def format_coords(geo):
""" format the coords section
"""
# Get the number of atoms
natoms = len(geo)
# Get the geometry information
symbols = geom.symbols(geo)
coordinates = geom.coordinates(geo)
masses = geom.masses(geo)
print(masses)
# Build a string with the formatted coordinates string
if geom.is_atom(geo):
geo_str = '{0:<4s}{1:<6d}'.format(symbols[0], masses[0])
else:
geo_str = '{0} \n'.format(str(natoms))
for symbol, mass, coords in zip(symbols, masses, coordinates):
coords = [coord * phycon.BOHR2ANG for coord in coords]
coords_str = '{0:>14.8f}{1:>14.8f}{2:>14.8f}'.format(
coords[0], coords[1], coords[2])
geo_str += '{0:<4s}{1:<6.0f}{2}\n'.format(symbol, mass, coords_str)
# Remove final newline character from the string
geo_str = geo_str.rstrip()
return natoms, geo_str
def format_coords(geo):
""" format the coords section
"""
# Get the number of atoms
natoms = len(geo)
# Get the geometry information
symbs = geom.symbols(geo)
coords = geom.coordinates(geo)
masses = tuple(round(mass) for mass in geom.masses(geo))
# Build a string with the formatted coordinates string
if geom.is_atom(geo):
geo_str = f'{symbs[0]:<4s}{masses[0]:<6d}'
else:
geo_str = f'{str(natoms)} \n'
for symb, mass, xyzs in zip(symbs, masses, coords):
_xyzs = [x * phycon.BOHR2ANG for x in xyzs]
xyzs_str = f'{_xyzs[0]:>14.8f}{_xyzs[1]:>14.8f}{_xyzs[2]:>14.8f}'
geo_str += f'{symb:<4s}{mass:<6.0f}{xyzs_str}\n'
# Remove final newline character from the string
geo_str = geo_str.rstrip()
return natoms, geo_str
def test__mass():
""" test geom.masses
test geom.center_of_mass()
test geom.mass_centered()
"""
ref_masses = (1.00782503223, 15.99491461957, 1.00782503223)
assert numpy.allclose(geom.masses(H2O_GEO, amu=True), ref_masses)
ref_masses2 = (1837.1526464817923, 29156.94568388855, 1837.1526464817923)
assert numpy.allclose(geom.masses(H2O_GEO, amu=False), ref_masses2)
ref_red_mass = 0.9544182343494726
assert numpy.isclose(geom.reduced_mass(H2O_GEO, H_GEO), ref_red_mass)
# make sure the COM for an uncentered geometry is non-zero
cm_xyz = automol.geom.center_of_mass(C2H2CLF_GEO)
assert not numpy.allclose(cm_xyz, 0.)
# now make sure centering it yields a COM at the origin
geo = automol.geom.mass_centered(C2H2CLF_GEO)
cm_xyz = automol.geom.center_of_mass(geo)
assert numpy.allclose(cm_xyz, 0.)