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 get_wf_gibbs_SQS(structure,
num_deformations=7,
deformation_fraction=(-0.1, 0.1),
phonon=False,
phonon_supercell_matrix=None,
run_isif2=False,
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 to get_gibbs.
pass_isif4: bool
Whether pass isif=4 calculation, pass to get_gibbs.
"""
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 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)
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)
fws = []
prestatic_calcs = []
if relax_path != '':
pass
else:
for i, deformation in enumerate(np.linspace(0.85, 1.15, 7)):
structure1 = deepcopy(structure)
structure1.scale_lattice(deformation * structure.volume)
vis_PreStatic = PreStaticSet(structure1)
prestatic = StaticFW(structure=structure1,
scale_lattice=deformation,
name='VR_%.3f-PreStatic' % deformation,
prev_calc_loc=False,
vasp_input_set=vis_PreStatic,
vasp_cmd=vasp_cmd,
db_file=db_file,
metadata=metadata,
Prestatic=True,
store_volumetric_data=store_volumetric_data)
fws.append(prestatic)
prestatic_calcs.append(prestatic)
check_result = Firework(
PreEV_check(db_file=db_file,
tag=tag,
relax_path=relax_path,
deformations=deformations,
structure=structure,
tolerance=tolerance,
threshold=14,
vol_spacing=vol_spacing,
vasp_cmd=vasp_cmd,
run_isif2=run_isif2,
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,
pass_isif4=pass_isif4,
modify_incar_params=modify_incar_params,
modify_kpoints_params=modify_kpoints_params),
parents=prestatic_calcs,
name='%s-PreEV_check' % 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 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 get_wf_gibbs_robust(structure,
num_deformations=7,
deformation_fraction=(-0.1, 0.1),
phonon=False,
isif4=False,
phonon_supercell_matrix=None,
override_symmetry_tolerances=None,
t_min=5,
t_max=2000,
t_step=5,
eos_tolerance=0.01,
volume_spacing_min=0.03,
vasp_cmd=None,
db_file=None,
metadata=None,
name='EV_QHA',
override_default_vasp_params=None,
modify_incar_params={},
modify_kpoints_params={},
verbose=False,
level=1,
phonon_supercell_matrix_min=60,
phonon_supercell_matrix_max=120,
optimize_sc=False,
force_phonon=False,
stable_tor=0.01,
store_volumetric_data=False):
"""
E - V
curve
workflow
Parameters
------
structure: pymatgen.Structure
The initial structure
num_deformations: int
The number of deformation
deformation_fraction: float
Can be a float (a single value) or a 2-type of a min,max deformation fraction.
Default is (-0.1, 0.1) leading to volumes of 0.90-1.10. 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/str
3x3 array of the supercell matrix, e.g. [[2,0,0],[0,2,0],[0,0,2]]. Must be specified if phonon is specified.
if string, choose from 'atoms', 'lattice' or 'volume' (only the first letter works, case insensitive),
which determine who to determin the matrix
override_symmetry_tolerances : dict
The symmetry tolerance. It contains three keys, default: {'tol_energy':0.025, 'tol_strain':0.05, 'tol_bond':0.1}
t_min : float
Minimum temperature
t_step : float
Temperature step size
t_max : float
Maximum temperature (inclusive)
eos_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
override_default_vasp_params: dict
Override vasp parameters for all vasp jobs. e.g override_default_vasp_params={'user_incar_settings': {'ISIF': 4}}
modify_incar_params : dict
Override vasp settings in firework level
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.
phonon_supercell_matrix_min/max: int
minimum/maximum atoms/lattice/volume(controlled by scale_object, default is using atoms)
optimize_sc: bool
Optimize the super cell matrix (True) or not (False)
If False, then use the closest integer transformation matrix of ideal matrix
stable_tor: float
The tolerance for phonon stability (the percentage of negative part frequency)
"""
vasp_cmd = vasp_cmd or VASP_CMD
db_file = db_file or DB_FILE
override_symmetry_tolerances = override_symmetry_tolerances or {
'tol_energy': 0.025,
'tol_strain': 0.05,
'tol_bond': 0.10
}
override_default_vasp_params = override_default_vasp_params or {}
site_properties = deepcopy(structure).site_properties
metadata = metadata or {}
tag = metadata.get('tag', '{}'.format(str(uuid4())))
metadata.update({'tag': tag})
deformations = _get_deformations(deformation_fraction, num_deformations)
vol_spacing = max(
(deformations[-1] - deformations[0]) / (num_deformations - 1),
volume_spacing_min)
common_kwargs = {
'vasp_cmd': vasp_cmd,
'db_file': ">>db_file<<",
"metadata": metadata,
"tag": tag,
'override_default_vasp_params': override_default_vasp_params
}
robust_opt_kwargs = {
'isif': 7,
'isif4': isif4,
'level': level,
'override_symmetry_tolerances': override_symmetry_tolerances
}
vasp_kwargs = {
'modify_incar_params': modify_incar_params,
'modify_kpoints_params': modify_kpoints_params
}
t_kwargs = {'t_min': t_min, 't_max': t_max, 't_step': t_step}
eos_kwargs = {
'deformations': deformations,
'vol_spacing': vol_spacing,
'eos_tolerance': eos_tolerance,
'threshold': 14
}
fws = []
robust_opt_fw = RobustOptimizeFW(
structure,
prev_calc_loc=False,
name='Full relax',
store_volumetric_data=store_volumetric_data,
**robust_opt_kwargs,
**vasp_kwargs,
**common_kwargs)
fws.append(robust_opt_fw)
check_qha_parent = []
if phonon:
if isinstance(phonon_supercell_matrix, str):
if phonon_supercell_matrix == 'Yphon':
phonon_supercell_matrix = supercell_scaling_by_Yphon(
structure, supercellsize=phonon_supercell_matrix_max)
else:
phonon_supercell_matrix = supercell_scaling_by_atom_lat_vol(
structure,
min_obj=phonon_supercell_matrix_min,
max_obj=phonon_supercell_matrix_max,
scale_object=phonon_supercell_matrix,
target_shape='sc',
lower_search_limit=-2,
upper_search_limit=2,
verbose=verbose,
sc_tolerance=1e-5,
optimize_sc=optimize_sc)
ph_scm_size = np.array(phonon_supercell_matrix).shape
if not (ph_scm_size[0] == 3 and ph_scm_size[1] == 3):
raise ValueError(
'Current phonon_supercell_matrix({}) is not correct.'.format(
phonon_supercell_matrix))
phonon_wf = PhononFW(structure,
phonon_supercell_matrix,
parents=robust_opt_fw,
prev_calc_loc='static',
name='structure_{:.3f}-phonon'.format(
structure.volume),
stable_tor=stable_tor,
**t_kwargs,
**common_kwargs)
fws.append(phonon_wf)
check_qha_parent.append(phonon_wf)
check_relax_fw = Firework(CheckRelaxScheme(db_file=">>db_file<<", tag=tag),
parents=robust_opt_fw,
name="{}-CheckRelaxScheme".format(
structure.composition.reduced_formula))
fws.append(check_relax_fw)
check_qha_parent.append(check_relax_fw)
check_qha_fw = Firework(
EVcheck_QHA(site_properties=site_properties,
verbose=verbose,
stable_tor=stable_tor,
phonon=phonon,
phonon_supercell_matrix=phonon_supercell_matrix,
force_phonon=force_phonon,
override_symmetry_tolerances=override_symmetry_tolerances,
store_volumetric_data=store_volumetric_data,
**eos_kwargs,
**vasp_kwargs,
**t_kwargs,
**common_kwargs),
parents=check_qha_parent,
name='{}-EVcheck_QHA'.format(structure.composition.reduced_formula))
fws.append(check_qha_fw)
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 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:
eos_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;
'''
# Get the parameters from the object
max_run = 10
db_file = env_chk(self.get('db_file', DB_FILE),
fw_spec) #always concrete db_fiel
vasp_cmd = ">>vasp_cmd<<" #chould change for user to provide the change
deformations = self.get('deformations', [])
run_num = self.get('run_num', 0)
eos_tolerance = self.get('eos_tolerance', 0.005)
threshold = self.get('threshold', 14)
del_limited = self.get('del_limited', 0.3)
vol_spacing = self.get('vol_spacing', 0.05)
t_min = self.get('t_min', 5)
t_max = self.get('t_max', 2000)
t_step = self.get('t_step', 5)
phonon = self.get('phonon', False)
force_phonon = self.get('force_phonon', False)
phonon_supercell_matrix = self.get('phonon_supercell_matrix', None)
verbose = self.get('verbose', False)
modify_kpoints_params = self.get('modify_kpoints_params', {})
site_properties = self.get('site_properties', None)
modify_incar_params = self.get('modify_incar_params', {})
powerups_options = modify_incar_params.get('powerups', None)
override_default_vasp_params = self.get('override_default_vasp_params',
{})
user_incar_settings = override_default_vasp_params.get(
'user_incar_settings', {})
powerups_options = user_incar_settings.get('powerups',
powerups_options)
override_symmetry_tolerances = self.get('override_symmetry_tolerances',
{})
store_volumetric_data = self.get('store_volumetric_data', False)
stable_tor = self.get('stable_tor', 0.01)
force_phonon = self.get('force_phonon', False)
test = self.get('test', False)
relax_structure = self.get('structure') or fw_spec.get(
'structure', None)
relax_scheme = self.get('relax_scheme') or fw_spec.get(
'relax_scheme', [2])
relax_phonon = fw_spec.get('relax_phonon', False)
#Only set phonon=True and ISIF=4 passed, then run phonon
if not force_phonon:
phonon = phonon and relax_phonon
metadata = self.get('metadata', {})
tag = self.get('tag', metadata.get('tag', None))
if tag is None:
tag = str(uuid4())
metadata['tag'] = tag
common_kwargs = {
'vasp_cmd': vasp_cmd,
'db_file': self.get('db_file', DB_FILE),
"metadata": metadata,
"tag": tag,
'override_default_vasp_params': override_default_vasp_params,
}
vasp_kwargs = {
'modify_incar_params': modify_incar_params,
'modify_kpoints_params': modify_kpoints_params
}
t_kwargs = {'t_min': t_min, 't_max': t_max, 't_step': t_step}
eos_kwargs = {
'vol_spacing': vol_spacing,
'eos_tolerance': eos_tolerance,
'threshold': 14
}
run_num += 1
#Some initial checks
#TODO: add phonon after RobustOptimizeFW
if phonon:
#To check if the consistent of phonon and optimize
if not consistent_check_db(db_file, tag):
print('Please check DB, DFTTK running ended!')
return
if relax_structure is not None:
structure = deepcopy(relax_structure)
else:
raise ValueError(
'Not structure in spec, please provide structure as input')
if site_properties:
for pkey in site_properties:
structure.add_site_property(pkey, site_properties[pkey])
# get original EV curve
volumes, energies, dos_objs = self.get_orig_EV(db_file, tag)
vol_adds = check_deformations_in_volumes(deformations, volumes,
structure.volume)
if (len(vol_adds)) == 0:
self.check_points(db_file, metadata, eos_tolerance, threshold,
del_limited, volumes, energies, verbose)
else:
self.correct = True
self.error = 1e10
EVcheck_result = init_evcheck_result(append_run_num=run_num,
correct=self.correct,
volumes=volumes,
energies=energies,
eos_tolerance=eos_tolerance,
threshold=threshold,
vol_spacing=vol_spacing,
error=self.error,
metadata=metadata)
if self.correct:
vol_orig = structure.volume
if (len(vol_adds)) == 0:
volume, energy, dos_obj = 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['selected'] = volume
EVcheck_result['append'] = (vol_adds).tolist()
# Marked as adopted in db
mark_adopted(tag, db_file, volume, phonon=phonon)
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).tolist())
calcs = []
#vis_relax = RelaxSet(structure)
#vis_static = StaticSet(structure)
#isif2 = 5 if 'infdet' in relax_path else 4
for vol_add in vol_adds:
struct = deepcopy(structure)
struct.scale_lattice(structure.volume * vol_add)
relax_parents_fw = None
for isif_i in relax_scheme:
#record_path=record_path
relax_fw = OptimizeFW(
struct,
isif=isif_i,
store_volumetric_data=store_volumetric_data,
name="relax_Vol{:.3f}".format(vol_add),
vasp_input_set=None,
job_type="normal",
override_symmetry_tolerances=
override_symmetry_tolerances,
prev_calc_loc=True,
parents=relax_parents_fw,
db_insert=False,
force_gamma=True,
modify_incar={},
**vasp_kwargs,
**common_kwargs)
relax_parents_fw = deepcopy(relax_fw)
fws.append(relax_fw)
calcs.append(relax_fw)
static_fw = StaticFW(
struct,
isif=relax_scheme[-1],
name='static_Vol{:.3f}'.format(vol_add),
vasp_input_set=None,
prev_calc_loc=True,
parents=relax_parents_fw,
store_volumetric_data=store_volumetric_data,
**common_kwargs)
fws.append(static_fw)
calcs.append(static_fw)
if phonon:
#visphonon = ForceConstantsSet(struct)
phonon_fw = PhononFW(
struct,
phonon_supercell_matrix,
vasp_input_set=None,
stable_tor=stable_tor,
name='structure_{:.3f}-phonon'.format(vol_add),
prev_calc_loc=True,
parents=static_fw,
**t_kwargs,
**common_kwargs)
fws.append(phonon_fw)
calcs.append(phonon_fw)
check_result = Firework(
EVcheck_QHA(
structure=relax_structure,
relax_scheme=relax_scheme,
store_volumetric_data=store_volumetric_data,
run_num=run_num,
verbose=verbose,
site_properties=site_properties,
stable_tor=stable_tor,
phonon=phonon,
phonon_supercell_matrix=phonon_supercell_matrix,
force_phonon=force_phonon,
**eos_kwargs,
**vasp_kwargs,
**t_kwargs,
**common_kwargs),
parents=calcs,
name='{}-EVcheck_QHA'.format(
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)
wfs = Customizing_Workflows(
wfs, powerups_options=powerups_options)
if not test: lpad.add_wf(wfs)
else:
too_many_run_error()
else: # No need to do more VASP calculation, QHA could be running
print('Success in Volumes-Energies checking, enter QHA ...')
debye_fw = Firework(QHAAnalysis(phonon=phonon,
t_min=t_min,
t_max=t_max,
t_step=t_step,
db_file=self.get(
'db_file', DB_FILE),
tag=tag,
metadata=metadata),
name="{}-qha_analysis".format(
structure.composition.reduced_formula))
fws.append(debye_fw)
'''
# 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 Staticore 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)
wfs = Customizing_Workflows(wfs,
powerups_options=powerups_options)
if not test: 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('EV_check_summary.json', 'w') as fp:
json.dump(EVcheck_result, fp, indent=4)
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)