def test__struct_check():
""" test geom.is_atom
test geom.is_linear
"""
assert geom.is_atom(H_GEO)
assert not geom.is_atom(C2H2CLF_GEO)
assert not geom.is_linear(H_GEO)
assert geom.is_linear(H2_GEO)
assert not geom.is_linear(C2H2CLF_GEO)
assert geom.is_linear(HCCH_GEO)
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 determine_struct_type(geo):
""" determines the linear string
"""
# Remove dummy atoms
geo = [coords for coords in geo if coords[0] != 'X']
if geom.is_atom(geo):
struct_type = 'Monoatomic'
else:
if geom.is_linear(geo):
struct_type = 'Linear'
else:
struct_type = 'Nonlinear'
return struct_type