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):
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 run_task(self, fw_spec):
from magdesign.diffusion.neb_structures import neb_structures_insert_in_existing
terminal_start_rundir = fw_spec['previous_fws'][
self.terminal_start_task_type][0]['dir']
terminal_end_rundir = fw_spec['previous_fws'][
self.terminal_end_task_type][0]['dir']
if 'structures' in fw_spec:
if fw_spec['structures'] is not None:
structs = neb_structures_insert_in_existing(
fw_spec['structures'], n_insert=self.n_insert)
else:
# Get the structures from the previous nebs ...
if len(fw_spec['previous_fws'][self.prev_neb_task_type]) != 1:
raise RuntimeError(
'Multiple or no fws with task_type "{}"'.format(
self.prev_neb_task_type))
prev_neb_rundir = fw_spec['previous_fws'][
self.prev_neb_task_type][0]['dir']
prev_neb_analysis = NEBAnalysis.from_dir(
prev_neb_rundir,
relaxation_dirs=(terminal_start_rundir,
terminal_end_rundir))
structs = neb_structures_insert_in_existing(
prev_neb_analysis.structures, n_insert=self.n_insert)
else:
if fw_spec['terminal_start'] is not None:
structs = neb_structures_insert_in_existing(
[fw_spec['terminal_start'], fw_spec['terminal_end']],
n_insert=self.n_insert)
else:
# Get the terminals from the relaxation of the terminals.
if len(fw_spec['previous_fws'][
self.terminal_start_task_type]) != 1:
raise RuntimeError(
'Multiple or no fws with task_type "{}"'.format(
self.terminal_start_task_type))
if len(fw_spec['previous_fws'][
self.terminal_end_task_type]) != 1:
raise RuntimeError(
'Multiple or no fws with task_type "{}"'.format(
self.terminal_end_task_type))
terminal_start_rundir = fw_spec['previous_fws'][
self.terminal_start_task_type][0]['dir']
terminal_end_rundir = fw_spec['previous_fws'][
self.terminal_end_task_type][0]['dir']
terminal_start_vasprun = Vasprun(
os.path.join(terminal_start_rundir, 'vasprun.xml'))
terminal_end_vasprun = Vasprun(
os.path.join(terminal_end_rundir, 'vasprun.xml'))
terminal_start_structure = terminal_start_vasprun.final_structure
terminal_end_structure = terminal_end_vasprun.final_structure
structs = neb_structures_insert_in_existing(
[terminal_start_structure, terminal_end_structure],
n_insert=self.n_insert)
if self.climbing_image:
neb_vis = MPcNEBSet(structures=structs,
user_incar_settings=self.user_incar_settings)
task_helper = MPcNEBTaskHelper()
else:
neb_vis = MPNEBSet(structures=structs,
user_incar_settings=self.user_incar_settings)
task_helper = MPNEBTaskHelper()
if 'additional_controllers' in fw_spec:
additional_controllers = fw_spec['additional_controllers']
fw_spec.pop('additional_controllers')
else:
additional_controllers = [
WalltimeController(),
MemoryController(),
VaspNEBValidatorController()
]
control_procedure = ControlProcedure(
controllers=additional_controllers)
if self.task_index is None:
# Define the task_index as "MPNEBVaspN" where N is the number of structures in the NEB (e.g. 3 when two end
# points plus one structure are computed)
if self.climbing_image:
task_index = 'MPcNEBVasp{:d}'.format(len(structs))
else:
task_index = 'MPNEBVasp{:d}'.format(len(structs))
else:
task_index = self.task_index
task_index = SRCTaskIndex.from_any(task_index)
task_type = task_index.task_type
src_fws = createVaspSRCFireworks(vasp_input_set=neb_vis,
task_helper=task_helper,
task_type=task_type,
control_procedure=control_procedure,
custodian_handlers=[],
max_restarts=10,
src_cleaning=None,
task_index=task_index,
spec={
'additional_vasp_wf_info': {
'terminal_start_run_dir':
terminal_start_rundir,
'terminal_end_run_dir':
terminal_end_rundir
}
},
setup_spec_update=None,
run_spec_update=None)
wf = Workflow(fireworks=src_fws['fws'],
links_dict=src_fws['links_dict'])
return FWAction(detours=[wf])