Changeset c738f1 for src/Fragmentation

Timestamp:

Nov 11, 2016, 2:25:35 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:

884d8c

Parents:

2124aa

git-author:

Frederik Heber <heber@…> (10/04/16 20:01:24)

git-committer:

Frederik Heber <heber@…> (11/11/16 14:25:35)

Message:

FIX: SaturatedFragment::getEdges().

• SaturatedFragment now keeps track of which hydrogens have been added in replacement for which atom not contained in the fragment.

Location:

src/Fragmentation/Exporters

Files:

• SaturatedFragment.cpp (modified) (5 diffs)
• SaturatedFragment.hpp (modified) (3 diffs)

src/Fragmentation/Exporters/SaturatedFragment.cpp

@@ -294 +294 @@
         LOG(4, "DEBUG: Places to saturate for atom " << *OtherWalker
             << " are " << positionsiter->second);
-        atom * const father = Walker;
+        atom * const father = OtherWalker;
         for (SaturationsPositions_t::const_iterator positer = positionsiter->second.begin();
             positer != positionsiter->second.end(); ++positer) {
@@ -320 +320 @@
   _atom->setFather(_father);
   SaturationHydrogens.insert(_atom->getId());
+  // note down the id of the replaced atom
+  replaced_atoms.insert( std::make_pair(_father->getId(), _atom->getId()) );
 
   return *_atom;
@@ -670 +672 @@
 static FragmentationEdges::edges_t createEdgesFromAtoms(
     const std::vector<atom *> &_atoms,
+    const SaturatedFragment::replaced_atoms_t &replaced_atoms,
     const KeySet &_FullMolecule)
 {
@@ -682 +685 @@
       const atom * const OtherWalker = (*bonditer)->GetOtherAtom(walker);
       const atomId_t &otherwalkerid = OtherWalker->getId();
-      if (walkerid < otherwalkerid) {
-        // check if it's in fullkeysets (also contains excluded and saturation hydrogens)
-        if (_FullMolecule.count(otherwalkerid))
-          edges.push_back( FragmentationEdges::edge_t(walkerid, otherwalkerid) );
+      if (_FullMolecule.count(otherwalkerid)) {
+        if (walkerid < otherwalkerid) {
+          // check if it's in fullkeysets (also contains excluded and saturation hydrogens)
+          if (_FullMolecule.count(otherwalkerid))
+            edges.push_back( FragmentationEdges::edge_t(walkerid, otherwalkerid) );
+        }
+      } else {
+        ASSERT( replaced_atoms.count(otherwalkerid),
+            "createEdgesFromAtoms() - atom #"+toString(otherwalkerid)
+            +" to a cut bond  is not in replaced_atoms.");
+        // add bond to every saturation hydrogen instead
+        const std::pair<
+            SaturatedFragment::replaced_atoms_t::const_iterator,
+            SaturatedFragment::replaced_atoms_t::const_iterator> range = replaced_atoms.equal_range(otherwalkerid);
+        for (SaturatedFragment::replaced_atoms_t::const_iterator replaceiter = range.first;
+            replaceiter != range.second; ++replaceiter) {
+          edges.push_back( FragmentationEdges::edge_t(walkerid, replaceiter->second) );
+        }
       }
     }
@@ -739 +756 @@
   // gather all edges
   const std::vector<atom *> atoms = gatherAllAtoms(FullMolecule);
-  FragmentationEdges::edges_t edges = createEdgesFromAtoms(atoms, FullMolecule);
+  FragmentationEdges::edges_t edges = createEdgesFromAtoms(atoms, replaced_atoms, FullMolecule);
 
   // translate each edge
-  std::map<atomId_t, atomId_t> idtable = createIdTable(atoms);
+  const std::map<atomId_t, atomId_t> idtable = createIdTable(atoms);
 
   // rewrite indices of edges in correct order

src/Fragmentation/Exporters/SaturatedFragment.hpp

@@ -15 +15 @@
 
 #include <iosfwd>
+#include <map>
 #include <set>
 #include <string>
@@ -122 +123 @@
       std::ostream &out,
       const ParserTypes _type) const;
+
+  //!> typedef for the replaced atom (due to cut bonds) and their replacement hydrogens
+  typedef std::multimap<atomId_t, atomId_t> replaced_atoms_t;
 
 private:
@@ -220 +224 @@
   //!> whether to actually saturate or not
   const enum HydrogenSaturation saturation;
+  //!> list of saturated hydrogens to their original atoms
+  replaced_atoms_t replaced_atoms;
 };