Changeset 2d701e for src

Timestamp:

Sep 9, 2014, 6:26:21 PM (10 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:

833b15

Parents:

40bb9e

git-author:

Frederik Heber <heber@…> (08/20/14 12:36:11)

git-committer:

Frederik Heber <heber@…> (09/09/14 18:26:21)

Message:

FIX: molecule::Translate() used in CenterInBox(), CenterEdge(), CenterPeriodic(), and CenterAtVector().

File:

• src/molecule_geometry.cpp (modified) (4 diffs)

src/molecule_geometry.cpp

@@ -70 +70 @@
 
   // go through all atoms
-  for (iterator iter = begin(); iter != end(); ++iter) {
-    if (DoLog(4) && (*Center != *CenterBox))
-      LOG(4, "INFO: atom before is at " << **iter);
-    **iter -= *Center;
-    **iter += *CenterBox;
-    if (DoLog(4) && (*Center != *CenterBox))
-      LOG(4, "INFO: atom after is at " << **iter);
-  }
+  const Vector difference = *CenterBox - *Center;
+  Translate(&difference);
   getAtomSet().transformNodes(boost::bind(&Box::enforceBoundaryConditions,domain,_1));
 
@@ -106 +100 @@
 void molecule::CenterEdge(Vector *max)
 {
-//  Info info(__func__);
-  Vector *min = new Vector;
-
-  const_iterator iter = begin();  // start at first in list
-  if (iter != end()) { //list not empty?
-    for (int i=NDIM;i--;) {
-      max->at(i) = (*iter)->at(i);
-      min->at(i) = (*iter)->at(i);
-    }
-    for (; iter != end(); ++iter) {// continue with second if present
-      //(*iter)->Output(1,1,out);
-      for (int i=NDIM;i--;) {
-        max->at(i) = (max->at(i) < (*iter)->at(i)) ? (*iter)->at(i) : max->at(i);
-        min->at(i) = (min->at(i) > (*iter)->at(i)) ? (*iter)->at(i) : min->at(i);
+  const_iterator iter = begin();
+  if (iter != end()) {   //list not empty?
+    Vector min = (*begin())->getPosition();
+    *max = min;
+    for (;iter != end(); ++iter) { // continue with second if present
+      const Vector &currentPos = (*iter)->getPosition();
+      for (size_t i=0;i<NDIM;++i) {
+        if (min[i] > currentPos[i])
+          min[i] = currentPos[i];
+        if ((*max)[i] < currentPos[i])
+          (*max)[i] = currentPos[i];
       }
     }
-    LOG(1, "INFO: Maximum is " << *max << ", Minimum is " << *min << ".");
-    min->Scale(-1.);
-    (*max) += (*min);
-    Translate(min);
-  }
-  delete(min);
+    LOG(1, "INFO: Maximum is " << *max << ", Minimum is " << min << ".");
+    const Vector temp = -1.*min;
+    Translate(&temp);
+  }
 };
 
@@ -216 +205 @@
   Vector NewCenter;
   DeterminePeriodicCenter(NewCenter);
-  // go through all atoms
-  for (iterator iter = begin(); iter != end(); ++iter) {
-    **iter -= NewCenter;
-  }
+  NewCenter *= -1.;
+  Translate(&NewCenter);
 };
 
@@ -229 +216 @@
 void molecule::CenterAtVector(Vector *newcenter)
 {
-  // go through all atoms
-  for (iterator iter = begin(); iter != end(); ++iter) {
-    **iter -= *newcenter;
-  }
+  const Vector temp = -1.**newcenter;
+  Translate(&temp);
 };