def test_cleanupfiles_calc_dir(self):
# will test deleting from some folder specified by calc_dir
with ScratchDir(".", copy_from_current_on_enter=True) as d:
current_path = os.getcwd()
os.mkdir("to_remove.relax0")
os.mkdir("to_remove.relax1")
os.mkdir("dont_remove.relax0")
os.mkdir("shouldnt_touch")
fw1 = Firework(
[
DeleteFilesPrevFolder(files=["to_remove*", "dont_remove"],
calc_dir=current_path),
PassCalcLocs(name="fw1"),
],
name="fw1",
)
fw2 = Firework([PassCalcLocs(name="fw2")], name="fw2", parents=fw1)
wf = Workflow([fw1, fw2])
self.lp.add_wf(wf)
rapidfire(self.lp)
self.assertTrue(
os.path.exists(os.path.join(current_path,
"dont_remove.relax0")))
self.assertTrue(
os.path.exists(os.path.join(current_path, "shouldnt_touch")))
self.assertFalse(
os.path.exists(os.path.join(current_path, "to_remove.relax0")))
self.assertFalse(
os.path.exists(os.path.join(current_path, "to_remove.relax1")))
def test_copyfilesfromcalcloc(self):
fw1 = Firework(
[
CopyVaspOutputs(calc_dir=self.plain_outdir),
PassCalcLocs(name="fw1")
],
name="fw1",
)
fw2 = Firework(
[
CopyVaspOutputs(calc_dir=self.relax2_outdir),
PassCalcLocs(name="fw2")
],
name="fw2",
)
fw3 = Firework(
[
CopyFilesFromCalcLoc(
calc_loc="fw1",
filenames=["POSCAR"],
name_prepend="",
name_append="_0",
),
CopyFilesFromCalcLoc(
calc_loc="fw2",
filenames=["POSCAR"],
name_prepend="",
name_append="_1",
),
PassCalcLocs(name="fw3"),
],
name="fw3",
parents=[fw1, fw2],
)
fw4 = Firework([PassCalcLocs(name="fw4")], name="fw4", parents=fw3)
wf = Workflow([fw1, fw2, fw3, fw4])
self.lp.add_wf(wf)
rapidfire(self.lp)
fw4 = self.lp.get_fw_by_id(self.lp.get_fw_ids({"name": "fw4"})[0])
calc_locs = fw4.spec["calc_locs"]
self.assertTrue(
os.path.exists(
get_calc_loc("fw3", calc_locs)["path"] + "/POSCAR_0"))
self.assertTrue(
os.path.exists(
get_calc_loc("fw3", calc_locs)["path"] + "/POSCAR_1"))
def test_cleanupfiles_calc_loc(self):
# will test deleting files from previous folder
fw1 = Firework(
[
CreateFolder(folder_name="to_remove.relax0"),
CreateFolder(folder_name="to_remove.relax1"),
CreateFolder(folder_name="dont_remove.relax0"),
CreateFolder(folder_name="shouldnt_touch"),
PassCalcLocs(name="fw1"),
],
name="fw1",
)
fw2 = Firework(
[
DeleteFilesPrevFolder(files=["to_remove*", "dont_remove"],
calc_loc=True),
PassCalcLocs(name="fw2"),
],
name="fw2",
parents=fw1,
)
wf = Workflow([fw1, fw2])
self.lp.add_wf(wf)
rapidfire(self.lp)
fw2 = self.lp.get_fw_by_id(self.lp.get_fw_ids({"name": "fw2"})[0])
calc_locs = fw2.spec["calc_locs"]
self.assertTrue(
os.path.exists(
os.path.join(
get_calc_loc("fw1", calc_locs)["path"],
"dont_remove.relax0")))
self.assertTrue(
os.path.exists(
os.path.join(
get_calc_loc("fw1", calc_locs)["path"], "shouldnt_touch")))
self.assertFalse(
os.path.exists(
os.path.join(
get_calc_loc("fw1", calc_locs)["path"],
"to_remove.relax0")))
self.assertFalse(
os.path.exists(
os.path.join(
get_calc_loc("fw1", calc_locs)["path"],
"to_remove.relax1")))
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,
parents=None,
prev_calc_dir=None,
structure=None,
mode="gap",
name=None,
vasp_cmd=VASP_CMD,
db_file=DB_FILE,
**kwargs,
):
"""
For getting a more accurate band gap or a full band structure with HSE - requires previous
calculation that gives VBM/CBM info or the high-symmetry kpoints.
Args:
parents (Firework): Parents of this particular Firework. FW or list of FWS.
prev_calc_dir (str): Path to a previous calculation to copy from
structure (Structure): Input structure - used only to set the name of the FW.
mode (string): options:
"line" to get a full band structure along symmetry lines or
"uniform" for uniform mesh band structure or
"gap" to get the energy at the CBM and VBM
name (str): Name for the Firework.
vasp_cmd (str): Command to run vasp.
db_file (str): Path to file specifying db credentials.
**kwargs: Other kwargs that are passed to Firework.__init__.
"""
name = name if name else "{} {}".format("hse", mode)
fw_name = "{}-{}".format(
structure.composition.reduced_formula if structure else "unknown",
name)
t = []
if prev_calc_dir:
t.append(
CopyVaspOutputs(calc_dir=prev_calc_dir,
additional_files=["CHGCAR"]))
elif parents:
t.append(
CopyVaspOutputs(calc_loc=True, additional_files=["CHGCAR"]))
else:
raise ValueError("Must specify a previous calculation for HSEBSFW")
t.append(WriteVaspHSEBSFromPrev(prev_calc_dir=".", mode=mode))
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd))
t.append(PassCalcLocs(name=name))
parse_dos = True if mode == "uniform" else False
bandstructure_mode = mode if mode in ["line", "uniform"] else "line"
t.append(
VaspToDb(
db_file=db_file,
additional_fields={"task_label": name},
parse_dos=parse_dos,
bandstructure_mode=bandstructure_mode,
))
super().__init__(t, parents=parents, name=fw_name, **kwargs)
def __init__(
self,
parents=None,
structure=None,
name="vasp2trace",
db_file=None,
prev_calc_dir=None,
vasp2trace_out=None,
vasp_cmd=None,
**kwargs
):
"""
Run Vasp2Trace on a spin-polarized calculation and parse the output data.
Assumes you have a previous FW with the calc_locs passed into the current FW.
Args:
structure (Structure): - only used for setting name of FW
name (str): name of this FW
db_file (str): path to the db file
parents (Firework): Parents of this particular Firework. FW or list of FWS.
prev_calc_dir (str): Path to a previous calculation to copy from
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
fw_name = "{}-{}".format(
structure.composition.reduced_formula if structure else "unknown", name
)
t = []
if prev_calc_dir:
t.append(
CopyVaspOutputs(
calc_dir=prev_calc_dir,
additional_files=["CHGCAR", "WAVECAR", "PROCAR"],
contcar_to_poscar=True,
)
)
elif parents:
t.append(
CopyVaspOutputs(
calc_loc=True,
additional_files=["CHGCAR", "WAVECAR", "PROCAR"],
contcar_to_poscar=True,
)
)
else:
raise ValueError("Must specify structure or previous calculation")
t.extend(
[
RunVasp2TraceMagnetic(),
PassCalcLocs(name=name),
Vasp2TraceToDb(db_file=db_file, vasp2trace_out=vasp2trace_out),
]
)
super(Vasp2TraceMagneticFW, self).__init__(
t, parents=parents, name=fw_name, **kwargs
)
def __init__(self, structure, isif=2, scale_lattice=None, name="static", vasp_input_set=None,
vasp_cmd="vasp", metadata=None, prev_calc_loc=True, Prestatic=False, modify_incar=None,
db_file=None, parents=None, tag=None, override_default_vasp_params=None,
store_volumetric_data=False, **kwargs):
# 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
metadata = metadata or {}
tag = tag or metadata.get('tag')
# generate a tag with a warning
if tag is None:
tag = str(uuid4())
metadata['tag'] = tag
if isinstance(store_volumetric_data, (list, tuple)):
store_volumetric_data = store_volumetric_data
elif isinstance(store_volumetric_data, bool):
if store_volumetric_data:
store_volumetric_data = STORE_VOLUMETRIC_DATA
else:
store_volumetric_data = ()
else:
raise ValueError('The store_volumetric_data should be list or bool')
override_default_vasp_params = override_default_vasp_params or {}
self.override_default_vasp_params = override_default_vasp_params
vasp_input_set = vasp_input_set or StaticSet(structure, isif=isif, **override_default_vasp_params)
site_properties = deepcopy(structure).site_properties
# Avoids delivery (prev_calc_loc == '' (instead by True))
t = []
if type(prev_calc_loc) == str:
t.append(CopyVaspOutputs(calc_dir=prev_calc_loc, contcar_to_poscar=True))
t.append(WriteVaspFromIOSetPrevStructure(vasp_input_set=vasp_input_set, site_properties=site_properties))
elif parents:
if prev_calc_loc:
t.append(CopyVaspOutputs(calc_loc=prev_calc_loc, contcar_to_poscar=True))
t.append(WriteVaspFromIOSetPrevStructure(vasp_input_set=vasp_input_set, site_properties=site_properties))
else:
t.append(WriteVaspFromIOSetPrevStructure(structure=structure, vasp_input_set=vasp_input_set, site_properties=site_properties))
if (scale_lattice is not None) and not Prestatic:
t.append(ScaleVolumeTransformation(scale_factor=scale_lattice, structure=structure))
t.append(ModifyIncar(incar_update=">>incar_update<<"))
if modify_incar != None:
t.append(ModifyIncar(incar_update=modify_incar))
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd, auto_npar=">>auto_npar<<", gzip_output=False))
t.append(PassCalcLocs(name=name))
if Prestatic:
t.append(Record_PreStatic_result(db_file = ">>db_file<<", metadata = metadata, structure = structure, scale_lattice = scale_lattice))
else:
t.append(VaspToDb(db_file=">>db_file<<", parse_dos=True, additional_fields={"task_label": name, "metadata": metadata,
"version_atomate": atomate_ver, "version_dfttk": dfttk_ver, "adopted": True, "tag": tag},
store_volumetric_data=store_volumetric_data))
run_task_ext(t,vasp_cmd,">>db_file<<",structure,tag,self.override_default_vasp_params)
t.append(CheckSymmetryToDb(db_file=">>db_file<<", tag=tag, site_properties=site_properties))
super(StaticFW, self).__init__(t, parents=parents, name="{}-{}".format(
structure.composition.reduced_formula, 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,
scale_lattice=None,
name="static",
vasp_input_set=None,
vasp_cmd="vasp",
metadata=None,
prev_calc_loc=True,
db_file=None,
parents=None,
**kwargs):
# 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
metadata = metadata or {}
vasp_input_set = vasp_input_set or StaticSet(structure)
site_properties = deepcopy(structure).site_properties
t = []
if parents:
if prev_calc_loc:
t.append(
CopyVaspOutputs(calc_loc=prev_calc_loc,
contcar_to_poscar=True))
t.append(
WriteVaspFromIOSetPrevStructure(
vasp_input_set=vasp_input_set,
site_properties=site_properties))
else:
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
if scale_lattice is not None:
t.append(ScaleVolumeTransformation(scale_factor=scale_lattice))
t.append(ModifyIncar(incar_update=">>incar_update<<"))
t.append(
RunVaspCustodian(vasp_cmd=vasp_cmd,
auto_npar=">>auto_npar<<",
gzip_output=False))
t.append(PassCalcLocs(name=name))
t.append(
VaspToDb(
db_file=db_file,
parse_dos=True,
additional_fields={
"task_label": name,
"metadata": metadata
},
))
super(StaticFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, 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="nscf",
mode="uniform",
vasp_cmd="vasp",
copy_vasp_outputs=True,
db_file=None,
parents=None,
**kwargs):
"""
Standard NonSCF Calculation Firework supporting both
uniform and line modes.
Args:
structure (Structure): Input structure - used only to set the name of the FW.
name (str): Name for the Firework.
mode (str): "uniform" or "line" mode.
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.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
t = []
if copy_vasp_outputs:
t.append(
CopyVaspOutputs(calc_loc=True, additional_files=["CHGCAR"]))
mode = mode.lower()
if mode == "uniform":
t.append(
WriteVaspNSCFFromPrev(prev_calc_dir=".",
mode="uniform",
reciprocal_density=1000))
else:
t.append(
WriteVaspNSCFFromPrev(prev_calc_dir=".",
mode="line",
reciprocal_density=20))
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 + " " + mode},
parse_dos=(mode == "uniform"),
bandstructure_mode=mode))
super(NonSCFFW, self).__init__(
t,
parents=parents,
name="%s-%s %s" %
(structure.composition.reduced_formula, name, mode),
**kwargs)
def __init__(self, structure, scale_lattice=None, isif=4, override_symmetry_tolerances=None,
name="structure optimization", vasp_input_set=None, job_type="normal", vasp_cmd="vasp",
metadata=None, override_default_vasp_params=None, db_file=None, record_path=False,
prev_calc_loc=True, parents=None, db_insert=False, tag=None,
run_isif2=False, pass_isif4=False, force_gamma=True, store_volumetric_data=False,
modify_incar=None, modify_incar_params={}, modify_kpoints_params={}, **kwargs):
metadata = metadata or {}
tag = tag or metadata.get('tag')
# generate a tag with a warning
if tag is None:
tag = str(uuid4())
metadata['tag'] = tag
metadata.update({'tag': tag})
if isinstance(store_volumetric_data, (list, tuple)):
store_volumetric_data = store_volumetric_data
elif isinstance(store_volumetric_data, bool):
if store_volumetric_data:
store_volumetric_data = STORE_VOLUMETRIC_DATA
else:
store_volumetric_data = ()
else:
raise ValueError('The store_volumetric_data should be list or bool')
override_default_vasp_params = override_default_vasp_params or {}
override_symmetry_tolerances = override_symmetry_tolerances or {}
vasp_input_set = vasp_input_set or RelaxSet(structure, isif=isif, force_gamma=force_gamma,
**override_default_vasp_params)
site_properties = deepcopy(structure).site_properties
t = []
# Avoids delivery (prev_calc_loc == '' (instead by True))
if type(prev_calc_loc) == str:
t.append(CopyVaspOutputs(calc_dir=prev_calc_loc, contcar_to_poscar=True))
t.append(WriteVaspFromIOSetPrevStructure(vasp_input_set=vasp_input_set, site_properties=site_properties))
elif parents:
if prev_calc_loc:
t.append(CopyVaspOutputs(calc_loc=prev_calc_loc, contcar_to_poscar=True))
t.append(WriteVaspFromIOSetPrevStructure(vasp_input_set=vasp_input_set, site_properties=site_properties))
else:
#vasp_input_set = vasp_input_set or RelaxSet(structure) # ??
t.append(WriteVaspFromIOSetPrevStructure(structure=structure, vasp_input_set=vasp_input_set, site_properties=site_properties))
if scale_lattice is not None:
t.append(ScaleVolumeTransformation(scale_factor=scale_lattice, structure=structure))
t.append(ModifyIncar(incar_update=">>incar_update<<"))
if modify_incar != None:
t.append(ModifyIncar(incar_update=modify_incar))
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd, job_type=job_type, gzip_output=False))
t.append(PassCalcLocs(name=name))
if record_path:
t.append(Record_relax_running_path(db_file = db_file, metadata = metadata, run_isif2=run_isif2, pass_isif4=pass_isif4))
if db_insert:
t.append(VaspToDb(db_file=db_file, additional_fields={"task_label": name, "metadata": metadata}, store_volumetric_data=store_volumetric_data))
t.append(CheckSymmetryToDb(db_file=db_file, tag=tag, override_symmetry_tolerances=override_symmetry_tolerances, site_properties=site_properties))
super(OptimizeFW, self).__init__(t, parents=parents, name="{}-{}".format(structure.composition.reduced_formula, name), **kwargs)
def test_createfolder(self):
folder_name = "test_folder"
fw1 = Firework([
CreateFolder(folder_name=folder_name, change_dir=False),
PassCalcLocs(name="fw1")
],
name="fw3")
fw2 = Firework([PassCalcLocs(name="fw2")], name="fw2", parents=fw1)
wf = Workflow([fw1, fw2])
self.lp.add_wf(wf)
rapidfire(self.lp)
fw2 = self.lp.get_fw_by_id(self.lp.get_fw_ids({"name": "fw2"})[0])
calc_locs = fw2.spec["calc_locs"]
self.assertTrue(
os.path.exists(
get_calc_loc("fw1", calc_locs)["path"] + "/" + folder_name))
def __init__(self, structure, start_temp, end_temp, nsteps,
name="molecular dynamics",
vasp_input_set=None, vasp_cmd=VASP_CMD,
override_default_vasp_params=None,
wall_time=19200, db_file=DB_FILE, parents=None,
copy_vasp_outputs=True, **kwargs):
"""
Standard firework for a single MD run.
Args:
structure (Structure): Input structure.
start_temp (float): Start temperature of MD run.
end_temp (float): End temperature of MD run.
nsteps (int): Number of MD steps
name (string): Name for the Firework.
vasp_input_set (string): string name for the VASP input set (e.g.,
"MITMDVaspInputSet").
vasp_cmd (string): Command to run vasp.
override_default_vasp_params (dict): If this is not None,
these params are passed to the default vasp_input_set, i.e.,
MITMDSet. This allows one to easily override some
settings, e.g., user_incar_settings, etc. Particular to MD,
one can control time_step and all other settings of the input set.
wall_time (int): Total wall time in seconds before writing STOPCAR.
copy_vasp_outputs (bool): Whether to copy outputs from previous run. Defaults to True.
db_file (string): 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__.
"""
override_default_vasp_params = override_default_vasp_params or {}
vasp_input_set = vasp_input_set or MITMDSet(structure,
start_temp=start_temp,
end_temp=end_temp,
nsteps=nsteps,
**override_default_vasp_params)
t = []
if copy_vasp_outputs:
t.append(CopyVaspOutputs(calc_loc=True, additional_files=["CHGCAR"],
contcar_to_poscar=True))
t.append(WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd,
gamma_vasp_cmd=">>gamma_vasp_cmd<<",
handler_group="md", wall_time=wall_time))
t.append(PassCalcLocs(name=name))
t.append(VaspToDb(db_file=db_file,
additional_fields={"task_label": name},
defuse_unsuccessful=False))
super(MDFW, self).__init__(t, parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula,
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,
structure,
magmom,
name="spin-orbit coupling",
saxis=(0, 0, 1),
vasp_cmd="vasp_ncl",
copy_vasp_outputs=True,
db_file=None,
parents=None,
**kwargs):
"""
Firework for spin orbit coupling calculation.
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.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
t = []
if copy_vasp_outputs:
t.append(
CopyVaspOutputs(calc_loc=True,
additional_files=["CHGCAR"],
contcar_to_poscar=True))
t.append(
WriteVaspSOCFromPrev(prev_calc_dir=".",
magmom=magmom,
saxis=saxis))
else:
vasp_input_set = MPSOCSet(structure)
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
t.extend([
RunVaspCustodian(vasp_cmd=vasp_cmd, auto_npar=">>auto_npar<<"),
PassCalcLocs(name=name),
VaspToDb(db_file=db_file, additional_fields={"task_label": name})
])
super(SOCFW, self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula,
name),
**kwargs)
def __init__(self,
structure,
name="static",
previous_structure=False,
vasp_input_set=None,
vasp_cmd="vasp",
db_file=None,
parents=None,
override_default_vasp_params=None,
pass_structure=True,
prev_calc_loc=False,
**kwargs):
"""
This Firework is modified from atomate.vasp.fireworks.core.StaticFW to fit the needs of mpmorph
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__.
"""
t = []
override_default_vasp_params = override_default_vasp_params or {}
vasp_input_set = vasp_input_set or MPStaticSet(
structure, **override_default_vasp_params)
if prev_calc_loc:
t.append(
CopyVaspOutputs(calc_loc=prev_calc_loc,
contcar_to_poscar=True))
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
if previous_structure:
t.append(PreviousStructureTask())
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd,
auto_npar=">>auto_npar<<"))
t.append(SaveStructureTask())
t.append(PassCalcLocs(name=name))
t.append(
VaspToDb(db_file=db_file, additional_fields={"task_label": name}))
name = f'{structure.composition.reduced_formula}-{name}'
super(StaticFW, self).__init__(t, parents=parents, name=name, **kwargs)
def __init__(
self,
parents=None,
structure=None,
name="standardize",
db_file=None,
prev_calc_dir=None,
vasp_cmd=None,
**kwargs
):
"""
Standardize the structure with spglib.
Args:
structure (Structure): pmg structure.
name (str): name of this FW
db_file (str): path to the db file
parents (Firework): Parents of this particular Firework. FW or list of FWS.
prev_calc_dir (str): Path to a previous calculation to copy from
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
fw_name = "{}-{}".format(
structure.composition.reduced_formula if structure else "unknown", name
)
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 structure or previous calculation")
t.extend(
[
StandardizeCell(),
PassCalcLocs(name=name),
]
)
super(StandardizeFW, self).__init__(t, parents=parents, name=fw_name, **kwargs)
def __init__(self,
molecules,
packing_config,
tolerance=2.0,
filetype="xyz",
control_params=None,
output_file="packed.xyz",
copy_to_current_on_exit=False,
site_property=None,
parents=None,
name="PackmolFW",
packmol_cmd="packmol",
**kwargs):
"""
Args:
molecules (list): list of constituent molecules(Molecule objects)
packing_config (list): list of dict config settings for each molecule in the
molecules list. eg: config settings for a single molecule
[{"number": 1, "inside box":[0,0,0,100,100,100]}]
tolerance (float): packmol tolerance
filetype (string): input/output structure file type
control_params (dict): packmol control parameters dictionary. Basically all parameters
other than structure/atoms.
output_file (str): output file name. The extension will be adjusted according to the filetype.
copy_to_current_on_exit (bool): whether or not to copy the packed molecule output file
to the current directory.
site_property (str): the specified site property will be restored for the final Molecule object.
parents ([Firework]): parent fireworks
name (str): firework name
packmol_cmd (str): path to packmol bin
**kwargs:
"""
control_params = control_params or {'maxit': 20, 'nloop': 600}
tasks = [
RunPackmol(molecules=molecules,
packing_config=packing_config,
tolerance=tolerance,
filetype=filetype,
control_params=control_params,
output_file=output_file,
copy_to_current_on_exit=copy_to_current_on_exit,
site_property=site_property,
packmol_cmd=packmol_cmd),
PassCalcLocs(name=name)
]
super(PackmolFW, self).__init__(tasks,
parents=parents,
name=name,
**kwargs)
def __init__(self, structure, isif=7, name="structure optimization", isif4=False, level=1,
override_symmetry_tolerances=None, job_type="normal", vasp_input_set=None,
vasp_cmd="vasp", metadata=None, override_default_vasp_params=None, db_file=None,
prev_calc_loc=True, parents=None, db_insert=False, tag=None, modify_incar_params={},
modify_kpoints_params={}, energy_with_isif={}, store_volumetric_data=False,
**kwargs):
metadata = metadata or {}
tag = tag or metadata.get('tag')
# generate a tag with a warning
if tag is None:
tag = str(uuid4())
metadata['tag'] = tag
if isinstance(store_volumetric_data, (list, tuple)):
store_volumetric_data = store_volumetric_data
elif isinstance(store_volumetric_data, bool):
if store_volumetric_data:
store_volumetric_data = STORE_VOLUMETRIC_DATA
else:
store_volumetric_data = ()
else:
raise ValueError('The store_volumetric_data should be list or bool')
override_default_vasp_params = override_default_vasp_params or {}
override_symmetry_tolerances = override_symmetry_tolerances or {}
vasp_input_set = vasp_input_set or RelaxSet(structure, isif=isif, **override_default_vasp_params)
site_properties = deepcopy(structure).site_properties
t = []
if parents:
if prev_calc_loc:
t.append(CopyVaspOutputs(calc_loc=prev_calc_loc, contcar_to_poscar=True))
t.append(WriteVaspFromIOSetPrevStructure(vasp_input_set=vasp_input_set, site_properties=site_properties))
else:
t.append(WriteVaspFromIOSetPrevStructure(structure=structure, vasp_input_set=vasp_input_set, site_properties=site_properties))
t.append(ModifyIncar(incar_update=">>incar_update<<"))
t.append(RunVaspCustodian(vasp_cmd=vasp_cmd, job_type=job_type, gzip_output=False))
t.append(PassCalcLocs(name=name))
if db_insert:
t.append(VaspToDb(db_file=">>db_file<<", additional_fields={"task_label": name, "metadata": metadata}, store_volumetric_data=store_volumetric_data))
t.append(CheckSymmetryToDb(db_file=">>db_file<<", tag=tag, site_properties=site_properties))
common_kwargs = {'vasp_cmd': vasp_cmd, 'db_file': ">>db_file<<", "metadata": metadata, "tag": tag,
'override_default_vasp_params': override_default_vasp_params}
static_kwargs = {}
relax_kwargs = {}
t.append(CheckRelaxation(db_file=">>db_file<<", metadata=metadata, tag=tag, isif4=isif4, level=level, energy_with_isif=energy_with_isif,
common_kwargs=common_kwargs, relax_kwargs=relax_kwargs, static_kwargs=static_kwargs, site_properties=site_properties,
store_volumetric_data=store_volumetric_data,
**override_symmetry_tolerances))
super().__init__(t, parents=parents, name="{}-{}".format(structure.composition.reduced_formula, name), **kwargs)
def __init__(self, spec, neb_label, from_images=True,
user_incar_settings=None,
user_kpoints_settings=None, additional_cust_args=None,
**kwargs):
"""
Args:
spec (dict): Specification of the job to run.
neb_label (str): "1", "2"..., label neb run.
from_images (bool): Set True to initialize from image structures, False starting
from relaxed endpoint structures.
user_incar_settings (dict): Additional INCAR settings.
user_kpoints_settings (dict): Additional KPOINTS settings.
additional_cust_args (dict): Other kwargs that are passed to RunVaspCustodian.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
assert neb_label.isdigit() and int(neb_label) >= 1
label = "neb{}".format(neb_label)
sort_tol = spec["sort_tol"]
d_img = spec["d_img"]
interpolation_type = spec["interpolation_type"]
# Task 1: Write NEB input sets
user_incar_settings = user_incar_settings or {}
user_kpoints_settings = user_kpoints_settings or {}
additional_cust_args = additional_cust_args or {}
if from_images:
write_neb_task = WriteNEBFromImages(neb_label=neb_label,
user_incar_settings=user_incar_settings,
user_kpoints_settings=user_kpoints_settings)
else: # from endpoints
write_neb_task = WriteNEBFromEndpoints(
user_incar_settings=user_incar_settings,
user_kpoints_settings=user_kpoints_settings,
sort_tol=sort_tol, d_img=d_img,
interpolation_type=interpolation_type)
# Task 2: Run NEB using Custodian
cust_args = {"job_type": "neb", "gzip_output": False,
"handler_group": "no_handler"}
cust_args.update(additional_cust_args)
run_neb_task = RunVaspCustodian(vasp_cmd=">>vasp_cmd<<",
gamma_vasp_cmd=">>gamma_vasp_cmd<<",
**cust_args)
# Task 3, 4: Transfer and PassCalcLocs
tasks = [write_neb_task, run_neb_task, TransferNEBTask(label=label),
PassCalcLocs(name=label)]
super(NEBFW, self).__init__(tasks, spec=spec, name=label, **kwargs)
def __init__(self, spec, label, user_incar_settings=None,
user_kpoints_settings=None,
additional_cust_args=None, **kwargs):
"""
Args:
spec (dict): Specification of the job to run.
label (str): "parent", "ep0" or "ep1"
vasp_input_set (VaspInputSet): Input set to use.
user_kpoints_settings (dict): Additional KPOINTS settings.
additional_cust_args (dict): Other kwargs that are passed to RunVaspCustodian.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
# Get structure from spec
assert label in ["parent", "ep0", "ep1"]
structure_dict = spec[label]
structure = Structure.from_dict(structure_dict)
user_incar_settings = user_incar_settings or {}
user_kpoints_settings = user_kpoints_settings or {}
additional_cust_args = additional_cust_args or {}
# Task 1: Write input sets
if label == 'parent':
vasp_input_set = MITRelaxSet(structure,
user_incar_settings=user_incar_settings,
user_kpoints_settings=user_kpoints_settings)
else: # label == "ep0" or "ep1"
from pymatgen_diffusion.neb.io import MVLCINEBEndPointSet
vasp_input_set = MVLCINEBEndPointSet(structure,
user_incar_settings=user_incar_settings,
user_kpoints_settings=user_kpoints_settings)
write_ep_task = WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set)
# Task 2: Run VASP using Custodian
cust_args = {"job_type": "normal", "gzip_output": False,
"handler_group": "no_handler"}
cust_args.update(additional_cust_args)
run_vasp = RunVaspCustodian(vasp_cmd=">>vasp_cmd<<",
gamma_vasp_cmd=">>gamma_vasp_cmd<<",
**cust_args)
# Task 3, 4: Transfer and PassCalLocs
tasks = [write_ep_task, run_vasp, TransferNEBTask(label=label),
PassCalcLocs(name=label)]
super(NEBRelaxationFW, self).__init__(tasks, spec=spec, name=label,
**kwargs)
def __init__(self,
structure,
name="structure optimization",
vasp_input_set=None,
job_type="normal",
vasp_cmd="vasp",
metadata=None,
override_default_vasp_params=None,
db_file=None,
force_gamma=True,
prev_calc_loc=True,
parents=None,
db_insert=False,
**kwargs):
metadata = metadata or {}
override_default_vasp_params = override_default_vasp_params or {}
vasp_input_set = vasp_input_set or PRLRelaxSet(
structure, force_gamma=force_gamma, **override_default_vasp_params)
t = []
if parents:
if prev_calc_loc:
t.append(
CopyVaspOutputs(calc_loc=prev_calc_loc,
contcar_to_poscar=True))
t.append(
WriteVaspFromIOSetPrevStructure(vasp_input_set=vasp_input_set))
else:
vasp_input_set = vasp_input_set or PRLRelaxSet(structure)
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
t.append(
RunVaspCustodian(vasp_cmd=vasp_cmd,
job_type=job_type,
gzip_output=False))
t.append(PassCalcLocs(name=name))
if db_insert:
t.append(
VaspToDb(db_file=db_file,
additional_fields={
"task_label": name,
"metadata": metadata
}))
super(PRLOptimizeFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
def test_passcalclocs(self):
fw1 = Firework([PassCalcLocs(name="fw1")], name="fw1")
fw2 = Firework([PassCalcLocs(name="fw2")], name="fw2", parents=fw1)
fw3 = Firework([PassCalcLocs(name="fw3")], name="fw3", parents=fw2)
wf = Workflow([fw1, fw2, fw3])
self.lp.add_wf(wf)
rapidfire(self.lp)
fw2 = self.lp.get_fw_by_id(self.lp.get_fw_ids({"name": "fw2"})[0])
fw3 = self.lp.get_fw_by_id(self.lp.get_fw_ids({"name": "fw3"})[0])
self.assertEqual(len(fw2.spec["calc_locs"]), 1)
self.assertEqual(len(fw3.spec["calc_locs"]), 2)
self.assertEqual(fw3.spec["calc_locs"][0]["name"], "fw1")
self.assertEqual(fw3.spec["calc_locs"][1]["name"], "fw2")
self.assertNotEqual(fw3.spec["calc_locs"][0]["path"],
fw3.spec["calc_locs"][1]["path"])
calc_locs = fw3.spec["calc_locs"]
self.assertEqual(get_calc_loc("fw1", calc_locs), calc_locs[0])
self.assertEqual(get_calc_loc("fw2", calc_locs), calc_locs[1])
self.assertEqual(get_calc_loc(True, calc_locs), calc_locs[1])
def __init__(self,
structure,
name="boltztrap",
db_file=None,
parents=None,
scissor=0.0,
doping=None,
tmax=1300,
tgrid=50,
soc=False,
additional_fields=None,
**kwargs):
"""
Run Boltztrap (which includes writing bolztrap input files and parsing outputs). Assumes
you have a previous FW with the calc_locs passed into the current FW.
Args:
structure (Structure): - only used for setting name of FW
name (str): name of this FW
db_file (str): path to the db file
parents (Firework): Parents of this particular Firework. FW or list of FWS.
scissor (float): if scissor > 0, apply scissor on the band structure so that new
band gap = scissor (in eV)
doping: ([float]) doping levels you want to compute
tmax: (float) max temperature to evaluate
tgrid: (float) temperature interval
soc (bool): whether the band structure is calculated with spin-orbit coupling
additional_fields (dict): fields added to the document such as user-defined tags or name, ids, etc
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
additional_fields = additional_fields or {}
t = [
CopyVaspOutputs(calc_loc=True, contcar_to_poscar=True),
RunBoltztrap(scissor=scissor,
soc=soc,
doping=doping,
tmax=tmax,
tgrid=tgrid),
BoltztrapToDb(db_file=db_file,
additional_fields=additional_fields),
PassCalcLocs(name=name)
]
super(BoltztrapFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
def __init__(self,
control,
structure,
name="TDDFT",
aims_cmd='mpirun aims',
job_type="tddft",
max_force_threshold=0.01,
parents=None,
**kwargs):
"""
Optimize the given structure.
Args:
structure (Structure): Input structure.
name (str): Name for the Firework.
vasp_input_set (VaspInputSet): input set to use. Defaults to MPRelaxSet() if None.
override_default_vasp_params (dict): If this is not None, these params are passed to
the default vasp_input_set, i.e., MPRelaxSet. This allows one to easily override
some settings, e.g., user_incar_settings, etc.
vasp_cmd (str): Command to run vasp.
ediffg (float): Shortcut to set ediffg in certain jobs
db_file (str): Path to file specifying db credentials to place output parsing.
force_gamma (bool): Force gamma centered kpoint generation
job_type (str): custodian job type (default "double_relaxation_run")
max_force_threshold (float): max force on a site allowed at end; otherwise, reject job
auto_npar (bool or str): whether to set auto_npar. defaults to env_chk: ">>auto_npar<<"
half_kpts_first_relax (bool): whether to use half the kpoints for the first relaxation
parents ([Firework]): Parents of this particular Firework.
**kwargs: Other kwargs that are passed to Firework.__init__.
"""
t = list()
t.append(WriteAimsFromIOSet(control=control, structure=structure))
t.append(
RunAimsCustodian(aims_cmd=aims_cmd,
job_type=job_type,
max_force_threshold=max_force_threshold))
t.append(PassCalcLocs(name=name))
# t.append(
# VaspToDb(db_file=db_file, additional_fields={"task_label": name}))
super(TDDFTFW, self).__init__(
t,
parents=parents,
name="{}-{}".format(
'-'.join(structure.composition.reduced_formula), name),
**kwargs)