def __init__(self, structure, supercell_matrix, t_min=5, t_max=2000, t_step=5,
name="phonon", vasp_input_set=None, override_default_vasp_params=None,
vasp_cmd="vasp", metadata=None, tag=None, qpoint_mesh=(50, 50, 50),
prev_calc_loc=True, db_file=None, parents=None, stable_tor=0.01,
**kwargs):
metadata = metadata or {}
tag = tag or metadata.get('tag')
# generate a tag with a warning
if tag is None:
tag = str(uuid4())
warnings.warn('No ``tag`` was passed explicitly or in ``metadata`` to PhononFW. In order to find this Firework later, you should assign one. This was assigned: {}'.format(tag))
metadata['tag'] = tag
override_default_vasp_params = override_default_vasp_params or {}
ncell = int(0.5+np.linalg.det(supercell_matrix))
tmp = copy.deepcopy(override_default_vasp_params)
if 'user_incar_settings' in tmp:
if 'magmom' in tmp['user_incar_settings']:
mag = tmp['user_incar_settings']['magmom']
supermag = []
for site in mag:
n = str(site).split('*')
if len(n)==1:
supermag.append('{}*{}'.format(ncell,float(n[0])))
else:
supermag.append('{}*{}'.format(ncell*int(n[0]),float(n[1])))
tmp['user_incar_settings']['magmom']=supermag
print("phonon setting", tmp)
vasp_input_set = vasp_input_set or ForceConstantsSet(structure, **tmp)
supercell_structure = deepcopy(structure)
supercell_structure.make_supercell(supercell_matrix)
supercell_site_properties = deepcopy(supercell_structure.site_properties)
t = []
# We need to get the POSCAR from the previous run or from the passed Structure
# so it can be transformed to a supercell in the next step
if parents:
if prev_calc_loc:
t.append(CopyVaspOutputs(calc_loc=prev_calc_loc, contcar_to_poscar=True))
else:
# write the input set first, just to get the POSCAR file in the directory
# the other inputs will get overridden by WriteVaspFromIOSetPrevStructure
t.append(WriteVaspFromIOSetPrevStructure(structure=structure, vasp_input_set=vasp_input_set, site_properties=site_properties))
t.append(SupercellTransformation(supercell_matrix=supercell_matrix))
t.append(WriteVaspFromIOSetPrevStructure(vasp_input_set=vasp_input_set, site_properties=supercell_site_properties))
t.append(RunVaspCustodianNoValidate(vasp_cmd=vasp_cmd, auto_npar=">>auto_npar<<", gzip_output=False))
# we skipped the validation so we can potentially fix the vasprun.xml file.
# Fix and validate here.
t.append(PyTask(func='dfttk.vasprun_fix.fix_vasprun', args=['vasprun.xml']))
t.append(PassCalcLocs(name=name))
t.append(CalculatePhononThermalProperties(supercell_matrix=supercell_matrix, t_min=t_min, t_max=t_max, t_step=t_step, db_file=">>db_file<<", tag=tag, metadata=metadata))
t.append(PhononStable(supercell_matrix=supercell_matrix, db_file=">>db_file<<", tag=tag, metadata=metadata, qpoint_mesh=qpoint_mesh, stable_tor=stable_tor))
super(PhononFW, self).__init__(t, parents=parents, name="{}-{}".format(
structure.composition.reduced_formula, name), **kwargs)
def __init__(self,
structure,
supercell_matrix,
t_min=5,
t_max=2000,
t_step=5,
name="phonon",
vasp_input_set=None,
vasp_cmd="vasp",
metadata=None,
tag=None,
prev_calc_loc=True,
db_file=None,
parents=None,
**kwargs):
metadata = metadata or {}
tag = tag or metadata.get('tag')
# generate a tag with a warning
if tag is None:
tag = str(uuid4())
warnings.warn(
'No ``tag`` was passed explicitly or in ``metadata`` to PhononFW. In order to find this Firework later, you should assign one. This was assigned: {}'
.format(tag))
metadata['tag'] = tag
vasp_input_set = vasp_input_set or ForceConstantsSet(structure)
supercell_structure = deepcopy(structure)
supercell_structure.make_supercell(supercell_matrix)
supercell_site_properties = deepcopy(
supercell_structure.site_properties)
t = []
# We need to get the POSCAR from the previous run or from the passed Structure
# so it can be transformed to a supercell in the next step
if parents:
if prev_calc_loc:
t.append(
CopyVaspOutputs(calc_loc=prev_calc_loc,
contcar_to_poscar=True))
else:
# write the input set first, just to get the POSCAR file in the directory
# the other inputs will get overridden by WriteVaspFromIOSetPrevStructure
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
t.append(SupercellTransformation(supercell_matrix=supercell_matrix))
t.append(
WriteVaspFromIOSetPrevStructure(
vasp_input_set=vasp_input_set,
site_properties=supercell_site_properties))
t.append(
RunVaspCustodianNoValidate(vasp_cmd=vasp_cmd,
auto_npar=">>auto_npar<<",
gzip_output=False))
# we skipped the validation so we can potentially fix the vasprun.xml file.
# Fix and validate here.
t.append(
PyTask(func='dfttk.vasprun_fix.fix_vasprun', args=['vasprun.xml']))
t.append(PassCalcLocs(name=name))
t.append(
CalculatePhononThermalProperties(supercell_matrix=supercell_matrix,
t_min=t_min,
t_max=t_max,
t_step=t_step,
db_file=db_file,
tag=tag,
metadata=metadata))
super(PhononFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)