Changeset e0aee2b

Timestamp:

Jun 1, 2010, 9:04:17 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:

d51975

Parents:

15b670

Message:

Bugfix of FillBoxWithMolecule() and Testfix of Filling/1

• BUGFIX: FillBoxWithMolecule() - increased filler in loop instead of iter (and iter is const now)
• FillBoxWithMolecule() - uses now const int FillerCount instead of filler->getAtomCount()
• TESTFIX: Filling/1 - replaced test.conf, as is exactly the same (after filling!) except ordering of initial atoms (of butane), checked visually and by diff.

Files:

• src/boundary.cpp (modified) (2 diffs)
• tests/regression/Filling/1/post/test.conf (modified) (1 diff)

src/boundary.cpp

@@ -816 +816 @@
   filler->CenterEdge(&Inserter);
   filler->Center.Zero();
+  const int FillerCount = filler->getAtomCount();
   DoLog(2) && (Log() << Verbose(2) << "INFO: Filler molecule has the following bonds:" << endl);
   for(molecule::iterator AtomRunner = filler->begin(); AtomRunner != filler->end(); ++AtomRunner)
     for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); BondRunner != (*AtomRunner)->ListOfBonds.end(); ++BondRunner)
       if ((*BondRunner)->leftatom == *AtomRunner)
-        DoLog(2) && (Log() << Verbose(2) << "  " << *Binder << endl);
-
-  atom * CopyAtoms[filler->getAtomCount()];
+        DoLog(2) && (Log() << Verbose(2) << "  " << *(*BondRunner) << endl);
+
+  atom * CopyAtoms[FillerCount];
 
   // calculate filler grid in [0,1]^3
@@ -847 +848 @@
 
         // go through all atoms
-        for (int i=0;i<filler->getAtomCount();i++)
+        for (int i=0;i<FillerCount;i++)
           CopyAtoms[i] = NULL;
-        for(molecule::iterator iter = filler->begin(); iter !=filler->end();++filler){
+        for(molecule::const_iterator iter = filler->begin(); iter !=filler->end();++iter){
 
           // create atomic random translation vector ...

tests/regression/Filling/1/post/test.conf

@@ -72 +72 @@
 Ion_Type3       335     8       1.0     3       3       15.99900000000  Oxygen  O
 #Ion_TypeNr._Nr.R[0]    R[1]    R[2]    MoveType (0 MoveIon, 1 FixedIon)
-Ion_Type2_1     9.782085945     3.275186040     3.535886037     0 # molecule nr 0
-Ion_Type2_2     8.532785963     4.158586027     3.535886037     0 # molecule nr 1
-Ion_Type2_3     7.283585982     3.275186040     3.535886037     0 # molecule nr 2
-Ion_Type1_1     9.782085945     2.645886050     2.645886050     0 # molecule nr 3
-Ion_Type1_2     9.782085945     2.645886050     4.425886024     0 # molecule nr 4
-Ion_Type1_3     10.672039608    3.904536878     3.535886037     0 # molecule nr 5
-Ion_Type1_4     8.532785963     4.787886018     2.645886050     0 # molecule nr 6
-Ion_Type1_5     8.532785963     4.787886018     4.425886024     0 # molecule nr 7
-Ion_Type1_6     6.393632318     3.904536877     3.535886037     0 # molecule nr 8
-Ion_Type1_7     7.283585982     2.645886050     2.645886050     0 # molecule nr 9
-Ion_Type1_8     7.283585982     2.645886050     4.425886024     0 # molecule nr 10
+Ion_Type1_1     9.782085945     2.645886050     2.645886050     0 # molecule nr 0
+Ion_Type1_2     9.782085945     2.645886050     4.425886024     0 # molecule nr 1
+Ion_Type1_3     10.672039608    3.904536878     3.535886037     0 # molecule nr 2
+Ion_Type1_4     8.532785963     4.787886018     2.645886050     0 # molecule nr 3
+Ion_Type1_5     8.532785963     4.787886018     4.425886024     0 # molecule nr 4
+Ion_Type1_6     6.393632318     3.904536877     3.535886037     0 # molecule nr 5
+Ion_Type1_7     7.283585982     2.645886050     2.645886050     0 # molecule nr 6
+Ion_Type1_8     7.283585982     2.645886050     4.425886024     0 # molecule nr 7
+Ion_Type2_1     9.782085945     3.275186040     3.535886037     0 # molecule nr 8
+Ion_Type2_2     8.532785963     4.158586027     3.535886037     0 # molecule nr 9
+Ion_Type2_3     7.283585982     3.275186040     3.535886037     0 # molecule nr 10
 Ion_Type3_1     0.000000000     0.000000000     0.504284000     0 # molecule nr 11
 Ion_Type1_9     0.758602000     0.000000000     1.008568000     0 # molecule nr 12