Changeset 17c03f for src


Ignore:
Timestamp:
Dec 14, 2012, 5:39:41 PM (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:
e71325
Parents:
766767
git-author:
Frederik Heber <heber@…> (09/28/12 08:00:23)
git-committer:
Frederik Heber <heber@…> (12/14/12 17:39:41)
Message:

Extracted parseKeySetFile from FragmentationResults, FragmentationChargeDensity, FragmentationAutomationAction.

  • this removes the code duplication.
Location:
src
Files:
2 added
4 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

    r766767 r17c03f  
    5959#include "Fragmentation/Automation/FragmentationResults.hpp"
    6060#include "Fragmentation/Automation/MPQCFragmentController.hpp"
     61#include "Fragmentation/Automation/parseKeySetFile.hpp"
    6162#include "Fragmentation/Automation/VMGDebugGridFragmentController.hpp"
    6263#include "Fragmentation/Automation/VMGFragmentController.hpp"
    … …  
    7576#include "Fragmentation/Summation/writeTable.hpp"
    7677#include "Graph/DepthFirstSearchAnalysis.hpp"
    77 #include "Helpers/defs.hpp"
    7878#include "Jobs/MPQCJob.hpp"
    7979#include "Jobs/MPQCData.hpp"
    … …  
    251251    return false;
    252252
     253  if (!Energy.InitialiseIndices()) return false;
     254
     255  if (!Force.ParseIndices(KeySetFilename.c_str())) return false;
     256
    253257  // initialise keysets
    254258  KeySetsContainer KeySet;
     259  parseKeySetFile(KeySet, KeySetFilename, FragmentCounter, NonHydrogenKeySets);
    255260  KeySetsContainer ForceKeySet;
    256   if (!Energy.InitialiseIndices()) return false;
    257 
    258   if (!Force.ParseIndices(KeySetFilename.c_str())) return false;
    259 
    260   {
    261     // else needs keysets without hydrogens
    262     std::stringstream filename;
    263     filename << FRAGMENTPREFIX << KEYSETFILE;
    264     if (!KeySet.ParseKeySets(KeySetFilename, filename.str(), FragmentCounter)) return false;
    265   }
    266 
    267   {
    268     // forces need keysets including hydrogens
    269     std::stringstream filename;
    270     filename << FRAGMENTPREFIX << FORCESFILE;
    271     if (!ForceKeySet.ParseKeySets(KeySetFilename, filename.str(), FragmentCounter)) return false;
    272   }
     261  parseKeySetFile(ForceKeySet, KeySetFilename, FragmentCounter, HydrogenKeySets);
    273262
    274263  // combine all found data
    … …  
    412401  // append all fragments to a HomologyContainer
    413402  HomologyContainer::container_t values;
     403  const size_t FragmentCounter = results.Result_perIndexSet_Energy.size();
     404  KeySetsContainer KeySet;
     405  parseKeySetFile(KeySet, KeySetFilename, FragmentCounter, NonHydrogenKeySets);
    414406  KeySetsContainer ForceKeySet;
    415   {
    416     // forces need keysets including hydrogens
    417     std::stringstream filename;
    418     filename << FRAGMENTPREFIX << FORCESFILE;
    419 #ifndef NDEBUG
    420     bool status =
    421 #endif
    422         ForceKeySet.ParseKeySets(KeySetFilename, filename.str(), results.Result_perIndexSet_Energy.size());
    423     ASSERT( status,
    424         "FragmentationResults::FragmentationResults() - ParseKeySets() of "
    425         +toString(FORCESFILE)+" failed.");
    426   }
     407  parseKeySetFile(ForceKeySet, KeySetFilename, FragmentCounter, HydrogenKeySets);
     408
    427409  // convert KeySetContainer to IndexSetContainer
    428410  IndexSetContainer::ptr container(new IndexSetContainer(ForceKeySet));

  • src/Fragmentation/Automation/FragmentationChargeDensity.cpp

    r766767 r17c03f  
    4848#include "Fragmentation/Automation/createMatrixNrLookup.hpp"
    4949#include "Fragmentation/Automation/extractJobIds.hpp"
     50#include "Fragmentation/Automation/parseKeySetFile.hpp"
    5051#include "Fragmentation/Summation/IndexSetContainer.hpp"
    5152#include "Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp"
    … …  
    7273  // initialise keysets
    7374  KeySetsContainer KeySet;
    74   {
    75     // else needs keysets without hydrogens
    76     std::stringstream filename;
    77     filename << FRAGMENTPREFIX << KEYSETFILE;
    78 #ifndef NDEBUG
    79     bool status =
    80 #endif
    81         KeySet.ParseKeySets(KeySetFilename, filename.str(), FragmentCounter);
    82     ASSERT( status,
    83         "FragmentationResults::FragmentationResults() - ParseKeySets() of "
    84         +toString(KEYSETFILE)+" failed.");
    85   }
     75  parseKeySetFile(KeySet, KeySetFilename, FragmentCounter, NonHydrogenKeySets);
    8676
    8777  /// prepare for OrthogonalSummation

  • src/Fragmentation/Automation/FragmentationResults.cpp

    r766767 r17c03f  
    4949#include "Fragmentation/Automation/createMatrixNrLookup.hpp"
    5050#include "Fragmentation/Automation/extractJobIds.hpp"
     51#include "Fragmentation/Automation/parseKeySetFile.hpp"
    5152#include "Fragmentation/Summation/AllLevelOrthogonalSummator.hpp"
    5253#include "Fragmentation/Summation/IndexSetContainer.hpp"
    … …  
    7980  // initialise keysets
    8081  KeySetsContainer KeySet;
     82  parseKeySetFile(KeySet, KeySetFilename, MPQCFragmentCounter, NonHydrogenKeySets);
    8183  KeySetsContainer ForceKeySet;
    82   {
    83     // else needs keysets without hydrogens
    84     std::stringstream filename;
    85     filename << FRAGMENTPREFIX << KEYSETFILE;
    86 #ifndef NDEBUG
    87     bool status =
    88 #endif
    89         KeySet.ParseKeySets(KeySetFilename, filename.str(), MPQCFragmentCounter);
    90     ASSERT( status,
    91         "FragmentationResults::FragmentationResults() - ParseKeySets() of "
    92         +toString(KEYSETFILE)+" failed.");
    93   }
    94 
    95   {
    96     // forces need keysets including hydrogens
    97     std::stringstream filename;
    98     filename << FRAGMENTPREFIX << FORCESFILE;
    99 #ifndef NDEBUG
    100     bool status =
    101 #endif
    102         ForceKeySet.ParseKeySets(KeySetFilename, filename.str(), MPQCFragmentCounter);
    103     ASSERT( status,
    104         "FragmentationResults::FragmentationResults() - ParseKeySets() of "
    105         +toString(FORCESFILE)+" failed.");
    106   }
     84  parseKeySetFile(ForceKeySet, KeySetFilename, MPQCFragmentCounter, HydrogenKeySets);
    10785
    10886  /// prepare for OrthogonalSummation

  • src/Fragmentation/Automation/Makefile.am

    r766767 r17c03f  
    77        Fragmentation/Automation/FragmentationResults.cpp \
    88        Fragmentation/Automation/MPQCFragmentController.cpp \
     9        Fragmentation/Automation/parseKeySetFile.cpp \
    910        Fragmentation/Automation/SpecificFragmentController.cpp
    1011
    … …  
    2122        Fragmentation/Automation/FragmentationResults.hpp \
    2223        Fragmentation/Automation/MPQCFragmentController.hpp \
     24        Fragmentation/Automation/parseKeySetFile.hpp \
    2325        Fragmentation/Automation/SpecificFragmentController.hpp \
    2426        Fragmentation/Automation/SpecificFragmentController_impl.hpp
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