MPQC
2.3.1
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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 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 // symmetry equiv info 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 // these are optional 00147 double *mass_; 00148 char **labels_; 00149 00150 // The Z that represents a "Q" type atom. 00151 int q_Z_; 00152 00153 // If true, include the q terms in the charge and efield routines 00154 bool include_q_; 00155 00156 // If true, include the coupling between q-q pairs when 00157 // computing nuclear repulsion energy and gradients. 00158 bool include_qq_; 00159 00160 // These vectors contain the atom indices of atoms that are not type 00161 // "Q" and those that are. 00162 std::vector<int> q_atoms_; 00163 std::vector<int> non_q_atoms_; 00164 00165 void clear(); 00166 00167 // Throw an exception if an atom is duplicated. The 00168 // atoms in the range [begin, natom_) are checked. 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 00355 SCVector3 center_of_charge() const; 00356 00358 double nuclear_repulsion_energy(); 00359 00362 void nuclear_repulsion_1der(int center, double xyz[3]); 00363 00365 void nuclear_efield(const double *position, double* efield); 00366 00369 void nuclear_charge_efield(const double *charges, 00370 const double *position, double* efield); 00371 00377 void symmetrize(double tol = 0.5); 00378 00380 void symmetrize(const Ref<PointGroup> &pg, double tol = 0.5); 00381 00385 void cleanup_molecule(double tol = 0.1); 00386 00387 void translate(const double *r); 00388 void move_to_com(); 00389 void transform_to_principal_axes(int trans_frame=1); 00390 void transform_to_symmetry_frame(); 00391 void print_pdb(std::ostream& =ExEnv::out0(), char *title =0) const; 00392 00393 void read_pdb(const char *filename); 00394 00397 void principal_moments_of_inertia(double *evals, double **evecs=0) const; 00398 00400 int nunique() const { return nuniq_; } 00402 int unique(int iuniq) const { return equiv_[iuniq][0]; } 00404 int nequivalent(int iuniq) const { return nequiv_[iuniq]; } 00406 int equivalent(int iuniq, int j) const { return equiv_[iuniq][j]; } 00409 int atom_to_unique(int iatom) const { return atom_to_uniq_[iatom]; } 00412 int atom_to_unique_offset(int iatom) const; 00413 00415 int n_core_electrons(); 00416 00418 int max_z(); 00419 00421 Ref<AtomInfo> atominfo() const { return atominfo_; } 00422 00424 std::string atom_name(int iatom) const; 00425 00427 std::string atom_symbol(int iatom) const; 00428 00431 void set_include_q(bool iq) { include_q_ = iq; } 00433 bool include_q() const { return include_q_; } 00434 00437 void set_include_qq(bool iqq) { include_qq_ = iqq; } 00439 bool include_qq() const { return include_qq_; } 00440 00442 int n_q_atom() const { return q_atoms_.size(); } 00444 int q_atom(int i) const { return q_atoms_[i]; } 00445 00447 int n_non_q_atom() const { return non_q_atoms_.size(); } 00449 int non_q_atom(int i) const { return non_q_atoms_[i]; } 00450 00451 void save_data_state(StateOut&); 00452 }; 00453 00454 } 00455 00456 #endif 00457 00458 // Local Variables: 00459 // mode: c++ 00460 // c-file-style: "CLJ" 00461 // End: