def get_wf_single(structure,
WORKFLOW="get_wf_gibbs",
settings={},
db_file=None):
"""
Get a single workflow
Parameters
structure: pymatgen.Structure
The structure
WORKFLOW: str
The name of the workflow, now only gibbs energy workflow(get_wf_gibbs) is supported
settings: dict
User settings for the workflow
Return
"""
################ PARAMETERS FOR WF #############################
#str, the absolute path of db.json file, e.g. /storage/home/mjl6505/atomate/config/db.json
# If None, it will use the configuration in fireworks
if db_file is None:
db_file = settings.get('db_file', None)
#list, the MAGMOM of the structure, e.g. [4.0, 4.0, -4.0, -4.0]
magmom = settings.get('magmom', None)
magmom = parse_magmom(magmom=magmom, nvalue=len(structure.sites))
#int, the number of initial deformations, e.g. 7
num_deformations = settings.get('num_deformations', 7)
#list/tuple(min, max) or float(-max, max), the maximum amplitude of deformation, e.g. (-0.15, 0.15) means (0.95, 1.1) in volume
deformation_fraction = settings.get('deformation_fraction', (-0.15, 0.20))
#float, minimum ratio of Volumes spacing, e.g. 0.05
volume_spacing_min = settings.get('volume_spacing_min', 0.05)
#bool, run phonon(True) or not(False)
phonon = settings.get('phonon', False)
#list(3x3), the supercell matrix for phonon, e.g. [[2.0, 0, 0], [0, 2.0, 0], [0, 0, 2.0]]
phonon_supercell_matrix = settings.get('phonon_supercell_matrix', None)
phonon_supercell_matrix_min = settings.get('phonon_supercell_matrix_min',
None)
phonon_supercell_matrix_max = settings.get('phonon_supercell_matrix_max',
None)
optimize_sc = settings.get('optimize_sc', False)
#run phonon always, no matter ISIF=4 passed or not
force_phonon = settings.get('force_phonon', False)
#The tolerance for phonon stable
stable_tor = settings.get('stable_tor', 0.01)
#float, the mimimum of temperature in QHA process, e.g. 5
t_min = settings.get('t_min', 5)
#float, the maximum of temperature in QHA process, e.g. 2000
t_max = settings.get('t_max', 2000)
#float, the step of temperature in QHA process, e.g. 5
t_step = settings.get('t_step', 5)
#float, acceptable value for average RMS, recommend >= 0.005
eos_tolerance = settings.get('eos_tolerance', 0.01)
#str, the vasp command, if None then find in the FWorker configuration
vasp_cmd = settings.get('vasp_cmd', None)
#dict, metadata to be included, this parameter is useful for filter the data, e.g. metadata={"phase": "BCC_A2", "tag": "AFM"}
metadata = settings.get('metadata', None)
#It is for RobustOptimizeFW, if run ISIF=4 followed ISIF=7
isif4 = settings.get('isif4', False)
#The level for robust optimization
level = settings.get('level', 1)
#float, the tolerannce for symmetry, e.g. 0.05
symmetry_tolerance = settings.get('symmetry_tolerance', 0.05)
#bool, set True to pass initial VASP running if the results exist in DB, use carefully to keep data consistent.
passinitrun = settings.get('passinitrun', False)
#bool, Whether run isif=2 calculation before isif=4 running
run_isif2 = settings.get('run_isif2', False)
#bool, Whether pass isif=4 calculation.
pass_isif4 = settings.get('pass_isif4', False)
#Set the path already exists for new static calculations; if set as '', will try to get the path from db_file
relax_path = settings.get('relax_path', '')
#The symmetry tolerance, including three keys,
#e.g. override_symmetry_tolerances={'tol_strain': 0.05, 'tol_energy': 0.025, 'tol_bond': 0.10}
override_symmetry_tolerances = settings.get('override_symmetry_tolerances',
None)
#Global settings for all vasp job, e.g.
#override_default_vasp_params = {'user_incar_settings': {}, 'user_kpoints_settings': {}, 'user_potcar_functional': str}
#If some value in 'user_incar_settings' is set to None, it will use vasp's default value
override_default_vasp_params = settings.get('override_default_vasp_params',
{})
#dict, dict of class ModifyIncar with keywords in Workflow name. e.g.
"""
modify_incar_params = { 'Full relax': {'incar_update': {"LAECHG":False,"LCHARG":False,"LWAVE":False}},
'PreStatic': {'incar_update': {"LAECHG":False,"LCHARG":False,"LWAVE":False}},
'PS2': {'incar_update': {"LAECHG":False,"LCHARG":False,"LWAVE":False}},
'static': {'incar_update': {"LAECHG":False,"LCHARG":False,"LWAVE":False}},
"""
modify_incar_params = settings.get('modify_incar_params', {})
#check if fworker_name is assigned
powerups = settings.get('powerups', {})
"""
if len(powerups)>0:
if 'user_incar_settings' not in override_default_vasp_params:
override_default_vasp_params.update({'user_incar_settings':{}})
override_default_vasp_params['user_incar_settings'].update({'powerups':powerups})
modify_incar_params.update({'powerups':powerups})
"""
#dict, dict of class ModifyKpoints with keywords in Workflow name, similar with modify_incar_params
modify_kpoints_params = settings.get('modify_kpoints_params', {})
#bool, print(True) or not(False) some informations, used for debug
verbose = settings.get('verbose', False)
#Save the volume data or not ("chgcar", "aeccar0", "aeccar2", "elfcar", "locpot")
store_volumetric_data = settings.get('store_volumetric_data', False)
## The following settings only work for elastic constants workflow
strain_states = settings.get('strain_states', None)
stencils = settings.get('stencils', None)
analysis = settings.get('analysis', True)
sym_reduce = settings.get('sym_reduce', False)
order = settings.get('order', 2)
conventional = settings.get('conventional', False)
"""
stencils = settings.get('stencils', [0.01])
#sym_reduce = settings.get('sym_reduce', True)
stencils = settings.get('stencils', [-0.01,0.01])
#conventional = settings.get('conventional', True)
"""
#Set the default value for phonon_supercell_matrix_min/max
if isinstance(phonon_supercell_matrix,
str) and (phonon_supercell_matrix_min is None):
if phonon_supercell_matrix.lower().startswith('a'):
phonon_supercell_matrix_min = 60
phonon_supercell_matrix_max = 130
elif phonon_supercell_matrix.lower().startswith('l'):
phonon_supercell_matrix_min = 8
phonon_supercell_matrix_max = 12
elif phonon_supercell_matrix.lower().startswith('v'):
phonon_supercell_matrix_min = 512
phonon_supercell_matrix_max = 1728
else:
raise ValueError(
"Unknown parameters for phonon_supercell_matrix({}), support 'atoms', 'lattice' or 'volume' or 3x3 list."
.format(phonon_supercell_matrix))
uis = override_default_vasp_params.get('user_incar_settings', {})
if magmom:
structure.add_site_property('magmom', magmom)
elif 'MAGMOM' in uis:
magmom = uis['MAGMOM']
if isinstance(magmom, str):
magmom = Incar.from_string(
'MAGMOM={}'.format(magmom)).as_dict()['MAGMOM']
magmom = parse_magmom(magmom=magmom, nvalue=len(structure.sites))
structure.add_site_property('magmom', magmom)
if not db_file:
#from fireworks.fw_config import config_to_dict
#db_file = loadfn(config_to_dict()["FWORKER_LOC"])["env"]["db_file"]
db_file = ">>db_file<<"
"""
if WORKFLOW == "get_wf_gibbs":
#Currently, only this workflow is supported
wf = get_wf_gibbs(structure, num_deformations=num_deformations, deformation_fraction=deformation_fraction,
phonon=phonon, phonon_supercell_matrix=phonon_supercell_matrix, t_min=t_min, t_max=t_max,
t_step=t_step, eos_tolerance=eos_tolerance, volume_spacing_min=volume_spacing_min,vasp_cmd=vasp_cmd,
db_file=db_file, metadata=metadata, name='EV_QHA', symmetry_tolerance=symmetry_tolerance,
run_isif2=run_isif2, pass_isif4=pass_isif4, passinitrun=passinitrun, relax_path=relax_path,
modify_incar_params=modify_incar_params, modify_kpoints_params=modify_kpoints_params,
verbose=verbose, store_volumetric_data=store_volumetric_data)
elif WORKFLOW == "eos":
"""
if WORKFLOW == "eos":
wf = get_wf_EV_bjb(
structure,
deformation_fraction=deformation_fraction,
store_volumetric_data=store_volumetric_data,
num_deformations=num_deformations,
settings=settings,
override_symmetry_tolerances=override_default_vasp_params,
metadata=metadata)
elif WORKFLOW == "singleV":
wf = get_wf_singleV(
structure,
store_volumetric_data=store_volumetric_data,
metadata=metadata,
override_default_vasp_params=override_default_vasp_params,
settings=settings)
elif WORKFLOW == "crosscom":
wf = get_wf_crosscom(structure, metadata=metadata, settings=settings)
elif WORKFLOW == "robust" or WORKFLOW == "get_wf_gibbs":
wf = get_wf_gibbs_robust(
structure,
num_deformations=num_deformations,
deformation_fraction=deformation_fraction,
phonon=phonon,
phonon_supercell_matrix=phonon_supercell_matrix,
t_min=t_min,
t_max=t_max,
t_step=t_step,
eos_tolerance=eos_tolerance,
volume_spacing_min=volume_spacing_min,
vasp_cmd=">>vasp_cmd<<",
db_file=">>db_file<<",
isif4=isif4,
metadata=metadata,
name='EV_QHA',
override_symmetry_tolerances=override_symmetry_tolerances,
override_default_vasp_params=override_default_vasp_params,
modify_incar_params=modify_incar_params,
modify_kpoints_params=modify_kpoints_params,
verbose=verbose,
phonon_supercell_matrix_min=phonon_supercell_matrix_min,
phonon_supercell_matrix_max=phonon_supercell_matrix_max,
optimize_sc=optimize_sc,
level=level,
force_phonon=force_phonon,
stable_tor=stable_tor,
store_volumetric_data=store_volumetric_data,
settings=settings)
elif WORKFLOW == "born":
wf = get_wf_borncharge(
structure=structure,
metadata=metadata,
db_file=db_file,
isif=2,
name="born charge",
vasp_cmd=">>vasp_cmd<<",
override_default_vasp_params=override_default_vasp_params,
modify_incar=modify_incar_params,
settings=settings)
elif WORKFLOW == 'elastic':
wf = get_wf_elastic(
structure=structure,
metadata=metadata,
vasp_cmd=">>vasp_cmd<<",
db_file=">>db_file<<",
name="elastic",
override_default_vasp_params=override_default_vasp_params,
settings=settings,
strain_states=strain_states,
stencils=stencils,
analysis=analysis,
sym_reduce=sym_reduce,
order=order,
conventional=conventional)
else:
raise ValueError(
"Currently, only the gibbs energy workflow is supported.")
return wf
###################### DO NOT CHANGE THE FOLLOWING LINES ##############################
from pymatgen import Structure
from dfttk.wflows import get_wf_gibbs_robust
from fireworks.fw_config import config_to_dict
from monty.serialization import loadfn, dumpfn
from fireworks import LaunchPad
structure = Structure.from_file(TEMPLATE_STRUCTURE_FILENAME)
if magmom:
structure.add_site_property('magmom', magmom)
if not db_file:
db_file = loadfn(config_to_dict()["FWORKER_LOC"])["env"]["db_file"]
wf = get_wf_gibbs_robust(structure, num_deformations=num_deformations, deformation_fraction=deformation_fraction,
phonon=phonon, phonon_supercell_matrix=phonon_supercell_matrix, t_min=t_min, t_max=t_max, t_step=t_step,
eos_tolerance=eos_tolerance, volume_spacing_min=volume_spacing_min, vasp_cmd=vasp_cmd, db_file=db_file,
isif4=isif4, metadata=metadata, name='EV_QHA', override_symmetry_tolerances=override_symmetry_tolerances,
override_default_vasp_params=override_default_vasp_params, modify_incar_params=modify_incar_params,
modify_kpoints_params=modify_kpoints_params, verbose=verbose, phonon_supercell_matrix_min=phonon_supercell_matrix_min,
phonon_supercell_matrix_max=phonon_supercell_matrix_max, optimize_sc=optimize_sc, level=level,
force_phonon=force_phonon, stable_tor=stable_tor)
if not DRY_RUN:
lpad = LaunchPad.auto_load()
lpad.add_wf(wf)
if WRITE_OUT_WF:
dumpfn(wf.to_dict(), 'dfttk_wf.yaml')