Changeset dadc74 for src/Fragmentation

Timestamp:

Oct 25, 2011, 12:08:03 PM (13 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:

ba94c5

Parents:

f0674a

git-author:

Frederik Heber <heber@…> (10/20/11 09:02:58)

git-committer:

Frederik Heber <heber@…> (10/25/11 12:08:03)

Message:

Extracted Graph (map of KeySets) into own class from graph.hpp.

• Placed InsertGraphIntoGraph() as its member function.

Location:

src/Fragmentation

Files:

• BondsPerShortestPath.hpp (modified) (1 diff)
• Fragmentation.cpp (modified) (1 diff)
• Fragmentation.hpp (modified) (1 diff)
• Graph.cpp (added)
• Graph.hpp (added)
• Makefile.am (modified) (2 diffs)
• PowerSetGenerator.hpp (modified) (1 diff)
• UniqueFragments.cpp (modified) (1 diff)
• UniqueFragments.hpp (modified) (1 diff)
• fragmentation_helpers.cpp (modified) (2 diffs)
• fragmentation_helpers.hpp (modified) (1 diff)

src/Fragmentation/BondsPerShortestPath.hpp

@@ -17 +17 @@
 #include <vector>
 
-#include "graph.hpp"
-
 class atom;
 class bond;
+class KeySet;
 
 class BondsPerShortestPath

src/Fragmentation/Fragmentation.cpp

@@ -29 +29 @@
 #include "Element/periodentafel.hpp"
 #include "Fragmentation/fragmentation_helpers.hpp"
+#include "Fragmentation/Graph.hpp"
 #include "Fragmentation/KeySet.hpp"
 #include "Fragmentation/PowerSetGenerator.hpp"

src/Fragmentation/Fragmentation.hpp

@@ -16 +16 @@
 #include <string>
 
-#include "graph.hpp"
 #include "Graph/DepthFirstSearchAnalysis.hpp"
 
+#include "graph.hpp"
+
 class atom;
+class Graph;
 class KeySet;
 class molecule;

src/Fragmentation/Makefile.am

@@ -8 +8 @@
         Fragmentation/Fragmentation.cpp \
         Fragmentation/fragmentation_helpers.cpp \
+        Fragmentation/Graph.cpp \
         Fragmentation/helpers.cpp \
         Fragmentation/HessianMatrix.cpp \
@@ -23 +24 @@
         Fragmentation/Fragmentation.hpp \
         Fragmentation/fragmentation_helpers.hpp \
+        Fragmentation/Graph.hpp \
+        Fragmentation/helpers.cpp \
         Fragmentation/helpers.hpp \
         Fragmentation/HessianMatrix.hpp \

src/Fragmentation/PowerSetGenerator.hpp

@@ -18 +18 @@
 
 #include "Fragmentation/BondsPerShortestPath.hpp"
-#include "graph.hpp"
 
 class bond;
-class UniqueFragment;
+class UniqueFragments;
 
 class PowerSetGenerator

src/Fragmentation/UniqueFragments.cpp

@@ -27 +27 @@
 #include "Bond/bond.hpp"
 #include "Element/element.hpp"
+#include "Fragmentation/Graph.hpp"
 #include "Fragmentation/KeySet.hpp"
 #include "graph.hpp"

src/Fragmentation/UniqueFragments.hpp

@@ -17 +17 @@
 #include <vector>
 
-#include "graph.hpp"
-
 class atom;
 class bond;
 class config;
+class Graph;
+class KeySet;
 
 /** Structure containing all values in power set combination generation.

src/Fragmentation/fragmentation_helpers.cpp

@@ -29 +29 @@
 #include "Bond/bond.hpp"
 #include "Element/element.hpp"
+#include "Fragmentation/Graph.hpp"
 #include "Fragmentation/KeySet.hpp"
+#include "graph.hpp"
 #include "Helpers/defs.hpp"
 #include "Helpers/helpers.hpp"
@@ -457 +459 @@
     for(int i=0;i<NumLevels;i++) {
       if (FragmentLowerOrdersList[RootNr][i] != NULL) {
-        InsertGraphIntoGraph(*FragmentList, (*FragmentLowerOrdersList[RootNr][i]), &counter);
+        (*FragmentList).InsertGraph((*FragmentLowerOrdersList[RootNr][i]), &counter);
       }
     }

src/Fragmentation/fragmentation_helpers.hpp

@@ -22 +22 @@
 
 class bond;
+class Graph;
+class KeySet;
 class molecule;