def vac_antisite_def_struct_gen(c_size=15,
mpid="",
struct=None,
write_file=True):
"""
Vacancy, antisite generator
Args:
c_size: cell size
struct: Structure object or
mpid: materials project id
Returns:
def_str: defect structures in Poscar object format
"""
def_str = []
if struct == None:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
if mpid == "":
print("Provide structure")
c_size = c_size
prim_struct_sites = len(struct.sites)
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
dim1 = int((float(c_size) / float(max(abs(struct.lattice.matrix[0]))))) + 1
dim2 = int(float(c_size) / float(max(abs(struct.lattice.matrix[1])))) + 1
dim3 = int(float(c_size) / float(max(abs(struct.lattice.matrix[2])))) + 1
cellmax = max(dim1, dim2, dim3)
conv_struct_sites = len(struct.sites)
conv_prim_rat = int(conv_struct_sites / prim_struct_sites)
sc_scale = [dim1, dim2, dim3]
print("sc_scale", sc_scale)
tmp = struct.copy()
tmp.make_supercell(sc_scale)
sc_tmp = tmp # Poscar(tmp).structure .make_supercell(list(sc_scale))
scs = list(VacancyGenerator(struct))
supercell = Poscar(sc_tmp)
supercell.comment = str("bulk") + str("@") + str("cellmax") + str(cellmax)
def_str.append(supercell)
if write_file == True:
supercell.write_file("POSCAR-" + str("bulk") + str(".vasp"))
for i in range(len(scs)):
sc = scs[i].generate_defect_structure(sc_scale)
poscar = Poscar(sc) # mpvis.get_poscar(sc)
pmg_name = str(scs[i].name).split("_")
sitespecie = pmg_name[1]
mult = pmg_name[2].split("mult")[1]
name = (str("vacancy_") + str(i + 1) + str("_mult-") + str(mult) +
str("_sitespecie-") + str(sitespecie) + str("@cellmax") +
str(cellmax))
poscar.comment = str(name)
def_str.append(poscar)
if write_file == True:
filename = (str("POSCAR-") + str("vacancy_") + str(i + 1) +
str("_mult-") + str(mult) + str("_sitespecie-") +
str(sitespecie) + str(".vasp"))
poscar.write_file(filename)
return def_str
def surfer(mpid='',
vacuum=15,
layers=2,
mat=None,
max_index=1,
write_file=True):
"""
ASE surface bulder
Args:
vacuum: vacuum region
mat: Structure object
max_index: maximum miller index
min_slab_size: minimum slab size
Returns:
structures: list of surface Structure objects
"""
if mat == None:
with MPRester() as mp:
mat = mp.get_structure_by_material_id(mpid)
if mpid == '':
print('Provide structure')
sg_mat = SpacegroupAnalyzer(mat)
mat_cvn = sg_mat.get_conventional_standard_structure()
mat_cvn.sort()
indices = get_symmetrically_distinct_miller_indices(mat_cvn, max_index)
ase_atoms = AseAtomsAdaptor().get_atoms(mat_cvn)
structures = []
pos = Poscar(mat_cvn)
try:
pos.comment = str('sbulk') + str('@') + str('vac') + str(vacuum) + str(
'@') + str('layers') + str(layers)
except:
pass
structures.append(pos)
if write_file == True:
mat_cvn.to(fmt='poscar',
filename=str('POSCAR-') + str('cvn') + str('.vasp'))
for i in indices:
ase_slab = surface(ase_atoms, i, layers)
ase_slab.center(vacuum=vacuum, axis=2)
slab_pymatgen = AseAtomsAdaptor().get_structure(ase_slab)
slab_pymatgen.sort()
surf_name = '_'.join(map(str, i))
pos = Poscar(slab_pymatgen)
try:
pos.comment = str("Surf-") + str(surf_name) + str('@') + str(
'vac') + str(vacuum) + str('@') + str('layers') + str(layers)
except:
pass
if write_file == True:
pos.write_file(filename=str('POSCAR-') + str("Surf-") +
str(surf_name) + str('.vasp'))
structures.append(pos)
return structures
def vac_intl(cellmax=2, mpid='', struct=None):
"""
Vacancy and interstitial generator
Args:
cellmax: maximum cell size
struct: Structure object
Returns:
def_str: defect structures
"""
if struct == None:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
if mpid == '':
print("Provide structure")
sg_mat = SpacegroupAnalyzer(struct)
struct = sg_mat.get_conventional_standard_structure()
def_str = []
count = 0
cell_arr = [cellmax, cellmax, cellmax]
vac = Vacancy(struct, {}, {})
for el in list(struct.symbol_set):
scs = vac.make_supercells_with_defects(cell_arr, el)
for i in range(len(scs)):
if i == 0:
pos = Poscar(scs[i])
pos.comment = str('bulk') + str('.') + str('cellmax') + str(
cellmax)
if count == 0:
def_str.append(pos)
count = count + 1
else:
pos = Poscar(scs[i])
pos.comment = str('vac') + str('cellmax') + str(cellmax) + str(
'@') + str(vac.get_defectsite_multiplicity(i)) + str(
'Element') + str(el)
if pos not in def_str:
def_str.append(pos)
struct_valrad_eval = ValenceIonicRadiusEvaluator(struct)
val = struct_valrad_eval.valences
rad = struct_valrad_eval.radii
struct_val = val
struct_rad = rad
intl = Interstitial(struct, val, rad)
for el in struct.composition.elements:
scs = intl.make_supercells_with_defects(cell_arr, el)
for i in range(1, len(scs)):
pos = Poscar(scs[i])
pos.comment = str('intl') + str('cellmax') + str(cellmax) + str(
'@') + str(intl.get_defectsite_coordination_number(
i - 1)) + str('Element') + str(el)
if pos not in def_str:
def_str.append(pos)
print(len(def_str))
return def_str
def pmg_surfer(mpid='', vacuum=15, mat=None, max_index=1, min_slab_size=15):
if mat == None:
with MPRester() as mp:
mat = mp.get_structure_by_material_id(mpid)
if mpid == '':
print('Provide structure')
sg_mat = SpacegroupAnalyzer(mat)
mat_cvn = sg_mat.get_conventional_standard_structure()
mat_cvn.sort()
indices = get_symmetrically_distinct_miller_indices(mat_cvn, max_index)
#ase_atoms = AseAtomsAdaptor().get_atoms(mat_cvn)
structures = []
pos = Poscar(mat_cvn)
try:
pos.comment = str('sbulk') + str('@') + str('vac') + str(vacuum) + str(
'@') + str('size') + str(min_slab_size)
except:
pass
structures.append(pos)
mat_cvn.to(fmt='poscar',
filename=str('POSCAR-') + str('cvn') + str('.vasp'))
for i in indices:
slab = SlabGenerator(initial_structure=mat_cvn,
miller_index=i,
min_slab_size=min_slab_size,
min_vacuum_size=vacuum,
lll_reduce=False,
center_slab=True,
primitive=False).get_slab()
normal_slab = slab.get_orthogonal_c_slab()
slab_pymatgen = Poscar(normal_slab).structure
#ase_slab.center(vacuum=vacuum, axis=2)
#slab_pymatgen = AseAtomsAdaptor().get_structure(ase_slab)
xy_size = min_slab_size
dim1 = int((float(xy_size) /
float(max(abs(slab_pymatgen.lattice.matrix[0]))))) + 1
dim2 = int(
float(xy_size) /
float(max(abs(slab_pymatgen.lattice.matrix[1])))) + 1
slab_pymatgen.make_supercell([dim1, dim2, 1])
slab_pymatgen.sort()
surf_name = '_'.join(map(str, i))
pos = Poscar(slab_pymatgen)
try:
pos.comment = str("Surf-") + str(surf_name) + str('@') + str(
'vac') + str(vacuum) + str('@') + str('size') + str(
min_slab_size)
except:
pass
pos.write_file(filename=str('POSCAR-') + str("Surf-") +
str(surf_name) + str('.vasp'))
structures.append(pos)
return structures
def surfer(vacuum=15, layers=2, mat=None, max_index=1, write_file=True):
"""
ASE surface bulder
Args:
vacuum: vacuum region
mat: Structure object
max_index: maximum miller index
min_slab_size: minimum slab size
Returns:
structures: list of surface Structure objects
"""
if mat == None:
print("Provide structure")
sg_mat = SpacegroupAnalyzer(mat)
mat_cvn = sg_mat.get_conventional_standard_structure()
mat_cvn.sort()
indices = get_symmetrically_distinct_miller_indices(mat_cvn, max_index)
ase_atoms = AseAtomsAdaptor().get_atoms(mat_cvn)
structures = []
pos = Poscar(mat_cvn)
try:
pos.comment = (str("sbulk") + str("@") + str("vac") + str(vacuum) +
str("@") + str("layers") + str(layers))
except:
pass
structures.append(pos)
if write_file == True:
mat_cvn.to(fmt="poscar",
filename=str("POSCAR-") + str("cvn") + str(".vasp"))
for i in indices:
ase_slab = surface(ase_atoms, i, layers)
ase_slab.center(vacuum=vacuum, axis=2)
slab_pymatgen = AseAtomsAdaptor().get_structure(ase_slab)
slab_pymatgen.sort()
surf_name = "_".join(map(str, i))
pos = Poscar(slab_pymatgen)
try:
pos.comment = (str("Surf-") + str(surf_name) + str("@") +
str("vac") + str(vacuum) + str("@") +
str("layers") + str(layers))
except:
pass
if write_file == True:
pos.write_file(filename=str("POSCAR-") + str("Surf-") +
str(surf_name) + str(".vasp"))
structures.append(pos)
return structures
def constrain(structs, fnames, atom_index, in_str=" "):
#len(structs)==1
mlog.debug("len(structs): {} ".format(len(structs)))
mlog.debug("fnames: {} ".format(fnames[0]))
for struct, fname in zip(structs, fnames):
mlog.debug(fname)
mlog.debug(struct)
natom = struct.num_sites
selective_dynamics = [[True for col in range(3)]
for row in range(natom)]
for i in range(natom):
if i in atom_index:
selective_dynamics[i] = [False, False, False]
tmp_struct = Structure(
struct.lattice,
struct.species,
struct.frac_coords,
site_properties={'selective_dynamics': selective_dynamics})
poscar = Poscar(tmp_struct)
poscar.comment = poscar.comment + ' |--> ' + in_str
filename = 'Fixed_' + fname + '.vasp'
poscar.write_file(filename)
def vac_antisite_def_struct_gen(c_size=15,
mpid='',
struct=None,
write_file=True):
"""
Vacancy, antisite generator
Args:
c_size: cell size
struct: Structure object or
mpid: materials project id
Returns:
def_str: defect structures in Poscar object format
"""
def_str = []
if struct == None:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
if mpid == '':
print("Provide structure")
c_size = c_size
dim1 = int((float(c_size) / float(max(abs(struct.lattice.matrix[0]))))) + 1
dim2 = int(float(c_size) / float(max(abs(struct.lattice.matrix[1])))) + 1
dim3 = int(float(c_size) / float(max(abs(struct.lattice.matrix[2])))) + 1
cellmax = max(dim1, dim2, dim3)
prim_struct_sites = len(struct.sites)
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
conv_struct_sites = len(struct.sites)
conv_prim_rat = int(conv_struct_sites / prim_struct_sites)
sc_scale = [dim1, dim2, dim3]
print("sc_scale", sc_scale)
struct_valrad_eval = ValenceIonicRadiusEvaluator(struct)
val = struct_valrad_eval.valences
rad = struct_valrad_eval.radii
struct_val = val
struct_rad = rad
vac = Vacancy(struct, {}, {})
scs = vac.make_supercells_with_defects(sc_scale)
for i in range(len(scs)):
sc = scs[i]
poscar = Poscar(sc) #mpvis.get_poscar(sc)
interdir = mpid
if not i:
fin_dir = os.path.join(interdir, 'bulk')
poscar.comment = str('bulk') + str('@') + str('cellmax') + str(
cellmax)
def_str.append(poscar)
if write_file == True:
poscar.write_file('POSCAR-' + str('bulk') + str(".vasp"))
else:
blk_str_sites = set(scs[0].sites)
vac_str_sites = set(sc.sites)
vac_sites = blk_str_sites - vac_str_sites
vac_site = list(vac_sites)[0]
site_mult = int(
vac.get_defectsite_multiplicity(i - 1) / conv_prim_rat)
vac_site_specie = vac_site.specie
vac_symbol = vac_site.specie.symbol
vac_dir = 'vacancy_{}_mult-{}_sitespecie-{}'.format(
str(i), site_mult, vac_symbol)
fin_dir = os.path.join(interdir, vac_dir)
try:
poscar.comment = str(vac_dir) + str('@') + str(
'cellmax') + str(cellmax)
except:
pass
pos = poscar
def_str.append(pos)
if write_file == True:
poscar.write_file('POSCAR-' + str(vac_dir) + str(".vasp"))
struct_species = scs[0].types_of_specie
for specie in set(struct_species) - set([vac_site_specie]):
subspecie_symbol = specie.symbol
anti_struct = sc.copy()
anti_struct.append(specie, vac_site.frac_coords)
poscar = Poscar(anti_struct)
as_dir = 'antisite_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
str(i), site_mult, vac_symbol, subspecie_symbol)
fin_dir = os.path.join(interdir, as_dir)
poscar.comment = str(as_dir) + str('@') + str('cellmax') + str(
cellmax)
pos = poscar
def_str.append(pos)
if write_file == True:
poscar.write_file('POSCAR-' + str(as_dir) + str(".vasp"))
return def_str
def vac_antisite_def_struct_gen(c_size=15,mpid='',struct=None):
"""
Vacancy, antisite generator
Args:
c_size: cell size
struct: Structure object or
mpid: materials project id
Returns:
def_str: defect structures in Poscar object format
"""
def_str=[]
if struct ==None:
with MPRester() as mp:
struct = mp.get_structure_by_material_id(mpid)
if mpid == '':
print ("Provide structure")
c_size=c_size
dim1=int((float(c_size)/float( max(abs(struct.lattice.matrix[0])))))+1
dim2=int(float(c_size)/float( max(abs(struct.lattice.matrix[1]))))+1
dim3=int(float(c_size)/float( max(abs(struct.lattice.matrix[2]))))+1
cellmax=max(dim1,dim2,dim3)
#print ("in vac_def cellmax=",cell
prim_struct_sites = len(struct.sites)
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
conv_struct_sites = len(struct.sites)
conv_prim_rat = int(conv_struct_sites/prim_struct_sites)
#sc_scale = get_sc_scale(struct,cellmax)
sc_scale=[dim1,dim2,dim3]
#sc_scale=[cellmax,cellmax,cellmax]
print ("sc_scale",sc_scale)
#mpvis = MITRelaxSet #MPGGAVaspInputSet()
# Begin defaults: All default settings.
#blk_vasp_incar_param = {'IBRION':-1,'EDIFF':1e-4,'EDIFFG':0.001,'NSW':0,}
#def_vasp_incar_param = {'ISIF':2,'NELM':99,'IBRION':2,'EDIFF':1e-6,
# 'EDIFFG':0.001,'NSW':40,}
#kpoint_den = 6000
# End defaults
#ptcr_flag = True
#try:
# potcar = mpvis.get_potcar(struct)
#except:
# print ("VASP POTCAR folder not detected.\n" \
# "Only INCAR, POSCAR, KPOINTS are generated.\n" \
# "If you have VASP installed on this system, \n" \
# "refer to pymatgen documentation for configuring the settings.")
# ptcr_flag = False
struct_valrad_eval = ValenceIonicRadiusEvaluator(struct)
val = struct_valrad_eval.valences
rad = struct_valrad_eval.radii
struct_val = val
struct_rad = rad
vac = Vacancy(struct, {}, {})
scs = vac.make_supercells_with_defects(sc_scale)
#site_no = scs[0].num_sites
#if site_no > cellmax:
# max_sc_dim = max(sc_scale)
# i = sc_scale.index(max_sc_dim)
# sc_scale[i] -= 1
# scs = vac.make_supercells_with_defects(sc_scale)
#print ('struct',scs)
for i in range(len(scs)):
sc = scs[i]
#print (type(sc))
poscar = Poscar(sc) #mpvis.get_poscar(sc)
#kpoints = Kpoints.automatic_density(sc,kpoint_den)
#incar = mpvis.get_incar(sc)
#if ptcr_flag:
# potcar = mpvis.get_potcar(sc)
interdir = mpid
if not i:
fin_dir = os.path.join(interdir,'bulk')
#try:
# os.makedirs(fin_dir)
#except:
# pass
#incar.update(blk_vasp_incar_param)
#incar.write_file(os.path.join(fin_dir,'INCAR'))
#poscar.write_file(os.path.join(fin_dir,'POSCAR'))
poscar.comment=str('bulk')+str('@')+str('cellmax')+str(cellmax)
def_str.append(poscar)
poscar.write_file('POSCAR-'+str('bulk')+str(".vasp"))
#if ptcr_flag:
# potcar.write_file(os.path.join(fin_dir,'POTCAR'))
#kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
else:
blk_str_sites = set(scs[0].sites)
vac_str_sites = set(sc.sites)
vac_sites = blk_str_sites - vac_str_sites
vac_site = list(vac_sites)[0]
site_mult = int(vac.get_defectsite_multiplicity(i-1)/conv_prim_rat)
#try:
# site_mult = int(vac.get_defectsite_multiplicity(i-1)/conv_prim_rat)
#except:
# site_mult=1
# pass
vac_site_specie = vac_site.specie
vac_symbol = vac_site.specie.symbol
vac_dir ='vacancy_{}_mult-{}_sitespecie-{}'.format(str(i),
site_mult, vac_symbol)
fin_dir = os.path.join(interdir,vac_dir)
#try:
# os.makedirs(fin_dir)
#except:
# pass
#incar.update(def_vasp_incar_param)
try:
poscar.comment=str(vac_dir)+str('@')+str('cellmax')+str(cellmax)
except:
pass
pos=poscar
#pos=poscar.structure
def_str.append(pos)
#poscar.write_file(os.path.join(fin_dir,'POSCAR'))
poscar.write_file('POSCAR-'+str(vac_dir)+str(".vasp"))
#incar.write_file(os.path.join(fin_dir,'INCAR'))
#if ptcr_flag:
# potcar.write_file(os.path.join(fin_dir,'POTCAR'))
#kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
# Antisite generation at all vacancy sites
struct_species = scs[0].types_of_specie
for specie in set(struct_species)-set([vac_site_specie]):
subspecie_symbol = specie.symbol
anti_struct = sc.copy()
anti_struct.append(specie, vac_site.frac_coords)
poscar = Poscar(anti_struct)
#incar = mpvis.get_incar(anti_struct)
#incar.update(def_vasp_incar_param)
as_dir ='antisite_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
str(i), site_mult, vac_symbol, subspecie_symbol)
fin_dir = os.path.join(interdir,as_dir)
#try:
# os.makedirs(fin_dir)
#except:
# pass
poscar.comment=str(as_dir)+str('@')+str('cellmax')+str(cellmax)
pos=poscar
#pos=poscar.structure
def_str.append(pos)
#poscar.write_file(os.path.join(fin_dir,'POSCAR'))
poscar.write_file('POSCAR-'+str(as_dir)+str(".vasp"))
#incar.write_file(os.path.join(fin_dir,'INCAR'))
#if ptcr_flag:
# potcar.write_file(os.path.join(fin_dir,'POTCAR'))
#kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
#try:
# struct.make_supercell(sc_scale)
# intl = Interstitial(struct, val, rad)
# cell_arr=sc_scale
# for el in struct.composition.elements:
# scs = intl.make_supercells_with_defects(1,el)
# #scs = intl.make_supercells_with_defects(cell_arr,el)
# for i in range(1,len(scs)):
# pos=Poscar(scs[i])
# pos.comment=str('intl_')+str('cellmax')+str(cellmax)+str('@')+str(intl.get_defectsite_coordination_number(i-1))+str('Element')+str(el)
# def_str.append(pos)
# pos.write_file('POSCAR-'+str('intl_')+str('cellmax')+str(cellmax)+str('@')+str(intl.get_defectsite_coordination_number(i-1))+str('Element')+str(el))
#except:
# pass
return def_str
def twoD_operation():
#sepline(ch='2D structure operation',sp='=')
print('your choice ?')
print('{} >>> {}'.format('1', 'build rippled structure'))
print('{} >>> {}'.format('2', 'build multi-layered structure'))
print('{} >>> {}'.format('3', 'split multi-layered structure'))
print('{} >>> {}'.format('4', 'resize vacuum layer'))
print('{} >>> {}'.format('5', 'center atomic-layer along z direction'))
print('{} >>> {}'.format('6', 'apply strain along different direction'))
print('{} >>> {}'.format('7', 'constrain atom in specific range'))
print('{} >>> {}'.format('8',
'get a substrate for 2D material (online!!!)'))
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
choice = int(in_str)
if choice == 1:
struct = readstructure()
margin_dist = 1.0 #
assert (struct.lattice.is_orthogonal)
print("input the supercell scaling factor")
print('for x direction can be: 10 1 1')
print('for y direction can be: 1 10 1')
wait_sep()
scale_str = input()
scaling = [int(x) for x in scale_str.split()]
if (len(scaling) != 3):
print('unknow format')
else:
if scaling[0] >= scaling[1]:
direction = 0 # for x direction
else:
direction = 1 # for y direction
print("input the strain range")
print("example: 0.02:0.1:10 ")
wait_sep()
strain_str = input()
tmp = [float(x) for x in strain_str.split(":")]
strain = []
if len(tmp) == 3:
strain_range = np.linspace(tmp[0], tmp[1], int(tmp[2]))
# print(strain_range)
else:
print("unknow format")
return
print("input the index of atom need to be fixed")
print("example: 1 10 11 20 ")
print("0 means fix the atom automatically")
wait_sep()
atom_index_str = input()
try:
atom_index = [int(x) for x in strain_str.split("")]
auto_fix = False
except:
atom_index = [int(atom_index_str)]
auto_fix = True
struct_sc = struct.copy()
struct_sc.make_supercell(scaling)
natom = struct_sc.num_sites
min_z = np.min(struct_sc.cart_coords[:, 2])
tmp_coords = np.ones((struct_sc.num_sites, 1)) * min_z
cart_coords = struct_sc.cart_coords
cart_coords[:, 2] = cart_coords[:, 2] - tmp_coords.T + 0.01
frac_coords_new = np.dot(cart_coords,
np.linalg.inv(struct_sc.lattice.matrix))
for i_strain in strain_range:
new_lat_matrix = struct_sc.lattice.matrix
new_lat_matrix[direction, direction] = struct_sc.lattice.matrix[
direction, direction] * (1 - i_strain)
fname = "%10.5f" % (
i_strain
) + '_wo.vasp' # structure only applied with in-plan strain
struct_wo_ripple = Structure(new_lat_matrix, struct_sc.species,
frac_coords_new)
struct_wo_ripple.to(filename=fname.strip(), fmt='poscar')
frac_coords_new_cp = struct_wo_ripple.frac_coords.copy()
cart_coords_new_cp = struct_wo_ripple.cart_coords.copy()
nz = 0
selective_dynamics = [[True for col in range(3)]
for row in range(natom)]
z_shift = np.zeros((natom, 3))
for i_atom in range(natom):
z_shift[i_atom,
2] = 40 * (2 * i_strain - 10 * i_strain**2) * np.sin(
cart_coords_new_cp[i_atom, direction] * np.pi /
new_lat_matrix[direction, direction])
if cart_coords_new_cp[i_atom,
direction] < nz or cart_coords_new_cp[
i_atom, direction] > new_lat_matrix[
direction, direction] - nz:
z_shift[i_atom, 2] = 0.0
if auto_fix:
if struct_wo_ripple[i_atom].coords[direction]<margin_dist or \
struct_wo_ripple[i_atom].coords[direction] > new_lat_matrix[direction,direction]-margin_dist:
selective_dynamics[i_atom] = [False, False, False]
else:
if i_atom in atom_index:
selective_dynamics[i_atom] = [False, False, False]
struct_w_ripple=Structure(new_lat_matrix,struct_sc.species,cart_coords_new_cp+z_shift,coords_are_cartesian=True,\
site_properties={'selective_dynamics':selective_dynamics})
fname = "%10.5f" % (
i_strain
) + '_w.vasp' # structure applied with in-plan strain and ripple
struct_w_ripple.to(filename=fname.strip(), fmt='poscar')
elif choice == 2:
struct = readstructure()
print("input the number of layers")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
layer_number = int(in_str)
print("input the layer distance")
wait_sep()
species = []
in_str = ""
while in_str == "":
in_str = input().strip()
layer_distance = float(in_str)
new_struct = move_to_zcenter(struct)
struct_thickness = np.max(new_struct.cart_coords[:, 2]) - np.min(
new_struct.cart_coords[:, 2])
natom = new_struct.num_sites
new_cart_coords = np.zeros((natom * layer_number, 3))
for i in range(layer_number):
new_cart_coords[i * natom:(i + 1) * natom,
0:2] = new_struct.cart_coords[:, 0:2]
new_cart_coords[i * natom:(i + 1) * natom,
2] = new_struct.cart_coords[:, 2] + i * (
layer_distance + struct_thickness)
species.extend(new_struct.species)
new_lat = new_struct.lattice.matrix
new_lat[2, 2] = new_lat[2, 2] + layer_distance * layer_number
tmp_struct = Structure(new_lat,
species,
new_cart_coords,
coords_are_cartesian=True)
tmp1_struct = move_to_zcenter(tmp_struct)
tmp2_struct = tmp1_struct.get_sorted_structure()
tmp2_struct.to(filename='layer_' + str(layer_number) + '.vasp',
fmt='poscar')
elif choice == 3:
ProperDist = 3.5 # Ang
struct = readstructure()
(atom_index, in_str) = atom_selection(struct)
print("input the splitting distance, 10 Ang is enough!")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
SplitDistance = float(in_str)
print("numbers of splitting site, 50 sites are enough!")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
NumberSplitSite = int(in_str)
DensityN = int(NumberSplitSite * 0.75)
SparseN = NumberSplitSite - DensityN + 1
# print(DensityN,SparseN)
dist = ProperDist / (DensityN - 1)
SplitDistanceArray = np.zeros(NumberSplitSite + 1)
for Nsite in range(DensityN):
SplitDistanceArray[Nsite] = (Nsite) * dist
dist = (SplitDistance - ProperDist) / SparseN
for Nsite in range(SparseN):
SplitDistanceArray[Nsite +
DensityN] = ProperDist + (Nsite + 1) * dist
# print(SplitDistanceArray)
coords = struct.cart_coords
for Nsite in range(NumberSplitSite + 1):
coords = struct.cart_coords
for atom in atom_index:
coords[atom, 2] = coords[atom, 2] + SplitDistanceArray[Nsite]
tmp_struct = Structure(struct.lattice,
struct.species,
coords,
coords_are_cartesian=True)
fname = str(Nsite) + '.vasp'
tmp_struct.to(filename=fname, fmt='poscar')
data = np.zeros((NumberSplitSite + 1, 2))
for i, j in enumerate(SplitDistanceArray):
data[i][0] = i
data[i][1] = j
head_line = "#%(key1)+12s %(key2)+12s" % {
'key1': 'index',
'key2': 'distance/Ang'
}
fmt = "%12d %12.6f" + '\n'
write_col_data('split.dat', data, head_line, sp_fmt=fmt)
return
elif choice == 4:
struct = readstructure()
new_struct = move_to_zcenter(struct)
struct_thickness = np.max(new_struct.cart_coords[:, 2]) - np.min(
new_struct.cart_coords[:, 2])
vac_layer_thickness = new_struct.lattice.c - struct_thickness
print("current vacuum layer thickness is %6.3f Ang" %
(vac_layer_thickness))
print("input the new value of vacuum layer thickness")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
nvac_layer_thickness = float(in_str)
assert (nvac_layer_thickness > struct_thickness)
new_lat = new_struct.lattice.matrix
new_lat[2, 2] = nvac_layer_thickness
tmp_struct = Structure(new_lat,
new_struct.species,
new_struct.cart_coords,
coords_are_cartesian=True)
center_struct = move_to_zcenter(tmp_struct)
center_struct.to(filename='new_vacuum.vasp', fmt='poscar')
return
elif choice == 5:
struct = readstructure()
new_struct = move_to_zcenter(struct)
new_struct.to(filename='z-center.vasp', fmt='poscar')
return
elif choice == 6:
struct = readstructure()
assert (struct.lattice.is_orthogonal)
try:
import sympy
except:
print("you must install sympy module")
return
new_struct = move_to_zcenter(struct)
print("input the elastic of material by order : C11 C12 C22 C66")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip().split()
elastic_constant = [float(x) for x in in_str]
if len(elastic_constant) != 4:
print("you must input C11 C12 C22 C66")
return
C11 = elastic_constant[0]
C12 = elastic_constant[1]
C22 = elastic_constant[2]
C66 = elastic_constant[3]
print("input applied force: e.x. 1.0 GPa nm")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
sigma = float(in_str)
orig_struct = new_struct.copy()
new_struct = new_struct.copy()
natom = orig_struct.num_sites
lat = orig_struct.lattice.matrix
pos = orig_struct.frac_coords
nps = 37
phi = np.linspace(0, 360, nps) * np.pi / 180
vzz = C12 / C22
temp_num = (C11 * C22 - C12**2) / (C22 * C66)
d1 = C11 / C22 + 1.0 - temp_num
d2 = -(2.0 * C12 / C22 - temp_num)
d3 = C11 / C22
F = sigma * C22 / (C11 * C22 - C12**2.0)
Poisson=(vzz*(np.cos(phi))**4.0-d1*(np.cos(phi))**2.0*(np.sin(phi))**2.0+vzz*(np.sin(phi))**4.0)/\
((np.cos(phi))**4.0+d2*(np.cos(phi))**2.0*(np.sin(phi))**2.0+d3*(np.sin(phi))**4.0)
eps_theta = F * ((np.cos(phi))**4 + d2 * (np.cos(phi))**2.0 *
(np.sin(phi))**2.0 + d3 * (np.sin(phi))**4.0)
t = sympy.Symbol('t', real=True)
e = sympy.Symbol('e', real=True)
v = sympy.Symbol('v', real=True)
eprim = sympy.Matrix([[e + 1, 0], [0, 1 - e * v]])
R = sympy.Matrix([[sympy.cos(t), -sympy.sin(t)],
[sympy.sin(t), sympy.cos(t)]])
eps_mat = R * eprim * R.adjugate()
for k in range(len(phi)):
cur__phi = phi[k] * 180 / np.pi
Rot = eps_mat.subs({e: eps_theta[k], v: Poisson[k], t: phi[k]})
fname = str(k) + '.vasp'
final_lat = np.matrix(np.eye(3))
final_lat[0, 0] = Rot[0, 0]
final_lat[0, 1] = Rot[0, 1]
final_lat[1, 0] = Rot[1, 0]
final_lat[1, 1] = Rot[1, 1]
lat_new = lat * final_lat
tmp_struct = Structure(lat_new, new_struct.species, pos)
tmp_struct.to(filename=fname, fmt='poscar')
return
elif choice == 7:
struct = readstructure()
natom = struct.num_sites
atom_index, in_str = atom_selection(struct)
selective_dynamics = [[True for col in range(3)]
for row in range(natom)]
for i in range(natom):
if i in atom_index:
selective_dynamics[i] = [False, False, False]
tmp_struct = Structure(
struct.lattice,
struct.species,
struct.frac_coords,
site_properties={'selective_dynamics': selective_dynamics})
poscar = Poscar(tmp_struct)
poscar.comment = poscar.comment + ' |--> ' + in_str
poscar.write_file('Fixed.vasp')
return
elif choice == 8:
print('your choice ?')
print('{} >>> {}'.format('1', 'input 2D structure from local disk'))
print('{} >>> {}'.format('2', 'get 2D structure online'))
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
choice = int(in_str)
if choice == 1:
mpid = None
struct = readstructure()
else:
print("input the mp-id for your structure")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
mpid = in_str
struct = None
film, substrates = make_connect(mpid=mpid, struct=struct)
df = get_subs(film, substrates)
df.to_csv('substrate.csv', sep=',', header=True, index=True)
return
else:
print("unkonw choice")
return
def pmg_surfer(vacuum=15,
mat=None,
max_index=1,
min_slab_size=15,
write_file=True):
"""
Pymatgen surface builder for a Poscar
Args:
vacuum: vacuum region
mat: Structure object
max_index: maximum miller index
min_slab_size: minimum slab size
Returns:
structures: list of surface Structure objects
"""
if mat == None:
print("Provide structure")
sg_mat = SpacegroupAnalyzer(mat)
mat_cvn = sg_mat.get_conventional_standard_structure()
mat_cvn.sort()
indices = get_symmetrically_distinct_miller_indices(mat_cvn, max_index)
structures = []
pos = Poscar(mat_cvn)
try:
pos.comment = (str("sbulk") + str("@") + str("vac") + str(vacuum) +
str("@") + str("size") + str(min_slab_size))
except:
pass
structures.append(pos)
if write_file == True:
mat_cvn.to(fmt="poscar",
filename=str("POSCAR-") + str("cvn") + str(".vasp"))
for i in indices:
slab = SlabGenerator(
initial_structure=mat_cvn,
miller_index=i,
min_slab_size=min_slab_size,
min_vacuum_size=vacuum,
lll_reduce=False,
center_slab=True,
primitive=False,
).get_slab()
normal_slab = slab.get_orthogonal_c_slab()
slab_pymatgen = Poscar(normal_slab).structure
xy_size = min_slab_size
dim1 = (int((float(xy_size) /
float(max(abs(slab_pymatgen.lattice.matrix[0]))))) + 1)
dim2 = (int(
float(xy_size) / float(max(abs(slab_pymatgen.lattice.matrix[1]))))
+ 1)
slab_pymatgen.make_supercell([dim1, dim2, 1])
slab_pymatgen.sort()
surf_name = "_".join(map(str, i))
pos = Poscar(slab_pymatgen)
try:
pos.comment = (str("Surf-") + str(surf_name) + str("@") +
str("vac") + str(vacuum) + str("@") + str("size") +
str(min_slab_size))
except:
pass
if write_file == True:
pos.write_file(filename=str("POSCAR-") + str("Surf-") +
str(surf_name) + str(".vasp"))
structures.append(pos)
return structures