def __call__(self,
structure,
outdir=None,
names=None,
functionals=None,
previous=None,
**kwargs):
from Generate_Surface import get_bottom, get_SD_along_vector
from Helpers import pyl_to_pmg
if not functionals:
functionals = self.functionals
outdir = os.getcwd() if outdir is None else RelativePath(outdir).path
sp_functionals = [
CustomFunctional(functional.base,
functional.modifications + [no_relax],
functional.type)
for functional in functionals[self.to_run:]
]
structure_frozen_bot = structure.copy()
pmg_s = pyl_to_pmg(structure)
sd_bottom = get_SD_along_vector(pmg_s, 2,
get_bottom(pmg_s, region='bot'))
for (atom, sd) in zip(structure_frozen_bot, sd_bottom):
if sd[0]:
atom.freeze = 'xyz'
structure_frozen_top = structure.copy()
sd_top = get_SD_along_vector(pmg_s, 2, get_bottom(pmg_s, region='top'))
for (atom, sd) in zip(structure_frozen_top, sd_top):
if sd[0]:
atom.freeze = 'xyz'
# Clevage Energy
(clevage, previous) = self.call_with_output(structure,
outdir=outdir,
names=self.names[-3:],
functionals=sp_functionals,
previous=previous)
# Frozen Bottom
(bottom, clevage) = self.call_with_output(structure_frozen_bot,
outdir=os.path.join(
outdir, 'bottom'),
names=names,
functionals=functionals,
previous=clevage)
# Frozen Top
(bottom,
clevage) = self.call_with_output(structure_frozen_top,
outdir=os.path.join(outdir, 'top'),
names=names,
functionals=functionals,
previous=clevage)
return clevage
def __init__(self, vaspobj: Vasp, bulk_structure, standard=[], override=[], incar_settings='../INCAR.defaults', kpt_modifier=1):
from Helpers import pyl_to_pmg
standard = [load_default_vasp, ws_bulk, load_optimized_U_species, set_kpar_2, idipol_3, no_relax]
with open(incar_settings) as f:
lines = [line.strip().split('=') for line in f.readlines()]
incar = {f[0].strip(): float(f[1]) for f in lines}
kpts = math.ceil((incar['KPOINTS'] - 0.25) * max(pyl_to_pmg(bulk_structure).lattice.abc) / kpt_modifier)
get_nopsin_eig = CustomFunctional(Vasp, standard + [get_eigen_nospin, set_algo_fast, set_nelm_200] + override)
get_eigenvalues = CustomFunctional(Vasp, standard + [get_eigen, set_nelm_200] + override)
final_converge = CustomFunctional(Vasp, standard + [full_converge, set_algo_normal, all_output, set_nelm_200] + override)
ldipol = CustomFunctional(Vasp, standard + [full_converge, set_algo_fast, all_output, set_nelm_200, surface_final] + override)
names = ['2_nospin_eig', '3_get_eigenvalues', '4_final_converge', '5_ldipol']
functionals = [get_nopsin_eig, get_eigenvalues, final_converge, ldipol]
super().__init__(functionals, names=names, vaspobj=vaspobj, encut=incar['ENCUT'], kpoints=kpts)
def make_surfaces_to_pylada(root, bulk_structure, incar_settings=None, label='', depth=8, frozen_depth=2, override=[], kpt_modifier=1):
'''
:param root: root directory of run
:param bulk_structure: pylada bulk strucutre
:param incar_settings: location of INCAR.defaults
:return:
'''
from pylada.crystal import write
from Generate_Surface import Generate_Surface
from Helpers import pyl_to_pmg, pmg_to_pyl
from Generate_Surface import get_bottom, get_SD_along_vector
# small_surfaces = Generate_Surface(pyl_to_pmg(bulk_structure), 1, 1, 1, 3, vacuum=8, orth=True)
for i, surface in enumerate(Generate_Surface(pyl_to_pmg(bulk_structure), 1, 1, 1, depth, vacuum=8, orth=False)):
# Frozen Surface
# surface_small = small_surfaces[i]
surf_folder = root / label / str(i).zfill(2)
surf_folder.functional = WSBulkToFrozenSurfacePBE(Vasp(), bulk_structure=bulk_structure,
incar_settings=incar_settings, override=override,
kpt_modifier=kpt_modifier)
surf_folder.params['structure'] = pmg_to_pyl(surface).copy()
os.makedirs(surf_folder.name[1:], exist_ok=True)
surface.to('poscar', os.path.join(surf_folder.name[1:], 'surface.vasp'))
with open(os.path.join(surf_folder.name[1:], 'DATABASE'), 'w') as f:
f.write('''
surface
surface_cut {}
surface_termination {}
convergence_study
convergence_type surface
misc_labels {}
'''.format(i, 'None', label))
# Frozen Surfaces
for frozen_region in ['top', 'bottom']:
froz_folder = surf_folder / frozen_region
froz_folder.functional = WSBulkToSurfacePBE(Vasp(), bulk_structure=bulk_structure,
incar_settings=incar_settings, override=override,
kpt_modifier=kpt_modifier)
surface_frozen = surface.copy()
# print(surface_frozen)
sd = get_SD_along_vector(surface_frozen, 2, get_bottom(surface_frozen, length=frozen_depth, region=frozen_region))
# Poscar(surface_frozen, selective_dynamics=sd).write_file(os.path.join(froz_folder.name[1:], 'surface.vasp'))
surface_frozen_pyl = pmg_to_pyl(surface_frozen)
# sd_small = get_SD_along_vector(surface_frozen, frozen_depth, get_bottom(surface_frozen, region=frozen_region))
for (atom, sd) in zip(surface_frozen_pyl, sd):
if sd[0]:
atom.freeze = 'xyz'
os.makedirs(froz_folder.name[1:], exist_ok=True)
write.poscar(surface_frozen_pyl, os.path.join(froz_folder.name[1:], 'surface.vasp'), vasp5=True)
froz_folder.params['structure'] = surface_frozen_pyl.copy()
os.makedirs(froz_folder.name[1:], exist_ok=True)
with open(os.path.join(froz_folder.name[1:], 'DATABASE'), 'w') as f:
f.write('''
surface
surface_cut {}
surface_termination {}
misc_labels {}
'''.format(i, frozen_region, label))
def set_kpoints_1704(vasp: Vasp, structure=None):
kpts = Kpoints.automatic_density(pyl_to_pmg(structure), 1704)
vasp.kpoints = str(kpts)
return vasp