def snl_to_wf_elastic(snl, parameters):
# parameters["user_vasp_settings"] specifies user defined incar/kpoints parameters
fws = []
connections = defaultdict(list)
parameters = parameters if parameters else {}
snl_priority = parameters.get('priority', 1)
priority = snl_priority * 2 # once we start a job, keep going!
f = Composition(snl.structure.composition.reduced_formula).alphabetical_formula
# add the SNL to the SNL DB and figure out duplicate group
tasks = [AddSNLTask()]
spec = {'task_type': 'Add to SNL database', 'snl': snl.as_dict(),
'_queueadapter': QA_DB, '_priority': snl_priority}
if 'snlgroup_id' in parameters and isinstance(snl, MPStructureNL):
spec['force_mpsnl'] = snl.as_dict()
spec['force_snlgroup_id'] = parameters['snlgroup_id']
del spec['snl']
fws.append(Firework(tasks, spec,
name=get_slug(f + '--' + spec['task_type']), fw_id=0))
connections[0] = [1]
parameters["exact_structure"] = True
# run GGA structure optimization for force convergence
spec = snl_to_wf._snl_to_spec(snl, parameters=parameters)
user_vasp_settings = parameters.get("user_vasp_settings")
spec = update_spec_force_convergence(spec, user_vasp_settings)
spec['run_tags'].append("origin")
spec['_priority'] = priority
spec['_queueadapter'] = QA_VASP
del spec['_dupefinder']
spec['task_type'] = "Vasp force convergence optimize structure (2x)"
tasks = [VaspWriterTask(), get_custodian_task(spec)]
fws.append(Firework(tasks, spec,
name=get_slug(f + '--' + spec['task_type']), fw_id=1))
# insert into DB - GGA structure optimization
spec = {'task_type': 'VASP db insertion', '_priority': priority,
'_allow_fizzled_parents': True, '_queueadapter': QA_DB,
'clean_task_doc':True, 'elastic_constant':"force_convergence"}
fws.append(Firework([VaspToDBTask()], spec,
name=get_slug(f + '--' + spec['task_type']), fw_id=2))
connections[1] = [2]
spec = {'task_type': 'Setup Deformed Struct Task', '_priority': priority,
'_queueadapter': QA_CONTROL}
fws.append(Firework([SetupDeformedStructTask()], spec,
name=get_slug(f + '--' + spec['task_type']),fw_id=3))
connections[2] = [3]
wf_meta = get_meta_from_structure(snl.structure)
wf_meta['run_version'] = 'May 2013 (1)'
if '_materialsproject' in snl.data and 'submission_id' in snl.data['_materialsproject']:
wf_meta['submission_id'] = snl.data['_materialsproject']['submission_id']
return Workflow(fws, connections, name=Composition(
snl.structure.composition.reduced_formula).alphabetical_formula, metadata=wf_meta)
def snl_to_wf_phonon(snl, parameters):
# parameters["user_vasp_settings"] specifies user defined incar/kpoints parameters
fws = []
connections = defaultdict(list)
parameters = parameters if parameters else {}
snl_priority = parameters.get('priority', 1)
priority = snl_priority * 2 # once we start a job, keep going!
f = Composition(snl.structure.composition.reduced_formula).alphabetical_formula
# add the SNL to the SNL DB and figure out duplicate group
tasks = [AddSNLTask()]
spec = {'task_type': 'Add to SNL database', 'snl': snl.as_dict(),
'_queueadapter': QA_DB, '_priority': snl_priority}
if 'snlgroup_id' in parameters and isinstance(snl, MPStructureNL):
spec['force_mpsnl'] = snl.as_dict()
spec['force_snlgroup_id'] = parameters['snlgroup_id']
del spec['snl']
fws.append(Firework(tasks, spec,
name=get_slug(f + '--' + spec['task_type']), fw_id=0))
connections[0] = [1]
parameters["exact_structure"] = True
# run GGA structure optimization for force convergence
spec = snl_to_wf._snl_to_spec(snl, parameters=parameters)
user_vasp_settings = parameters.get("user_vasp_settings")
spec = update_spec_force_convergence(spec, user_vasp_settings)
spec['run_tags'].append("origin")
spec['_priority'] = priority
spec['_queueadapter'] = QA_VASP
del spec['_dupefinder']
spec['task_type'] = "Vasp force convergence optimize structure (2x)"
tasks = [VaspWriterTask(), get_custodian_task(spec)]
fws.append(Firework(tasks, spec,
name=get_slug(f + '--' + spec['task_type']), fw_id=1))
# insert into DB - GGA structure optimization
spec = {'task_type': 'VASP db insertion', '_priority': priority,
'_allow_fizzled_parents': True, '_queueadapter': QA_DB,
'clean_task_doc':True, 'elastic_constant':"force_convergence"}
fws.append(Firework([VaspToDBTask()], spec,
name=get_slug(f + '--' + spec['task_type']), fw_id=2))
connections[1] = [2]
spec = {'task_type': 'Setup Deformed Struct Task', '_priority': priority,
'_queueadapter': QA_CONTROL}
fws.append(Firework([SetupDeformedStructTask()], spec,
name=get_slug(f + '--' + spec['task_type']),fw_id=3))
connections[2] = [3]
wf_meta = get_meta_from_structure(snl.structure)
wf_meta['run_version'] = 'May 2013 (1)'
if '_materialsproject' in snl.data and 'submission_id' in snl.data['_materialsproject']:
wf_meta['submission_id'] = snl.data['_materialsproject']['submission_id']
return Workflow(fws, connections, name=Composition(
snl.structure.composition.reduced_formula).alphabetical_formula, metadata=wf_meta)
def run_task(self, fw_spec):
# Read structure from previous relaxation
relaxed_struct = fw_spec['output']['crystal']
# Generate deformed structures
d_struct_set = DeformedStructureSet(relaxed_struct, ns=0.06)
wf=[]
for i, d_struct in enumerate(d_struct_set.def_structs):
fws=[]
connections={}
f = Composition(d_struct.formula).alphabetical_formula
snl = StructureNL(d_struct, 'Joseph Montoya <*****@*****.**>',
projects=["Elasticity"])
tasks = [AddSNLTask()]
snl_priority = fw_spec.get('priority', 1)
spec = {'task_type': 'Add Deformed Struct to SNL database',
'snl': snl.as_dict(),
'_queueadapter': QA_DB,
'_priority': snl_priority}
if 'snlgroup_id' in fw_spec and isinstance(snl, MPStructureNL):
spec['force_mpsnl'] = snl.as_dict()
spec['force_snlgroup_id'] = fw_spec['snlgroup_id']
del spec['snl']
fws.append(Firework(tasks, spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-1000+i*10))
connections[-1000+i*10] = [-999+i*10]
spec = snl_to_wf._snl_to_spec(snl,
parameters={'exact_structure':True})
spec = update_spec_force_convergence(spec)
spec['deformation_matrix'] = d_struct_set.deformations[i].tolist()
spec['original_task_id'] = fw_spec["task_id"]
spec['_priority'] = fw_spec['_priority']*2
#Turn off dupefinder for deformed structure
del spec['_dupefinder']
spec['task_type'] = "Optimize deformed structure"
fws.append(Firework([VaspWriterTask(), SetupElastConstTask(),
get_custodian_task(spec)],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-999+i*10))
priority = fw_spec['_priority']*3
spec = {'task_type': 'VASP db insertion',
'_priority': priority,
'_allow_fizzled_parents': True,
'_queueadapter': QA_DB,
'elastic_constant':"deformed_structure",
'clean_task_doc':True,
'deformation_matrix':d_struct_set.deformations[i].tolist(),
'original_task_id':fw_spec["task_id"]}
fws.append(Firework([VaspToDBTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-998+i*10))
connections[-999+i*10] = [-998+i*10]
wf.append(Workflow(fws, connections))
return FWAction(additions=wf)
def run_task(self, fw_spec):
# Read structure from previous relaxation
relaxed_struct = fw_spec['output']['crystal']
# Generate deformed structures
d_struct_set = DeformedStructureSet(relaxed_struct, ns=0.06)
wf=[]
for i, d_struct in enumerate(d_struct_set.def_structs):
fws=[]
connections={}
f = Composition(d_struct.formula).alphabetical_formula
snl = StructureNL(d_struct, 'Joseph Montoya <*****@*****.**>',
projects=["Elasticity"])
tasks = [AddSNLTask()]
snl_priority = fw_spec.get('priority', 1)
spec = {'task_type': 'Add Deformed Struct to SNL database',
'snl': snl.as_dict(),
'_queueadapter': QA_DB,
'_priority': snl_priority}
if 'snlgroup_id' in fw_spec and isinstance(snl, MPStructureNL):
spec['force_mpsnl'] = snl.as_dict()
spec['force_snlgroup_id'] = fw_spec['snlgroup_id']
del spec['snl']
fws.append(Firework(tasks, spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-1000+i*10))
connections[-1000+i*10] = [-999+i*10]
spec = snl_to_wf._snl_to_spec(snl,
parameters={'exact_structure':True})
spec = update_spec_force_convergence(spec)
spec['deformation_matrix'] = d_struct_set.deformations[i].tolist()
spec['original_task_id'] = fw_spec["task_id"]
spec['_priority'] = fw_spec['_priority']*2
#Turn off dupefinder for deformed structure
del spec['_dupefinder']
spec['task_type'] = "Optimize deformed structure"
fws.append(Firework([VaspWriterTask(), SetupElastConstTask(),
get_custodian_task(spec)],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-999+i*10))
priority = fw_spec['_priority']*3
spec = {'task_type': 'VASP db insertion',
'_priority': priority,
'_allow_fizzled_parents': True,
'_queueadapter': QA_DB,
'elastic_constant':"deformed_structure",
'clean_task_doc':True,
'deformation_matrix':d_struct_set.deformations[i].tolist(),
'original_task_id':fw_spec["task_id"]}
fws.append(Firework([VaspToDBTask(), AddElasticDataToDBTask()], spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-998+i*10))
connections[-999+i*10] = [-998+i*10]
wf.append(Workflow(fws, connections))
return FWAction(additions=wf)
