Index: src/Actions/PotentialAction/FitPartialChargesAction.cpp
===================================================================
--- src/Actions/PotentialAction/FitPartialChargesAction.cpp	(revision 50d49dca91aa5db281d312ca5ee0fbad52557a21)
+++ src/Actions/PotentialAction/FitPartialChargesAction.cpp	(revision 50d49dca91aa5db281d312ca5ee0fbad52557a21)
@@ -0,0 +1,206 @@
+/*
+ * Project: MoleCuilder
+ * Description: creates and alters molecular systems
+ * Copyright (C)  2013 Frederik Heber. All rights reserved.
+ * 
+ *
+ *   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/>.
+ */
+
+/*
+ * FitPartialChargesAction.cpp
+ *
+ *  Created on: Jul 03, 2013
+ *      Author: heber
+ */
+
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+// needs to come before MemDebug due to placement new
+#include <boost/archive/text_iarchive.hpp>
+
+#include "CodePatterns/MemDebug.hpp"
+
+#include "Atom/atom.hpp"
+#include "CodePatterns/Log.hpp"
+#include "Fragmentation/Exporters/ExportGraph_ToFiles.hpp"
+#include "Fragmentation/Graph.hpp"
+#include "World.hpp"
+
+#include <boost/filesystem.hpp>
+#include <boost/foreach.hpp>
+#include <algorithm>
+#include <functional>
+#include <iostream>
+#include <string>
+
+#include "Actions/PotentialAction/FitPartialChargesAction.hpp"
+
+#include "Potentials/PartialNucleiChargeFitter.hpp"
+
+#include "Element/element.hpp"
+#include "Fragmentation/Homology/HomologyContainer.hpp"
+#include "Fragmentation/Homology/HomologyGraph.hpp"
+#include "Fragmentation/Summation/SetValues/SamplingGrid.hpp"
+#include "FunctionApproximation/Extractors.hpp"
+#include "Potentials/PartialNucleiChargeFitter.hpp"
+#include "Potentials/SerializablePotential.hpp"
+#include "World.hpp"
+
+using namespace MoleCuilder;
+
+// and construct the stuff
+#include "FitPartialChargesAction.def"
+#include "Action_impl_pre.hpp"
+/** =========== define the function ====================== */
+
+inline
+HomologyGraph getFirstGraphwithSpecifiedElements(
+    const HomologyContainer &homologies,
+    const SerializablePotential::ParticleTypes_t &types)
+{
+  ASSERT( !types.empty(),
+      "getFirstGraphwithSpecifiedElements() - charges is empty?");
+  // create charges
+  Fragment::charges_t charges;
+  charges.resize(types.size());
+  std::transform(types.begin(), types.end(),
+      charges.begin(), boost::lambda::_1);
+  // convert into count map
+  Extractors::elementcounts_t counts_per_charge =
+      Extractors::_detail::getElementCounts(charges);
+  ASSERT( !counts_per_charge.empty(),
+      "getFirstGraphwithSpecifiedElements() - charge counts are empty?");
+  LOG(2, "DEBUG: counts_per_charge is " << counts_per_charge << ".");
+  // we want to check each (unique) key only once
+  HomologyContainer::const_key_iterator olditer = homologies.key_end();
+  for (HomologyContainer::const_key_iterator iter =
+      homologies.key_begin(); iter != homologies.key_end();
+      iter = homologies.getNextKey(iter)) {
+    // if it's the same as the old one, skip it
+    if (olditer == iter)
+      continue;
+    else
+      olditer = iter;
+    // if it's a new key, check if every element has the right number of counts
+    Extractors::elementcounts_t::const_iterator countiter = counts_per_charge.begin();
+    for (; countiter != counts_per_charge.end(); ++countiter)
+      if (!(*iter).hasTimesAtomicNumber(
+          static_cast<size_t>(countiter->first),
+          static_cast<size_t>(countiter->second))
+          )
+        break;
+    if( countiter == counts_per_charge.end())
+      return *iter;
+  }
+  return HomologyGraph();
+}
+
+ActionState::ptr PotentialFitPartialChargesAction::performCall() {
+
+  // fragment specifies the homology fragment to use
+  SerializablePotential::ParticleTypes_t fragmentnumbers;
+  {
+    const std::vector<const element *> &fragment = params.fragment.get();
+    std::transform(fragment.begin(), fragment.end(), std::back_inserter(fragmentnumbers),
+        boost::bind(&element::getAtomicNumber, _1));
+  }
+
+  // parse homologies into container
+  HomologyContainer &homologies = World::getInstance().getHomologies();
+  const HomologyGraph graph = getFirstGraphwithSpecifiedElements(homologies,fragmentnumbers);
+  HomologyContainer::range_t range = homologies.getHomologousGraphs(graph);
+  // for the moment just use the very first fragment
+  if (range.first == range.second) {
+    STATUS("HomologyContainer does not contain specified fragment.");
+    return Action::failure;
+  }
+
+  // average partial charges over all fragments
+  HomologyContainer::const_iterator iter = range.first;
+  if (!iter->second.containsGrids) {
+    STATUS("This HomologyGraph does not contain sampled grids.");
+    return Action::failure;
+  }
+  PartialNucleiChargeFitter::charges_t averaged_charges;
+  averaged_charges.resize(iter->second.fragment.getCharges().size(), 0.);
+  size_t NoFragments = 0;
+  for (;
+      iter != range.second; ++iter, ++NoFragments) {
+    if (!iter->second.containsGrids) {
+      ELOG(2, "This HomologyGraph does not contain sampled grids,\ndid you forget to add '--store-grids 1' to AnalyseFragmentResults.");
+      return Action::failure;
+    }
+    const Fragment &fragment = iter->second.fragment;
+  //  const double &energy = iter->second.energy;
+  //  const SamplingGrid &charge = iter->second.charge_distribution;
+    const SamplingGrid &potential = iter->second.potential_distribution;
+    if ((potential.level == 0)
+        || ((potential.begin[0] == potential.end[0])
+            && (potential.begin[1] == potential.end[1])
+            && (potential.begin[2] == potential.end[2]))) {
+      ELOG(1, "Sampled grid contains grid made of zero points.");
+      return Action::failure;
+    }
+
+    // then we extract positions from fragment
+    PartialNucleiChargeFitter::positions_t positions;
+    Fragment::positions_t fragmentpositions = fragment.getPositions();
+    positions.reserve(fragmentpositions.size());
+    BOOST_FOREACH( Fragment::position_t pos, fragmentpositions) {
+      positions.push_back( Vector(pos[0], pos[1], pos[2]) );
+    }
+    PartialNucleiChargeFitter fitter(potential, positions, params.radius.get());
+    fitter();
+    PartialNucleiChargeFitter::charges_t return_charges = fitter.getSolutionAsCharges_t();
+    std::transform(
+        return_charges.begin(), return_charges.end(),
+        averaged_charges.begin(),
+        averaged_charges.begin(),
+        std::plus<PartialNucleiChargeFitter::charge_t>());
+  }
+  std::transform(averaged_charges.begin(),averaged_charges.end(),
+      averaged_charges.begin(),
+      std::bind1st(std::multiplies<PartialNucleiChargeFitter::charge_t>(),1./NoFragments)
+  );
+
+
+  // output fitted charges
+  LOG(0, "STATUS: We have fitted the following charges " << averaged_charges
+      << ", averaged over " << NoFragments << " fragments.");
+
+  return Action::success;
+}
+
+ActionState::ptr PotentialFitPartialChargesAction::performUndo(ActionState::ptr _state) {
+  return Action::success;
+}
+
+ActionState::ptr PotentialFitPartialChargesAction::performRedo(ActionState::ptr _state){
+  return Action::success;
+}
+
+bool PotentialFitPartialChargesAction::canUndo() {
+  return false;
+}
+
+bool PotentialFitPartialChargesAction::shouldUndo() {
+  return false;
+}
+/** =========== end of function ====================== */
