Changeset d8821e for src/Actions


Ignore:
Timestamp:
Jul 14, 2014, 11:16:23 AM (11 years ago)
Author:
Frederik Heber <heber@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable
Children:
2a03b0
Parents:
c73e35 (diff), a61dbb (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.
Message:

Merge branch 'Fragmentation_Automation_wo_JobMarket' into stable

Conflicts:

src/Actions/ActionQueue.cpp
src/Actions/FragmentationAction/FragmentationAction.cpp
src/Actions/PotentialAction/FitParticleChargesAction.cpp

Location:
src/Actions
Files:
10 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/ActionQueue.cpp

    rc73e35 rd8821e  
    5858    AR(new ActionRegistry()),
    5959    history(new ActionHistory),
     60    CurrentAction(0),
    6061#ifndef HAVE_ACTION_THREAD
    61     CurrentAction(0)
     62    lastActionOk(true)
    6263#else
    63     CurrentAction(0),
     64    lastActionOk(true),
    6465    run_thread(boost::bind(&ActionQueue::run, this)),
    6566    run_thread_isIdle(true)
    … …  
    99100  try {
    100101    newaction->call();
     102    lastActionOk = true;
    101103  } catch(ActionFailureException &e) {
    102104    std::cerr << "Action " << *boost::get_error_info<ActionNameString>(e) << " has failed." << std::endl;
    103105    World::getInstance().setExitFlag(5);
     106    actionqueue.clear();
     107    tempqueue.clear();
     108    lastActionOk = false;
     109    std::cerr << "ActionQueue cleared." << std::endl;
    104110  }
    105111#else
    … …  
    157163        actionqueue[CurrentAction]->call();
    158164        pushStatus("SUCCESS: Action "+actionqueue[CurrentAction]->getName()+" successful.");
     165        lastActionOk = true;
    159166      } catch(ActionFailureException &e) {
    160167        pushStatus("FAIL: Action "+*boost::get_error_info<ActionNameString>(e)+" has failed.");
    161168        World::getInstance().setExitFlag(5);
     169        actionqueue.clear();
     170        tempqueue.clear();
     171        lastActionOk = false;
     172        std::cerr << "ActionQueue cleared." << std::endl;
     173        CurrentAction = (size_t)-1;
    162174      }
    163175      // access actionqueue, hence using mutex

  • src/Actions/ActionQueue.hpp

    rc73e35 rd8821e  
    123123  void redoLast();
    124124
     125  /** Return status of last executed action.
     126   *
     127   * \return true - action executed correctly, false - else
     128   */
     129  bool getLastActionOk() const
     130  {  return lastActionOk; }
     131
    125132#ifdef HAVE_ACTION_THREAD
    126133  boost::thread &getRunThread()
    … …  
    221228  ActionQueue_t tempqueue;
    222229
     230  //!> indicates that the last action has failed
     231  bool lastActionOk;
     232
    223233#ifdef HAVE_ACTION_THREAD
    224234  //!> internal thread to call Actions

  • src/Actions/CommandAction/ElementDbAction.cpp

    rc73e35 rd8821e  
    4141#include "config.hpp"
    4242#include "Element/element.hpp"    // we need element because of serialization!
     43#include "Element/ion.hpp"    // we need element because of serialization!
    4344#include "Element/periodentafel.hpp"
    4445#include "CodePatterns/Log.hpp"

  • src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp

    rc73e35 rd8821e  
    6363#include "Descriptors/AtomIdDescriptor.hpp"
    6464#include "Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp"
    65 #include "Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp"
    6665#include "Fragmentation/Summation/Containers/FragmentationResultContainer.hpp"
    6766#include "Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp"
    … …  
    7877#include "Fragmentation/Summation/writeIndexedTable.hpp"
    7978#include "Fragmentation/Summation/writeTable.hpp"
    80 #ifdef HAVE_VMG
     79#if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
     80#include "Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp"
    8181#include "Fragmentation/Summation/Containers/VMGData.hpp"
    8282#include "Fragmentation/Summation/Containers/VMGDataFused.hpp"
    … …  
    232232
    233233
     234#if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
    234235/** Print long range energy from received results.
    235236 *
    … …  
    261262  }
    262263}
     264#endif
    263265
    264266void appendToHomologies(
    265267    const FragmentationShortRangeResults &shortrangeresults,
     268#if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
    266269    const FragmentationLongRangeResults &longrangeresults,
     270#endif
    267271    const bool storeGrids
    268272    )
    … …  
    311315    // only store sampled grids if desired
    312316    if (storeGrids) {
     317#if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
    313318      // obtain charge distribution
    314319      std::map<IndexSet::ptr, std::pair< MPQCDataGridMap_t, MPQCDataGridMap_t> >::const_iterator chargeiter
    … …  
    338343//          ++iter)
    339344//        *iter -= offset;
     345#else
     346      ELOG(1, "Long-range information in homology desired but long-range analysis capability not compiled in.");
     347#endif
    340348    }
    341349    values.insert( std::make_pair( graph, value) );
    … …  
    362370          << ", associated energy " << iter->second.energy;
    363371      if (iter->second.containsGrids)
     372#if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
    364373        output  << ", and sampled grid integral " << iter->second.charge_distribution.integral();
     374#else
     375        output << ", and there are sampled grids but capability not compiled in";
     376#endif
    365377      output << ".";
    366378      LOG(2, output.str());
    … …  
    610622  }
    611623
    612 #ifdef HAVE_VMG
     624#if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
    613625  if (DoLongrange) {
    614626    if ( World::getInstance().getAllAtoms().size() == 0) {
    … …  
    651663  }
    652664#else
    653   if (DoLongrange)
     665  if (DoLongrange) {
    654666    ELOG(2, "File contains long-range information but long-range analysis capability not compiled in.");
     667  }
    655668
    656669  // append all keysets to homology file with short-range info only (without grids)
    657   {
    658     std::map<JobId_t, VMGData> longrangeData;
    659     FragmentationLongRangeResults longrangeresults(
    660         shortrangedata,longrangeData,keysets, forcekeysets);
    661     appendToHomologies(shortrangeresults, longrangeresults, false);
    662   }
     670  appendToHomologies(shortrangeresults, false);
    663671#endif
    664672

  • src/Actions/FragmentationAction/FragmentationAction.cpp

    rc73e35 rd8821e  
    4141#include "Descriptors/AtomSelectionDescriptor.hpp"
    4242#include "Fragmentation/Exporters/ExportGraph_ToFiles.hpp"
    43 #ifdef HAVE_JOBMARKET
    4443#include "Fragmentation/Exporters/ExportGraph_ToJobs.hpp"
    45 #endif
    4644#include "Fragmentation/Fragmentation.hpp"
    4745#include "Fragmentation/Graph.hpp"
    … …  
    273271      exporter();
    274272    } else {
    275 #ifdef HAVE_JOBMARKET
    276273      // store molecule's fragment in FragmentJobQueue
    277274      ExportGraph_ToJobs exporter(TotalGraph, treatment, saturation);
    278275      exporter.setLevel(params.level.get());
    279276      exporter();
    280 #else
    281       STATUS("No output file types specified and JobMarket support is not compiled in.");
    282       return Action::failure;
    283 #endif
    284277    }
    285278  }

  • src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

    rc73e35 rd8821e  
    5353#include "CodePatterns/Info.hpp"
    5454#include "CodePatterns/Log.hpp"
     55
     56#ifdef HAVE_JOBMARKET
    5557#include "JobMarket/Jobs/FragmentJob.hpp"
     58#else
     59#include "Jobs/JobMarket/FragmentJob.hpp"
     60#endif
    5661
    5762#include "Fragmentation/Automation/FragmentJobQueue.hpp"
     63#ifdef HAVE_JOBMARKET
    5864#include "Fragmentation/Automation/MPQCFragmentController.hpp"
     65#else
     66#include "Fragmentation/Automation/MPQCCommandFragmentController.hpp"
     67#endif
    5968#include "Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp"
    6069#include "Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp"
    … …  
    6372#include "Fragmentation/Summation/Containers/MPQCData.hpp"
    6473#include "Fragmentation/KeySetsContainer.hpp"
    65 #ifdef HAVE_VMG
     74#if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
    6675#include "Fragmentation/Automation/VMGDebugGridFragmentController.hpp"
    6776#include "Fragmentation/Automation/VMGFragmentController.hpp"
    … …  
    99108}
    100109
     110#ifdef HAVE_JOBMARKET
    101111static void updateSteps(Process &p, const size_t step, const size_t total)
    102112{
    … …  
    104114  p.setCurrStep(step);
    105115}
     116#endif
    106117
    107118ActionState::ptr FragmentationFragmentationAutomationAction::performCall() {
    … …  
    117128  size_t Exitflag = 0;
    118129  std::map<JobId_t, MPQCData> shortrangedata;
     130#ifdef HAVE_JOBMARKET
    119131  {
    120132    const size_t NumberJobs = FragmentJobQueue::getInstance().size();
    … …  
    126138
    127139    // Phase Two: add MPQCJobs and send
    128     const size_t NoJobs = mpqccontroller.addJobsFromQueue(
     140    const bool AddJobsStatus = mpqccontroller.addJobsFromQueue(
    129141        params.DoLongrange.get() ? MPQCData::DoSampleDensity : MPQCData::DontSampleDensity,
    130142        params.DoValenceOnly.get() ? MPQCData::DoSampleValenceOnly : MPQCData::DontSampleValenceOnly
    131143        );
    132     LOG(1, "INFO: Added " << NoJobs << " from FragmentJobsQueue.");
     144    if (AddJobsStatus)
     145      LOG(1, "INFO: Added jobs from FragmentJobsQueue.");
     146    else {
     147      ELOG(1, "Adding jobs failed.");
     148      return Action::failure;
     149    }
    133150    mpqccontroller.run();
    134151
    … …  
    148165    Exitflag += mpqccontroller.getExitflag();
    149166  }
    150 
    151 #ifdef HAVE_VMG
     167#else
     168  {
     169    const size_t NumberJobs = FragmentJobQueue::getInstance().size();
     170    MPQCCommandFragmentController mpqccontroller;
     171    // Phase One: obtain ids: not needed, we have infinite pool
     172
     173    // Phase Two: add MPQCJobs and send
     174    const size_t NoJobs = mpqccontroller.addJobsFromQueue(
     175        params.DoLongrange.get() ? MPQCData::DoSampleDensity : MPQCData::DontSampleDensity,
     176        params.DoValenceOnly.get() ? MPQCData::DoSampleValenceOnly : MPQCData::DontSampleValenceOnly,
     177        params.executable.get().string()
     178        );
     179    LOG(1, "INFO: Added " << NoJobs << " from FragmentJobsQueue.");
     180    mpqccontroller.run();
     181
     182    // get back the results and place them in shortrangedata
     183    mpqccontroller.getResults(shortrangedata);
     184    ASSERT( shortrangedata.size() == NumberJobs,
     185        "FragmentationFragmentationAutomationAction::performCall() - number of converted results "
     186        +toString(shortrangedata.size())+" and number of jobs "+toString(NumberJobs)+ " differ.");
     187
     188    Exitflag += mpqccontroller.getExitflag();
     189  }
     190#endif
     191
     192#if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
    152193  if (params.DoLongrange.get()) {
    153194  if ( World::getInstance().getAllAtoms().size() == 0) {

  • src/Actions/GlobalListOfActions.hpp

    rc73e35 rd8821e  
    122122  (SelectionNotShapeByName) \
    123123  (FragmentationAnalyseFragmentationResults) \
     124  (FragmentationFragmentationAutomation) \
    124125  (FragmentationClearFragmentationResults) \
    125126  (FragmentationFragmentation) \
     127  (FragmentationMolecularDynamics) \
     128  (FragmentationParseFragmentJobs) \
    126129  (FragmentationStoreSaturatedFragment) \
    127130  (PotentialFitParticleCharges) \
    … …  
    137140  (ShapeTranslateShape)
    138141
    139 // we need to append the automation action in case we have the JobMarket
    140 #ifdef HAVE_JOBMARKET
    141 #define GLOBALLISTOFACTIONS_JOBMARKET \
    142     BOOST_PP_SEQ_PUSH_BACK( \
    143         BOOST_PP_SEQ_PUSH_BACK( \
    144             BOOST_PP_SEQ_PUSH_BACK( \
    145                 GLOBALLISTOFACTIONS_initial, \
    146                 FragmentationFragmentationAutomation \
    147             ), \
    148             FragmentationMolecularDynamics \
    149         ), \
    150         FragmentationParseFragmentJobs \
    151     )
    152 #else
    153 #define GLOBALLISTOFACTIONS_JOBMARKET \
    154     GLOBALLISTOFACTIONS_initial
    155 #endif /* HAVE_JOBMARKET */
    156 
     142// extend list of actions in case levmar is available
    157143#ifdef HAVE_LEVMAR
    158144#define GLOBALLISTOFACTIONS_LEVMAR \
    159145    BOOST_PP_SEQ_PUSH_BACK( \
    160         GLOBALLISTOFACTIONS_JOBMARKET, \
     146        GLOBALLISTOFACTIONS_initial, \
    161147        PotentialFitPotential \
    162148    )
    163149#else
    164150#define GLOBALLISTOFACTIONS_LEVMAR \
    165     GLOBALLISTOFACTIONS_JOBMARKET
     151    GLOBALLISTOFACTIONS_initial
    166152#endif /* HAVE_LEVMAR */
    167153

  • src/Actions/Makefile.am

    rc73e35 rd8821e  
    228228  Actions/FragmentationAction/ClearFragmentationResultsAction.cpp \
    229229  Actions/FragmentationAction/FragmentationAction.cpp \
     230  Actions/FragmentationAction/FragmentationAutomationAction.cpp \
     231  Actions/FragmentationAction/MolecularDynamicsAction.cpp \
     232  Actions/FragmentationAction/ParseFragmentJobsAction.cpp \
    230233  Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp
    231234FRAGMENTATIONACTIONHEADER = \
    … …  
    233236  Actions/FragmentationAction/ClearFragmentationResultsAction.hpp \
    234237  Actions/FragmentationAction/FragmentationAction.hpp \
     238  Actions/FragmentationAction/FragmentationAutomationAction.hpp \
     239  Actions/FragmentationAction/MolecularDynamicsAction.hpp \
     240  Actions/FragmentationAction/ParseFragmentJobsAction.hpp \
    235241  Actions/FragmentationAction/StoreSaturatedFragmentAction.hpp
    236242FRAGMENTATIONACTIONDEFS = \
    … …  
    238244  Actions/FragmentationAction/ClearFragmentationResultsAction.def \
    239245  Actions/FragmentationAction/FragmentationAction.def \
    240   Actions/FragmentationAction/StoreSaturatedFragmentAction.def
    241 
    242 if CONDJOBMARKET
    243 FRAGMENTATIONACTIONSOURCE += \
    244   Actions/FragmentationAction/FragmentationAutomationAction.cpp \
    245   Actions/FragmentationAction/MolecularDynamicsAction.cpp \
    246   Actions/FragmentationAction/ParseFragmentJobsAction.cpp
    247 FRAGMENTATIONACTIONHEADER += \
    248   Actions/FragmentationAction/FragmentationAutomationAction.hpp \
    249   Actions/FragmentationAction/MolecularDynamicsAction.hpp \
    250   Actions/FragmentationAction/ParseFragmentJobsAction.hpp
    251 FRAGMENTATIONACTIONDEFS += \
    252246  Actions/FragmentationAction/FragmentationAutomationAction.def \
    253247  Actions/FragmentationAction/MolecularDynamicsAction.def \
    254   Actions/FragmentationAction/ParseFragmentJobsAction.def
    255 endif
     248  Actions/FragmentationAction/ParseFragmentJobsAction.def \
     249  Actions/FragmentationAction/StoreSaturatedFragmentAction.def
    256250
    257251GRAPHACTIONSOURCE = \

  • src/Actions/PotentialAction/FitParticleChargesAction.cpp

    rc73e35 rd8821e  
    4747#include <boost/foreach.hpp>
    4848#include <algorithm>
     49#include <functional>
    4950#include <iostream>
    5051#include <string>
    … …  
    128129    return Action::failure;
    129130  }
     131
     132  // average partial charges over all fragments
    130133  HomologyContainer::const_iterator iter = range.first;
    131134  if (!iter->second.containsGrids) {
    … …  
    133136    return Action::failure;
    134137  }
    135   const Fragment &fragment = iter->second.fragment;
    136 //  const double &energy = iter->second.energy;
    137 //  const SamplingGrid &charge = iter->second.charge_distribution;
    138   const SamplingGrid &potential = iter->second.potential_distribution;
    139 
    140   // then we extract positions from fragment
    141   PartialNucleiChargeFitter::positions_t positions;
    142   Fragment::positions_t fragmentpositions = fragment.getPositions();
    143   positions.reserve(fragmentpositions.size());
    144   BOOST_FOREACH( Fragment::position_t pos, fragmentpositions) {
    145     positions.push_back( Vector(pos[0], pos[1], pos[2]) );
    146   }
    147   PartialNucleiChargeFitter fitter(potential, positions, params.radius.get());
    148   fitter();
    149   PartialNucleiChargeFitter::charges_t return_charges = fitter.getSolutionAsCharges_t();
     138  PartialNucleiChargeFitter::charges_t averaged_charges;
     139  averaged_charges.resize(iter->second.fragment.getCharges().size(), 0.);
     140  size_t NoFragments = 0;
     141  for (;
     142      iter != range.second; ++iter, ++NoFragments) {
     143    if (!iter->second.containsGrids) {
     144      ELOG(2, "This HomologyGraph does not contain sampled grids,\ndid you forget to add '--store-grids 1' to AnalyseFragmentResults.");
     145      return Action::failure;
     146    }
     147    const Fragment &fragment = iter->second.fragment;
     148  //  const double &energy = iter->second.energy;
     149  //  const SamplingGrid &charge = iter->second.charge_distribution;
     150    const SamplingGrid &potential = iter->second.potential_distribution;
     151    if ((potential.level == 0)
     152        || ((potential.begin[0] == potential.end[0])
     153            && (potential.begin[1] == potential.end[1])
     154            && (potential.begin[2] == potential.end[2]))) {
     155      ELOG(1, "Sampled grid contains grid made of zero points.");
     156      return Action::failure;
     157    }
     158
     159    // then we extract positions from fragment
     160    PartialNucleiChargeFitter::positions_t positions;
     161    Fragment::positions_t fragmentpositions = fragment.getPositions();
     162    positions.reserve(fragmentpositions.size());
     163    BOOST_FOREACH( Fragment::position_t pos, fragmentpositions) {
     164      positions.push_back( Vector(pos[0], pos[1], pos[2]) );
     165    }
     166    PartialNucleiChargeFitter fitter(potential, positions, params.radius.get());
     167    fitter();
     168    PartialNucleiChargeFitter::charges_t return_charges = fitter.getSolutionAsCharges_t();
     169    std::transform(
     170        return_charges.begin(), return_charges.end(),
     171        averaged_charges.begin(),
     172        averaged_charges.begin(),
     173        std::plus<PartialNucleiChargeFitter::charge_t>());
     174  }
     175  std::transform(averaged_charges.begin(),averaged_charges.end(),
     176      averaged_charges.begin(),
     177      std::bind1st(std::multiplies<PartialNucleiChargeFitter::charge_t>(),1./NoFragments)
     178  );
     179
    150180
    151181  // output fitted charges
    152   LOG(0, "STATUS: We have fitted the following charges " << return_charges << ".");
     182  LOG(0, "STATUS: We have fitted the following charges " << averaged_charges
     183      << ", averaged over " << NoFragments << " fragments.");
    153184
    154185  return Action::success;

  • src/Actions/PotentialAction/FitPotentialAction.cpp

    rc73e35 rd8821e  
    113113}
    114114
     115SerializablePotential::ParticleTypes_t getNumbersFromElements(
     116    const std::vector<const element *> &fragment)
     117{
     118  SerializablePotential::ParticleTypes_t fragmentnumbers;
     119  std::transform(fragment.begin(), fragment.end(), std::back_inserter(fragmentnumbers),
     120      boost::bind(&element::getAtomicNumber, _1));
     121  return fragmentnumbers;
     122}
     123
     124
    115125ActionState::ptr PotentialFitPotentialAction::performCall() {
    116126  // fragment specifies the homology fragment to use
    117   SerializablePotential::ParticleTypes_t fragmentnumbers;
    118   {
    119     const std::vector<const element *> &fragment = params.fragment.get();
    120     std::transform(fragment.begin(), fragment.end(), std::back_inserter(fragmentnumbers),
    121         boost::bind(&element::getAtomicNumber, _1));
    122   }
     127  SerializablePotential::ParticleTypes_t fragmentnumbers =
     128      getNumbersFromElements(params.fragment.get());
    123129
    124130  // either charges and a potential is specified or a file
    … …  
    158164    } else {
    159165      // charges specify the potential type
    160       SerializablePotential::ParticleTypes_t chargenumbers;
    161       {
    162         const std::vector<const element *> &charges = params.charges.get();
    163         std::transform(charges.begin(), charges.end(), std::back_inserter(chargenumbers),
    164             boost::bind(&element::getAtomicNumber, _1));
    165       }
     166      SerializablePotential::ParticleTypes_t chargenumbers =
     167          getNumbersFromElements(params.charges.get());
    166168
    167169      LOG(0, "STATUS: I'm training now a " << params.potentialtype.get()
    … …  
    240242      size_t counter=1;
    241243      if (DoLog(3)) {
    242         const FunctionModel::arguments_t &inputs = data.getTrainingInputs()[0];
     244        const FunctionModel::arguments_t &inputs = data.getAllArguments()[0];
    243245        for (FunctionModel::arguments_t::const_iterator iter = inputs.begin();
    244246            iter != inputs.end(); ++iter) {
    … …  
    265267    }
    266268
     269    if ((params.threshold.get() < 1) && (params.best_of_howmany.isSet()))
     270      ELOG(2, "threshold parameter always overrules max_runs, both are specified.");
    267271    // now perform the function approximation by optimizing the model function
    268272    FunctionApproximation approximator(data, *model);
    … …  
    304308
    305309    // create a map of each fragment with error.
    306     typedef std::multimap< double, size_t > WorseFragmentMap_t;
    307     WorseFragmentMap_t WorseFragmentMap;
    308310    HomologyContainer::range_t fragmentrange = homologies.getHomologousGraphs(graph);
    309     // fragments make it into the container in reversed order, hence count from top down
    310     size_t index= std::distance(fragmentrange.first, fragmentrange.second)-1;
    311     for (HomologyContainer::const_iterator iter = fragmentrange.first;
    312         iter != fragmentrange.second;
    313         ++iter) {
    314       const Fragment& fragment = iter->second.fragment;
    315       const double &energy = iter->second.energy;
    316 
    317       // create arguments from the fragment
    318       FunctionModel::extractor_t extractor = model->getSpecificExtractor();
    319       FunctionModel::arguments_t args = extractor(fragment, 1);
    320 
    321       // calculate value from potential
    322       const double fitvalue = (*model)(args)[0];
    323 
    324       // insert difference into map
    325       const double error = fabs(energy - fitvalue);
    326       WorseFragmentMap.insert( std::make_pair( error, index-- ) );
    327 
    328       {
    329         // give only the distances in the debugging text
    330         std::stringstream streamargs;
    331         BOOST_FOREACH (argument_t arg, args) {
    332           streamargs << " " << arg.distance*AtomicLengthToAngstroem;
    333         }
    334         LOG(2, "DEBUG: frag.#" << index+1 << "'s error is |" << energy << " - " << fitvalue
    335             << "| = " << error << " for args " << streamargs.str() << ".");
    336       }
    337     }
     311    TrainingData::L2ErrorConfigurationIndexMap_t WorseFragmentMap =
     312        data.getWorstFragmentMap(*model, fragmentrange);
    338313    LOG(0, "RESULT: WorstFragmentMap " << WorseFragmentMap << ".");
    339314
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