Changeset 1883f9

Timestamp:

Aug 10, 2010, 2:47:43 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:

61951b

Parents:

8eca62

Message:

Removed molecule::Center.

• QTWorldView now more has entry "Center".
• Center..() all act on the atoms, not on molecule::Center.

Location:

src

Files:

• UIElements/Views/QT4/QTWorldView.cpp (modified) (2 diffs)
• UIElements/Views/QT4/QTWorldView.hpp (modified) (1 diff)
• boundary.cpp (modified) (1 diff)
• config.cpp (modified) (1 diff)
• molecule.hpp (modified) (1 diff)
• molecule_geometry.cpp (modified) (7 diffs)
• moleculelist.cpp (modified) (2 diffs)

src/UIElements/Views/QT4/QTWorldView.cpp

@@ -20 +20 @@
 // these attributes are skiped so far
 const int QTWorldView::COLUMNCOUNT = COLUMNTYPES_MAX;
-const char *QTWorldView::COLUMNNAMES[QTWorldView::COLUMNCOUNT]={"Name","Atoms"/*,"Formula"*/,"Center"/*,"Size"*/};
+const char *QTWorldView::COLUMNNAMES[QTWorldView::COLUMNCOUNT]={"Name","Atoms"/*,"Formula"*//*,"Size"*/};
 
 QTWorldView::QTWorldView(QWidget * _parent) :
@@ -81 +81 @@
     setItem(i,ATOMS,countWidget);
 
-    const Vector center = (*iter)->Center;
-    QTableWidgetItem *centerWidget = new QTableWidgetItem();
-    stringstream centersstr;
-    centersstr << center;
-    centerWidget->setText(QString(centersstr.str().c_str()));
-    setItem(i,CENTER,centerWidget);
-    centerWidget->setFlags(Qt::ItemIsSelectable | Qt::ItemIsUserCheckable | Qt::ItemIsEnabled);
-
     molSelection[i]=nameWidget->isSelected();
   }

src/UIElements/Views/QT4/QTWorldView.hpp

@@ -28 +28 @@
 
   static const int COLUMNCOUNT;
-  enum {NAME,ATOMS,CENTER,COLUMNTYPES_MAX} COLUMNTYPES;
+  enum {NAME,ATOMS,COLUMNTYPES_MAX} COLUMNTYPES;
   static const char *COLUMNNAMES[];
 

src/boundary.cpp

@@ -804 +804 @@
   // Center filler at origin
   filler->CenterEdge(&Inserter);
-  filler->Center.Zero();
   const int FillerCount = filler->getAtomCount();
   DoLog(2) && (Log() << Verbose(2) << "INFO: Filler molecule has the following bonds:" << endl);

src/config.cpp

@@ -1586 +1586 @@
     for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
       src[N++] = (*ListRunner)->IndexNr;
-      (*ListRunner)->Translate(&(*ListRunner)->Center);
     }
     mol = World::getInstance().createMolecule();

src/molecule.hpp

@@ -104 +104 @@
     double BondDistance;  //!< typical bond distance used in CreateAdjacencyList() and furtheron
     bool ActiveFlag;    //!< in a MoleculeListClass used to discern active from inactive molecules
-    Vector Center;      //!< Center of molecule in a global box
+    //Vector Center;      //!< Center of molecule in a global box
     int IndexNr;        //!< index of molecule in a MoleculeListClass
     char name[MAXSTRINGSIZE];         //!< arbitrary name

src/molecule_geometry.cpp

@@ -104 +104 @@
     (*max) += (*min);
     Translate(min);
-    Center.Zero();
   }
   delete(min);
@@ -118 +117 @@
   int Num = 0;
   molecule::const_iterator iter = begin();  // start at first in list
+  Vector Center;
 
   Center.Zero();
-
   if (iter != end()) {   //list not empty?
     for (; iter != end(); ++iter) {  // continue with second if present
@@ -128 +127 @@
     Center.Scale(-1./(double)Num); // divide through total number (and sign for direction)
     Translate(&Center);
-    Center.Zero();
   }
 };
@@ -197 +195 @@
 void molecule::CenterPeriodic()
 {
-  DeterminePeriodicCenter(Center);
+  Vector NewCenter;
+  DeterminePeriodicCenter(NewCenter);
+  // go through all atoms
+  BOOST_FOREACH(atom* iter, atoms){
+    *iter -= NewCenter;
+  }
 };
 
@@ -207 +210 @@
 void molecule::CenterAtVector(Vector *newcenter)
 {
-  Center = *newcenter;
+  // go through all atoms
+  BOOST_FOREACH(atom* iter, atoms){
+    *iter -= *newcenter;
+  }
 };
 
@@ -277 +283 @@
   bool flag;
   Vector Testvector, Translationvector;
+  Vector Center;
 
   do {
@@ -322 +329 @@
 
   Center.Scale(1./static_cast<double>(getAtomCount()));
+  CenterAtVector(&Center);
 };
 

src/moleculelist.cpp

@@ -193 +193 @@
       }
       // Center and size
-      (*out) << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl;
+      Vector *Center = (*ListRunner)->DetermineCenterOfAll();
+      (*out) << "\t" << *Center << "\t" << sqrt(size) << endl;
+      delete(Center);
     }
   }
@@ -309 +311 @@
     // get pointer to src molecule
     molecule *srcmol = ReturnIndex(src[i]);
-    //srcmol->Center.Zero();
-    srcmol->Translate(&srcmol->Center);
   }
   // perform a simple multi merge