def test__from_data():
""" test getters
"""
assert C2H2CLF_GEO == geom.from_data(
syms=geom.symbols(C2H2CLF_GEO),
xyzs=geom.coordinates(C2H2CLF_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 test__from_data():
""" test geom.from_data
"""
assert C2H2CLF_GEO == geom.from_data(
symbols=geom.symbols(C2H2CLF_GEO),
coordinates=geom.coordinates(C2H2CLF_GEO),
)
def test__is_valid():
""" test geom.is_valid
"""
# Check validity
assert geom.is_valid(C2H2CLF_GEO)
# with pytest.raises(ValueError):
# geom.is_valid(BAD_GEO)
# Check empty geom returns empty information
assert not geom.symbols(())
assert not geom.coordinates(())
