Changeset 833b15 for src/Tesselation/boundary.cpp

Timestamp:

Sep 9, 2014, 7:42:32 PM (11 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:

a090e3

Parents:

2d701e

git-author:

Frederik Heber <heber@…> (09/01/14 15:54:02)

git-committer:

Frederik Heber <heber@…> (09/09/14 19:42:32)

Message:

FIX: Changes to function signatures in molecule_geometry.

• no more returning allocated pointer (Vector *)
• no more Pointers as parameters.
• removed functions that are only convenience and have nothing to do with the molecule.
• changes elsewhere due to signature changes.

File:

• src/Tesselation/boundary.cpp (modified) (15 diffs)

src/Tesselation/boundary.cpp

@@ -183 +183 @@
   LineMap LinesOnBoundary;
   TriangleMap TrianglesOnBoundary;
-  Vector *MolCenter = mol->DetermineCenterOfAll();
+  Vector MolCenter = mol->DetermineCenterOfAll();
   Vector helper;
   BoundariesTestPair BoundaryTestPair;
@@ -207 +207 @@
     // Boundaries stores non-const TesselPoint ref, hence we need iterator here
     for (molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-      ProjectedVector = (*iter)->getPosition() - (*MolCenter);
+      ProjectedVector = (*iter)->getPosition() - (MolCenter);
       ProjectedVector.ProjectOntoPlane(AxisVector);
 
@@ -233 +233 @@
           LOG(2, "Keeping new vector due to larger projected distance " << ProjectedVectorNorm << ".");
         } else if (fabs(ProjectedVectorNorm - BoundaryTestPair.first->second.first) < MYEPSILON) {
-          helper = (*iter)->getPosition() - (*MolCenter);
+          helper = (*iter)->getPosition() - (MolCenter);
           const double oldhelperNorm = helper.NormSquared();
-          helper = BoundaryTestPair.first->second.second->getPosition() - (*MolCenter);
+          helper = BoundaryTestPair.first->second.second->getPosition() - (MolCenter);
           if (helper.NormSquared() < oldhelperNorm) {
             BoundaryTestPair.first->second.second = (*iter);
@@ -289 +289 @@
         {
           Vector SideA, SideB, SideC, SideH;
-          SideA = left->second.second->getPosition() - (*MolCenter);
+          SideA = left->second.second->getPosition() - (MolCenter);
           SideA.ProjectOntoPlane(AxisVector);
           //          LOG(1, "SideA: " << SideA);
 
-          SideB = right->second.second->getPosition() -(*MolCenter);
+          SideB = right->second.second->getPosition() -(MolCenter);
           SideB.ProjectOntoPlane(AxisVector);
           //          LOG(1, "SideB: " << SideB);
@@ -301 +301 @@
           //          LOG(1, "SideC: " << SideC);
 
-          SideH = runner->second.second->getPosition() -(*MolCenter);
+          SideH = runner->second.second->getPosition() -(MolCenter);
           SideH.ProjectOntoPlane(AxisVector);
           //          LOG(1, "SideH: " << SideH);
@@ -329 +329 @@
     } while (flag);
   }
-  delete(MolCenter);
   return BoundaryPoints;
 };
@@ -726 +725 @@
     for (int i = 0; i < NDIM; i++)
       BoxLengths[i] = GreatestDiameter[i];
-    mol->CenterEdge(&BoxLengths);
+    mol->CenterEdge();
   } else {
     BoxLengths[0] = (repetition[0] * GreatestDiameter[0] + repetition[1] * GreatestDiameter[1] + repetition[2] * GreatestDiameter[2]);
@@ -749 +748 @@
     // set new box dimensions
     LOG(0, "Translating to box with these boundaries.");
-    mol->SetBoxDimension(&BoxLengths);
+    {
+      RealSpaceMatrix domain;
+      for(int i =0; i<NDIM;++i)
+        domain.at(i,i) = BoxLengths[i];
+      World::getInstance().setDomain(domain);
+    }
     mol->CenterInBox();
   }
   delete[] GreatestDiameter;
   // update Box of atoms by boundary
-  mol->SetBoxDimension(&BoxLengths);
+  {
+    RealSpaceMatrix domain;
+    for(int i =0; i<NDIM;++i)
+      domain.at(i,i) = BoxLengths[i];
+    World::getInstance().setDomain(domain);
+  }
   LOG(0, "RESULT: The resulting cell dimensions are: " << BoxLengths[0] << " and " << BoxLengths[1] << " and " << BoxLengths[2] << " with total volume of " << cellvolume << " " << (IsAngstroem ? "angstrom" : "atomiclength") << "^3.");
 };
@@ -804 +813 @@
 
   // Center filler at origin
-  filler->CenterEdge(&Inserter);
+  filler->CenterEdge();
   const int FillerCount = filler->getAtomCount();
   LOG(2, "INFO: Filler molecule has the following bonds:");
@@ -1099 +1108 @@
 
   // Center filler at its center of gravity
-  Vector *gravity = filler->DetermineCenterOfGravity();
+  const Vector gravity = filler->DetermineCenterOfGravity();
   filler->CenterAtVector(gravity);
-  delete gravity;
   //const int FillerCount = filler->getAtomCount();
   LOG(2, "INFO: Filler molecule has the following bonds:");
@@ -1165 +1173 @@
           RandomizeMoleculePositions(Filling, RandomAtomDisplacement, Rotations, random);
           // translation
-          Filling->Translate(&Inserter);
+          Filling->Translate(Inserter);
           // remove out-of-bounds atoms
           const bool status = RemoveAtomsOutsideDomain(Filling);
@@ -1203 +1211 @@
     RandomizeMoleculePositions(filler, RandomAtomDisplacement, Rotations, random);
     // translation
-    filler->Translate(&firstInserter);
+    filler->Translate(firstInserter);
     // remove out-of-bounds atoms
     RemoveAtomsOutsideDomain(filler);
@@ -1277 +1285 @@
 
   // Center filler at origin
-  filler->CenterEdge(&Inserter);
+  filler->CenterEdge();
 //  const int FillerCount = filler->getAtomCount();
   LOG(2, "INFO: Filler molecule has the following bonds:");
@@ -1378 +1386 @@
           RandomizeMoleculePositions(Filling, RandomAtomDisplacement, Rotations, random);
           // translation
-          Filling->Translate(&Inserter);
+          Filling->Translate(Inserter);
           // remove out-of-bounds atoms
           const bool status = RemoveAtomsOutsideDomain(Filling);
@@ -1416 +1424 @@
     RandomizeMoleculePositions(filler, RandomAtomDisplacement, Rotations, random);
     // translation
-    filler->Translate(&firstInserter);
+    filler->Translate(firstInserter);
     // remove out-of-bounds atoms
     RemoveAtomsOutsideDomain(filler);