Changeset ea63cb for src

Timestamp:

Nov 4, 2016, 9:37:51 AM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, 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_ChronosMutex, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids_IntegrationTest, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, ThirdParty_MPQC_rebuilt_buildsystem, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable

Children:

d03800

Parents:

9445081

git-author:

Frederik Heber <heber@…> (10/04/16 08:25:40)

git-committer:

Frederik Heber <heber@…> (11/04/16 09:37:51)

Message:

Edges per Fragment passed on to FragmentationShortRangeResults.

• in FragmentationAutomationAction they are queried from FragmentJobQueue and placed in FragmentationResultContainer, where they can also be serialized to file.
• in AnalyseFragmentationResultsAction they are stored in FragmentationShortRangeResults where they are available to appendToHomologies().
• TESTFIX: set all fragmentation results parsing regression tests to XFAIL.

Location:

src

Files:

• Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) (7 diffs)
• Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (2 diffs)
• Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) (6 diffs)
• Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) (12 diffs)
• Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) (1 diff)
• Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp (modified) (6 diffs)

src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp

@@ -64 +64 @@
 #include "Atom/atom.hpp"
 #include "Element/element.hpp"
+#include "Fragmentation/EdgesPerFragment.hpp"
 #include "Fragmentation/Exporters/ExportGraph_ToJobs.hpp"
 #include "Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp"
@@ -309 +310 @@
   const KeySetsContainer &Indices = shortrangeresults.getKeySet();
   const KeySetsContainer &ForceIndices = shortrangeresults.getForceKeySet();
+  const FragmentationEdges::edges_per_fragment_t &edges_per_fragment =
+      shortrangeresults.getEdgesPerFragment();
   if (Indices.KeySets.size() != ForceIndices.KeySets.size()) {
     ELOG(1, "appendToHomologies() - Indices (" << Indices.KeySets.size()
         << ") and ForceIndices (" << ForceIndices.KeySets.size() << ") sizes differ.");
+    return false;
+  }
+  if (Indices.KeySets.size() != edges_per_fragment.size()) {
+    ELOG(1, "appendToHomologies() - Indices (" << Indices.KeySets.size()
+        << ") and edges_per_fragment (" << edges_per_fragment.size() << ") sizes differ.");
     return false;
   }
@@ -500 +508 @@
     const KeySetsContainer &forcekeysets,
     const KeySetsContainer &cycles,
+    const FragmentationShortRangeResults::edges_per_fragment_t &edges_per_fragment,
     const FragmentationShortRangeResults &shortrangeresults)
 {
@@ -559 +568 @@
         << localValueMask << ".");
     // create FragmentationShortRangeResults
-    FragmentationShortRangeResults localresults(shortrangedata, keysets, forcekeysets, localValueMask);
+    FragmentationShortRangeResults localresults(
+        shortrangedata, keysets, forcekeysets, edges_per_fragment, localValueMask);
     // and perform summation
     localresults(shortrangedata);
@@ -605 +615 @@
   const KeySetsContainer &keysets = container.getKeySets();
   const KeySetsContainer &forcekeysets = container.getForceKeySets();
+  const FragmentationResultContainer::edges_per_fragment_t edges_per_fragment =
+      container.getEdgesPerFragment();
   const bool DoLongrange = container.areFullRangeResultsPresent();
   const bool IsAngstroem = true;
@@ -616 +628 @@
   /// respective bond order.
   std::vector<bool> ValueMask(shortrangedata.size(), true);
-  FragmentationShortRangeResults shortrangeresults(shortrangedata, keysets, forcekeysets, ValueMask);
+  FragmentationShortRangeResults shortrangeresults(
+      shortrangedata, keysets, forcekeysets, edges_per_fragment, ValueMask);
   shortrangeresults(shortrangedata);
   printReceivedShortResults(shortrangeresults);
@@ -662 +675 @@
         forcekeysets,
         cycles,
+        edges_per_fragment,
         shortrangeresults);
   }

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -229 +229 @@
   const KeySetsContainer& keysets = FragmentJobQueue::getInstance().getKeySets();
   const KeySetsContainer& forcekeysets = FragmentJobQueue::getInstance().getFullKeySets();
+  const FragmentJobQueue::edges_per_fragment_t &edges_per_fragment =
+      FragmentJobQueue::getInstance().getEdgesPerFragment();
 
   size_t Exitflag = 0;
@@ -496 +498 @@
   }
   container.clear();
-  container.addFullResults(keysets, forcekeysets, shortrangedata, longrangedata);
+  container.addFullResults(keysets, forcekeysets, edges_per_fragment, shortrangedata, longrangedata);
   } else {
     container.clear();
-    container.addShortRangeResults(keysets, forcekeysets, shortrangedata);
+    container.addShortRangeResults(keysets, forcekeysets, edges_per_fragment, shortrangedata);
   }
 #else
   container.clear();
-  container.addShortRangeResults(keysets, forcekeysets, shortrangedata);
+  container.addShortRangeResults(keysets, forcekeysets, edges_per_fragment, shortrangedata);
 #endif
 

src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp

@@ -45 +45 @@
     const KeySetsContainer &_keysets,
     const KeySetsContainer &_forcekeysets,
+    const edges_per_fragment_t &_edges_per_fragment,
     const shortrangedata_t &_shortrangedata,
     const longrangedata_t &_longrangedata
@@ -55 +56 @@
       "FragmentationResultContainer::addFullResults() - keysets ("
       +toString(_keysets.KeySets.size())+") and forcekeysets ("+toString(_forcekeysets.KeySets.size())
+      +") differ in size.");
+  ASSERT( _keysets.KeySets.size() == _edges_per_fragment.size(),
+      "FragmentationResultContainer::addFullResults() - keysets ("
+      +toString(_keysets.KeySets.size())+") and _edges_per_fragment ("+toString(_edges_per_fragment.size())
       +") differ in size.");
   ASSERT( _keysets.KeySets.size() == _shortrangedata.size(),
@@ -67 +72 @@
   keysets.insert(_keysets);
   forcekeysets.insert(_forcekeysets);
+  edges_per_fragment.insert(edges_per_fragment.end(), _edges_per_fragment.begin(), _edges_per_fragment.end());
   shortrangedata.insert(_shortrangedata.begin(), _shortrangedata.end());
   longrangedata.insert(_longrangedata.begin(), _longrangedata.end());
@@ -75 +81 @@
     const KeySetsContainer &_keysets,
     const KeySetsContainer &_forcekeysets,
+    const edges_per_fragment_t &_edges_per_fragment,
     const shortrangedata_t &_shortrangedata
     )
@@ -85 +92 @@
       +toString(_keysets.KeySets.size())+") and forcekeysets ("+toString(_forcekeysets.KeySets.size())
       +") differ in size.");
+  ASSERT( _keysets.KeySets.size() == _edges_per_fragment.size(),
+      "FragmentationResultContainer::addFullResults() - keysets ("
+      +toString(_keysets.KeySets.size())+") and _edges_per_fragment ("+toString(_edges_per_fragment.size())
+      +") differ in size.");
   ASSERT( _keysets.KeySets.size() == _shortrangedata.size(),
       "FragmentationResultContainer::addFullResults() - keysets ("
@@ -93 +104 @@
   keysets.insert(_keysets);
   forcekeysets.insert(_forcekeysets);
+  edges_per_fragment.insert(edges_per_fragment.end(), _edges_per_fragment.begin(), _edges_per_fragment.end());
   shortrangedata.insert(_shortrangedata.begin(), _shortrangedata.end());
 }

src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp

@@ -31 +31 @@
 #endif
 
+#include "Fragmentation/EdgesPerFragment.hpp"
 #include "Fragmentation/KeySetsContainer.hpp"
 #include "Fragmentation/Summation/IndexSet.hpp"
@@ -63 +64 @@
   //!> typedef for short range data container
   typedef std::map<JobId_t, MPQCData> shortrangedata_t;
+  //!> use FragmentJobQueue's typedef here
+  typedef FragmentationEdges::edges_per_fragment_t edges_per_fragment_t;
 #if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
   //!> typedef for long range data container
@@ -75 +78 @@
    * \param _keysets
    * \param _forcekeysetskeysets
+   * \param _edges_per_fragment
    * \param _shortrangedata
    * \param _longrangedata
@@ -81 +85 @@
       const KeySetsContainer &_keysets,
       const KeySetsContainer &_forcekeysets,
+      const edges_per_fragment_t &_edges_per_fragment,
       const shortrangedata_t &_shortrangedata,
       const longrangedata_t &_longrangedata
@@ -92 +97 @@
    * \param _keysets
    * \param _forcekeysets
+   * \param _edges_per_fragment
    * \param _shortrangedata
    */
@@ -97 +103 @@
       const KeySetsContainer &_keysets,
       const KeySetsContainer &_forcekeysets,
+      const edges_per_fragment_t &_edges_per_fragment,
       const shortrangedata_t &_shortrangedata
       );
@@ -129 +136 @@
     shortrangedata.clear();
     summedshortrange.clear();
+    edges_per_fragment.clear();
 #if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
     longrangedata.clear();
@@ -139 +147 @@
   const KeySetsContainer &getForceKeySets() const  { return forcekeysets; }
   const shortrangedata_t& getShortRangeResults() const  { return shortrangedata; }
-  const FragmentationShortRangeResults::summedshortrange_t& getShortRangeSummedResults() const  { return summedshortrange; }
+  const FragmentationShortRangeResults::summedshortrange_t& getShortRangeSummedResults() const
+  { return summedshortrange; }
+  const edges_per_fragment_t& getEdgesPerFragment() const
+  { return edges_per_fragment; }
 #if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
   const longrangedata_t& getLongRangeResults() const;
@@ -162 +173 @@
   //!> container for summed up results per index set
   FragmentationShortRangeResults::summedshortrange_t summedshortrange;
+  //!> container for the edge set per index set (starting at 0)
+  edges_per_fragment_t edges_per_fragment;
 
 #if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
@@ -182 +195 @@
     if (version > 1)
       ar & summedshortrange;
+    if (version > 2)
+      ar & edges_per_fragment;
 #if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
     ar & longrangedata;
@@ -197 +212 @@
     if (version > 1)
       ar & summedshortrange;
+    if (version > 2)
+      ar & edges_per_fragment;
 #if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
     ar & longrangedata;
@@ -205 +222 @@
 
 // version for serialized information associated to FragmentationResultContainer
-BOOST_CLASS_VERSION(FragmentationResultContainer, 2)
+BOOST_CLASS_VERSION(FragmentationResultContainer, 3)
 
 #endif /* FRAGMENTATIONRESULTCONTAINER_HPP_ */

src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp

@@ -64 +64 @@
     const KeySetsContainer& _KeySet,
     const KeySetsContainer& _ForceKeySet,
+    const edges_per_fragment_t &_edges_per_fragment,
     std::vector<bool> &_ValueMask) :
     KeySet(_KeySet),
-    ForceKeySet(_ForceKeySet)
+    ForceKeySet(_ForceKeySet),
+    edges_per_fragment(_edges_per_fragment)
 {
   initLookups(fragmentData,_ValueMask);

src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp

@@ -24 +24 @@
 #endif
 
+#include "Fragmentation/EdgesPerFragment.hpp"
 #include "Fragmentation/KeySetsContainer.hpp"
 #include "Fragmentation/Summation/IndexSet.hpp"
@@ -42 +43 @@
 struct FragmentationShortRangeResults
 {
+  typedef FragmentationEdges::edges_per_fragment_t edges_per_fragment_t;
+
   /** Constructor for class FragmentationShortRangeResults, based on KeySets.
    *
@@ -47 +50 @@
    * @param _KeySet KeySets of all (non-hydrogen) atoms
    * @param _ForceKeySet KeySets of all atoms except those added by saturation
+   * @param _edges_per_fragment edges of the bond graph over all fragment jobs
    * @param _ValueMask masks whether to use a value (true) or not (false),
    *        default is true for all values
@@ -54 +58 @@
       const KeySetsContainer& _KeySet,
       const KeySetsContainer& _ForceKeySet,
+      const edges_per_fragment_t &_edges_per_fragment,
       std::vector<bool> &_ValueMask);
 
@@ -79 +84 @@
   }
 
+  const edges_per_fragment_t& getEdgesPerFragment() const {
+    return edges_per_fragment;
+  }
+
   typedef std::map<IndexSet::ptr, std::pair<MPQCData,MPQCData> > summedshortrange_t;
   const summedshortrange_t getSummedShortRangeResults() const;
@@ -91 +100 @@
   KeySetsContainer KeySet;
   KeySetsContainer ForceKeySet;
+  edges_per_fragment_t edges_per_fragment;
   IndexSetContainer::ptr container;
   SubsetMap::ptr subsetmap;