def generate_elastic_workflow(structure, tags=None):
"""
Generates a standard production workflow.
Notes:
Uses a primitive structure transformed into
the conventional basis (for equivalent deformations).
Adds the "minimal" category to the minimal portion
of the workflow necessary to generate the elastic tensor,
and the "minimal_full_stencil" category to the portion that
includes all of the strain stencil, but is symmetrically complete
"""
if tags == None:
tags = []
# transform the structure
ieee_rot = Tensor.get_ieee_rotation(structure)
if not SquareTensor(ieee_rot).is_rotation(tol=0.005):
raise ValueError(
"Rotation matrix does not satisfy rotation conditions")
symm_op = SymmOp.from_rotation_and_translation(ieee_rot)
ieee_structure = structure.copy()
ieee_structure.apply_operation(symm_op)
# construct workflow
wf = wf_elastic_constant(ieee_structure)
# Set categories, starting with optimization
opt_fws = get_fws_and_tasks(wf, fw_name_constraint="optimization")
wf.fws[opt_fws[0][0]].spec['elastic_category'] = "minimal"
# find minimal set of fireworks using symmetry reduction
fws_by_strain = {
Strain(fw.tasks[-1]['pass_dict']['strain']): n
for n, fw in enumerate(wf.fws) if 'deformation' in fw.name
}
unique_tensors = symmetry_reduce(list(fws_by_strain.keys()),
ieee_structure)
for unique_tensor in unique_tensors:
fw_index = get_tkd_value(fws_by_strain, unique_tensor)
if np.isclose(unique_tensor, 0.005).any():
wf.fws[fw_index].spec['elastic_category'] = "minimal"
else:
wf.fws[fw_index].spec['elastic_category'] = "minimal_full_stencil"
# Add tags
if tags:
wf = add_tags(wf, tags)
wf = add_modify_incar(wf)
priority = 500 - structure.num_sites
wf = add_priority(wf, priority)
for fw in wf.fws:
if fw.spec.get('elastic_category') == 'minimal':
fw.spec['_priority'] += 2000
elif fw.spec.get('elastic_category') == 'minimal_full_stencil':
fw.spec['_priority'] += 1000
return wf
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 setUpClass(cls):
if not SETTINGS.get("VASP_PSP_DIR"):
SETTINGS["VASP_PSP_DIR"] = os.path.join(module_dir, "..", "..", "tests", "reference_files")
print('This system is not set up to run VASP jobs. '
'Please set VASP_PSP_DIR variable in your ~/.pmgrc.yaml file.')
cls.struct_si = SpacegroupAnalyzer(
PymatgenTest.get_structure("Si")).get_conventional_standard_structure()
cls.scratch_dir = os.path.join(module_dir, "scratch")
cls.elastic_config = {"norm_deformations":[0.01],
"shear_deformations":[0.03],
"vasp_cmd": ">>vasp_cmd<<", "db_file": ">>db_file<<"}
cls.wf = wf_elastic_constant(cls.struct_si, cls.elastic_config)
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)