def test_get_atomic_mass(self):
"""Test of the periodic_table.atomic_mass() method."""
# Check the proton weight.
weight = periodic_table.atomic_mass(id='H')
self.assertEqual(weight, 1.007975)
# Check the 1H weight.
weight = periodic_table.atomic_mass(id='1H')
self.assertEqual(weight, 1.0078250322)
# Check the 2H weight.
weight = periodic_table.atomic_mass(id='2H')
self.assertEqual(weight, 2.0141017781)
def test_get_atomic_mass(self):
"""Test of the periodic_table.atomic_mass() method."""
# Check the proton weight.
weight = periodic_table.atomic_mass(id="H")
self.assertEqual(weight, 1.007975)
# Check the 1H weight.
weight = periodic_table.atomic_mass(id="1H")
self.assertEqual(weight, 1.0078250322)
# Check the 2H weight.
weight = periodic_table.atomic_mass(id="2H")
self.assertEqual(weight, 2.0141017781)
def centre_of_mass(pos=None, elements=None, verbosity=1):
"""Calculate and return the centre of mass for the given atomic coordinates.
@keyword pos: The list of atomic coordinates.
@type pos: list of lists of float
@keyword elements: The list of elements corresponding to the atoms.
@type elements: list of str
@keyword verbosity: The amount of text to print out. 0 results in no printouts, 1 the full amount.
@type verbosity: int
@return: The centre of mass vector and the mass.
@rtype: 3D list of floats, float
"""
# Print out.
if verbosity:
print("Calculating the centre of mass.")
# Initialise the centre of mass.
R = zeros(3, float64)
# Initialise the total mass.
M = 0.0
# Loop over all atoms.
for i in range(len(pos)):
# Atomic mass.
try:
mass = periodic_table.atomic_mass(elements[i])
except RelaxError:
warn(
RelaxWarning(
"Skipping the atom index %s as the element '%s' is unknown."
% (i, elements[i])))
# Total mass.
M = M + mass
# Sum of mass * position.
R = R + mass * pos[i]
# Normalise.
R = R / M
# Final printout.
if verbosity:
print(" Total mass: M = " + repr(M))
print(" Centre of mass: R = " + repr(R))
# Return the centre of mass and total mass
return R, M
def centre_of_mass(pos=None, elements=None, verbosity=1):
"""Calculate and return the centre of mass for the given atomic coordinates.
@keyword pos: The list of atomic coordinates.
@type pos: list of lists of float
@keyword elements: The list of elements corresponding to the atoms.
@type elements: list of str
@keyword verbosity: The amount of text to print out. 0 results in no printouts, 1 the full amount.
@type verbosity: int
@return: The centre of mass vector and the mass.
@rtype: 3D list of floats, float
"""
# Print out.
if verbosity:
print("Calculating the centre of mass.")
# Initialise the centre of mass.
R = zeros(3, float64)
# Initialise the total mass.
M = 0.0
# Loop over all atoms.
for i in range(len(pos)):
# Atomic mass.
try:
mass = periodic_table.atomic_mass(elements[i])
except RelaxError:
warn(RelaxWarning("Skipping the atom index %s as the element '%s' is unknown." % (i, elements[i])))
# Total mass.
M = M + mass
# Sum of mass * position.
R = R + mass * pos[i]
# Normalise.
R = R / M
# Final printout.
if verbosity:
print(" Total mass: M = " + repr(M))
print(" Centre of mass: R = " + repr(R))
# Return the centre of mass and total mass
return R, M
