MPQC 2.3.1

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molecule.h
1 //
2 // molecule.h
3 //
4 // Copyright (C) 1996 Limit Point Systems, Inc.
5 //
6 // Author: Curtis Janssen <cljanss@limitpt.com>
7 // Maintainer: LPS
8 //
9 // This file is part of the SC Toolkit.
10 //
11 // The SC Toolkit is free software; you can redistribute it and/or modify
12 // it under the terms of the GNU Library General Public License as published by
13 // the Free Software Foundation; either version 2, or (at your option)
14 // any later version.
15 //
16 // The SC Toolkit is distributed in the hope that it will be useful,
17 // but WITHOUT ANY WARRANTY; without even the implied warranty of
18 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
19 // GNU Library General Public License for more details.
20 //
21 // You should have received a copy of the GNU Library General Public License
22 // along with the SC Toolkit; see the file COPYING.LIB. If not, write to
23 // the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.
24 //
25 // The U.S. Government is granted a limited license as per AL 91-7.
26 //
27
28 #ifndef _chemistry_molecule_molecule_h
29 #define _chemistry_molecule_molecule_h
30
31 #ifdef __GNUC__
32 #pragma interface
33 #endif
34
35 #include <stdio.h>
36 #include <iostream>
37 #include <util/class/class.h>
38 #include <util/state/state.h>
39 #include <util/keyval/keyval.h>
40 #include <util/misc/units.h>
41 #include <math/symmetry/pointgrp.h>
42 #include <math/scmat/vector3.h>
43 #include <math/scmat/matrix.h>
44 #include <chemistry/molecule/atominfo.h>
45
46 namespace sc {
47
127 class Molecule: public SavableState
128 {
129 protected:
130 int natoms_;
131 Ref<AtomInfo> atominfo_;
132 Ref<PointGroup> pg_;
133 Ref<Units> geometry_units_;
134 double **r_;
135 int *Z_;
136 double *charges_;
137
138 // symmetry equiv info
139 int nuniq_;
140 int *nequiv_;
141 int **equiv_;
142 int *atom_to_uniq_;
143 void init_symmetry_info(double tol=0.5);
144 void clear_symmetry_info();
145
146 // these are optional
147 double *mass_;
148 char **labels_;
149
150 // The Z that represents a "Q" type atom.
151 int q_Z_;
152
153 // If true, include the q terms in the charge and efield routines
154 bool include_q_;
155
156 // If true, include the coupling between q-q pairs when
157 // computing nuclear repulsion energy and gradients.
158 bool include_qq_;
159
160 // These vectors contain the atom indices of atoms that are not type
161 // "Q" and those that are.
162 std::vector<int> q_atoms_;
163 std::vector<int> non_q_atoms_;
164
165 void clear();
166
167 // Throw an exception if an atom is duplicated. The
168 // atoms in the range [begin, natom_) are checked.
169 void throw_if_atom_duplicated(int begin=0, double tol = 1e-3);
170 public:
171 Molecule();
172 Molecule(const Molecule&);
173 Molecule(StateIn&);
269 Molecule(const Ref<KeyVal>&input);
270
271 virtual ~Molecule();
272
273 Molecule& operator=(const Molecule&);
274
276 void add_atom(int Z,double x,double y,double z,
277 const char * = 0, double mass = 0.0,
278 int have_charge = 0, double charge = 0.0);
279
281 virtual void print(std::ostream& =ExEnv::out0()) const;
282 virtual void print_parsedkeyval(std::ostream& =ExEnv::out0(),
283 int print_pg = 1,
284 int print_unit = 1,
285 int number_atoms = 1) const;
286
288 int natom() const { return natoms_; }
289
290 int Z(int atom) const { return Z_[atom]; }
291 double &r(int atom, int xyz) { return r_[atom][xyz]; }
292 const double &r(int atom, int xyz) const { return r_[atom][xyz]; }
293 double *r(int atom) { return r_[atom]; }
294 const double *r(int atom) const { return r_[atom]; }
295 double mass(int atom) const;
298 const char *label(int atom) const;
299
302 int atom_at_position(double *, double tol = 0.05) const;
303
306 int atom_label_to_index(const char *label) const;
307
311 double *charges() const;
312
314 double charge(int iatom) const;
315
317 double nuclear_charge() const;
318
320 void set_point_group(const Ref<PointGroup>&, double tol=1.0e-7);
322 Ref<PointGroup> point_group() const;
323
327 Ref<PointGroup> highest_point_group(double tol = 1.0e-8) const;
328
331 int is_axis(SCVector3 &origin,
332 SCVector3 &udirection, int order, double tol=1.0e-8) const;
333
336 int is_plane(SCVector3 &origin, SCVector3 &uperp, double tol=1.0e-8) const;
337
339 int has_inversion(SCVector3 &origin, double tol = 1.0e-8) const;
340
342 int is_linear(double tolerance = 1.0e-5) const;
344 int is_planar(double tolerance = 1.0e-5) const;
347 void is_linear_planar(int&linear,int&planar,double tol = 1.0e-5) const;
348
351 SCVector3 center_of_mass() const;
352
355 SCVector3 center_of_charge() const;
356
358 double nuclear_repulsion_energy();
359
362 void nuclear_repulsion_1der(int center, double xyz[3]);
363
365 void nuclear_efield(const double *position, double* efield);
366
369 void nuclear_charge_efield(const double *charges,
370 const double *position, double* efield);
371
377 void symmetrize(double tol = 0.5);
378
380 void symmetrize(const Ref<PointGroup> &pg, double tol = 0.5);
381
385 void cleanup_molecule(double tol = 0.1);
386
387 void translate(const double *r);
388 void move_to_com();
389 void transform_to_principal_axes(int trans_frame=1);
390 void transform_to_symmetry_frame();
391 void print_pdb(std::ostream& =ExEnv::out0(), char *title =0) const;
392
393 void read_pdb(const char *filename);
394
397 void principal_moments_of_inertia(double *evals, double **evecs=0) const;
398
400 int nunique() const { return nuniq_; }
402 int unique(int iuniq) const { return equiv_[iuniq][0]; }
404 int nequivalent(int iuniq) const { return nequiv_[iuniq]; }
406 int equivalent(int iuniq, int j) const { return equiv_[iuniq][j]; }
409 int atom_to_unique(int iatom) const { return atom_to_uniq_[iatom]; }
412 int atom_to_unique_offset(int iatom) const;
413
415 int n_core_electrons();
416
418 int max_z();
419
421 Ref<AtomInfo> atominfo() const { return atominfo_; }
422
424 std::string atom_name(int iatom) const;
425
427 std::string atom_symbol(int iatom) const;
428
431 void set_include_q(bool iq) { include_q_ = iq; }
433 bool include_q() const { return include_q_; }
434
437 void set_include_qq(bool iqq) { include_qq_ = iqq; }
439 bool include_qq() const { return include_qq_; }
440
442 int n_q_atom() const { return q_atoms_.size(); }
444 int q_atom(int i) const { return q_atoms_[i]; }
445
447 int n_non_q_atom() const { return non_q_atoms_.size(); }
449 int non_q_atom(int i) const { return non_q_atoms_[i]; }
450
451 void save_data_state(StateOut&);
452 };
453
454 }
455
456 #endif
457
458 // Local Variables:
459 // mode: c++
460 // c-file-style: "CLJ"
461 // End: