def test_supercell_scaling_by_atom_lat_vol():
min_atoms = 60
max_atoms = 90
lower_search_limit = -2
upper_search_limit = 2
target_shape = 'sc'
#test for cubic
stru1 = Structure.from_str(POSCAR_STR_check_symbol, fmt="POSCAR")
#optimal_sc_shape = dfttkutils.supercell_scaling_by_target_atoms(stru1, min_atoms=min_atoms, max_atoms=max_atoms,
# target_shape=target_shape, lower_search_limit=lower_search_limit,
# upper_search_limit=upper_search_limit, verbose=False)
stru2 = Structure.from_str(POSCAR_scalling_t1, fmt='POSCAR')
optimal_sc_shape = dfttkutils.supercell_scaling_by_atom_lat_vol(
stru2,
min_obj=min_atoms,
max_obj=max_atoms,
target_shape=target_shape,
lower_search_limit=lower_search_limit,
upper_search_limit=upper_search_limit,
verbose=False)
print(optimal_sc_shape)
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