Changeset c7aac9 for src/FunctionApproximation

Timestamp:

Nov 4, 2016, 9:37:50 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:

c5e75f3

Parents:

e47ac7

git-author:

Frederik Heber <heber@…> (10/02/16 14:03:57)

git-committer:

Frederik Heber <heber@…> (11/04/16 09:37:50)

Message:

FIX: TrainingData used charges instead of atomic numbers to recognize fragments.

• this only works if we do not DoSampleValenceOnly. Otherwise charges are no longer directly associable with the atomic number of the nuclei.
• Extractors::gatherAllSymmetricDistanceArguments now needs atomicnumbers instead of charges.
• TESTFIX: needed to adapt ExtractorsUnitTest.

Location:

src/FunctionApproximation

Files:

• Extractors.cpp (modified) (2 diffs)
• Extractors.hpp (modified) (4 diffs)
• TrainingData.cpp (modified) (1 diff)
• unittests/ExtractorsUnitTest.cpp (modified) (1 diff)

src/FunctionApproximation/Extractors.cpp

@@ -59 +59 @@
 Extractors::gatherAllSymmetricDistanceArguments(
     const Fragment::positions_t& positions,
-    const Fragment::charges_t& charges,
+    const Fragment::atomicnumbers_t& atomicnumbers,
     const size_t globalid)
 {
@@ -76 +76 @@
       arg.distance = firsttemp.distance(secondtemp);
       arg.types = std::make_pair(
-          charges[ std::distance(positions.begin(), firstpositer) ],
-          charges[ std::distance(positions.begin(), secondpositer) ]
+          (int)atomicnumbers[ std::distance(positions.begin(), firstpositer) ],
+          (int)atomicnumbers[ std::distance(positions.begin(), secondpositer) ]
           );
       arg.indices = std::make_pair(

src/FunctionApproximation/Extractors.hpp

@@ -69 +69 @@
    *
    * \param positions all nuclei positions
-   * \param charges all nuclei charges
+   * \param atomicNumber all nuclei atomic numbers
    * \param globalid index to associated in argument_t with
    * \return vector of argument_ , each with a distance
@@ -76 +76 @@
   gatherAllSymmetricDistanceArguments(
       const Fragment::positions_t& positions,
-      const Fragment::charges_t& charges,
+      const Fragment::atomicnumbers_t& atomicnumbers,
       const size_t globalid);
 
@@ -83 +83 @@
    *
    * \param positions all nuclei positions
-   * \param charges all nuclei charges
+   * \param atomicNumber all nuclei atomic numbers
    * \param index index refers to the index within the global set of configurations
    * \return vector of of argument_t containing all found distances
@@ -89 +89 @@
   inline FunctionModel::arguments_t gatherAllSymmetricDistances(
       const Fragment::positions_t& positions,
-      const Fragment::charges_t& charges,
+      const Fragment::atomicnumbers_t& atomicnumbers,
       const size_t index
       ) {
     // get distance out of Fragment
-    return gatherAllSymmetricDistanceArguments(positions, charges, index);
+    return gatherAllSymmetricDistanceArguments(positions, atomicnumbers, index);
   }
 

src/FunctionApproximation/TrainingData.cpp

@@ -58 +58 @@
   for (HomologyContainer::const_iterator iter = range.first; iter != range.second; ++iter) {
     const Fragment &fragment = iter->second.fragment;
-    // create internal list of arguments
     FunctionModel::arguments_t all_args = Extractors::gatherAllSymmetricDistances(
         fragment.getPositions(),
-        fragment.getCharges(),
+        fragment.getAtomicNumbers(),
         DistanceVector.size()
         );

src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp

@@ -85 +85 @@
 
   // create charges
-  Fragment::charges_t charges;
-  charges += 6., 6., 1., 1., 1.;
+  Fragment::atomicnumbers_t atomicnumbers;
+  atomicnumbers += 6, 6, 1, 1, 1;
 
   // create distances
   FunctionModel::arguments_t args =
-      Extractors::gatherAllSymmetricDistances(positions, charges, 0);
+      Extractors::gatherAllSymmetricDistances(positions, atomicnumbers, 0);
   CPPUNIT_ASSERT_EQUAL( (size_t)(5*4/2), args.size() );