#include <molecule.h>
Public Member Functions | |
| void | init_with_chkpt (shared_ptr< PSIO > psio) |
| Pull information from a chkpt object created from psio. | |
| void | init_with_chkpt (shared_ptr< Chkpt > chkpt) |
| Pull information from the chkpt object passed. | |
| void | add_atom (int Z, double x, double y, double z, const char *=0, double mass=0.0, int have_charge=0, double charge=0.0) |
| Add an atom to the molecule. | |
| int | natom () const |
| Number of atoms. | |
| int | Z (int atom) const |
| Nuclear charge of atom. | |
| double | x (int atom) const |
| double | y (int atom) const |
| double | z (int atom) const |
| const atom_info & | r (int atom) const |
| Return reference to atom_info struct for atom. | |
| atom_info | r (int atom) |
| Return copy of atom_info for atom. | |
| const Vector3 | xyz (int atom) const |
| Returns a Vector3 with x, y, z position of atom. | |
| double | mass (int atom) const |
| Returns mass atom atom. | |
| const std::string | label (int atom) const |
| Returns label of atom. | |
| double | charge (int atom) const |
| Returns charge of atom. | |
| int | atom_at_position (double *, double tol=0.05) const |
| Tests to see of an atom is at the passed position with a given tolerance. | |
| Vector3 | center_of_mass () const |
| Computes center of mass of molecule (does not translate molecule). | |
| double | nuclear_repulsion_energy () |
| Computes nuclear repulsion energy. | |
| SimpleVector | nuclear_repulsion_energy_deriv1 () |
| Computes nuclear repulsion energy derivatives. Free with delete[]. | |
| SimpleMatrix * | nuclear_repulsion_energy_deriv2 () |
| Computes nuclear repulsion energy second derivatives. | |
| SimpleVector | nuclear_dipole_contribution () |
| Returns the nuclear contribution to the dipole moment. | |
| SimpleVector | nuclear_quadrupole_contribution () |
| Returns the nuclear contribution to the quadrupole moment. | |
| void | translate (const Vector3 &r) |
| Translates molecule by r. | |
| void | move_to_com () |
| Moves molecule to center of mass. | |
| SimpleMatrix * | inertia_tensor () |
| Compute inertia tensor. | |
| int | nirrep () const |
| Returns the number of irreps. | |
| void | nirrep (int nirreps) |
| Sets the number of irreps. | |
| void | print (FILE *out=outfile) |
| Print the molecule. | |
Protected Member Functions | |
| void | clear () |
| Zero it out. | |
Protected Attributes | |
| int | natoms_ |
| Number of atoms. | |
| std::vector< atom_info > | atoms_ |
| Atom info vector. | |
| int | nirreps_ |
| Symmetry information about the molecule. | |
Classes | |
| struct | atom_info |
1.5.6