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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
00127 class Molecule: public SavableState
00128 {
00129 protected:
00130 int natoms_;
00131 Ref<AtomInfo> atominfo_;
00132 Ref<PointGroup> pg_;
00133 Ref<Units> geometry_units_;
00134 double **r_;
00135 int *Z_;
00136 double *charges_;
00137
00138
00139 int nuniq_;
00140 int *nequiv_;
00141 int **equiv_;
00142 int *atom_to_uniq_;
00143 void init_symmetry_info(double tol=0.5);
00144 void clear_symmetry_info();
00145
00146
00147 double *mass_;
00148 char **labels_;
00149
00150
00151 int q_Z_;
00152
00153
00154 bool include_q_;
00155
00156
00157
00158 bool include_qq_;
00159
00160
00161
00162 std::vector<int> q_atoms_;
00163 std::vector<int> non_q_atoms_;
00164
00165 void clear();
00166 public:
00167 Molecule();
00168 Molecule(const Molecule&);
00169 Molecule(StateIn&);
00171 Molecule(const Ref<KeyVal>&input);
00172
00173 virtual ~Molecule();
00174
00175 Molecule& operator=(const Molecule&);
00176
00178 void add_atom(int Z,double x,double y,double z,
00179 const char * = 0, double mass = 0.0,
00180 int have_charge = 0, double charge = 0.0);
00181
00183 virtual void print(std::ostream& =ExEnv::out0()) const;
00184 virtual void print_parsedkeyval(std::ostream& =ExEnv::out0(),
00185 int print_pg = 1,
00186 int print_unit = 1,
00187 int number_atoms = 1) const;
00188
00190 int natom() const { return natoms_; }
00191
00192 int Z(int atom) const { return Z_[atom]; }
00193 double &r(int atom, int xyz) { return r_[atom][xyz]; }
00194 const double &r(int atom, int xyz) const { return r_[atom][xyz]; }
00195 double *r(int atom) { return r_[atom]; }
00196 const double *r(int atom) const { return r_[atom]; }
00197 double mass(int atom) const;
00200 const char *label(int atom) const;
00201
00204 int atom_at_position(double *, double tol = 0.05) const;
00205
00208 int atom_label_to_index(const char *label) const;
00209
00213 double *charges() const;
00214
00216 double charge(int iatom) const;
00217
00219 double nuclear_charge() const;
00220
00222 void set_point_group(const Ref<PointGroup>&, double tol=1.0e-7);
00224 Ref<PointGroup> point_group() const;
00225
00229 Ref<PointGroup> highest_point_group(double tol = 1.0e-8) const;
00230
00233 int is_axis(SCVector3 &origin,
00234 SCVector3 &udirection, int order, double tol=1.0e-8) const;
00235
00238 int is_plane(SCVector3 &origin, SCVector3 &uperp, double tol=1.0e-8) const;
00239
00241 int has_inversion(SCVector3 &origin, double tol = 1.0e-8) const;
00242
00244 int is_linear(double tolerance = 1.0e-5) const;
00246 int is_planar(double tolerance = 1.0e-5) const;
00249 void is_linear_planar(int&linear,int&planar,double tol = 1.0e-5) const;
00250
00253 SCVector3 center_of_mass() const;
00254
00256 double nuclear_repulsion_energy();
00257
00260 void nuclear_repulsion_1der(int center, double xyz[3]);
00261
00263 void nuclear_efield(const double *position, double* efield);
00264
00267 void nuclear_charge_efield(const double *charges,
00268 const double *position, double* efield);
00269
00275 void symmetrize(double tol = 0.5);
00276
00278 void symmetrize(const Ref<PointGroup> &pg, double tol = 0.5);
00279
00283 void cleanup_molecule(double tol = 0.1);
00284
00285 void translate(const double *r);
00286 void move_to_com();
00287 void transform_to_principal_axes(int trans_frame=1);
00288 void transform_to_symmetry_frame();
00289 void print_pdb(std::ostream& =ExEnv::out0(), char *title =0) const;
00290
00291 void read_pdb(const char *filename);
00292
00295 void principal_moments_of_inertia(double *evals, double **evecs=0) const;
00296
00298 int nunique() const { return nuniq_; }
00300 int unique(int iuniq) const { return equiv_[iuniq][0]; }
00302 int nequivalent(int iuniq) const { return nequiv_[iuniq]; }
00304 int equivalent(int iuniq, int j) const { return equiv_[iuniq][j]; }
00307 int atom_to_unique(int iatom) const { return atom_to_uniq_[iatom]; }
00310 int atom_to_unique_offset(int iatom) const;
00311
00313 int n_core_electrons();
00314
00316 int max_z();
00317
00319 Ref<AtomInfo> atominfo() const { return atominfo_; }
00320
00322 std::string atom_name(int iatom) const;
00323
00325 std::string atom_symbol(int iatom) const;
00326
00329 void set_include_q(bool iq) { include_q_ = iq; }
00331 bool include_q() const { return include_q_; }
00332
00335 void set_include_qq(bool iqq) { include_qq_ = iqq; }
00337 bool include_qq() const { return include_qq_; }
00338
00340 int n_q_atom() const { return q_atoms_.size(); }
00342 int q_atom(int i) const { return q_atoms_[i]; }
00343
00345 int n_non_q_atom() const { return non_q_atoms_.size(); }
00347 int non_q_atom(int i) const { return non_q_atoms_[i]; }
00348
00349 void save_data_state(StateOut&);
00350 };
00351
00352 }
00353
00354 #endif
00355
00356
00357
00358
00359