def _snl_to_spec(snl, enforce_gga=False):
spec = {}
incar_enforce = {'NPAR': 2}
structure = snl.structure
mpvis = MPGGAVaspInputSet(user_incar_settings=incar_enforce) if enforce_gga else MPVaspInputSet(user_incar_settings=incar_enforce)
incar = mpvis.get_incar(structure)
poscar = mpvis.get_poscar(structure)
kpoints = mpvis.get_kpoints(structure)
potcar = mpvis.get_potcar(structure)
spec['vasp'] = {}
spec['vasp']['incar'] = incar.to_dict
spec['vasp']['poscar'] = poscar.to_dict
spec['vasp']['kpoints'] = kpoints.to_dict
spec['vasp']['potcar'] = potcar.to_dict
# Add run tags of pseudopotential
spec['run_tags'] = spec.get('run_tags', [potcar.functional])
spec['run_tags'].extend(potcar.symbols)
# Add run tags of +U
u_tags = ['%s=%s' % t for t in
zip(poscar.site_symbols, incar.get('LDAUU', [0] * len(poscar.site_symbols)))]
spec['run_tags'].extend(u_tags)
spec['_dupefinder'] = DupeFinderVasp().to_dict()
spec['vaspinputset_name'] = mpvis.__class__.__name__
spec['task_type'] = 'GGA+U optimize structure (2x)' if spec['vasp'][
'incar'].get('LDAU', False) else 'GGA optimize structure (2x)'
return spec
def _snl_to_spec(snl, enforce_gga=False, parameters=None):
parameters = parameters if parameters else {}
parameters['boltztrap'] = parameters.get('boltztrap',
True) # by default run boltztrap
spec = {'parameters': parameters}
incar_enforce = {'NPAR': 2}
if 'exact_structure' in parameters and parameters['exact_structure']:
structure = snl.structure
else:
structure = snl.structure.get_primitive_structure()
mpvis = MPGGAVaspInputSet(
user_incar_settings=incar_enforce) if enforce_gga else MPVaspInputSet(
user_incar_settings=incar_enforce)
incar = mpvis.get_incar(structure)
poscar = mpvis.get_poscar(structure)
kpoints = mpvis.get_kpoints(structure)
potcar = mpvis.get_potcar(structure)
spec['vasp'] = {}
spec['vasp']['incar'] = incar.as_dict()
spec['vasp']['poscar'] = poscar.as_dict()
spec['vasp']['kpoints'] = kpoints.as_dict()
spec['vasp']['potcar'] = potcar.as_dict()
# Add run tags of pseudopotential
spec['run_tags'] = spec.get('run_tags', [potcar.functional])
spec['run_tags'].extend(potcar.symbols)
# Add run tags of +U
u_tags = [
'%s=%s' % t
for t in zip(poscar.site_symbols,
incar.get('LDAUU', [0] * len(poscar.site_symbols)))
]
spec['run_tags'].extend(u_tags)
# add user run tags
if 'run_tags' in parameters:
spec['run_tags'].extend(parameters['run_tags'])
del spec['parameters']['run_tags']
# add exact structure run tag automatically if we have a unique situation
if 'exact_structure' in parameters and parameters[
'exact_structure'] and snl.structure != snl.structure.get_primitive_structure(
):
spec['run_tags'].extend('exact_structure')
spec['_dupefinder'] = DupeFinderVasp().to_dict()
spec['vaspinputset_name'] = mpvis.__class__.__name__
spec['task_type'] = 'GGA+U optimize structure (2x)' if spec['vasp'][
'incar'].get('LDAU', False) else 'GGA optimize structure (2x)'
return spec
def _snl_to_spec(snl, enforce_gga=False, parameters=None):
parameters = parameters if parameters else {}
spec = {'parameters': parameters}
incar_enforce = {'NPAR': 2}
if 'exact_structure' in parameters and parameters['exact_structure']:
structure = snl.structure
else:
structure = snl.structure.get_primitive_structure()
mpvis = MPGGAVaspInputSet(user_incar_settings=incar_enforce) if enforce_gga else MPVaspInputSet(user_incar_settings=incar_enforce)
incar = mpvis.get_incar(structure)
poscar = mpvis.get_poscar(structure)
kpoints = mpvis.get_kpoints(structure)
potcar = mpvis.get_potcar(structure)
spec['vasp'] = {}
spec['vasp']['incar'] = incar.to_dict
spec['vasp']['poscar'] = poscar.to_dict
spec['vasp']['kpoints'] = kpoints.to_dict
spec['vasp']['potcar'] = potcar.to_dict
# Add run tags of pseudopotential
spec['run_tags'] = spec.get('run_tags', [potcar.functional])
spec['run_tags'].extend(potcar.symbols)
# Add run tags of +U
u_tags = ['%s=%s' % t for t in
zip(poscar.site_symbols, incar.get('LDAUU', [0] * len(poscar.site_symbols)))]
spec['run_tags'].extend(u_tags)
# add user run tags
if 'run_tags' in parameters:
spec['run_tags'].extend(parameters['run_tags'])
del spec['parameters']['run_tags']
# add exact structure run tag automatically if we have a unique situation
if 'exact_structure' in parameters and parameters['exact_structure'] and snl.structure != snl.structure.get_primitive_structure():
spec['run_tags'].extend('exact_structure')
spec['_dupefinder'] = DupeFinderVasp().to_dict()
spec['vaspinputset_name'] = mpvis.__class__.__name__
spec['task_type'] = 'GGA+U optimize structure (2x)' if spec['vasp'][
'incar'].get('LDAU', False) else 'GGA optimize structure (2x)'
return spec
def _snl_to_spec(snl, enforce_gga=False):
spec = {}
incar_enforce = {'NPAR': 2}
structure = snl.structure
mpvis = MPGGAVaspInputSet(
user_incar_settings=incar_enforce) if enforce_gga else MPVaspInputSet(
user_incar_settings=incar_enforce)
incar = mpvis.get_incar(structure)
poscar = mpvis.get_poscar(structure)
kpoints = mpvis.get_kpoints(structure)
potcar = mpvis.get_potcar(structure)
spec['vasp'] = {}
spec['vasp']['incar'] = incar.to_dict
spec['vasp']['poscar'] = poscar.to_dict
spec['vasp']['kpoints'] = kpoints.to_dict
spec['vasp']['potcar'] = potcar.to_dict
# Add run tags of pseudopotential
spec['run_tags'] = spec.get('run_tags', [potcar.functional])
spec['run_tags'].extend(potcar.symbols)
# Add run tags of +U
u_tags = [
'%s=%s' % t
for t in zip(poscar.site_symbols,
incar.get('LDAUU', [0] * len(poscar.site_symbols)))
]
spec['run_tags'].extend(u_tags)
spec['_dupefinder'] = DupeFinderVasp().to_dict()
spec['vaspinputset_name'] = mpvis.__class__.__name__
spec['task_type'] = 'GGA+U optimize structure (2x)' if spec['vasp'][
'incar'].get('LDAU', False) else 'GGA optimize structure (2x)'
return spec
def _snl_to_spec(snl, enforce_gga=True):
spec = {}
mpvis = MPGGAVaspInputSet() if enforce_gga else MPVaspInputSet()
structure = snl.structure
spec['vasp'] = {}
spec['vasp']['incar'] = mpvis.get_incar(structure).to_dict
spec['vasp']['incar']['NPAR'] = 2
spec['vasp']['poscar'] = mpvis.get_poscar(structure).to_dict
spec['vasp']['kpoints'] = mpvis.get_kpoints(structure).to_dict
spec['vasp']['potcar'] = mpvis.get_potcar(structure).to_dict
spec['_dupefinder'] = DupeFinderVasp().to_dict()
spec['_priority'] = 2
# TODO: restore category
# spec['_category'] = 'Materials Project'
spec['vaspinputset_name'] = mpvis.__class__.__name__
spec['task_type'] = 'GGA+U optimize structure (2x)' if spec['vasp'][
'incar'].get('LDAU', False) else 'GGA optimize structure (2x)'
spec.update(_get_metadata(snl))
return spec
def structure_to_wf(structure):
"""
This method starts with a Structure object and creates a Workflow object
The workflow has two steps - a structure relaxation and a static run
:param structure:
:return:
"""
fws = [] # list of FireWorks to run
connections = defaultdict(list) # dependencies between FireWorks
# generate VASP input objects for 1st VASP run - this is put in the FW spec
mpvis = MPGGAVaspInputSet(user_incar_settings={'NPAR': 2})
incar = mpvis.get_incar(structure)
poscar = mpvis.get_poscar(structure)
kpoints = mpvis.get_kpoints(structure)
potcar = mpvis.get_potcar(structure)
# serialize the VASP input objects to the FW spec
spec = {}
spec['vasp'] = {}
spec['vasp']['incar'] = incar.as_dict()
spec['vasp']['poscar'] = poscar.as_dict()
spec['vasp']['kpoints'] = kpoints.as_dict()
spec['vasp']['potcar'] = potcar.as_dict()
spec['vaspinputset_name'] = mpvis.__class__.__name__
spec['task_type'] = 'GGA optimize structure (2x) example'
# set up the custodian that we want to run
jobs = VaspJob.double_relaxation_run('', gzipped=False)
for j in jobs: # turn off auto npar, it doesn't work for >1 node
j.auto_npar = False
handlers = [VaspErrorHandler(), FrozenJobErrorHandler(), MeshSymmetryErrorHandler(),
NonConvergingErrorHandler()]
c_params = {'jobs': [j.as_dict() for j in jobs], 'handlers': [h.as_dict() for h in handlers], 'max_errors': 5}
custodiantask = VaspCustodianTaskEx(c_params)
# 1st Firework - run GGA optimize structure
# VaspWriterTask - write input files (INCAR, POSCAR, KPOINTS, POSCAR) based on spec
# CustodianTaskEx - run VASP within a custodian
tasks = [VaspWriterTask(), custodiantask]
fws.append(Firework(tasks, spec, name=get_name(structure, spec['task_type']), fw_id=1))
# 2nd Firework - insert previous run into DB
spec = {'task_type': 'VASP db insertion example'}
fws.append(
Firework([VaspToDBTaskEx()], spec, name=get_name(structure, spec['task_type']), fw_id=2))
connections[1] = [2]
# 3rd Firework - static run.
# VaspCopyTask - copy output from previous run to this directory
# SetupStaticRunTask - override old parameters for static run
# CustodianTaskEx - run VASP within a custodian
spec = {'task_type': 'GGA static example'}
copytask = VaspCopyTask({'use_CONTCAR': True, 'skip_CHGCAR': True})
setuptask = SetupStaticRunTask()
custodiantask = VaspCustodianTaskEx({'jobs': [VaspJob('', auto_npar=False).as_dict()], 'handlers': [h.as_dict() for h in handlers], 'max_errors': 5})
fws.append(Firework([copytask, setuptask, custodiantask], spec, name=get_name(structure, spec['task_type']), fw_id=3))
connections[2] = [3]
# 4th Firework - insert previous run into DB
spec = {'task_type': 'VASP db insertion example'}
fws.append(
Firework([VaspToDBTaskEx()], spec, name=get_name(structure, spec['task_type']), fw_id=4))
connections[3] = [4]
return Workflow(fws, connections, name=get_slug(structure.formula))
def structure_to_wf(structure):
"""
This method starts with a Structure object and creates a Workflow object
The workflow has two steps - a structure relaxation and a static run
:param structure:
:return:
"""
fws = [] # list of FireWorks to run
connections = defaultdict(list) # dependencies between FireWorks
# generate VASP input objects for 1st VASP run - this is put in the FW spec
mpvis = MPGGAVaspInputSet(user_incar_settings={'NPAR': 2})
incar = mpvis.get_incar(structure)
poscar = mpvis.get_poscar(structure)
kpoints = mpvis.get_kpoints(structure)
potcar = mpvis.get_potcar(structure)
# serialize the VASP input objects to the FW spec
spec = {}
spec['vasp'] = {}
spec['vasp']['incar'] = incar.to_dict
spec['vasp']['poscar'] = poscar.to_dict
spec['vasp']['kpoints'] = kpoints.to_dict
spec['vasp']['potcar'] = potcar.to_dict
spec['vaspinputset_name'] = mpvis.__class__.__name__
spec['task_type'] = 'GGA optimize structure (2x) example'
# set up the custodian that we want to run
jobs = VaspJob.double_relaxation_run('', gzipped=False)
for j in jobs: # turn off auto npar, it doesn't work for >1 node
j.auto_npar = False
handlers = [VaspErrorHandler(), FrozenJobErrorHandler(), MeshSymmetryErrorHandler(),
NonConvergingErrorHandler()]
c_params = {'jobs': [j.to_dict for j in jobs], 'handlers': [h.to_dict for h in handlers], 'max_errors': 5}
custodiantask = VaspCustodianTaskEx(c_params)
# 1st FireWork - run GGA optimize structure
# VaspWriterTask - write input files (INCAR, POSCAR, KPOINTS, POSCAR) based on spec
# CustodianTaskEx - run VASP within a custodian
tasks = [VaspWriterTask(), custodiantask]
fws.append(FireWork(tasks, spec, name=get_name(structure, spec['task_type']), fw_id=1))
# 2nd FireWork - insert previous run into DB
spec = {'task_type': 'VASP db insertion example'}
fws.append(
FireWork([VaspToDBTaskEx()], spec, name=get_name(structure, spec['task_type']), fw_id=2))
connections[1] = [2]
# 3rd FireWork - static run.
# VaspCopyTask - copy output from previous run to this directory
# SetupStaticRunTask - override old parameters for static run
# CustodianTaskEx - run VASP within a custodian
spec = {'task_type': 'GGA static example'}
copytask = VaspCopyTask({'use_CONTCAR': True, 'skip_CHGCAR': True})
setuptask = SetupStaticRunTask()
custodiantask = VaspCustodianTaskEx({'jobs': [VaspJob('', auto_npar=False).to_dict], 'handlers': [h.to_dict for h in handlers], 'max_errors': 5})
fws.append(FireWork([copytask, setuptask, custodiantask], spec, name=get_name(structure, spec['task_type']), fw_id=3))
connections[2] = [3]
# 4th FireWork - insert previous run into DB
spec = {'task_type': 'VASP db insertion example'}
fws.append(
FireWork([VaspToDBTaskEx()], spec, name=get_name(structure, spec['task_type']), fw_id=4))
connections[3] = [4]
return Workflow(fws, connections, name=get_slug(structure.formula))