Changeset 129204 for src/molecule_fragmentation.cpp

Timestamp:

Mar 2, 2011, 9:53:08 PM (14 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, 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_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

111387

Parents:

766ba5

git-author:

Frederik Heber <heber@…> (02/25/11 19:58:54)

git-committer:

Frederik Heber <heber@…> (03/02/11 21:53:08)

Message:

Moved bond.* to Bond/, new class GraphEdge which contains graph parts of bond.

• enums Shading and EdgeType are now part of GraphEdge, hence bigger change in the code where these are used.

File:

• src/molecule_fragmentation.cpp (modified) (6 diffs)

src/molecule_fragmentation.cpp

@@ -22 +22 @@
 #include <cstring>
 
-#include "World.hpp"
 #include "atom.hpp"
-#include "bond.hpp"
-#include "Graph/BondGraph.hpp"
+#include "Bond/bond.hpp"
+#include "Box.hpp"
+#include "CodePatterns/Verbose.hpp"
+#include "CodePatterns/Log.hpp"
 #include "config.hpp"
 #include "element.hpp"
 #include "Helpers/helpers.hpp"
-#include "CodePatterns/Verbose.hpp"
-#include "CodePatterns/Log.hpp"
+#include "Graph/BondGraph.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "molecule.hpp"
 #include "periodentafel.hpp"
 #include "World.hpp"
-#include "LinearAlgebra/RealSpaceMatrix.hpp"
-#include "Box.hpp"
 
 /************************************* Functions for class molecule *********************************/
@@ -1783 +1782 @@
   atom *OtherWalker = NULL;
   RealSpaceMatrix matrix = World::getInstance().getDomain().getM();
-  enum bond::Shading *ColorList = NULL;
+  enum GraphEdge::Shading *ColorList = NULL;
   double tmp;
   //bool LastBond = true; // only needed to due list construct
@@ -1794 +1793 @@
   DoLog(2) && (Log() << Verbose(2) << "Begin of ScanForPeriodicCorrection." << endl);
 
-  ColorList = new enum bond::Shading[getAtomCount()];
+  ColorList = new enum GraphEdge::Shading[getAtomCount()];
   for (int i=0;i<getAtomCount();i++)
-    ColorList[i] = (enum bond::Shading)0;
+    ColorList[i] = (enum GraphEdge::Shading)0;
   if (flag) {
     // remove bonds that are beyond bonddistance
@@ -1836 +1835 @@
       // apply to all atoms of first component via BFS
       for (int i=getAtomCount();i--;)
-        ColorList[i] = bond::white;
+        ColorList[i] = GraphEdge::white;
       AtomStack->push_front(Binder->leftatom);
       while (!AtomStack->empty()) {
@@ -1842 +1841 @@
         AtomStack->pop_front();
         //Log() << Verbose (3) << "Current Walker is: " << *Walker << "." << endl;
-        ColorList[Walker->getNr()] = bond::black;    // mark as explored
+        ColorList[Walker->getNr()] = GraphEdge::black;    // mark as explored
         *Walker += Translationvector; // translate
         const BondList& ListOfBonds = Walker->getListOfBonds();
@@ -1850 +1849 @@
           if ((*Runner) != Binder) {
             OtherWalker = (*Runner)->GetOtherAtom(Walker);
-            if (ColorList[OtherWalker->getNr()] == bond::white) {
+            if (ColorList[OtherWalker->getNr()] == GraphEdge::white) {
               AtomStack->push_front(OtherWalker); // push if yet unexplored
             }