def reject2(args):
"""
原子が 0 意外を出力
"""
path, pos = args
strs = CVMStrs.from_str_file(path)
tmpstr = []
for structure in strs:
a = structure.label.num_atoms[int(pos)]
if a != 0:
tmpstr.append(structure)
outstr = CVMStrs(tmpstr)
fname = path + "_rejcted"
outstr.make_file(fname)
def reject(path, limit):
"""
条件で構造を絞る
"""
strs = CVMStrs.from_str_file(path)
tmpstr = []
for structure in strs:
a = structure.label.num_atoms[0] / (structure.label.num_atoms[0] +
structure.label.num_atoms[2] +
structure.label.num_atoms[3])
if a != 0 and a < limit:
tmpstr.append(structure)
outstr = CVMStrs(tmpstr)
fname = path + "_rejcted"
outstr.make_file(fname)
def reject_bin(args):
"""
条件で構造を絞る
二元系用
"""
path, limit = args
strs = CVMStrs.from_str_file(path)
tmpstr = []
for structure in strs:
a = structure.label.num_atoms[0] / (structure.label.num_atoms[0] +
structure.label.num_atoms[1])
if a <= limit:
tmpstr.append(structure)
outstr = CVMStrs(tmpstr)
fname = path + "_rejcted"
outstr.make_file(fname)
def replace(path, site, rep):
"""
* 元素ラベルを交換する\n
* e.g.: cvm_input.py ファイル名 --site "0011" --rep "AC BD"\n
* --site は左から順に第一、第二、第三...サイトに対応\n
0 で交換判定しない、 1 で交換判定するサイトを指定\n
* "0011" では 4 副格子中の 3 番目と 4 番目の site 原子ラベルを交換する設定\n
* --rep で交換するラベルの組み合わせを指定する\n
* "AC BD" は A を C に B を D に置き換える
* ラベルを変えない場合は "AA" のように同じラベルを振る
"""
d = len(site)
site_ids = [j + k*d for k in range(100)
for j in [int(i) for i in range(len(site)) if site[i] == "1"]]
print(site_ids)
replace_dict = {x[0]:x[1] for x in rep.split()}
strs = CVMStrs.from_str_file(path)
strs.replace_site_elements(site_ids, replace_dict)
fname = path + "_rev"
for s in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
if s in rep:
largest = s
strs.complete_elements("ABCDEFGHIJKLMNOPQRSTUVWXYZ".index(largest)+1)
strs.make_file(fname)
try:
enes = CVMEnergies.from_energies_file("energies.txt")
enes.rename_from_str_labels(strs)
enes.make_file("energies.txt_rev")
except IOError:
pass
def make_poscar(args, disord):
"""
POSCAR を作成する
str ファイルを引数に指定する
"""
path = args
strs = CVMStrs.from_str_file(path, disord=disord)
# strs[0] | fnc.echo
strs.make_poscar()
def stack(args):
"""
hcp-fcc Mg stacking 構造を作成する
"""
path = args
strs = CVMStrs.from_str_file(path)
for structure in strs:
dirc = str(structure.label).split('*')[0]
Bash.mkdir(dirc)
structure.make_stack_poscar(os.path.join(dirc, "POSCAR"))
def rename_energies(path):
"""
energies.txt を str ファイルから修正する
"""
path = "hcp.str"
strs = CVMStrs.from_str_file(path)
enes = CVMEnergies.from_energies_file("energies.txt")
enes.rename_from_str_labels(strs)
enes.make_file("energies.txt_rev")
def test_make_poscar(self):
""" for make poscar """
path = os.path.join(self.PATH, 'str')
strs = CVMStrs.from_str_file(os.path.join(path, 'bcci.str'))
# print(strs[100])
# print(strs[100].sites)
# strs[100].sites.set_sorted()
print(strs[100])
strs[100].make_poscar(1, path)
def make_sc(path, dim, disord, rep, key):
"""
supercell を作成
e.g.: cvm_input.py make_sc hcpi.str --dim 2 1 1 --rep "BA" --key GS7_
"""
strs = CVMStrs.from_str_file(path, disord=disord)
replace_dict = {x[0]:x[1] for x in rep.split()}
# strs[2].make_supercell(strs.disord.lattice.array, replace_dict, dim)
supercells = strs.make_supercells(key, replace_dict, dim)
# supercells.make_poscar()
supercells.make_file('supercells.str')
def exchange_elements(path, elem1, elem2):
"""
原子ラベルを交換したファイルを作成
"""
strs = CVMStrs.from_str_file(path)
enes = CVMEnergies.from_energies_file("energies.txt")
strs.exchange_elements(elem1, elem2)
enes.exchange_elements(elem1, elem2)
fname = path + "_rev"
strs.make_file(fname)
enes.make_file("energies.txt_rev")
def alt_scale(args):
"""
str ファイルの格子長の scale を変更する
args: fname_str, scale
scale は分数表記
小数を与えることができないので、整数に通分する
"""
path = args[0]
scale = Fraction(args[1])
strs = CVMStrs.from_str_file(path)
strs.alt_lattice(scale)
fname = path + '_rev'
strs.make_file(fname)
def add_site(path, input_file):
"""
サイトを追加
"""
with open(input_file, 'r') as rfile:
lines = rfile.readlines()
args = {}
for line in lines:
key = line.split("=")[0].split()[0]
tmp = line.split("=")[1].split()
if len(tmp) == 1:
try:
value = int(tmp[0])
except ValueError:
value = tmp[0]
else:
value = [Fraction(x) for x in tmp]
args.update({key: value})
strs = CVMStrs.from_str_file(path)
strs.add_site(**args) #pylint: disable=W0142
fname = path + "_added"
strs.make_file(fname)
def add_site(args):
"""
サイトを追加
引数は path input_file
"""
path, input_file = args
with open(input_file, 'r') as rfile:
lines = rfile.readlines()
args = {}
for line in lines:
key = line.split("=")[0].split()[0]
if key in ['primitive_z', 'origin']:
args.update({key: int(line.split('=')[1].split()[0])})
elif key == 'trans':
value = [[Fraction(x) for x in y.split()]
for y in line.split('=')[1].split(',')]
args.update({key: value})
elif key == 'label':
args.update({key: line.split('=')[1].split()[0]})
elif key == 'insert_idx':
value = [int(x) for x in line.split('=')[1].split(',')]
args.update({key: value})
else:
print(key)
strs = CVMStrs.from_str_file(path)
tmp_args = {}
tmp_args.update({'primitive_z': args['primitive_z'],
'origin': args['origin'],
'label': args['label']})
for i, idx in enumerate(args['insert_idx']):
tmp_args.update({'insert_idx': idx})
tmp_args.update({'trans': args['trans'][i]})
strs.add_site(**tmp_args) #pylint: disable=W0142
if tmp_args['origin'] >= idx:
tmp_args['origin'] += 1
tmp_args['primitive_z'] += 1
fname = path + '_added'
strs.make_file(fname)