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<h1>bem.h</h1><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//</span>
<a name="l00002"></a>00002 <span class="comment">// bem.h</span>
<a name="l00003"></a>00003 <span class="comment">//</span>
<a name="l00004"></a>00004 <span class="comment">// Copyright (C) 1996 Limit Point Systems, Inc.</span>
<a name="l00005"></a>00005 <span class="comment">//</span>
<a name="l00006"></a>00006 <span class="comment">// Author: Curtis Janssen <cljanss@limitpt.com></span>
<a name="l00007"></a>00007 <span class="comment">// Maintainer: LPS</span>
<a name="l00008"></a>00008 <span class="comment">//</span>
<a name="l00009"></a>00009 <span class="comment">// This file is part of the SC Toolkit.</span>
<a name="l00010"></a>00010 <span class="comment">//</span>
<a name="l00011"></a>00011 <span class="comment">// The SC Toolkit is free software; you can redistribute it and/or modify</span>
<a name="l00012"></a>00012 <span class="comment">// it under the terms of the GNU Library General Public License as published by</span>
<a name="l00013"></a>00013 <span class="comment">// the Free Software Foundation; either version 2, or (at your option)</span>
<a name="l00014"></a>00014 <span class="comment">// any later version.</span>
<a name="l00015"></a>00015 <span class="comment">//</span>
<a name="l00016"></a>00016 <span class="comment">// The SC Toolkit is distributed in the hope that it will be useful,</span>
<a name="l00017"></a>00017 <span class="comment">// but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00018"></a>00018 <span class="comment">// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
<a name="l00019"></a>00019 <span class="comment">// GNU Library General Public License for more details.</span>
<a name="l00020"></a>00020 <span class="comment">//</span>
<a name="l00021"></a>00021 <span class="comment">// You should have received a copy of the GNU Library General Public License</span>
<a name="l00022"></a>00022 <span class="comment">// along with the SC Toolkit; see the file COPYING.LIB. If not, write to</span>
<a name="l00023"></a>00023 <span class="comment">// the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.</span>
<a name="l00024"></a>00024 <span class="comment">//</span>
<a name="l00025"></a>00025 <span class="comment">// The U.S. Government is granted a limited license as per AL 91-7.</span>
<a name="l00026"></a>00026 <span class="comment">//</span>
<a name="l00027"></a>00027
<a name="l00028"></a>00028 <span class="preprocessor">#ifndef _chemistry_solvent_bem_h</span>
<a name="l00029"></a>00029 <span class="preprocessor"></span><span class="preprocessor">#define _chemistry_solvent_bem_h</span>
<a name="l00030"></a>00030 <span class="preprocessor"></span>
<a name="l00031"></a>00031 <span class="preprocessor">#include <util/class/class.h></span>
<a name="l00032"></a>00032 <span class="preprocessor">#include <util/state/state.h></span>
<a name="l00033"></a>00033 <span class="preprocessor">#include <util/keyval/keyval.h></span>
<a name="l00034"></a>00034 <span class="preprocessor">#include <math/isosurf/volume.h></span>
<a name="l00035"></a>00035 <span class="preprocessor">#include <math/isosurf/surf.h></span>
<a name="l00036"></a>00036 <span class="preprocessor">#include <math/scmat/matrix.h></span>
<a name="l00037"></a>00037 <span class="preprocessor">#include <chemistry/molecule/molecule.h></span>
<a name="l00038"></a>00038
<a name="l00039"></a>00039 <span class="keyword">namespace </span>sc {
<a name="l00040"></a>00040
<a name="l00041"></a>00041 <span class="comment">// This represents a solvent by a polarization charge on a dielectric</span>
<a name="l00042"></a>00042 <span class="comment">// boundary surface.</span>
<a name="l00043"></a>00043 <span class="keyword">class </span>BEMSolvent: <span class="keyword">public</span> DescribedClass {
<a name="l00044"></a>00044 <span class="keyword">private</span>:
<a name="l00045"></a>00045 <span class="keywordtype">int</span> debug_;
<a name="l00046"></a>00046
<a name="l00047"></a>00047 Ref<Molecule> solute_;
<a name="l00048"></a>00048 Ref<Molecule> solvent_;
<a name="l00049"></a>00049 <span class="keywordtype">double</span> solvent_density_;
<a name="l00050"></a>00050 <span class="keywordtype">double</span> dielectric_constant_;
<a name="l00051"></a>00051 Ref<SCMatrixKit> matrixkit_;
<a name="l00052"></a>00052 RefSCMatrix system_matrix_i_;
<a name="l00053"></a>00053 <span class="keywordtype">double</span> f_;
<a name="l00054"></a>00054 Ref<MessageGrp> grp_;
<a name="l00055"></a>00055
<a name="l00056"></a>00056 <span class="keywordtype">double</span> area_;
<a name="l00057"></a>00057 <span class="keywordtype">double</span> volume_;
<a name="l00058"></a>00058 <span class="keywordtype">double</span> computed_enclosed_charge_;
<a name="l00059"></a>00059 <span class="keywordtype">double</span> edisp_;
<a name="l00060"></a>00060 <span class="keywordtype">double</span> erep_;
<a name="l00061"></a>00061
<a name="l00062"></a>00062 Ref<TriangulatedImplicitSurface> surf_;
<a name="l00063"></a>00063
<a name="l00064"></a>00064 <span class="keywordtype">double</span>** alloc_array(<span class="keywordtype">int</span> n, <span class="keywordtype">int</span> m);
<a name="l00065"></a>00065 <span class="keywordtype">void</span> free_array(<span class="keywordtype">double</span>**);
<a name="l00066"></a>00066
<a name="l00067"></a>00067 <span class="comment">// This holds the area associated with each vertex. It is used</span>
<a name="l00068"></a>00068 <span class="comment">// to convert charges to charge densities and back.</span>
<a name="l00069"></a>00069 <span class="keywordtype">double</span>* vertex_area_;
<a name="l00070"></a>00070
<a name="l00071"></a>00071 <span class="comment">// Given charges compute surface charge density.</span>
<a name="l00072"></a>00072 <span class="keywordtype">void</span> charges_to_surface_charge_density(<span class="keywordtype">double</span> *charges);
<a name="l00073"></a>00073
<a name="l00074"></a>00074 <span class="comment">// Given surface charge density compute charges.</span>
<a name="l00075"></a>00075 <span class="keywordtype">void</span> surface_charge_density_to_charges(<span class="keywordtype">double</span> *charges);
<a name="l00076"></a>00076 <span class="keyword">public</span>:
<a name="l00077"></a>00077 BEMSolvent(<span class="keyword">const</span> Ref<KeyVal>&);
<a name="l00078"></a>00078 <span class="keyword">virtual</span> ~BEMSolvent();
<a name="l00079"></a>00079
<a name="l00080"></a>00080 <span class="comment">// This should be called after everything is setup--the</span>
<a name="l00081"></a>00081 <span class="comment">// molecule has the correct the geometry and all of the</span>
<a name="l00082"></a>00082 <span class="comment">// parameters have been adjusted.</span>
<a name="l00083"></a>00083 <span class="keywordtype">void</span> init();
<a name="l00084"></a>00084 <span class="comment">// This gets rid of the system matrix inverse and, optionally, the surface.</span>
<a name="l00085"></a>00085 <span class="keywordtype">void</span> done(<span class="keywordtype">int</span> clear_surface = 1);
<a name="l00086"></a>00086
<a name="l00087"></a>00087 <span class="keywordtype">int</span> ncharge() { <span class="keywordflow">return</span> surf_->nvertex(); }
<a name="l00088"></a>00088
<a name="l00089"></a>00089 Ref<Molecule> solvent() { <span class="keywordflow">return</span> solvent_ ;}
<a name="l00090"></a>00090 <span class="keywordtype">double</span> solvent_density() { <span class="keywordflow">return</span> solvent_density_ ;}
<a name="l00091"></a>00091
<a name="l00092"></a>00092 <span class="comment">// NOTE: call allocation routines after init and free routines before done</span>
<a name="l00093"></a>00093 <span class="keywordtype">double</span>** alloc_charge_positions() { <span class="keywordflow">return</span> alloc_array(ncharge(), 3); }
<a name="l00094"></a>00094 <span class="keywordtype">void</span> free_charge_positions(<span class="keywordtype">double</span>**a) { free_array(a); }
<a name="l00095"></a>00095
<a name="l00096"></a>00096 <span class="keywordtype">double</span>** alloc_normals() { <span class="keywordflow">return</span> alloc_array(ncharge(), 3); }
<a name="l00097"></a>00097 <span class="keywordtype">void</span> free_normals(<span class="keywordtype">double</span>**a) { free_array(a); }
<a name="l00098"></a>00098
<a name="l00099"></a>00099 <span class="keywordtype">double</span>* alloc_efield_dot_normals() { <span class="keywordflow">return</span> <span class="keyword">new</span> <span class="keywordtype">double</span>[ncharge()]; }
<a name="l00100"></a>00100 <span class="keywordtype">void</span> free_efield_dot_normals(<span class="keywordtype">double</span>*a) { <span class="keyword">delete</span>[] a; }
<a name="l00101"></a>00101
<a name="l00102"></a>00102 <span class="keywordtype">double</span>* alloc_charges() { <span class="keywordflow">return</span> <span class="keyword">new</span> <span class="keywordtype">double</span>[ncharge()]; }
<a name="l00103"></a>00103 <span class="keywordtype">void</span> free_charges(<span class="keywordtype">double</span>*a) { <span class="keyword">delete</span>[] a; }
<a name="l00104"></a>00104
<a name="l00105"></a>00105 <span class="keywordtype">void</span> charge_positions(<span class="keywordtype">double</span>**);
<a name="l00106"></a>00106 <span class="keywordtype">void</span> normals(<span class="keywordtype">double</span>**);
<a name="l00107"></a>00107
<a name="l00108"></a>00108 <span class="comment">// Given the efield dotted with the normals at the charge positions this</span>
<a name="l00109"></a>00109 <span class="comment">// will compute a new set of charges.</span>
<a name="l00110"></a>00110 <span class="keywordtype">void</span> compute_charges(<span class="keywordtype">double</span>* efield_dot_normals, <span class="keywordtype">double</span>* charge);
<a name="l00111"></a>00111
<a name="l00112"></a>00112 <span class="comment">// Given a set of charges and a total charge, this will normalize</span>
<a name="l00113"></a>00113 <span class="comment">// the integrated charge to the charge that would be expected on</span>
<a name="l00114"></a>00114 <span class="comment">// the surface if the given total charge were enclosed within it.</span>
<a name="l00115"></a>00115 <span class="keywordtype">void</span> normalize_charge(<span class="keywordtype">double</span> enclosed_charge, <span class="keywordtype">double</span>* charges);
<a name="l00116"></a>00116
<a name="l00117"></a>00117 <span class="comment">// Given charges and nuclear charges compute their interation energy.</span>
<a name="l00118"></a>00118 <span class="keywordtype">double</span> nuclear_charge_interaction_energy(<span class="keywordtype">double</span> *nuclear_charge,
<a name="l00119"></a>00119 <span class="keywordtype">double</span>** charge_positions,
<a name="l00120"></a>00120 <span class="keywordtype">double</span>* charge);
<a name="l00121"></a>00121
<a name="l00122"></a>00122 <span class="comment">// Given charges compute the interaction energy between the nuclei</span>
<a name="l00123"></a>00123 <span class="comment">// and the point charges.</span>
<a name="l00124"></a>00124 <span class="keywordtype">double</span> nuclear_interaction_energy(<span class="keywordtype">double</span>** charge_positions,
<a name="l00125"></a>00125 <span class="keywordtype">double</span>* charge);
<a name="l00126"></a>00126
<a name="l00127"></a>00127 <span class="comment">// Given charges compute the interaction energy for just the surface.</span>
<a name="l00128"></a>00128 <span class="keywordtype">double</span> self_interaction_energy(<span class="keywordtype">double</span>** charge_positions, <span class="keywordtype">double</span> *charge);
<a name="l00129"></a>00129
<a name="l00130"></a>00130 <span class="comment">// Given the charges, return the total polarization charge on the surface.</span>
<a name="l00131"></a>00131 <span class="keywordtype">double</span> polarization_charge(<span class="keywordtype">double</span>* charge);
<a name="l00132"></a>00132
<a name="l00133"></a>00133 <span class="comment">// Return the area (available after compute_charges called).</span>
<a name="l00134"></a>00134 <span class="keywordtype">double</span> area()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> area_; }
<a name="l00135"></a>00135 <span class="comment">// Return the volume (available after compute_charges called).</span>
<a name="l00136"></a>00136 <span class="keywordtype">double</span> volume()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> volume_; }
<a name="l00137"></a>00137 <span class="comment">// Return the enclosed charge (available after compute_charges called).</span>
<a name="l00138"></a>00138 <span class="keywordtype">double</span> computed_enclosed_charge()<span class="keyword"> const </span>{
<a name="l00139"></a>00139 <span class="keywordflow">return</span> computed_enclosed_charge_;
<a name="l00140"></a>00140 }
<a name="l00141"></a>00141
<a name="l00142"></a>00142 <span class="keywordtype">double</span> disp() {<span class="keywordflow">return</span> edisp_;}
<a name="l00143"></a>00143 <span class="keywordtype">double</span> rep() {<span class="keywordflow">return</span> erep_;}
<a name="l00144"></a>00144 <span class="keywordtype">double</span> disprep();
<a name="l00145"></a>00145
<a name="l00146"></a>00146 <span class="comment">// this never needs to be called explicitly, but is here now for debugging</span>
<a name="l00147"></a>00147 <span class="keywordtype">void</span> init_system_matrix();
<a name="l00148"></a>00148
<a name="l00149"></a>00149 Ref<TriangulatedImplicitSurface> surface()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> surf_; }
<a name="l00150"></a>00150
<a name="l00151"></a>00151 Ref<SCMatrixKit> matrixkit() { <span class="keywordflow">return</span> matrixkit_; }
<a name="l00152"></a>00152 };
<a name="l00153"></a>00153
<a name="l00154"></a>00154 }
<a name="l00155"></a>00155
<a name="l00156"></a>00156 <span class="preprocessor">#endif</span>
<a name="l00157"></a>00157 <span class="preprocessor"></span>
<a name="l00158"></a>00158 <span class="comment">// Local Variables:</span>
<a name="l00159"></a>00159 <span class="comment">// mode: c++</span>
<a name="l00160"></a>00160 <span class="comment">// c-file-style: "CLJ"</span>
<a name="l00161"></a>00161 <span class="comment">// End:</span>
</pre></div></div>
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<address>
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Generated at Wed Oct 14 14:12:09 2009 for <a
href="http://www.mpqc.org">MPQC</a>
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distrib
>
Mandriva
>
2010.0
>
i586
>
media
>
contrib-release
>
by-pkgid
>
247b28499c443e092731ffba814075f2
>
files
>
33
