def test_check_symbol():
struc = Structure.from_str(POSCAR_STR_check_symbol, fmt="POSCAR")
magmoms = [4.0, 4.0, -4.0, -4.0]
struc.add_site_property("magmom", magmoms)
InputSet = RelaxSet(struc)
symbols, natom = dfttkutils.check_symbol(InputSet)
assert (symbols == ["Fe", "Fe"])
assert (natom == ["2", "2"])
def test_update_pot_by_symbols():
struc = Structure.from_str(POSCAR_STR_check_symbol, fmt="POSCAR")
magmoms = [4.0, 4.0, -4.0, -4.0]
struc.add_site_property("magmom", magmoms)
InputSet = RelaxSet(struc)
potcar = dfttkutils.update_pot_by_symbols(InputSet, write_file=False)
syms = potcar.symbols
assert (syms == ["Fe", "Fe"])
def run_task(self, fw_spec):
# unrelaxed cell
cell = Structure.from_file('POSCAR')
cell.to(filename='str.out', fmt='mcsqs')
# relaxed cell
cell = Structure.from_file('CONTCAR')
cell.to(filename='str_relax.out', fmt='mcsqs')
# check the symmetry
out = subprocess.run(['checkrelax', '-1'], stdout=subprocess.PIPE)
relaxation = float(out.stdout)
# we relax too much, add a volume relax and inflection detection WF as a detour
if relaxation > self['tolerance']:
from dfttk.fworks import OptimizeFW, InflectionDetectionFW
from fireworks import Workflow
from dfttk.input_sets import RelaxSet
from dfttk.utils import add_modify_incar_by_FWname, add_modify_kpoints_by_FWname
fws = []
vis = RelaxSet(self.get('structure'), volume_relax=True)
vol_relax_fw = OptimizeFW(
self.get('structure'),
symmetry_tolerance=None,
job_type='normal',
name='Volume relax', #record_path = True,
vasp_input_set=vis,
modify_incar={'ISIF': 7},
vasp_cmd=self.get('vasp_cmd'),
db_file=self.get('db_file'),
metadata=self.get('metadata'),
)
fws.append(vol_relax_fw)
modify_incar_params = self.get('modify_incar_params')
modify_kpoints_params = self.get('modify_kpoints_params')
# we have to add the calc locs for this calculation by hand
# because the detour action seems to disable spec mods
fws.append(
InflectionDetectionFW(
self.get('structure'),
parents=[vol_relax_fw],
Pos_Shape_relax=self.get('Pos_Shape_relax') or False,
metadata=self.get('metadata'),
db_file=self.get('db_file'),
spec={
'calc_locs':
extend_calc_locs(self.get('name', 'Full relax'),
fw_spec)
}))
infdet_wf = Workflow(fws)
add_modify_incar_by_FWname(infdet_wf,
modify_incar_params=modify_incar_params)
add_modify_kpoints_by_FWname(
infdet_wf, modify_kpoints_params=modify_kpoints_params)
return FWAction(detours=[infdet_wf])
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_update_pos_by_symbols():
struc = Structure.from_str(POSCAR_STR_check_symbol, fmt="POSCAR")
magmoms = [4.0, 4.0, -4.0, -4.0]
struc.add_site_property("magmom", magmoms)
InputSet = RelaxSet(struc)
poscar_str = dfttkutils.update_pos_by_symbols(InputSet, write_file=False)
syms = poscar_str.split("\n")[5]
natom = poscar_str.split("\n")[6]
assert (syms == "Fe Fe")
assert (natom == "2 2")
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 get_wf_gibbs(structure,
num_deformations=7,
deformation_fraction=(-0.1, 0.1),
run_isif2=False,
phonon=False,
phonon_supercell_matrix=None,
pass_isif4=False,
t_min=5,
t_max=2000,
t_step=5,
tolerance=0.01,
volume_spacing_min=0.03,
vasp_cmd=None,
db_file=None,
metadata=None,
name='EV_QHA',
symmetry_tolerance=0.05,
passinitrun=False,
relax_path='',
modify_incar_params={},
modify_kpoints_params={},
verbose=False,
store_volumetric_data=False):
"""
E - V
curve
workflow
Parameters
------
structure: pymatgen.Structure
num_deformations: int
deformation_fraction: float
Can be a float (a single value) or a 2-type of a min,max deformation fraction.
Default is (-0.05, 0.1) leading to volumes of 0.95-1.10. A single value gives plus/minus
by default.
phonon : bool
Whether to do a phonon calculation. Defaults to False, meaning the Debye model.
phonon_supercell_matrix : list
3x3 array of the supercell matrix, e.g. [[2,0,0],[0,2,0],[0,0,2]]. Must be specified if phonon is specified.
t_min : float
Minimum temperature
t_step : float
Temperature step size
t_max : float
Maximum temperature (inclusive)
tolerance: float
Acceptable value for average RMS, recommend >= 0.005.
volume_spacing_min: float
Minimum ratio of Volumes spacing
vasp_cmd : str
Command to run VASP. If None (the default) is passed, the command will be looked up in the FWorker.
db_file : str
Points to the database JSON file. If None (the default) is passed, the path will be looked up in the FWorker.
name : str
Name of the workflow
metadata : dict
Metadata to include
passinitrun : bool
Set True to pass initial VASP running if the results exist in DB, use carefully to keep data consistent.
relax_path : str
Set the path already exists for new static calculations; if set as '', will try to get the path from db_file.
modify_incar_params : dict
User can use these params to modify the INCAR set. It is a dict of class ModifyIncar with keywords in Workflow name.
modify_kpoints_params : dict
User can use these params to modify the KPOINTS set. It is a dict of class ModifyKpoints with keywords in Workflow name.
Only 'kpts' supported now.
run_isif2: bool
Whether run isif=2 calculation before isif=4 running.
pass_isif4: bool
Whether pass isif=4 calculation.
"""
vasp_cmd = vasp_cmd or VASP_CMD
db_file = db_file or DB_FILE
if db_file == ">>db_file<<":
#In PengGao's version, some function used the absolute db_file
from fireworks.fw_config import config_to_dict
from monty.serialization import loadfn
db_file = loadfn(config_to_dict()["FWORKER_LOC"])["env"]["db_file"]
site_properties = deepcopy(structure).site_properties
metadata = metadata or {}
tag = metadata.get('tag', '{}'.format(str(uuid4())))
if isinstance(deformation_fraction, (list, tuple)):
deformations = np.linspace(1 + deformation_fraction[0],
1 + deformation_fraction[1],
num_deformations)
vol_spacing = max((deformation_fraction[1] - deformation_fraction[0]) /
(num_deformations - 0.999999) + 0.001,
volume_spacing_min)
else:
deformations = np.linspace(1 - deformation_fraction,
1 + deformation_fraction, num_deformations)
vol_spacing = max(
deformation_fraction / (num_deformations - 0.999999) * 2 + 0.001,
volume_spacing_min)
fws = []
if 'tag' not in metadata.keys():
metadata['tag'] = tag
relax_path, run_isif2, pass_isif4 = check_relax_path(
relax_path, db_file, tag, run_isif2, pass_isif4)
if (relax_path == ''):
# follow a scheme of
# 1. Full relax + symmetry check
# 2. If symmetry check fails, detour to 1. Volume relax, 2. inflection detection
# 3. Inflection detection
# 4. Static EV
# 5. Phonon EV
# for each FW, we set the structure to the original structure to verify to ourselves that the
# volume deformed structure is set by input set.
vis_relax = RelaxSet(structure)
print('Full relax will be running ...')
full_relax_fw = OptimizeFW(structure,
symmetry_tolerance=symmetry_tolerance,
job_type='normal',
name='Full relax',
prev_calc_loc=False,
vasp_input_set=vis_relax,
vasp_cmd=vasp_cmd,
db_file=db_file,
metadata=metadata,
record_path=True,
run_isif2=run_isif2,
pass_isif4=pass_isif4,
modify_incar_params=modify_incar_params,
modify_kpoints_params=modify_kpoints_params,
store_volumetric_data=store_volumetric_data,
spec={'_preserve_fworker': True})
fws.append(full_relax_fw)
else:
full_relax_fw = None
check_result = Firework(
EVcheck_QHA(db_file=db_file,
tag=tag,
relax_path=relax_path,
deformations=deformations,
site_properties=site_properties,
tolerance=tolerance,
threshold=14,
vol_spacing=vol_spacing,
vasp_cmd=vasp_cmd,
metadata=metadata,
t_min=t_min,
t_max=t_max,
t_step=t_step,
phonon=phonon,
symmetry_tolerance=symmetry_tolerance,
phonon_supercell_matrix=phonon_supercell_matrix,
verbose=verbose,
run_isif2=run_isif2,
pass_isif4=pass_isif4,
modify_incar_params=modify_incar_params,
modify_kpoints_params=modify_kpoints_params,
store_volumetric_data=store_volumetric_data),
parents=full_relax_fw,
name='%s-EVcheck_QHA' % structure.composition.reduced_formula)
fws.append(check_result)
wfname = "{}:{}".format(structure.composition.reduced_formula, name)
wf = Workflow(fws, name=wfname, metadata=metadata)
add_modify_incar_by_FWname(wf, modify_incar_params=modify_incar_params)
add_modify_kpoints_by_FWname(wf,
modify_kpoints_params=modify_kpoints_params)
return wf
def run_task(self, fw_spec):
'''
run_num: maximum number of appending VASP running; this limitation is to avoid always running due to bad settings;
only for internal usage;
Important args:
tolerance: acceptable value for average RMS, recommend >= 0.005;
threshold: total point number above the value should be reduced, recommend < 16 or much time to run;
del_limited: maximum deletion ration for large results;
vol_spacing: the maximum ratio step between two volumes, larger step will be inserted points to calculate;
'''
max_run = 10
deformations = self.get('deformations') or []
db_file = self['db_file']
tag = self['tag']
vasp_cmd = self['vasp_cmd']
metadata = self['metadata']
relax_path = self['relax_path'] or ''
structure = self.get('structure') or None
run_num = self.get('run_num') or 0
tolerance = self.get('tolerance') or 0.005
threshold = self.get('threshold') or 14
del_limited = self.get('del_limited') or 0.3
vol_spacing = self.get('vol_spacing') or 0.05
t_min = self.get('t_min') or 5
t_max = self.get('t_max') or 2000
t_step = self.get('t_step') or 5
phonon = self.get('phonon') or False
phonon_supercell_matrix = self.get('phonon_supercell_matrix') or None
verbose = self.get('verbose') or False
modify_incar_params = self.get('modify_incar_params') or {}
modify_kpoints_params = self.get('modify_kpoints_params') or {}
powerups_options = modify_incar_params.get('powerups', None)
symmetry_tolerance = self.get('symmetry_tolerance') or None
run_isif2 = self.get('run_isif2') or None
pass_isif4 = self.get('pass_isif4') or False
site_properties = self.get('site_properties') or None
store_volumetric_data = self.get('store_volumetric_data', False)
run_num += 1
volumes, energies = self.get_orig_EV_structure(db_file, tag)
self.check_points(db_file, metadata, tolerance, 0.1, del_limited,
volumes, energies, verbose)
EVcheck_result = init_evcheck_result(run_num, self.correct, volumes,
energies, tolerance, threshold,
vol_spacing, self.error, metadata)
structure.scale_lattice(self.minE_value)
if site_properties:
for pkey in site_properties:
structure.add_site_property(pkey, site_properties[pkey])
vol_orig = structure.volume
volume, energy = gen_volenergdos(self.points, volumes, energies)
vol_adds = self.check_vol_coverage(volume, vol_spacing, vol_orig,
run_num, energy, structure, phonon,
db_file, tag, t_min, t_max, t_step,
EVcheck_result) # Normalized to 1
if self.correct or len(vol_adds) > 0:
EVcheck_result['sellected'] = volume
EVcheck_result['minE_value'] = self.minE_value
EVcheck_result['append'] = (vol_adds).tolist()
# Marked as adopted in db
lpad = LaunchPad.auto_load()
fws = []
if len(vol_adds) > 0: # VASP calculations need to append
if run_num < max_run:
# Do VASP and check again
print('Appending PreStatic of : %s to calculate in VASP!' %
(vol_adds * vol_orig).tolist())
fws = []
prestatic_calcs = []
vis_prestatic = PreStaticSet(structure)
for vol_add in vol_adds:
prestatic = StaticFW(
structure=structure,
job_type='normal',
name='VR_%.3f-PreStatic' % vol_add,
prev_calc_loc=False,
vasp_input_set=vis_prestatic,
vasp_cmd=">>vasp_cmd<<",
db_file=self.get('db_file', DB_FILE),
metadata=metadata,
Prestatic=True)
fws.append(prestatic)
prestatic_calcs.append(prestatic)
check_result = Firework(
PreEV_check(
db_file=self.get('db_file', DB_FILE),
tag=tag,
relax_path=relax_path,
deformations=deformations,
run_isif2=run_isif2,
tolerance=tolerance,
threshold=14,
vol_spacing=vol_spacing,
vasp_cmd=">>vasp_cmd<<",
pass_isif4=pass_isif4,
metadata=metadata,
t_min=t_min,
t_max=t_max,
t_step=t_step,
phonon=phonon,
symmetry_tolerance=symmetry_tolerance,
phonon_supercell_matrix=phonon_supercell_matrix,
verbose=verbose,
site_properties=site_properties,
modify_incar_params=modify_incar_params,
modify_kpoints_params=modify_kpoints_params),
parents=prestatic_calcs,
name='%s-PreEV_check%s' %
(structure.composition.reduced_formula, run_num))
fws.append(check_result)
strname = "{}:{}".format(
structure.composition.reduced_formula, 'PreEV_check')
wfs = Workflow(fws, name=strname, metadata=metadata)
if modify_incar_params != {}:
from dfttk.utils import add_modify_incar_by_FWname
add_modify_incar_by_FWname(
wfs, modify_incar_params=modify_incar_params)
if modify_kpoints_params != {}:
from dfttk.utils import add_modify_kpoints_by_FWname
add_modify_kpoints_by_FWname(
wfs, modify_kpoints_params=modify_kpoints_params)
wfs = Customizing_Workflows(
wfs, powerups_options=powerups_options)
lpad.add_wf(wfs)
else:
too_many_run_error()
else: # No need to do more VASP calculation, QHA could be running
relax_path, run_isif2, pass_isif4 = check_relax_path(
relax_path, db_file, tag, run_isif2, pass_isif4)
if relax_path == '':
print(
'Success in PreStatic calculations, entering Position relax ...'
)
vis_relax = RelaxSet(structure)
ps2_relax_fw = OptimizeFW(
structure,
symmetry_tolerance=symmetry_tolerance,
job_type='normal',
name='MinE V=%.3f relax' % vol_orig,
prev_calc_loc=False,
vasp_input_set=vis_relax,
vasp_cmd=">>vasp_cmd<<",
db_file=self.get('db_file', DB_FILE),
metadata=metadata,
record_path=True,
modify_incar={'ISIF': 2},
run_isif2=run_isif2,
pass_isif4=pass_isif4,
modify_incar_params=modify_incar_params,
modify_kpoints_params=modify_kpoints_params,
spec={'_preserve_fworker': True},
store_volumetric_data=store_volumetric_data)
fws.append(ps2_relax_fw)
else:
print(
'Initial setting found, enter static claculations ...')
ps2_relax_fw = None
check_result = Firework(
EVcheck_QHA(
db_file=self.get('db_file', DB_FILE),
tag=tag,
relax_path=relax_path,
tolerance=tolerance,
run_isif2=run_isif2,
threshold=threshold,
vol_spacing=vol_spacing,
vasp_cmd=">>vasp_cmd<<",
run_num=run_num,
metadata=metadata,
t_min=t_min,
t_max=t_max,
t_step=t_step,
phonon=phonon,
deformations=deformations,
phonon_supercell_matrix=phonon_supercell_matrix,
symmetry_tolerance=symmetry_tolerance,
modify_incar_params=modify_incar_params,
verbose=verbose,
pass_isif4=pass_isif4,
modify_kpoints_params=modify_kpoints_params,
site_properties=site_properties),
parents=ps2_relax_fw,
name='%s-EVcheck_QHA' %
structure.composition.reduced_formula,
store_volumetric_data=store_volumetric_data)
fws.append(check_result)
strname = "{}:{}".format(structure.composition.reduced_formula,
'prePS2_Relax')
wfs = Workflow(fws, name=strname, metadata=metadata)
if modify_incar_params != {}:
from dfttk.utils import add_modify_incar_by_FWname
add_modify_incar_by_FWname(
wfs, modify_incar_params=modify_incar_params)
if modify_kpoints_params != {}:
from dfttk.utils import add_modify_kpoints_by_FWname
add_modify_kpoints_by_FWname(
wfs, modify_kpoints_params=modify_kpoints_params)
wfs = Customizing_Workflows(wfs,
powerups_options=powerups_options)
lpad.add_wf(wfs)
else: # failure to meet the tolerance
if len(volumes
) == 0: #self.error == 1e10: # Bad initial running set
pass_result_error()
else: # fitting fails
tol_error()
import json
with open('PreStatic_check_summary.json', 'w') as fp:
json.dump(EVcheck_result, fp)
def __init__(self,
structure,
symmetry_tolerance=None,
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 RelaxSet(
structure, force_gamma=force_gamma, **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:
vasp_input_set = vasp_input_set or RelaxSet(structure)
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
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
}))
# This has to happen at the end because dynamically adding Fireworks if the symmetry breaks skips the rest of the tasks in the Firework.
if symmetry_tolerance is not None:
t.append(
CheckSymmetry(tolerance=symmetry_tolerance,
vasp_cmd=vasp_cmd,
db_file=db_file,
structure=structure,
metadata=metadata,
name=name))
super(OptimizeFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
def __init__(self,
structure,
scale_lattice=None,
symmetry_tolerance=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,
modify_incar=None,
force_gamma=True,
prev_calc_loc=True,
parents=None,
db_insert=False,
Pos_Shape_relax=False,
modify_incar_params={},
modify_kpoints_params={},
**kwargs):
metadata = metadata or {}
override_default_vasp_params = override_default_vasp_params or {}
vasp_input_set = vasp_input_set or RelaxSet(
structure, 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(
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<<"))
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,
Pos_Shape_relax=Pos_Shape_relax))
if db_insert:
t.append(
VaspToDb(db_file=db_file,
additional_fields={
"task_label": name,
"metadata": metadata
}))
# This has to happen at the end because dynamically adding Fireworks if the symmetry breaks skips the rest of the tasks in the Firework.
if symmetry_tolerance is not None:
t.append(
CheckSymmetry(tolerance=symmetry_tolerance,
vasp_cmd=vasp_cmd,
db_file=db_file,
structure=structure,
metadata=metadata,
name=name,
modify_incar_params=modify_incar_params,
modify_kpoints_params=modify_kpoints_params,
Pos_Shape_relax=Pos_Shape_relax))
super(OptimizeFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
def __init__(self,
structure,
isif=4,
name="structure optimization",
override_symmetry_tolerances=None,
job_type="normal",
vasp_cmd="vasp_std",
metadata=None,
override_default_vasp_params=None,
db_file=None,
prev_calc_loc=True,
parents=None,
db_insert=False,
tag=None,
**kwargs):
metadata = metadata or {}
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
override_default_vasp_params = override_default_vasp_params or {}
override_symmetry_tolerances = override_symmetry_tolerances or {}
vasp_input_set = 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(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
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
}))
common_kwargs = {
'vasp_cmd': vasp_cmd,
'db_file': db_file,
"metadata": metadata,
"tag": tag
}
relax_kwargs = {}
static_kwargs = {}
t.append(
CheckRelaxation(db_file=db_file,
metadata=metadata,
tag=tag,
common_kwargs=common_kwargs,
relax_kwargs=relax_kwargs,
static_kwargs=static_kwargs,
**override_symmetry_tolerances))
super().__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
def run_task(self, fw_spec):
'''
run_num: maximum number of appending VASP running; this limitation is to avoid always running due to bad settings;
only for internal usage;
Important args:
tolerance: acceptable value for average RMS, recommend >= 0.005;
threshold: total point number above the value should be reduced, recommend < 16 or much time to run;
del_limited: maximum deletion ration for large results;
vol_spacing: the maximum ratio step between two volumes, larger step will be inserted points to calculate;
'''
max_run = 10
deformations = self.get('deformations') or []
db_file = self['db_file']
tag = self['tag']
vasp_cmd = self['vasp_cmd']
metadata = self['metadata']
relax_path = self['relax_path'] or ''
run_num = self.get('run_num') or 0
tolerance = self.get('tolerance') or 0.005
threshold = self.get('threshold') or 14
del_limited = self.get('del_limited') or 0.3
vol_spacing = self.get('vol_spacing') or 0.03
t_min = self.get('t_min') or 5
t_max = self.get('t_max') or 2000
t_step = self.get('t_step') or 5
phonon = self.get('phonon') or False
phonon_supercell_matrix = self.get('phonon_supercell_matrix') or None
verbose = self.get('verbose') or False
modify_incar_params = self.get('modify_incar_params') or {}
modify_kpoints_params = self.get('modify_kpoints_params') or {}
Pos_Shape_relax = self.get('Pos_Shape_relax') or False
symmetry_tolerance = self.get('symmetry_tolerance') or None
run_num += 1
relax_path, Pos_Shape_relax = check_relax_path(relax_path, db_file, tag, Pos_Shape_relax)
if relax_path == '':
print('''
#######################################################################
# #
# Cannot find relax path for static calculations, exit! #
# You can modify the tag and run again! #
# #
#######################################################################
''')
return
from pymatgen.io.vasp.inputs import Poscar
poscar = Poscar.from_file(relax_path + '/CONTCAR')
structure = poscar.structure
if phonon:
if not consistent_check_db(db_file, tag):
print('Please check DB, DFTTK running ended!')
return
volumes, energies, dos_objs = self.get_orig_EV(db_file, tag)
vol_adds = self.check_deformations_in_volumes(deformations, volumes, structure.volume)
if (len(vol_adds)) == 0:
self.check_points(db_file, metadata, tolerance, threshold, del_limited, volumes, energies, verbose)
else:
self.correct = True
self.error = 1e10
EVcheck_result = {}
EVcheck_result['append_run_num'] = run_num
EVcheck_result['correct'] = self.correct
EVcheck_result['volumes'] = volumes
EVcheck_result['energies'] = energies
EVcheck_result['tolerance'] = tolerance
EVcheck_result['threshold'] = threshold
EVcheck_result['vol_spacing'] = vol_spacing
EVcheck_result['error'] = self.error
EVcheck_result['metadata'] = metadata
if self.correct:
vol_orig = structure.volume
if (len(vol_adds)) == 0:
volume, energy, dos_obj = self.gen_volenergdos(self.points, volumes, energies, dos_objs)
vol_adds = self.check_vol_coverage(volume, vol_spacing, vol_orig, run_num,
energy, structure, dos_obj, phonon,
db_file, tag, t_min, t_max, t_step,
EVcheck_result) # Normalized to 1
EVcheck_result['sellected'] = volume
EVcheck_result['append'] = (vol_adds * vol_orig).tolist()
# Marked as adopted in db
mark_adopted(tag, db_file, volume)
lpad = LaunchPad.auto_load()
fws = []
if len(vol_adds) > 0: # VASP calculations need to append
if run_num < max_run:
# Do VASP and check again
print('Appending the volumes of : %s to calculate in VASP!' %(vol_adds * vol_orig).tolist())
calcs = []
vis_relax = RelaxSet(structure)
vis_static = StaticSet(structure)
isif = 5 if 'infdet' in relax_path else 4
for vol_add in vol_adds:
if Pos_Shape_relax:
ps_relax_fw = OptimizeFW(structure, scale_lattice=vol_add, symmetry_tolerance=None, modify_incar = {'ISIF': isif},
job_type='normal', name='Pos_Shape_%.3f-relax' %(vol_add * vol_orig), prev_calc_loc=relax_path,
vasp_input_set=vis_relax, vasp_cmd=vasp_cmd, db_file=db_file, metadata=metadata, Pos_Shape_relax = True,
modify_incar_params=modify_incar_params, modify_kpoints_params = modify_kpoints_params,
parents=None)
calcs.append(ps_relax_fw)
fws.append(ps_relax_fw)
static = StaticFW(structure, name = 'structure_%.3f-static' %(vol_add * vol_orig), vasp_input_set=vis_static, vasp_cmd=vasp_cmd,
db_file=db_file, metadata=metadata, prev_calc_loc=True, parents=ps_relax_fw)
else:
static = StaticFW(structure, scale_lattice=vol_add, name = 'structure_%.3f-static' %(vol_add * vol_orig), vasp_input_set=vis_static, vasp_cmd=vasp_cmd,
db_file=db_file, metadata=metadata, prev_calc_loc=relax_path, parents=None)
fws.append(static)
calcs.append(static)
if phonon:
visphonon = ForceConstantsSet(structure)
phonon_fw = PhononFW(structure, phonon_supercell_matrix, t_min=t_min, t_max=t_max, t_step=t_step,
name='structure_%.3f-phonon' %(vol_add * vol_orig), vasp_input_set=visphonon,
vasp_cmd=vasp_cmd, db_file=db_file, metadata=metadata,
prev_calc_loc=True, parents=static)
fws.append(phonon_fw)
calcs.append(phonon_fw)
check_result = Firework(EVcheck_QHA(db_file = db_file, tag = tag, relax_path = relax_path, tolerance = tolerance,
threshold = threshold, vol_spacing = vol_spacing, vasp_cmd = vasp_cmd, run_num = run_num,
metadata = metadata, t_min = t_min, t_max = t_max, t_step = t_step, phonon = phonon,
phonon_supercell_matrix = phonon_supercell_matrix, symmetry_tolerance = symmetry_tolerance,
modify_incar_params = modify_incar_params, verbose = verbose, Pos_Shape_relax = Pos_Shape_relax,
modify_kpoints_params = modify_kpoints_params),
parents = calcs, name='%s-EVcheck_QHA' %structure.composition.reduced_formula)
fws.append(check_result)
strname = "{}:{}".format(structure.composition.reduced_formula, 'EV_QHA_Append')
wfs = Workflow(fws, name = strname, metadata=metadata)
if modify_incar_params != {}:
from dfttk.utils import add_modify_incar_by_FWname
add_modify_incar_by_FWname(wfs, modify_incar_params = modify_incar_params)
if modify_kpoints_params != {}:
from dfttk.utils import add_modify_kpoints_by_FWname
add_modify_kpoints_by_FWname(wfs, modify_kpoints_params = modify_kpoints_params)
lpad.add_wf(wfs)
else:
print('''
#######################################################################
# #
# Too many appended VASP running times, abort! #
# Please check VASP setting! #
# #
#######################################################################
''')
else: # No need to do more VASP calculation, QHA could be running
print('Success in Volumes-Energies checking, enter QHA ...')
# Debye
debye_fw = Firework(QHAAnalysis(phonon=False, t_min=t_min, t_max=t_max, t_step=t_step, db_file=db_file, tag=tag, metadata=metadata),
name="{}-qha_analysis-Debye".format(structure.composition.reduced_formula))
fws.append(debye_fw)
if phonon:
phonon_supercell_matrix = self.get('phonon_supercell_matrix')
# do a Debye run before the phonon, so they can be done in stages.
phonon_fw = Firework(QHAAnalysis(phonon=True, t_min=t_min, t_max=t_max, t_step=t_step, db_file=db_file, tag=tag,
metadata=metadata), parents=debye_fw, name="{}-qha_analysis-phonon".format(structure.composition.reduced_formula))
fws.append(phonon_fw)
strname = "{}:{}".format(structure.composition.reduced_formula, 'QHA')
wfs = Workflow(fws, name = strname, metadata=metadata)
lpad.add_wf(wfs)
else: # failure to meet the tolerance
if len(volumes) == 0: #self.error == 1e10: # Bad initial running set
print('''
#######################################################################
# #
# "passinitrun = True" could not set while initial results absent. #
# #
#######################################################################
''')
else: # fitting fails
print('''
#######################################################################
# #
# Can not achieve the tolerance requirement, abort! #
# #
#######################################################################
''')
import json
with open('E-V check_summary.json', 'w') as fp:
json.dump(EVcheck_result, fp)
def get_wf_gibbs(structure, num_deformations=7, deformation_fraction=(-0.05, 0.1),
phonon=False, phonon_supercell_matrix=None,
t_min=5, t_max=2000, t_step=5,
vasp_cmd=None, db_file=None, metadata=None, name='EV_QHA'):
"""
E - V
curve
workflow
Parameters
------
structure: pymatgen.Structure
num_deformations: int
deformation_fraction: float
Can be a float (a single value) or a 2-type of a min,max deformation fraction.
Default is (-0.05, 0.1) leading to volumes of 0.95-1.10. A single value gives plus/minus
by default.
phonon : bool
Whether to do a phonon calculation. Defaults to False, meaning the Debye model.
phonon_supercell_matrix : list
3x3 array of the supercell matrix, e.g. [[2,0,0],[0,2,0],[0,0,2]]. Must be specified if phonon is specified.
t_min : float
Minimum temperature
t_step : float
Temperature step size
t_max : float
Maximum temperature (inclusive)
vasp_cmd : str
Command to run VASP. If None (the default) is passed, the command will be looked up in the FWorker.
db_file : str
Points to the database JSON file. If None (the default) is passed, the path will be looked up in the FWorker.
name : str
Name of the workflow
metadata : dict
Metadata to include
"""
vasp_cmd = vasp_cmd or VASP_CMD
db_file = db_file or DB_FILE
metadata = metadata or {}
tag = metadata.get('tag', '{}'.format(str(uuid4())))
if 'tag' not in metadata.keys():
metadata['tag'] = tag
if isinstance(deformation_fraction, (list, tuple)):
deformations = np.linspace(1+deformation_fraction[0], 1+deformation_fraction[1], num_deformations)
else:
deformations = np.linspace(1-deformation_fraction, 1+deformation_fraction, num_deformations)
# follow a scheme of
# 1. Full relax + symmetry check
# 2. If symmetry check fails, detour to 1. Volume relax, 2. inflection detection
# 3. Inflection detection
# 4. Static EV
# 5. Phonon EV
fws = []
static_calcs = []
phonon_calcs = []
# for each FW, we set the structure to the original structure to verify to ourselves that the
# volume deformed structure is set by input set.
# Full relax
vis = RelaxSet(structure)
full_relax_fw = OptimizeFW(structure, symmetry_tolerance=0.05, job_type='normal', name='Full relax', prev_calc_loc=False, vasp_input_set=vis, vasp_cmd=vasp_cmd, db_file=db_file, metadata=metadata, spec={'_preserve_fworker': True})
fws.append(full_relax_fw)
for i, deformation in enumerate(deformations):
vis = StaticSet(structure)
static = StaticFW(structure, scale_lattice=deformation, name='structure_{}-static'.format(i), vasp_input_set=vis, vasp_cmd=vasp_cmd, db_file=db_file, metadata=metadata, parents=full_relax_fw)
fws.append(static)
static_calcs.append(static)
if phonon:
vis = ForceConstantsSet(structure)
phonon_fw = PhononFW(structure, phonon_supercell_matrix, t_min=t_min, t_max=t_max, t_step=t_step,
name='structure_{}-phonon'.format(i), vasp_input_set=vis,
vasp_cmd=vasp_cmd, db_file=db_file, metadata=metadata,
prev_calc_loc=True, parents=static)
fws.append(phonon_fw)
phonon_calcs.append(static)
phonon_calcs.append(phonon_fw)
# always do a Debye after the static calculations. That way we can set up a phonon calculation, do a Debye fitting, then do the phonon if we want.
debye_fw = Firework(QHAAnalysis(phonon=False, t_min=t_min, t_max=t_max, t_step=t_step, db_file=db_file, tag=tag, metadata=metadata), parents=static_calcs, name="{}-qha_analysis-Debye".format(structure.composition.reduced_formula))
fws.append(debye_fw)
if phonon:
# do a Debye run before the phonon, so they can be done in stages.
phonon_fw = Firework(QHAAnalysis(phonon=True, t_min=t_min, t_max=t_max, t_step=t_step, db_file=db_file, tag=tag, metadata=metadata), parents=phonon_calcs, name="{}-qha_analysis-phonon".format(structure.composition.reduced_formula))
fws.append(phonon_fw)
wfname = "{}:{}".format(structure.composition.reduced_formula, name)
return Workflow(fws, name=wfname, metadata=metadata)