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<hr><h1>molecule.h</h1><div class="fragment"><pre>00001 <font class="comment">//</font>
00002 <font class="comment">// molecule.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_molecule_molecule_h</font>
00029 <font class="preprocessor"></font><font class="preprocessor">#define _chemistry_molecule_molecule_h</font>
00030 <font class="preprocessor"></font>
00031 <font class="preprocessor">#ifdef __GNUC__</font>
00032 <font class="preprocessor"></font><font class="preprocessor">#pragma interface</font>
00033 <font class="preprocessor"></font><font class="preprocessor">#endif</font>
00034 <font class="preprocessor"></font>
00035 <font class="preprocessor">#include <stdio.h></font>
00036 <font class="preprocessor">#include <iostream></font>
00037 <font class="preprocessor">#include <util/class/class.h></font>
00038 <font class="preprocessor">#include <util/state/state.h></font>
00039 <font class="preprocessor">#include <util/keyval/keyval.h></font>
00040 <font class="preprocessor">#include <util/misc/units.h></font>
00041 <font class="preprocessor">#include <math/symmetry/pointgrp.h></font>
00042 <font class="preprocessor">#include <math/scmat/vector3.h></font>
00043 <font class="preprocessor">#include <math/scmat/matrix.h></font>
00044 <font class="preprocessor">#include <chemistry/molecule/atominfo.h></font>
00045
00046 <font class="keyword">namespace </font>sc {
00047
<a name="l00099"></a><a class="code" href="class_sc__Molecule.html">00099</a> <font class="keyword">class </font>Molecule: <font class="keyword">public</font> SavableState
00100 {
00101 <font class="keyword">protected</font>:
00102 <font class="keywordtype">int</font> natoms_;
00103 Ref<AtomInfo> atominfo_;
00104 Ref<PointGroup> pg_;
00105 Ref<Units> geometry_units_;
00106 <font class="keywordtype">double</font> **r_;
00107 <font class="keywordtype">int</font> *Z_;
00108 <font class="keywordtype">double</font> *charges_;
00109
00110 <font class="comment">// symmetry equiv info</font>
00111 <font class="keywordtype">int</font> nuniq_;
00112 <font class="keywordtype">int</font> *nequiv_;
00113 <font class="keywordtype">int</font> **equiv_;
00114 <font class="keywordtype">int</font> *atom_to_uniq_;
00115 <font class="keywordtype">void</font> init_symmetry_info(<font class="keywordtype">double</font> tol=0.5);
00116 <font class="keywordtype">void</font> clear_symmetry_info();
00117
00118 <font class="comment">// these are optional</font>
00119 <font class="keywordtype">double</font> *mass_;
00120 <font class="keywordtype">char</font> **labels_;
00121
00122 <font class="keywordtype">void</font> clear();
00123 <font class="keyword">public</font>:
00124 <a class="code" href="class_sc__Molecule.html#a3">Molecule</a>();
00125 <a class="code" href="class_sc__Molecule.html#a3">Molecule</a>(<font class="keyword">const</font> Molecule&);
00126 <a class="code" href="class_sc__Molecule.html#a3">Molecule</a>(StateIn&);
00128 <a class="code" href="class_sc__Molecule.html#a3">Molecule</a>(<font class="keyword">const</font> Ref<KeyVal>&input);
00129
00130 <font class="keyword">virtual</font> ~Molecule();
00131
00132 Molecule& operator=(<font class="keyword">const</font> Molecule&);
00133
00135 <font class="keywordtype">void</font> <a class="code" href="class_sc__Molecule.html#a6">add_atom</a>(<font class="keywordtype">int</font> Z,<font class="keywordtype">double</font> x,<font class="keywordtype">double</font> y,<font class="keywordtype">double</font> z,
00136 <font class="keyword">const</font> <font class="keywordtype">char</font> * = 0, <font class="keywordtype">double</font> mass = 0.0,
00137 <font class="keywordtype">int</font> have_charge = 0, <font class="keywordtype">double</font> charge = 0.0);
00138
00140 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__Molecule.html#a7">print</a>(std::ostream& =ExEnv::out0()) <font class="keyword">const</font>;
00141 <font class="keyword">virtual</font> <font class="keywordtype">void</font> print_parsedkeyval(std::ostream& =ExEnv::out0(),
00142 <font class="keywordtype">int</font> print_pg = 1,
00143 <font class="keywordtype">int</font> print_unit = 1,
00144 <font class="keywordtype">int</font> number_atoms = 1) <font class="keyword">const</font>;
00145
<a name="l00147"></a><a class="code" href="class_sc__Molecule.html#a9">00147</a> <font class="keywordtype">int</font> <a class="code" href="class_sc__Molecule.html#a9">natom</a>()<font class="keyword"> const </font>{ <font class="keywordflow">return</font> natoms_; }
00148
00149 <font class="keywordtype">int</font> Z(<font class="keywordtype">int</font> atom)<font class="keyword"> const </font>{ <font class="keywordflow">return</font> Z_[atom]; }
00150 <font class="keywordtype">double</font> &r(<font class="keywordtype">int</font> atom, <font class="keywordtype">int</font> xyz)<font class="keyword"> </font>{ <font class="keywordflow">return</font> r_[atom][xyz]; }
00151 <font class="keyword">const</font> <font class="keywordtype">double</font> &r(<font class="keywordtype">int</font> atom, <font class="keywordtype">int</font> xyz)<font class="keyword"> const </font>{ <font class="keywordflow">return</font> r_[atom][xyz]; }
00152 <font class="keywordtype">double</font> *r(<font class="keywordtype">int</font> atom)<font class="keyword"> </font>{ <font class="keywordflow">return</font> r_[atom]; }
00153 <font class="keyword">const</font> <font class="keywordtype">double</font> *r(<font class="keywordtype">int</font> atom)<font class="keyword"> const </font>{ <font class="keywordflow">return</font> r_[atom]; }
00154 <font class="keywordtype">double</font> mass(<font class="keywordtype">int</font> atom) <font class="keyword">const</font>;
00157 <font class="keyword">const</font> <font class="keywordtype">char</font> *<a class="code" href="class_sc__Molecule.html#a16">label</a>(<font class="keywordtype">int</font> atom) <font class="keyword">const</font>;
00158
00161 <font class="keywordtype">int</font> <a class="code" href="class_sc__Molecule.html#a17">atom_at_position</a>(<font class="keywordtype">double</font> *, <font class="keywordtype">double</font> tol = 0.05) <font class="keyword">const</font>;
00162
00165 <font class="keywordtype">int</font> <a class="code" href="class_sc__Molecule.html#a18">atom_label_to_index</a>(<font class="keyword">const</font> <font class="keywordtype">char</font> *label) <font class="keyword">const</font>;
00166
00170 <font class="keywordtype">double</font> *<a class="code" href="class_sc__Molecule.html#a19">charges</a>() <font class="keyword">const</font>;
00171
00173 <font class="keywordtype">double</font> <a class="code" href="class_sc__Molecule.html#a20">charge</a>(<font class="keywordtype">int</font> iatom) <font class="keyword">const</font>;
00174
00176 <font class="keywordtype">double</font> <a class="code" href="class_sc__Molecule.html#a21">nuclear_charge</a>() <font class="keyword">const</font>;
00177
00179 <font class="keywordtype">void</font> <a class="code" href="class_sc__Molecule.html#a22">set_point_group</a>(<font class="keyword">const</font> Ref<PointGroup>&, <font class="keywordtype">double</font> tol=1.0e-7);
00181 Ref<PointGroup> <a class="code" href="class_sc__Molecule.html#a23">point_group</a>() <font class="keyword">const</font>;
00182
00186 Ref<PointGroup> <a class="code" href="class_sc__Molecule.html#a24">highest_point_group</a>(<font class="keywordtype">double</font> tol = 1.0e-8) <font class="keyword">const</font>;
00187
00190 <font class="keywordtype">int</font> <a class="code" href="class_sc__Molecule.html#a25">is_axis</a>(SCVector3 &origin,
00191 SCVector3 &udirection, <font class="keywordtype">int</font> order, <font class="keywordtype">double</font> tol=1.0e-8) <font class="keyword">const</font>;
00192
00195 <font class="keywordtype">int</font> <a class="code" href="class_sc__Molecule.html#a26">is_plane</a>(SCVector3 &origin, SCVector3 &uperp, <font class="keywordtype">double</font> tol=1.0e-8) <font class="keyword">const</font>;
00196
00198 <font class="keywordtype">int</font> <a class="code" href="class_sc__Molecule.html#a27">has_inversion</a>(SCVector3 &origin, <font class="keywordtype">double</font> tol = 1.0e-8) <font class="keyword">const</font>;
00199
00201 <font class="keywordtype">int</font> <a class="code" href="class_sc__Molecule.html#a28">is_linear</a>(<font class="keywordtype">double</font> tolerance = 1.0e-5) <font class="keyword">const</font>;
00203 <font class="keywordtype">int</font> <a class="code" href="class_sc__Molecule.html#a29">is_planar</a>(<font class="keywordtype">double</font> tolerance = 1.0e-5) <font class="keyword">const</font>;
00206 <font class="keywordtype">void</font> <a class="code" href="class_sc__Molecule.html#a30">is_linear_planar</a>(<font class="keywordtype">int</font>&linear,<font class="keywordtype">int</font>&planar,<font class="keywordtype">double</font> tol = 1.0e-5) <font class="keyword">const</font>;
00207
00210 SCVector3 <a class="code" href="class_sc__Molecule.html#a31">center_of_mass</a>() <font class="keyword">const</font>;
00211
00213 <font class="keywordtype">double</font> <a class="code" href="class_sc__Molecule.html#a32">nuclear_repulsion_energy</a>();
00214
00217 <font class="keywordtype">void</font> <a class="code" href="class_sc__Molecule.html#a33">nuclear_repulsion_1der</a>(<font class="keywordtype">int</font> center, <font class="keywordtype">double</font> xyz[3]);
00218
00220 <font class="keywordtype">void</font> <a class="code" href="class_sc__Molecule.html#a34">nuclear_efield</a>(<font class="keyword">const</font> <font class="keywordtype">double</font> *position, <font class="keywordtype">double</font>* efield);
00221
00224 <font class="keywordtype">void</font> <a class="code" href="class_sc__Molecule.html#a35">nuclear_charge_efield</a>(<font class="keyword">const</font> <font class="keywordtype">double</font> *charges,
00225 <font class="keyword">const</font> <font class="keywordtype">double</font> *position, <font class="keywordtype">double</font>* efield);
00226
00232 <font class="keywordtype">void</font> <a class="code" href="class_sc__Molecule.html#a36">symmetrize</a>(<font class="keywordtype">double</font> tol = 0.5);
00233
00235 <font class="keywordtype">void</font> <a class="code" href="class_sc__Molecule.html#a36">symmetrize</a>(<font class="keyword">const</font> Ref<PointGroup> &pg, <font class="keywordtype">double</font> tol = 0.5);
00236
00240 <font class="keywordtype">void</font> <a class="code" href="class_sc__Molecule.html#a38">cleanup_molecule</a>(<font class="keywordtype">double</font> tol = 0.1);
00241
00242 <font class="keywordtype">void</font> translate(<font class="keyword">const</font> <font class="keywordtype">double</font> *r);
00243 <font class="keywordtype">void</font> move_to_com();
00244 <font class="keywordtype">void</font> transform_to_principal_axes(<font class="keywordtype">int</font> trans_frame=1);
00245 <font class="keywordtype">void</font> transform_to_symmetry_frame();
00246 <font class="keywordtype">void</font> print_pdb(std::ostream& =ExEnv::out0(), <font class="keywordtype">char</font> *title =0) <font class="keyword">const</font>;
00247
00248 <font class="keywordtype">void</font> read_pdb(<font class="keyword">const</font> <font class="keywordtype">char</font> *filename);
00249
00252 <font class="keywordtype">void</font> <a class="code" href="class_sc__Molecule.html#a45">principal_moments_of_inertia</a>(<font class="keywordtype">double</font> *evals, <font class="keywordtype">double</font> **evecs=0) <font class="keyword">const</font>;
00253
<a name="l00255"></a><a class="code" href="class_sc__Molecule.html#a46">00255</a> <font class="keywordtype">int</font> <a class="code" href="class_sc__Molecule.html#a46">nunique</a>()<font class="keyword"> const </font>{ <font class="keywordflow">return</font> nuniq_; }
<a name="l00257"></a><a class="code" href="class_sc__Molecule.html#a47">00257</a> <font class="keywordtype">int</font> <a class="code" href="class_sc__Molecule.html#a47">unique</a>(<font class="keywordtype">int</font> iuniq)<font class="keyword"> const </font>{ <font class="keywordflow">return</font> equiv_[iuniq][0]; }
<a name="l00259"></a><a class="code" href="class_sc__Molecule.html#a48">00259</a> <font class="keywordtype">int</font> <a class="code" href="class_sc__Molecule.html#a48">nequivalent</a>(<font class="keywordtype">int</font> iuniq)<font class="keyword"> const </font>{ <font class="keywordflow">return</font> nequiv_[iuniq]; }
<a name="l00261"></a><a class="code" href="class_sc__Molecule.html#a49">00261</a> <font class="keywordtype">int</font> <a class="code" href="class_sc__Molecule.html#a49">equivalent</a>(<font class="keywordtype">int</font> iuniq, <font class="keywordtype">int</font> j)<font class="keyword"> const </font>{ <font class="keywordflow">return</font> equiv_[iuniq][j]; }
<a name="l00264"></a><a class="code" href="class_sc__Molecule.html#a50">00264</a> <font class="keywordtype">int</font> <a class="code" href="class_sc__Molecule.html#a50">atom_to_unique</a>(<font class="keywordtype">int</font> iatom)<font class="keyword"> const </font>{ <font class="keywordflow">return</font> atom_to_uniq_[iatom]; }
00267 <font class="keywordtype">int</font> <a class="code" href="class_sc__Molecule.html#a51">atom_to_unique_offset</a>(<font class="keywordtype">int</font> iatom) <font class="keyword">const</font>;
00268
00270 <font class="keywordtype">int</font> <a class="code" href="class_sc__Molecule.html#a52">n_core_electrons</a>();
00271
00273 <font class="keywordtype">int</font> <a class="code" href="class_sc__Molecule.html#a53">max_z</a>();
00274
<a name="l00276"></a><a class="code" href="class_sc__Molecule.html#a54">00276</a> Ref<AtomInfo> <a class="code" href="class_sc__Molecule.html#a54">atominfo</a>()<font class="keyword"> const </font>{ <font class="keywordflow">return</font> atominfo_; }
00277
00278 <font class="keywordtype">void</font> <a class="code" href="class_sc__Molecule.html#a55">save_data_state</a>(StateOut&);
00279 };
00280
00281 }
00282
00283 <font class="preprocessor">#endif</font>
00284 <font class="preprocessor"></font>
00285 <font class="comment">// Local Variables:</font>
00286 <font class="comment">// mode: c++</font>
00287 <font class="comment">// c-file-style: "CLJ"</font>
00288 <font class="comment">// End:</font>
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