Index: src/LevMartester.cpp
===================================================================
--- src/LevMartester.cpp	(revision f06d528db608aa670621118d65d43dc67a5b5fd2)
+++ src/LevMartester.cpp	(revision f06d528db608aa670621118d65d43dc67a5b5fd2)
@@ -0,0 +1,241 @@
+/*
+ * Project: MoleCuilder
+ * Description: creates and alters molecular systems
+ * Copyright (C)  2012 University of Bonn. All rights reserved.
+ * Please see the COPYING file or "Copyright notice" in builder.cpp for details.
+ * 
+ *
+ *   This file is part of MoleCuilder.
+ *
+ *    MoleCuilder is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 2 of the License, or
+ *    (at your option) any later version.
+ *
+ *    MoleCuilder is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with MoleCuilder.  If not, see <http://www.gnu.org/licenses/>. 
+ */
+
+/*
+ * LevMartester.cpp
+ *
+ *  Created on: Sep 27, 2012
+ *      Author: heber
+ */
+
+
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "CodePatterns/MemDebug.hpp"
+
+#include <boost/archive/text_iarchive.hpp>
+#include <boost/filesystem.hpp>
+#include <boost/program_options.hpp>
+
+#include <fstream>
+#include <iostream>
+#include <iterator>
+#include <vector>
+
+#include <levmar.h>
+
+#include "CodePatterns/Assert.hpp"
+#include "CodePatterns/Log.hpp"
+
+#include "LinearAlgebra/Vector.hpp"
+
+#include "Fragmentation/Homology/HomologyContainer.hpp"
+#include "Fragmentation/SetValues/Fragment.hpp"
+
+namespace po = boost::program_options;
+
+HomologyGraph getFirstGraphWithTwoCarbons(const HomologyContainer &homologies)
+{
+  FragmentNode SaturatedCarbon(6,4); // carbon has atomic number 6 and should have 4 bonds for C2H6
+  for (HomologyContainer::container_t::const_iterator iter =
+      homologies.begin(); iter != homologies.end(); ++iter) {
+    if (iter->first.hasNode(SaturatedCarbon,2))
+      return iter->first;
+  }
+  return HomologyGraph();
+}
+
+/* Meyer's (reformulated) problem, minimum at (2.48, 6.18, 3.45) */
+void meyer(double *p, double *x, int m, int n, void *data)
+{
+register int i;
+double ui;
+
+        for(i=0; i<n; ++i){
+                ui=0.45+0.05*i;
+                x[i]=p[0]*exp(10.0*p[1]/(ui+p[2]) - 13.0);
+        }
+}
+
+void jacmeyer(double *p, double *jac, int m, int n, void *data)
+{
+register int i, j;
+double ui, tmp;
+
+  for(i=j=0; i<n; ++i){
+          ui=0.45+0.05*i;
+          tmp=exp(10.0*p[1]/(ui+p[2]) - 13.0);
+
+          jac[j++]=tmp;
+          jac[j++]=10.0*p[0]*tmp/(ui+p[2]);
+          jac[j++]=-10.0*p[0]*p[1]*tmp/((ui+p[2])*(ui+p[2]));
+  }
+}
+
+
+int main(int argc, char **argv)
+{
+  std::cout << "Hello to the World from LevMar!" << std::endl;
+
+  // load homology file
+  po::options_description desc("Allowed options");
+  desc.add_options()
+      ("help", "produce help message")
+      ("homology-file", po::value< boost::filesystem::path >(), "homology file to parse")
+  ;
+
+  po::variables_map vm;
+  po::store(po::parse_command_line(argc, argv, desc), vm);
+  po::notify(vm);
+
+  if (vm.count("help")) {
+      std::cout << desc << "\n";
+      return 1;
+  }
+
+  boost::filesystem::path homology_file;
+  if (vm.count("homology-file")) {
+    homology_file = vm["homology-file"].as<boost::filesystem::path>();
+    LOG(1, "INFO: Parsing " << homology_file.string() << ".");
+  } else {
+    LOG(0, "homology-file level was not set.");
+  }
+  HomologyContainer homologies;
+  if (boost::filesystem::exists(homology_file)) {
+    std::ifstream returnstream(homology_file.string().c_str());
+    if (returnstream.good()) {
+      boost::archive::text_iarchive ia(returnstream);
+      ia >> homologies;
+    } else {
+      ELOG(2, "Failed to parse from " << homology_file.string() << ".");
+    }
+    returnstream.close();
+  } else {
+    ELOG(0, homology_file << " does not exist.");
+  }
+
+  // first we try to look into the HomologyContainer
+  LOG(1, "INFO: Listing all present homologies ...");
+  for (HomologyContainer::container_t::const_iterator iter =
+      homologies.begin(); iter != homologies.end(); ++iter) {
+    LOG(1, "INFO: graph " << iter->first << " has Fragment "
+        << iter->second.first << " and associated energy " << iter->second.second << ".");
+  }
+
+  // then we ought to pick the right HomologyGraph ...
+  const HomologyGraph graph = getFirstGraphWithTwoCarbons(homologies);
+  LOG(1, "First representative graph containing two saturated carbons is " << graph << ".");
+
+  // Afterwards we go through all of this type and gather the distance and the energy value
+  typedef std::vector< std::pair<double, double> > DistanceEnergyVector_t;
+  DistanceEnergyVector_t DistanceEnergyVector;
+  std::pair<HomologyContainer::const_iterator, HomologyContainer::const_iterator> range =
+      homologies.getHomologousGraphs(graph);
+  for (HomologyContainer::const_iterator iter = range.first; iter != range.second; ++iter) {
+    // get distance out of Fragment
+    const Fragment &fragment = iter->second.first;
+    const Fragment::charges_t charges = fragment.getCharges();
+    const Fragment::positions_t positions = fragment.getPositions();
+    std::vector< Vector > DistanceVectors;
+    for (Fragment::charges_t::const_iterator chargeiter = charges.begin();
+        chargeiter != charges.end(); ++chargeiter) {
+      if (*chargeiter == 6) {
+        Fragment::positions_t::const_iterator positer = positions.begin();
+        const size_t steps = std::distance(charges.begin(), chargeiter);
+        std::advance(positer, steps);
+        DistanceVectors.push_back(Vector((*positer)[0], (*positer)[1], (*positer)[2]));
+      }
+    }
+    ASSERT( DistanceVectors.size() == (size_t)2,
+        "main() - found not exactly two carbon atoms in fragment.");
+    const double distance = DistanceVectors[0].distance(DistanceVectors[1]);
+    const double energy = iter->second.second;
+    DistanceEnergyVector.push_back( std::make_pair(distance, energy) );
+  }
+  LOG(1, "INFO: I gathered the following " << DistanceEnergyVector.size() << " data pairs: ");
+  for (DistanceEnergyVector_t::const_iterator dataiter = DistanceEnergyVector.begin();
+      dataiter != DistanceEnergyVector.end(); ++dataiter) {
+    LOG(1, "INFO: " << dataiter->first << " with energy " << dataiter->second);
+  }
+  // NOTICE that distance are in bohrradi as they come from MPQC!
+
+  // let levmar optimize
+  register int i, j;
+  int ret;
+  double p[5], // 5 is max(2, 3, 5)
+             x[16]; // 16 is max(2, 3, 5, 6, 16)
+  int m, n;
+  double opts[LM_OPTS_SZ], info[LM_INFO_SZ];
+
+  opts[0]=LM_INIT_MU; opts[1]=1E-15; opts[2]=1E-15; opts[3]=1E-20;
+  opts[4]= LM_DIFF_DELTA; // relevant only if the Jacobian is approximated using finite differences; specifies forward differencing
+  //opts[4]=-LM_DIFF_DELTA; // specifies central differencing to approximate Jacobian; more accurate but more expensive to compute!
+
+  m=3; n=16;
+  p[0]=8.85; p[1]=4.0; p[2]=2.5;
+  x[0]=34.780;        x[1]=28.610; x[2]=23.650; x[3]=19.630;
+  x[4]=16.370;        x[5]=13.720; x[6]=11.540; x[7]=9.744;
+  x[8]=8.261; x[9]=7.030; x[10]=6.005; x[11]=5.147;
+  x[12]=4.427;        x[13]=3.820; x[14]=3.307; x[15]=2.872;
+  ret=dlevmar_der(meyer, jacmeyer, p, x, m, n, 1000, opts, info, NULL, NULL, NULL); // with analytic Jacobian
+
+ { double *work, *covar;
+  work=(double *)malloc((LM_DIF_WORKSZ(m, n)+m*m)*sizeof(double));
+  if(!work){
+      fprintf(stderr, "memory allocation request failed in main()\n");
+    exit(1);
+  }
+  covar=work+LM_DIF_WORKSZ(m, n);
+
+  ret=dlevmar_dif(meyer, p, x, m, n, 1000, opts, info, work, covar, NULL); // no Jacobian, caller allocates work memory, covariance estimated
+
+  printf("Covariance of the fit:\n");
+  for(i=0; i<m; ++i){
+    for(j=0; j<m; ++j)
+      printf("%g ", covar[i*m+j]);
+    printf("\n");
+  }
+  printf("\n");
+
+  free(work);
+ }
+
+//  {
+//   double err[16];
+//   dlevmar_chkjac(meyer, jacmeyer, p, m, n, NULL, err);
+//   for(i=0; i<n; ++i) printf("gradient %d, err %g\n", i, err[i]);
+//  }
+
+  printf("Levenberg-Marquardt returned %d in %g iter, reason %g\nSolution: ", ret, info[5], info[6]);
+  for(i=0; i<m; ++i)
+    printf("%.7g ", p[i]);
+  printf("\n\nMinimization info:\n");
+  for(i=0; i<LM_INFO_SZ; ++i)
+    printf("%g ", info[i]);
+  printf("\n");
+
+  return 0;
+}
