def get_csv(group, para_type):
### group = 'CH3ab' para_type = 'da'
### local file
cons_dir = '../data/' + group + '_data/' + group + '_cons'
cifs_dir = '../data/' + group + '_data/' + group + '_cifs'
### MS file
MS_dir = os.path.join(os.path.expanduser('~'),
'Documents/USRP/DopRutile_Files/Documents')
MS_cifs_dir = os.path.join(MS_dir, group + '_cifs')
### csv file
csv_name = group + '_data_' + time.strftime("%Y%m%d",
time.localtime()) + '.csv'
csv_path = os.path.join(os.path.expanduser('~'),
'Desktop/CH4_DS/' + csv_name)
### pd.DataFrame
row_index = 1
group_df = pd.DataFrame()
###
for file_name in os.listdir(cons_dir):
f = os.path.join(cons_dir, file_name)
if re.match(r'.*.cif', file_name):
os.remove(f)
for con_name in os.listdir(cons_dir):
if row_index % 4 == 0:
print('{:<5}{:^5}{:<30}{:^3}'.format(row_index, ' --> ', con_name,
' | '))
else:
print('{:<5}{:^5}{:<30}{:^3}'.format(row_index, ' --> ', con_name,
' | '),
end='')
###
con = os.path.join(cons_dir, con_name)
abc, elements, numbers, xyzs, l1, l2, group_dict = sc.std_contcars(
con, group)
##
cif_name = os.path.basename(con) + '.cif'
p2c.write_cif(con + '.cif', abc, elements, numbers, xyzs)
##
total_paras = gp.get_paras(abc, l1, l2, group, group_dict, cif_name,
para_type)
###
if row_index == 1:
group_df = pd.DataFrame(columns=tuple(total_paras.keys()))
group_df.loc[row_index] = list(total_paras.values())
row_index += 1
###
cif = os.path.join(cifs_dir, cif_name)
###
ms_xsd = os.path.join(MS_cifs_dir, os.path.basename(con) + '.xsd')
if not os.path.exists(ms_xsd):
ms_cif = os.path.join(MS_cifs_dir, cif_name)
shutil.copy(con + '.cif', cif)
shutil.move(con + '.cif', ms_cif)
else:
os.remove(con + '.cif')
###
group_df = group_df.sort_values(by=['cell', 'name', 'dop'], ascending=True)
group_df = group_df.reset_index(drop=True)
print('\n', group_df.shape[1], '\n')
group_df.to_csv(csv_path)
def std_cons(CONTCAR):
abc, elements, numbers, xyzs = p2c.get_cell(CONTCAR)
contcar_name = os.path.basename(CONTCAR)
dopM = contcar_name.split('_')[-3]
### Special edition
if 'IrO2' in CONTCAR:
for xyz in xyzs:
xyz[1] = 1 - xyz[1]
### round xyz by 8
for xyz in xyzs:
for i in range(len(xyz)):
xyz[i] = round(xyz[i], 8)
### std xyz
for xyz in xyzs:
if xyz[2] >= 0.99:
xyz[2] -= 1.00
### make dict
element_dict = {}
count = 0
for element, number in zip(elements, numbers):
for i in range(int(number)):
element_dict[element + str(i + 1)] = xyzs[count]
count += 1
###
metals = ['Ti', 'V', 'Ge', 'Mo', 'Ru', 'Rh', 'Os', 'Ir']
### first layer
H_dict = {}
O_dict = {}
M_dict = {}
for element_name in element_dict.keys():
if element_name.strip(string.digits) == 'H':
H_dict[element_name] = element_dict[element_name]
elif element_name.strip(string.digits) == 'O':
O_dict[element_name] = element_dict[element_name]
elif element_name.strip(string.digits) in metals:
M_dict[element_name] = element_dict[element_name]
##
def tuple2dict(t):
d = {}
for name, xyz in t:
d[name] = xyz
return d
##
def get_layer(O_dict, M_dict):
##
O_dict_z = sorted(O_dict.items(), key=lambda e: e[1][2], reverse=True)
# get O1 O2
O12_dict = tuple2dict(O_dict_z[:2])
O12_dict_x = sorted(O12_dict.items(),
key=lambda e: e[1][0],
reverse=True)
O1_tuple = O12_dict_x[1]
O2_tuple = O12_dict_x[0]
# get O3 O4 O5 O6
O3456_dict = tuple2dict(O_dict_z[2:6])
O3456_dict_y = sorted(O3456_dict.items(),
key=lambda e: e[1][1],
reverse=True)
#
O34_dict = tuple2dict(O3456_dict_y[-2:])
O34_dict_x = sorted(O34_dict.items(),
key=lambda e: e[1][0],
reverse=True)
O3_tuple = O34_dict_x[1]
O4_tuple = O34_dict_x[0]
#
O56_dict = tuple2dict(O3456_dict_y[:2])
O56_dict_x = sorted(O56_dict.items(),
key=lambda e: e[1][0],
reverse=True)
O5_tuple = O56_dict_x[1]
O6_tuple = O56_dict_x[0]
# get O7 O8
O78_dict = tuple2dict(O_dict_z[6:8])
O78_dict_x = sorted(O78_dict.items(),
key=lambda e: e[1][0],
reverse=True)
O7_tuple = O78_dict_x[1]
O8_tuple = O78_dict_x[0]
## get M1 M2 M3 M4
M_dict_z = sorted(M_dict.items(), key=lambda e: e[1][2], reverse=True)
M1234_dict = tuple2dict(M_dict_z[:4])
M1234_dict_y = sorted(M1234_dict.items(),
key=lambda e: e[1][1],
reverse=True)
#
M12_dict = tuple2dict(M1234_dict_y[-2:])
M12_dict_x = sorted(M12_dict.items(),
key=lambda e: e[1][0],
reverse=True)
M1_tuple = M12_dict_x[1]
M2_tuple = M12_dict_x[0]
#
M34_dict = tuple2dict(M1234_dict_y[:2])
M34_dict_x = sorted(M34_dict.items(),
key=lambda e: e[1][0],
reverse=True)
M3_tuple = M34_dict_x[1]
M4_tuple = M34_dict_x[0]
##
layer = {}
layer['O1'] = list(O1_tuple)
O_dict.pop(O1_tuple[0])
layer['O2'] = list(O2_tuple)
O_dict.pop(O2_tuple[0])
layer['O3'] = list(O3_tuple)
O_dict.pop(O3_tuple[0])
layer['O4'] = list(O4_tuple)
O_dict.pop(O4_tuple[0])
layer['O5'] = list(O5_tuple)
O_dict.pop(O5_tuple[0])
layer['O6'] = list(O6_tuple)
O_dict.pop(O6_tuple[0])
layer['O7'] = list(O7_tuple)
O_dict.pop(O7_tuple[0])
layer['O8'] = list(O8_tuple)
O_dict.pop(O8_tuple[0])
layer['M1'] = list(M1_tuple)
M_dict.pop(M1_tuple[0])
layer['M2'] = list(M2_tuple)
M_dict.pop(M2_tuple[0])
layer['M3'] = list(M3_tuple)
M_dict.pop(M3_tuple[0])
layer['M4'] = list(M4_tuple)
M_dict.pop(M4_tuple[0])
return O_dict, M_dict, layer
###
def get_Hab(H_dict):
Hab_dict = {}
#
H_dict_y = sorted(H_dict.items(), key=lambda e: e[1][1], reverse=True)
H1_tuple = H_dict_y[0]
#
Hab_dict['H1'] = list(H1_tuple)
return Hab_dict
### adjust atom location
def mv_xyz(xyz, d, s):
if d == 'x':
xyz[0] = xyz[0] + s
elif d == 'y':
xyz[1] = xyz[1] + s
elif d == 'z':
xyz[2] = xyz[2] + s
return xyz
##
O2_dict, M2_dict, l1 = get_layer(O_dict, M_dict)
O3_dict, M3_dict, l2 = get_layer(O2_dict, M2_dict)
Hab_dict = get_Hab(H_dict)
## C D
## A B
## C D
def adjust_AtomPair(A, B, C, D, loc):
if D[1][0] < A[1][0]:
C[1] = mv_xyz(C[1], 'x', 1)
D[1] = mv_xyz(D[1], 'x', 1)
if C[1][0] > B[1][0]:
C[1] = mv_xyz(C[1], 'x', -1)
D[1] = mv_xyz(D[1], 'x', -1)
if loc == 1:
if C[1][0] < A[1][0] and (A[1][0] < D[1][0] < B[1][0]):
C[1] = mv_xyz(C[1], 'x', 1)
C, D = D, C
elif loc == -1:
if (A[1][0] < C[1][0] < B[1][0]) and B[1][0] < D[1][0]:
D[1] = mv_xyz(D[1], 'x', -1)
C, D = D, C
return C, D
## set O1 O2 unchanged
if l1['O3'][1][1] < l1['M1'][1][1]:
l1['O3'][1] = mv_xyz(l1['O3'][1], 'y', 1)
l1['O4'][1] = mv_xyz(l1['O4'][1], 'y', 1)
l1['O3'], l1['O5'] = l1['O5'], l1['O3']
l1['O4'], l1['O6'] = l1['O6'], l1['O4']
##
if l1['O1'][1][0] > l1['M1'][1][0]:
l1['O2'][1] = mv_xyz(l1['O2'][1], 'x', -1)
l1['O1'], l1['O2'] = l1['O2'], l1['O1']
##
if l1['M3'][0].strip(string.digits) == dopM:
l1['M4'][1] = mv_xyz(l1['M4'][1], 'x', -1)
l1['M3'], l1['M4'] = l1['M4'], l1['M3']
##
l1['O3'], l1['O4'] = adjust_AtomPair(l1['O1'], l1['O2'], \
l1['O3'], l1['O4'], 1)
##
l1['O5'], l1['O6'] = adjust_AtomPair(l1['O1'], l1['O2'], \
l1['O5'], l1['O6'], 1)
##
l1['M1'], l1['M2'] = adjust_AtomPair(l1['O1'], l1['O2'], \
l1['M1'], l1['M2'], 1)
##
l1['M3'], l1['M4'] = adjust_AtomPair(l1['M1'], l1['M2'], \
l1['M3'], l1['M4'], -1)
#l1['M3'], l1['M4'] = l1['M4'], l1['M3']
##
l1['O7'], l1['O8'] = adjust_AtomPair(l1['M1'], l1['M2'], \
l1['O7'], l1['O8'], -1)
##
l2['O1'], l2['O2'] = adjust_AtomPair(l1['M1'], l1['M2'], \
l2['O1'], l2['O2'], -1)
##
##
std_layer = []
for i in l1.values():
std_layer.append(i)
for i in l2.values():
std_layer.append(i)
### change xyz
for A in std_layer:
element_dict[A[0]] = A[1]
##
xyzs = []
for key, value in element_dict.items():
xyzs.append(value)
### round xyz by 8
for xyz in xyzs:
for i in range(len(xyz)):
xyz[i] = round(xyz[i], 8)
###
cif_name = os.path.basename(CONTCAR) + '.cif'
p2c.write_cif(CONTCAR + '.cif', abc, elements, numbers, xyzs)
return abc, l1, l2, Hab_dict, cif_name
def std_cons(CONTCAR):
abc, elements, numbers, xyzs = p2c.get_cell(CONTCAR)
contcar_name = os.path.basename(CONTCAR)
dopM = contcar_name.split('_')[-3]
### Special edition
if 'IrO2' in CONTCAR:
for xyz in xyzs:
if xyz[1] > 0.75:
xyz[1] = xyz[1] - 1
### round xyz by 8
for xyz in xyzs:
for i in range(len(xyz)):
xyz[i] = round(xyz[i], 8)
### std xyz
for xyz in xyzs:
if xyz[2] >= 0.99:
xyz[2] -= 1.00
### make dict
## get element name and number
element_dict = {}
count = 0
for element, number in zip(elements, numbers):
for i in range(int(number)):
element_dict[element + str(i + 1)] = xyzs[count]
count += 1
###
metals = ['Ti', 'V', 'Ge', 'Mo', 'Ru', 'Rh', 'Os', 'Ir']
### first layer
H_dict = {}
C_dict = {}
O_dict = {}
M_dict = {}
for element_name in element_dict.keys():
if element_name.strip(string.digits) == 'H':
H_dict[element_name] = element_dict[element_name]
elif element_name.strip(string.digits) == 'C':
C_dict[element_name] = element_dict[element_name]
elif element_name.strip(string.digits) == 'O':
O_dict[element_name] = element_dict[element_name]
elif element_name.strip(string.digits) in metals:
M_dict[element_name] = element_dict[element_name]
##
### adjust atom location
def mv_xyz(xyz, d, s):
if d == 'x':
xyz[0] = xyz[0] + s
elif d == 'y':
xyz[1] = xyz[1] + s
elif d == 'z':
xyz[2] = xyz[2] + s
return xyz
##
O2_dict, M2_dict, l1 = get_layer(O_dict, M_dict)
O3_dict, M3_dict, l2 = get_layer(O2_dict, M2_dict)
CH3_dict = get_CH3(H_dict, C_dict)
## C D
## A B
## C D
def adjust_AtomPair(A, B, C, D, loc):
if D[1][0] < A[1][0]:
C[1] = mv_xyz(C[1], 'x', 1)
D[1] = mv_xyz(D[1], 'x', 1)
if C[1][0] > B[1][0]:
C[1] = mv_xyz(C[1], 'x', -1)
D[1] = mv_xyz(D[1], 'x', -1)
if loc == 1:
if C[1][0] < A[1][0] and (A[1][0] < D[1][0] < B[1][0]):
C[1] = mv_xyz(C[1], 'x', 1)
C, D = D, C
elif loc == -1:
if (A[1][0] < C[1][0] < B[1][0]) and B[1][0] < D[1][0]:
D[1] = mv_xyz(D[1], 'x', -1)
C, D = D, C
return C, D
## set O1 O2 unchanged
if l1['O3'][1][1] < l1['M1'][1][1]:
l1['O3'][1] = mv_xyz(l1['O3'][1], 'y', 1)
l1['O4'][1] = mv_xyz(l1['O4'][1], 'y', 1)
l1['O3'], l1['O5'] = l1['O5'], l1['O3']
l1['O4'], l1['O6'] = l1['O6'], l1['O4']
##
if l1['O1'][1][0] > l1['M1'][1][0]:
l1['O2'][1] = mv_xyz(l1['O2'][1], 'x', -1)
l1['O1'], l1['O2'] = l1['O2'], l1['O1']
##
if l1['M3'][0].strip(string.digits) == dopM:
l1['M4'][1] = mv_xyz(l1['M4'][1], 'x', -1)
l1['M3'], l1['M4'] = l1['M4'], l1['M3']
##
l1['O3'], l1['O4'] = adjust_AtomPair(l1['O1'], l1['O2'], \
l1['O3'], l1['O4'], 1)
##
l1['O5'], l1['O6'] = adjust_AtomPair(l1['O1'], l1['O2'], \
l1['O5'], l1['O6'], 1)
##
l1['M1'], l1['M2'] = adjust_AtomPair(l1['O1'], l1['O2'], \
l1['M1'], l1['M2'], 1)
##
l1['M3'], l1['M4'] = adjust_AtomPair(l1['M1'], l1['M2'], \
l1['M3'], l1['M4'], -1)
#l1['M3'], l1['M4'] = l1['M4'], l1['M3']
##
l1['O7'], l1['O8'] = adjust_AtomPair(l1['M1'], l1['M2'], \
l1['O7'], l1['O8'], -1)
##
l2['O1'], l2['O2'] = adjust_AtomPair(l1['M1'], l1['M2'], \
l2['O1'], l2['O2'], -1)
##
##
std_layer = []
for i in l1.values():
std_layer.append(i)
for i in l2.values():
std_layer.append(i)
### change xyz
for A in std_layer:
element_dict[A[0]] = A[1]
##
xyzs = []
for key, value in element_dict.items():
xyzs.append(value)
### round xyz by 8
for xyz in xyzs:
for i in range(len(xyz)):
xyz[i] = round(xyz[i], 8)
###
cif_name = os.path.basename(CONTCAR) + '.cif'
p2c.write_cif(CONTCAR + '.cif', abc, elements, numbers, xyzs)
return abc, l1, l2, CH3_dict, cif_name
