Changeset 6d551c for src/Fragmentation

Timestamp:

Oct 26, 2012, 1:24:01 PM (12 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:

f96874

Parents:

dbe3b9

git-author:

Frederik Heber <heber@…> (09/07/12 08:47:35)

git-committer:

Frederik Heber <heber@…> (10/26/12 13:24:01)

Message:

ListOfLocalAtoms is now a map, inherited into a distinct class.

• this is preparatory for allowing arbitrary fragmentation of atoms not only of a single molecule.

File:

• src/Fragmentation/Fragmentation.cpp (modified) (3 diffs)

src/Fragmentation/Fragmentation.cpp

@@ -53 +53 @@
 #include "Graph/BondGraph.hpp"
 #include "Graph/CheckAgainstAdjacencyFile.hpp"
+#include "Graph/ListOfLocalAtoms.hpp"
 #include "molecule.hpp"
 #include "MoleculeLeafClass.hpp"
@@ -106 +107 @@
   Graph TotalGraph;     // graph with all keysets however local numbers
   int TotalNumberOfKeySets = 0;
-  atom ***ListOfLocalAtoms = NULL;
   bool *AtomMask = NULL;
 
@@ -161 +161 @@
   // ===== 6a. assign each keyset to its respective subgraph =====
   const int MolCount = World::getInstance().numMolecules();
-  ListOfLocalAtoms = new atom **[MolCount];
-  for (int i=0;i<MolCount;i++)
-    ListOfLocalAtoms[i] = NULL;
   FragmentCounter = 0;
-  Subgraphs->next->AssignKeySetsToFragment(mol, &ParsedFragmentList, ListOfLocalAtoms, FragmentList, FragmentCounter, true);
-  delete[](ListOfLocalAtoms);
+  {
+    ListOfLocalAtoms_t *ListOfLocalAtoms = new ListOfLocalAtoms_t[MolCount];
+    Subgraphs->next->AssignKeySetsToFragment(mol, &ParsedFragmentList, ListOfLocalAtoms, FragmentList, FragmentCounter, true);
+    delete[] ListOfLocalAtoms;
+  }
 
   // ===== 6b. prepare and go into the adaptive (Order<0), single-step (Order==0) or incremental (Order>0) cycle