Changeset 9c793c for src/FunctionApproximation

Timestamp:

Nov 11, 2016, 2:25:36 PM (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:

f5dbea

Parents:

bc069f

git-author:

Frederik Heber <heber@…> (10/05/16 21:33:40)

git-committer:

Frederik Heber <heber@…> (11/11/16 14:25:36)

Message:

All ..Potentials now return BindingModel instead of HomologyGraph, Extractors::reorderArg..() uses it.

• Extractors::filterArg..() and ::reorderArg..() expect BindingModel instead of HomologyGraph.
• TESTFIX: Lennard Jones potential fitting regression test no longer fails because it is purely non-bonded.

Location:

src/FunctionApproximation

Files:

• Extractors.cpp (modified) (12 diffs)
• Extractors.hpp (modified) (3 diffs)

src/FunctionApproximation/Extractors.cpp

@@ -61 +61 @@
 #include "LinearAlgebra/Vector.hpp"
 
+#include "Fragmentation/Homology/HomologyGraph.hpp"
 #include "FunctionApproximation/Extractors.hpp"
 #include "FunctionApproximation/FunctionArgument.hpp"
-
-#include "Fragmentation/Homology/HomologyGraph.hpp"
+#include "Potentials/BindingModel.hpp"
 
 using namespace boost::assign;
@@ -535 +535 @@
     const HomologyGraph &_graph,
     const ParticleTypes_t &_types,
-    const HomologyGraph &_bindingmodel
+    const BindingModel &_bindingmodel
     )
 {
@@ -545 +545 @@
     // deal with the case when there are no distances (ConstantPotential)
     if (_bindingmodel.getNodes().size() < 2) {
-      LOG(3, "DEBUG: Potential requires only zero or no particle types, needs no distances.");
+      LOG(3, "DEBUG: Potential requires only one or no particle types, needs no distances.");
       continue;
     }
-    if (_bindingmodel.getEdges().empty()) {
+    if (_bindingmodel.getGraph().getEdges().empty()) {
       LOG(3, "DEBUG: Potential represents non-bonded interactions, gets all distances.");
+      // TODO: Here we need to constrain to all distances matching the types?
       returnargs.push_back(args);
       continue;
@@ -604 +605 @@
 
     /// 2. grab first node of the binding model (gives a type)
-    const FragmentNode &firstnode = _bindingmodel.getNodes().begin()->first;
-    const size_t &firsttimes = _bindingmodel.getNodes().begin()->second;
-    const size_t &firsttype = firstnode.getAtomicNumber(); // TODO: convert to ParticleNumber_t ?
+    const BindingModel::vector_nodes_t::const_iterator firstiter = _bindingmodel.getNodes().begin();
+    const FragmentNode &firstnode = *firstiter;
+    const Extractors::ParticleType_t &firsttype = firstnode.getAtomicNumber();
 
     /// 3. grab all candidate nodes contained in arguments_t
@@ -612 +613 @@
         type_index_lookup_t::right_const_iterator,
         type_index_lookup_t::right_const_iterator> range = type_index_lookup.right.equal_range(firsttype);
-#ifndef NDEBUG
-    const size_t checktimes = std::distance(range.first, range.second);
-    ASSERT( firsttimes == checktimes,
-        "Extractors::reorderArgumentsByParticleTypes() - unequal amounts of same first type "
-        +toString(firsttype)+" in HomologyGraph and in type lookup "+toString(checktimes));
-#endif
 
     /// 4. go over all candidate nodes (gives index)
+    const size_t nodes_in_bindingmodel = _bindingmodel.getNodes().size();
+    LOG(2, "DEBUG: There are " << nodes_in_bindingmodel << " nodes in the binding model.");
     set_of_nodes_t set_of_nodes;
     for (type_index_lookup_t::right_const_iterator rangeiter = range.first;
@@ -648 +645 @@
 
       generateAllInducedConnectedSubgraphs(
-          N-1, level, nodes, set_of_nodes, nodes_per_level, fragmentgraph, distances, index_map);
+          nodes_in_bindingmodel-1, level, nodes, set_of_nodes, nodes_per_level, fragmentgraph, distances, index_map);
       LOG(2, "DEBUG: We have found " << set_of_nodes.size() << " unique induced, connected subgraphs.");
     }
@@ -661 +658 @@
 
       /// 10. compare each converted HomologyGraph with _bindingmodel: Accept or Reject
-      if (nodes_graph == _bindingmodel) {
-        LOG(2, "ACCEPT: " << nodes_graph << " is identical to " << _bindingmodel);
+      if (nodes_graph == _bindingmodel.getGraph()) {
+        LOG(2, "ACCEPT: " << nodes_graph << " is identical to " << _bindingmodel.getGraph());
         /// 11. for each accepted keyset, pick _all_ symmetric distances from arguments_t
         FunctionModel::arguments_t argumentbunch;
@@ -687 +684 @@
          */
 
-        /// So, we need to store for each node its type and the number of connected
-        /// edges, which we extract from the argumentbunch.
+        /// So, we need to extract from the argumentbunch the information contained in each
+        /// FragmentNode, namely its type and the number of connected edges
         node_FragmentNode_map_t node_FragmentNode_map = fillNodeFragmentMap(argumentbunch);
 
-        /// Then, we step through the nodes of the bindingmodel
-        const HomologyGraph::nodes_t bindingmodel_nodes = _bindingmodel.getNodes();
+        /// Then, we step through the nodes of the bindingmodel ...
+        /// ... and find a suitable mapping from indices in the arguments to
+        /// the index in the order of the HomologyGraph's nodes
+        const BindingModel::vector_nodes_t bindingmodel_nodes = _bindingmodel.getNodes();
         argindex_to_nodeindex_t argindex_to_nodeindex;
         size_t nodeindex = 0;
-        for (HomologyGraph::nodes_t::const_iterator nodeiter = bindingmodel_nodes.begin();
+        for (BindingModel::vector_nodes_t::const_iterator nodeiter = bindingmodel_nodes.begin();
             nodeiter != bindingmodel_nodes.end(); ++nodeiter) {
-          const FragmentNode &node = nodeiter->first;
+          const FragmentNode &node = *nodeiter;
           LOG(3, "DEBUG: Binding model's node #" << node << ".");
-          // might have to pick several
-          for (size_t pick_no = 0; pick_no < nodeiter->second; ++pick_no) {
-            /// ... and pick for each the first (and unique) from these stored nodes.
-            node_FragmentNode_map_t::iterator mapiter = node_FragmentNode_map.begin();
-            for (;mapiter != node_FragmentNode_map.end(); ++mapiter) {
-              if ((mapiter->second.first == node.getAtomicNumber())
-                  && (mapiter->second.second == node.getConnectedEdges())) {
-                LOG(3, "DEBUG: #" << mapiter->first << " with type " << mapiter->second.first
-                    << " and " << mapiter->second.second << " connected edges matches as choice #"
-                    << pick_no << ".");
-                break;
-              }
+          /// ... and pick for each the first (and unique) from these stored nodes.
+          node_FragmentNode_map_t::iterator mapiter = node_FragmentNode_map.begin();
+          for (;mapiter != node_FragmentNode_map.end(); ++mapiter) {
+            if ((mapiter->second.first == node.getAtomicNumber())
+                && (mapiter->second.second == node.getConnectedEdges())) {
+              LOG(3, "DEBUG: #" << mapiter->first << " with type " << mapiter->second.first
+                  << " and " << mapiter->second.second << " connected edges matches.");
+              break;
             }
-            ASSERT( mapiter != node_FragmentNode_map.end(),
-                "Extractors::reorderArgumentsByParticleTypes() - could not find a suitable node for #"+
-                toString(mapiter->first)+" with type "+toString(mapiter->second.first)+" and "+
-                toString(mapiter->second.second)+" connected edges");
-            std::pair<argindex_to_nodeindex_t::iterator, bool> inserter =
-                argindex_to_nodeindex.insert( std::make_pair(mapiter->first, nodeindex++) );
-            ASSERT( inserter.second,
-                "Extractors::reorderArgumentsByParticleTypes() - node #"+toString(mapiter->first)+
-                " is already present?");
-            // remove to ensure uniqueness of choice
-            node_FragmentNode_map.erase(mapiter);
           }
+          ASSERT( mapiter != node_FragmentNode_map.end(),
+              "Extractors::reorderArgumentsByParticleTypes() - could not find a suitable node for #"+
+              toString(mapiter->first)+" with type "+toString(mapiter->second.first)+" and "+
+              toString(mapiter->second.second)+" connected edges");
+          std::pair<argindex_to_nodeindex_t::iterator, bool> inserter =
+              argindex_to_nodeindex.insert( std::make_pair(mapiter->first, nodeindex++) );
+          ASSERT( inserter.second,
+              "Extractors::reorderArgumentsByParticleTypes() - node #"+toString(mapiter->first)+
+              " is already present?");
+          // remove to ensure uniqueness of choice
+          node_FragmentNode_map.erase(mapiter);
         }
-        /// This gives then the desired mapping from indices in the arguments to
-        /// the index in the order of the HomologyGraph's nodes
+        LOG(4, "DEBUG: argument's indices to node index map is " << argindex_to_nodeindex);
+        // i.e. this is not the arg's index in argumentbunch, but the index of the position
+        // contained in the argument_t
 
         /// Finally, we only need to bring the arguments in the typical order:
         /// 01 02 03 04 ... 0n, 12 13 14 ... 1n, 23 24 25 ... 2n, ...,  (n-1)n
+        /// These ordering we store in a map for each argument's indices
         const size_t num_args = argindex_to_nodeindex.size();
         argument_placement_map_t argument_placement_map = fillArgumentsPlacementMap(num_args);
@@ -737 +734 @@
             toString(argument_placement_map.size())+" and we expected "+toString(argumentbunch.size()));
 
-        // and finally resort the arguments with the known placement map
-        FunctionModel::arguments_t sortedargs(argumentbunch);
+        // and finally resort the arguments with the constructed placement map
+        FunctionModel::arguments_t sortedargs(argumentbunch.size());
         for (FunctionModel::arguments_t::const_iterator argiter = argumentbunch.begin();
             argiter != argumentbunch.end(); ++argiter) {
           const argument_t &arg = *argiter;
+          const argument_t::indices_t translatedIndices =
+              translateIndices(argindex_to_nodeindex, arg.indices);
           const argument_placement_map_t::const_iterator indexiter =
-              argument_placement_map.find( translateIndices(argindex_to_nodeindex, arg.indices) );
+              argument_placement_map.find( translatedIndices );
           ASSERT( indexiter != argument_placement_map.end(),
               "Extractors::reorderArgumentsByParticleTypes() - could not find place for edge "+
@@ -749 +748 @@
           sortedargs[indexiter->second] = arg;
           LOG(3, "DEBUG: Placed argument " << arg << " at #" << indexiter->second
-              << " as translated indices are " << translateIndices(argindex_to_nodeindex, arg.indices));
+              << " as translated indices are " << translatedIndices);
         }
         LOG(2, "DEBUG: Sorted arguments are " << sortedargs << ".");
@@ -755 +754 @@
         returnargs.push_back(sortedargs);
       } else {
-        LOG(2, "REJECT: " << nodes_graph << " is not identical to " << _bindingmodel);
+        LOG(2, "REJECT: " << nodes_graph << " is not identical to " << _bindingmodel.getGraph());
       }
     }
@@ -767 +766 @@
     const HomologyGraph &_graph,
     const ParticleTypes_t &_types,
-    const HomologyGraph &_bindingmodel
+    const BindingModel &_bindingmodel
     )
 {

src/FunctionApproximation/Extractors.hpp

@@ -20 +20 @@
 #include "FunctionApproximation/FunctionModel.hpp"
 
+class BindingModel;
 class Fragment;
 class HomologyGraph;
@@ -118 +119 @@
       const HomologyGraph &_graph,
       const ParticleTypes_t &_types,
-      const HomologyGraph &_bindingmodel
+      const BindingModel &_bindingmodel
       );
 
@@ -135 +136 @@
       const HomologyGraph &_graph,
       const ParticleTypes_t &_types,
-      const HomologyGraph &_bindingmodel
+      const BindingModel &_bindingmodel
       );