from_index_amount(ind, amount)
for ind in [(0, 0), (1, 1), (2, 2)]
for amount in norm_deformations
]
)
if shear_deformations is not None:
deformations.extend(
[
Deformation.from_index_amount(ind, amount)
for ind in [(0, 1), (0, 2), (1, 2)]
for amount in shear_deformations
]
)
if additional_deformations:
deformations.extend([Deformation(defo_mat) for defo_mat in additional_deformations])
if not deformations:
raise ValueError("deformations list empty")
wf_elastic = get_wf_deformations(
structure,
deformations,
vasp_input_set=vasp_input_set,
lepsilon=False,
vasp_cmd=vasp_cmd,
db_file=db_file,
user_kpoints_settings=user_kpoints_settings,
pass_stress_strain=True,
name="deformation",
relax_deformed=True,
tag="elastic",
)
if add_analysis_task:
fw_analysis = Firework(
ElasticTensorToDbTask(structure=structure, db_file=db_file),
name="Analyze Elastic Data",
spec={"_allow_fizzled_parents": True},
)
append_fw_wf(wf_elastic, fw_analysis)
wf_elastic.name = "{}:{}".format(structure.composition.reduced_formula, "elastic constants")
return wf_elastic
