def __init__(self, vasp_input_set, spec):
# Initializes fws list and links_dict
fws = []
links_dict = {}
if 'additional_controllers' in spec:
additional_controllers = spec['additional_controllers']
spec.pop('additional_controllers')
else:
additional_controllers = [
WalltimeController(),
MemoryController(),
VaspXMLValidatorController()
]
control_procedure = ControlProcedure(
controllers=additional_controllers)
task_helper = MPRelaxTaskHelper()
task_type = task_helper.task_type
src_fws = createVaspSRCFireworks(vasp_input_set=vasp_input_set,
task_helper=task_helper,
task_type=task_type,
control_procedure=control_procedure,
custodian_handlers=[],
max_restarts=10,
src_cleaning=None,
task_index=None,
spec=None,
setup_spec_update=None,
run_spec_update=None)
fws.extend(src_fws['fws'])
links_dict_update(links_dict=links_dict,
links_update=src_fws['links_dict'])
self.wf = Workflow(fireworks=fws,
links_dict=links_dict,
metadata={
'workflow_class': self.workflow_class,
'workflow_module': self.workflow_module
},
name='MPRelaxFWWorkflowSRC')
def __init__(self, neb_vasp_input_set, spec, neb_terminals, relax_terminals=True, n_insert=1, n_nebs=3,
relax_vasp_input_set=None, initial_neb_structures=None, climbing_image=True, sort_structure=False,
neb_optimizer=None, neb_optimizing_procedure=None):
user_incar_settings = {'NPAR': 4, 'ISIF': 0, 'SIGMA': 0.2, 'ISMEAR': 0, 'EDIFF': 5.0e-05}
neb_user_incar_settings = {'NPAR': 4, 'ISIF': 0, 'SIGMA': 0.2, 'ISMEAR': 0, 'EDIFF': 5.0e-05, 'NSW': 25}
if n_nebs < 1:
raise ValueError('Minimum one NEB ...')
if relax_terminals and initial_neb_structures is not None:
raise ValueError('Cannot relax terminals and start from initial NEB structures')
# Initializes fws list and links_dict
fws = []
links_dict = {}
if 'additional_controllers' in spec:
additional_controllers = spec['additional_controllers']
spec.pop('additional_controllers')
else:
additional_controllers = [WalltimeController(), MemoryController(), VaspXMLValidatorController()]
# Control procedure
control_procedure = ControlProcedure(controllers=additional_controllers)
# First NEB
gen_neb_spec = spec.copy()
if relax_terminals:
gen_neb_spec['terminal_start'] = None
gen_neb_spec['terminal_end'] = None
else:
gen_neb_spec['terminal_start'] = neb_terminals[0]
gen_neb_spec['terminal_end'] = neb_terminals[1]
# gen_neb_spec['structures'] = neb_terminals
gen_neb_spec = set_short_single_core_to_spec(gen_neb_spec)
terminal_start_relax_task_type = 'MPRelaxVasp-start'
terminal_end_relax_task_type = 'MPRelaxVasp-end'
terminal_start_task_type = None
terminal_end_task_type = None
if relax_terminals:
terminal_start_task_type = terminal_start_relax_task_type
terminal_end_task_type = terminal_end_relax_task_type
gen_neb_task = GenerateNEBRelaxationTask(n_insert=n_insert, user_incar_settings=neb_user_incar_settings,
climbing_image=climbing_image, task_index='neb1',
terminal_start_task_type=terminal_start_task_type,
terminal_end_task_type=terminal_end_task_type,
neb_optimizer=neb_optimizer,
neb_optimizing_procedure=neb_optimizing_procedure)
gen_neb_fw = Firework([gen_neb_task], spec=gen_neb_spec, name='gen-neb1')
fws.append(gen_neb_fw)
if relax_terminals:
# Start terminal
relax_task_helper = MPRelaxTaskHelper()
vis_start = relax_vasp_input_set(neb_terminals[0], user_incar_settings=user_incar_settings,
sort_structure=sort_structure)
start_src_fws = createVaspSRCFireworks(vasp_input_set=vis_start, task_helper=relax_task_helper,
task_type=terminal_start_relax_task_type,
control_procedure=control_procedure,
custodian_handlers=[], max_restarts=10, src_cleaning=None,
task_index=None,
spec=None,
setup_spec_update=None, run_spec_update=None)
fws.extend(start_src_fws['fws'])
links_dict_update(links_dict=links_dict, links_update=start_src_fws['links_dict'])
linkupdate = {start_src_fws['control_fw'].fw_id: gen_neb_fw.fw_id}
links_dict_update(links_dict=links_dict,
links_update=linkupdate)
# End terminal
vis_end = relax_vasp_input_set(neb_terminals[1], user_incar_settings=user_incar_settings,
sort_structure=sort_structure)
end_src_fws = createVaspSRCFireworks(vasp_input_set=vis_end, task_helper=relax_task_helper,
task_type=terminal_end_relax_task_type,
control_procedure=control_procedure,
custodian_handlers=[], max_restarts=10, src_cleaning=None,
task_index=None,
spec=None,
setup_spec_update=None, run_spec_update=None)
fws.extend(end_src_fws['fws'])
links_dict_update(links_dict=links_dict, links_update=end_src_fws['links_dict'])
linkupdate = {end_src_fws['control_fw'].fw_id: gen_neb_fw.fw_id}
links_dict_update(links_dict=links_dict,
links_update=linkupdate)
if n_nebs > 1:
for ineb in range(2, n_nebs+1):
prev_gen_neb_fw = gen_neb_fw
gen_neb_spec = spec.copy()
gen_neb_spec['structures'] = None
gen_neb_spec = set_short_single_core_to_spec(gen_neb_spec)
gen_neb_task = GenerateNEBRelaxationTask(n_insert=n_insert,
user_incar_settings=neb_user_incar_settings,
climbing_image=climbing_image,
task_index='neb{:d}'.format(ineb),
prev_neb_task_type='neb{:d}'.format(ineb-1),
terminal_start_task_type=terminal_start_task_type,
terminal_end_task_type=terminal_end_task_type,
neb_optimizer=neb_optimizer,
neb_optimizing_procedure=neb_optimizing_procedure)
gen_neb_fw = Firework([gen_neb_task], spec=gen_neb_spec, name='gen-neb{:d}'.format(ineb))
fws.append(gen_neb_fw)
linkupdate = {prev_gen_neb_fw.fw_id: gen_neb_fw.fw_id}
links_dict_update(links_dict=links_dict,
links_update=linkupdate)
if relax_terminals:
linkupdate = {start_src_fws['control_fw'].fw_id: gen_neb_fw.fw_id}
links_dict_update(links_dict=links_dict,
links_update=linkupdate)
linkupdate = {end_src_fws['control_fw'].fw_id: gen_neb_fw.fw_id}
links_dict_update(links_dict=links_dict,
links_update=linkupdate)
if climbing_image:
wfname = "MPcNEBRelaxFWWorkflowSRC"
else:
wfname = "MPcNEBRelaxFWWorkflowSRC"
self.wf = Workflow(fireworks=fws, links_dict=links_dict,
metadata={'workflow_class': self.workflow_class,
'workflow_module': self.workflow_module},
name=wfname)
def __init__(self,
neb_vasp_input_set,
spec,
neb_terminals,
relax_terminals=True,
n_insert=1,
n_nebs=3,
relax_vasp_input_set=None,
initial_neb_structures=None,
climbing_image=True):
user_incar_settings = {'NPAR': 4, 'ISIF': 0, 'SIGMA': 0.2, 'ISMEAR': 0}
if n_nebs < 1:
raise ValueError('Minimum one NEB ...')
if relax_terminals and initial_neb_structures is not None:
raise ValueError(
'Cannot relax terminals and start from initial NEB structures')
# Initializes fws list and links_dict
fws = []
links_dict = {}
if 'additional_controllers' in spec:
additional_controllers = spec['additional_controllers']
spec.pop('additional_controllers')
else:
additional_controllers = [
WalltimeController(),
MemoryController(),
VaspXMLValidatorController()
]
# Control procedure
control_procedure = ControlProcedure(
controllers=additional_controllers)
# First NEB
gen_neb_spec = spec.copy()
if relax_terminals:
gen_neb_spec['terminal_start'] = None
gen_neb_spec['terminal_end'] = None
else:
gen_neb_spec['terminal_start'] = neb_terminals[0]
gen_neb_spec['terminal_end'] = neb_terminals[1]
# gen_neb_spec['structures'] = neb_terminals
gen_neb_spec = set_short_single_core_to_spec(gen_neb_spec)
terminal_start_relax_task_type = 'MPRelaxVasp-start'
terminal_end_relax_task_type = 'MPRelaxVasp-end'
terminal_start_task_type = None
terminal_end_task_type = None
if relax_terminals:
terminal_start_task_type = terminal_start_relax_task_type
terminal_end_task_type = terminal_end_relax_task_type
gen_neb_task = GenerateNEBRelaxationTask(
n_insert=n_insert,
user_incar_settings=user_incar_settings,
climbing_image=climbing_image,
task_index='neb1',
terminal_start_task_type=terminal_start_task_type,
terminal_end_task_type=terminal_end_task_type)
gen_neb_fw = Firework([gen_neb_task],
spec=gen_neb_spec,
name='gen-neb1')
fws.append(gen_neb_fw)
if relax_terminals:
# Start terminal
relax_task_helper = MPRelaxTaskHelper()
vis_start = relax_vasp_input_set(
neb_terminals[0], user_incar_settings=user_incar_settings)
start_src_fws = createVaspSRCFireworks(
vasp_input_set=vis_start,
task_helper=relax_task_helper,
task_type=terminal_start_relax_task_type,
control_procedure=control_procedure,
custodian_handlers=[],
max_restarts=10,
src_cleaning=None,
task_index=None,
spec=None,
setup_spec_update=None,
run_spec_update=None)
fws.extend(start_src_fws['fws'])
links_dict_update(links_dict=links_dict,
links_update=start_src_fws['links_dict'])
linkupdate = {start_src_fws['control_fw'].fw_id: gen_neb_fw.fw_id}
links_dict_update(links_dict=links_dict, links_update=linkupdate)
# End terminal
vis_end = relax_vasp_input_set(
neb_terminals[1], user_incar_settings=user_incar_settings)
end_src_fws = createVaspSRCFireworks(
vasp_input_set=vis_end,
task_helper=relax_task_helper,
task_type=terminal_end_relax_task_type,
control_procedure=control_procedure,
custodian_handlers=[],
max_restarts=10,
src_cleaning=None,
task_index=None,
spec=None,
setup_spec_update=None,
run_spec_update=None)
fws.extend(end_src_fws['fws'])
links_dict_update(links_dict=links_dict,
links_update=end_src_fws['links_dict'])
linkupdate = {end_src_fws['control_fw'].fw_id: gen_neb_fw.fw_id}
links_dict_update(links_dict=links_dict, links_update=linkupdate)
if n_nebs > 1:
for ineb in range(2, n_nebs + 1):
prev_gen_neb_fw = gen_neb_fw
gen_neb_spec = spec.copy()
gen_neb_spec['structures'] = None
gen_neb_spec = set_short_single_core_to_spec(gen_neb_spec)
gen_neb_task = GenerateNEBRelaxationTask(
n_insert=n_insert,
user_incar_settings=user_incar_settings,
climbing_image=climbing_image,
task_index='neb{:d}'.format(ineb),
prev_neb_task_type='neb{:d}'.format(ineb - 1),
terminal_start_task_type=terminal_start_task_type,
terminal_end_task_type=terminal_end_task_type)
gen_neb_fw = Firework([gen_neb_task],
spec=gen_neb_spec,
name='gen-neb{:d}'.format(ineb))
fws.append(gen_neb_fw)
linkupdate = {prev_gen_neb_fw.fw_id: gen_neb_fw.fw_id}
links_dict_update(links_dict=links_dict,
links_update=linkupdate)
if relax_terminals:
linkupdate = {
start_src_fws['control_fw'].fw_id: gen_neb_fw.fw_id
}
links_dict_update(links_dict=links_dict,
links_update=linkupdate)
linkupdate = {
end_src_fws['control_fw'].fw_id: gen_neb_fw.fw_id
}
links_dict_update(links_dict=links_dict,
links_update=linkupdate)
if climbing_image:
wfname = "MPcNEBRelaxFWWorkflowSRC"
else:
wfname = "MPcNEBRelaxFWWorkflowSRC"
self.wf = Workflow(fireworks=fws,
links_dict=links_dict,
metadata={
'workflow_class': self.workflow_class,
'workflow_module': self.workflow_module
},
name=wfname)
def __init__(self, vasp_input_set, spec, relaxation_type='IONS_SHAPE_VOLUME',
relaxation_strategy=DEFAULT_RELAXATION_STRATEGY):
vasp_input_set.user_incar_settings.update(relaxation_type_to_vasp_variables[relaxation_type])
# Initializes fws list and links_dict
fws = []
links_dict = {}
if 'additional_controllers' in spec:
additional_controllers = spec['additional_controllers']
spec.pop('additional_controllers')
else:
additional_controllers = [WalltimeController(), MemoryController(), VaspXMLValidatorController()]
control_procedure = ControlProcedure(controllers=additional_controllers)
task_helper = MPRelaxTaskHelper()
if relaxation_strategy == self.DEFAULT_RELAXATION_STRATEGY:
if relaxation_type in ['NONE', 'IONS']:
task_type = task_helper.task_type
else:
task_type = '{}-1'.format(task_helper.task_type)
src_fws = createVaspSRCFireworks(vasp_input_set=vasp_input_set, task_helper=task_helper, task_type=task_type,
control_procedure=control_procedure,
custodian_handlers=[], max_restarts=10, src_cleaning=None, task_index=None,
spec=spec,
setup_spec_update=None, run_spec_update=None)
fws.extend(src_fws['fws'])
links_dict_update(links_dict=links_dict, links_update=src_fws['links_dict'])
if relaxation_type not in ['NONE', 'IONS']:
task_type2 = '{}-2'.format(task_helper.task_type)
src_fws2 = createVaspSRCFireworks(vasp_input_set=vasp_input_set, task_helper=task_helper,
task_type=task_type2,
control_procedure=control_procedure,
custodian_handlers=[], max_restarts=10, src_cleaning=None,
task_index=None,
spec=spec,
setup_spec_update=None, run_spec_update=None,
deps={task_type: '@final_structure'})
fws.extend(src_fws2['fws'])
links_dict_update(links_dict=links_dict, links_update=src_fws2['links_dict'])
linkupdate = {src_fws['control_fw'].fw_id: src_fws2['setup_fw'].fw_id}
links_dict_update(links_dict=links_dict,
links_update=linkupdate)
else:
if relaxation_strategy == self.IMPROVED_RELAXATION_STRATEGY:
steps = [{'user_incar_settings': {'ENCUT': '$VALUE=300.0_float'},
'user_kpoints_settings': {'reciprocal_density': '$FORMULA=0.6*$FINAL_int'}},
{'user_incar_settings': {'ENCUT': '$FORMULA=0.8*$FINAL_float'},
'user_kpoints_settings': {'reciprocal_density': '$FORMULA=0.8*$FINAL_int'}},
{},
{}
]
elif isinstance(relaxation_strategy, (list, tuple)):
steps = relaxation_strategy
else:
raise ValueError('Wrong value for relaxation_strategy')
deps = None
prev_src_fws = None
for istep, step in enumerate(steps):
task_type = '{}-{:d}'.format(task_helper.task_type, istep+1)
vis = self._modify_vasp_input_set(vasp_input_set, step)
src_fws = createVaspSRCFireworks(vasp_input_set=vis, task_helper=task_helper,
task_type=task_type,
control_procedure=control_procedure,
custodian_handlers=[], max_restarts=10, src_cleaning=None,
task_index=None,
spec=spec,
setup_spec_update=None, run_spec_update=None, deps=deps)
fws.extend(src_fws['fws'])
links_dict_update(links_dict=links_dict, links_update=src_fws['links_dict'])
if prev_src_fws is not None:
linkupdate = {prev_src_fws['control_fw'].fw_id: src_fws['setup_fw'].fw_id}
links_dict_update(links_dict=links_dict,
links_update=linkupdate)
deps = {task_type: '@final_structure'}
prev_src_fws = src_fws
self.wf = Workflow(fireworks=fws, links_dict=links_dict,
metadata={'workflow_class': self.workflow_class,
'workflow_module': self.workflow_module},
name='MPRelaxFWWorkflowSRC')
