Changeset ac9ca4 for src


Ignore:
Timestamp:
Apr 15, 2013, 10:28:22 AM (12 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:
4f44ae
Parents:
dd0c8f
git-author:
Frederik Heber <heber@…> (03/04/13 13:54:11)
git-committer:
Frederik Heber <heber@…> (04/15/13 10:28:22)
Message:

FragmentAction creates FragmentJobs if no output-types are given.

Location:
src
Files:
2 added
16 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/FragmentationAction/FragmentationAction.cpp

    rdd0c8f rac9ca4  
    3939#include "CodePatterns/Log.hpp"
    4040#include "Fragmentation/Exporters/ExportGraph_ToFiles.hpp"
     41#ifdef HAVE_JOBMARKET
     42#include "Fragmentation/Exporters/ExportGraph_ToJobs.hpp"
     43#endif
    4144#include "Fragmentation/Fragmentation.hpp"
    4245#include "Fragmentation/Graph.hpp"
    … …  
    167170  }
    168171
    169   // store molecule's fragment to file
    170172  {
    171173    const enum HydrogenSaturation saturation =  params.DoSaturation.get() ? DoSaturate : DontSaturate;
    172174    const enum HydrogenTreatment treatment =  params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
    173     ExportGraph_ToFiles exporter(TotalGraph, treatment, saturation);
    174     exporter.setPrefix(params.prefix.get());
    175     exporter.setOutputTypes(params.types.get());
    176     exporter();
     175    if (params.types.get().size() != 0) {
     176      // store molecule's fragment to file
     177      ExportGraph_ToFiles exporter(TotalGraph, treatment, saturation);
     178      exporter.setPrefix(params.prefix.get());
     179      exporter.setOutputTypes(params.types.get());
     180      exporter();
     181    } else {
     182#ifdef HAVE_JOBMARKET
     183      // store molecule's fragment in FragmentJobQueue
     184      ExportGraph_ToJobs exporter(TotalGraph, treatment, saturation);
     185      exporter.setLevel(params.level.get());
     186      exporter();
     187#else
     188      ELOG(1, "No output file types specified and JobMarket support is not compiled in.");
     189      return Action::failure;
     190#endif
     191    }
    177192  }
    178193

  • src/Actions/FragmentationAction/FragmentationAction.def

    rdd0c8f rac9ca4  
    1313#include "Parameters/Validators/DummyValidator.hpp"
    1414#include "Parameters/Validators/GenericValidators.hpp"
     15#include "Parameters/Validators/RangeValidator.hpp"
    1516#include "Parameters/Validators/STLVectorValidator.hpp"
    1617#include "Parameters/Validators/Specific/BoxLengthValidator.hpp"
    … …  
    2021// ValueStorage by the token "Z" -> first column: int, Z, "Z"
    2122// "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
    22 #define paramtypes (std::string)(double)(unsigned int)(bool)(bool)(std::vector<std::string>)
    23 #define paramtokens ("fragment-molecule")("distance")("order")("DoSaturate")("ExcludeHydrogen")("output-types")
    24 #define paramdescriptions ("prefix of each fragment file")("distance in space")("order of a discretization, dissection, ...")("do saturate dangling bonds with hydrogen")("whether to exclude hydrogen in the bond graph dissection or not")("type(s) of parsers that output fragment config files")
    25 #define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(true))(PARAM_DEFAULT(true))(PARAM_DEFAULT(std::vector<std::string>(1, std::string("pcp"))))
    26 #define paramreferences (prefix)(distance)(order)(DoSaturation)(HowtoTreatHydrogen)(types)
     23#define paramtypes (std::string)(double)(unsigned int)(bool)(bool)(std::vector<std::string>)(unsigned int)
     24#define paramtokens ("fragment-molecule")("distance")("order")("DoSaturate")("ExcludeHydrogen")("output-types")("grid-level")
     25#define paramdescriptions ("prefix of each fragment file")("distance in space")("order of a discretization, dissection, ...")("do saturate dangling bonds with hydrogen")("whether to exclude hydrogen in the bond graph dissection or not")("type(s) of parsers that output fragment config files")("resolution of density sampling multigrid")
     26#define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(true))(PARAM_DEFAULT(true))(NOPARAM_DEFAULT)(PARAM_DEFAULT(5))
     27#define paramreferences (prefix)(distance)(order)(DoSaturation)(HowtoTreatHydrogen)(types)(level)
    2728#define paramvalids \
    2829(DummyValidator< std::string >()) \
    … …  
    3132(DummyValidator< bool >()) \
    3233(DummyValidator< bool >()) \
    33 (STLVectorValidator< std::vector<std::string> >(1, 10, ParserTypeValidator()))
     34(STLVectorValidator< std::vector<std::string> >(0, 10, ParserTypeValidator())) \
     35(RangeValidator< unsigned int >(1, 10))
    3436
    3537#undef statetypes

  • src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

    rdd0c8f rac9ca4  
    5757#include "Fragmentation/Automation/extractJobIds.hpp"
    5858#include "Fragmentation/Automation/FragmentationChargeDensity.hpp"
     59#include "Fragmentation/Automation/FragmentJobQueue.hpp"
    5960#include "Fragmentation/Automation/FragmentationResults.hpp"
    6061#include "Fragmentation/Automation/MPQCFragmentController.hpp"
    … …  
    478479  // TODO: Have io_service run in second thread and merge with current again eventually
    479480
     481  // check some things prior to work
     482  enum OutputType_t {
     483    ToFiles,
     484    ToJobs,
     485    ToNone
     486  };
     487  enum OutputType_t outputtype = ToNone;
     488  if (params.jobfiles.get().size() != 0) {
     489    // we got no job files, hence we use FragmentJobQueue
     490    if (params.path.get().size() == 0) {
     491      ELOG(1, "Missing path to fragment files.");
     492      return Action::failure;
     493    }
     494    outputtype = ToFiles;
     495
     496    // parse in fragment-jobs if given
     497    if(!FragmentJobQueue::getInstance().addJobsFromFiles(
     498        params.jobfiles.get(),
     499        params.level.get()))
     500      return Action::failure;
     501  } else {
     502    if (params.path.get().size() != 0) {
     503      ELOG(2, "Path to fragment given although we use FragmentJobQueue.");
     504    }
     505    outputtype = ToJobs;
     506  }
     507
    480508  size_t Exitflag = 0;
    481509  std::map<JobId_t, MPQCData> fragmentData;
    482510  {
     511    const size_t NumberJobs = FragmentJobQueue::getInstance().size();
    483512    MPQCFragmentController mpqccontroller(io_service);
    484513    mpqccontroller.setHost(params.host.get());
    485514    mpqccontroller.setPort(params.port.get());
    486     mpqccontroller.setLevel(params.level.get());
    487515    // Phase One: obtain ids
    488     std::vector< boost::filesystem::path > jobfiles = params.jobfiles.get();
    489     mpqccontroller.requestIds(jobfiles.size());
    490 
    491     // Phase Two: create and add MPQCJobs
    492     if (!mpqccontroller.addJobsFromFiles(params.executable.get().string(), jobfiles))
    493       return Action::failure;
     516    mpqccontroller.requestIds(NumberJobs);
     517
     518    // Phase Two: add MPQCJobs and send
     519    mpqccontroller.addJobsFromQueue();
     520    mpqccontroller.run();
    494521
    495522    // Phase Three: calculate result
    496     mpqccontroller.waitforResults(jobfiles.size());
     523    mpqccontroller.waitforResults(NumberJobs);
    497524    mpqccontroller.getResults(fragmentData);
    498525
    … …  
    572599
    573600  // append all keysets to homology file
    574   if (Exitflag == 0) {
     601  if ((Exitflag == 0) && (!params.homology_file.get().empty())) {
    575602    const boost::filesystem::path &homology_file = params.homology_file.get();
    576603    if (homology_file.string() != "") {

  • src/Actions/FragmentationAction/FragmentationAutomationAction.def

    rdd0c8f rac9ca4  
    2424#define paramtokens ("fragment-jobs")("fragment-path")("server-address")("server-port")("fragment-executable")("grid-level")("near-field-cells")("interpolation-degree")("DoLongrange")("homology-file")
    2525#define paramdescriptions ("vector of fragment files")("prefix of each fragment file")("hostname of server")("controller port of server")("executable to launch on clients")("resolution of multigrid")("number of cells used in smearing out core charge")("interpolation degree for getting the nuclei potential from the grid")("whether to calculate long-range contributions")("path to file containing homology containerto append to")
    26 #define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT("127.0.0.1"))(PARAM_DEFAULT("1026"))(NOPARAM_DEFAULT)(PARAM_DEFAULT(5))(PARAM_DEFAULT(3))(PARAM_DEFAULT(3))(PARAM_DEFAULT("0"))(PARAM_DEFAULT(""))
     26#define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT("127.0.0.1"))(NOPARAM_DEFAULT)(PARAM_DEFAULT("mpqc"))(PARAM_DEFAULT(5))(PARAM_DEFAULT(3))(PARAM_DEFAULT(3))(PARAM_DEFAULT("0"))(PARAM_DEFAULT(""))
    2727#define paramreferences (jobfiles)(path)(host)(port)(executable)(level)(near_field_cells)(interpolation_degree)(DoLongrange)(homology_file)
    2828#define paramvalids \

  • src/Actions/FragmentationAction/StoreSaturatedFragmentAction.def

    rdd0c8f rac9ca4  
    2020#define paramtokens ("store-saturated-fragment")("DoSaturate")("output-types")
    2121#define paramdescriptions ("name of fragment file")("do saturate dangling bonds with hydrogen")("type(s) of parsers that output fragment config files")
    22 #define paramdefaults (NOPARAM_DEFAULT)(PARAM_DEFAULT(true))(PARAM_DEFAULT(std::vector<std::string>(1, std::string("pcp"))))
     22#define paramdefaults (NOPARAM_DEFAULT)(PARAM_DEFAULT(true))(NOPARAM_DEFAULT)
    2323#define paramreferences (prefix)(DoSaturation)(types)
    2424#define paramvalids \

  • src/Fragmentation/Automation/MPQCFragmentController.cpp

    rdd0c8f rac9ca4  
    4545#include "Box.hpp"
    4646#include "Helpers/defs.hpp"
     47#include "Fragmentation/Automation/FragmentJobQueue.hpp"
    4748#include "Jobs/MPQCJob.hpp"
    4849#include "LinearAlgebra/RealSpaceMatrix.hpp"
    4950#include "World.hpp"
    5051
    51 bool MPQCFragmentController::addJobsFromFiles(
    52     const std::string &executable,
    53     const std::vector< boost::filesystem::path > &jobfiles)
     52bool MPQCFragmentController::addJobsFromQueue()
    5453{
    55   std::vector<FragmentJob::ptr> jobs;
    56   for (std::vector< boost::filesystem::path >::const_iterator iter = jobfiles.begin();
    57       iter != jobfiles .end(); ++iter) {
    58     const std::string &filename = (*iter).string();
    59     if (boost::filesystem::exists(filename)) {
    60       const JobId_t next_id = getAvailableId();
    61       LOG(1, "INFO: Creating MPQCCommandJob with filename'"
    62           +filename+"', and id "+toString(next_id)+".");
    63       parsejob(jobs, executable, filename, next_id);
    64     } else {
    65       ELOG(1, "Fragment job "+filename+" does not exist.");
    66       return false;
    67     }
     54  // give them all valid ids
     55  std::vector<FragmentJob::ptr> newjobs = FragmentJobQueue::getInstance().getJobs();
     56  for (std::vector<FragmentJob::ptr>::iterator jobiter = newjobs.begin();
     57      jobiter != newjobs.end();
     58      ++jobiter) {
     59    changeJobId((*jobiter), getAvailableId());
    6860  }
    69   addJobs(jobs);
     61  // add the jobs
     62  addJobs(newjobs);
     63
     64  return (newjobs.size() != 0);
     65}
     66
     67void MPQCFragmentController::run()
     68{
     69  // take jobs from queue and add them
    7070  sendJobs(host, port);
    7171  RunService("Adding MPQCJobs");
    72 
    73   return true;
    7472}
    75 
    76 /** Creates a MPQCCommandJob with argument \a filename.
    77  *
    78  * @param jobs created job is added to this vector
    79  * @param command mpqc command to execute
    80  * @param filename filename being argument to job
    81  * @param nextid id for this job
    82  */
    83 void MPQCFragmentController::parsejob(
    84     std::vector<FragmentJob::ptr> &jobs,
    85     const std::string &command,
    86     const std::string &filename,
    87     const JobId_t nextid)
    88 {
    89   std::ifstream file;
    90   file.open(filename.c_str());
    91   ASSERT( file.good(), "parsejob() - file "+filename+" does not exist.");
    92   std::string output((std::istreambuf_iterator<char>(file)),
    93       std::istreambuf_iterator<char>());
    94   double begin[NDIM] = { 0., 0., 0. };
    95   RealSpaceMatrix M = World::getInstance().getDomain().getM();
    96   M *= 1./AtomicLengthToAngstroem;  // scale to atomic length units
    97   const double size = M.at(0,0);
    98   double end[NDIM] = { size, size, size };
    99   ASSERT( M.determinant() == size*size*size,
    100       "parsejob() - current domain matrix "+toString(M)+" is not cubic.");
    101   FragmentJob::ptr testJob( new MPQCJob(nextid, output, begin, end, level) );
    102   jobs.push_back(testJob);
    103   file.close();
    104   LOG(1, "INFO: Added MPQCCommandJob from file "+filename+".");
    105 }

  • src/Fragmentation/Automation/MPQCFragmentController.hpp

    rdd0c8f rac9ca4  
    3434public:
    3535  MPQCFragmentController(boost::asio::io_service &io_service) :
    36     SpecificFragmentController(io_service),
    37     level(5)
     36    SpecificFragmentController(io_service)
    3837  {}
    3938  virtual ~MPQCFragmentController()
    4039  {}
    4140
    42   bool addJobsFromFiles(
    43       const std::string &executable,
    44       const std::vector< boost::filesystem::path > &jobfiles);
     41  /** Command Controller to fill its hold of jobs from FragmentJobQueue.
     42   *
     43   * \return true - jobs obtained, false - queue empty
     44   */
     45  bool addJobsFromQueue();
     46
     47  /** Get results map of calculated jobs.
     48   *
     49   * \param fragmentData contains map of results on output
     50   */
    4551  void getResults(std::map<JobId_t, MPQCData> &fragmentData) {
    4652    SpecificFragmentController::getResults<MPQCData>(fragmentData);
    4753  }
    4854
    49   void setLevel(const size_t _level) { level = _level; }
    50 
    51 private:
    52   void parsejob(
    53       std::vector<FragmentJob::ptr> &jobs,
    54       const std::string &command,
    55       const std::string &filename,
    56       const JobId_t nextid);
    57 
    58 private:
    59   //!> resolution of sampled electron density as \f$2^{\mathrm{level}}\f$
    60   size_t level;
     55  /** Runs the service.
     56   *
     57   * Here, we finalize each job's id and push them to the server.
     58   */
     59  void run();
    6160};
    6261

  • src/Fragmentation/Automation/Makefile.am

    rdd0c8f rac9ca4  
    66        Fragmentation/Automation/FragmentationChargeDensity.cpp \
    77        Fragmentation/Automation/FragmentationResults.cpp \
     8        Fragmentation/Automation/FragmentJobQueue.cpp \
    89        Fragmentation/Automation/MPQCFragmentController.cpp \
    910        Fragmentation/Automation/parseKeySetFile.cpp \
    … …  
    2122        Fragmentation/Automation/FragmentationChargeDensity.hpp \
    2223        Fragmentation/Automation/FragmentationResults.hpp \
     24        Fragmentation/Automation/FragmentJobQueue.hpp \
    2325        Fragmentation/Automation/MPQCFragmentController.hpp \
    2426        Fragmentation/Automation/parseKeySetFile.hpp \

  • src/Fragmentation/Exporters/ExportGraph.cpp

    rdd0c8f rac9ca4  
    8181    BondFragments.ListOfMolecules.erase(iter);
    8282  }
    83 }
    84 
    85 void ExportGraph::operator()()
    86 {
    87   if (BondFragments.ListOfMolecules.size() == 0)
    88     prepareMolecule();
    8983}
    9084

  • src/Fragmentation/Exporters/ExportGraph.hpp

    rdd0c8f rac9ca4  
    4646  typedef boost::shared_ptr<SaturatedFragment> SaturatedFragment_ptr;
    4747
    48   virtual void operator()();
     48  virtual void operator()()=0;
    4949
    5050  /** Returns a saturated fragment for immediate use only.

  • src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp

    rdd0c8f rac9ca4  
    103103void ExportGraph_ToFiles::operator()()
    104104{
    105   LOG(1, "INFO: Writing " << TotalGraph.size() << " possible bond fragmentation configs");
     105  LOG(1, "INFO: Writing " << TotalGraph.size() << " possible bond fragmentation configs.");
    106106  size_t FragmentCounter = 0;
    107107  char *FragmentNumber = NULL;

  • src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp

    rdd0c8f rac9ca4  
    3333#endif
    3434
     35// boost asio required before MemDebug due to placement new
     36#include <boost/asio.hpp>
     37
    3538#include "CodePatterns/MemDebug.hpp"
    3639
    3740#include "Fragmentation/Exporters/ExportGraph_ToJobs.hpp"
    3841
     42#include <algorithm>
     43
     44#include "Box.hpp"
     45#include "Fragmentation/KeySet.hpp"
     46#include "Fragmentation/Automation/FragmentJobQueue.hpp"
     47#include "Fragmentation/Automation/MPQCFragmentController.hpp"
     48#include "Helpers/defs.hpp"
     49#include "Jobs/MPQCJob.hpp"
     50#include "LinearAlgebra/RealSpaceMatrix.hpp"
     51#include "Parser/FormatParserStorage.hpp"
    3952#include "World.hpp"
    4053
    … …  
    4356    const enum HydrogenTreatment _treatment,
    4457    const enum HydrogenSaturation _saturation) :
    45     ExportGraph(_graph, _treatment, _saturation)
     58    ExportGraph(_graph, _treatment, _saturation),
     59    level(5)
    4660{}
    4761
    … …  
    5165void ExportGraph_ToJobs::operator()()
    5266{
    53   ExportGraph::operator()();
     67  std::vector<FragmentJob::ptr> jobs;
     68  KeySetsContainer KeySets;
     69  KeySetsContainer FullKeySets;
     70  jobs.reserve(TotalGraph.size());
     71  LOG(1, "INFO: Creating " << TotalGraph.size() << " possible bond fragmentation jobs.");
     72
     73  // gather info about the domain
     74  double begin[NDIM] = { 0., 0., 0. };
     75  RealSpaceMatrix M = World::getInstance().getDomain().getM();
     76  M *= 1./AtomicLengthToAngstroem;  // scale to atomic length units
     77  const double size = M.at(0,0);
     78  double end[NDIM] = { size, size, size };
     79  const ParserTypes jobtype =
     80      FormatParserStorage::getInstance().getTypeFromName("mpqc");
     81
     82  // go through all fragments, output to stream and create job therefrom
     83  ExportGraph::SaturatedFragment_ptr CurrentFragment = getNextFragment();
     84  for (; (CurrentFragment != NULL) && (CurrentFragment->getKeySet() != ExportGraph::EmptySet);
     85      CurrentFragment = getNextFragment()) {
     86    const KeySet &set = CurrentFragment->getKeySet();
     87    LOG(2, "INFO: Creating bond fragment job for set " << set << ".");
     88    // store config in stream
     89    {
     90      std::stringstream output;
     91      // save to stream
     92      CurrentFragment->OutputConfig(output, jobtype);
     93      // create job and insert
     94      FragmentJob::ptr testJob( new MPQCJob(JobId::IllegalJob, output.str(), begin, end, level) );
     95      jobs.push_back(testJob);
     96
     97      // order is the same as the number of non-hydrogen atoms
     98      const KeySet &keyset = CurrentFragment->getKeySet();
     99      const size_t order = keyset.size();
     100      const KeySet &fullmolecule = CurrentFragment->getFullMolecule();
     101      const KeySet &saturationhydrogens = CurrentFragment->getSaturationHydrogens();
     102      KeySetsContainer::IntVector indices(keyset.begin(), keyset.end());
     103      KeySetsContainer::IntVector forceindices(fullmolecule.begin(), fullmolecule.end());
     104      {
     105        // replace all saturated hydrogen indices by "-1"
     106        for (KeySetsContainer::IntVector::iterator iter = forceindices.begin();
     107            iter != forceindices.end();
     108            ++iter)
     109          if (saturationhydrogens.find(*iter) != saturationhydrogens.end())
     110            *iter = -1;
     111      }
     112      KeySets.insert(indices, order);
     113      FullKeySets.insert(forceindices, order);
     114    }
     115    // store force index reference file
     116    // explicitly release fragment
     117    CurrentFragment.reset();
     118  }
     119  if (CurrentFragment == NULL) {
     120    ELOG(1, "Some error while obtaining the next fragment occured.");
     121    return;
     122  }
     123
     124  // push final jobs
     125  FragmentJobQueue::getInstance().addJobs(jobs, KeySets, FullKeySets);
    54126}

  • src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp

    rdd0c8f rac9ca4  
    2828{
    2929public:
     30  /** Constructor for ExportGraph_ToJobs.
     31   *
     32   * Sets default level.
     33   *
     34   * \param _graph Graph with all KeySet's
     35   * \param _treatment whether hydrogen is excluded in the _graph or not
     36   * \param _saturation whether we saturate dangling bonds or not
     37   */
    3038  ExportGraph_ToJobs(
    3139      const Graph &_graph,
    … …  
    3644        void operator()();
    3745
     46  /** Sets the level for the sampling of the density.
     47   *
     48   * \param _level level to set
     49   */
     50  void setLevel(const size_t _level) { level = _level; }
     51
     52private:
     53  //!> resolution of sampled electron density as \f$2^{\mathrm{level}}\f$
     54  size_t level;
    3855};
    3956

  • src/Fragmentation/KeySetsContainer.cpp

    rdd0c8f rac9ca4  
    233233  return true;
    234234}
     235
     236void KeySetsContainer::clear()
     237{
     238  KeySets.clear();
     239  OrderSet.clear();
     240  AtomCounter.clear();
     241  FragmentCounter = 0;
     242  Order = 0;
     243  FragmentsPerOrder.clear();
     244}
     245
     246void KeySetsContainer::insert(const KeySetsContainer &other)
     247{
     248  KeySets.reserve(KeySets.size()+other.KeySets.size());
     249  AtomCounter.reserve(AtomCounter.size()+other.AtomCounter.size());
     250  for (ArrayOfIntVectors::const_iterator iter = other.KeySets.begin();
     251      iter != other.KeySets.end(); ++iter)
     252    insert(*iter, iter->size());
     253}
     254
     255void KeySetsContainer::insert(const IntVector &indices, const size_t order)
     256{
     257  KeySets.push_back(indices);
     258  AtomCounter.push_back(indices.size());
     259  if (order > OrderSet.size() )
     260    OrderSet.resize(order);
     261  OrderSet[order-1].push_back(FragmentCounter);
     262  if (order > FragmentsPerOrder.size())
     263    FragmentsPerOrder.resize(order);
     264  ++(FragmentsPerOrder[order-1]);
     265  ++FragmentCounter;
     266}

  • src/Fragmentation/KeySetsContainer.hpp

    rdd0c8f rac9ca4  
    4545  }
    4646
     47  void clear();
     48
     49  void insert(const KeySetsContainer &other);
     50
     51  void insert(const IntVector &set, const size_t order);
     52
    4753private:
    4854  friend class boost::serialization::access;

  • src/Fragmentation/Makefile.am

    rdd0c8f rac9ca4  
    7272libMolecuilderFragmentation_getFromKeyset_la_includedir = $(includedir)/MoleCuilder/Fragmentation/
    7373libMolecuilderFragmentation_getFromKeysetStub_la_includedir = $(includedir)/MoleCuilder/Fragmentation/
     74libMolecuilderFragmentation_la_CPPFLAGS = $(AM_CPPFLAGS)
     75libMolecuilderFragmentation_la_LDFLAGS = $(AM_LDFLAGS)
     76libMolecuilderFragmentation_la_LIBADD =
     77if CONDJOBMARKET
     78libMolecuilderFragmentation_la_CPPFLAGS += ${JobMarket_CFLAGS}
     79libMolecuilderFragmentation_la_LDFLAGS += $(JobMarket_LDFLAGS)
     80libMolecuilderFragmentation_la_LIBADD += $(JobMarket_LIBS)
     81endif
    7482
    7583nobase_libMolecuilderFragmentation_la_include_HEADERS = ${FRAGMENTATIONHEADER}
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