Changeset 95e6b1 for src

Timestamp:

Aug 10, 2010, 7:25:28 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:

fa1830

Parents:

7aa3cf (diff), 61951b (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'SmallFixes' into stable

Location:

src

Files:

• Legacy/oldmenu.cpp (deleted)
• Legacy/oldmenu.hpp (deleted)
• UIElements/Views/QT4/QTStatusBar.cpp (modified) (1 diff)
• 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) (2 diffs)
• molecule_geometry.cpp (modified) (7 diffs)
• moleculelist.cpp (modified) (2 diffs)
• periodentafel.cpp (modified) (1 diff)

src/UIElements/Views/QT4/QTStatusBar.cpp

@@ -21 +21 @@
   QStatusBar(_parent),
   Observer("QTStatusBar"),
-  parent(_parent),
   atomCount(World::getInstance().numAtoms()),
-  moleculeCount(World::getInstance().numMolecules())
+  moleculeCount(World::getInstance().numMolecules()),
+  parent(_parent)
 {
   World::getInstance().signOn(this);

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();
     mol->SetNameFromFilename(ConfigFileName);
-    molecules->SimpleMultiMerge(mol, src, N);
     //mol->CalculateOrbitals(*this);
     delete[](src);

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
@@ -379 +379 @@
   void eraseMolecule();
 
-
-  // merging of molecules
-  bool SimpleMerge(molecule *mol, molecule *srcmol);
-  bool SimpleAdd(molecule *mol, molecule *srcmol);
-  bool SimpleMultiMerge(molecule *mol, int *src, int N);
-  bool SimpleMultiAdd(molecule *mol, int *src, int N);
-  bool ScatterMerge(molecule *mol, int *src, int N);
-  bool EmbedMerge(molecule *mol, molecule *srcmol);
-
   private:
   World *world; //!< The world this List belongs to. Needed to avoid deadlocks in the destructor

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);
     }
   }
@@ -210 +212 @@
 };
 
-/** Simple merge of two molecules into one.
- * \param *mol destination molecule
- * \param *srcmol source molecule
- * \return true - merge successful, false - merge failed (probably due to non-existant indices
- */
-bool MoleculeListClass::SimpleMerge(molecule *mol, molecule *srcmol)
-{
-  if (srcmol == NULL)
-    return false;
-
-  // put all molecules of src into mol
-  for (molecule::iterator iter = srcmol->begin(); !srcmol->empty(); iter=srcmol->begin()) {
-    atom * const Walker = *iter;
-    srcmol->UnlinkAtom(Walker);
-    mol->AddAtom(Walker);
-  }
-
-  // remove src
-  ListOfMolecules.remove(srcmol);
-  World::getInstance().destroyMolecule(srcmol);
-  return true;
-};
-
-/** Simple add of one molecules into another.
- * \param *mol destination molecule
- * \param *srcmol source molecule
- * \return true - merge successful, false - merge failed (probably due to non-existant indices
- */
-bool MoleculeListClass::SimpleAdd(molecule *mol, molecule *srcmol)
-{
-  if (srcmol == NULL)
-    return false;
-
-  // put all molecules of src into mol
-  atom *Walker = NULL;
-  for (molecule::iterator iter = srcmol->begin(); iter != srcmol->end(); ++iter) {
-    Walker = mol->AddCopyAtom((*iter));
-    Walker->father = Walker;
-  }
-
-  return true;
-};
-
-/** Simple merge of a given set of molecules into one.
- * \param *mol destination molecule
- * \param *src index of set of source molecule
- * \param N number of source molecules
- * \return true - merge successful, false - some merges failed (probably due to non-existant indices)
- */
-bool MoleculeListClass::SimpleMultiMerge(molecule *mol, int *src, int N)
-{
-  bool status = true;
-  // check presence of all source molecules
-  for (int i=0;i<N;i++) {
-    molecule *srcmol = ReturnIndex(src[i]);
-    status = status && SimpleMerge(mol, srcmol);
-  }
-  insert(mol);
-  return status;
-};
-
-/** Simple add of a given set of molecules into one.
- * \param *mol destination molecule
- * \param *src index of set of source molecule
- * \param N number of source molecules
- * \return true - merge successful, false - some merges failed (probably due to non-existant indices)
- */
-bool MoleculeListClass::SimpleMultiAdd(molecule *mol, int *src, int N)
-{
-  bool status = true;
-  // check presence of all source molecules
-  for (int i=0;i<N;i++) {
-    molecule *srcmol = ReturnIndex(src[i]);
-    status = status && SimpleAdd(mol, srcmol);
-  }
-  return status;
-};
-
-/** Scatter merge of a given set of molecules into one.
- * Scatter merge distributes the molecules in such a manner that they don't overlap.
- * \param *mol destination molecule
- * \param *src index of set of source molecule
- * \param N number of source molecules
- * \return true - merge successful, false - merge failed (probably due to non-existant indices
- * \TODO find scatter center for each src molecule
- */
-bool MoleculeListClass::ScatterMerge(molecule *mol, int *src, int N)
-{
-  // check presence of all source molecules
-  for (int i=0;i<N;i++) {
-    // get pointer to src molecule
-    molecule *srcmol = ReturnIndex(src[i]);
-    if (srcmol == NULL)
-      return false;
-  }
-  // adapt each Center
-  for (int i=0;i<N;i++) {
-    // get pointer to src molecule
-    molecule *srcmol = ReturnIndex(src[i]);
-    //srcmol->Center.Zero();
-    srcmol->Translate(&srcmol->Center);
-  }
-  // perform a simple multi merge
-  SimpleMultiMerge(mol, src, N);
-  return true;
-};
-
-/** Embedding merge of a given set of molecules into one.
- * Embedding merge inserts one molecule into the other.
- * \param *mol destination molecule (fixed one)
- * \param *srcmol source molecule (variable one, where atoms are taken from)
- * \return true - merge successful, false - merge failed (probably due to non-existant indices)
- * \TODO linked cell dimensions for boundary points has to be as big as inner diameter!
- */
-bool MoleculeListClass::EmbedMerge(molecule *mol, molecule *srcmol)
-{
-  LinkedCell *LCList = NULL;
-  Tesselation *TesselStruct = NULL;
-  if ((srcmol == NULL) || (mol == NULL)) {
-    DoeLog(1) && (eLog()<< Verbose(1) << "Either fixed or variable molecule is given as NULL." << endl);
-    return false;
-  }
-
-  // calculate envelope for *mol
-  LCList = new LinkedCell(mol, 8.);
-  FindNonConvexBorder(mol, TesselStruct, (const LinkedCell *&)LCList, 4., NULL);
-  if (TesselStruct == NULL) {
-    DoeLog(1) && (eLog()<< Verbose(1) << "Could not tesselate the fixed molecule." << endl);
-    return false;
-  }
-  delete(LCList);
-  LCList = new LinkedCell(TesselStruct, 8.);  // re-create with boundary points only!
-
-  // prepare index list for bonds
-  atom ** CopyAtoms = new atom*[srcmol->getAtomCount()];
-  for(int i=0;i<srcmol->getAtomCount();i++)
-    CopyAtoms[i] = NULL;
-
-  // for each of the source atoms check whether we are in- or outside and add copy atom
-  int nr=0;
-  for (molecule::const_iterator iter = srcmol->begin(); iter != srcmol->end(); ++iter) {
-    DoLog(2) && (Log() << Verbose(2) << "INFO: Current Walker is " << **iter << "." << endl);
-    if (!TesselStruct->IsInnerPoint((*iter)->getPosition(), LCList)) {
-      CopyAtoms[(*iter)->nr] = (*iter)->clone();
-      mol->AddAtom(CopyAtoms[(*iter)->nr]);
-      nr++;
-    } else {
-      // do nothing
-    }
-  }
-  DoLog(1) && (Log() << Verbose(1) << nr << " of " << srcmol->getAtomCount() << " atoms have been merged.");
-
-  // go through all bonds and add as well
-  for(molecule::iterator AtomRunner = srcmol->begin(); AtomRunner != srcmol->end(); ++AtomRunner)
-    for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); BondRunner != (*AtomRunner)->ListOfBonds.end(); ++BondRunner)
-      if ((*BondRunner)->leftatom == *AtomRunner) {
-        DoLog(3) && (Log() << Verbose(3) << "Adding Bond between " << *CopyAtoms[(*BondRunner)->leftatom->nr] << " and " << *CopyAtoms[(*BondRunner)->rightatom->nr]<< "." << endl);
-        mol->AddBond(CopyAtoms[(*BondRunner)->leftatom->nr], CopyAtoms[(*BondRunner)->rightatom->nr], (*BondRunner)->BondDegree);
-      }
-  delete(LCList);
-  return true;
-};
 
 /** Simple output of the pointers in ListOfMolecules.

src/periodentafel.cpp

@@ -295 +295 @@
     getline(input,header1tmp);
     getline(input,header2tmp); // skip first two header lines
-    cout << "First header: " << header1tmp << endl;
-    cout << "Second header: " << header2tmp << endl;
+    //cout << "First header: " << header1tmp << endl;
+    //cout << "Second header: " << header2tmp << endl;
     DoLog(0) && (Log() << Verbose(0) <<  "Parsed elements:");
     while (!input.eof()) {