def createVaspSRCFireworks(vasp_input_set, task_helper, task_type, control_procedure,
custodian_handlers, max_restarts, src_cleaning, task_index, spec,
setup_spec_update=None, run_spec_update=None):
# Make a full copy of the spec
if spec is None:
spec = {}
spec = copy.deepcopy(spec)
spec['_add_launchpad_and_fw_id'] = True
spec['_add_fworker'] = True
# Initialize the SRC task_index
if task_index is not None:
src_task_index = SRCTaskIndex.from_any(task_index)
else:
src_task_index = SRCTaskIndex.from_string(task_type)
spec['SRC_task_index'] = src_task_index
# SetupTask
setup_spec = copy.deepcopy(spec)
# Remove any initial queue_adapter_update from the spec
setup_spec.pop('queue_adapter_update', None)
setup_spec = set_short_single_core_to_spec(setup_spec)
setup_spec['_preserve_fworker'] = True
setup_spec['_pass_job_info'] = True
setup_spec.update({} if setup_spec_update is None else setup_spec_update)
setup_task = VaspSetupTask(vasp_input_set=vasp_input_set, deps=None, task_helper=task_helper, task_type=task_type)
setup_fw = Firework(setup_task, spec=setup_spec, name=src_task_index.setup_str)
# RunTask
run_spec = copy.deepcopy(spec)
run_spec['SRC_task_index'] = src_task_index
run_spec['_preserve_fworker'] = True
run_spec['_pass_job_info'] = True
run_spec.update({} if run_spec_update is None else run_spec_update)
run_task = VaspRunTask(control_procedure=control_procedure, task_helper=task_helper, task_type=task_type,
custodian_handlers=custodian_handlers)
run_fw = Firework(run_task, spec=run_spec, name=src_task_index.run_str)
# ControlTask
control_spec = copy.deepcopy(spec)
control_spec = set_short_single_core_to_spec(control_spec)
control_spec['SRC_task_index'] = src_task_index
control_spec['_allow_fizzled_parents'] = True
control_task = VaspControlTask(control_procedure=control_procedure, manager=None, max_restarts=max_restarts,
src_cleaning=src_cleaning, task_helper=task_helper)
control_fw = Firework(control_task, spec=control_spec, name=src_task_index.control_str)
links_dict = {setup_fw.fw_id: [run_fw.fw_id],
run_fw.fw_id: [control_fw.fw_id]}
return {'setup_fw': setup_fw, 'run_fw': run_fw, 'control_fw': control_fw, 'links_dict': links_dict,
'fws': [setup_fw, run_fw, control_fw]}
def createVaspSRCFireworks(vasp_input_set, task_helper, task_type, control_procedure,
custodian_handlers, max_restarts, src_cleaning, task_index, spec,
setup_spec_update=None, run_spec_update=None):
# Make a full copy of the spec
if spec is None:
spec = {}
spec = copy.deepcopy(spec)
spec['_add_launchpad_and_fw_id'] = True
spec['_add_fworker'] = True
# Initialize the SRC task_index
if task_index is not None:
src_task_index = SRCTaskIndex.from_any(task_index)
else:
src_task_index = SRCTaskIndex.from_string(task_type)
spec['SRC_task_index'] = src_task_index
# SetupTask
setup_spec = copy.deepcopy(spec)
# Remove any initial queue_adapter_update from the spec
setup_spec.pop('queue_adapter_update', None)
setup_spec = set_short_single_core_to_spec(setup_spec)
setup_spec['_preserve_fworker'] = True
setup_spec['_pass_job_info'] = True
setup_spec.update({} if setup_spec_update is None else setup_spec_update)
setup_task = VaspSetupTask(vasp_input_set=vasp_input_set, deps=None, task_helper=task_helper, task_type=task_type)
setup_fw = Firework(setup_task, spec=setup_spec, name=src_task_index.setup_str)
# RunTask
run_spec = copy.deepcopy(spec)
run_spec['SRC_task_index'] = src_task_index
run_spec['_preserve_fworker'] = True
run_spec['_pass_job_info'] = True
run_spec.update({} if run_spec_update is None else run_spec_update)
run_task = VaspRunTask(control_procedure=control_procedure, task_helper=task_helper, task_type=task_type,
custodian_handlers=custodian_handlers)
run_fw = Firework(run_task, spec=run_spec, name=src_task_index.run_str)
# ControlTask
control_spec = copy.deepcopy(spec)
control_spec = set_short_single_core_to_spec(control_spec)
control_spec['SRC_task_index'] = src_task_index
control_spec['_allow_fizzled_parents'] = True
control_task = VaspControlTask(control_procedure=control_procedure, manager=None, max_restarts=max_restarts,
src_cleaning=src_cleaning, task_helper=task_helper)
control_fw = Firework(control_task, spec=control_spec, name=src_task_index.control_str)
links_dict = {setup_fw.fw_id: [run_fw.fw_id],
run_fw.fw_id: [control_fw.fw_id]}
return {'setup_fw': setup_fw, 'run_fw': run_fw, 'control_fw': control_fw, 'links_dict': links_dict,
'fws': [setup_fw, run_fw, control_fw]}
def createSRCFireworksOld(task_class, task_input, SRC_spec, initialization_info, wf_task_index_prefix, current_task_index=1,
handlers=None, validators=None,
deps=None, task_type=None, queue_adapter_update=None):
SRC_spec = copy.deepcopy(SRC_spec)
SRC_spec['initialization_info'] = initialization_info
SRC_spec['_add_launchpad_and_fw_id'] = True
SRC_spec['SRCScheme'] = True
prefix_allowed_chars = ['-']
prefix_test_string = str(wf_task_index_prefix)
for allowed_char in prefix_allowed_chars:
prefix_test_string = prefix_test_string.replace(allowed_char, "")
if not prefix_test_string.isalnum():
raise ValueError('wf_task_index_prefix should only contain letters '
'and the following characters : {}'.format(prefix_test_string))
SRC_spec['wf_task_index_prefix'] = wf_task_index_prefix
# Remove any initial queue_adapter_update from the spec
SRC_spec.pop('queue_adapter_update', None)
if queue_adapter_update is not None:
SRC_spec['queue_adapter_update'] = queue_adapter_update
# Setup (Autoparal) run
SRC_spec_setup = copy.deepcopy(SRC_spec)
SRC_spec_setup = set_short_single_core_to_spec(SRC_spec_setup)
SRC_spec_setup['wf_task_index'] = '_'.join(['setup', wf_task_index_prefix, str(current_task_index)])
setup_task = task_class(task_input, is_autoparal=True, use_SRC_scheme=True, deps=deps, task_type=task_type)
setup_fw = Firework(setup_task, spec=SRC_spec_setup, name=SRC_spec_setup['wf_task_index'])
# Actual run of simulation
SRC_spec_run = copy.deepcopy(SRC_spec)
SRC_spec_run['wf_task_index'] = '_'.join(['run', wf_task_index_prefix, str(current_task_index)])
run_task = task_class(task_input, is_autoparal=False, use_SRC_scheme=True, deps=deps, task_type=task_type)
run_fw = Firework(run_task, spec=SRC_spec_run, name=SRC_spec_run['wf_task_index'])
# Check memory firework
SRC_spec_check = copy.deepcopy(SRC_spec)
SRC_spec_check = set_short_single_core_to_spec(SRC_spec_check)
SRC_spec_check['wf_task_index'] = '_'.join(['check', wf_task_index_prefix, str(current_task_index)])
check_task = CheckTask(handlers=handlers, validators=validators)
SRC_spec_check['_allow_fizzled_parents'] = True
check_fw = Firework(check_task, spec=SRC_spec_check, name=SRC_spec_check['wf_task_index'])
links_dict = {setup_fw.fw_id: [run_fw.fw_id],
run_fw.fw_id: [check_fw.fw_id]}
return {'setup_fw': setup_fw, 'run_fw': run_fw, 'check_fw': check_fw, 'links_dict': links_dict,
'fws': [setup_fw, run_fw, check_fw]}
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, 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 createSRCFireworksOld(task_class,
task_input,
SRC_spec,
initialization_info,
wf_task_index_prefix,
current_task_index=1,
handlers=None,
validators=None,
deps=None,
task_type=None,
queue_adapter_update=None):
SRC_spec = copy.deepcopy(SRC_spec)
SRC_spec['initialization_info'] = initialization_info
SRC_spec['_add_launchpad_and_fw_id'] = True
SRC_spec['SRCScheme'] = True
prefix_allowed_chars = ['-']
prefix_test_string = str(wf_task_index_prefix)
for allowed_char in prefix_allowed_chars:
prefix_test_string = prefix_test_string.replace(allowed_char, "")
if not prefix_test_string.isalnum():
raise ValueError(
'wf_task_index_prefix should only contain letters '
'and the following characters : {}'.format(prefix_test_string))
SRC_spec['wf_task_index_prefix'] = wf_task_index_prefix
# Remove any initial queue_adapter_update from the spec
SRC_spec.pop('queue_adapter_update', None)
if queue_adapter_update is not None:
SRC_spec['queue_adapter_update'] = queue_adapter_update
# Setup (Autoparal) run
SRC_spec_setup = copy.deepcopy(SRC_spec)
SRC_spec_setup = set_short_single_core_to_spec(SRC_spec_setup)
SRC_spec_setup['wf_task_index'] = '_'.join(
['setup', wf_task_index_prefix,
str(current_task_index)])
setup_task = task_class(task_input,
is_autoparal=True,
use_SRC_scheme=True,
deps=deps,
task_type=task_type)
setup_fw = Firework(setup_task,
spec=SRC_spec_setup,
name=SRC_spec_setup['wf_task_index'])
# Actual run of simulation
SRC_spec_run = copy.deepcopy(SRC_spec)
SRC_spec_run['wf_task_index'] = '_'.join(
['run', wf_task_index_prefix,
str(current_task_index)])
run_task = task_class(task_input,
is_autoparal=False,
use_SRC_scheme=True,
deps=deps,
task_type=task_type)
run_fw = Firework(run_task,
spec=SRC_spec_run,
name=SRC_spec_run['wf_task_index'])
# Check memory firework
SRC_spec_check = copy.deepcopy(SRC_spec)
SRC_spec_check = set_short_single_core_to_spec(SRC_spec_check)
SRC_spec_check['wf_task_index'] = '_'.join(
['check', wf_task_index_prefix,
str(current_task_index)])
check_task = CheckTask(handlers=handlers, validators=validators)
SRC_spec_check['_allow_fizzled_parents'] = True
check_fw = Firework(check_task,
spec=SRC_spec_check,
name=SRC_spec_check['wf_task_index'])
links_dict = {
setup_fw.fw_id: [run_fw.fw_id],
run_fw.fw_id: [check_fw.fw_id]
}
return {
'setup_fw': setup_fw,
'run_fw': run_fw,
'check_fw': check_fw,
'links_dict': links_dict,
'fws': [setup_fw, run_fw, check_fw]
}
