Changeset 205ccd

Timestamp:

Jul 10, 2009, 9:19:23 PM (16 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:

042f82

Parents:

d1df9b

Message:

BUGFIX: Due to stupid mistake, first atom was overlooked in periodic translation

• molecule::TranslatePeriodically() is fixed (while is ptr != end) and next pointer moved to its end

File:

• src/molecules.cpp (modified) (2 diffs)

src/molecules.cpp

@@ -853 +853 @@
   // 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);
+  while (ptr != end) {  // continue with second if present
+    //ptr->Output(1,1,out);
+    // multiply its vector with matrix inverse
+    x.CopyVector(&ptr->x);
+    x.Translate(trans);
+    x.MatrixMultiplication(Minv);
+    // truncate to [0,1] for each axis
+    for (int i=0;i<NDIM;i++) {
+      value = floor(fabs(x.x[i]));  // next lower integer
+      if (x.x[i] >=0) {
+        x.x[i] -= value;
+      } else {
+        x.x[i] += value+1;
+      }
+    }
+    // matrix multiply
+    x.MatrixMultiplication(M);
+    ptr->x.CopyVector(&x);
+    for (int j=0;j<MDSteps;j++) {
+      x.CopyVector(&Trajectories[ptr].R.at(j));
       x.Translate(trans);
       x.MatrixMultiplication(Minv);
       // truncate to [0,1] for each axis
       for (int i=0;i<NDIM;i++) {
-        value = floor(fabs(x.x[i]));  // next lower integer
+        value = floor(x.x[i]);  // next lower integer
         if (x.x[i] >=0) {
           x.x[i] -= value;
@@ -872 +886 @@
       // matrix multiply
       x.MatrixMultiplication(M);
-      ptr->x.CopyVector(&x);
-      for (int j=0;j<MDSteps;j++) {
-        x.CopyVector(&Trajectories[ptr].R.at(j));
-        x.Translate(trans);
-        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;
-          }
-        }
-        // matrix multiply
-        x.MatrixMultiplication(M);
-        Trajectories[ptr].R.at(j).CopyVector(&x);
-      }
+      Trajectories[ptr].R.at(j).CopyVector(&x);
     }
+    ptr = ptr->next;
   }
   delete(M);