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<hr><h1>coor.h</h1><div class="fragment"><pre>00001 <font class="comment">//</font>
00002 <font class="comment">// coor.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_coor_h</font>
00029 <font class="preprocessor"></font><font class="preprocessor">#define _chemistry_molecule_coor_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 <iostream></font>
00036 <font class="preprocessor">#include <vector></font>
00037
00038 <font class="preprocessor">#include <math/scmat/matrix.h></font>
00039 <font class="preprocessor">#include <math/optimize/transform.h></font>
00040 <font class="preprocessor">#include <chemistry/molecule/molecule.h></font>
00041
00042 <font class="keyword">namespace </font>sc {
00043
<a name="l00046"></a><a class="code" href="class_sc__IntCoor.html">00046</a> <font class="keyword">class </font>IntCoor: <font class="keyword">public</font> SavableState {
00047 <font class="keyword">protected</font>:
00048 <font class="comment">// conversion factors from radians, bohr to the preferred units</font>
00049 <font class="keyword">static</font> <font class="keywordtype">double</font> bohr_conv;
00050 <font class="keyword">static</font> <font class="keywordtype">double</font> radian_conv;
00051 <font class="keywordtype">char</font> *label_;
00052 <font class="keywordtype">double</font> value_;
00053 <font class="keyword">public</font>:
00054 <a class="code" href="class_sc__IntCoor.html#a2">IntCoor</a>(StateIn&);
00055 <a class="code" href="class_sc__IntCoor.html#a2">IntCoor</a>(<font class="keyword">const</font> IntCoor&);
00058 <a class="code" href="class_sc__IntCoor.html#a2">IntCoor</a>(<font class="keyword">const</font> <font class="keywordtype">char</font>* label = 0);
00075 <a class="code" href="class_sc__IntCoor.html#a2">IntCoor</a>(<font class="keyword">const</font> Ref<KeyVal>&);
00076
00077 <font class="keyword">virtual</font> ~IntCoor();
00078 <font class="keywordtype">void</font> <a class="code" href="class_sc__IntCoor.html#a5">save_data_state</a>(StateOut&);
00079
00081 <font class="keyword">virtual</font> <font class="keyword">const</font> <font class="keywordtype">char</font>* <a class="code" href="class_sc__IntCoor.html#a6">label</a>() <font class="keyword">const</font>;
00083 <font class="keyword">virtual</font> <font class="keywordtype">double</font> <a class="code" href="class_sc__IntCoor.html#a7">value</a>() <font class="keyword">const</font>;
00085 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__IntCoor.html#a8">set_value</a>(<font class="keywordtype">double</font>);
00087 <font class="keyword">virtual</font> <font class="keywordtype">double</font> <a class="code" href="class_sc__IntCoor.html#a9">preferred_value</a>() <font class="keyword">const</font>;
00089 <font class="keyword">virtual</font> <font class="keyword">const</font> <font class="keywordtype">char</font>* <a class="code" href="class_sc__IntCoor.html#a10">ctype</a>() <font class="keyword">const</font> = 0;
00091 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__IntCoor.html#a11">print</a>(std::ostream & o=ExEnv::out0()) <font class="keyword">const</font>;
00092 <font class="keyword">virtual</font> <font class="keywordtype">void</font> print_details(<font class="keyword">const</font> Ref<Molecule> &, std::ostream& =ExEnv::out0()) <font class="keyword">const</font>;
00095 <font class="keyword">virtual</font> <font class="keywordtype">double</font> <a class="code" href="class_sc__IntCoor.html#a13">force_constant</a>(Ref<Molecule>&) = 0;
00097 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__IntCoor.html#a14">update_value</a>(<font class="keyword">const</font> Ref<Molecule>&) = 0;
00099 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__IntCoor.html#a15">bmat</a>(<font class="keyword">const</font> Ref<Molecule>&,RefSCVector&bmat,<font class="keywordtype">double</font> coef=1.0) = 0;
00103 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__IntCoor.html#a16">equivalent</a>(Ref<IntCoor>&) = 0;
00104 };
00105
<a name="l00120"></a><a class="code" href="class_sc__SumIntCoor.html">00120</a> <font class="keyword">class </font>SumIntCoor: <font class="keyword">public</font> IntCoor {
00121 <font class="keyword">private</font>:
00122 std::vector<double> coef_;
00123 std::vector<Ref<IntCoor> > coor_;
00124 <font class="keyword">public</font>:
00125 <a class="code" href="class_sc__SumIntCoor.html#a1">SumIntCoor</a>(StateIn&);
00128 <a class="code" href="class_sc__SumIntCoor.html#a1">SumIntCoor</a>(<font class="keyword">const</font> <font class="keywordtype">char</font> *);
00139 <a class="code" href="class_sc__SumIntCoor.html#a1">SumIntCoor</a>(<font class="keyword">const</font> Ref<KeyVal>&);
00140
00141 ~SumIntCoor();
00142 <font class="keywordtype">void</font> <a class="code" href="class_sc__SumIntCoor.html#a4">save_data_state</a>(StateOut&);
00143
00145 <font class="keywordtype">int</font> <a class="code" href="class_sc__SumIntCoor.html#a5">n</a>();
00148 <font class="keywordtype">void</font> <a class="code" href="class_sc__SumIntCoor.html#a6">add</a>(Ref<IntCoor>&,<font class="keywordtype">double</font> coef);
00150 <font class="keywordtype">void</font> <a class="code" href="class_sc__SumIntCoor.html#a7">normalize</a>();
00151
00152 <font class="comment">// IntCoor overrides</font>
00154 <font class="comment"> double preferred_value() const;</font>
00156 <font class="comment"> const char* ctype() const;</font>
00158 <font class="comment"> void print_details(const Ref<Molecule> &, std::ostream& =ExEnv::out0()) const;</font>
00160 <font class="comment"> double force_constant(Ref<Molecule>&);</font>
00162 <font class="comment"> void update_value(const Ref<Molecule>&);</font>
00164 <font class="comment"> void bmat(const Ref<Molecule>&,RefSCVector&bmat,double coef = 1.0);</font>
00166 <font class="comment"> int equivalent(Ref<IntCoor>&);</font>
00167 };
00168
<a name="l00189"></a><a class="code" href="class_sc__SetIntCoor.html">00189</a> <font class="keyword">class </font>SetIntCoor: <font class="keyword">public</font> SavableState {
00190 <font class="keyword">private</font>:
00191 std::vector<Ref<IntCoor> > coor_;
00192 <font class="keyword">public</font>:
00193 <a class="code" href="class_sc__SetIntCoor.html#a2">SetIntCoor</a>();
00194 <a class="code" href="class_sc__SetIntCoor.html#a2">SetIntCoor</a>(StateIn&);
00205 <a class="code" href="class_sc__SetIntCoor.html#a2">SetIntCoor</a>(<font class="keyword">const</font> Ref<KeyVal>&);
00206
00207 <font class="keyword">virtual</font> ~SetIntCoor();
00208 <font class="keywordtype">void</font> <a class="code" href="class_sc__SetIntCoor.html#a4">save_data_state</a>(StateOut&);
00209
00211 <font class="keywordtype">void</font> <a class="code" href="class_sc__SetIntCoor.html#a5">add</a>(<font class="keyword">const</font> Ref<IntCoor>&);
00213 <font class="keywordtype">void</font> <a class="code" href="class_sc__SetIntCoor.html#a5">add</a>(<font class="keyword">const</font> Ref<SetIntCoor>&);
00215 <font class="keywordtype">void</font> <a class="code" href="class_sc__SetIntCoor.html#a7">pop</a>();
00217 <font class="keywordtype">void</font> <a class="code" href="class_sc__SetIntCoor.html#a8">clear</a>();
00219 <font class="keywordtype">int</font> <a class="code" href="class_sc__SetIntCoor.html#a9">n</a>() <font class="keyword">const</font>;
00221 Ref<IntCoor> <a class="code" href="class_sc__SetIntCoor.html#a10">coor</a>(<font class="keywordtype">int</font> i) <font class="keyword">const</font>;
00223 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__SetIntCoor.html#a11">fd_bmat</a>(<font class="keyword">const</font> Ref<Molecule>&,RefSCMatrix&);
00225 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__SetIntCoor.html#a12">bmat</a>(<font class="keyword">const</font> Ref<Molecule>&, RefSCMatrix&);
00229 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__SetIntCoor.html#a13">guess_hessian</a>(Ref<Molecule>&,RefSymmSCMatrix&);
00231 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__SetIntCoor.html#a14">print_details</a>(<font class="keyword">const</font> Ref<Molecule> &,std::ostream& =ExEnv::out0()) <font class="keyword">const</font>;
00233 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__SetIntCoor.html#a15">update_values</a>(<font class="keyword">const</font> Ref<Molecule>&);
00235 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__SetIntCoor.html#a16">values_to_vector</a>(<font class="keyword">const</font> RefSCVector&);
00236 };
00237
00238
00239 <font class="comment">// ////////////////////////////////////////////////////////////////////////</font>
00240
00241 <font class="keyword">class </font>BitArrayLTri;
00242
<a name="l00245"></a><a class="code" href="class_sc__IntCoorGen.html">00245</a> <font class="keyword">class </font>IntCoorGen: <font class="keyword">public</font> SavableState
00246 {
00247 <font class="keyword">protected</font>:
00248 Ref<Molecule> molecule_;
00249
00250 <font class="keywordtype">int</font> linear_bends_;
00251 <font class="keywordtype">int</font> linear_lbends_;
00252 <font class="keywordtype">int</font> linear_tors_;
00253 <font class="keywordtype">int</font> linear_stors_;
00254 <font class="keywordtype">int</font> nextra_bonds_;
00255 <font class="keywordtype">int</font> *extra_bonds_;
00256 <font class="keywordtype">double</font> linear_bend_thres_;
00257 <font class="keywordtype">double</font> linear_tors_thres_;
00258 <font class="keywordtype">double</font> radius_scale_factor_;
00259
00260 <font class="keywordtype">void</font> init_constants();
00261
00262 <font class="keywordtype">double</font> cos_ijk(Molecule& m, <font class="keywordtype">int</font> i, <font class="keywordtype">int</font> j, <font class="keywordtype">int</font> k);
00263 <font class="keywordtype">int</font> hterminal(Molecule& m, BitArrayLTri& bonds, <font class="keywordtype">int</font> i);
00264 <font class="keywordtype">int</font> nearest_contact(<font class="keywordtype">int</font> i, Molecule& m);
00265
00266 <font class="keywordtype">void</font> add_bonds(<font class="keyword">const</font> Ref<SetIntCoor>& list, BitArrayLTri& bonds, Molecule& m);
00267 <font class="keywordtype">void</font> add_bends(<font class="keyword">const</font> Ref<SetIntCoor>& list, BitArrayLTri& bonds, Molecule& m);
00268 <font class="keywordtype">void</font> add_tors(<font class="keyword">const</font> Ref<SetIntCoor>& list, BitArrayLTri& bonds, Molecule& m);
00269 <font class="keywordtype">void</font> add_out(<font class="keyword">const</font> Ref<SetIntCoor>& list, BitArrayLTri& bonds, Molecule& m);
00270 <font class="keyword">public</font>:
00274 <a class="code" href="class_sc__IntCoorGen.html#a0">IntCoorGen</a>(<font class="keyword">const</font> Ref<Molecule>&, <font class="keywordtype">int</font> nextra=0, <font class="keywordtype">int</font> *extra=0);
00316 <a class="code" href="class_sc__IntCoorGen.html#a0">IntCoorGen</a>(<font class="keyword">const</font> Ref<KeyVal>&);
00317 <a class="code" href="class_sc__IntCoorGen.html#a0">IntCoorGen</a>(StateIn&);
00318
00319 ~IntCoorGen();
00320
00322 <font class="keywordtype">void</font> <a class="code" href="class_sc__IntCoorGen.html#a4">save_data_state</a>(StateOut&);
00323
00325 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__IntCoorGen.html#a5">generate</a>(<font class="keyword">const</font> Ref<SetIntCoor>&);
00326
00328 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__IntCoorGen.html#a6">print</a>(std::ostream& out=ExEnv::out0()) <font class="keyword">const</font>;
00329 };
00330
00331
00332 <font class="comment">// ////////////////////////////////////////////////////////////////////////</font>
00333
00334
<a name="l00338"></a><a class="code" href="class_sc__MolecularCoor.html">00338</a> <font class="keyword">class </font>MolecularCoor: <font class="keyword">public</font> SavableState
00339 {
00340 <font class="keyword">protected</font>:
00341 Ref<Molecule> molecule_;
00342 RefSCDimension dnatom3_; <font class="comment">// the number of atoms x 3</font>
00343 Ref<SCMatrixKit> matrixkit_; <font class="comment">// used to construct matrices</font>
00344
00345 <font class="keywordtype">int</font> debug_;
00346 <font class="keyword">public</font>:
00347 <a class="code" href="class_sc__MolecularCoor.html#a2">MolecularCoor</a>(Ref<Molecule>&);
00348 <a class="code" href="class_sc__MolecularCoor.html#a2">MolecularCoor</a>(StateIn&);
00365 <a class="code" href="class_sc__MolecularCoor.html#a2">MolecularCoor</a>(<font class="keyword">const</font> Ref<KeyVal>&);
00366
00367 <font class="keyword">virtual</font> ~MolecularCoor();
00368
00369 <font class="keywordtype">void</font> <a class="code" href="class_sc__MolecularCoor.html#a4">save_data_state</a>(StateOut&);
00370
<a name="l00373"></a><a class="code" href="class_sc__MolecularCoor.html#a5">00373</a> RefSCDimension <a class="code" href="class_sc__MolecularCoor.html#a5">dim_natom3</a>()<font class="keyword"> </font>{ <font class="keywordflow">return</font> dnatom3_; }
00374
<a name="l00376"></a><a class="code" href="class_sc__MolecularCoor.html#a6">00376</a> Ref<Molecule> <a class="code" href="class_sc__MolecularCoor.html#a6">molecule</a>()<font class="keyword"> const </font>{ <font class="keywordflow">return</font> molecule_; }
00377
00379 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__MolecularCoor.html#a7">print</a>(std::ostream& =ExEnv::out0()) <font class="keyword">const</font> = 0;
00380 <font class="keyword">virtual</font> <font class="keywordtype">void</font> print_simples(std::ostream& =ExEnv::out0()) <font class="keyword">const</font> = 0;
00381
00385 <font class="keyword">virtual</font> RefSCDimension <a class="code" href="class_sc__MolecularCoor.html#a9">dim</a>() = 0;
00386
00390 <font class="keywordtype">int</font> <a class="code" href="class_sc__MolecularCoor.html#a10">to_cartesian</a>(<font class="keyword">const</font> RefSCVector&internal);
00391 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__MolecularCoor.html#a10">to_cartesian</a>(<font class="keyword">const</font> Ref<Molecule>&mol,
00392 <font class="keyword">const</font> RefSCVector&internal) = 0;
00393
00397 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__MolecularCoor.html#a12">to_internal</a>(RefSCVector&internal) = 0;
00398
00403 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__MolecularCoor.html#a10">to_cartesian</a>(RefSCVector&cartesian,RefSCVector&internal) = 0;
00404
00409 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__MolecularCoor.html#a12">to_internal</a>(RefSCVector&internal,RefSCVector&cartesian) = 0;
00410
00414 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__MolecularCoor.html#a10">to_cartesian</a>(RefSymmSCMatrix&cartesian,
00415 RefSymmSCMatrix&internal) =0;
00416
00420 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__MolecularCoor.html#a12">to_internal</a>(RefSymmSCMatrix&internal,
00421 RefSymmSCMatrix&cartesian) = 0;
00422
00425 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__MolecularCoor.html#a17">guess_hessian</a>(RefSymmSCMatrix&hessian) = 0;
00426
00429 <font class="keyword">virtual</font> RefSymmSCMatrix <a class="code" href="class_sc__MolecularCoor.html#a18">inverse_hessian</a>(RefSymmSCMatrix&) = 0;
00430
00432 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__MolecularCoor.html#a19">nconstrained</a>();
00433
00437 <font class="keyword">virtual</font> Ref<NonlinearTransform> <a class="code" href="class_sc__MolecularCoor.html#a20">change_coordinates</a>();
00438
00439 Ref<SCMatrixKit> matrixkit()<font class="keyword"> const </font>{ <font class="keywordflow">return</font> matrixkit_; }
00440 };
00441
00442
<a name="l00445"></a><a class="code" href="class_sc__IntMolecularCoor.html">00445</a> <font class="keyword">class </font>IntMolecularCoor: <font class="keyword">public</font> MolecularCoor
00446 {
00447 <font class="keyword">protected</font>:
00448 Ref<IntCoorGen> generator_;
00449
00450 <font class="keywordtype">void</font> form_K_matrix(RefSCDimension& dredundant,
00451 RefSCDimension& dfixed,
00452 RefSCMatrix& K,
00453 <font class="keywordtype">int</font>*& is_totally_symmetric);
00454
00455 RefSCDimension dim_; <font class="comment">// corresponds to the number of variable coordinates</font>
00456 RefSCDimension dvc_; <font class="comment">// the number of variable + constant coordinates</font>
00457
00458 Ref<SetIntCoor> variable_; <font class="comment">// the variable internal coordinates</font>
00459 Ref<SetIntCoor> constant_; <font class="comment">// the constant internal coordinates</font>
00460
00461 Ref<SetIntCoor> fixed_;
00462 Ref<SetIntCoor> watched_;
00463 Ref<IntCoor> followed_;
00464
00465 <font class="comment">// these are all of the basic coordinates</font>
00466 Ref<SetIntCoor> bonds_;
00467 Ref<SetIntCoor> bends_;
00468 Ref<SetIntCoor> tors_;
00469 Ref<SetIntCoor> outs_;
00470 <font class="comment">// these are provided by the user or generated coordinates that</font>
00471 <font class="comment">// could not be assigned to any of the above catagories</font>
00472 Ref<SetIntCoor> extras_;
00473
00474 Ref<SetIntCoor> all_;
00475
00476 <font class="comment">// Useful relationships</font>
00477 <font class="comment">// variable_->n() + constant_->n() = 3N-6(5)</font>
00478 <font class="comment">// symm_->n() + asymm_->n() = 3N-6(5)</font>
00479
00480 <font class="keywordtype">int</font> update_bmat_; <font class="comment">// if 1 recompute the b matrix during to_cartesian</font>
00481 <font class="keywordtype">int</font> only_totally_symmetric_; <font class="comment">// only coors with tot. symm comp. are varied</font>
00482 <font class="keywordtype">double</font> symmetry_tolerance_; <font class="comment">// tol used to find coors with tot. sym. comp.</font>
00483 <font class="keywordtype">double</font> simple_tolerance_; <font class="comment">// tol used to see if a simple is included</font>
00484 <font class="keywordtype">double</font> coordinate_tolerance_; <font class="comment">// tol used to see if a coor is included</font>
00485 <font class="keywordtype">double</font> cartesian_tolerance_; <font class="comment">// tol used in intco->cart transformation</font>
00486 <font class="keywordtype">double</font> scale_bonds_; <font class="comment">// scale factor for bonds</font>
00487 <font class="keywordtype">double</font> scale_bends_; <font class="comment">// scale factor for bends</font>
00488 <font class="keywordtype">double</font> scale_tors_; <font class="comment">// scale factor for tors</font>
00489 <font class="keywordtype">double</font> scale_outs_; <font class="comment">// scale factor for outs</font>
00490
00491 <font class="keywordtype">int</font> nextra_bonds_;
00492 <font class="keywordtype">int</font>* extra_bonds_;
00493
00494 <font class="keywordtype">int</font> given_fixed_values_; <font class="comment">// if true make molecule have given fixed values</font>
00495
00496 <font class="keywordtype">int</font> decouple_bonds_;
00497 <font class="keywordtype">int</font> decouple_bends_;
00498
00499 <font class="keywordtype">int</font> max_update_steps_;
00500 <font class="keywordtype">double</font> max_update_disp_;
00501
00505 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__IntMolecularCoor.html#b1">init</a>();
00508 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__IntMolecularCoor.html#b2">new_coords</a>();
00510 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__IntMolecularCoor.html#b3">read_keyval</a>(<font class="keyword">const</font> Ref<KeyVal>&);
00511
00512 <font class="comment">// control whether or not to print coordinates when they are formed</font>
00513 <font class="keywordtype">int</font> form_print_simples_;
00514 <font class="keywordtype">int</font> form_print_variable_;
00515 <font class="keywordtype">int</font> form_print_constant_;
00516 <font class="keywordtype">int</font> form_print_molecule_;
00517 <font class="keyword">public</font>:
00518 <a class="code" href="class_sc__IntMolecularCoor.html#a2">IntMolecularCoor</a>(StateIn&);
00519 <a class="code" href="class_sc__IntMolecularCoor.html#a2">IntMolecularCoor</a>(Ref<Molecule>&mol);
00624 <a class="code" href="class_sc__IntMolecularCoor.html#a2">IntMolecularCoor</a>(<font class="keyword">const</font> Ref<KeyVal>&);
00625
00626 <font class="keyword">virtual</font> ~IntMolecularCoor();
00627 <font class="keywordtype">void</font> <a class="code" href="class_sc__IntMolecularCoor.html#a4">save_data_state</a>(StateOut&);
00628
00631 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__IntMolecularCoor.html#a5">form_coordinates</a>(<font class="keywordtype">int</font> keep_variable=0) =0;
00632
00635 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__IntMolecularCoor.html#a6">all_to_cartesian</a>(<font class="keyword">const</font> Ref<Molecule> &,RefSCVector&internal);
00638 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__IntMolecularCoor.html#a7">all_to_internal</a>(<font class="keyword">const</font> Ref<Molecule> &,RefSCVector&internal);
00639
00642 <font class="keyword">virtual</font> RefSCDimension <a class="code" href="class_sc__IntMolecularCoor.html#a8">dim</a>();
00643 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__IntMolecularCoor.html#a11">to_cartesian</a>(<font class="keyword">const</font> Ref<Molecule> &,<font class="keyword">const</font> RefSCVector&internal);
00644 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__IntMolecularCoor.html#a10">to_internal</a>(RefSCVector&internal);
00645 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__IntMolecularCoor.html#a11">to_cartesian</a>(RefSCVector&cartesian,RefSCVector&internal);
00646 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__IntMolecularCoor.html#a10">to_internal</a>(RefSCVector&internal,RefSCVector&cartesian);
00647 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__IntMolecularCoor.html#a11">to_cartesian</a>(RefSymmSCMatrix&cart,RefSymmSCMatrix&internal);
00648 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__IntMolecularCoor.html#a10">to_internal</a>(RefSymmSCMatrix&internal,RefSymmSCMatrix&cart);
00649 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__IntMolecularCoor.html#a15">print</a>(std::ostream& =ExEnv::out0()) <font class="keyword">const</font>;
00650 <font class="keyword">virtual</font> <font class="keywordtype">void</font> print_simples(std::ostream& =ExEnv::out0()) <font class="keyword">const</font>;
00651 <font class="keyword">virtual</font> <font class="keywordtype">void</font> print_variable(std::ostream& =ExEnv::out0()) <font class="keyword">const</font>;
00652 <font class="keyword">virtual</font> <font class="keywordtype">void</font> print_constant(std::ostream& =ExEnv::out0()) <font class="keyword">const</font>;
00653 <font class="keywordtype">int</font> <a class="code" href="class_sc__IntMolecularCoor.html#a19">nconstrained</a>();
00654 };
00655
00656 <font class="comment">// ///////////////////////////////////////////////////////////////////////</font>
00657
<a name="l00667"></a><a class="code" href="class_sc__SymmMolecularCoor.html">00667</a> <font class="keyword">class </font>SymmMolecularCoor: <font class="keyword">public</font> IntMolecularCoor
00668 {
00669 <font class="keyword">protected</font>:
00670 <font class="comment">// true if coordinates should be changed during optimization</font>
00671 <font class="keywordtype">int</font> change_coordinates_;
00672 <font class="comment">// true if hessian should be transformed too (should always be true)</font>
00673 <font class="keywordtype">int</font> transform_hessian_;
00674 <font class="comment">// max value for the condition number if coordinates can be changed</font>
00675 <font class="keywordtype">double</font> max_kappa2_;
00676
00677 <font class="keywordtype">void</font> <a class="code" href="class_sc__SymmMolecularCoor.html#b0">init</a>();
00678 <font class="keyword">public</font>:
00679 <a class="code" href="class_sc__SymmMolecularCoor.html#a2">SymmMolecularCoor</a>(Ref<Molecule>&mol);
00680 <a class="code" href="class_sc__SymmMolecularCoor.html#a2">SymmMolecularCoor</a>(StateIn&);
00699 <a class="code" href="class_sc__SymmMolecularCoor.html#a2">SymmMolecularCoor</a>(<font class="keyword">const</font> Ref<KeyVal>&);
00700
00701 <font class="keyword">virtual</font> ~SymmMolecularCoor();
00702 <font class="keywordtype">void</font> <a class="code" href="class_sc__SymmMolecularCoor.html#a4">save_data_state</a>(StateOut&);
00703
00706 <font class="keywordtype">void</font> <a class="code" href="class_sc__SymmMolecularCoor.html#a5">form_coordinates</a>(<font class="keywordtype">int</font> keep_variable=0);
00707
00709 <font class="keywordtype">void</font> <a class="code" href="class_sc__SymmMolecularCoor.html#a6">guess_hessian</a>(RefSymmSCMatrix&hessian);
00711 RefSymmSCMatrix <a class="code" href="class_sc__SymmMolecularCoor.html#a7">inverse_hessian</a>(RefSymmSCMatrix&);
00712
00715 Ref<NonlinearTransform> <a class="code" href="class_sc__SymmMolecularCoor.html#a8">change_coordinates</a>();
00716
00717 <font class="keywordtype">void</font> <a class="code" href="class_sc__SymmMolecularCoor.html#a9">print</a>(std::ostream& =ExEnv::out0()) <font class="keyword">const</font>;
00718 };
00719
00720 <font class="comment">// ///////////////////////////////////////////////////////////////////////</font>
00721
<a name="l00724"></a><a class="code" href="class_sc__RedundMolecularCoor.html">00724</a> <font class="keyword">class </font>RedundMolecularCoor: <font class="keyword">public</font> IntMolecularCoor
00725 {
00726
00727 <font class="keyword">public</font>:
00728 <a class="code" href="class_sc__RedundMolecularCoor.html#a2">RedundMolecularCoor</a>(Ref<Molecule>&mol);
00729 <a class="code" href="class_sc__RedundMolecularCoor.html#a2">RedundMolecularCoor</a>(StateIn&);
00731 <a class="code" href="class_sc__RedundMolecularCoor.html#a2">RedundMolecularCoor</a>(<font class="keyword">const</font> Ref<KeyVal>&);
00732
00733 <font class="keyword">virtual</font> ~RedundMolecularCoor();
00734 <font class="keywordtype">void</font> <a class="code" href="class_sc__RedundMolecularCoor.html#a4">save_data_state</a>(StateOut&);
00735
00738 <font class="keywordtype">void</font> <a class="code" href="class_sc__RedundMolecularCoor.html#a5">form_coordinates</a>(<font class="keywordtype">int</font> keep_variable=0);
00740 <font class="keywordtype">void</font> <a class="code" href="class_sc__RedundMolecularCoor.html#a6">guess_hessian</a>(RefSymmSCMatrix&hessian);
00742 RefSymmSCMatrix <a class="code" href="class_sc__RedundMolecularCoor.html#a7">inverse_hessian</a>(RefSymmSCMatrix&);
00743 };
00744
00745 <font class="comment">// ///////////////////////////////////////////////////////////////////////</font>
00746
<a name="l00751"></a><a class="code" href="class_sc__CartMolecularCoor.html">00751</a> <font class="keyword">class </font>CartMolecularCoor: <font class="keyword">public</font> MolecularCoor
00752 {
00753 <font class="keyword">private</font>:
00754 <font class="keyword">protected</font>:
00755 RefSCDimension dim_; <font class="comment">// the number of atoms x 3</font>
00756
00758 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__CartMolecularCoor.html#b0">init</a>();
00759 <font class="keyword">public</font>:
00760 <a class="code" href="class_sc__CartMolecularCoor.html#a2">CartMolecularCoor</a>(Ref<Molecule>&mol);
00761 <a class="code" href="class_sc__CartMolecularCoor.html#a2">CartMolecularCoor</a>(StateIn&);
00763 <a class="code" href="class_sc__CartMolecularCoor.html#a2">CartMolecularCoor</a>(<font class="keyword">const</font> Ref<KeyVal>&);
00764
00765 <font class="keyword">virtual</font> ~CartMolecularCoor();
00766
00767 <font class="keywordtype">void</font> <a class="code" href="class_sc__CartMolecularCoor.html#a4">save_data_state</a>(StateOut&);
00768
00770 <font class="keyword">virtual</font> RefSCDimension <a class="code" href="class_sc__CartMolecularCoor.html#a5">dim</a>();
00771 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__CartMolecularCoor.html#a8">to_cartesian</a>(<font class="keyword">const</font> Ref<Molecule>&,<font class="keyword">const</font> RefSCVector&internal);
00772 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__CartMolecularCoor.html#a7">to_internal</a>(RefSCVector&internal);
00773 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__CartMolecularCoor.html#a8">to_cartesian</a>(RefSCVector&cartesian,RefSCVector&internal);
00774 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__CartMolecularCoor.html#a7">to_internal</a>(RefSCVector&internal,RefSCVector&cartesian);
00775 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__CartMolecularCoor.html#a8">to_cartesian</a>(RefSymmSCMatrix&cart,RefSymmSCMatrix&internal);
00776 <font class="keyword">virtual</font> <font class="keywordtype">int</font> <a class="code" href="class_sc__CartMolecularCoor.html#a7">to_internal</a>(RefSymmSCMatrix&internal,RefSymmSCMatrix&cart);
00777 <font class="keyword">virtual</font> <font class="keywordtype">void</font> <a class="code" href="class_sc__CartMolecularCoor.html#a12">print</a>(std::ostream& =ExEnv::out0()) <font class="keyword">const</font>;
00778 <font class="keyword">virtual</font> <font class="keywordtype">void</font> print_simples(std::ostream& =ExEnv::out0()) <font class="keyword">const</font>;
00779 <font class="keywordtype">void</font> <a class="code" href="class_sc__CartMolecularCoor.html#a14">guess_hessian</a>(RefSymmSCMatrix&hessian);
00780 RefSymmSCMatrix <a class="code" href="class_sc__CartMolecularCoor.html#a15">inverse_hessian</a>(RefSymmSCMatrix&);
00781 };
00782
00783 }
00784
00785 <font class="preprocessor">#endif</font>
00786 <font class="preprocessor"></font>
00787 <font class="comment">// Local Variables:</font>
00788 <font class="comment">// mode: c++</font>
00789 <font class="comment">// c-file-style: "CLJ"</font>
00790 <font class="comment">// End:</font>
</div></pre><hr>
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