def _snl_to_spec(snl, enforce_gga=False, parameters=None):
parameters = parameters if parameters else {}
parameters.setdefault('boltztrap', True) # by default run boltztrap
parameters.setdefault('force_gamma', False) # by default not force gamma
parameters.setdefault('exact_structure', True)
spec = {'parameters': parameters}
incar_enforce = {'NCORE': 8}
if parameters['exact_structure']:
structure = snl.structure
else:
structure = snl.structure.get_primitive_structure()
if enforce_gga:
incar_enforce.update({"LDAU": False})
mpvis = MPRelaxSet(structure,
user_incar_settings=incar_enforce,
force_gamma=parameters['force_gamma'])
incar = mpvis.incar
poscar = mpvis.poscar
kpoints = mpvis.kpoints
potcar = mpvis.potcar
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 \
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 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 run_task(self, fw_spec):
if '_fizzled_parents' in fw_spec and not 'prev_vasp_dir' in fw_spec:
prev_dir = get_loc(
fw_spec['_fizzled_parents'][0]['launches'][0]['launch_dir'])
update_spec = {} # add this later when creating new FW
fizzled_parent = True
parse_dos = False
else:
prev_dir = get_loc(fw_spec['prev_vasp_dir'])
update_spec = {
'prev_vasp_dir': prev_dir,
'prev_task_type': fw_spec['prev_task_type'],
'run_tags': fw_spec['run_tags'],
'parameters': fw_spec.get('parameters')
}
fizzled_parent = False
parse_dos = 'Uniform' in fw_spec['prev_task_type']
if 'run_tags' in fw_spec:
self.additional_fields['run_tags'] = fw_spec['run_tags']
else:
self.additional_fields['run_tags'] = fw_spec['_fizzled_parents'][
0]['spec']['run_tags']
if MOVE_TO_GARDEN_DEV:
prev_dir = move_to_garden(prev_dir, prod=False)
elif MOVE_TO_GARDEN_PROD:
prev_dir = move_to_garden(prev_dir, prod=True)
# get the directory containing the db file
db_dir = os.environ['DB_LOC']
db_path = os.path.join(db_dir, 'tasks_db.json')
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger('MPVaspDrone')
logger.setLevel(logging.INFO)
sh = logging.StreamHandler(stream=sys.stdout)
sh.setLevel(getattr(logging, 'INFO'))
logger.addHandler(sh)
with open(db_path) as f:
db_creds = json.load(f)
drone = MPVaspDrone(host=db_creds['host'],
port=db_creds['port'],
database=db_creds['database'],
user=db_creds['admin_user'],
password=db_creds['admin_password'],
collection=db_creds['collection'],
parse_dos=parse_dos,
additional_fields=self.additional_fields,
update_duplicates=self.update_duplicates)
t_id, d = drone.assimilate(
prev_dir, launches_coll=LaunchPad.auto_load().launches)
mpsnl = d['snl_final'] if 'snl_final' in d else d['snl']
snlgroup_id = d['snlgroup_id_final'] if 'snlgroup_id_final' in d else d[
'snlgroup_id']
update_spec.update({'mpsnl': mpsnl, 'snlgroup_id': snlgroup_id})
print 'ENTERED task id:', t_id
stored_data = {'task_id': t_id}
if d['state'] == 'successful':
update_spec['analysis'] = d['analysis']
update_spec['output'] = d['output']
update_spec['vasp'] = {
'incar': d['calculations'][-1]['input']['incar'],
'kpoints': d['calculations'][-1]['input']['kpoints']
}
update_spec["task_id"] = t_id
return FWAction(stored_data=stored_data, update_spec=update_spec)
# not successful - first test to see if UnconvergedHandler is needed
if not fizzled_parent:
unconverged_tag = 'unconverged_handler--{}'.format(
fw_spec['prev_task_type'])
output_dir = last_relax(os.path.join(prev_dir, 'vasprun.xml'))
ueh = UnconvergedErrorHandler(output_filename=output_dir)
# TODO: make this a little more flexible
if ueh.check() and unconverged_tag not in fw_spec['run_tags']:
print 'Unconverged run! Creating dynamic FW...'
spec = {
'prev_vasp_dir': prev_dir,
'prev_task_type': fw_spec['task_type'],
'mpsnl': mpsnl,
'snlgroup_id': snlgroup_id,
'task_type': fw_spec['prev_task_type'],
'run_tags': list(fw_spec['run_tags']),
'parameters': fw_spec.get('parameters'),
'_dupefinder': DupeFinderVasp().to_dict(),
'_priority': fw_spec['_priority']
}
# Pass elastic tensor spec
if 'deformation_matrix' in fw_spec.keys():
spec['deformation_matrix'] = fw_spec['deformation_matrix']
spec['original_task_id'] = fw_spec['original_task_id']
snl = StructureNL.from_dict(spec['mpsnl'])
spec['run_tags'].append(unconverged_tag)
spec['_queueadapter'] = QA_VASP
fws = []
connections = {}
f = Composition(snl.structure.composition.reduced_formula
).alphabetical_formula
fws.append(
Firework([
VaspCopyTask({
'files': [
'INCAR', 'KPOINTS', 'POSCAR', 'POTCAR',
'CONTCAR'
],
'use_CONTCAR':
False
}),
SetupUnconvergedHandlerTask(),
get_custodian_task(spec)
],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-2))
spec = {
'task_type': 'VASP db insertion',
'_allow_fizzled_parents': True,
'_priority': fw_spec['_priority'],
'_queueadapter': QA_DB,
'run_tags': list(fw_spec['run_tags'])
}
if 'deformation_matrix' in fw_spec.keys():
spec['deformation_matrix'] = fw_spec['deformation_matrix']
spec['original_task_id'] = fw_spec['original_task_id']
spec['run_tags'].append(unconverged_tag)
fws.append(
Firework([VaspToDBTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-1))
connections[-2] = -1
wf = Workflow(fws, connections)
return FWAction(detours=wf)
# not successful and not due to convergence problem - FIZZLE
raise ValueError("DB insertion successful, but don't know how to \
fix this Firework! Can't continue with workflow...")
