Changeset 15b670 for src

Timestamp:

Jun 1, 2010, 8:25:36 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:

e0aee2b

Parents:

0de7e8

Message:

Testfixes for Tesselations/1-3 and bugfixes for molecule::DetermineCenterOfAll()

• BUGFIX: molecule::DetermineCenterOfAll() - would scale by -1./Num, which is not the right center.
• TESTFIX: Tesselations/1-3 all suffered ... replaced in regression dir.
  • (Non)ConvexEnvelope.r3d to be disordered, due to IonType2 appear before IonType1 in test.conf
  • (Non)ConvexEnvelope.r3d from test and from regression to differ by 4.4e-16 and 0 (now nodes coordinates are set to 0, if fabs(.) is below MYEPSILON)
  • Tesselations/3: NonConvexEnvelope.dat was disorder (but the exactly same tesselation) due to IonType (did not occur for Tesselations/1-2)

Location:

src

Files:

• molecule_geometry.cpp (modified) (2 diffs)
• tesselationhelpers.cpp (modified) (4 diffs)

src/molecule_geometry.cpp

@@ -133 +133 @@
   if (iter != end()) {   //list not empty?
     for (; iter != end(); ++iter) {  // continue with second if present
-      Num += 1.;
+      Num++;
       (*a) += (*iter)->x;
     }
@@ -175 +175 @@
       (*a) += tmp;
     }
-    a->Scale(-1./Num); // divide through total mass (and sign for direction)
+    a->Scale(1./Num); // divide through total mass (and sign for direction)
   }
 //  Log() << Verbose(1) << "Resulting center of gravity: ";

src/tesselationhelpers.cpp

@@ -785 +785 @@
       Walker = cloud->GetPoint();
       *rasterfile << "2" << endl << "  ";  // 2 is sphere type
-      for (i=0;i<NDIM;i++)
-        *rasterfile << Walker->node->at(i)-center->at(i) << " ";
+      for (int j=0;j<NDIM;j++) { // and for each node all NDIM coordinates
+        const double tmp = Walker->node->at(j)-center->at(j);
+        *rasterfile << ((fabs(tmp) < MYEPSILON) ? 0 : tmp) << " ";
+      }
       *rasterfile << "\t0.1\t1. 1. 1." << endl; // radius 0.05 and white as colour
       cloud->GoToNext();
@@ -796 +798 @@
       *rasterfile << "1" << endl << "  ";  // 1 is triangle type
       for (i=0;i<3;i++) {  // print each node
-        for (int j=0;j<NDIM;j++)  // and for each node all NDIM coordinates
-          *rasterfile << TriangleRunner->second->endpoints[i]->node->node->at(j)-center->at(j) << " ";
+        for (int j=0;j<NDIM;j++) { // and for each node all NDIM coordinates
+          const double tmp = TriangleRunner->second->endpoints[i]->node->node->at(j)-center->at(j);
+          *rasterfile << ((fabs(tmp) < MYEPSILON) ? 0 : tmp) << " ";
+        }
         *rasterfile << "\t";
       }
@@ -836 +840 @@
     }
     *tecplot << "\", N=" << TesselStruct->PointsOnBoundary.size() << ", E=" << TesselStruct->TrianglesOnBoundary.size() << ", DATAPACKING=POINT, ZONETYPE=FETRIANGLE" << endl;
-    int i=cloud->GetMaxId();
-    int *LookupList = new int[i];
-    for (cloud->GoToFirst(), i=0; !cloud->IsEnd(); cloud->GoToNext(), i++){
+    const int MaxId=cloud->GetMaxId();
+    int *LookupList = new int[MaxId];
+    for (int i=0; i< MaxId ; i++){
       LookupList[i] = -1;
     }
@@ -848 +852 @@
       Walker = target->second->node;
       LookupList[Walker->nr] = Counter++;
-      *tecplot << Walker->node->at(0) << " " << Walker->node->at(1) << " " << Walker->node->at(2) << " " << target->second->value << endl;
+      for (int i=0;i<NDIM;i++) {
+        const double tmp = Walker->node->at(i);
+        *tecplot << ((fabs(tmp) < MYEPSILON) ? 0 : tmp) << " ";
+      }
+      *tecplot << target->second->value << endl;
     }
     *tecplot << endl;