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('')
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 run_task(self, fw_spec):
print 'sleeping 10s for Mongo'
time.sleep(10)
print 'done sleeping'
print 'the gap is {}, the cutoff is {}'.format(
fw_spec['analysis']['bandgap'], self.gap_cutoff)
if fw_spec['analysis']['bandgap'] >= self.gap_cutoff:
static_dens = 90
uniform_dens = 1000
line_dens = 20
else:
static_dens = 450
uniform_dens = 1500
line_dens = 30
if fw_spec['analysis']['bandgap'] <= self.metal_cutoff:
user_incar_settings = {"ISMEAR": 1, "SIGMA": 0.2}
else:
user_incar_settings = {}
print 'Adding more runs...'
type_name = 'GGA+U' if 'GGA+U' in fw_spec['prev_task_type'] else 'GGA'
snl = StructureNL.from_dict(fw_spec['mpsnl'])
f = Composition(
snl.structure.composition.reduced_formula).alphabetical_formula
fws = []
connections = {}
priority = fw_spec['_priority']
trackers = [
Tracker('FW_job.out'),
Tracker('FW_job.error'),
Tracker('vasp.out'),
Tracker('OUTCAR'),
Tracker('OSZICAR')
]
trackers_db = [Tracker('FW_job.out'), Tracker('FW_job.error')]
# run GGA static
spec = fw_spec # pass all the items from the current spec to the new
spec.update({
'task_type': '{} static v2'.format(type_name),
'_queueadapter': QA_VASP_SMALL,
'_dupefinder': DupeFinderVasp().to_dict(),
'_priority': priority,
'_trackers': trackers
})
fws.append(
Firework([
VaspCopyTask({
'use_CONTCAR': True,
'skip_CHGCAR': True
}),
SetupStaticRunTask({
"kpoints_density": static_dens,
'user_incar_settings': user_incar_settings
}),
get_custodian_task(spec)
],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-10))
# insert into DB - GGA static
spec = {
'task_type': 'VASP db insertion',
'_queueadapter': QA_DB,
'_allow_fizzled_parents': True,
'_priority': priority * 2,
"_dupefinder": DupeFinderDB().to_dict(),
'_trackers': trackers_db
}
fws.append(
Firework([VaspToDBTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-9))
connections[-10] = -9
# run GGA Uniform
spec = {
'task_type': '{} Uniform v2'.format(type_name),
'_queueadapter': QA_VASP,
'_dupefinder': DupeFinderVasp().to_dict(),
'_priority': priority,
'_trackers': trackers
}
fws.append(
Firework([
VaspCopyTask({'use_CONTCAR': False}),
SetupNonSCFTask({
'mode': 'uniform',
"kpoints_density": uniform_dens
}),
get_custodian_task(spec)
],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-8))
connections[-9] = -8
# insert into DB - GGA Uniform
spec = {
'task_type': 'VASP db insertion',
'_queueadapter': QA_DB,
'_allow_fizzled_parents': True,
'_priority': priority * 2,
"_dupefinder": DupeFinderDB().to_dict(),
'_trackers': trackers_db
}
fws.append(
Firework([VaspToDBTask({'parse_uniform': True})],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-7))
connections[-8] = -7
# run GGA Band structure
spec = {
'task_type': '{} band structure v2'.format(type_name),
'_queueadapter': QA_VASP,
'_dupefinder': DupeFinderVasp().to_dict(),
'_priority': priority,
'_trackers': trackers
}
fws.append(
Firework([
VaspCopyTask({'use_CONTCAR': False}),
SetupNonSCFTask({
'mode': 'line',
"kpoints_line_density": line_dens
}),
get_custodian_task(spec)
],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-6))
connections[-7] = [-6]
# insert into DB - GGA Band structure
spec = {
'task_type': 'VASP db insertion',
'_queueadapter': QA_DB,
'_allow_fizzled_parents': True,
'_priority': priority * 2,
"_dupefinder": DupeFinderDB().to_dict(),
'_trackers': trackers_db
}
fws.append(
Firework([VaspToDBTask({})],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-5))
connections[-6] = -5
if fw_spec.get('parameters') and fw_spec['parameters'].get(
'boltztrap'):
# run Boltztrap
from mpworks.firetasks.boltztrap_tasks import BoltztrapRunTask
spec = {
'task_type': '{} Boltztrap'.format(type_name),
'_queueadapter': QA_DB,
'_dupefinder': DupeFinderDB().to_dict(),
'_priority': priority
}
fws.append(
Firework([BoltztrapRunTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-4))
connections[-7].append(-4)
wf = Workflow(fws, connections)
print 'Done adding more runs...'
return FWAction(additions=wf)
def run_task(self, fw_spec):
print 'sleeping 10s for Mongo'
time.sleep(10)
print 'done sleeping'
print 'the gap is {}, the cutoff is {}'.format(
fw_spec['analysis']['bandgap'], self.gap_cutoff)
if fw_spec['analysis']['bandgap'] >= self.gap_cutoff:
print 'Adding more runs...'
type_name = 'GGA+U' if 'GGA+U' in fw_spec[
'prev_task_type'] else 'GGA'
snl = StructureNL.from_dict(fw_spec['mpsnl'])
f = Composition(
snl.structure.composition.reduced_formula).alphabetical_formula
fws = []
connections = {}
priority = fw_spec['_priority']
# run GGA static
spec = fw_spec # pass all the items from the current spec to the new
# one
spec.update({
'task_type': '{} static'.format(type_name),
'_queueadapter': QA_VASP,
'_dupefinder': DupeFinderVasp().to_dict(),
'_priority': priority
})
fws.append(
Firework([
VaspCopyTask({'use_CONTCAR': True}),
SetupStaticRunTask(),
get_custodian_task(spec)
],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-10))
# insert into DB - GGA static
spec = {
'task_type': 'VASP db insertion',
'_queueadapter': QA_DB,
'_allow_fizzled_parents': True,
'_priority': priority,
"_dupefinder": DupeFinderDB().to_dict()
}
fws.append(
Firework([VaspToDBTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-9))
connections[-10] = -9
# run GGA Uniform
spec = {
'task_type': '{} Uniform'.format(type_name),
'_queueadapter': QA_VASP,
'_dupefinder': DupeFinderVasp().to_dict(),
'_priority': priority
}
fws.append(
Firework([
VaspCopyTask({'use_CONTCAR': False}),
SetupNonSCFTask({'mode': 'uniform'}),
get_custodian_task(spec)
],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-8))
connections[-9] = -8
# insert into DB - GGA Uniform
spec = {
'task_type': 'VASP db insertion',
'_queueadapter': QA_DB,
'_allow_fizzled_parents': True,
'_priority': priority,
"_dupefinder": DupeFinderDB().to_dict()
}
fws.append(
Firework([VaspToDBTask({'parse_uniform': True})],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-7))
connections[-8] = -7
# run GGA Band structure
spec = {
'task_type': '{} band structure'.format(type_name),
'_queueadapter': QA_VASP,
'_dupefinder': DupeFinderVasp().to_dict(),
'_priority': priority
}
fws.append(
Firework([
VaspCopyTask({'use_CONTCAR': False}),
SetupNonSCFTask({'mode': 'line'}),
get_custodian_task(spec)
],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-6))
connections[-7] = -6
# insert into DB - GGA Band structure
spec = {
'task_type': 'VASP db insertion',
'_queueadapter': QA_DB,
'_allow_fizzled_parents': True,
'_priority': priority,
"_dupefinder": DupeFinderDB().to_dict()
}
fws.append(
Firework([VaspToDBTask({})],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-5))
connections[-6] = -5
wf = Workflow(fws, connections)
print 'Done adding more runs...'
return FWAction(additions=wf)
return FWAction()
def snl_to_wf(snl, parameters=None):
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
snl_spec = {}
if 'snlgroup_id' in parameters:
if 'mpsnl' in parameters:
snl_spec['mpsnl'] = parameters['mpsnl']
elif isinstance(snl, MPStructureNL):
snl_spec['mpsnl'] = snl.as_dict()
else:
raise ValueError("improper use of force SNL")
snl_spec['snlgroup_id'] = parameters['snlgroup_id']
else:
# 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
}
fws.append(
Firework(tasks,
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=0))
connections[0] = [1]
trackers = [
Tracker('FW_job.out'),
Tracker('FW_job.error'),
Tracker('vasp.out'),
Tracker('OUTCAR'),
Tracker('OSZICAR'),
Tracker('OUTCAR.relax1'),
Tracker('OUTCAR.relax2')
]
trackers_db = [Tracker('FW_job.out'), Tracker('FW_job.error')]
# run GGA structure optimization
spec = _snl_to_spec(snl, enforce_gga=True, parameters=parameters)
spec.update(snl_spec)
spec['_priority'] = priority
spec['_queueadapter'] = QA_VASP
spec['_trackers'] = trackers
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 * 2,
'_allow_fizzled_parents': True,
'_queueadapter': QA_DB,
"_dupefinder": DupeFinderDB().to_dict(),
'_trackers': trackers_db
}
fws.append(
Firework([VaspToDBTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=2))
connections[1] = [2]
# determine if GGA+U FW is needed
incar = MPVaspInputSet().get_incar(snl.structure).as_dict()
ggau_compound = ('LDAU' in incar and incar['LDAU'])
if not parameters.get('skip_bandstructure', False) and (
not ggau_compound
or parameters.get('force_gga_bandstructure', False)):
spec = {
'task_type': 'Controller: add Electronic Structure v2',
'_priority': priority,
'_queueadapter': QA_CONTROL
}
fws.append(
Firework([AddEStructureTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=3))
connections[2] = [3]
if ggau_compound:
spec = _snl_to_spec(snl, enforce_gga=False, parameters=parameters)
del spec[
'vasp'] # we are stealing all VASP params and such from previous run
spec['_priority'] = priority
spec['_queueadapter'] = QA_VASP
spec['_trackers'] = trackers
fws.append(
Firework(
[VaspCopyTask(),
SetupGGAUTask(),
get_custodian_task(spec)],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=10))
connections[2].append(10)
spec = {
'task_type': 'VASP db insertion',
'_queueadapter': QA_DB,
'_allow_fizzled_parents': True,
'_priority': priority,
"_dupefinder": DupeFinderDB().to_dict(),
'_trackers': trackers_db
}
fws.append(
Firework([VaspToDBTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=11))
connections[10] = [11]
if not parameters.get('skip_bandstructure', False):
spec = {
'task_type': 'Controller: add Electronic Structure v2',
'_priority': priority,
'_queueadapter': QA_CONTROL
}
fws.append(
Firework([AddEStructureTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=12))
connections[11] = [12]
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(snl, parameters=None):
fws = []
connections = {}
parameters = parameters if parameters else {}
snl_priority = parameters.get('priority', 1)
priority = snl_priority * 2 # once we start a job, keep going!
f = Composition.from_formula(
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.to_dict,
'_queueadapter': QA_DB,
'_priority': snl_priority
}
if 'snlgroup_id' in parameters and isinstance(snl, MPStructureNL):
spec['force_mpsnl'] = snl.to_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]
# run GGA structure optimization
spec = _snl_to_spec(snl, enforce_gga=True)
spec['_priority'] = priority
spec['_queueadapter'] = QA_VASP
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
}
fws.append(
FireWork([VaspToDBTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=2))
connections[1] = [2]
if not parameters.get('skip_bandstructure', False):
spec = {
'task_type': 'Controller: add Electronic Structure v2',
'_priority': priority,
'_queueadapter': QA_CONTROL
}
fws.append(
FireWork([AddEStructureTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=3))
connections[2] = [3]
# determine if GGA+U FW is needed
incar = MPVaspInputSet().get_incar(snl.structure).to_dict
if 'LDAU' in incar and incar['LDAU']:
spec = _snl_to_spec(snl, enforce_gga=False)
del spec[
'vasp'] # we are stealing all VASP params and such from previous run
spec['_priority'] = priority
spec['_queueadapter'] = QA_VASP
fws.append(
FireWork(
[VaspCopyTask(),
SetupGGAUTask(),
get_custodian_task(spec)],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=10))
connections[2].append(10)
spec = {
'task_type': 'VASP db insertion',
'_queueadapter': QA_DB,
'_allow_fizzled_parents': True,
'_priority': priority
}
fws.append(
FireWork([VaspToDBTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=11))
connections[10] = [11]
if not parameters.get('skip_bandstructure', False):
spec = {
'task_type': 'Controller: add Electronic Structure v2',
'_priority': priority,
'_queueadapter': QA_CONTROL
}
fws.append(
FireWork([AddEStructureTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=12))
connections[11] = [12]
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.from_formula(
snl.structure.composition.reduced_formula).alphabetical_formula,
metadata=wf_meta)
from mpworks.firetasks.vasp_io_tasks import VaspCopyTask, VaspToDBTask
from mpworks.workflows.wf_utils import last_relax, get_loc, move_to_garden
import os
import shutil
shutil.copyfile(
'/lustre/home/umjzhh-2/pv_me2/config/config_SjtuPi/my_launchpad.yaml',
'my_launchpad.yaml')
shutil.copyfile(
'/lustre/home/umjzhh-2/pv_me2/config/config_SjtuPi/FW_config.yaml',
'FW_config.yaml')
shutil.copyfile(
'/lustre/home/umjzhh-2/pv_me2/config/config_SjtuPi/my_fworker.yaml',
'my_fworker.yaml')
shutil.copyfile(
'/lustre/home/umjzhh-2/pv_me2/config/config_SjtuPi/my_qadapter.yaml',
'my_qadapter.yaml')
fw_spec = {
"prev_vasp_dir": os.getcwd(),
"prev_task_type": "GGA static v2",
"run_tags": "GGA static v2",
"dir_name": os.getcwd()
} #GGA optimize structure (2x)"#"run_tags":"GGA static v2"#GGA static v2 #GGA optimize structure (2x)
copy = VaspCopyTask()
#copy.run_task(fw_spec)
parameters = {"additional_fields": {}}
to_db = VaspToDBTask()
to_db.run_task(fw_spec)
