Changeset 1024cb for src/Actions/WorldAction

Timestamp:

May 31, 2010, 5:32:27 PM (15 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:

e08c46

Parents:

42af9e (diff), a7b761b (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

git-author:

Frederik Heber <heber@…> (05/31/10 17:29:30)

git-committer:

Frederik Heber <heber@…> (05/31/10 17:32:27)

Message:

Merge commit 'jupiter/MoleculeStartEndSwitch' into CommandLineActionMapping

Conflicts:

molecuilder/src/Makefile.am
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/helpers.hpp
molecuilder/src/molecule.cpp
molecuilder/src/molecule_dynamics.cpp
molecuilder/src/molecule_fragmentation.cpp
molecuilder/src/molecule_geometry.cpp
molecuilder/src/molecule_graph.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp
molecuilder/src/unittests/listofbondsunittest.cpp

Integration of MoleculeStartEndSwitch had the following consequences:

• no more AtomCount -> getAtomCount()
• no more start/end -> begin(), end() and iterator
• no more decent ordering in atomic ids (hence, Simple_configuration/8 and Domain/5, Domain/6 now check by comparing sorted xyz, not confs)

There is still a huge problem with bonds. One test runs into an endless loop.

Signed-off-by: Frederik Heber <heber@…>

File:

• src/Actions/WorldAction/RepeatBoxAction.cpp (modified) (3 diffs)

src/Actions/WorldAction/RepeatBoxAction.cpp

@@ -40 +40 @@
   molecule *mol = NULL;
   int j = 0;
+  atom *Walker = NULL;
 
   dialog->queryVector(NAME, &Repeater, World::getInstance().getDomain(), false, MapOfActions::getInstance().getDescription(NAME));
@@ -54 +55 @@
         Repeater[axis] = 1;
       }
-      mol->CountAtoms();  // recount atoms
-      if (mol->AtomCount != 0) {  // if there is more than none
-        count = mol->AtomCount;   // is changed becausing of adding, thus has to be stored away beforehand
+      if (mol->getAtomCount() != 0) {  // if there is more than none
+        count = mol->getAtomCount();   // is changed becausing of adding, thus has to be stored away beforehand
         Elements = new const element *[count];
         vectors = new Vector *[count];
         j = 0;
-        atom *first = mol->start;
-        while (first->next != mol->end) {  // make a list of all atoms with coordinates and element
-          first = first->next;
-          Elements[j] = first->type;
-          vectors[j] = &first->x;
+        for(molecule::iterator AtomRunner = mol->begin(); AtomRunner != mol->end(); ++AtomRunner) {
+          Elements[j] = (*AtomRunner)->type;
+          vectors[j] = &(*AtomRunner)->x;
           j++;
         }
@@ -75 +73 @@
           x += y; // per factor one cell width further
           for (int k=count;k--;) { // go through every atom of the original cell
-            first = World::getInstance().createAtom(); // create a new body
-            first->x = (*vectors[k]) + x;
-            first->type = Elements[k];  // insert original element
-            mol->AddAtom(first);        // and add to the molecule (which increments ElementsInMolecule, AtomCount, ...)
+            Walker = World::getInstance().createAtom(); // create a new body
+            Walker->x = (*vectors[k]) + x;
+            Walker->type = Elements[k];  // insert original element
+            mol->AddAtom(Walker);        // and add to the molecule (which increments ElementsInMolecule, AtomCount, ...)
           }
         }