def test_check_correct_electronic_repeat(self):
shutil.copy("vasprun.xml.electronic2", "vasprun.xml")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d, {"errors": ["Unconverged"], "actions": None})
os.remove("vasprun.xml")
def test_check_correct_ionic(self):
shutil.copy("vasprun.xml.ionic", "vasprun.xml")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d["errors"], ['Unconverged'])
os.remove("vasprun.xml")
def test_check_correct_ionic(self):
shutil.copy("vasprun.xml.ionic", "vasprun.xml")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d["errors"], ['Unconverged'])
os.remove("vasprun.xml")
def test_check_correct_electronic_repeat(self):
shutil.copy("vasprun.xml.electronic2", "vasprun.xml")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d, {"errors": ["Unconverged"], "actions": None})
os.remove("vasprun.xml")
def test_check_correct_electronic_repeat(self):
shutil.copy("vasprun.xml.electronic2", "vasprun.xml")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d, {'actions': [{'action': {'_set': {'ALGO': 'All'}}, 'dict': 'INCAR'}],
'errors': ['Unconverged']})
os.remove("vasprun.xml")
def test_check_correct_scan(self):
shutil.copy("vasprun.xml.scan", "vasprun.xml")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d["errors"], ['Unconverged'])
self.assertIn({"dict": "INCAR",
"action": {"_set": {"ALGO": "All"}}},d["actions"])
os.remove("vasprun.xml")
def test_check_correct_scan(self):
shutil.copy("vasprun.xml.scan", "vasprun.xml")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d["errors"], ['Unconverged'])
self.assertIn({"dict": "INCAR",
"action": {"_set": {"ALGO": "All"}}},d["actions"])
os.remove("vasprun.xml")
def test_is_converged(self):
import pymatgen
print(pymatgen.__file__)
print(pymatgen.__version__)
import custodian
print(custodian.__version__)
path = os.path.join(TEST_PATH, self.path, 'unconverged', 'vasprun.xml')
handler = UnconvergedErrorHandler(path)
print(handler.check())
def test_check_correct(self):
subdir = os.path.join(test_dir, "unconverged")
os.chdir(subdir)
shutil.copy("INCAR", "INCAR.orig")
shutil.copy("KPOINTS", "KPOINTS.orig")
shutil.copy("POSCAR", "POSCAR.orig")
shutil.copy("CONTCAR", "CONTCAR.orig")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d["errors"], ['Unconverged'])
os.remove(os.path.join(subdir, "error.1.tar.gz"))
shutil.move("INCAR.orig", "INCAR")
shutil.move("KPOINTS.orig", "KPOINTS")
shutil.move("POSCAR.orig", "POSCAR")
shutil.move("CONTCAR.orig", "CONTCAR")
def test_check_correct_electronic_repeat(self):
shutil.copy("vasprun.xml.electronic2", "vasprun.xml")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(
d,
{
"actions": [{
"action": {
"_set": {
"ALGO": "All"
}
},
"dict": "INCAR"
}],
"errors": ["Unconverged"],
},
)
os.remove("vasprun.xml")
def test_check_correct(self):
subdir = os.path.join(test_dir, "unconverged")
os.chdir(subdir)
shutil.copy("INCAR", "INCAR.orig")
shutil.copy("KPOINTS", "KPOINTS.orig")
shutil.copy("POSCAR", "POSCAR.orig")
shutil.copy("CONTCAR", "CONTCAR.orig")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d["errors"], ['Unconverged'])
os.remove(os.path.join(subdir, "error.1.tar.gz"))
shutil.move("INCAR.orig", "INCAR")
shutil.move("KPOINTS.orig", "KPOINTS")
shutil.move("POSCAR.orig", "POSCAR")
shutil.move("CONTCAR.orig", "CONTCAR")
def test_check_correct_electronic(self):
shutil.copy("vasprun.xml.electronic", "vasprun.xml")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d["errors"], ["Unconverged"])
self.assertEqual(
d,
{
"actions": [{
"action": {
"_set": {
"ALGO": "Normal"
}
},
"dict": "INCAR"
}],
"errors": ["Unconverged"],
},
)
shutil.copy("vasprun.xml.electronic_veryfast", "vasprun.xml")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d["errors"], ["Unconverged"])
self.assertEqual(
d,
{
"actions": [{
"action": {
"_set": {
"ALGO": "Fast"
}
},
"dict": "INCAR"
}],
"errors": ["Unconverged"],
},
)
shutil.copy("vasprun.xml.electronic_normal", "vasprun.xml")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d["errors"], ["Unconverged"])
self.assertEqual(
d,
{
"actions": [{
"action": {
"_set": {
"ALGO": "All"
}
},
"dict": "INCAR"
}],
"errors": ["Unconverged"],
},
)
shutil.copy("vasprun.xml.electronic_metagga_fast", "vasprun.xml")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d["errors"], ["Unconverged"])
self.assertEqual(
d,
{
"actions": [{
"action": {
"_set": {
"ALGO": "All"
}
},
"dict": "INCAR"
}],
"errors": ["Unconverged"],
},
)
shutil.copy("vasprun.xml.electronic_hybrid_fast", "vasprun.xml")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d["errors"], ["Unconverged"])
self.assertEqual(
d,
{
"actions": [{
"action": {
"_set": {
"ALGO": "All"
}
},
"dict": "INCAR"
}],
"errors": ["Unconverged"],
},
)
os.remove("vasprun.xml")
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...")
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']
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)
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']}
snl = StructureNL.from_dict(spec['mpsnl'])
spec['run_tags'].append(unconverged_tag)
spec['_queueadapter'] = QA_VASP
fws = []
connections = {}
f = Composition.from_formula(
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'])}
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...")
