def setUp(self):
super().setUp()
self.tf_loc = os.path.join(ref_dir, "elastic_wf")
self.struct_si = PymatgenTest.get_structure("Si")
self.struct_si = SpacegroupAnalyzer(
self.struct_si
).get_conventional_standard_structure()
self.opt_struct = Structure.from_file(
os.path.join(self.tf_loc, "1", "inputs", "POSCAR")
)
# Base WF
self.base_wf = get_wf(
self.struct_si, "optimize_only.yaml", params=[{"db_file": ">>db_file<<"}]
)
self.base_wf.append_wf(
get_wf_elastic_constant(
self.struct_si,
db_file=">>db_file<<",
stencils=[[0.01]] * 3 + [[0.03]] * 3,
copy_vasp_outputs=True,
),
self.base_wf.leaf_fw_ids,
)
self.base_wf_noopt = get_wf_elastic_constant(
self.opt_struct,
stencils=[[0.01]] * 3 + [[0.03]] * 3,
copy_vasp_outputs=False,
sym_reduce=False,
db_file=">>db_file<<",
)
ec_incar_update = {"incar_update": {"EDIFF": 1e-6, "ENCUT": 700}}
self.base_wf = add_modify_incar(self.base_wf, ec_incar_update)
self.base_wf_noopt = add_modify_incar(self.base_wf_noopt, ec_incar_update)
# Full preset WF
self.preset_wf = wf_elastic_constant(self.struct_si)
# Minimal WF
self.minimal_wf = wf_elastic_constant_minimal(self.opt_struct)
self.minimal_wf = add_modify_incar(self.minimal_wf, ec_incar_update)
# TOEC WF (minimal)
self.toec_wf = wf_elastic_constant_minimal(self.struct_si, order=3)
self.toec_wf = add_modify_incar(self.toec_wf, ec_incar_update)
toec_data = loadfn(os.path.join(self.tf_loc, "toec_data.json"))
# Rather than run entire workflow, preload the spec to test the analysis
toec_analysis = Firework(
[
ElasticTensorToDb(
structure=self.struct_si, order=3, db_file=">>db_file<<"
)
],
spec={"deformation_tasks": toec_data["deformation_tasks"]},
)
self.toec_analysis = Workflow([toec_analysis])
# Check 4th order to see if constructed correctly
self.foec_wf = wf_elastic_constant_minimal(self.struct_si, order=4)
def setUp(self):
super(TestElasticWorkflow, self).setUp()
self.tf_loc = os.path.join(ref_dir, 'elastic_wf')
self.struct_si = PymatgenTest.get_structure("Si")
self.struct_si = SpacegroupAnalyzer(
self.struct_si).get_conventional_standard_structure()
self.opt_struct = Structure.from_file(
os.path.join(self.tf_loc, '1', 'inputs', 'POSCAR'))
# Base WF
self.base_wf = get_wf(self.struct_si,
"optimize_only.yaml",
params=[{
"db_file": ">>db_file<<"
}])
self.base_wf.append_wf(
get_wf_elastic_constant(self.struct_si,
db_file='>>db_file<<',
stencils=[[0.01]] * 3 + [[0.03]] * 3,
copy_vasp_outputs=True),
self.base_wf.leaf_fw_ids)
self.base_wf_noopt = get_wf_elastic_constant(self.opt_struct,
stencils=[[0.01]] * 3 +
[[0.03]] * 3,
copy_vasp_outputs=False,
sym_reduce=False,
db_file='>>db_file<<')
ec_incar_update = {'incar_update': {'EDIFF': 1e-6, 'ENCUT': 700}}
self.base_wf = add_modify_incar(self.base_wf, ec_incar_update)
self.base_wf_noopt = add_modify_incar(self.base_wf_noopt,
ec_incar_update)
# Full preset WF
self.preset_wf = wf_elastic_constant(self.struct_si)
# Minimal WF
self.minimal_wf = wf_elastic_constant_minimal(self.opt_struct)
self.minimal_wf = add_modify_incar(self.minimal_wf, ec_incar_update)
# TOEC WF (minimal)
self.toec_wf = wf_elastic_constant_minimal(self.struct_si, order=3)
self.toec_wf = add_modify_incar(self.toec_wf, ec_incar_update)
toec_data = loadfn(os.path.join(self.tf_loc, 'toec_data.json'))
# Rather than run entire workflow, preload the spec to test the analysis
toec_analysis = Firework(
[
ElasticTensorToDb(
structure=self.struct_si, order=3, db_file=">>db_file<<")
],
spec={"deformation_tasks": toec_data['deformation_tasks']})
self.toec_analysis = Workflow([toec_analysis])
def setUp(self):
super(TestElasticWorkflow, self).setUp()
self.tf_loc = os.path.join(ref_dir, 'elastic_wf')
self.struct_si = PymatgenTest.get_structure("Si")
self.struct_si = SpacegroupAnalyzer(self.struct_si).get_conventional_standard_structure()
self.opt_struct = Structure.from_file(os.path.join(self.tf_loc, '1', 'inputs', 'POSCAR'))
# Base WF
self.base_wf = get_wf(self.struct_si, "optimize_only.yaml",
params=[{"db_file": ">>db_file<<"}])
self.base_wf.append_wf(get_wf_elastic_constant(self.struct_si, db_file='>>db_file<<',
stencils=[[0.01]]*3 + [[0.03]]*3,
copy_vasp_outputs=True),
self.base_wf.leaf_fw_ids)
self.base_wf_noopt = get_wf_elastic_constant(self.opt_struct, stencils=[[0.01]]*3 + [[0.03]]*3,
copy_vasp_outputs=False, sym_reduce=False,
db_file='>>db_file<<')
ec_incar_update = {'incar_update': {'EDIFF': 1e-6, 'ENCUT': 700}}
self.base_wf = add_modify_incar(self.base_wf, ec_incar_update)
self.base_wf_noopt = add_modify_incar(self.base_wf_noopt, ec_incar_update)
# Full preset WF
self.preset_wf = wf_elastic_constant(self.struct_si)
# Minimal WF
self.minimal_wf = wf_elastic_constant_minimal(self.opt_struct)
self.minimal_wf = add_modify_incar(self.minimal_wf, ec_incar_update)
# TOEC WF (minimal)
self.toec_wf = wf_elastic_constant_minimal(self.struct_si, order=3)
self.toec_wf = add_modify_incar(self.toec_wf, ec_incar_update)
toec_data = loadfn(os.path.join(self.tf_loc, 'toec_data.json'))
# Rather than run entire workflow, preload the spec to test the analysis
toec_analysis = Firework([ElasticTensorToDb(structure=self.struct_si, order=3,
db_file=">>db_file<<")],
spec={"deformation_tasks": toec_data['deformation_tasks']})
self.toec_analysis = Workflow([toec_analysis])
# Check 4th order to see if constructed correctly
self.foec_wf = wf_elastic_constant_minimal(self.struct_si, order=4)
def wf_elastic_constant_minimal(structure, c=None, order=2, sym_reduce=True):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
stencil = np.arange(0.01, 0.01 * order, step=0.01)
wf = get_wf_elastic_constant(structure, vasp_cmd=vasp_cmd, db_file=db_file,
sym_reduce=sym_reduce, stencils=stencil, order=order,
copy_vasp_outputs=False)
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def wf_elastic_constant(structure, c=None, order=2, sym_reduce=False):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
uis_optimize = {"ENCUT": 700, "EDIFF": 1e-6, "LAECHG": False}
if order > 2:
uis_optimize.update({"EDIFF": 1e-10, "EDIFFG": -0.001,
"ADDGRID": True, "LREAL": False, "ISYM": 0})
# This ensures a consistent k-point mesh across all calculations
# We also turn off symmetry to prevent VASP from changing the
# mesh internally
kpts_settings = Kpoints.automatic_density(structure, 40000, force_gamma=True)
stencils = np.linspace(-0.075, 0.075, 7)
else:
kpts_settings = {'grid_density': 7000}
stencils = None
uis_static = uis_optimize.copy()
uis_static.update({'ISIF': 2, 'IBRION': 2, 'NSW': 99, 'ISTART': 1, "PREC": "High"})
# input set for structure optimization
vis_relax = MPRelaxSet(structure, force_gamma=True, user_incar_settings=uis_optimize,
user_kpoints_settings=kpts_settings)
# optimization only workflow
wf = get_wf(structure, "optimize_only.yaml", vis=vis_relax,
params=[{"vasp_cmd": vasp_cmd, "db_file": db_file,
"name": "elastic structure optimization"}])
vis_static = MPStaticSet(structure, force_gamma=True, lepsilon=False,
user_kpoints_settings=kpts_settings,
user_incar_settings=uis_static)
# deformations wflow for elasticity calculation
wf_elastic = get_wf_elastic_constant(structure, vasp_cmd=vasp_cmd, db_file=db_file,
order=order, stencils=stencils, copy_vasp_outputs=True,
vasp_input_set=vis_static, sym_reduce=sym_reduce)
wf.append_wf(wf_elastic, wf.leaf_fw_ids)
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def wf_elastic_constant(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
user_kpoints_settings = c.get("user_kpoints_settings", {"grid_density": 7000})
norm_deformations = c.get("norm_deformations", [-0.01, -0.005, 0.005, 0.01])
shear_deformations = c.get("shear_deformations", [-0.06, -0.03, 0.03, 0.06])
wf = get_wf_elastic_constant(structure, vasp_cmd=vasp_cmd,
norm_deformations=norm_deformations,
shear_deformations=shear_deformations,
db_file=db_file, user_kpoints_settings=user_kpoints_settings)
mip = {"incar_update":{"ENCUT": 700, "EDIFF": 1e-6, "LAECHG":False}}
wf = add_modify_incar(wf, modify_incar_params=mip)
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
