rmgpy.cantherm.geometry.Geometry

class rmgpy.cantherm.geometry.Geometry(coordinates, number, mass)

The three-dimensional geometry of a molecular configuration. The attributes are:

Attribute Type Description
coordinates numpy.ndarray An N x 3 array containing the 3D coordinates of each atom
number numpy.ndarray An array containing the integer atomic number of each atom
mass numpy.ndarray An array containing the atomic mass in kg/mol of each atom

The integer index of each atom is consistent across all three attributes.

getCenterOfMass(atoms=None)

Calculate and return the [three-dimensional] position of the center of mass of the current geometry. If a list atoms of atoms is specified, only those atoms will be used to calculate the center of mass. Otherwise, all atoms will be used.

getInternalReducedMomentOfInertia(pivots, top1)

Calculate and return the reduced moment of inertia for an internal torsional rotation around the axis defined by the two atoms in pivots. The list top1 contains the atoms that should be considered as part of the rotating top; this list should contain the pivot atom connecting the top to the rest of the molecule. The procedure used is that of Pitzer [1], which is described as \(I^{(2,3)}\) by East and Radom [2]. In this procedure, the molecule is divided into two tops: those at either end of the hindered rotor bond. The moment of inertia of each top is evaluated using an axis passing through the center of mass of both tops. Finally, the reduced moment of inertia is evaluated from the moment of inertia of each top via the formula

\[\frac{1}{I^{(2,3)}} = \frac{1}{I_1} + \frac{1}{I_2}\]
[1]Pitzer, K. S. J. Chem. Phys. 14, p. 239-243 (1946).
[2]East, A. L. L. and Radom, L. J. Chem. Phys. 106, p. 6655-6674 (1997).
getMomentOfInertiaTensor()

Calculate and return the moment of inertia tensor for the current geometry in kg*m^2. If the coordinates are not at the center of mass, they are temporarily shifted there for the purposes of this calculation.

getPrincipalMomentsOfInertia()

Calculate and return the principal moments of inertia and corresponding principal axes for the current geometry. The moments of inertia are in kg*m^2, while the principal axes have unit length.

getTotalMass(atoms=None)

Calculate and return the total mass of the atoms in the geometry in kg/mol. If a list atoms of atoms is specified, only those atoms will be used to calculate the center of mass. Otherwise, all atoms will be used.