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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
00167
00168
00169 void throw_if_atom_duplicated(int begin=0, double tol = 1e-3);
00170 public:
00171 Molecule();
00172 Molecule(const Molecule&);
00173 Molecule(StateIn&);
00269 Molecule(const Ref<KeyVal>&input);
00270
00271 virtual ~Molecule();
00272
00273 Molecule& operator=(const Molecule&);
00274
00276 void add_atom(int Z,double x,double y,double z,
00277 const char * = 0, double mass = 0.0,
00278 int have_charge = 0, double charge = 0.0);
00279
00281 virtual void print(std::ostream& =ExEnv::out0()) const;
00282 virtual void print_parsedkeyval(std::ostream& =ExEnv::out0(),
00283 int print_pg = 1,
00284 int print_unit = 1,
00285 int number_atoms = 1) const;
00286
00288 int natom() const { return natoms_; }
00289
00290 int Z(int atom) const { return Z_[atom]; }
00291 double &r(int atom, int xyz) { return r_[atom][xyz]; }
00292 const double &r(int atom, int xyz) const { return r_[atom][xyz]; }
00293 double *r(int atom) { return r_[atom]; }
00294 const double *r(int atom) const { return r_[atom]; }
00295 double mass(int atom) const;
00298 const char *label(int atom) const;
00299
00302 int atom_at_position(double *, double tol = 0.05) const;
00303
00306 int atom_label_to_index(const char *label) const;
00307
00311 double *charges() const;
00312
00314 double charge(int iatom) const;
00315
00317 double nuclear_charge() const;
00318
00320 void set_point_group(const Ref<PointGroup>&, double tol=1.0e-7);
00322 Ref<PointGroup> point_group() const;
00323
00327 Ref<PointGroup> highest_point_group(double tol = 1.0e-8) const;
00328
00331 int is_axis(SCVector3 &origin,
00332 SCVector3 &udirection, int order, double tol=1.0e-8) const;
00333
00336 int is_plane(SCVector3 &origin, SCVector3 &uperp, double tol=1.0e-8) const;
00337
00339 int has_inversion(SCVector3 &origin, double tol = 1.0e-8) const;
00340
00342 int is_linear(double tolerance = 1.0e-5) const;
00344 int is_planar(double tolerance = 1.0e-5) const;
00347 void is_linear_planar(int&linear,int&planar,double tol = 1.0e-5) const;
00348
00351 SCVector3 center_of_mass() const;
00352
00354 double nuclear_repulsion_energy();
00355
00358 void nuclear_repulsion_1der(int center, double xyz[3]);
00359
00361 void nuclear_efield(const double *position, double* efield);
00362
00365 void nuclear_charge_efield(const double *charges,
00366 const double *position, double* efield);
00367
00373 void symmetrize(double tol = 0.5);
00374
00376 void symmetrize(const Ref<PointGroup> &pg, double tol = 0.5);
00377
00381 void cleanup_molecule(double tol = 0.1);
00382
00383 void translate(const double *r);
00384 void move_to_com();
00385 void transform_to_principal_axes(int trans_frame=1);
00386 void transform_to_symmetry_frame();
00387 void print_pdb(std::ostream& =ExEnv::out0(), char *title =0) const;
00388
00389 void read_pdb(const char *filename);
00390
00393 void principal_moments_of_inertia(double *evals, double **evecs=0) const;
00394
00396 int nunique() const { return nuniq_; }
00398 int unique(int iuniq) const { return equiv_[iuniq][0]; }
00400 int nequivalent(int iuniq) const { return nequiv_[iuniq]; }
00402 int equivalent(int iuniq, int j) const { return equiv_[iuniq][j]; }
00405 int atom_to_unique(int iatom) const { return atom_to_uniq_[iatom]; }
00408 int atom_to_unique_offset(int iatom) const;
00409
00411 int n_core_electrons();
00412
00414 int max_z();
00415
00417 Ref<AtomInfo> atominfo() const { return atominfo_; }
00418
00420 std::string atom_name(int iatom) const;
00421
00423 std::string atom_symbol(int iatom) const;
00424
00427 void set_include_q(bool iq) { include_q_ = iq; }
00429 bool include_q() const { return include_q_; }
00430
00433 void set_include_qq(bool iqq) { include_qq_ = iqq; }
00435 bool include_qq() const { return include_qq_; }
00436
00438 int n_q_atom() const { return q_atoms_.size(); }
00440 int q_atom(int i) const { return q_atoms_[i]; }
00441
00443 int n_non_q_atom() const { return non_q_atoms_.size(); }
00445 int non_q_atom(int i) const { return non_q_atoms_[i]; }
00446
00447 void save_data_state(StateOut&);
00448 };
00449
00450 }
00451
00452 #endif
00453
00454
00455
00456
00457