Changeset 9d613f

Timestamp:

Nov 7, 2011, 12:24:05 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:

874597

Parents:

f27fa7

git-author:

Frederik Heber <heber@…> (10/10/11 14:18:16)

git-committer:

Frederik Heber <heber@…> (11/07/11 12:24:05)

Message:

FIX: RepeatBoxAction did not use CopyMolecule() but copied by hand. Kudos: Gregor Bollerhey.

• this causes trouble with FormatParsers such as Tremolo... who have internally additional information stored.
• extended regression tests Domain/RepeatBox with a test of a repeated .data file with "special" element names.

Kudos to Gregor Bollerhey for finding this bug.

Files:

• src/Actions/WorldAction/RepeatBoxAction.cpp (modified) (4 diffs)
• tests/regression/Domain/RepeatBox/post/ec.data (added)
• tests/regression/Domain/RepeatBox/pre/ec.data (added)
• tests/regression/Domain/RepeatBox/pre/ec.potentials (added)
• tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) (3 diffs)

src/Actions/WorldAction/RepeatBoxAction.cpp

@@ -47 +47 @@
 void repeatMoleculesinDomain(Vector Repeater, const std::vector<molecule *> &AllMolecules)
 {
-  int count;
-  const element ** Elements;
-  int j = 0;
-  atom *Walker = NULL;
-  MoleculeListClass *molecules = World::getInstance().getMolecules();
-
   LOG(0, "STATUS: Repeating box " << Repeater << " times for (x,y,z) axis.");
 
@@ -75 +69 @@
   molecule *newmol = NULL;
   std::vector<Vector> vectors;
+  MoleculeListClass *molecules = World::getInstance().getMolecules();
   for (n[0] = 0; n[0] < Repeater[0]; n[0]++) {
     y[0] = n[0];
@@ -84 +79 @@
           continue;
         for (vector<molecule *>::const_iterator MolRunner = AllMolecules.begin(); MolRunner != AllMolecules.end(); ++MolRunner) {
-          const molecule *mol = *MolRunner;
-          LOG(2, "INFO: Current mol is " << mol->name << ".");
-          count = mol->getAtomCount();   // is changed becausing of adding, thus has to be stored away beforehand
-          if (count != 0) {  // if there is more than none
-            Elements = new const element *[count];
-            vectors.resize(count);
-            j = 0;
-            for(molecule::const_iterator AtomRunner = mol->begin(); AtomRunner != mol->end(); ++AtomRunner) {
-              Elements[j] = (*AtomRunner)->getType();
-              vectors[j] = (*AtomRunner)->getPosition();
-              j++;
-            }
-            if (count != j)
-              ELOG(1, "AtomCount " << count << " is not equal to number of atoms in molecule " << j << "!");
-            x = y;
-            x *= M;
-            newmol = World::getInstance().createMolecule();
-            // TODO: Remove this when World don't has deprecated MoleculeListClass anymore
-            molecules->insert(newmol);
-            for (int k=count;k--;) { // go through every atom of the original cell
-              Walker = World::getInstance().createAtom(); // create a new body
-              Walker->setPosition((vectors[k]) + x);
-              Walker->setType(Elements[k]);  // insert original element
-              cout << "new atom is " << *Walker << endl;
-              newmol->AddAtom(Walker);        // and add to the molecule (which increments ElementsInMolecule, AtomCount, ...)
-            }
-            // free memory
-            delete[](Elements);
-          } else {
-            LOG(1, "\t ... is empty.");
-          }
+          molecule * const mol = *MolRunner;
+          DoLog(1) && (Log() << Verbose(1) << "Current mol is " << mol->name << "." << endl);
+          newmol = mol->CopyMolecule();
+          // TODO: remove this when World does not have MoleculeListClass anymore.
+          molecules->insert(newmol);
+          x = y;
+          x *= M;
+          // shift each atom into new position
+          for(molecule::iterator iter = newmol->begin(); iter != newmol->end(); ++iter)
+            (*iter)->setPosition((*iter)->getPosition() + x);
         }
       }
@@ -122 +96 @@
 
 Action::state_ptr WorldRepeatBoxAction::performCall() {
-  molecule *mol = NULL;
-
   // obtain information
   getParametersfromValueStorage();
 
   std::vector<molecule *> AllMolecules;
-  if (mol != NULL) {
-    LOG(0, "Using molecule " << mol->name << ".");
-    AllMolecules = World::getInstance().getAllMolecules(MoleculeByPtr(mol));
-  } else {
-    LOG(0, "Using all molecules.");
-    AllMolecules = World::getInstance().getAllMolecules();
-  }
+  DoLog(0) && (Log() << Verbose(0) << "Using all molecules." << endl);
+  AllMolecules = World::getInstance().getAllMolecules();
 
   // prepare undo state

tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at

@@ -39 +39 @@
 AT_CHECK([file=test-z.xyz;sort -n ${abs_top_srcdir}/tests/regression/Domain/RepeatBox/post/test-z.xyz  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
 AT_CHECK([file=test-z.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
+
+file=ec.data
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Domain/RepeatBox/pre/ec.* .], 0)
+AT_CHECK([../../molecuilder --parse-tremolo-potentials ec.potentials -i $file  -o tremolo -d "2, 2, 2"], 0, [stdout], [stderr])
+AT_CHECK([fgrep "Box domain is now" stdout], 0, [ignore], [ignore])
+AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Domain/RepeatBox/post/$file], 0, [ignore], [ignore])
 
 AT_CLEANUP
@@ -82 +88 @@
 AT_CHECK([file=test-z.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
 
+file=ec.data
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Domain/RepeatBox/pre/ec.* .], 0)
+AT_CHECK([../../molecuilder --parse-tremolo-potentials ec.potentials  -i $file  -o tremolo -d "2, 2, 2" --undo], 0, [stdout], [stderr])
+AT_CHECK([fgrep "Box domain is now" stdout], 0, [ignore], [ignore])
+AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Domain/RepeatBox/pre/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP
 
@@ -124 +136 @@
 AT_CHECK([file=test-z.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
 
+file=ec.data
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Domain/RepeatBox/pre/ec.* .], 0)
+AT_CHECK([../../molecuilder --parse-tremolo-potentials ec.potentials -i $file  -o tremolo -d "2, 2, 2" --undo --redo], 0, [stdout], [stderr])
+AT_CHECK([fgrep "Box domain is now" stdout], 0, [ignore], [ignore])
+AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Domain/RepeatBox/post/$file], 0, [ignore], [ignore])
+
 AT_CLEANUP