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import numpy as np
from ase import Atoms
from ase.units import Bohr, Ry
from ase.utils import reader, writer
def read_scf(filename):
try:
with open(filename + '.scf') as fd:
pip = fd.readlines()
ene = []
for line in pip:
if line[0:4] == ':ENE':
ene.append(float(line[43:59]) * Ry)
return ene
except Exception: # XXX Which kind of exception exactly?
return None
@reader
def read_struct(fd, ase=True):
pip = fd.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:
raise RuntimeError('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 _ 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 _ 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
@writer
def write_struct(fd, atoms2=None, rmt=None, lattice='P', zza=None):
atoms = atoms2.copy()
atoms.wrap()
fd.write('ASE generated\n')
nat = len(atoms)
if rmt is None:
rmt = [2.0] * nat
fd.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
fd.write(('%10.6f' * 6) % tuple(cell2) + '\n')
if zza is None:
zza = atoms.get_atomic_numbers()
for ii in range(nat):
fd.write('ATOM %3i: ' % (ii + 1))
pos = atoms.get_scaled_positions()[ii]
fd.write('X=%10.8f Y=%10.8f Z=%10.8f\n' % tuple(pos))
fd.write(' MULT= 1 ISPLIT= 1\n')
zz = zza[ii]
if zz > 71:
ro = 0.000005
elif zz > 36:
ro = 0.00001
elif zz > 18:
ro = 0.00005
else:
ro = 0.0001
fd.write('%-10s NPT=%5i R0=%9.8f RMT=%10.4f Z:%10.5f\n' %
(atoms.get_chemical_symbols()[ii], 781, ro, rmt[ii], zz))
fd.write(f'LOCAL ROT MATRIX: {1.0:9.7f} {0.0:9.7f} {0.0:9.7f}\n')
fd.write(f' {0.0:9.7f} {1.0:9.7f} {0.0:9.7f}\n')
fd.write(f' {0.0:9.7f} {0.0:9.7f} {1.0:9.7f}\n')
fd.write(' 0\n')
def cellconst(metT):
""" metT=np.dot(cell,cell.T) """
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)
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(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 == 'B':
cell = np.array([[0.5, 0.0, 0.5], [0.0, 1.0, 0.0], [0.5, 0.0, -0.5]])
elif lattice == 'A':
cell = np.array([[-1.0, 0.0, 0.0], [0.0, -0.5, 0.5], [0.0, 0.5, 0.5]])
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:
raise ValueError('lattice is ' + lattice + '!')
return cell
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