Index: src/Actions/PotentialAction/FitFragmentPartialChargesAction.cpp
===================================================================
--- src/Actions/PotentialAction/FitFragmentPartialChargesAction.cpp	(revision 2f9fafed8550e71352c619338faefe51479ec428)
+++ src/Actions/PotentialAction/FitFragmentPartialChargesAction.cpp	(revision 2f9fafed8550e71352c619338faefe51479ec428)
@@ -0,0 +1,612 @@
+/*
+ * Project: MoleCuilder
+ * Description: creates and alters molecular systems
+ * Copyright (C)  2016 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/>.
+ */
+
+/*
+ * FitFragmentPartialChargesAction.cpp
+ *
+ *  Created on: Oct 09, 2016
+ *      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/bimap.hpp>
+#include <boost/bimap/multiset_of.hpp>
+#include <boost/bind.hpp>
+#include <boost/filesystem.hpp>
+#include <boost/foreach.hpp>
+#include <boost/mpl/for_each.hpp>
+
+#include <algorithm>
+#include <functional>
+#include <iostream>
+#include <string>
+
+#include "Actions/PotentialAction/FitFragmentPartialChargesAction.hpp"
+
+#include "Potentials/PartialNucleiChargeFitter.hpp"
+
+#include "AtomIdSet.hpp"
+#include "Descriptors/AtomIdDescriptor.hpp"
+#include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
+#include "Fragmentation/Homology/AtomFragmentsMap.hpp"
+#include "Fragmentation/Homology/HomologyGraph.hpp"
+#include "Fragmentation/Summation/Containers/FragmentationResultContainer.hpp"
+#include "Fragmentation/Summation/Containers/PartialChargesFused.hpp"
+#include "Fragmentation/Summation/Containers/PartialChargesMap.hpp"
+#include "Fragmentation/Summation/SetValues/IndexedPartialCharges.hpp"
+#include "Fragmentation/Summation/SetValues/SamplingGrid.hpp"
+#include "Fragmentation/Summation/ZeroInstanceInitializer.hpp"
+#include "FunctionApproximation/Extractors.hpp"
+#include "Potentials/PartialNucleiChargeFitter.hpp"
+#include "Potentials/Particles/ParticleFactory.hpp"
+#include "Potentials/Particles/ParticleRegistry.hpp"
+#include "Potentials/SerializablePotential.hpp"
+#include "World.hpp"
+
+using namespace MoleCuilder;
+
+// and construct the stuff
+#include "FitFragmentPartialChargesAction.def"
+#include "Action_impl_pre.hpp"
+/** =========== define the function ====================== */
+
+namespace detail {
+  typedef std::map<KeySet, HomologyGraph> KeysetsToGraph_t;
+
+  typedef std::map<HomologyGraph, PartialNucleiChargeFitter::charges_t> GraphFittedChargeMap_t;
+
+  typedef std::map<atomId_t, double> fitted_charges_t;
+
+  typedef std::map<HomologyGraph, size_t> GraphIndex_t;
+
+  typedef std::set<size_t> AtomsGraphIndices_t;
+  typedef boost::bimaps::bimap<
+      boost::bimaps::multiset_of<AtomsGraphIndices_t>,
+      atomId_t > GraphIndices_t;
+
+  typedef std::map<std::set<size_t>, std::map<atomicNumber_t, std::string> > AtomParticleNames_t;
+
+  typedef std::map<std::set<size_t>, std::string> GraphToNameMap_t;
+
+  typedef std::map<KeySet, IndexedPartialCharges::values_t> fittedcharges_per_fragment_t;
+
+  typedef std::map<AtomFragmentsMap::indices_t, KeySet> indices_to_keysets_t;
+
+  typedef std::map< std::string, std::pair<double, size_t> > average_charge_map_t;
+};
+
+static void enforceZeroTotalCharge(
+    PartialNucleiChargeFitter::charges_t &_averaged_charges)
+{
+  double charge_sum = 0.;
+  charge_sum = std::accumulate(_averaged_charges.begin(), _averaged_charges.end(), charge_sum);
+  if (fabs(charge_sum) > MYEPSILON) {
+    std::transform(
+        _averaged_charges.begin(), _averaged_charges.end(),
+        _averaged_charges.begin(),
+        boost::bind(std::minus<double>(), _1, charge_sum/_averaged_charges.size()));
+  }
+  charge_sum = 0.;
+  charge_sum = std::accumulate(_averaged_charges.begin(), _averaged_charges.end(), charge_sum);
+  ASSERT( fabs(charge_sum) < MYEPSILON,
+      "enforceZeroTotalCharge() - enforcing neutral net charge failed, "
+      +toString(charge_sum)+" is the remaining net charge.");
+
+  LOG(2, "DEBUG: final charges with net zero charge are " << _averaged_charges);
+}
+
+static
+std::set<KeySet> accumulateKeySetsForAtoms(
+    const AtomFragmentsMap::AtomFragmentsMap_t &_atommap,
+    const std::vector<const atom *> &_selected_atoms)
+{
+  std::set<KeySet> fragments;
+  for (std::vector<const atom *>::const_iterator iter = _selected_atoms.begin();
+      iter != _selected_atoms.end(); ++iter) {
+    const atomId_t atomid = (*iter)->getId();
+    const AtomFragmentsMap::AtomFragmentsMap_t::const_iterator atomiter =
+        _atommap.find(atomid);
+    if ((*iter)->getElementNo() != 1) {
+      if (atomiter == _atommap.end()) {
+        ELOG(2, "There are no fragments associated to " << atomid << ".");
+        continue;
+      }
+      const AtomFragmentsMap::keysets_t &keysets = atomiter->second;
+      LOG(2, "DEBUG: atom " << atomid << " has " << keysets.size() << " fragments.");
+      fragments.insert( keysets.begin(), keysets.end() );
+    } else {
+      LOG(3, "DEBUG: Skipping atom " << atomid << " as it's hydrogen.");
+    }
+  }
+  return fragments;
+}
+
+static
+void getKeySetsToGraphMapping(
+    detail::KeysetsToGraph_t &_keyset_graphs,
+    const std::set<KeySet> &_fragments,
+    const AtomFragmentsMap &_atomfragments)
+{
+  for (std::set<KeySet>::const_iterator fragmentiter = _fragments.begin();
+      fragmentiter != _fragments.end(); ++fragmentiter) {
+    const KeySet &keyset = *fragmentiter;
+    const AtomFragmentsMap::indices_t &forceindices = _atomfragments.getFullKeyset(keyset);
+    ASSERT( !forceindices.empty(),
+        "getKeySetsToGraphMapping() - force keyset to "+toString(keyset)+" is empty.");
+    KeySet forcekeyset;
+    forcekeyset.insert(forceindices.begin(), forceindices.end());
+    forcekeyset.erase(-1);
+    const HomologyGraph graph(forcekeyset);
+    LOG(2, "DEBUG: Associating keyset " << forcekeyset << " with graph " << graph);
+    _keyset_graphs.insert( std::make_pair(keyset, graph) );
+  }
+}
+
+static
+bool getPartialChargesForAllIndexSets(
+    detail::fittedcharges_per_fragment_t &_fittedcharges_per_fragment,
+    const FragmentationResultContainer &_container,
+    const std::set<KeySet> &_fragments,
+    const double _mask_radius,
+    const bool enforceZeroCharge)
+{
+  const std::map<JobId_t, MPQCData> &shortrangedata = _container.getShortRangeResults();
+  const std::map<JobId_t, VMGData> &longrangedata = _container.getLongRangeResults();
+  const KeySetsContainer &keysets = _container.getKeySets();
+
+  std::map<JobId_t, MPQCData>::const_iterator shortiter = shortrangedata.begin();
+  std::map<JobId_t, VMGData>::const_iterator longiter = longrangedata.begin();
+  KeySetsContainer::ArrayOfIntVectors::const_iterator keysetiter = keysets.KeySets.begin();
+  for (; keysetiter != keysets.KeySets.end(); ++keysetiter, ++shortiter, ++longiter) {
+    // check whether its an allowed keyset (atomfragments has keyset, not forcekeyset)
+    KeySet currentset;
+    currentset.insert(keysetiter->begin(), keysetiter->end());
+    if (_fragments.find(currentset) == _fragments.end())
+      continue;
+
+    // obtain positions and sampled potential
+    const Fragment::positions_t &fragmentpositions = shortiter->second.positions;
+    const SamplingGrid &potential = longiter->second.both_sampled_potential;
+    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 0;
+    }
+
+    // convert std::vector<double> to Vector
+    PartialNucleiChargeFitter::positions_t positions;
+    positions.reserve(fragmentpositions.size());
+    BOOST_FOREACH( Fragment::position_t pos, fragmentpositions) {
+      positions.push_back( Vector(pos[0], pos[1], pos[2]) );
+    }
+
+    // fit charges
+    PartialNucleiChargeFitter fitter(potential, positions, _mask_radius);
+    fitter();
+    PartialNucleiChargeFitter::charges_t return_charges = fitter.getSolutionAsCharges_t();
+    LOG(2, "DEBUG: fitted charges are " << return_charges);
+
+    // make sum of charges zero if desired
+    if (enforceZeroCharge)
+      enforceZeroTotalCharge(return_charges);
+
+    // output status info fitted charges
+    LOG(2, "DEBUG: For fragment " << *keysetiter
+        << " we have fitted the following charges " << return_charges << ".");
+
+    IndexedPartialCharges::values_t values;
+    for (PartialNucleiChargeFitter::charges_t::const_iterator chargeiter = return_charges.begin();
+        chargeiter != return_charges.end(); ++chargeiter) {
+      values.push_back(partial_charge_t(*chargeiter));
+    }
+    _fittedcharges_per_fragment.insert( std::make_pair(currentset, values) );
+  }
+  return true;
+}
+
+static const atom * getNonHydrogenSurrogate(const atom * const _walker)
+{
+  const atom * surrogate = _walker;
+  if (surrogate->getElementNo() == 1) {
+    // it's hydrogen, check its bonding and use its bond partner instead to request
+    // keysets
+    const BondList &ListOfBonds = surrogate->getListOfBonds();
+    if ( ListOfBonds.size() != 1) {
+      ELOG(1, "Solitary hydrogen in atom " << surrogate->getId() << " detected.");
+      return _walker;
+    }
+    surrogate = (*ListOfBonds.begin())->GetOtherAtom(surrogate);
+  }
+  return surrogate;
+}
+
+static void addToParticleRegistry(
+    const ParticleFactory &factory,
+    ParticleRegistry &registry,
+    const periodentafel &periode,
+    const detail::fitted_charges_t &_fitted_charges,
+    const detail::GraphIndices_t &_GraphIndices,
+    detail::AtomParticleNames_t &_atom_particlenames)
+{
+  /// We step here through the atoms and check for all atoms of the
+  /// same element and which belong to the same set of graphs (via the set
+  /// of their unique enumeration indices) then they get the same particle
+  detail::average_charge_map_t average_charge_map;
+  for (detail::fitted_charges_t::const_iterator chargeiter = _fitted_charges.begin();
+      chargeiter != _fitted_charges.end(); ++chargeiter) {
+    const atomId_t &atomid = chargeiter->first;
+    const double &charge = chargeiter->second;
+    const atom * const walker = World::getInstance().getAtom(AtomById(atomid));
+    ASSERT( walker != NULL,
+        "addToParticleRegistry() - atom "+toString(atomid)
+        +" not present in the World?");
+    const detail::GraphIndices_t::right_const_iterator graphiter =
+        _GraphIndices.right.find(atomid);
+    ASSERT(graphiter != _GraphIndices.right.end(),
+        "addToParticleRegistry() - atom #"+toString(atomid)
+        +" not contained in GraphIndices.");
+    const detail::AtomParticleNames_t::iterator nameiter =
+        _atom_particlenames.find(graphiter->second);
+    const atomicNumber_t elementno = walker->getElementNo();
+    std::string name;
+    if ((nameiter != _atom_particlenames.end()) && (nameiter->second.count(elementno))) {
+        name = (nameiter->second)[elementno];
+        detail::average_charge_map_t::iterator averageiter = average_charge_map.find(name);
+        ASSERT( averageiter != average_charge_map.end(),
+            "addToParticleRegistry() - could not find name "+toString(nameiter->second)
+            +" in average charge map.");
+        // add charge to particle
+        averageiter->second.first += charge;
+        ++(averageiter->second.second);
+        LOG(1, "INFO: Adding additional charge " << charge << " to particle " << name << " for atom "
+            << *walker << " with element " << elementno << ".");
+    } else {
+      if (nameiter == _atom_particlenames.end())
+        _atom_particlenames.insert(
+            std::make_pair(graphiter->second, std::map<atomicNumber_t, std::string>()) );
+      name = Particle::findFreeName(periode, elementno);
+      _atom_particlenames[graphiter->second][elementno] = name;
+      LOG(1, "INFO: Adding particle " << name << " for atom "
+          << *walker << " with element " << elementno << " and initial charge "
+          << charge << ".");
+      factory.createInstance(name, elementno, charge);
+#ifndef NDEBUG
+      std::pair< detail::average_charge_map_t::iterator, bool> inserter =
+#endif
+          average_charge_map.insert( std::make_pair(name, std::make_pair(charge,1)) );
+      ASSERT( inserter.second,
+          "addToParticleRegistry() - name "+name+" already present in average charge map?");
+    }
+  }
+
+  // go through map, average and insert average charge into factory
+  for (detail::average_charge_map_t::const_iterator averageiter = average_charge_map.begin();
+      averageiter != average_charge_map.end(); ++averageiter) {
+    const std::string &name = averageiter->first;
+    const double &charge = averageiter->second.first;
+    const size_t &times = averageiter->second.second;
+    ASSERT( times != 0,
+        "addToParticleRegistry() - zero times in average charge map is not allowed.");
+    Particle *particle = registry.getByName(name);
+    particle->charge = charge/(double)times;
+  }
+}
+
+static bool isNotHydrogen(const atom * const _atom)
+{
+  return (_atom->getElementNo() != (atomicNumber_t) 1);
+}
+
+static struct KeySetSizeComp {
+  bool operator() (const KeySet &a, const KeySet &b) { return a.size()<b.size(); }
+} keyset_comparator;
+
+#include <boost/fusion/sequence.hpp>
+#include <boost/mpl/for_each.hpp>
+
+#include "Fragmentation/Summation/AllLevelOrthogonalSummator.hpp"
+#include "Fragmentation/Summation/IndexSet.hpp"
+#include "Fragmentation/Summation/IndexSetContainer.hpp"
+#include "Fragmentation/Summation/SubsetMap.hpp"
+#include "Fragmentation/Summation/Containers/PartialChargesFused.hpp"
+#include "Fragmentation/Summation/Containers/PartialChargesMap.hpp"
+#include "Fragmentation/Summation/SetValues/IndexedPartialCharges.hpp"
+
+ActionState::ptr PotentialFitFragmentPartialChargesAction::performCall()
+{
+  // check for selected atoms
+  const World &world = World::getConstInstance();
+  const std::vector<const atom *> selected_atoms = world.getSelectedAtoms();
+  if (selected_atoms.empty()) {
+    STATUS("There are no atoms selected for fitting partial charges to.");
+    return Action::failure;
+  }
+  LOG(3, "There are  " << selected_atoms.size() << " selected atoms.");
+
+  /// obtain possible fragments to each selected atom
+  const AtomFragmentsMap &atomfragments = AtomFragmentsMap::getConstInstance();
+  if (!atomfragments.checkCompleteness()) {
+    ELOG(0, "AtomFragmentsMap failed internal consistency check, missing forcekeysets?");
+    return Action::failure;
+  }
+  const std::set<KeySet> fragments =
+      accumulateKeySetsForAtoms( atomfragments.getMap(), selected_atoms);
+  const size_t NoNonHydrogens =
+      std::count_if(selected_atoms.begin(), selected_atoms.end(), isNotHydrogen);
+  if (fragments.size() < NoNonHydrogens) {
+    ELOG(0, "Obtained fewer fragments than there are atoms, has AtomFragments been loaded?");
+    return Action::failure;
+  }
+
+  // get results from container
+  FragmentationResultContainer& resultscontainer = FragmentationResultContainer::getInstance();
+#if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
+  const bool DoLongrange = resultscontainer.areFullRangeResultsPresent();
+  if (!DoLongrange) {
+    ELOG(1, "FragmentationResultContainer does not contain long-range results, cannot fit partial charges.");
+    return Action::failure;
+  }
+
+  if (resultscontainer.getKeySets().KeySets.empty()) {
+    STATUS("There are no results in the container.");
+    return Action::failure;
+  }
+
+  // reduce given fragments to homologous graphs for later lookup
+  detail::KeysetsToGraph_t keyset_graphs;
+  detail::fittedcharges_per_fragment_t fittedcharges_per_fragment;
+  getKeySetsToGraphMapping(keyset_graphs, fragments, atomfragments);
+
+  /// then go through all fragments and get partial charges for each
+  const bool status = getPartialChargesForAllIndexSets(
+      fittedcharges_per_fragment,
+      resultscontainer,
+      fragments,
+      params.radius.get(),
+      params.enforceZeroCharge.get());
+  if (!status)
+    return Action::failure;
+
+  /// obtain average charge for each atom the fitted charges over all its fragments
+  detail::fitted_charges_t fitted_charges;
+  {
+    // place all into boost::fusion map for summation
+    std::map<JobId_t, PartialChargesMap_t> PartialCharges_fused;
+    std::vector<IndexSet> indexsets;
+    JobId_t counter = 0;
+    for (detail::fittedcharges_per_fragment_t::const_iterator iter = fittedcharges_per_fragment.begin();
+        iter != fittedcharges_per_fragment.end(); ++iter) {
+      const KeySet &currentset = iter->first;
+      // place as IndexSet into container
+      {
+        IndexSet tempset;
+        tempset.insert(currentset.begin(), currentset.end());
+        indexsets.push_back(tempset);
+      }
+      LOG(3, "Inserting " << iter->first << " with charges " << iter->second << " into chargemap instance.");
+      PartialChargesMap_t chargemap;
+      const AtomFragmentsMap::indices_t &full_currentset = atomfragments.getFullKeyset(currentset);
+      IndexedPartialCharges::indices_t indices(full_currentset.begin(), full_currentset.end());
+      boost::fusion::at_key<PartialChargesFused::partial_charges_t>(chargemap) =
+          IndexedPartialCharges(full_currentset, iter->second);
+      PartialCharges_fused.insert( std::make_pair(counter++, chargemap) );
+    }
+    ASSERT( counter == fragments.size(),
+        "PotentialFitPartialChargesAction::performCall() - not all fragments' keysets were created?");
+    ASSERT( indexsets.size() == fragments.size(),
+        "PotentialFitPartialChargesAction::performCall() - not all fragments' keysets were created?");
+
+    // prepare index set hierarchy
+    std::map< JobId_t, size_t > IdentityLookup;
+    size_t MaxLevel = std::max_element(fragments.begin(), fragments.end(), keyset_comparator)->size();
+    LOG(3, "The maximum level is " << MaxLevel);
+    size_t max_indices = fragments.size();
+    LOG(3, "There are " << max_indices << " keysets for the selected atoms.");
+    {
+      for (size_t index = 0; index < max_indices; ++index)
+        IdentityLookup.insert( std::make_pair( (JobId_t)index, index ) );
+    }
+    IndexSetContainer::ptr container(new IndexSetContainer(indexsets));
+    SubsetMap::ptr subsetmap(new SubsetMap(*container));
+
+    // and sum up
+    PartialChargesMap_t ZeroInstances;
+    ZeroInstanceInitializer<PartialChargesMap_t> initZeroInstance(ZeroInstances);
+    boost::mpl::for_each<PartialChargesVector_t>(boost::ref(initZeroInstance));
+    //!> results per level of summed up partial charges
+    std::vector<PartialChargesMap_t> Result_PartialCharges_fused(MaxLevel);
+    //!> results per index set in terms of value and contribution
+    std::map<
+        IndexSet::ptr,
+        std::pair<PartialChargesMap_t, PartialChargesMap_t> > Result_perIndexSet_PartialCharges;
+    AllLevelOrthogonalSummator<PartialChargesMap_t> partialchargeSummer(
+                subsetmap,
+                PartialCharges_fused,
+                container->getContainer(),
+                IdentityLookup,
+                Result_PartialCharges_fused,
+                Result_perIndexSet_PartialCharges,
+                ZeroInstances);
+    boost::mpl::for_each<PartialChargesVector_t>(boost::ref(partialchargeSummer));
+
+    // TODO: place results into fitted_charges
+    const IndexedPartialCharges::indexedvalues_t indexed_partial_charges =
+        boost::fusion::at_key<PartialChargesFused::partial_charges_t>(
+            Result_PartialCharges_fused.back()
+            ).getValues();
+    for (IndexedPartialCharges::indexedvalues_t::const_iterator iter = indexed_partial_charges.begin();
+        iter != indexed_partial_charges.end(); ++iter)
+      fitted_charges.insert( std::make_pair( iter->first, iter->second.charge));
+    LOG(3, "Summation has brought forth the following charges per atom index: " << fitted_charges);
+  }
+
+  // make a unique list of the present HomologyGraphs
+  typedef std::set<HomologyGraph> unique_graphs_t;
+  unique_graphs_t unique_graphs;
+  for (detail::KeysetsToGraph_t::const_iterator keysetiter = keyset_graphs.begin();
+      keysetiter != keyset_graphs.end(); ++keysetiter)
+    unique_graphs.insert(keysetiter->second);
+
+  /// make Particles be used for every atom that was fitted on the same number of graphs
+  detail::GraphIndex_t GraphIndex;
+  size_t index = 0;
+  for (unique_graphs_t::const_iterator graphiter = unique_graphs.begin();
+      graphiter != unique_graphs.end(); ++graphiter) {
+    GraphIndex.insert( std::make_pair( *graphiter, index++));
+  }
+  LOG(2, "DEBUG: There are " << index << " unique graphs in the homology container.");
+  ASSERT( index == unique_graphs.size(),
+      "PotentialFitFragmentPartialChargesAction::performCall() - could not enumerate all unique graphs?");
+
+  // go through every non-hydrogen atom, get all graphs, convert to GraphIndex and store
+  detail::GraphIndices_t GraphIndices;
+  const AtomFragmentsMap::AtomFragmentsMap_t &atommap = atomfragments.getMap();
+  for (std::vector<const atom *>::const_iterator atomiter = selected_atoms.begin();
+      atomiter != selected_atoms.end(); ++atomiter) {
+    // use the non-hydrogen here
+    const atomId_t walkerid = (*atomiter)->getId();
+    const atomId_t surrogateid = getNonHydrogenSurrogate(*atomiter)->getId();
+    if (surrogateid != walkerid)
+      continue;
+    const AtomFragmentsMap::AtomFragmentsMap_t::const_iterator keysetsiter =
+        atommap.find(walkerid);
+    ASSERT(keysetsiter != atommap.end(),
+        "PotentialFitFragmentPartialChargesAction::performCall() - we checked already that "
+        +toString(surrogateid)+" should be present!");
+    const AtomFragmentsMap::keysets_t & keysets = keysetsiter->second;
+
+    // go over all fragments associated to this atom
+    detail::AtomsGraphIndices_t AtomsGraphIndices;
+    for (AtomFragmentsMap::keysets_t::const_iterator keysetsiter = keysets.begin();
+        keysetsiter != keysets.end(); ++keysetsiter) {
+      const KeySet &keyset = *keysetsiter;
+      const std::map<KeySet, HomologyGraph>::const_iterator keysetgraphiter =
+          keyset_graphs.find(keyset);
+      ASSERT( keysetgraphiter != keyset_graphs.end(),
+          "PotentialFitFragmentPartialChargesAction::performCall() - keyset "+toString(keyset)
+          +" not contained in keyset_graphs.");
+      const HomologyGraph &graph = keysetgraphiter->second;
+      const detail::GraphIndex_t::const_iterator indexiter = GraphIndex.find(graph);
+      ASSERT( indexiter != GraphIndex.end(),
+          "PotentialFitFragmentPartialChargesAction::performCall() - graph "+toString(graph)
+          +" not contained in GraphIndex.");
+      AtomsGraphIndices.insert( indexiter->second );
+    }
+
+    GraphIndices.insert( detail::GraphIndices_t::value_type(AtomsGraphIndices, walkerid) );
+
+    LOG(2, "DEBUG: Atom #" << walkerid << "," << **atomiter << ". has graph indices "
+        << AtomsGraphIndices);
+  }
+  // then graphs from non-hydrogen bond partner for all hydrogens
+  for (std::vector<const atom *>::const_iterator atomiter = selected_atoms.begin();
+      atomiter != selected_atoms.end(); ++atomiter) {
+    // use the non-hydrogen here
+    const atomId_t walkerid = (*atomiter)->getId();
+    const atomId_t surrogateid = getNonHydrogenSurrogate((*atomiter))->getId();
+    if (surrogateid == walkerid)
+      continue;
+    detail::GraphIndices_t::right_const_iterator graphiter = GraphIndices.right.find(surrogateid);
+    ASSERT( graphiter != GraphIndices.right.end(),
+        "PotentialFitFragmentPartialChargesAction::performCall() - atom #"+toString(surrogateid)
+        +" not contained in GraphIndices.");
+    const detail::AtomsGraphIndices_t &AtomsGraphIndices = graphiter->second;
+    GraphIndices.insert( detail::GraphIndices_t::value_type(AtomsGraphIndices, walkerid) );
+    LOG(2, "DEBUG: Hydrogen #" << walkerid << ", " << **atomiter
+        << ", has graph indices " << AtomsGraphIndices);
+  }
+
+  /// place all fitted (and now averaged) charges into ParticleRegistry
+  detail::AtomParticleNames_t atom_particlenames;
+  addToParticleRegistry(
+      ParticleFactory::getConstInstance(),
+      ParticleRegistry::getInstance(),
+      *World::getInstance().getPeriode(),
+      fitted_charges,
+      GraphIndices,
+      atom_particlenames);
+
+  for (World::AtomSelectionIterator atomiter = World::getInstance().beginAtomSelection();
+      atomiter != World::getInstance().endAtomSelection(); ++atomiter) {
+    atom * const walker = atomiter->second;
+    const atomId_t walkerid = atomiter->first;
+    const detail::GraphIndices_t::right_const_iterator graphiter =
+        GraphIndices.right.find(walkerid);
+    ASSERT( graphiter != GraphIndices.right.end(),
+        "PotentialFitFragmentPartialChargesAction::performCall() - cannot find "
+        +toString(walkerid)+" in GraphIndices.");
+    const detail::AtomsGraphIndices_t &graphindex = graphiter->second;
+    const detail::AtomParticleNames_t::const_iterator particlesetiter =
+        atom_particlenames.find(graphindex);
+    ASSERT( particlesetiter != atom_particlenames.end(),
+        "PotentialFitFragmentPartialChargesAction::performCall() - cannot find "
+        +toString(graphindex)+" in atom_particlenames.");
+    const std::map<atomicNumber_t, std::string>::const_iterator nameiter =
+        particlesetiter->second.find(walker->getElementNo());
+    ASSERT( nameiter != particlesetiter->second.end(),
+        "PotentialFitFragmentPartialChargesAction::performCall() - ");
+    walker->setParticleName(nameiter->second);
+    LOG(1, "INFO: atom " << *walker << " received the following particle "
+        << walker->getParticleName());
+  }
+
+  return Action::success;
+#else
+  ELOG(0, "Long-range support not compiled in, cannot fit partial charges to fragment's potential grids.");
+  return Action::failure;
+#endif
+}
+
+ActionState::ptr PotentialFitFragmentPartialChargesAction::performUndo(ActionState::ptr _state) {
+  return Action::success;
+}
+
+ActionState::ptr PotentialFitFragmentPartialChargesAction::performRedo(ActionState::ptr _state){
+  return Action::success;
+}
+
+bool PotentialFitFragmentPartialChargesAction::canUndo() {
+  return false;
+}
+
+bool PotentialFitFragmentPartialChargesAction::shouldUndo() {
+  return false;
+}
+/** =========== end of function ====================== */
Index: src/Actions/PotentialAction/FitFragmentPartialChargesAction.def
===================================================================
--- src/Actions/PotentialAction/FitFragmentPartialChargesAction.def	(revision 2f9fafed8550e71352c619338faefe51479ec428)
+++ src/Actions/PotentialAction/FitFragmentPartialChargesAction.def	(revision 2f9fafed8550e71352c619338faefe51479ec428)
@@ -0,0 +1,43 @@
+/*
+ * FitFragmentPartialChargesAction.def
+ *
+ *  Created on: Oct 09, 2016
+ *      Author: heber
+ */
+
+// all includes and forward declarations necessary for non-integral types below
+#include <boost/filesystem/path.hpp>
+#include "Element/element.hpp"
+#include <vector>
+
+#include "Parameters/Validators/DummyValidator.hpp"
+#include "Parameters/Validators/GenericValidators.hpp"
+#include "Parameters/Validators/STLVectorValidator.hpp"
+#include "Parameters/Validators/Specific/ElementValidator.hpp"
+
+// i.e. there is an integer with variable name Z that can be found in
+// ValueStorage by the token "Z" -> first column: int, Z, "Z"
+// "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
+#define paramtypes (double)(bool)
+#define paramtokens ("radius")("enforce-net-zero-charge")
+#define paramdescriptions ("radius of sphere around nuclei where potential does not need to match")("whether to make the sum of fitted charged become zero")
+#define paramdefaults (PARAM_DEFAULT(0))(PARAM_DEFAULT(1))
+#define paramreferences (radius)(enforceZeroCharge)
+#define paramvalids \
+(NonNegativeValidator<double>()) \
+(DummyValidator<bool>())
+
+#undef statetypes
+#undef statereferences
+
+// some defines for all the names, you may use ACTION, STATE and PARAMS
+#define CATEGORY Potential
+#define MENUNAME "potential"
+#define MENUPOSITION 5
+#define ACTIONNAME FitFragmentPartialCharges
+#define TOKEN "fit-fragment-partial-charges"
+
+
+// finally the information stored in the ActionTrait specialization
+#define DESCRIPTION "fits partial nuclear charges to selected atoms from averages over fragments' sampled grids stored in FragmentResultContainer."
+#undef SHORTFORM
Index: src/Actions/PotentialAction/FitFragmentPartialChargesAction.hpp
===================================================================
--- src/Actions/PotentialAction/FitFragmentPartialChargesAction.hpp	(revision 2f9fafed8550e71352c619338faefe51479ec428)
+++ src/Actions/PotentialAction/FitFragmentPartialChargesAction.hpp	(revision 2f9fafed8550e71352c619338faefe51479ec428)
@@ -0,0 +1,22 @@
+/*
+ * FitFragmentPartialChargesAction.hpp
+ *
+ *  Created on: Oct 09, 2016
+ *      Author: heber
+ */
+
+#ifndef FITFRAGMENTPARTICLECHARGESACTION_HPP_
+#define FITFRAGMENTPARTICLECHARGESACTION_HPP_
+
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include "Actions/Action.hpp"
+
+#include "FitFragmentPartialChargesAction.def"
+#include "Action_impl_header.hpp"
+
+#endif /* FITFRAGMENTPARTICLECHARGESACTION_HPP_ */
Index: src/Actions/PotentialAction/FitPartialChargesAction.cpp
===================================================================
--- src/Actions/PotentialAction/FitPartialChargesAction.cpp	(revision bb8b0ad03160a4d002def3445d1d4d98e1ad3e25)
+++ src/Actions/PotentialAction/FitPartialChargesAction.cpp	(revision 2f9fafed8550e71352c619338faefe51479ec428)
@@ -184,16 +184,4 @@
 }
 
-inline SerializablePotential::ParticleTypes_t
-getParticleTypesForAtomIdSet(const AtomIdSet &_atoms)
-{
-  SerializablePotential::ParticleTypes_t particletypes;
-  particletypes.resize(_atoms.size());
-  std::transform(
-      _atoms.begin(), _atoms.end(),
-      particletypes.begin(),
-      boost::bind(&atom::getElementNo, _1));
-  return particletypes;
-}
-
 static
 std::set<KeySet> accumulateKeySetsForAtoms(
@@ -282,5 +270,5 @@
 }
 
-const atom * getNonHydrogenSurrogate(const atom * const _walker)
+static const atom * getNonHydrogenSurrogate(const atom * const _walker)
 {
   const atom * surrogate = _walker;
@@ -298,5 +286,5 @@
 }
 
-double fitAverageChargeToAtom(
+static double fitAverageChargeToAtom(
     const atom * const _walker,
     const AtomFragmentsMap &_atomfragments,
@@ -361,5 +349,5 @@
 }
 
-void addToParticleRegistry(
+static void addToParticleRegistry(
     const ParticleFactory &factory,
     const periodentafel &periode,
@@ -400,10 +388,10 @@
 }
 
-bool isNotHydrogen(const atom * const _atom)
+static bool isNotHydrogen(const atom * const _atom)
 {
   return (_atom->getElementNo() != (atomicNumber_t) 1);
 }
 
-struct KeySetSizeComp {
+static struct KeySetSizeComp {
   bool operator() (const KeySet &a, const KeySet &b) { return a.size()<b.size(); }
 } keyset_comparator;
