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<hr><h1>bem.h</h1><div class="fragment"><pre>00001 <font class="comment">//</font>
00002 <font class="comment">// bem.h</font>
00003 <font class="comment">//</font>
00004 <font class="comment">// Copyright (C) 1996 Limit Point Systems, Inc.</font>
00005 <font class="comment">//</font>
00006 <font class="comment">// Author: Curtis Janssen <cljanss@limitpt.com></font>
00007 <font class="comment">// Maintainer: LPS</font>
00008 <font class="comment">//</font>
00009 <font class="comment">// This file is part of the SC Toolkit.</font>
00010 <font class="comment">//</font>
00011 <font class="comment">// The SC Toolkit is free software; you can redistribute it and/or modify</font>
00012 <font class="comment">// it under the terms of the GNU Library General Public License as published by</font>
00013 <font class="comment">// the Free Software Foundation; either version 2, or (at your option)</font>
00014 <font class="comment">// any later version.</font>
00015 <font class="comment">//</font>
00016 <font class="comment">// The SC Toolkit is distributed in the hope that it will be useful,</font>
00017 <font class="comment">// but WITHOUT ANY WARRANTY; without even the implied warranty of</font>
00018 <font class="comment">// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</font>
00019 <font class="comment">// GNU Library General Public License for more details.</font>
00020 <font class="comment">//</font>
00021 <font class="comment">// You should have received a copy of the GNU Library General Public License</font>
00022 <font class="comment">// along with the SC Toolkit; see the file COPYING.LIB. If not, write to</font>
00023 <font class="comment">// the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.</font>
00024 <font class="comment">//</font>
00025 <font class="comment">// The U.S. Government is granted a limited license as per AL 91-7.</font>
00026 <font class="comment">//</font>
00027
00028 <font class="preprocessor">#ifndef _chemistry_solvent_bem_h</font>
00029 <font class="preprocessor"></font><font class="preprocessor">#define _chemistry_solvent_bem_h</font>
00030 <font class="preprocessor"></font>
00031 <font class="preprocessor">#include <util/class/class.h></font>
00032 <font class="preprocessor">#include <util/state/state.h></font>
00033 <font class="preprocessor">#include <util/keyval/keyval.h></font>
00034 <font class="preprocessor">#include <math/isosurf/volume.h></font>
00035 <font class="preprocessor">#include <math/isosurf/surf.h></font>
00036 <font class="preprocessor">#include <math/scmat/matrix.h></font>
00037 <font class="preprocessor">#include <chemistry/molecule/molecule.h></font>
00038
00039 <font class="keyword">namespace </font>sc {
00040
00041 <font class="comment">// This represents a solvent by a polarization charge on a dielectric</font>
00042 <font class="comment">// boundary surface.</font>
00043 <font class="keyword">class </font>BEMSolvent: <font class="keyword">public</font> DescribedClass {
00044 <font class="keyword">private</font>:
00045 <font class="keywordtype">int</font> debug_;
00046
00047 Ref<Molecule> solute_;
00048 Ref<Molecule> solvent_;
00049 <font class="keywordtype">double</font> solvent_density_;
00050 <font class="keywordtype">double</font> dielectric_constant_;
00051 Ref<SCMatrixKit> matrixkit_;
00052 RefSCMatrix system_matrix_i_;
00053 <font class="keywordtype">double</font> f_;
00054 Ref<MessageGrp> grp_;
00055
00056 <font class="keywordtype">double</font> area_;
00057 <font class="keywordtype">double</font> volume_;
00058 <font class="keywordtype">double</font> computed_enclosed_charge_;
00059 <font class="keywordtype">double</font> edisp_;
00060 <font class="keywordtype">double</font> erep_;
00061
00062 Ref<TriangulatedImplicitSurface> surf_;
00063
00064 <font class="keywordtype">double</font>** alloc_array(<font class="keywordtype">int</font> n, <font class="keywordtype">int</font> m);
00065 <font class="keywordtype">void</font> free_array(<font class="keywordtype">double</font>**);
00066
00067 <font class="comment">// This holds the area associated with each vertex. It is used</font>
00068 <font class="comment">// to convert charges to charge densities and back.</font>
00069 <font class="keywordtype">double</font>* vertex_area_;
00070
00071 <font class="comment">// Given charges compute surface charge density.</font>
00072 <font class="keywordtype">void</font> charges_to_surface_charge_density(<font class="keywordtype">double</font> *charges);
00073
00074 <font class="comment">// Given surface charge density compute charges.</font>
00075 <font class="keywordtype">void</font> surface_charge_density_to_charges(<font class="keywordtype">double</font> *charges);
00076 <font class="keyword">public</font>:
00077 BEMSolvent(<font class="keyword">const</font> Ref<KeyVal>&);
00078 <font class="keyword">virtual</font> ~BEMSolvent();
00079
00080 <font class="comment">// This should be called after everything is setup--the</font>
00081 <font class="comment">// molecule has the correct the geometry and all of the</font>
00082 <font class="comment">// parameters have been adjusted.</font>
00083 <font class="keywordtype">void</font> init();
00084 <font class="comment">// This gets rid of the system matrix inverse and, optionally, the surface.</font>
00085 <font class="keywordtype">void</font> done(<font class="keywordtype">int</font> clear_surface = 1);
00086
00087 <font class="keywordtype">int</font> ncharge()<font class="keyword"> </font>{ <font class="keywordflow">return</font> surf_->nvertex(); }
00088
00089 Ref<Molecule> solvent()<font class="keyword"> </font>{ <font class="keywordflow">return</font> solvent_ ;}
00090 <font class="keywordtype">double</font> solvent_density()<font class="keyword"> </font>{ <font class="keywordflow">return</font> solvent_density_ ;}
00091
00092 <font class="comment">// NOTE: call allocation routines after init and free routines before done</font>
00093 <font class="keywordtype">double</font>** alloc_charge_positions()<font class="keyword"> </font>{ <font class="keywordflow">return</font> alloc_array(ncharge(), 3); }
00094 <font class="keywordtype">void</font> free_charge_positions(<font class="keywordtype">double</font>**a)<font class="keyword"> </font>{ free_array(a); }
00095
00096 <font class="keywordtype">double</font>** alloc_normals()<font class="keyword"> </font>{ <font class="keywordflow">return</font> alloc_array(ncharge(), 3); }
00097 <font class="keywordtype">void</font> free_normals(<font class="keywordtype">double</font>**a)<font class="keyword"> </font>{ free_array(a); }
00098
00099 <font class="keywordtype">double</font>* alloc_efield_dot_normals()<font class="keyword"> </font>{ <font class="keywordflow">return</font> <font class="keyword">new</font> <font class="keywordtype">double</font>[ncharge()]; }
00100 <font class="keywordtype">void</font> free_efield_dot_normals(<font class="keywordtype">double</font>*a)<font class="keyword"> </font>{ <font class="keyword">delete</font>[] a; }
00101
00102 <font class="keywordtype">double</font>* alloc_charges()<font class="keyword"> </font>{ <font class="keywordflow">return</font> <font class="keyword">new</font> <font class="keywordtype">double</font>[ncharge()]; }
00103 <font class="keywordtype">void</font> free_charges(<font class="keywordtype">double</font>*a)<font class="keyword"> </font>{ <font class="keyword">delete</font>[] a; }
00104
00105 <font class="keywordtype">void</font> charge_positions(<font class="keywordtype">double</font>**);
00106 <font class="keywordtype">void</font> normals(<font class="keywordtype">double</font>**);
00107
00108 <font class="comment">// Given the efield dotted with the normals at the charge positions this</font>
00109 <font class="comment">// will compute a new set of charges.</font>
00110 <font class="keywordtype">void</font> compute_charges(<font class="keywordtype">double</font>* efield_dot_normals, <font class="keywordtype">double</font>* charge);
00111
00112 <font class="comment">// Given a set of charges and a total charge, this will normalize</font>
00113 <font class="comment">// the integrated charge to the charge that would be expected on</font>
00114 <font class="comment">// the surface if the given total charge were enclosed within it.</font>
00115 <font class="keywordtype">void</font> normalize_charge(<font class="keywordtype">double</font> enclosed_charge, <font class="keywordtype">double</font>* charges);
00116
00117 <font class="comment">// Given charges and nuclear charges compute their interation energy.</font>
00118 <font class="keywordtype">double</font> nuclear_charge_interaction_energy(<font class="keywordtype">double</font> *nuclear_charge,
00119 <font class="keywordtype">double</font>** charge_positions,
00120 <font class="keywordtype">double</font>* charge);
00121
00122 <font class="comment">// Given charges compute the interaction energy between the nuclei</font>
00123 <font class="comment">// and the point charges.</font>
00124 <font class="keywordtype">double</font> nuclear_interaction_energy(<font class="keywordtype">double</font>** charge_positions,
00125 <font class="keywordtype">double</font>* charge);
00126
00127 <font class="comment">// Given charges compute the interaction energy for just the surface.</font>
00128 <font class="keywordtype">double</font> self_interaction_energy(<font class="keywordtype">double</font>** charge_positions, <font class="keywordtype">double</font> *charge);
00129
00130 <font class="comment">// Given the charges, return the total polarization charge on the surface.</font>
00131 <font class="keywordtype">double</font> polarization_charge(<font class="keywordtype">double</font>* charge);
00132
00133 <font class="comment">// Return the area (available after compute_charges called).</font>
00134 <font class="keywordtype">double</font> area()<font class="keyword"> const </font>{ <font class="keywordflow">return</font> area_; }
00135 <font class="comment">// Return the volume (available after compute_charges called).</font>
00136 <font class="keywordtype">double</font> volume()<font class="keyword"> const </font>{ <font class="keywordflow">return</font> volume_; }
00137 <font class="comment">// Return the enclosed charge (available after compute_charges called).</font>
00138 <font class="keywordtype">double</font> computed_enclosed_charge()<font class="keyword"> const </font>{
00139 <font class="keywordflow">return</font> computed_enclosed_charge_;
00140 }
00141
00142 <font class="keywordtype">double</font> disp()<font class="keyword"> </font>{<font class="keywordflow">return</font> edisp_;}
00143 <font class="keywordtype">double</font> rep()<font class="keyword"> </font>{<font class="keywordflow">return</font> erep_;}
00144 <font class="keywordtype">double</font> disprep();
00145
00146 <font class="comment">// this never needs to be called explicitly, but is here now for debugging</font>
00147 <font class="keywordtype">void</font> init_system_matrix();
00148
00149 Ref<TriangulatedImplicitSurface> surface()<font class="keyword"> const </font>{ <font class="keywordflow">return</font> surf_; }
00150
00151 Ref<SCMatrixKit> matrixkit()<font class="keyword"> </font>{ <font class="keywordflow">return</font> matrixkit_; }
00152 };
00153
00154 }
00155
00156 <font class="preprocessor">#endif</font>
00157 <font class="preprocessor"></font>
00158 <font class="comment">// Local Variables:</font>
00159 <font class="comment">// mode: c++</font>
00160 <font class="comment">// c-file-style: "CLJ"</font>
00161 <font class="comment">// End:</font>
</div></pre><hr>
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