def _format_grad_str(geom, grad):
""" Formats the gradient into a string used for the ProjRot input file.
:param geom: geometries (Angstrom)
:type geom: list
:param grads: gradients (Eh/Bohr)
:type grads: list
:rtype: str
"""
atom_list = []
for i, (sym, _) in enumerate(geom):
atom_list.append(int(ptab.to_Z(sym)))
# Format the strings for the xyz gradients
full_grads_str = ''
for i, grads in enumerate(grad):
grads_str = '{0:>14.8f}{1:>14.8f}{2:>14.8f}'.format(
grads[0], grads[1], grads[2])
full_grads_str += '{0:2d}{1:4d}{2}\n'.format(i + 1, atom_list[i],
grads_str)
return remove_trail_whitespace(full_grads_str)
def test__string_remove():
""" test ioformat.remove_whitespace
test ioformat.remove_trail_whitespace
test ioformat.remove_comment_lines
"""
out_str = ioformat.remove_whitespace_from_string(INI_STR)
assert out_str == ('! From Theory\n'
'A + B = C + D 1.00 0.00 0.00\n'
'PLOG / 0.01 3.0E+8 2.0 100.0\n'
'A + D = E 2.00 0.00 0.00\n'
'! From Experiment\n'
'E = F 3.00 0.00 0.00\n'
'PLOG / 0.01 6.0 2.5 105\n')
out_str = ioformat.remove_trail_whitespace(INI_STR)
assert out_str == ('! From Theory\n'
'A + B = C + D 1.00 0.00 0.00\n'
' PLOG / 0.01 3.0E+8 2.0 100.0\n'
'A + D = E 2.00 0.00 0.00\n'
'! From Experiment\n'
'E = F 3.00 0.00 0.00\n'
' PLOG / 0.01 6.0 2.5 105\n')
out_str = ioformat.remove_comment_lines(INI_STR, '!')
assert out_str == ('\n'
'A + B = C + D 1.00 0.00 0.00 \n'
' PLOG / 0.01 3.0E+8 2.0 100.0\n'
'\n'
'A + D = E 2.00 0.00 0.00 \n'
'\n'
'\n'
'E = F 3.00 0.00 0.00 \n'
' PLOG / 0.01 6.0 2.5 105\n'
'\n'
'\n')
def mdhr_data(potentials, freqs=()):
""" Writes the string for an auxiliary data file for MESS containing
potentials and vibrational frequencies of a
multidimensional hindered rotor, up to four dimensions.
:param potentials: potential values along torsional modes of rotor
:type potentials: list(list(float))
:param freqs: vibrational frequenciess along torsional modes of rotor
:type freqs: list(list(float))
:rtype: str
"""
# Determine the dimensions of the rotor potential list
dims = numpy.array(potentials).shape
ndims = len(dims)
# Write top line string with number of points in potential
if ndims == 1:
dat_str = '{0:>6d}'.format(*dims)
nfreqs = len(freqs[0]) if freqs else None
elif ndims == 2:
dat_str = '{0:>6d}{1:>6d}'.format(*dims)
nfreqs = len(freqs[0][0]) if freqs else None
elif ndims == 3:
dat_str = '{0:>6d}{1:>6d}{2:>6d}'.format(*dims)
nfreqs = len(freqs[0][0][0]) if freqs else None
elif ndims == 4:
dat_str = '{0:>6d}{1:>6d}{2:>6d}{3:>6d}'.format(*dims)
nfreqs = len(freqs[0][0][0][0]) if freqs else None
# Add the nofreq line
if freqs:
dat_str += '\n '
dat_str += ' '.join('{0:d}'.format(idx + 1) for idx in range(nfreqs))
dat_str += '\n\n'
else:
dat_str += '\n nofreq\n\n'
# Write the strings with the potential values
if ndims == 1:
for i in range(dims[0]):
dat_str += ('{0:>6d}{1:>15.8f}'.format(i + 1, potentials[i]))
if freqs:
' {}'.join((freq for freq in freqs[i]))
dat_str += '\n'
elif ndims == 2:
for i in range(dims[0]):
for j in range(dims[1]):
dat_str += ('{0:>6d}{1:>6d}{2:>15.8f}'.format(
i + 1, j + 1, potentials[i][j]))
if freqs:
strs = ('{0:d}'.format(int(val)) for val in freqs[i][j])
dat_str += ' ' + ' '.join(strs)
dat_str += '\n'
elif ndims == 3:
for i in range(dims[0]):
for j in range(dims[1]):
for k in range(dims[2]):
dat_str += ('{0:>6d}{1:>6d}{2:>6d}{3:>15.8f}'.format(
i + 1, j + 1, k + 1, potentials[i][j][k]))
if freqs:
' {}'.join((freq for freq in freqs[i][j][k]))
dat_str += '\n'
elif ndims == 4:
for i in range(dims[0]):
for j in range(dims[1]):
for k in range(dims[2]):
for lma in range(dims[3]):
dat_str += (
'{0:>6d}{1:>6d}{2:>6d}{3:>6d}{4:>15.8f}'.format(
i + 1, j + 1, k + 1, lma + 1,
potentials[i][j][k][lma]))
if freqs:
' {}'.join((freq for freq in freqs[i][j][k][lma]))
dat_str += '\n'
return remove_trail_whitespace(dat_str)