Changeset d5ca1a for src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp

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:

67044a

Parents:

c5e75f3

git-author:

Frederik Heber <heber@…> (10/03/16 18:26:30)

git-committer:

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

Message:

Added HomologyGraph describing binding model to every EmpiricalPotential.

File:

• src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) (3 diffs)

src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp

@@ -67 +67 @@
 Coordinator::ptr ThreeBodyPotential_Angle::coordinator(Memory::ignore(new ThreeBody_Angle()));
 
+static HomologyGraph generateBindingModel(const EmpiricalPotential::ParticleTypes_t &_ParticleTypes)
+{
+  // fill nodes
+  HomologyGraph::nodes_t nodes;
+  {
+    ASSERT( _ParticleTypes.size() == (size_t)3,
+        "generateBindingModel() - ThreeBodyPotential_Angle needs three types.");
+    std::pair<HomologyGraph::nodes_t::iterator, bool > inserter;
+    inserter = nodes.insert( std::make_pair(FragmentNode(_ParticleTypes[0], 1), 1) );
+    if (!inserter.second)
+      ++(inserter.first->second);
+    inserter = nodes.insert( std::make_pair(FragmentNode(_ParticleTypes[1], 2), 1) );
+    if (!inserter.second)
+      ++(inserter.first->second);
+    inserter = nodes.insert( std::make_pair(FragmentNode(_ParticleTypes[2], 1), 1) );
+    if (!inserter.second)
+      ++(inserter.first->second);
+  }
+
+  // there are no edges
+  HomologyGraph::edges_t edges;
+  {
+    std::pair<HomologyGraph::edges_t::iterator, bool > inserter;
+    inserter = edges.insert( std::make_pair( FragmentEdge(_ParticleTypes[0], _ParticleTypes[1]), 1) );
+    if (!inserter.second)
+      ++(inserter.first->second);
+    inserter = edges.insert( std::make_pair( FragmentEdge(_ParticleTypes[1], _ParticleTypes[2]), 1) );
+    if (!inserter.second)
+      ++(inserter.first->second);
+  }
+
+  return HomologyGraph(nodes, edges);
+}
+
 ThreeBodyPotential_Angle::ThreeBodyPotential_Angle() :
   EmpiricalPotential(),
-  params(parameters_t(MAXPARAMS, 0.))
+  params(parameters_t(MAXPARAMS, 0.)),
+  bindingmodel(HomologyGraph())
 {
   // have some decent defaults for parameter_derivative checking
@@ -80 +115 @@
     ) :
   EmpiricalPotential(_ParticleTypes),
-  params(parameters_t(MAXPARAMS, 0.))
+  params(parameters_t(MAXPARAMS, 0.)),
+  bindingmodel(generateBindingModel(_ParticleTypes))
 {
   // have some decent defaults for parameter_derivative checking
@@ -92 +128 @@
     const double _equilibrium_distance) :
   EmpiricalPotential(_ParticleTypes),
-  params(parameters_t(MAXPARAMS, 0.))
+  params(parameters_t(MAXPARAMS, 0.)),
+  bindingmodel(generateBindingModel(_ParticleTypes))
 {
   params[spring_constant] = _spring_constant;