Main Page Class Hierarchy Compound List File List Compound Members Related Pages

# molecule.h

    00001 //
    00002 // molecule.h
    00003 //
    00004 // Copyright (C) 1996 Limit Point Systems, Inc.
    00005 //
    00006 // Author: Curtis Janssen <cljanss@limitpt.com>
    00007 // Maintainer: LPS
    00008 //
    00009 // This file is part of the SC Toolkit.
    00010 //
    00011 // The SC Toolkit is free software; you can redistribute it and/or modify
    00012 // it under the terms of the GNU Library General Public License as published by
    00013 // the Free Software Foundation; either version 2, or (at your option)
    00014 // any later version.
    00015 //
    00016 // The SC Toolkit is distributed in the hope that it will be useful,
    00017 // but WITHOUT ANY WARRANTY; without even the implied warranty of
    00018 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    00019 // GNU Library General Public License for more details.
    00020 //
    00021 // You should have received a copy of the GNU Library General Public License
    00022 // along with the SC Toolkit; see the file COPYING.LIB.  If not, write to
    00023 // the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.
    00024 //
    00025 // The U.S. Government is granted a limited license as per AL 91-7.
    00026 //
    00027
    00028 #ifndef _chemistry_molecule_molecule_h
    00029 #define _chemistry_molecule_molecule_h
    00030
    00031 #ifdef __GNUC__
    00032 #pragma interface
    00033 #endif
    00034
    00035 #include <stdio.h>
    00036 #include <iostream>
    00037 #include <util/class/class.h>
    00038 #include <util/state/state.h>
    00039 #include <util/keyval/keyval.h>
    00040 #include <util/misc/units.h>
    00041 #include <math/symmetry/pointgrp.h>
    00042 #include <math/scmat/vector3.h>
    00043 #include <math/scmat/matrix.h>
    00044 #include <chemistry/molecule/atominfo.h>
    00045
    00046 namespace sc {
    00047
    00099 class Molecule: public SavableState
    00100 {
    00101   protected:
    00102     int natoms_;
    00103     Ref<AtomInfo> atominfo_;
    00104     Ref<PointGroup> pg_;
    00105     Ref<Units> geometry_units_;
    00106     double **r_;
    00107     int *Z_;
    00108     double *charges_;
    00109
    00110     // symmetry equiv info
    00111     int nuniq_;
    00112     int *nequiv_;
    00113     int **equiv_;
    00114     int *atom_to_uniq_;
    00115     void init_symmetry_info(double tol=0.5);
    00116     void clear_symmetry_info();
    00117
    00118     // these are optional
    00119     double *mass_;
    00120     char **labels_;
    00121
    00122     void clear();
    00123   public:
    00124     Molecule();
    00125     Molecule(const Molecule&);
    00126     Molecule(StateIn&);
    00128     Molecule(const Ref<KeyVal>&input);
    00129
    00130     virtual ~Molecule();
    00131
    00132     Molecule& operator=(const Molecule&);
    00133
    00135     void add_atom(int Z,double x,double y,double z,
    00136                   const char * = 0, double mass = 0.0,
    00137                   int have_charge = 0, double charge = 0.0);
    00138
    00140     virtual void print(std::ostream& =ExEnv::out0()) const;
    00141     virtual void print_parsedkeyval(std::ostream& =ExEnv::out0(),
    00142                                     int print_pg = 1,
    00143                                     int print_unit = 1,
    00144                                     int number_atoms = 1) const;
    00145
    00147     int natom() const { return natoms_; }
    00148
    00149     int Z(int atom) const { return Z_[atom]; }
    00150     double &r(int atom, int xyz) { return r_[atom][xyz]; }
    00151     const double &r(int atom, int xyz) const { return r_[atom][xyz]; }
    00152     double *r(int atom) { return r_[atom]; }
    00153     const double *r(int atom) const { return r_[atom]; }
    00154     double mass(int atom) const;
    00157     const char *label(int atom) const;
    00158
    00161     int atom_at_position(double *, double tol = 0.05) const;
    00162
    00165     int atom_label_to_index(const char *label) const;
    00166
    00170     double *charges() const;
    00171
    00173     double charge(int iatom) const;
    00174
    00176     double nuclear_charge() const;
    00177
    00179     void set_point_group(const Ref<PointGroup>&, double tol=1.0e-7);
    00181     Ref<PointGroup> point_group() const;
    00182
    00186     Ref<PointGroup> highest_point_group(double tol = 1.0e-8) const;
    00187
    00190     int is_axis(SCVector3 &origin,
    00191                 SCVector3 &udirection, int order, double tol=1.0e-8) const;
    00192
    00195     int is_plane(SCVector3 &origin, SCVector3 &uperp, double tol=1.0e-8) const;
    00196
    00198     int has_inversion(SCVector3 &origin, double tol = 1.0e-8) const;
    00199
    00201     int is_linear(double tolerance = 1.0e-5) const;
    00203     int is_planar(double tolerance = 1.0e-5) const;
    00206     void is_linear_planar(int&linear,int&planar,double tol = 1.0e-5) const;
    00207
    00210     SCVector3 center_of_mass() const;
    00211
    00213     double nuclear_repulsion_energy();
    00214
    00217     void nuclear_repulsion_1der(int center, double xyz[3]);
    00218
    00220     void nuclear_efield(const double *position, double* efield);
    00221
    00224     void nuclear_charge_efield(const double *charges,
    00225                                const double *position, double* efield);
    00226
    00232     void symmetrize(double tol = 0.5);
    00233
    00235     void symmetrize(const Ref<PointGroup> &pg, double tol = 0.5);
    00236
    00240     void cleanup_molecule(double tol = 0.1);
    00241
    00242     void translate(const double *r);
    00243     void move_to_com();
    00244     void transform_to_principal_axes(int trans_frame=1);
    00245     void transform_to_symmetry_frame();
    00246     void print_pdb(std::ostream& =ExEnv::out0(), char *title =0) const;
    00247
    00248     void read_pdb(const char *filename);
    00249
    00252     void principal_moments_of_inertia(double *evals, double **evecs=0) const;
    00253
    00255     int nunique() const { return nuniq_; }
    00257     int unique(int iuniq) const { return equiv_[iuniq][0]; }
    00259     int nequivalent(int iuniq) const { return nequiv_[iuniq]; }
    00261     int equivalent(int iuniq, int j) const { return equiv_[iuniq][j]; }
    00264     int atom_to_unique(int iatom) const { return atom_to_uniq_[iatom]; }
    00267     int atom_to_unique_offset(int iatom) const;
    00268
    00270     int n_core_electrons();
    00271
    00273     int max_z();
    00274
    00276     Ref<AtomInfo> atominfo() const { return atominfo_; }
    00277
    00278     void save_data_state(StateOut&);
    00279 };
    00280
    00281 }
    00282
    00283 #endif
    00284
    00285 // Local Variables:
    00286 // mode: c++
    00287 // c-file-style: "CLJ"
    00288 // End: