MPQC  3.0.0-alpha
bem.h
1 //
2 // bem.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_solvent_bem_h
29 #define _chemistry_solvent_bem_h
30 
31 #include <util/class/class.h>
32 #include <util/state/state.h>
33 #include <util/keyval/keyval.h>
34 #include <math/isosurf/volume.h>
35 #include <math/isosurf/surf.h>
36 #include <math/scmat/matrix.h>
37 #include <chemistry/molecule/molecule.h>
38 
39 namespace sc {
40 
41 // This represents a solvent by a polarization charge on a dielectric
42 // boundary surface.
43 class BEMSolvent: public DescribedClass {
44  private:
45  int debug_;
46 
47  Ref<Molecule> solute_;
48  Ref<Molecule> solvent_;
49  double solvent_density_;
50  double dielectric_constant_;
51  Ref<SCMatrixKit> matrixkit_;
52  RefSCMatrix system_matrix_i_;
53  double f_;
54  Ref<MessageGrp> grp_;
55 
56  double area_;
57  double volume_;
58  double computed_enclosed_charge_;
59  double edisp_;
60  double erep_;
61 
63 
64  double** alloc_array(int n, int m);
65  void free_array(double**);
66 
67  // This holds the area associated with each vertex. It is used
68  // to convert charges to charge densities and back.
69  double* vertex_area_;
70 
71  // Given charges compute surface charge density.
72  void charges_to_surface_charge_density(double *charges);
73 
74  // Given surface charge density compute charges.
75  void surface_charge_density_to_charges(double *charges);
76  public:
77  BEMSolvent(const Ref<KeyVal>&);
78  virtual ~BEMSolvent();
79 
80  // This should be called after everything is setup--the
81  // molecule has the correct the geometry and all of the
82  // parameters have been adjusted.
83  void init();
84  // This gets rid of the system matrix inverse and, optionally, the surface.
85  void done(int clear_surface = 1);
86 
87  int ncharge() { return surf_->nvertex(); }
88 
89  Ref<Molecule> solvent() { return solvent_ ;}
90  double solvent_density() { return solvent_density_ ;}
91 
92  // NOTE: call allocation routines after init and free routines before done
93  double** alloc_charge_positions() { return alloc_array(ncharge(), 3); }
94  void free_charge_positions(double**a) { free_array(a); }
95 
96  double** alloc_normals() { return alloc_array(ncharge(), 3); }
97  void free_normals(double**a) { free_array(a); }
98 
99  double* alloc_efield_dot_normals() { return new double[ncharge()]; }
100  void free_efield_dot_normals(double*a) { delete[] a; }
101 
102  double* alloc_charges() { return new double[ncharge()]; }
103  void free_charges(double*a) { delete[] a; }
104 
105  void charge_positions(double**);
106  void normals(double**);
107 
108  // Given the efield dotted with the normals at the charge positions this
109  // will compute a new set of charges.
110  void compute_charges(double* efield_dot_normals, double* charge);
111 
112  // Given a set of charges and a total charge, this will normalize
113  // the integrated charge to the charge that would be expected on
114  // the surface if the given total charge were enclosed within it.
115  void normalize_charge(double enclosed_charge, double* charges);
116 
117  // Given charges and nuclear charges compute their interation energy.
118  double nuclear_charge_interaction_energy(double *nuclear_charge,
119  double** charge_positions,
120  double* charge);
121 
122  // Given charges compute the interaction energy between the nuclei
123  // and the point charges.
124  double nuclear_interaction_energy(double** charge_positions,
125  double* charge);
126 
127  // Given charges compute the interaction energy for just the surface.
128  double self_interaction_energy(double** charge_positions, double *charge);
129 
130  // Given the charges, return the total polarization charge on the surface.
131  double polarization_charge(double* charge);
132 
133  // Return the area (available after compute_charges called).
134  double area() const { return area_; }
135  // Return the volume (available after compute_charges called).
136  double volume() const { return volume_; }
137  // Return the enclosed charge (available after compute_charges called).
138  double computed_enclosed_charge() const {
139  return computed_enclosed_charge_;
140  }
141 
142  double disp() {return edisp_;}
143  double rep() {return erep_;}
144  double disprep();
145 
146  // this never needs to be called explicitly, but is here now for debugging
147  void init_system_matrix();
148 
149  Ref<TriangulatedImplicitSurface> surface() const { return surf_; }
150 
151  Ref<SCMatrixKit> matrixkit() { return matrixkit_; }
152 };
153 
154 }
155 
156 #endif
157 
158 // Local Variables:
159 // mode: c++
160 // c-file-style: "CLJ"
161 // End:
sc::BEMSolvent
Definition: bem.h:43
sc::RefSCMatrix
The RefSCMatrix class is a smart pointer to an SCMatrix specialization.
Definition: matrix.h:135
sc::Ref
A template class that maintains references counts.
Definition: ref.h:361
sc::DescribedClass
Classes which need runtime information about themselves and their relationship to other classes can v...
Definition: class.h:233
sc
Contains all MPQC code up to version 3.
Definition: mpqcin.h:14

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