def setUp(self):
self.norm_defo = Deformation.from_index_amount((0, 0), 0.02)
self.ind_defo = Deformation.from_index_amount((0, 1), 0.02)
self.non_ind_defo = Deformation([[1.0, 0.02, 0.02], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]])
lattice = Lattice(
[[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]
)
self.structure = Structure(lattice, ["Si", "Si"], [[0, 0, 0], [0.75, 0.5, 0.75]])
def setUp(self):
self.norm_defo = Deformation.from_index_amount((0, 0), 0.02)
self.ind_defo = Deformation.from_index_amount((0, 1), 0.02)
self.non_ind_defo = Deformation([[1.0, 0.02, 0.02], [0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]])
lattice = Lattice([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]])
self.structure = Structure(lattice, ["Si", "Si"],
[[0, 0, 0], [0.75, 0.5, 0.75]])
def test_properties(self):
# mean_stress
self.assertEqual(
self.rand_stress.mean_stress,
1. / 3. * (self.rand_stress[0, 0] + self.rand_stress[1, 1] +
self.rand_stress[2, 2]))
self.assertAlmostEqual(self.symm_stress.mean_stress, 3.66)
# deviator_stress
self.assertArrayAlmostEqual(
self.symm_stress.deviator_stress,
Stress([[-3.15, 2.29, 2.42], [2.29, 1.48, 5.07],
[2.42, 5.07, 1.67]]))
self.assertArrayAlmostEqual(
self.non_symm.deviator_stress,
[[-0.2666666667, 0.2, 0.3], [0.4, 0.133333333, 0.6],
[0.2, 0.5, 0.133333333]])
# deviator_principal_invariants
self.assertArrayAlmostEqual(self.symm_stress.dev_principal_invariants,
[0, 44.2563, 111.953628])
# von_mises
self.assertAlmostEqual(self.symm_stress.von_mises, 11.52253878275)
# piola_kirchoff 1, 2
f = Deformation.from_index_amount((0, 1), 0.03)
self.assertArrayAlmostEqual(
self.symm_stress.piola_kirchoff_1(f),
[[0.4413, 2.29, 2.42], [2.1358, 5.14, 5.07], [2.2679, 5.07, 5.33]])
self.assertArrayAlmostEqual(
self.symm_stress.piola_kirchoff_2(f),
[[0.377226, 2.1358, 2.2679], [2.1358, 5.14, 5.07],
[2.2679, 5.07, 5.33]])
# voigt
self.assertArrayEqual(self.symm_stress.voigt,
[0.51, 5.14, 5.33, 5.07, 2.42, 2.29])
with self.assertRaises(ValueError):
self.non_symm.voigt
def test_properties(self):
# mean_stress
self.assertEqual(self.rand_stress.mean_stress,
1. / 3. * (self.rand_stress[0, 0] +
self.rand_stress[1, 1] +
self.rand_stress[2, 2]))
self.assertAlmostEqual(self.symm_stress.mean_stress, 3.66)
# deviator_stress
self.assertArrayAlmostEqual(self.symm_stress.deviator_stress,
Stress([[-3.15, 2.29, 2.42],
[2.29, 1.48, 5.07],
[2.42, 5.07, 1.67]]))
self.assertArrayAlmostEqual(self.non_symm.deviator_stress,
[[-0.2666666667, 0.2, 0.3],
[0.4, 0.133333333, 0.6],
[0.2, 0.5, 0.133333333]])
# deviator_principal_invariants
self.assertArrayAlmostEqual(self.symm_stress.dev_principal_invariants,
[0, 44.2563, 111.953628])
# von_mises
self.assertAlmostEqual(self.symm_stress.von_mises,
11.52253878275)
# piola_kirchoff 1, 2
f = Deformation.from_index_amount((0, 1), 0.03)
self.assertArrayAlmostEqual(self.symm_stress.piola_kirchoff_1(f),
[[0.4413, 2.29, 2.42],
[2.1358, 5.14, 5.07],
[2.2679, 5.07, 5.33]])
self.assertArrayAlmostEqual(self.symm_stress.piola_kirchoff_2(f),
[[0.377226, 2.1358, 2.2679],
[2.1358, 5.14, 5.07],
[2.2679, 5.07, 5.33]])
# voigt
self.assertArrayEqual(self.symm_stress.voigt,
[0.51, 5.14, 5.33, 5.07, 2.42, 2.29])
def test_convert_strain_to_deformation(self):
defo = Deformation.from_index_amount((1, 2), 0.01)
pass
def get_wf_elastic_constant(structure, vasp_input_set=None, vasp_cmd="vasp",
norm_deformations=[-0.01, -0.005, 0.005, 0.01],
shear_deformations=[-0.06, -0.03, 0.03, 0.06],
db_file=None, reciprocal_density=None):
"""
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 - 25: Optimize Deformed Structure
Firework 26: 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
vasp_input_set (DictVaspInputSet): vasp input set.
vasp_cmd (str): command to run
db_file (str): path to file containing the database credentials.
reciprocal_density (int): k-points per reciprocal atom by volume
Returns:
Workflow
"""
v = vasp_input_set or MPRelaxSet(structure, force_gamma=True)
if reciprocal_density:
v.config_dict["KPOINTS"].update(
{"reciprocal_density":reciprocal_density})
v = DictSet(structure, v.config_dict)
fws = []
fws.append(OptimizeFW(structure=structure,
vasp_input_set=v,
vasp_cmd=vasp_cmd,
db_file=db_file))
deformations = []
# Generate deformations
for ind in [(0, 0), (1, 1), (2, 2)]:
for amount in norm_deformations:
defo = Deformation.from_index_amount(ind, amount)
deformations.append(defo)
for ind in [(0, 1), (0, 2), (1, 2)]:
for amount in shear_deformations:
defo = Deformation.from_index_amount(ind, amount)
deformations.append(defo)
def_vasp_params = {"user_incar_settings":{"ISIF":2, "IBRION":2,
"NSW":99, "LAECHG":False,
"LHVAR":False, "ALGO":"Fast",
"LWAVE":False}}
if reciprocal_density:
def_vasp_params.update(
{"reciprocal_density":reciprocal_density})
for deformation in deformations:
fw = TransmuterFW(name="elastic deformation",
structure=structure,
transformations=['DeformStructureTransformation'],
transformation_params=[
{"deformation": deformation.tolist()}],
copy_vasp_outputs=True,
db_file=db_file,
vasp_cmd=vasp_cmd,
parents=fws[0],
vasp_input_params = def_vasp_params
)
fw.spec['_tasks'].append(
PassStressStrainData(deformation=deformation.tolist()).to_dict())
fws.append(fw)
fws.append(Firework(AnalyzeStressStrainData(structure=structure,
db_file=db_file),
name="Analyze Elastic Data", parents=fws[1:],
spec = {"_allow_fizzled_parents":True}))
wfname = "{}:{}".format(structure.composition.reduced_formula,
"elastic constants")
return Workflow(fws, name=wfname)
def test_convert_strain_to_deformation(self):
defo = Deformation.from_index_amount((1, 2), 0.01)
pass
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
