Changeset 03e57a for src

Timestamp:

Aug 4, 2009, 1:47:05 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:

62bb91

Parents:

ab1932

Message:

Smaller FIXES to molecule class

• new pointer TesselStruct was not initialzied to NULL
• corrected molecule::CenterInBox(), it now really centers in the given cell_size box (no idea what it did before that)
• as TesselStruct is now a part of the molecule, we remove it on deleting the molecule if it's not NULL

File:

• src/molecules.cpp (modified) (3 diffs)

src/molecules.cpp

@@ -67 +67 @@
   IndexNr  = -1;
   ActiveFlag = false;
+  TesselStruct = NULL;
 };
 
@@ -79 +80 @@
   Free((void **)&ListOfBondsPerAtom, "molecule::~molecule: ListOfBondsPerAtom");
   Free((void **)&NumberOfBondsPerAtom, "molecule::~molecule: NumberOfBondsPerAtom");
+  if (TesselStruct != NULL)
+    delete(TesselStruct);
   CleanupMolecule();
   delete(first);
@@ -710 +713 @@
 {
   bool status = true;
-  atom *ptr = NULL;
   Vector x;
   double *M = ReturnFullMatrixforSymmetric(cell_size);
   double *Minv = x.InverseMatrix(M);
-  double value;
-
-//  cout << "The box matrix is :" << endl;
-//  for (int i=0;i<NDIM;++i) {
-//    for (int j=0;j<NDIM;++j)
-//      cout << M[i*NDIM+j] << "\t";
-//    cout << endl;
-//  }
-//  cout << "And its inverse is :" << endl;
-//  for (int i=0;i<NDIM;++i) {
-//    for (int j=0;j<NDIM;++j)
-//      cout << Minv[i*NDIM+j] << "\t";
-//    cout << endl;
-//  }
+  Vector *Center = DetermineCenterOfAll(out);
+
   // go through all atoms
-  ptr = start->next;  // start at first in list
-  if (ptr != end) {  //list not empty?
-    while (ptr->next != end) {  // continue with second if present
-      ptr = ptr->next;
-      //ptr->Output(1,1,out);
-      // multiply its vector with matrix inverse
-      x.CopyVector(&ptr->x);
-      x.MatrixMultiplication(Minv);
-      // truncate to [0,1] for each axis
-      for (int i=0;i<NDIM;i++) {
-        value = floor(x.x[i]);  // next lower integer
-        if (x.x[i] >=0) {
-          x.x[i] -= value;
-        } else {
-          x.x[i] += value+1;
-        }
-      }
-    }
+  atom *ptr = start;  // start at first in list
+  while (ptr->next != end) {  // continue with second if present
+    ptr = ptr->next;
+    //ptr->Output(1,1,out);
+    // multiply its vector with matrix inverse
+    x.CopyVector(&ptr->x);
+    x.SubtractVector(Center); // now, it's centered at origin
+    x.MatrixMultiplication(Minv);
+    // truncate to [0,1] for each axis
+    for (int i=0;i<NDIM;i++) {
+      x.x[i] += 0.5;  // set to center of box
+      while (x.x[i] >= 1.)
+        x.x[i] -= 1.;
+      while (x.x[i] < 0.)
+        x.x[i] += 1.;
+    }
+    x.MatrixMultiplication(M);
+    ptr->x.CopyVector(&x);
   }
   delete(M);
   delete(Minv);
+  delete(Center);
   return status;
 };