def __init__(self,
mol,
molname,
mission,
additional_user_tags=None,
dupefinder=None,
priority=1,
update_spec=None,
large=False):
self.molname = molname
self.mol = mol
self.large = large
initial_inchi = self.get_inchi(mol)
user_tags = {'mission': mission, "molname": molname}
if additional_user_tags:
user_tags.update(additional_user_tags)
spec = dict()
spec['user_tags'] = user_tags
spec['_priority'] = priority
spec['_dupefinder'] = dupefinder.to_dict() if dupefinder \
else DupeFinderEG().to_dict()
tracker_out = Tracker("mol.qcout", nlines=20)
tracker_std = Tracker("mol.qclog", nlines=10)
tracker_joberr = Tracker("FW_job.error", nlines=20)
tracker_jobout = Tracker("FW_job.out", nlines=20)
spec["_trackers"] = [
tracker_out, tracker_std, tracker_joberr, tracker_jobout
]
spec['run_tags'] = dict()
spec['implicit_solvent'] = {}
spec['inchi'] = initial_inchi
spec['num_atoms'] = len(mol)
if update_spec:
spec.update(update_spec)
self.base_spec = lambda: copy.deepcopy(spec)
def setUp(self):
self.old_wd = os.getcwd()
self.dest1 = os.path.join(MODULE_DIR, "numbers1.txt")
self.dest2 = os.path.join(MODULE_DIR, "numbers2.txt")
self.tracker1 = Tracker(self.dest1, nlines=2)
self.tracker2 = Tracker(self.dest2, nlines=2)
def add_trackers(original_wf, tracked_files=None, nlines=25):
"""
Every FireWork that runs VASP also tracks the OUTCAR, OSZICAR, etc using FWS
Trackers.
Args:
original_wf (Workflow)
tracked_files (list) : list of files to be tracked
nlines (int): number of lines at the end of files to be tracked
Returns:
Workflow
"""
if tracked_files is None:
tracked_files = ["OUTCAR", "OSZICAR"]
trackers = [
Tracker(f, nlines=nlines, allow_zipped=True) for f in tracked_files
]
idx_list = get_fws_and_tasks(original_wf, task_name_constraint="RunVasp")
for idx_fw, idx_t in idx_list:
if "_trackers" in original_wf.fws[idx_fw].spec:
original_wf.fws[idx_fw].spec["_trackers"].extend(trackers)
else:
original_wf.fws[idx_fw].spec["_trackers"] = trackers
return original_wf
def add_trackers(original_wf, tracked_files=None, nlines=25):
"""
Every FireWork that runs VASP also tracks the OUTCAR, OSZICAR, etc using FWS Trackers.
Args:
original_wf (Workflow)
tracked_files (list) : list of files to be tracked
nlines (int): number of lines at the end of files to be tracked
"""
if tracked_files == None:
tracked_files = ["OUTCAR", "OSZICAR"]
trackers = [
Tracker(f, nlines=nlines, allow_zipped=True) for f in tracked_files
]
wf_dict = original_wf.to_dict()
for idx_fw, idx_t in get_fws_and_tasks(original_wf,
task_name_constraint="RunVasp"):
if "_trackers" in wf_dict["fws"][idx_fw]["spec"]:
wf_dict["fws"][idx_fw]["spec"]["_trackers"].extend(trackers)
else:
wf_dict["fws"][idx_fw]["spec"]["_trackers"] = trackers
return Workflow.from_dict(wf_dict)
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 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)
