def test_append_fw(self):
fw_new = Firework(Task1())
fws = [self.fw1, self.fw2, self.fw3]
wflow = Workflow(fws)
leaf_ids = wflow.leaf_fw_ids
append_fw_wf(wflow, fw_new)
new_lead_ids = wflow.leaf_fw_ids
for i in leaf_ids:
self.assertEqual(wflow.links[i], [new_lead_ids[0]])
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"):
"""
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_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
