def main():
args = parse_args()
# Load system file
if args.fn_sys.endswith('.fchk'):
numbers, coords, energy, grad, hess, masses, rvecs, pbc = read_abinitio(
args.fn_sys, do_hess=False)
system = System(numbers,
coords,
rvecs=None,
charges=None,
radii=None,
masses=masses)
system.detect_bonds()
else:
system = System.from_file(args.fn_sys)
# Guess atom types if needed
if args.ffatypes is not None:
guess_ffatypes(system, args.ffatypes)
ffatypes = [system.ffatypes[i] for i in system.ffatype_ids]
# Load atomic charges
fn_charges, _, path = args.charges.partition(':')
if fn_charges.endswith('.h5'):
with h5.File(fn_charges, 'r') as f:
if not path in f:
raise IOError(
'Given HDF5 file %s does not contain a dataset %s' %
(fn_charges, path))
charges = f[path][:]
radii = None
if args.gaussian:
path_radii = os.path.join(os.path.dirname(path), 'radii')
if 'radii' in f[path]:
radii = average(f['%s/radii' % path][:],
ffatypes,
fmt='dict')
else:
radii = average(get_ei_radii(system.numbers),
ffatypes,
fmt='dict')
elif fn_charges.endswith('.chk'):
sample = load_chk(fn_charges)
if path in sample.keys():
charges = sample[path]
else:
raise IOError(
'Given CHK file %s does not contain a dataset with label %s' %
(fn_charges, path))
radii = None
if args.gaussian:
if 'radii' in sample.keys():
radii = average(sample['radii'], ffatypes, fmt='dict')
else:
raise IOError(
'Invalid extension, fn_charges should be a HDF5 or a CHK file.')
# Derive charge parameters
if args.bci:
constraints = {}
if args.bci_constraints is not None:
constraints = read_bci_constraints(args.bci_constraints)
bcis = charges_to_bcis(charges,
ffatypes,
system.bonds,
constraints=constraints,
verbose=args.verbose)
make_yaff_ei(args.fn_out, None, bcis=bcis, radii=radii)
else:
charges = average(charges, ffatypes, fmt='dict', verbose=args.verbose)
make_yaff_ei(args.fn_out, charges, radii=radii)
def main():
options, args = parse()
fn_sys, fn_in, path = args
if fn_sys.endswith('.fchk'):
numbers, coords, energy, grad, hess, masses, rvecs, pbc = read_abinitio(
fn_sys, do_hess=False)
system = System(numbers,
coords,
rvecs=None,
charges=None,
radii=None,
masses=masses)
system.detect_bonds()
else:
system = System.from_file(fn_sys)
if options.ffatypes is not None:
guess_ffatypes(system, options.ffatypes)
ffatypes = [system.ffatypes[i] for i in system.ffatype_ids]
if fn_in.endswith('.h5'):
h5 = h5py.File(fn_in)
if not path in h5 or 'charges' not in h5[path]:
raise IOError(
'Given HDF5 file %s does not contain dataset %s/charges' %
(fn_in, path))
charges = h5['%s/charges' % path][:]
radii = None
if options.gaussian:
if 'radii' in h5[path]:
radii = average(h5['%s/radii' % path][:], ffatypes, fmt='dict')
else:
radii = average(get_ei_radii(system.numbers),
ffatypes,
fmt='dict')
elif fn_in.endswith('.chk'):
sample = load_chk(fn_in)
if path in sample.keys():
charges = sample[path]
else:
raise IOError(
'Given CHK file %s does not contain dataset with label %s' %
(fn_in, path))
radii = None
if options.gaussian:
if 'radii' in sample.keys():
radii = average(sample['radii'], ffatypes, fmt='dict')
else:
raise IOError(
'Invalid extension, fn_in should be a HDF5 or a CHK file.')
if options.output is None:
if path == '.':
fn_out = 'pars_ei.txt'
else:
fn_out = 'pars_ei_%s.txt' % path.replace('/', '_')
else:
fn_out = options.output
if options.bci:
constraints = {}
if options.bci_constraints is not None:
constraints = read_bci_constraints(options.bci_constraints)
bcis = charges_to_bcis(charges,
ffatypes,
system.bonds,
constraints=constraints,
verbose=options.verbose)
make_yaff_ei(fn_out, None, bcis=bcis, radii=radii)
else:
charges = average(charges,
ffatypes,
fmt='dict',
verbose=options.verbose)
make_yaff_ei(fn_out, charges, radii=radii)