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 _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=True):
spec = {}
mpvis = MPGGAVaspInputSet() if enforce_gga else MPVaspInputSet()
structure = snl.structure
spec['vasp'] = {}
spec['vasp']['incar'] = mpvis.get_incar(structure).to_dict
spec['vasp']['incar']['NPAR'] = 2
spec['vasp']['poscar'] = mpvis.get_poscar(structure).to_dict
spec['vasp']['kpoints'] = mpvis.get_kpoints(structure).to_dict
spec['vasp']['potcar'] = mpvis.get_potcar(structure).to_dict
spec['_dupefinder'] = DupeFinderVasp().to_dict()
spec['_priority'] = 2
# TODO: restore category
# spec['_category'] = 'Materials Project'
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)'
spec.update(_get_metadata(snl))
return spec
def _snl_to_spec(snl, enforce_gga=False, parameters=None):
parameters = parameters if parameters else {}
parameters['boltztrap'] = parameters.get('boltztrap',
True) # by default run boltztrap
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.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 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 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('', gzipped=False)
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 vac_antisite_def_struct_gen(mpid, mapi_key, cellmax):
if not mpid:
print ("============\nERROR: Provide an mpid\n============")
return
if not mapi_key:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
else:
with MPRester(mapi_key) as mp:
struct = mp.get_structure_by_material_id(mpid)
prim_struct_sites = len(struct.sites)
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
conv_struct_sites = len(struct.sites)
conv_prim_rat = int(conv_struct_sites/prim_struct_sites)
sc_scale = get_sc_scale(struct,cellmax)
mpvis = MPGGAVaspInputSet()
# Begin defaults: All default settings.
blk_vasp_incar_param = {'IBRION':-1,'EDIFF':1e-4,'EDIFFG':0.001,'NSW':0,}
def_vasp_incar_param = {'ISIF':2,'NELM':99,'IBRION':2,'EDIFF':1e-6,
'EDIFFG':0.001,'NSW':40,}
kpoint_den = 6000
# End defaults
ptcr_flag = True
try:
potcar = mpvis.get_potcar(struct)
except:
print ("VASP POTCAR folder not detected.\n" \
"Only INCAR, POSCAR, KPOINTS are generated.\n" \
"If you have VASP installed on this system, \n" \
"refer to pymatgen documentation for configuring the settings.")
ptcr_flag = False
vac = Vacancy(struct, {}, {})
scs = vac.make_supercells_with_defects(sc_scale)
site_no = scs[0].num_sites
if site_no > cellmax:
max_sc_dim = max(sc_scale)
i = sc_scale.index(max_sc_dim)
sc_scale[i] -= 1
scs = vac.make_supercells_with_defects(sc_scale)
for i in range(len(scs)):
sc = scs[i]
poscar = mpvis.get_poscar(sc)
kpoints = Kpoints.automatic_density(sc,kpoint_den)
incar = mpvis.get_incar(sc)
if ptcr_flag:
potcar = mpvis.get_potcar(sc)
interdir = mpid
if not i:
fin_dir = os.path.join(interdir,'bulk')
try:
os.makedirs(fin_dir)
except:
pass
incar.update(blk_vasp_incar_param)
incar.write_file(os.path.join(fin_dir,'INCAR'))
poscar.write_file(os.path.join(fin_dir,'POSCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir,'POTCAR'))
kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
else:
blk_str_sites = set(scs[0].sites)
vac_str_sites = set(sc.sites)
vac_sites = blk_str_sites - vac_str_sites
vac_site = list(vac_sites)[0]
site_mult = int(vac.get_defectsite_multiplicity(i-1)/conv_prim_rat)
vac_site_specie = vac_site.specie
vac_symbol = vac_site.specie.symbol
vac_dir ='vacancy_{}_mult-{}_sitespecie-{}'.format(str(i),
site_mult, vac_symbol)
fin_dir = os.path.join(interdir,vac_dir)
try:
os.makedirs(fin_dir)
except:
pass
incar.update(def_vasp_incar_param)
poscar.write_file(os.path.join(fin_dir,'POSCAR'))
incar.write_file(os.path.join(fin_dir,'INCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir,'POTCAR'))
kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
# Antisite generation at all vacancy sites
struct_species = scs[0].types_of_specie
for specie in set(struct_species)-set([vac_site_specie]):
subspecie_symbol = specie.symbol
anti_struct = sc.copy()
anti_struct.append(specie, vac_site.frac_coords)
poscar = mpvis.get_poscar(anti_struct)
incar = mpvis.get_incar(anti_struct)
incar.update(def_vasp_incar_param)
as_dir ='antisite_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
str(i), site_mult, vac_symbol, subspecie_symbol)
fin_dir = os.path.join(interdir,as_dir)
try:
os.makedirs(fin_dir)
except:
pass
poscar.write_file(os.path.join(fin_dir,'POSCAR'))
incar.write_file(os.path.join(fin_dir,'INCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir,'POTCAR'))
kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
def vac_antisite_def_struct_gen(mpid, mapi_key, cellmax):
if not mpid:
print("============\nERROR: Provide an mpid\n============")
return
if not mapi_key:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
else:
with MPRester(mapi_key) as mp:
struct = mp.get_structure_by_material_id(mpid)
prim_struct_sites = len(struct.sites)
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
conv_struct_sites = len(struct.sites)
conv_prim_rat = int(conv_struct_sites / prim_struct_sites)
sc_scale = get_sc_scale(struct, cellmax)
mpvis = MPGGAVaspInputSet()
# Begin defaults: All default settings.
blk_vasp_incar_param = {
'IBRION': -1,
'EDIFF': 1e-4,
'EDIFFG': 0.001,
'NSW': 0,
}
def_vasp_incar_param = {
'ISIF': 2,
'NELM': 99,
'IBRION': 2,
'EDIFF': 1e-6,
'EDIFFG': 0.001,
'NSW': 40,
}
kpoint_den = 6000
# End defaults
ptcr_flag = True
try:
potcar = mpvis.get_potcar(struct)
except:
print ("VASP POTCAR folder not detected.\n" \
"Only INCAR, POSCAR, KPOINTS are generated.\n" \
"If you have VASP installed on this system, \n" \
"refer to pymatgen documentation for configuring the settings.")
ptcr_flag = False
vac = Vacancy(struct, {}, {})
scs = vac.make_supercells_with_defects(sc_scale)
site_no = scs[0].num_sites
if site_no > cellmax:
max_sc_dim = max(sc_scale)
i = sc_scale.index(max_sc_dim)
sc_scale[i] -= 1
scs = vac.make_supercells_with_defects(sc_scale)
for i in range(len(scs)):
sc = scs[i]
poscar = mpvis.get_poscar(sc)
kpoints = Kpoints.automatic_density(sc, kpoint_den)
incar = mpvis.get_incar(sc)
if ptcr_flag:
potcar = mpvis.get_potcar(sc)
interdir = mpid
if not i:
fin_dir = os.path.join(interdir, 'bulk')
try:
os.makedirs(fin_dir)
except:
pass
incar.update(blk_vasp_incar_param)
incar.write_file(os.path.join(fin_dir, 'INCAR'))
poscar.write_file(os.path.join(fin_dir, 'POSCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir, 'POTCAR'))
kpoints.write_file(os.path.join(fin_dir, 'KPOINTS'))
else:
blk_str_sites = set(scs[0].sites)
vac_str_sites = set(sc.sites)
vac_sites = blk_str_sites - vac_str_sites
vac_site = list(vac_sites)[0]
site_mult = int(
vac.get_defectsite_multiplicity(i - 1) / conv_prim_rat)
vac_site_specie = vac_site.specie
vac_symbol = vac_site.specie.symbol
vac_dir = 'vacancy_{}_mult-{}_sitespecie-{}'.format(
str(i), site_mult, vac_symbol)
fin_dir = os.path.join(interdir, vac_dir)
try:
os.makedirs(fin_dir)
except:
pass
incar.update(def_vasp_incar_param)
poscar.write_file(os.path.join(fin_dir, 'POSCAR'))
incar.write_file(os.path.join(fin_dir, 'INCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir, 'POTCAR'))
kpoints.write_file(os.path.join(fin_dir, 'KPOINTS'))
# Antisite generation at all vacancy sites
struct_species = scs[0].types_of_specie
for specie in set(struct_species) - set([vac_site_specie]):
subspecie_symbol = specie.symbol
anti_struct = sc.copy()
anti_struct.append(specie, vac_site.frac_coords)
poscar = mpvis.get_poscar(anti_struct)
incar = mpvis.get_incar(anti_struct)
incar.update(def_vasp_incar_param)
as_dir = 'antisite_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
str(i), site_mult, vac_symbol, subspecie_symbol)
fin_dir = os.path.join(interdir, as_dir)
try:
os.makedirs(fin_dir)
except:
pass
poscar.write_file(os.path.join(fin_dir, 'POSCAR'))
incar.write_file(os.path.join(fin_dir, 'INCAR'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir, 'POTCAR'))
kpoints.write_file(os.path.join(fin_dir, 'KPOINTS'))
def substitute_def_struct_gen(mpid, solute, mapi_key, cellmax):
print(mpid, solute, mapi_key, cellmax)
if not mpid:
print("============\nERROR: Provide an mpid\n============")
return
if not solute:
print("============\nERROR: Provide solute atom\n============")
return
if not mapi_key:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
else:
with MPRester(mapi_key) as mp:
struct = mp.get_structure_by_material_id(mpid)
print(struct.formula)
mpvis = MPGGAVaspInputSet()
# Begin defaults: All default settings.
blk_vasp_incar_param = {
'IBRION': -1,
'EDIFF': 1e-4,
'EDIFFG': 0.001,
'NSW': 0,
}
def_vasp_incar_param = {
'ISIF': 2,
'NELM': 99,
'IBRION': 2,
'EDIFF': 1e-6,
'EDIFFG': 0.001,
'NSW': 40,
}
kpoint_den = 6000
# End defaults
# Check if POTCAR file can be geneated
ptcr_flag = True
try:
potcar = mpvis.get_potcar(struct)
except:
print ("VASP POTCAR folder not detected.\n" \
"Only INCAR, POSCAR, KPOINTS are generated.\n" \
"If you have VASP installed on this system, \n" \
"refer to pymatgen documentation for configuring the settings.")
ptcr_flag = False
print(ptcr_flag)
vac = Vacancy(struct, {}, {})
sc_scale = get_sc_scale(struct, cellmax)
scs = vac.make_supercells_with_defects(sc_scale)
site_no = scs[0].num_sites
if site_no > cellmax:
max_sc_dim = max(sc_scale)
i = sc_scale.index(max_sc_dim)
sc_scale[i] -= 1
scs = vac.make_supercells_with_defects(sc_scale)
print len(scs)
interdir = mpid
blk_str_sites = set(scs[0].sites)
for i in range(1, len(scs)):
sc = scs[i]
vac_str_sites = set(sc.sites)
vac_sites = blk_str_sites - vac_str_sites
vac_site = list(vac_sites)[0]
site_mult = vac.get_defectsite_multiplicity(i - 1)
vac_site_specie = vac_site.specie
vac_specie = vac_site.specie.symbol
# Solute substitution defect generation at all vacancy sites
struct_species = scs[0].types_of_specie
solute_struct = sc.copy()
solute_struct.append(solute, vac_site.frac_coords)
incar = mpvis.get_incar(solute_struct)
incar.update(def_vasp_incar_param)
poscar = mpvis.get_poscar(solute_struct)
kpoints = Kpoints.automatic_density(solute_struct, kpoint_den)
if ptcr_flag:
potcar = mpvis.get_potcar(solute_struct)
sub_def_dir = 'solute_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
str(i), site_mult, vac_specie, solute)
fin_dir = os.path.join(interdir, sub_def_dir)
try:
os.makedirs(fin_dir)
except:
pass
poscar.write_file(os.path.join(fin_dir, 'POSCAR'))
incar.write_file(os.path.join(fin_dir, 'INCAR'))
kpoints.write_file(os.path.join(fin_dir, 'KPOINTS'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir, 'POTCAR'))
def substitute_def_struct_gen(mpid, solute, mapi_key, cellmax):
print (mpid, solute, mapi_key, cellmax)
if not mpid:
print ("============\nERROR: Provide an mpid\n============")
return
if not solute:
print ("============\nERROR: Provide solute atom\n============")
return
if not mapi_key:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
else:
with MPRester(mapi_key) as mp:
struct = mp.get_structure_by_material_id(mpid)
print (struct.formula)
mpvis = MPGGAVaspInputSet()
# Begin defaults: All default settings.
blk_vasp_incar_param = {'IBRION':-1,'EDIFF':1e-4,'EDIFFG':0.001,'NSW':0,}
def_vasp_incar_param = {'ISIF':2,'NELM':99,'IBRION':2,'EDIFF':1e-6,
'EDIFFG':0.001,'NSW':40,}
kpoint_den = 6000
# End defaults
# Check if POTCAR file can be geneated
ptcr_flag = True
try:
potcar = mpvis.get_potcar(struct)
except:
print ("VASP POTCAR folder not detected.\n" \
"Only INCAR, POSCAR, KPOINTS are generated.\n" \
"If you have VASP installed on this system, \n" \
"refer to pymatgen documentation for configuring the settings.")
ptcr_flag = False
print (ptcr_flag)
vac = Vacancy(struct, {}, {})
sc_scale = get_sc_scale(struct,cellmax)
scs = vac.make_supercells_with_defects(sc_scale)
site_no = scs[0].num_sites
if site_no > cellmax:
max_sc_dim = max(sc_scale)
i = sc_scale.index(max_sc_dim)
sc_scale[i] -= 1
scs = vac.make_supercells_with_defects(sc_scale)
print len(scs)
interdir = mpid
blk_str_sites = set(scs[0].sites)
for i in range(1,len(scs)):
sc = scs[i]
vac_str_sites = set(sc.sites)
vac_sites = blk_str_sites - vac_str_sites
vac_site = list(vac_sites)[0]
site_mult = vac.get_defectsite_multiplicity(i-1)
vac_site_specie = vac_site.specie
vac_specie = vac_site.specie.symbol
# Solute substitution defect generation at all vacancy sites
struct_species = scs[0].types_of_specie
solute_struct = sc.copy()
solute_struct.append(solute, vac_site.frac_coords)
incar = mpvis.get_incar(solute_struct)
incar.update(def_vasp_incar_param)
poscar = mpvis.get_poscar(solute_struct)
kpoints = Kpoints.automatic_density(solute_struct,kpoint_den)
if ptcr_flag:
potcar = mpvis.get_potcar(solute_struct)
sub_def_dir ='solute_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
str(i), site_mult, vac_specie, solute)
fin_dir = os.path.join(interdir,sub_def_dir)
try:
os.makedirs(fin_dir)
except:
pass
poscar.write_file(os.path.join(fin_dir,'POSCAR'))
incar.write_file(os.path.join(fin_dir,'INCAR'))
kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
if ptcr_flag:
potcar.write_file(os.path.join(fin_dir,'POTCAR'))
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.to_dict
spec['vasp']['poscar'] = poscar.to_dict
spec['vasp']['kpoints'] = kpoints.to_dict
spec['vasp']['potcar'] = potcar.to_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('', gzipped=False)
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.to_dict for j in jobs], 'handlers': [h.to_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).to_dict], 'handlers': [h.to_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))
