Changeset 32ea56

Timestamp:

Aug 26, 2010, 12:44:19 PM (14 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

8fd934

Parents:

e8a21f

Message:

Removed last occurences of molecule::SetIndexedArrayForEachAtomTo()

Location:

src

Files:

• molecule_dynamics.cpp (modified) (2 diffs)
• molecule_fragmentation.cpp (modified) (2 diffs)

src/molecule_dynamics.cpp

@@ -500 +500 @@
 bool molecule::LinearInterpolationBetweenConfiguration(int startstep, int endstep, std::string &prefix, config &configuration, bool MapByIdentity)
 {
+  // TODO: rewrite permutationMaps using enumeration objects
   molecule *mol = NULL;
   bool status = true;
@@ -510 +511 @@
     MinimiseConstrainedPotential(PermutationMap, startstep, endstep, configuration.GetIsAngstroem());
   else {
+    // TODO: construction of enumeration goes here
     PermutationMap = new atom *[getAtomCount()];
-    SetIndexedArrayForEachAtomTo( PermutationMap, &atom::nr );
+    for(internal_iterator iter = atoms.begin(); iter != atoms.end();++iter){
+      PermutationMap[(*iter)->nr] = (*iter);
+    }
   }
 

src/molecule_fragmentation.cpp

@@ -523 +523 @@
 
   int AtomNo = 0;
-  SetIndexedArrayForEachAtomTo( SortIndex, &atom::nr, &IncrementalAbsoluteValue, AtomNo );
+  for(internal_iterator iter=atoms.begin();iter!=atoms.end();++iter){
+    ASSERT(SortIndex[(*iter)->nr]==-1,"Same SortIndex set twice");
+    SortIndex[(*iter)->nr] = AtomNo++;
+  }
+  //SetIndexedArrayForEachAtomTo( SortIndex, &atom::nr, &IncrementalAbsoluteValue, AtomNo );
 
   return true;
@@ -858 +862 @@
 
     // set atom values
-    SetAtomValueToIndexedArray( OrderArray, &atom::nr, &atom::AdaptiveOrder );
-    SetAtomValueToIndexedArray( MaxArray, &atom::nr, &atom::MaxOrder );
+    for(internal_iterator iter=atoms.begin();iter!=atoms.end();++iter){
+      (*iter)->AdaptiveOrder = OrderArray[(*iter)->nr];
+      (*iter)->MaxOrder = MaxArray[(*iter)->nr];
+    }
+    //SetAtomValueToIndexedArray( OrderArray, &atom::nr, &atom::AdaptiveOrder );
+    //SetAtomValueToIndexedArray( MaxArray, &atom::nr, &atom::MaxOrder );
 
     DoLog(1) && (Log() << Verbose(1) << "\t ... done." << endl);