def getCentMass(self):
"""Gets the center of mass of the molecule."""
from BioNanoLEGO.DenseMatrix import zeros
self.cent_of_mass = zeros((3), "d")
total_mass = 0.0
for atom in self.atoms:
atom_mass = atom.getAtomcMass()
self.cent_of_mass += atom_mass * atom.getCoords()
total_mass += atom_mass
self.cent_of_mass /= total_mass
return
def getInertiaTensor(self):
"""Gets the moment of inertia tensor."""
from BioNanoLEGO.DenseMatrix import zeros, asmatrix
self.inertia_tensor = asmatrix(zeros((3, 3)), "d")
for atom in self.atoms:
atom_mass = atom.getAtomcMass()
x, y, z = atom.getCoords()
x2, y2, z2 = x * x, y * y, z * z
self.inertia_tensor[0, 0] += atom_mass * (y2 + z2)
self.inertia_tensor[1, 1] += atom_mass * (x2 + z2)
self.inertia_tensor[2, 2] += atom_mass * (x2 + y2)
self.inertia_tensor[0, 1] -= atom_mass * x * y
self.inertia_tensor[1, 0] = self.inertia_tensor[0, 1]
self.inertia_tensor[0, 2] -= atom_mass * x * z
self.inertia_tensor[2, 0] = self.inertia_tensor[0, 2]
self.inertia_tensor[1, 2] -= atom_mass * y * z
self.inertia_tensor[2, 1] = self.inertia_tensor[1, 2]
return
def __init__(self, name="molecule", atom_list=[], **options):
"""Creates a molecule.
name: The name of the molecule. Default is 'molecule'.
atom_list: A list of (atomic_symbol or atomic_number,(x,y,z)) of the molecule.
Default is [].
isotope_list: A list of isotope selection (atom_index,isotope), where the
atom index starts from 0. Default is the most abundant isotope.
unit: Length unit for the coordinates. Default is Bohr.
charge: The charge of the molecule. Default is 0.
multiplicity: The spin multiplicity of the molecule. Default is 1.
inertial_coord: Transforms the molecule to inertial coordinates, i.e.,
translating to let the center of mass be zero origin, and rotating
so that the moment of inertia tensor becomes a diagonal matrix.
Default is making such transformation.
"""
from BioNanoLEGO.Element import get_atomic_symbol, get_atomic_number
from BioNanoLEGO.DenseMatrix import asmatrix, zeros, eigh, diag
self.name = name
# Default is no pseudopotential
self.pseudopotential = False
unit = options.get("unit", "bohr")
unit = unit.lower()[:4]
if unit not in DEFINED_UNITS:
raise ValueError("Unknown length unit '%s'!" % unit)
self.charge = int(options.get("charge", 0))
self.multiplicity = int(options.get("multiplicity", 1))
inertial_coord = options.get("inertial_coord", True)
# Gets the user specified isotope selections
isotope_list = options.get("isotope_list", [])
# Initializes atoms
self.atoms = []
self.num_electrons = -int(self.charge)
if atom_list:
self.num_atoms = int(len(atom_list))
# Sets up the isotope selections
isotopes = [None] * self.num_atoms
for atom_idx, isotope in isotope_list:
isotopes[atom_idx] = int(isotope)
# Sets up the atoms
atom_idx = int(0)
for atomic_number, coords in atom_list:
if unit == "angs":
coords = angs_to_bhor(coords[0], coords[1], coords[2])
# The atomic symbol is given
if type(atomic_number) == type(""):
atom_name = atomic_number
atomic_number = get_atomic_number(atom_name)
# The atomic number is given
elif type(atomic_number) == type(0):
atom_name = get_atomic_symbol(atomic_number)
else:
raise TypeError("Atomic symbol or atomic number is expected for atom '%d'!" % atom_idx)
new_atom = Atom(atom_idx, atom_name, atomic_number, isotopes[atom_idx], coords)
self.atoms.append(new_atom)
self.num_electrons += new_atom.getNumElectrons()
atom_idx += 1
# Dumps coordinates
print "Coordinates: "
for atom in self.atoms:
print atom.getCoords()
# Gets the center of mass
self.getCentMass()
if inertial_coord:
print "Translating to center of mass: ", self.cent_of_mass
self.translate(-self.cent_of_mass)
self.cent_of_mass = zeros((3), "d")
# Gets the moment of inertia tensor
self.getInertiaTensor()
if inertial_coord:
E, U = eigh(self.inertia_tensor)
print "Rotation matrix: ", U
self.rotate(U)
self.inertia_tensor = asmatrix(diag(E))
print "New moment of inertia tensor: ", self.inertia_tensor
print "New coordinates: "
for atom in self.atoms:
print atom.getCoords()
else:
self.num_atoms = int(0)
return