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molecule.h // // molecule.h // // Copyright (C) 1996 Limit Point Systems, Inc. // // Author: Curtis Janssen <cljanss@limitpt.com> // Maintainer: LPS // // This file is part of the SC Toolkit. // // The SC Toolkit is free software; you can redistribute it and/or modify // it under the terms of the GNU Library General Public License as published by // the Free Software Foundation; either version 2, or (at your option) // any later version. // // The SC Toolkit is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU Library General Public License for more details. // // You should have received a copy of the GNU Library General Public License // along with the SC Toolkit; see the file COPYING.LIB. If not, write to // the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA. // // The U.S. Government is granted a limited license as per AL 91-7. // #ifndef _chemistry_molecule_molecule_h #define _chemistry_molecule_molecule_h #ifdef __GNUC__ #pragma interface #endif #include <stdio.h> #include <iostream> #include <util/class/class.h> #include <util/state/state.h> #include <util/keyval/keyval.h> #include <util/misc/units.h> #include <math/symmetry/pointgrp.h> #include <math/scmat/vector3.h> #include <math/scmat/matrix.h> #include <chemistry/molecule/atominfo.h> namespace sc { class Molecule: public SavableState { protected: int natoms_; Ref<AtomInfo> atominfo_; Ref<PointGroup> pg_; Ref<Units> geometry_units_; double **r_; int *Z_; double *charges_; // symmetry equiv info int nuniq_; int *nequiv_; int **equiv_; int *atom_to_uniq_; void init_symmetry_info(double tol=0.5); void clear_symmetry_info(); // these are optional double *mass_; char **labels_; void clear(); public: Molecule(); Molecule(const Molecule&); Molecule(StateIn&); Molecule(const Ref<KeyVal>&input); virtual ~Molecule(); Molecule& operator=(const Molecule&); 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); virtual void print(std::ostream& =ExEnv::out0()) const; virtual void print_parsedkeyval(std::ostream& =ExEnv::out0(), int print_pg = 1, int print_unit = 1, int number_atoms = 1) const; int natom() const { return natoms_; } int Z(int atom) const { return Z_[atom]; } double &r(int atom, int xyz) { return r_[atom][xyz]; } const double &r(int atom, int xyz) const { return r_[atom][xyz]; } double *r(int atom) { return r_[atom]; } const double *r(int atom) const { return r_[atom]; } double mass(int atom) const; const char *label(int atom) const; int atom_at_position(double *, double tol = 0.05) const; int atom_label_to_index(const char *label) const; double *charges() const; double charge(int iatom) const; double nuclear_charge() const; void set_point_group(const Ref<PointGroup>&, double tol=1.0e-7); Ref<PointGroup> point_group() const; Ref<PointGroup> highest_point_group(double tol = 1.0e-8) const; int is_axis(SCVector3 &origin, SCVector3 &udirection, int order, double tol=1.0e-8) const; int is_plane(SCVector3 &origin, SCVector3 &uperp, double tol=1.0e-8) const; int has_inversion(SCVector3 &origin, double tol = 1.0e-8) const; int is_linear(double tolerance = 1.0e-5) const; int is_planar(double tolerance = 1.0e-5) const; void is_linear_planar(int&linear,int&planar,double tol = 1.0e-5) const; SCVector3 center_of_mass() const; double nuclear_repulsion_energy(); void nuclear_repulsion_1der(int center, double xyz[3]); void nuclear_efield(const double *position, double* efield); void nuclear_charge_efield(const double *charges, const double *position, double* efield); void symmetrize(double tol = 0.5); void symmetrize(const Ref<PointGroup> &pg, double tol = 0.5); void cleanup_molecule(double tol = 0.1); void translate(const double *r); void move_to_com(); void transform_to_principal_axes(int trans_frame=1); void transform_to_symmetry_frame(); void print_pdb(std::ostream& =ExEnv::out0(), char *title =0) const; void read_pdb(const char *filename); void principal_moments_of_inertia(double *evals, double **evecs=0) const; int nunique() const { return nuniq_; } int unique(int iuniq) const { return equiv_[iuniq][0]; } int nequivalent(int iuniq) const { return nequiv_[iuniq]; } int equivalent(int iuniq, int j) const { return equiv_[iuniq][j]; } int atom_to_unique(int iatom) const { return atom_to_uniq_[iatom]; } int atom_to_unique_offset(int iatom) const; int n_core_electrons(); int max_z(); Ref<AtomInfo> atominfo() const { return atominfo_; } void save_data_state(StateOut&); }; } #endif // Local Variables: // mode: c++ // c-file-style: "CLJ" // End: