def __init__(self, structure=None, prev_calc_dir=None, name="static dielectric", vasp_cmd=VASP_CMD,
copy_vasp_outputs=True, lepsilon=True,
db_file=DB_FILE, parents=None, user_incar_settings=None,
pass_nm_results=False, **kwargs):
"""
Static DFPT calculation Firework
Args:
structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
name of the FW.
name (str): Name for the Firework.
lepsilon (bool): Turn on LEPSILON to calculate polar properties
vasp_cmd (str): Command to run vasp.
copy_vasp_outputs (str or bool): Whether to copy outputs from previous
run. Defaults to True.
prev_calc_dir (str): Path to a previous calculation to copy from
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework.
FW or list of FWS.
user_incar_settings (dict): Parameters in INCAR to override
pass_nm_results (bool): if true the normal mode eigen vals and vecs are passed so that
next firework can use it.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
name = "static dielectric" if lepsilon else "phonon"
fw_name = "{}-{}".format(structure.composition.reduced_formula if structure else "unknown", name)
user_incar_settings = user_incar_settings or {}
t = []
if prev_calc_dir:
t.append(CopyVaspOutputs(calc_dir=prev_calc_dir, contcar_to_poscar=True))
t.append(WriteVaspStaticFromPrev(lepsilon=lepsilon, other_params={
'user_incar_settings': user_incar_settings, 'force_gamma': True}))
elif parents and copy_vasp_outputs:
t.append(CopyVaspOutputs(calc_loc=True, contcar_to_poscar=True))
t.append(WriteVaspStaticFromPrev(lepsilon=lepsilon, other_params={
'user_incar_settings': user_incar_settings, 'force_gamma': True}))
elif structure:
vasp_input_set = MPStaticSet(structure, lepsilon=lepsilon, force_gamma=True,
user_incar_settings=user_incar_settings)
t.append(WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
else:
raise ValueError("Must specify structure or previous calculation")
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
if pass_nm_results:
t.append(pass_vasp_result({"structure": "a>>final_structure",
"eigenvals": "a>>normalmode_eigenvals",
"eigenvecs": "a>>normalmode_eigenvecs"},
parse_eigen=True,
mod_spec_key="normalmodes"))
t.append(PassCalcLocs(name=name))
t.append(VaspToDb(db_file=db_file, additional_fields={"task_label": name}))
super(DFPTFW, self).__init__(t, parents=parents, name=fw_name, **kwargs)
def __init__(self, structure=None, name="static", vasp_input_set=None, vasp_input_set_params=None,
vasp_cmd=VASP_CMD, prev_calc_loc=True, prev_calc_dir=None, db_file=DB_FILE, vasptodb_kwargs=None,
parents=None, **kwargs):
"""
Standard static calculation Firework - either from a previous location or from a structure.
Args:
structure (Structure): Input structure. Note that for prev_calc_loc jobs, the structure
is only used to set the name of the FW and any structure with the same composition
can be used.
name (str): Name for the Firework.
vasp_input_set (VaspInputSet): input set to use (for jobs w/no parents)
Defaults to MPStaticSet() if None.
vasp_input_set_params (dict): Dict of vasp_input_set kwargs.
vasp_cmd (str): Command to run vasp.
prev_calc_loc (bool or str): If true (default), copies outputs from previous calc. If
a str value, retrieves a previous calculation output by name. If False/None, will create
new static calculation using the provided structure.
prev_calc_dir (str): Path to a previous calculation to copy from
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework. FW or list of FWS.
vasptodb_kwargs (dict): kwargs to pass to VaspToDb
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
t = []
vasp_input_set_params = vasp_input_set_params or {}
vasptodb_kwargs = vasptodb_kwargs or {}
if "additional_fields" not in vasptodb_kwargs:
vasptodb_kwargs["additional_fields"] = {}
vasptodb_kwargs["additional_fields"]["task_label"] = name
fw_name = "{}-{}".format(structure.composition.reduced_formula if structure else "unknown", name)
if prev_calc_dir:
t.append(CopyVaspOutputs(calc_dir=prev_calc_dir, contcar_to_poscar=True))
t.append(WriteVaspStaticFromPrev(other_params=vasp_input_set_params))
elif parents:
if prev_calc_loc:
t.append(CopyVaspOutputs(calc_loc=prev_calc_loc,
contcar_to_poscar=True))
t.append(WriteVaspStaticFromPrev(other_params=vasp_input_set_params))
elif structure:
vasp_input_set = vasp_input_set or MPStaticSet(structure, **vasp_input_set_params)
t.append(WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
else:
raise ValueError("Must specify structure or previous calculation")
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd, auto_npar=">>auto_npar<<"))
t.append(PassCalcLocs(name=name))
t.append(
VaspToDb(db_file=db_file, **vasptodb_kwargs))
super(StaticFW, self).__init__(t, parents=parents, name=fw_name, **kwargs)
def __init__(self, mode, displacement, prev_calc_dir=None, structure=None, name="raman",
vasp_cmd=VASP_CMD, db_file=DB_FILE,
parents=None, user_incar_settings=None, **kwargs):
"""
Static calculation Firework that computes the DFPT dielectric constant for
structure displaced along the given normal mode direction.
Args:
structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
name of the FW.
mode (int): normal mode index.
displacement (float): displacement along the normal mode in Angstroms.
name (str): Name for the Firework.
prev_calc_dir (str): Path to a previous calculation to copy from
vasp_cmd (str): Command to run vasp.
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework.
FW or list of FWS.
user_incar_settings (dict): Parameters in INCAR to override
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
name = "{}_{}_{}".format(name, str(mode), str(displacement))
fw_name = "{}-{}".format(structure.composition.reduced_formula if structure else "unknown", name)
user_incar_settings = user_incar_settings or {}
t = []
if prev_calc_dir:
t.append(CopyVaspOutputs(calc_dir=prev_calc_dir, contcar_to_poscar=True))
elif parents:
t.append(CopyVaspOutputs(calc_loc=True, contcar_to_poscar=True))
else:
raise ValueError("Must specify a previous calculation")
t.append(WriteVaspStaticFromPrev(lepsilon=True, other_params={
'user_incar_settings': user_incar_settings}))
t.append(WriteNormalmodeDisplacedPoscar(mode=mode,
displacement=displacement))
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
key = "{}_{}".format(mode, displacement).replace('-', 'm').replace('.',
'd')
t.append(pass_vasp_result(pass_dict={"mode": mode,
"displacement": displacement,
"epsilon": "a>>epsilon_static"},
mod_spec_key="raman_epsilon->{}".format(key),
parse_eigen=True))
t.append(PassCalcLocs(name=name))
t.append(
VaspToDb(db_file=db_file, additional_fields={"task_label": name}))
super(RamanFW, self).__init__(t, parents=parents, name=fw_name, **kwargs)
def __init__(self,
structure,
name="static",
vasp_input_set=None,
vasp_cmd="vasp",
prev_calc_loc=True,
db_file=None,
parents=None,
**kwargs):
"""
Standard static calculation Firework - either from a previous location or from a structure.
Args:
structure (Structure): Input structure. Note that for prev_calc_loc jobs, the structure
is only used to set the name of the FW and any structure with the same composition
can be used.
name (str): Name for the Firework.
vasp_input_set (VaspInputSet): input set to use (for jobs w/no parents)
Defaults to MPStaticSet() if None.
vasp_cmd (str): Command to run vasp.
prev_calc_loc (bool or str): If true (default), copies outputs from previous calc. If
a str value, grabs a previous calculation output by name. If False/None, will create
new static calculation using the provided structure.
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework. FW or list of FWS.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
# TODO: @computron - I really don't like how you need to set the structure even for
# prev_calc_loc jobs. Sometimes it makes appending new FWs to an existing workflow
# difficult. Maybe think about how to remove this need? -computron
t = []
if parents:
if prev_calc_loc:
t.append(
CopyVaspOutputs(calc_loc=prev_calc_loc,
contcar_to_poscar=True))
t.append(WriteVaspStaticFromPrev())
else:
vasp_input_set = vasp_input_set or MPStaticSet(structure)
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd,
auto_npar=">>auto_npar<<"))
t.append(PassCalcLocs(name=name))
t.append(
VaspToDb(db_file=db_file, additional_fields={"task_label": name}))
super(StaticFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
def __init__(self,
structure,
name="static dielectric",
vasp_cmd=VASP_CMD,
copy_vasp_outputs=True,
db_file=DB_FILE,
parents=None,
phonon=False,
mode=None,
displacement=None,
user_incar_settings=None,
**kwargs):
"""
Standard static calculation Firework for dielectric constants using DFPT.
Args:
structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
name of the FW.
name (str): Name for the Firework.
vasp_cmd (str): Command to run vasp.
copy_vasp_outputs (bool): Whether to copy outputs from previous
run. Defaults to True.
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework.
FW or list of FWS.
phonon (bool): Whether or not to extract normal modes and pass it. This argument along
with the mode and displacement arguments must be set for the calculation of
dielectric constant in the Raman tensor workflow.
mode (int): normal mode index.
displacement (float): displacement along the normal mode in Angstroms.
user_incar_settings (dict): Parameters in INCAR to override
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
warnings.warn(
"This firework will be removed soon. Use DFPTFW and/or RamanFW fireworks."
)
user_incar_settings = user_incar_settings or {}
t = []
if copy_vasp_outputs:
t.append(
CopyVaspOutputs(calc_loc=True,
additional_files=["CHGCAR"],
contcar_to_poscar=True))
t.append(
WriteVaspStaticFromPrev(
lepsilon=True,
other_params={'user_incar_settings': user_incar_settings}))
else:
vasp_input_set = MPStaticSet(
structure,
lepsilon=True,
user_incar_settings=user_incar_settings)
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
if phonon:
if mode is None and displacement is None:
name = "{} {}".format("phonon", name)
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
t.append(
pass_vasp_result(
{
"structure": "a>>final_structure",
"eigenvals": "a>>normalmode_eigenvals",
"eigenvecs": "a>>normalmode_eigenvecs"
},
parse_eigen=True,
mod_spec_key="normalmodes"))
else:
name = "raman_{}_{} {}".format(str(mode), str(displacement),
name)
key = "{}_{}".format(mode, displacement).replace('-',
'm').replace(
'.', 'd')
pass_fw = pass_vasp_result(pass_dict={
"mode": mode,
"displacement": displacement,
"epsilon": "a>>epsilon_static"
},
mod_spec_key="raman_epsilon->" +
key,
parse_eigen=True)
t.extend([
WriteNormalmodeDisplacedPoscar(mode=mode,
displacement=displacement),
RunVaspCustodian(vasp_cmd=vasp_cmd), pass_fw
])
else:
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
t.extend([
PassCalcLocs(name=name),
VaspToDb(db_file=db_file, additional_fields={"task_label": name})
])
super(LepsFW, self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula,
name),
**kwargs)
def __init__(self,
structure,
mode,
displacement,
name="raman",
vasp_cmd="vasp",
db_file=None,
parents=None,
user_incar_settings=None,
**kwargs):
"""
Static calculation Firework that computes the DFPT dielectric constant for
structure displaced along the given normal mode direction.
Args:
structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
name of the FW.
mode (int): normal mode index.
displacement (float): displacement along the normal mode in Angstroms.
name (str): Name for the Firework.
vasp_cmd (str): Command to run vasp.
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework.
FW or list of FWS.
user_incar_settings (dict): Parameters in INCAR to override
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
name = "{}_{}_{} static dielectric".format(name, str(mode),
str(displacement))
user_incar_settings = user_incar_settings or {}
spec = kwargs.pop("spec", {})
spec.update({
"_files_in": {
"POSCAR": "POSCAR",
"OUTCAR": "OUTCAR",
"vasprunxml": "vasprun.xml"
}
})
t = []
t.append(
WriteVaspStaticFromPrev(
lepsilon=True,
other_params={'user_incar_settings': user_incar_settings}))
t.append(
WriteNormalmodeDisplacedPoscar(mode=mode,
displacement=displacement))
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
key = "{}_{}".format(mode,
displacement).replace('-', 'm').replace('.', 'd')
t.append(
pass_vasp_result(pass_dict={
"mode": mode,
"displacement": displacement,
"epsilon": "a>>epsilon_static"
},
mod_spec_key="raman_epsilon->{}".format(key),
parse_eigen=True))
t.append(PassCalcLocs(name=name))
t.append(
VaspToDb(db_file=db_file, additional_fields={"task_label": name}))
super(RamanFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
spec=spec,
**kwargs)
def __init__(self,
structure,
name="static dielectric",
vasp_cmd="vasp",
copy_vasp_outputs=True,
db_file=None,
parents=None,
user_incar_settings=None,
pass_nm_results=False,
**kwargs):
"""
Static DFPT calculation Firework
Args:
structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
name of the FW.
name (str): Name for the Firework.
vasp_cmd (str): Command to run vasp.
copy_vasp_outputs (bool): Whether to copy outputs from previous
run. Defaults to True.
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework.
FW or list of FWS.
user_incar_settings (dict): Parameters in INCAR to override
pass_nm_results (bool): if true the normal mode eigen vals and vecs are passed so that
next firework can use it.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
name = "{} {}".format("phonon", name)
user_incar_settings = user_incar_settings or {}
t = []
if copy_vasp_outputs:
t.append(CopyVaspOutputs(calc_loc=True, contcar_to_poscar=True))
t.append(
WriteVaspStaticFromPrev(lepsilon=True,
other_params={
'user_incar_settings':
user_incar_settings,
'force_gamma': True
}))
else:
vasp_input_set = MPStaticSet(
structure,
lepsilon=True,
force_gamma=True,
user_incar_settings=user_incar_settings)
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
if pass_nm_results:
t.append(
pass_vasp_result(
{
"structure": "a>>final_structure",
"eigenvals": "a>>normalmode_eigenvals",
"eigenvecs": "a>>normalmode_eigenvecs"
},
parse_eigen=True,
mod_spec_key="normalmodes"))
t.append(
VaspToDb(db_file=db_file, additional_fields={"task_label": name}))
spec = kwargs.pop("spec", {})
spec.update({
"_files_out": {
"POSCAR": "CONTCAR",
"OUTCAR": "OUTCAR*",
'vasprunxml': "vasprun.xml*"
}
})
super(DFPTFW, self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula,
name),
spec=spec,
**kwargs)
def __init__(self,
structure,
name="static dielectric",
vasp_cmd="vasp",
copy_vasp_outputs=True,
db_file=None,
parents=None,
phonon=False,
mode=None,
displacement=None,
user_incar_settings=None,
**kwargs):
"""
Standard static calculation Firework for dielectric constants using DFPT.
Args:
structure (Structure): Input structure. If copy_vasp_outputs, used only to set the
name of the FW.
name (str): Name for the Firework.
vasp_cmd (str): Command to run vasp.
copy_vasp_outputs (bool): Whether to copy outputs from previous
run. Defaults to True.
db_file (str): Path to file specifying db credentials.
parents (Firework): Parents of this particular Firework.
FW or list of FWS.
phonon (bool): Whether or not to extract normal modes and pass it. This argument along
with the mode and displacement arguments must be set for the calculation of
dielectric constant in the Raman tensor workflow.
mode (int): normal mode index.
displacement (float): displacement along the normal mode in Angstroms.
user_incar_settings (dict): Parameters in INCAR to override
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
user_incar_settings = user_incar_settings or {}
t = []
if copy_vasp_outputs:
t.append(
CopyVaspOutputs(calc_loc=True,
additional_files=["CHGCAR"],
contcar_to_poscar=True))
t.append(
WriteVaspStaticFromPrev(
lepsilon=True,
other_params={'user_incar_settings': user_incar_settings}))
else:
vasp_input_set = MPStaticSet(
structure,
lepsilon=True,
user_incar_settings=user_incar_settings)
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
if phonon:
if mode is None and displacement is None:
# TODO: @matk86 - I really don't understand the point of setting phonon=True w/o
# the mode or displacement. It seems to simply be running a regular static run and
# doing nothing else than changing the name of the Firework and perhaps passing
# normal modes data (but it's unclear how that data is generated. Why would anyone
# want to do this? -computron
name = "{} {}".format("phonon", name)
# TODO: @matk86 - not sure why this line is here. I understand you are trying to
# keep the code short but the logic is very confusing. The RunVaspCustodian is
# common to all 3 situations (phonon=F, phonon=T/mode=F, phonon=T/mode=T) yet is
# duplicated in each place. Instead, for better clarity construct the Firework
# sequentially (write inputs, run vasp, parse output data, pass output data) and
# add if/else for phonons where it is needed. Any name overrides can go near the
# top of the Firework. -computron
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
t.append(
pass_vasp_result(
{
"structure": "a>>final_structure",
"eigenvals": "a>>normalmode_eigenvals",
"eigenvecs": "a>>normalmode_eigenvecs"
},
parse_eigen=True,
mod_spec_key="normalmodes"))
else:
# TODO: @matk86 - Why is this second calculation being tacked on to the first one?
# It looks like it will overwrite INCAR/CHGCAR/etc of the first calculation and
# thus completely remove access to the original output files. Shouldn't this be a
# new Firework rather than a second calculation in the same Firework? -computron
name = "raman_{}_{} {}".format(str(mode), str(displacement),
name)
key = "{}_{}".format(mode, displacement).replace('-',
'm').replace(
'.', 'd')
pass_fw = pass_vasp_result(pass_dict={
"mode": mode,
"displacement": displacement,
"epsilon": "a>>epsilon_static"
},
mod_spec_key="raman_epsilon->" +
key,
parse_eigen=True)
t.extend([
WriteNormalmodeDisplacedPoscar(mode=mode,
displacement=displacement),
RunVaspCustodian(vasp_cmd=vasp_cmd), pass_fw
])
else:
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
t.extend([
PassCalcLocs(name=name),
VaspToDb(db_file=db_file, additional_fields={"task_label": name})
])
super(LepsFW, self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula,
name),
**kwargs)
