def test_cons_specific_volume(self):
wanted = [2, 6, 12, 41]
got = []
cg = CG(self.fcc_pcell)
for v in [1, 2, 3, 4]:
con = cg.cons_specific_volume([(1, 5), (2,)], v)
got.append(len([i for i in con]))
self.assertEqual(got, wanted)
def test_cons_specific_volume_c(self):
wanted = [7]
got = []
cg = CG(self.fcc_pcell)
for v in [4]:
con = cg.cons_specific_volume([(1, 5), (2,)], v, e_num=(3, 1))
got.append(len([i for i in con]))
self.assertEqual(got, wanted)
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')