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 wirite_poscar(cell, purity_atom='', folder='.', idx=0):
if purity_atom == '':
filename = 'POSCAR-idx-' + str(idx)
else:
comment = 'POSCAR-' + purity_atom + '-defect'
filename = '{:s}_id{:d}'.format(comment, idx)
file = path.join('./' + folder, filename)
write_vasp(cell, file)
def _export_supercell(pcell, comment, dimension, v, symprec, comprec, verbose):
cells = cells_nonredundant(
pcell, v, dimension, symprec=symprec, comprec=comprec)
for idx, c in enumerate(cells):
if verbose:
print(" " + "No.{:d}: Processing".format(idx))
filename = '{:s}_v{:d}_id{:d}'.format(comment, v, idx)
write_vasp(c, filename)
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 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 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 wirite_poscar(cell, purity_atom, folder, idx):
comment = 'POSCAR-' + purity_atom + '-defect'
filename = '{:s}_id{:d}'.format(comment, idx)
file = path.join('./' + folder, filename)
write_vasp(cell, file)
neig_list = np.zeros((n, 6))
for ii in range(pos.shape[0]):
d = np.linalg.norm(pos[ii] - extend_pos, axis=1)
idx = np.where(abs(d - d[np.argsort(d)[1]]) < 0.01)[0]
neig_list[ii] = idx % n
pos = np.dot(pos, np.linalg.inv(latt))
vac_str = [np.array([0])]
for vac in range(2, 6):
last_vac_str = vac_str[-1]
tmp_vac_str = []
n_prev = last_vac_str.shape[0]
for i in range(n_prev):
each_str = last_vac_str[i]
idx = np.setdiff1d(np.setdiff1d(range(n), each_str),
neig_list[each_str][:])
for ii in idx:
tmp_vac_str.append(get_min_serial(perms, np.hstack(
(each_str, ii))))
vac_str.append(np.unique(tmp_vac_str, axis=0))
idx = 0
os.makedirs('vac-' + str(vac))
for _str in vac_str[-1]:
_pos = pos[np.setdiff1d(range(n), _str), :]
_latt, _atoms = latt, np.ones((n - vac, )) * 5
write_vasp(Cell(_latt, _pos, _atoms),
'vac-' + str(vac) + '/POSCAR' + str(idx))
idx += 1
print(vac_str[-1].shape)
def write_poscar(cell, folder='.', idx=0, comment=""):
filename = '{:s}{:d}'.format('POSCAR' + comment, idx)
file = path.join(folder, filename)
write_vasp(cell, file, suffix='')
