Changeset e60558

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:

041a79

Parents:

67044a

git-author:

Frederik Heber <heber@…> (10/04/16 07:28:59)

git-committer:

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

Message:

Extractors require additionally the binding graph of the fragment itself.

• this is used in ::filterArguments..(), ::reorderArguments(), and CompountPotential::splitUpArgumentsByModelsFilter().

Location:

src

Files:

• FunctionApproximation/Extractors.cpp (modified) (3 diffs)
• FunctionApproximation/Extractors.hpp (modified) (4 diffs)
• FunctionApproximation/FunctionModel.hpp (modified) (2 diffs)
• FunctionApproximation/TrainingData.cpp (modified) (2 diffs)
• Potentials/CompoundPotential.cpp (modified) (3 diffs)
• Potentials/CompoundPotential.hpp (modified) (2 diffs)
• Potentials/Specifics/ConstantPotential.cpp (modified) (1 diff)
• Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) (1 diff)
• Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) (1 diff)
• Potentials/Specifics/PairPotential_Harmonic.cpp (modified) (1 diff)
• Potentials/Specifics/PairPotential_LennardJones.cpp (modified) (1 diff)
• Potentials/Specifics/PairPotential_Morse.cpp (modified) (1 diff)
• Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) (1 diff)
• UIElements/Views/Qt4/QtHomologyList.cpp (modified) (1 diff)

src/FunctionApproximation/Extractors.cpp

@@ -161 +161 @@
 FunctionModel::list_of_arguments_t Extractors::reorderArgumentsByParticleTypes(
     const FunctionModel::list_of_arguments_t &listargs,
+    const HomologyGraph &_graph,
     const ParticleTypes_t &_types,
     const HomologyGraph &_bindingmodel
@@ -305 +306 @@
 FunctionModel::list_of_arguments_t Extractors::filterArgumentsByParticleTypes(
     const FunctionModel::arguments_t &args,
+    const HomologyGraph &_graph,
     const ParticleTypes_t &_types,
     const HomologyGraph &_bindingmodel
@@ -365 +367 @@
   singlelist_allargs.push_back(allargs);
   FunctionModel::list_of_arguments_t sortedargs =
-      reorderArgumentsByParticleTypes(singlelist_allargs, _types, _bindingmodel);
+      reorderArgumentsByParticleTypes(singlelist_allargs, _graph, _types, _bindingmodel);
   ASSERT( sortedargs.size() == (size_t)1,
       "Extractors::filterArgumentsByParticleTypes() - reordering did not generate a single list.");

src/FunctionApproximation/Extractors.hpp

@@ -105 +105 @@
    *
    * \param listargs list of arguments to reorder each
+   * \param _graph contains binding model of graph
    * \param _types particle type vector
    * \return reordered args
@@ -110 +111 @@
   FunctionModel::list_of_arguments_t reorderArgumentsByParticleTypes(
       const FunctionModel::list_of_arguments_t &eachargs,
+      const HomologyGraph &_graph,
       const ParticleTypes_t &_types,
       const HomologyGraph &_bindingmodel
@@ -120 +122 @@
    *
    * \param args arguments to reorder
+   * \param _graph contains binding model of graph
    * \param _types particle type vector
    * \return filtered list of args
@@ -125 +128 @@
   FunctionModel::list_of_arguments_t filterArgumentsByParticleTypes(
       const FunctionModel::arguments_t &args,
+      const HomologyGraph &_graph,
       const ParticleTypes_t &_types,
       const HomologyGraph &_bindingmodel

src/FunctionApproximation/FunctionModel.hpp

@@ -21 +21 @@
 
 class Fragment;
+class HomologyGraph;
 class TrainingData;
 
@@ -70 +71 @@
   typedef boost::function< list_of_arguments_t (const Fragment &, const size_t)> extractor_t;
   //!> typedef for a function containing how to filter required distances from a full argument list.
-  typedef boost::function< list_of_arguments_t (const arguments_t &)> filter_t;
+  typedef boost::function< list_of_arguments_t (const HomologyGraph &, const arguments_t &)> filter_t;
   //!> typedef for the magic triple function that gets the other two distances for a given argument
   typedef boost::function< std::vector<arguments_t>(const argument_t &, const double)> triplefunction_t;

src/FunctionApproximation/TrainingData.cpp

@@ -57 +57 @@
 void TrainingData::operator()(const range_t &range) {
   for (HomologyContainer::const_iterator iter = range.first; iter != range.second; ++iter) {
+    const HomologyGraph &graph = iter->first;
     const Fragment &fragment = iter->second.fragment;
     FunctionModel::arguments_t all_args = Extractors::gatherAllSymmetricDistances(
@@ -67 +68 @@
     EnergyVector.push_back( FunctionModel::results_t(1, energy) );
     // filter distances out of list of all arguments
-    FunctionModel::list_of_arguments_t args = filter(all_args);
+    FunctionModel::list_of_arguments_t args = filter(graph, all_args);
     LOG(3, "DEBUG: Filtered arguments are " << args << ".");
     ArgumentVector.push_back( args );

src/Potentials/CompoundPotential.cpp

@@ -220 +220 @@
 
 CompoundPotential::arguments_by_model_t CompoundPotential::splitUpArgumentsByModelsFilter(
+    const HomologyGraph &graph,
     const arguments_t &arguments) const
 {
@@ -228 +229 @@
       modeliter != models.end(); ++modeliter) {
     FunctionModel::filter_t filterfunction = (*modeliter)->getSpecificFilter();
-    list_of_arguments_t tempargs = filterfunction(arguments);
+    list_of_arguments_t tempargs = filterfunction(graph, arguments);
     // then split up all the bunches, too.
     for (list_of_arguments_t::const_iterator argiter = tempargs.begin();
@@ -484 +485 @@
     returnfunction =
           boost::bind(&Extractors::concatenateListOfArguments,
-              boost::bind(returnfunction, _1),
-              boost::bind((*modeliter)->getSpecificFilter(), _1)
+              boost::bind(returnfunction, _1, _2),
+              boost::bind((*modeliter)->getSpecificFilter(), _1, _2)
         );
   }

src/Potentials/CompoundPotential.hpp

@@ -156 +156 @@
    * \return vector of partial arguments with associated model
    */
-  arguments_by_model_t splitUpArgumentsByModels(const list_of_arguments_t &listarguments) const;
+  arguments_by_model_t splitUpArgumentsByModels(
+      const list_of_arguments_t &listarguments) const;
 
   /** Helper function to split up total list of arguments for operator() calls.
@@ -164 +165 @@
    * bunches.
    *
+   * \param graph bindding graph of the arguments
    * \param arguments arguments to split up
    * \return vector of partial arguments with associated model
    */
-  arguments_by_model_t splitUpArgumentsByModelsFilter(const arguments_t &arguments) const;
+  arguments_by_model_t splitUpArgumentsByModelsFilter(
+      const HomologyGraph &graph,
+      const arguments_t &arguments) const;
 
   /** Helper function to check whether split up argument bunch matches with types.

src/Potentials/Specifics/ConstantPotential.cpp

@@ -201 +201 @@
   FunctionModel::filter_t returnfunction =
       boost::bind(&Extractors::filterArgumentsByParticleTypes,
-          _1,
+          _2, _1,
           boost::cref(getParticleTypes()), boost::cref(getBindingModel()));
   return returnfunction;

src/Potentials/Specifics/FourBodyPotential_Torsion.cpp

@@ -286 +286 @@
       boost::bind(&Extractors::reorderArgumentsByParticleTypes,
         boost::bind(&Extractors::filterArgumentsByParticleTypes,
-            _1,
+            _2, _1,
             boost::cref(getParticleTypes()), boost::cref(getBindingModel())),
+        _1,
         boost::cref(getParticleTypes()), boost::cref(getBindingModel())
       );

src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp

@@ -731 +731 @@
   FunctionModel::filter_t returnfunction =
       boost::bind(&Extractors::filterArgumentsByParticleTypes,
-          _1,
+          _2, _1,
           boost::cref(getParticleTypes()), boost::cref(getBindingModel()));
   return returnfunction;

src/Potentials/Specifics/PairPotential_Harmonic.cpp

@@ -229 +229 @@
   FunctionModel::filter_t returnfunction =
       boost::bind(&Extractors::filterArgumentsByParticleTypes,
-          _1,
+          _2, _1,
           boost::cref(getParticleTypes()), boost::cref(getBindingModel()));
   return returnfunction;

src/Potentials/Specifics/PairPotential_LennardJones.cpp

@@ -236 +236 @@
   FunctionModel::filter_t returnfunction =
       boost::bind(&Extractors::filterArgumentsByParticleTypes,
-          _1,
+          _2, _1,
           boost::cref(getParticleTypes()), boost::cref(getBindingModel()));
   return returnfunction;

src/Potentials/Specifics/PairPotential_Morse.cpp

@@ -255 +255 @@
   FunctionModel::filter_t returnfunction =
       boost::bind(&Extractors::filterArgumentsByParticleTypes,
-          _1,
+          _2, _1,
           boost::cref(getParticleTypes()), boost::cref(getBindingModel()));
   return returnfunction;

src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp

@@ -266 +266 @@
       boost::bind(&Extractors::reorderArgumentsByParticleTypes,
         boost::bind(&Extractors::filterArgumentsByParticleTypes,
-            _1,
-            boost::cref(getParticleTypes()), boost::cref(getBindingModel())),
+            _2, _1,
+          boost::cref(getParticleTypes()), boost::cref(getBindingModel())),
+        _1,
         boost::cref(getParticleTypes()), boost::cref(getBindingModel())
       );

src/UIElements/Views/Qt4/QtHomologyList.cpp

@@ -231 +231 @@
         Coordinator::ptr coordinator = potential.getCoordinator();
         // then we need to sample the potential
+        HomologyGraph dummy;
         xvalues.clear();
         for (TrainingData::InputVector_t::const_iterator inputiter = inputs.begin();
             inputiter != inputs.end(); ++inputiter) {
-          const FunctionModel::list_of_arguments_t specificargs = filter(*inputiter);
+          const FunctionModel::list_of_arguments_t specificargs = filter(dummy, *inputiter);
           double average = 0.;
           for (FunctionModel::list_of_arguments_t::const_iterator argiter = specificargs.begin();