Changeset 228340 for src/FunctionApproximation

Timestamp:

Nov 4, 2016, 11:47:34 AM (8 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:

2124aa

Parents:

814b8c

git-author:

Frederik Heber <heber@…> (10/03/16 18:04:17)

git-committer:

Frederik Heber <heber@…> (11/04/16 11:47:34)

Message:

Extractors::gatherAllSymmetricDistances..() additionaly gets edge set to set bonded flag.

Location:

src/FunctionApproximation

Files:

• Extractors.cpp (modified) (2 diffs)
• Extractors.hpp (modified) (5 diffs)
• TrainingData.cpp (modified) (2 diffs)
• unittests/ExtractorsUnitTest.cpp (modified) (1 diff)

src/FunctionApproximation/Extractors.cpp

@@ -62 +62 @@
     const Fragment::positions_t& positions,
     const Fragment::atomicnumbers_t& atomicnumbers,
+    const FragmentationEdges::edges_t &edges,
     const size_t globalid)
 {
@@ -88 +89 @@
           );
       arg.globalid = globalid;
+      arg.bonded = false;
       LOG(3, "DEBUG: Created argument " << arg << ".");
       result.push_back(arg);

src/FunctionApproximation/Extractors.hpp

@@ -16 +16 @@
 #include <boost/function.hpp>
 
+#include "Fragmentation/EdgesPerFragment.hpp"
 #include "Fragmentation/Summation/SetValues/Fragment.hpp"
 #include "FunctionApproximation/FunctionModel.hpp"
@@ -71 +72 @@
    * \param positions all nuclei positions
    * \param atomicNumber all nuclei atomic numbers
+   * \param edges edges of the fragment's bond graph
    * \param globalid index to associated in argument_t with
    * \return vector of argument_ , each with a distance
@@ -78 +80 @@
       const Fragment::positions_t& positions,
       const Fragment::atomicnumbers_t& atomicnumbers,
+      const FragmentationEdges::edges_t &edges,
       const size_t globalid);
 
@@ -85 +88 @@
    * \param positions all nuclei positions
    * \param atomicNumber all nuclei atomic numbers
+   * \param edges edges of the fragment's bond graph
    * \param index index refers to the index within the global set of configurations
    * \return vector of of argument_t containing all found distances
@@ -91 +95 @@
       const Fragment::positions_t& positions,
       const Fragment::atomicnumbers_t& atomicnumbers,
+      const FragmentationEdges::edges_t &edges,
       const size_t index
       ) {
     // get distance out of Fragment
-    return gatherAllSymmetricDistanceArguments(positions, atomicnumbers, index);
+    return gatherAllSymmetricDistanceArguments(positions, atomicnumbers, edges, index);
   }
 

src/FunctionApproximation/TrainingData.cpp

@@ -50 +50 @@
 #include "CodePatterns/toString.hpp"
 
+#include "Fragmentation/EdgesPerFragment.hpp"
 #include "Fragmentation/Summation/SetValues/Fragment.hpp"
 #include "FunctionApproximation/FunctionArgument.hpp"
@@ -59 +60 @@
     const HomologyGraph &graph = iter->first;
     const Fragment &fragment = iter->second.fragment;
+    const FragmentationEdges::edges_t &edges = iter->second.edges;
     FunctionModel::arguments_t all_args = Extractors::gatherAllSymmetricDistances(
         fragment.getPositions(),
         fragment.getAtomicNumbers(),
+        edges,
         DistanceVector.size()
         );

src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp

@@ -89 +89 @@
 
   // create distances
+  FragmentationEdges::edges_t edges; // maybe left empty
   FunctionModel::arguments_t args =
-      Extractors::gatherAllSymmetricDistances(positions, atomicnumbers, 0);
+      Extractors::gatherAllSymmetricDistances(positions, atomicnumbers, edges, 0);
   CPPUNIT_ASSERT_EQUAL( (size_t)(5*4/2), args.size() );