def get_delete_atom_num(no_defect_poscar, one_defect_poscar):
no_defect = read_vasp(no_defect_poscar)
one_defect = read_vasp(one_defect_poscar)
no_def_pos = no_defect.positions
one_def_pos = one_defect.positions
no_def_pos[abs(no_def_pos - 1) < 0.01] = 0
one_def_pos[abs(one_def_pos - 1) < 0.01] = 0
if len(no_defect.atoms) - 1 == len(one_defect.atoms):
num = no_def_pos.shape[0]
for ii in range(num):
d = np.linalg.norm(no_def_pos[ii] - one_def_pos, axis=1)
if min(d) > 0.1:
break
_no_def_pos = np.unique(np.delete(no_def_pos, ii, 0), axis=0)
_one_def_pos = np.unique(one_def_pos, axis=0)
d = 0
for i in _no_def_pos:
d = d + min(np.linalg.norm(i - _one_def_pos, axis=1))
for key, val in ptd.items():
if val == no_defect.atoms[ii]:
rm_atom = key
break
print('This is a vacancy defect', 'atom: \n', rm_atom, ii + 1,
'in the defect-free POSCAR has benn removed')
with open('element-in-out', 'w') as f:
f.writelines(str(rm_atom) + '=' + str(1) + '\n')
f.writelines('Vacc=-1 \n')
return ii, d
elif len(no_defect.atoms) == len(one_defect.atoms):
no_def_atoms, def_atoms = np.unique(no_defect.atoms), np.unique(
one_defect.atoms)
purity_atom = np.setdiff1d(def_atoms, no_def_atoms)
idx = np.where(one_defect.atoms == purity_atom)[0]
d = np.linalg.norm(one_def_pos[idx] - no_def_pos, axis=1)
ii, d = np.argmin(d), np.min(d)
for key, val in ptd.items():
if val == no_defect.atoms[ii]:
rm_atom = key
if val == purity_atom:
in_atom = key
print('This is a purity defect', 'atom: \n', rm_atom, ii + 1,
'in the defect-free POSCAR has benn dopped by', in_atom)
with open('element-in-out', 'w') as f:
f.writelines(str(rm_atom) + '=' + str(1) + '\n')
f.writelines(str(in_atom) + '=' + str(-1) + '\n')
return ii, d
else:
print('This kind of defect is not supported here right now')
def test_kpts(self,kw={}):
start,end,step = kw.get('start'),kw.get('end'),kw.get('step')
is_login_node,kw = run_vasp.clean_parse(kw,'is_login_node',False)
kw.pop('start');kw.pop('end');kw.pop('step')
kpts = Kpoints()
kpts_list = set()
kppa_list = []
for kppa in range(start,end,step):
kpts.automatic_density(structure=read_vasp(self.poscar),kppa=kppa)
if tuple(kpts.kpts[0]) not in kpts_list:
kpts_list.add(tuple(kpts.kpts[0]))
kppa_list.append(kppa)
idx = 0
for kppa in kppa_list:
_kw = kw.copy()
if 'style' not in _kw:
_kw.update({'kppa':kppa,'style':'auto','job_name':'test_kpts'+str(idx),'NSW':0})
prep_vasp.prep_single_vasp(poscar=self.poscar,kw=_kw)
idx += 1
for i in range(idx):
run_vasp.run_single_vasp(job_name='test_kpts'+str(i),is_login_node=is_login_node)
kpts_res = []
for ii in range(len(kppa_list)):
EV = ExtractValue(data_folder='test_kpts'+str(ii))
kpts_res.append([kppa_list[ii],EV.get_energy(),EV.get_cpu_time()])
with open('test_kpts.txt','w') as f:
f.writelines('KPTS\tEnergy\tcpu_time\n')
for line in kpts_res:
f.writelines(str(line[0])+'\t'+str(line[1])+'\t'+str(line[2])+'\n')
def symmetry(poscar,attr,sympre):
"""
argument:
poscar, the path of your initial POSCAR
attr, the attribute you want to get
Example:
pyvasp symmetry space POSCAR # get space_group
pyvasp symmetry equivalent POSCAR # get equivalent_atoms
pyvasp symmetry primitive POSCAR # get primitive cell
"""
c = read_vasp(poscar)
if 'space' in attr or 'group' in attr:
print('Space group: ', c.get_spacegroup(sympre))
elif 'equiv' in attr:
equ_atom = c.get_symmetry(sympre)['equivalent_atoms']
atom_type = np.unique(equ_atom)
atom_species,k = {},1
for ii in atom_type:
atom_species[k] = np.where(equ_atom==ii)[0]+1
k += 1
for key, val in atom_species.items():
print(key,val)
elif 'primi' in attr:
if c.is_primitive():
click.echo('This poscar is a primitive cell, or you can decrease symprec to try to get a primitive cell')
return
pc = c.get_primitive_cell(sympre)
write_vasp(pc,'primitive_cell')
def __init__(self, no_defect='POSCAR', no_defect_string=''):
# 初始化用 POSCAR路径？
if no_defect_string:
self.no_defect_cell = _read_string(no_defect_string)
else:
self.no_defect_cell = read_vasp(no_defect)
self.lattice = self.no_defect_cell.lattice
self.positions = self.no_defect_cell.positions
self.atoms = self.no_defect_cell.atoms
def extend_spec_direc(pcell_filename, volume):
"""
First parameter: filename, the path of your initial POSCAR
Sencond parameter: volume, the volume you want to extend
Example:
pyvasp extend_spec_direc -v 2 2 2 POSCAR
"""
pcell = read_vasp(pcell_filename)
supcell = pcell.extend(np.diag(volume))
write_vasp(supcell, 'supcell')
def diff_poscar(pri_pos,pos1,pos2,symprec=1e-3):
'''
To compare two structures are the same or not
'''
cell1,cell2 = read_vasp(pos1),read_vasp(pos2)
if sum(sum((cell1.lattice-cell2.lattice)**2))>0.01:
raise ValueError("Two POSCARs do not have the same lattice")
if len(cell1.atoms) != len(cell2.atoms):
raise ValueError("Two POSCARs do not have the same atoms number")
if sum(np.sort(cell1.atoms)-np.sort(cell2.atoms))>0.001:
raise ValueError("Two POSCARs do not have the same atoms")
cell = read_vasp(pri_pos)
if sum(sum((cell1.lattice-cell.lattice)**2))>0.01:
raise ValueError("Two POSCAR do not have the same lattice with the primitive POSCAR")
idx_1 = get_idx_in_pri_pos(cell.positions,cell1.positions)
idx_2 = get_idx_in_pri_pos(cell.positions,cell2.positions)
perms = get_perms(cell,symprec=symprec)
serial_1 = _get_min_serial(perms,idx_1)
serial_2 = _get_min_serial(perms,idx_2)
if sum(serial_1-serial_2) <= 0.001:
return True
return False
def extend_specific_volume(pcell_filename, dimension, volume, symprec, comprec, verbose):
"""
<primitive_cell_file> Primitive cell structure file, now only vasp POSCAR version5 supported.
"""
pcell = read_vasp(pcell_filename)
comment = 'cell'
(min_v, max_v) = volume
if min_v == -1:
click.echo("Expanding primitive to volume {:d}".format(max_v))
_export_supercell(pcell, comment, dimension, max_v, symprec, comprec, verbose)
else:
for v in range(min_v, max_v + 1):
click.echo("Expanding primitive to volume {:d}".format(v))
_export_supercell(pcell, comment, dimension, v, symprec, comprec, verbose)
def get_farther_atom_num(no_defect_poscar, one_defect_poscar):
'''
Return:
1: atom number of the farther atom in defect system
2: atom number of the farther atom in defect-free system
'''
all_basis = generate_all_basis(1, 1, 1)
no_defect = read_vasp(no_defect_poscar)
one_defect = read_vasp(one_defect_poscar)
no_def_pos = no_defect.positions
one_def_pos = one_defect.positions
c = no_defect.lattice
no_def_pos = np.dot(no_def_pos, c)
one_def_pos = np.dot(one_def_pos, c)
ii, d = get_delete_atom_num(no_defect_poscar, one_defect_poscar)
defect_atom = no_def_pos[ii]
extend_S = []
d, idx = np.zeros((no_def_pos.shape[0], 27)), 0
for basis in all_basis:
i, j, k = basis
d[:, idx] = np.linalg.norm(
defect_atom - (no_def_pos + i * c[0] + j * c[1] + k * c[2]),
axis=1)
idx += 1
max_idx_no_def = np.argmax(np.min(d,
axis=1)) #no-defect-farther-atom-number
# import pdb;pdb.set_trace()
d, idx = np.zeros((one_def_pos.shape[0], 27)), 0
for basis in all_basis:
i, j, k = basis
d[:, idx] = np.linalg.norm(
defect_atom - (one_def_pos + i * c[0] + j * c[1] + k * c[2]),
axis=1)
idx += 1
max_idx_one_def = np.argmax(np.min(d, axis=1))
return max_idx_one_def + 1, max_idx_no_def + 1
def cell(pcell_filename, volume):
"""
First parameter: pcell_filename, the path of your initial POSCAR
Sencond parameter: volume, the volume you want to extend
Example:
module load sagar #load the necessay package
pyvasp.py cell -v 2 2 2 POSCAR
"""
pcell = read_vasp(pcell_filename)
supcell = pcell.extend(np.diag(volume))
write_vasp(supcell, 'supcell')
def symmetry(poscar, attr, sympre):
"""
argument:
poscar, the path of your initial POSCAR
attr, the attribute you want to get
Example:
module load sagar #load the necessay package
pyvasp.py symmetry -a space POSCAR # get space_group
pyvasp.py symmetry -a translations POSCAR # get translations symmetry
pyvasp.py symmetry -a rotations POSCAR # get rotations symmetry
pyvasp.py symmetry -a equivalent POSCAR # get equivalent_atoms
pyvasp.py symmetry -a primitive POSCAR # get primitive cell
"""
c = read_vasp(poscar)
if 'space' in attr or 'group' in attr:
print('Space group: ', c.get_spacegroup(sympre))
elif 'symme' in attr:
print('Symmetry: ', c.get_symmetry(sympre))
elif 'trans' in attr:
print('Translations Symmetry: ',
c.get_symmetry(sympre)['translations'])
elif 'rotat' in attr:
print('Rotations Symmetry: ', c.get_symmetry(sympre)['rotations'])
elif 'equiv' in attr:
equ_atom = c.get_symmetry(sympre)['equivalent_atoms']
atom_type = np.unique(equ_atom)
atom_species, k = {}, 1
for ii in atom_type:
atom_species[k] = np.where(equ_atom == ii)[0] + 1
k += 1
for key, val in atom_species.items():
print(key, val)
elif 'primi' in attr:
pc = c.get_primitive_cell(sympre)
write_vasp(pc, 'primitive_cell')
def read_doscar(wd):
c = read_vasp(os.path.join(wd, 'POSCAR'))
line6 = np.genfromtxt(os.path.join(wd, 'DOSCAR'),
skip_header=5,
max_rows=1)
n_dos = int(line6[2])
sum_dos = np.genfromtxt(os.path.join(wd, 'DOSCAR'),
skip_header=6,
max_rows=n_dos)
np.savetxt(os.path.join(wd, 'sum_dos.txt'), sum_dos, fmt="%.5f")
incar = read_incar(os.path.join(wd, 'INCAR'))
if 'LORBIT' not in incar:
return
if int(incar['LORBIT']) == 11:
for ii in range(c.atoms.shape[0]):
p_dos = np.genfromtxt(os.path.join(wd, 'DOSCAR'),
skip_header=6 + (1 + n_dos) * (ii + 1),
max_rows=n_dos)
np.savetxt(os.path.join(wd, 'p_dos' + str(ii) + '.txt'),
p_dos,
fmt="%.5f")
def write_kpoints(poscar='POSCAR', kw={}):
if not path.isfile(poscar):
raise FileNotFoundError('Not found POSCAR')
stru = read_vasp(poscar)
style, kw = clean_parse(kw, 'style', 'auto')
if not path.isfile('KPOINTS'):
_kpts = Kpoints()
if 'auto' in style.lower():
if 'kpts' not in kw:
kppa, kw = clean_parse(kw, 'kppa', 3000)
kppa = float(kppa)
_kpts.automatic_density(structure=stru, kppa=kppa)
_kpts.write_file('KPOINTS')
else:
kpts, kw = clean_parse(kw, 'kpts', (1, 1, 1))
shift, kw = clean_parse(kw, 'shift', (0, 0, 0))
_kpts.gamma_automatic(kpts=kpts, shift=shift)
_kpts.write_file('KPOINTS')
elif 'gamma' in style.lower() and 'kpts' not in kw:
kppa, kw = clean_parse(kw, 'kppa', 3000)
kppa = float(kppa)
_kpts.automatic_gamma_density(structure=stru, kppa=kppa)
_kpts.write_file('KPOINTS')
elif 'gamma' in style.lower() and 'kpts' in kw:
kpts, kw = clean_parse(kw, 'kpts', (1, 1, 1))
shift, kw = clean_parse(kw, 'shift', (0, 0, 0))
_kpts.gamma_automatic(kpts=kpts, shift=shift)
_kpts.write_file('KPOINTS')
elif 'monk' in style.lower() and 'kpts' in kw:
kpts, kw = clean_parse(kw, 'kpts', (1, 1, 1))
shift, kw = clean_parse(kw, 'shift', (0, 0, 0))
_kpts.monkhorst_automatic(kpts=kpts, shift=shift)
_kpts.write_file('KPOINTS')
elif 'band' in style.lower() or 'line' in style.lower():
num_kpts, kw = clean_parse(kw, 'num_kpts', 16)
_kpts.automatic_linemode(structure=stru, num_kpts=num_kpts)
_kpts.write_file('KPOINTS')
return kw
if dimension == 2:
supercell = pcell.extend(h)._get_niggli_2D()
else:
supercell = pcell.extend(h)._get_niggli_3D()
_sites = np.repeat(sites, volume, axis=0)
for mol, _ in remove_redundant(supercell.positions, _sites, perms):
c = Cell(supercell.lattice, mol[0], mol[1])
if c.is_primitive(symprec):
yield c
def get_identity_atoms(cell, symprec, style="crystal"):
atom_number = cell.atoms
if style == "crystal":
equ_atom = cell.get_symmetry(symprec)['equivalent_atoms']
atom_uniq_type = np.unique(equ_atom)
atom_type = np.zeros(np.shape(equ_atom))
for idx, ea in enumerate(equ_atom):
atom_type[idx] = np.where(atom_uniq_type == ea)[0]
return atom_type
if __name__ == '__main__':
cell = read_vasp("/home/hecc/Desktop/Al_prim.vasp")
for idx, c in enumerate(get_max_volume(cell, [(13, 42)], 12,
min_volume=2)):
write_poscar(c, folder="/home/hecc/Desktop/fcc", idx=idx)
def __init__(self, poscar='POSCAR'):
self.poscar = poscar
if is_2d_structure(read_vasp(self.poscar)):
self.dimen = 2
else:
self.dimen = 3
def get_delete_atom_num(no_defect_poscar, one_defect_poscar):
no_defect = read_vasp(no_defect_poscar)
one_defect = read_vasp(one_defect_poscar)
no_def_pos = no_defect.positions
one_def_pos = one_defect.positions
no_def_pos[abs(no_def_pos - 1) < 0.01] = 0
one_def_pos[abs(one_def_pos - 1) < 0.01] = 0
if len(no_defect.atoms) - 1 == len(one_defect.atoms):
num = no_def_pos.shape[0]
for ii in range(num):
d = np.linalg.norm(no_def_pos[ii] - one_def_pos, axis=1)
if min(d) > 0.1:
break
_no_def_pos = np.unique(np.delete(no_def_pos, ii, 0), axis=0)
_one_def_pos = np.unique(one_def_pos, axis=0)
d = 0
for i in _no_def_pos:
d = d + min(np.linalg.norm(i - _one_def_pos, axis=1))
for key, val in ptd.items():
if val == no_defect.atoms[ii]:
rm_atom = key
break
print('This is a vacancy defect', 'atom: \n', rm_atom, ii + 1,
'in the defect-free POSCAR has benn removed')
with open('element-in-out', 'w') as f:
f.writelines(str(rm_atom) + '=' + str(1) + '\n')
f.writelines('Vacc=-1 \n')
return ii, d
elif len(no_defect.atoms) == len(one_defect.atoms):
no_def_atoms, def_atoms = np.unique(no_defect.atoms), np.unique(
one_defect.atoms)
purity_atom = np.setdiff1d(def_atoms, no_def_atoms)
if len(purity_atom) != 0: # introduce a new atom purity
idx = np.where(one_defect.atoms == purity_atom)[0]
d = np.linalg.norm(one_def_pos[idx] - no_def_pos, axis=1)
ii, d = np.argmin(d), np.min(d)
for key, val in ptd.items():
if val == no_defect.atoms[ii]:
rm_atom = key
if val == purity_atom:
in_atom = key
print('This is a purity defect', 'atom: \n', rm_atom, ii + 1,
'in the defect-free POSCAR has benn dopped by', in_atom)
with open('element-in-out', 'w') as f:
f.writelines(str(rm_atom) + '=' + str(1) + '\n')
f.writelines(str(in_atom) + '=' + str(-1) + '\n')
return ii, d
else:
purity_atom = []
for _atom in no_def_atoms:
idx_num_1, idx_num_2 = len(
np.where(_atom == no_defect.atoms)[0]), len(
np.where(_atom == one_defect.atoms)[0])
if abs(idx_num_2 - idx_num_1) == 1:
purity_atom.append(_atom)
elif abs(idx_num_1 - idx_num_2) > 1:
raise ValueError("The POSCAR has two or more defect atoms")
if len(purity_atom) > 2:
raise ValueError("The POSCAR has two or more defect atoms")
no_def_pos_0 = no_def_pos[no_defect.atoms == purity_atom[0]]
no_def_pos_1 = no_def_pos[no_defect.atoms == purity_atom[1]]
one_def_pos_0 = one_def_pos[one_defect.atoms == purity_atom[0]]
one_def_pos_1 = one_def_pos[one_defect.atoms == purity_atom[1]]
if no_def_pos_0.shape[0] - one_def_pos_0.shape[0] == 1:
purity_in = purity_atom[1]
purity_out = purity_atom[0]
d = [
min(np.linalg.norm(pos - one_def_pos_0, axis=1))
for pos in no_def_pos_0
]
ahead_num = np.where(no_defect.atoms == purity_out)[0][0]
idx = np.argmax(d)
for key, val in ptd.items():
if val == purity_out:
rm_atom = key
if val == purity_in:
in_atom = key
print('This is a purity defect', 'atom: \n', rm_atom,
ahead_num + idx + 1,
'in the defect-free POSCAR has benn dopped by', in_atom)
with open('element-in-out', 'w') as f:
f.writelines(str(rm_atom) + '=' + str(1) + '\n')
f.writelines(str(in_atom) + '=' + str(-1) + '\n')
return ahead_num + idx, d[idx]
else:
purity_in = purity_atom[0]
purity_out = purity_atom[1]
d = [
min(np.linalg.norm(pos - one_def_pos_1, axis=1))
for pos in no_def_pos_1
]
idx = np.argmax(d)
ahead_num = np.where(no_defect.atoms == purity_out)[0][0]
# import pdb; pdb.set_trace()
for key, val in ptd.items():
if val == purity_out:
rm_atom = key
if val == purity_in:
in_atom = key
print('This is a purity defect', 'atom: \n', rm_atom,
ahead_num + idx + 1,
'in the defect-free POSCAR has benn dopped by', in_atom)
with open('element-in-out', 'w') as f:
f.writelines(str(rm_atom) + '=' + str(1) + '\n')
f.writelines(str(in_atom) + '=' + str(-1) + '\n')
return ahead_num + idx, d[idx]
else:
print('This kind of defect is not supported here right now')
if is_int_np_array(mat):
mat = np.around(mat).astype('intc')
else:
print("cell:\n", lat_cell)
print("primitive cell:\n", lat_pcell)
raise ValueError(
"cell lattice and its primitive cell lattice not convertable")
hfpg = PG(pcell, mat)
return hfpg.get_symmetry_perms(symprec)
def get_min_serial(perms, num):
return np.unique(np.sort(perms[:, num], axis=1), axis=0)[0].tolist()
cell = read_vasp('POSCAR')
perms = get_perms(cell)
latt = cell.lattice
pos = cell.positions
pos = np.dot(pos, latt)
n = pos.shape[0]
basis = generate_all_basis(1, 1, 0)
extend_pos = np.zeros((9 * n, 3))
idx = 0
for ii in basis:
extend_pos[n * idx:n * (idx + 1), :] = (pos + ii[0] * latt[0] +
ii[1] * latt[1] + ii[2] * latt[2])
idx += 1
neig_list = np.zeros((n, 6))
for ii in range(pos.shape[0]):
def cell(pcell_filename, volume):
pcell = read_vasp(pcell_filename)
supcell = pcell.extend(np.diag(volume))
write_vasp(supcell, 'supcell')
def conf(cell_filename, comment, pmode, cmode, dimension, volume, element,
substitutes, number, symprec, comprec, verbose):
"""
<parent_cell_file> is the parent cell to generating configurations by sites disorder.\n
The non-primitive cell can only used as argument when '--pmode=sc'.\n
Command line tool only provide configurations generator for elements disorder, for more flexible usage such as specific site disorder, please see document http:// , or use python library directly.
"""
cell = read_vasp(cell_filename)
cg = ConfigurationGenerator(cell, symprec)
if pmode == 'varv' and cmode == 'vc':
click.secho("Expanding and generating configurations: ")
click.secho("(may take much time)",
blink=True,
bold=True,
bg='magenta',
fg='white')
spinner = Spinner()
spinner.start()
(min_v, max_v) = volume
if min_v == -1:
min_v = 1
sites = _get_sites(list(cell.atoms), element, substitutes)
confs = cg.cons_max_volume(sites,
max_v,
min_volume=min_v,
dimension=dimension,
symprec=symprec)
for idx, c in enumerate(confs):
c = c.get_primitive_cell()
filename = '{:s}_id{:d}'.format(comment, idx)
write_vasp(c, filename)
spinner.stop()
click.secho("DONE", bold=True, bg='green', fg='white')
elif pmode == 'svc' and cmode == 'vc':
click.secho("Expanding and generating configurations: ")
click.secho("(may take much time)",
blink=True,
bold=True,
bg='magenta',
fg='white')
spinner = Spinner()
spinner.start()
(min_v, max_v) = volume
sites = _get_sites(list(cell.atoms), element, substitutes)
confs = cg.cons_specific_volume(sites,
volume=max_v,
e_num=None,
dimension=dimension,
symprec=symprec)
f_deg = open('deg.txt', 'a')
for idx, (c, d) in enumerate(confs):
filename = '{:s}_id{:d}'.format(comment, idx)
write_vasp(c, filename)
deg_line = filename + '{:10d}'.format(d) + '\n'
f_deg.write(deg_line)
f_deg.close()
spinner.stop()
click.secho("DONE", bold=True, bg='green', fg='white')
elif pmode == 'svc' and cmode == 'cc':
click.secho("Expanding and generating configurations: ")
click.secho("(may take much time)",
blink=True,
bold=True,
bg='magenta',
fg='white')
spinner = Spinner()
spinner.start()
(min_v, max_v) = volume
l_atoms = cell.atoms.tolist()
sites = _get_sites(l_atoms, element, substitutes)
# number to enum
ele_n = s2n(element)
e_total = l_atoms.count(ele_n) * max_v
e_n = e_total - sum(number) # 第一个元素的数量
e_num = [e_n] + list(number) # 各个元素的数量
confs = cg.cons_specific_volume(sites,
volume=max_v,
e_num=e_num,
dimension=dimension,
symprec=symprec)
f_deg = open('deg.txt', 'a')
for idx, (c, d) in enumerate(confs):
filename = '{:s}_id{:d}'.format(comment, idx)
write_vasp(c, filename)
deg_line = filename + '{:10d}'.format(d) + '\n'
f_deg.write(deg_line)
f_deg.close()
spinner.stop()
click.secho("DONE", bold=True, bg='green', fg='white')
elif pmode == 'sc' and cmode == 'vc':
click.secho("Generating configurations: ")
click.secho("(may take much time)",
blink=True,
bold=True,
bg='magenta',
fg='white')
spinner = Spinner()
spinner.start()
l_atoms = cell.atoms.tolist()
sites = _get_sites(l_atoms, element, substitutes)
confs = cg.cons_specific_cell(sites, None, symprec=symprec)
f_deg = open('deg.txt', 'a')
for idx, (c, d) in enumerate(confs):
filename = '{:s}_id{:d}'.format(comment, idx)
write_vasp(c, filename)
# import pdb; pdb.set_trace()
deg_line = filename + '{:10d}'.format(d) + '\n'
f_deg.write(deg_line)
f_deg.close()
spinner.stop()
click.secho("DONE", bold=True, bg='green', fg='white')
elif pmode == 'sc' and cmode == 'cc':
click.secho("Generating configurations: ")
click.secho("(may take much time)",
blink=True,
bold=True,
bg='magenta',
fg='white')
spinner = Spinner()
spinner.start()
l_atoms = cell.atoms.tolist()
sites = _get_sites(l_atoms, element, substitutes)
# number to enum
ele_n = s2n(element)
e_total = l_atoms.count(ele_n)
e_n = e_total - sum(number) # 第一个元素的数量
e_num = [e_n] + list(number) # 各个元素的数量
confs = cg.cons_specific_cell(sites, e_num, symprec=symprec)
f_deg = open('deg.txt', 'a')
# TODO f.close()
for idx, (c, d) in enumerate(confs):
filename = '{:s}_id{:d}'.format(comment, idx)
write_vasp(c, filename)
deg_line = filename + '{:10d}'.format(d) + '\n'
f_deg.write(deg_line)
f_deg.close()
spinner.stop()
click.secho("DONE", bold=True, bg='green', fg='white')
else:
click.secho("ERROR: --pmode={:s} --cmode={:s} not supported.".format(
pmode, cmode),
bold=True,
bg='red',
fg='white')
def __init__(self, no_defect='POSCAR'):
# 初始化用 POSCAR路径？
self.no_defect_cell = read_vasp(no_defect)
self.lattice = self.no_defect_cell.lattice
self.positions = self.no_defect_cell.positions
self.atoms = self.no_defect_cell.atoms
optional_paras = ["genvec1", "genvec2", "genvec3", "shift"]
for para in optional_paras:
if para in self.__dict__:
d[para] = self.__dict__[para]
d["@module"] = self.__class__.__module__
d["@class"] = self.__class__.__name__
return d
@classmethod
def from_dict(cls, d):
comment = d.get("comment", "")
generation_style = d.get("generation_style")
kpts = d.get("kpoints", [[1, 1, 1]])
kpts_shift = d.get("usershift", [0, 0, 0])
num_kpts = d.get("nkpoints", 0)
return cls(comment=comment, kpts=kpts, style=generation_style,
kpts_shift=kpts_shift, num_kpts=num_kpts,
kpts_weights=d.get("kpts_weights"),
coord_type=d.get("coord_type"),
labels=d.get("labels"), tet_number=d.get("tet_number", 0),
tet_weight=d.get("tet_weight", 0),
tet_connections=d.get("tet_connections"))
if __name__ == '__main__':
from sagar.io.vasp import read_vasp
c = read_vasp('/home/hecc/Documents/python-package/Defect-Formation-Calculation/pyvaspflow/examples/POSCAR')
kpoints = Kpoints()
kpoints.automatic_density(structure=c,kppa=3000)
kpoints.write_file()
