def gen_fchk(mfn, data, ofn='', title=None, suffix='_rlo', overwrite=False):
# text: info, energy, coeff, rest
# data: energy, coeff, dim
if not ofn:
t, ext = os.path.splitext(mfn)
ofn = t + suffix + ext
if not overwrite and os.path.exists(ofn):
overwriteflag = raw_input('Overwrite file %s? Y/N ' % ofn)
if overwriteflag.lower() != 'y':
print ofn, 'skipped.'
return False
title = title or os.path.splitext(ofn)[0]
fchk = parse_fchk(mfn)
text = fchk['text']
dim_mo, dim_bs = fchk['data']['dim']
dim_nmo, dim_nbs = data.get('dim', (dim_mo, dim_bs))
assert dim_bs == dim_nbs
if dim_nmo == dim_mo:
for e in data['energy']:
assert e.shape == (dim_nmo, )
for c in data['coeff']:
assert c.shape == (dim_nmo, dim_bs)
elif dim_nmo < dim_mo:
for spin, e in enumerate(data['energy']):
data['energy'][spin] = np.append(e,
np.zeros(dim_mo - dim_nmo),
axis=0)
assert data['energy'][spin].shape == (dim_mo, )
for spin, c in enumerate(data['coeff']):
data['coeff'][spin] = np.append(c,
np.zeros(
(dim_mo - dim_nmo, dim_bs)),
axis=0)
assert data['coeff'][spin].shape == (dim_mo, dim_bs)
dim_nmo = dim_mo
else:
# raise AssertionError('Number of new orbitals exceeds number of original orbitals')
for lid, line in enumerate(text['info']):
text['info'][lid] = line.replace(str(dim_mo), str(dim_nmo))
text['energy'][0] = text['energy'][0].replace(str(dim_mo),
str(dim_nmo))
text['coeff'][0] = text['coeff'][0].replace(str(dim_mo * dim_bs),
str(dim_nmo * dim_bs))
if len(data['energy']) != len(text['energy']):
print 'Warning: Spin symmetry not match!'
amoeline = text['energy'][0]
bmoeline = amoeline.replace('Alpha Orbital Energies',
'Beta Orbital Energies ')
text['energy'] = [amoeline, bmoeline]
amocline = text['coeff'][0]
bmocline = amocline.replace('Alpha MO coefficients',
'Beta MO coefficients ')
text['coeff'] = [amocline, bmocline]
# print '%s generated.' % ofn
f = open(ofn, 'w')
write = f.write
writes = lambda s: write(s + '\n')
writel = lambda l: write('\n'.join(l) + '\n')
writes(title)
writel(text['info'][1:])
for spin, energy in enumerate(data['energy']):
writes(text['energy'][spin])
for i, e in enumerate(['%16.8E' % e for e in energy]):
write(e)
if (i + 1) % 5 == 0:
write('\n')
if (i + 1) % 5 != 0:
write('\n')
for spin, coeff in enumerate(data['coeff']):
writes(text['coeff'][spin])
# print coeff
for i, e in enumerate(['%16.8E' % e for e in coeff.reshape(1, -1)[0]]):
write(e)
if (i + 1) % 5 == 0:
write('\n')
if (i + 1) % 5 != 0:
write('\n')
writel(text['rest'])
f.close()
return ofn
if xoao.ndim == 2:
if fmxo.ndim == 2:
energies = np.diag(fmxo)
elif fmxo.ndim == 1:
energies = fmxo
else:
raise UserWarning('Invalid shape of fock matrix')
assert energies.shape[0] == xoao.shape[0]
data = {'energy': [energies], 'coeff': [xoao], 'dim': xoao.shape}
elif xoao.ndim == 3:
if fmxo.ndim == 3:
energies = np.diagonal(fmxo, axis1=1, axis2=2)
elif fmxo.ndim == 2:
energies = fmxo
else:
raise UserWarning('Invalid shape of fock matrix')
assert energies.shape[1] == xoao.shape[1]
assert energies.shape[0] == 2
assert xoao.shape[0] == 2
data = {'energy': energies, 'coeff': xoao, 'dim': xoao.shape[1:]}
else:
raise UserWarning('Unrecognized data shape: %s' % xoao.shape)
return gen_fchk(mfn, data, suffix=suffix, overwrite=overwrite)
if __name__ == '__main__':
import sys
mfn = sys.argv[1]
gen_fchk(mfn, parse_fchk(mfn)['data'])