/usr/share/pyshared/ase/io/wien2k.py is in python-ase 3.6.0.2515-1.1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 | from math import sin, cos, pi, sqrt
import numpy as np
from ase.atoms import Atoms, Atom
from ase.units import Bohr, Ry
def read_scf(filename):
try:
f = open(filename + '.scf', 'r')
pip = f.readlines()
ene = []
for line in pip:
if line[0:4] == ':ENE':
ene.append(float(line[43:59]) * Ry)
f.close()
return ene
except:
return None
def read_struct(filename, ase = True):
f = open(filename, 'r')
pip = f.readlines()
lattice = pip[1][0:3]
nat = int(pip[1][27:30])
cell = np.zeros(6)
for i in range(6):
cell[i] = float(pip[3][0 + i * 10:10 + i * 10])
cell[0:3] = cell[0:3] * Bohr
if lattice == 'P ':
lattice = 'P'
elif lattice == 'H ':
lattice = 'P'
cell[3:6] = [90.0, 90.0, 120.0]
elif lattice == 'R ':
lattice = 'R'
elif lattice == 'F ':
lattice = 'F'
elif lattice == 'B ':
lattice = 'I'
elif lattice == 'CXY':
lattice = 'C'
elif lattice == 'CXZ':
lattice = 'B'
elif lattice == 'CYZ':
lattice = 'A'
else:
print 'TEST needed'
pos = np.array([])
atomtype = []
rmt = []
neq = np.zeros(nat)
iline = 4
indif = 0
for iat in range(nat):
indifini = indif
if len(pos) == 0:
pos = np.array([[float(pip[iline][12:22]),
float(pip[iline][25:35]),
float(pip[iline][38:48])]])
else:
pos = np.append(pos, np.array([[float(pip[iline][12:22]),
float(pip[iline][25:35]),
float(pip[iline][38:48])]]),
axis = 0)
indif += 1
iline += 1
neq[iat] = int(pip[iline][15:17])
iline += 1
for ieq in range(1, int(neq[iat])):
pos = np.append(pos, np.array([[float(pip[iline][12:22]),
float(pip[iline][25:35]),
float(pip[iline][38:48])]]),
axis = 0)
indif += 1
iline += 1
for i in range(indif - indifini):
atomtype.append(pip[iline][0:2].replace(' ', ''))
rmt.append(float(pip[iline][43:48]))
iline += 4
if ase:
cell2 = coorsys(cell)
atoms = Atoms(atomtype, pos, pbc = True)
atoms.set_cell(cell2, scale_atoms = True)
cell2 = np.dot(c2p(lattice), cell2)
if lattice == 'R':
atoms.set_cell(cell2, scale_atoms = True)
else:
atoms.set_cell(cell2)
return atoms
else:
return cell, lattice, pos, atomtype, rmt
def write_struct(filename, atoms2 = None, rmt = None, lattice = 'P'):
atoms=atoms2.copy()
atoms.set_scaled_positions(atoms.get_scaled_positions())
f = file(filename, 'w')
f.write('ASE generated\n')
nat = len(atoms)
if rmt == None:
rmt = [2.0] * nat
f.write(lattice+' LATTICE,NONEQUIV.ATOMS:%3i\nMODE OF CALC=RELA\n'%nat)
cell = atoms.get_cell()
metT = np.dot(cell, np.transpose(cell))
cell2 = cellconst(metT)
cell2[0:3] = cell2[0:3] / Bohr
f.write(('%10.6f' * 6) % tuple(cell2) + '\n')
#print atoms.get_positions()[0]
for ii in range(nat):
f.write('ATOM %3i: ' % (ii + 1))
pos = atoms.get_scaled_positions()[ii]
f.write('X=%10.8f Y=%10.8f Z=%10.8f\n' % tuple(pos))
f.write(' MULT= 1 ISPLIT= 1\n')
zz = atoms.get_atomic_numbers()[ii]
if zz > 71:
ro = 0.000005
elif zz > 36:
ro = 0.00001
elif zz > 18:
ro = 0.00005
else:
ro = 0.0001
f.write('%-10s NPT=%5i R0=%9.8f RMT=%10.4f Z:%10.5f\n' %
(atoms.get_chemical_symbols()[ii], 781, ro, rmt[ii], zz))
f.write('LOCAL ROT MATRIX: %9.7f %9.7f %9.7f\n' % (1.0, 0.0, 0.0))
f.write(' %9.7f %9.7f %9.7f\n' % (0.0, 1.0, 0.0))
f.write(' %9.7f %9.7f %9.7f\n' % (0.0, 0.0, 1.0))
f.write(' 0\n')
def cellconst(metT):
aa = np.sqrt(metT[0, 0])
bb = np.sqrt(metT[1, 1])
cc = np.sqrt(metT[2, 2])
gamma = np.arccos(metT[0, 1] / (aa * bb)) / np.pi * 180.0
beta = np.arccos(metT[0, 2] / (aa * cc)) / np.pi * 180.0
alpha = np.arccos(metT[1, 2] / (bb * cc)) / np.pi * 180.0
return np.array([aa, bb, cc, alpha, beta, gamma])
def coorsys(latconst):
a = latconst[0]
b = latconst[1]
c = latconst[2]
cal = np.cos(latconst[3] * np.pi / 180.0)
cbe = np.cos(latconst[4] * np.pi / 180.0)
cga = np.cos(latconst[5] * np.pi / 180.0)
sal = np.sin(latconst[3] * np.pi / 180.0)
sbe = np.sin(latconst[4] * np.pi / 180.0)
sga = np.sin(latconst[5] * np.pi / 180.0)
return np.array([[a, b * cga, c * cbe],
[0, b * sga, c * (cal - cbe * cga) / sga],
[0, 0, c * np.sqrt(1 - cal**2 - cbe**2 - cga**2 + 2 * cal * cbe * cga) / sga]]).transpose()
def c2p(lattice):
# apply as eg. cell2 = np.dot(ct.c2p('F'), cell)
if lattice == 'P':
cell = np.eye(3)
elif lattice == 'F':
cell = np.array([[0.0, 0.5, 0.5], [0.5, 0.0, 0.5], [0.5, 0.5, 0.0]])
elif lattice == 'I':
cell = np.array([[-0.5, 0.5, 0.5], [0.5, -0.5, 0.5], [0.5, 0.5, -0.5]])
elif lattice == 'C':
cell = np.array([[0.5, 0.5, 0.0], [0.5, -0.5, 0.0], [0.0, 0.0, -1.0]])
elif lattice == 'R':
cell = np.array([[2.0 / 3.0, 1.0 / 3.0, 1.0 / 3.0], [-1.0 / 3.0, 1.0 / 3.0, 1.0 / 3.0], [-1.0 / 3.0, -2.0/3.0, 1.0 / 3.0]])
else:
print 'lattice is ' + lattice + '!'
return cell
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