Changeset e0ae58d for src/Fragmentation/Summation

Timestamp:

Oct 14, 2013, 11:42:04 PM (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:

955051

Parents:

7d507c

git-author:

Frederik Heber <heber@…> (09/26/13 16:17:59)

git-committer:

Frederik Heber <heber@…> (10/14/13 23:42:04)

Message:

createMatrixNrLookup now requires a ValueMask.

• adapted all Fragmentation..Results accordingly.
• FragmentationShortRangeResults' cstor now allows passing this ValueMask.

Location:

src/Fragmentation/Summation/Containers

Files:

• FragmentationChargeDensity.cpp (modified) (1 diff)
• FragmentationLongRangeResults.cpp (modified) (1 diff)
• FragmentationShortRangeResults.cpp (modified) (3 diffs)
• FragmentationShortRangeResults.hpp (modified) (2 diffs)
• createMatrixNrLookup.cpp (modified) (1 diff)
• createMatrixNrLookup.hpp (modified) (1 diff)

src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp

@@ -69 +69 @@
   // create lookup from job nr to fragment number
   size_t FragmentCounter = 0;
+  std::vector<bool> ValueMask(fragmentData.size(), true);
   const std::map< JobId_t, size_t > MatrixNrLookup =
-      createMatrixNrLookup(jobids, FragmentCounter);
+      createMatrixNrLookup(jobids, FragmentCounter, ValueMask);
 
   /// prepare for OrthogonalSummation

src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp

@@ -81 +81 @@
 {
   // create lookup from job nr to fragment number
-  size_t MPQCFragmentCounter = 0;
-  const std::vector<JobId_t> mpqcjobids = extractJobIds<MPQCData>(fragmentData);
-  MPQCMatrixNrLookup =
-      createMatrixNrLookup(mpqcjobids, MPQCFragmentCounter);
-
-  size_t VMGFragmentCounter = 0;
-  const std::vector<JobId_t> vmgjobids = extractJobIds<VMGData>(longrangeData);
-  VMGMatrixNrLookup =
-      createMatrixNrLookup(vmgjobids, VMGFragmentCounter);
+  {
+    size_t MPQCFragmentCounter = 0;
+    std::vector<bool> ValueMask(fragmentData.size(), true);
+    const std::vector<JobId_t> mpqcjobids = extractJobIds<MPQCData>(fragmentData);
+    MPQCMatrixNrLookup =
+        createMatrixNrLookup(mpqcjobids, MPQCFragmentCounter, ValueMask);
+  }
+
+  {
+    size_t VMGFragmentCounter = 0;
+    std::vector<bool> ValueMask(longrangeData.size(), true);
+    const std::vector<JobId_t> vmgjobids = extractJobIds<VMGData>(longrangeData);
+    VMGMatrixNrLookup =
+        createMatrixNrLookup(vmgjobids, VMGFragmentCounter, ValueMask);
+  }
 }
 

src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp

@@ -62 +62 @@
     const std::map<JobId_t,MPQCData> &fragmentData,
     const KeySetsContainer& _KeySet,
-    const KeySetsContainer& _ForceKeySet) :
+    const KeySetsContainer& _ForceKeySet,
+    std::vector<bool> &_ValueMask) :
     KeySet(_KeySet),
     ForceKeySet(_ForceKeySet)
 {
-  initLookups(fragmentData);
+  initLookups(fragmentData,_ValueMask);
 
   // convert KeySetContainer to IndexSetContainer
@@ -75 +76 @@
 
 void FragmentationShortRangeResults::initLookups(
-    const std::map<JobId_t,MPQCData> &fragmentData)
+    const std::map<JobId_t,MPQCData> &fragmentData,
+    std::vector<bool> &_ValueMask)
 {
   // create lookup from job nr to fragment number
@@ -81 +83 @@
   const std::vector<JobId_t> mpqcjobids = extractJobIds<MPQCData>(fragmentData);
   MPQCMatrixNrLookup =
-      createMatrixNrLookup(mpqcjobids, MPQCFragmentCounter);
+      createMatrixNrLookup(mpqcjobids, MPQCFragmentCounter, _ValueMask);
 }
 

src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp

@@ -47 +47 @@
    * @param _KeySet KeySets of all (non-hydrogen) atoms
    * @param _ForceKeySet KeySets of all atoms except those added by saturation
+   * @param _ValueMask masks whether to use a value (true) or not (false),
+   *        default is true for all values
    */
   FragmentationShortRangeResults(
       const std::map<JobId_t,MPQCData> &fragmentData,
       const KeySetsContainer& _KeySet,
-      const KeySetsContainer& _ForceKeySet);
+      const KeySetsContainer& _ForceKeySet,
+      std::vector<bool> &_ValueMask);
 
   /** Performs the summation and fills all result vectors.
@@ -78 +81 @@
 private:
   void initLookups(
-      const std::map<JobId_t,MPQCData> &fragmentData);
+      const std::map<JobId_t,MPQCData> &fragmentData,
+      std::vector<bool> &_ValueMask);
 
 private:

src/Fragmentation/Summation/Containers/createMatrixNrLookup.cpp

@@ -45 +45 @@
 std::map< JobId_t, size_t > createMatrixNrLookup(
     const std::vector<JobId_t> &jobids,
-    size_t &FragmentCounter)
+    size_t &FragmentCounter,
+    std::vector<bool> &ValueMask)
 {
   // align fragments
   std::map< JobId_t, size_t > MatrixNrLookup;
   FragmentCounter = 0;
+  ASSERT( ValueMask.size() == jobids.size(),
+      "createMatrixNrLookup() - jobids and ValueMask differ in size");
+  std::vector<bool>::const_iterator maskiter = ValueMask.begin();
   for (std::vector<JobId_t>::const_iterator iter = jobids.begin();
-      iter != jobids.end(); ++iter) {
+      iter != jobids.end(); ++iter, ++maskiter) {
     LOG(3, "DEBUG: Inserting (" << *iter << "," << FragmentCounter << ").");
 #ifndef NDEBUG
     std::pair< std::map< JobId_t, size_t >::iterator, bool> inserter =
 #endif
-        MatrixNrLookup.insert( std::make_pair(*iter, FragmentCounter++) );
+        // we either set to FragmentCounter or to -1 which is always outside
+        // of range and hence skipped by (Orthogonal)Summator.
+        MatrixNrLookup.insert(
+            std::make_pair(
+                *iter,
+                (*maskiter ? FragmentCounter : (size_t)-1)
+            )
+        );
     ASSERT( inserter.second,
         "createMatrixNrLookup() - two results have same id "
         +toString(*iter)+".");
+    ++FragmentCounter;  // in any case needs to be increased to skip the result
   }
   LOG(1, "INFO: There are " << FragmentCounter << " fragments.");

src/Fragmentation/Summation/Containers/createMatrixNrLookup.hpp

@@ -32 +32 @@
 std::map< JobId_t, size_t > createMatrixNrLookup(
     const std::vector<JobId_t> &jobids,
-    size_t &FragmentCounter);
+    size_t &FragmentCounter,
+    std::vector<bool> &ValueMask);
 
 #endif /* CREATEMATRIXNRLOOKUP_HPP_ */