Changeset ce4487 for src

Timestamp:

Jun 24, 2010, 10:33:22 AM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

04488a

Parents:

9f3b85 (diff), da3024 (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 'MenuRefactoring' into QT4Refactoring

Location:

src

Files:

• Actions/Process.cpp (modified) (1 diff)
• Actions/WorldAction/RepeatBoxAction.cpp (modified) (1 diff)
• Hbondangle.db (modified) (1 diff)
• Hbonddistance.db (modified) (1 diff)
• Patterns/ObservedIterator.hpp (modified) (1 diff)
• atom.cpp (modified) (1 diff)
• atom.hpp (modified) (1 diff)
• builder.cpp (modified) (5 diffs)
• config.cpp (modified) (3 diffs)
• molecule.cpp (modified) (7 diffs)
• molecule.hpp (modified) (2 diffs)
• molecule_pointcloud.cpp (modified) (1 diff)
• moleculelist.cpp (modified) (2 diffs)
• orbitals.db (modified) (1 diff)
• periodentafel.cpp (modified) (2 diffs)
• valence.db (modified) (1 diff)

src/Actions/Process.cpp

@@ -13 +13 @@
 
 Process::Process(int _maxSteps, std::string _name, bool _doRegister) :
+  Action(_name,_doRegister),
   Observable("Process"),
-  Action(_name,_doRegister),
   maxSteps(_maxSteps),
   active(false),

src/Actions/WorldAction/RepeatBoxAction.cpp

@@ -80 +80 @@
         for (n[2] = 0; n[2] < Repeater[2]; n[2]++) {
           y[2] = n[2];
-          if (n[0] == n[1] == n[2] == 0)
+          if ((n[0] == 0) && (n[1] == 0) && (n[2] == 0))
             continue;
           for (vector<molecule *>::iterator MolRunner = AllMolecules.begin(); MolRunner != AllMolecules.end(); ++MolRunner) {

src/Hbondangle.db

@@ +1 @@
+# atomicnumber angles for single, double and triple bond (-1 no angle)
 1       180     -1      -1
 5       180     131.0   109.2

src/Hbonddistance.db

@@ +1 @@
+#atomic number bond distances for single, double and triple bond (-1 no bond)
 1       0.74    -1      -1
 2       0.77429209      -1      -1

src/Patterns/ObservedIterator.hpp

@@ -84 +84 @@
   {
     --iter;
+    return *this;
   }
 

src/atom.cpp

@@ -315 +315 @@
 }
 
-atomId_t atom::getId() {
+atomId_t atom::getId() const {
   return id;
 }

src/atom.hpp

@@ -79 +79 @@
   void setWorld(World*);
 
-  virtual atomId_t getId();
+  virtual atomId_t getId() const;
   virtual bool changeId(atomId_t newId);
 

src/builder.cpp

@@ -1361 +1361 @@
 };
 
-#endif
 
 /** Tries given filename or standard on saving the config file.
@@ -1487 +1486 @@
 };
 
+#endif
+
 /** Parses the command line options.
  * Note that this function is from now on transitional. All commands that are not passed
@@ -1504 +1505 @@
 {
   Vector x,y,z,n;  // coordinates for absolute point in cell volume
-  double *factor; // unit factor if desired
   ifstream test;
   ofstream output;
   string line;
-  atom *first;
   bool SaveFlag = false;
   int ExitFlag = 0;
@@ -1514 +1513 @@
   double volume = 0.;
   enum ConfigStatus configPresent = absent;
-  clock_t start,end;
-  double MaxDistance = -1;
   int argptr;
   molecule *mol = NULL;
   string BondGraphFileName("\n");
-  bool DatabasePathGiven = false;
 
   if (argc > 1) { // config file specified as option
@@ -2204 +2200 @@
 int main(int argc, char **argv)
 {
-    config *configuration = World::getInstance().getConfig();
     // while we are non interactive, we want to abort from asserts
     //ASSERT_DO(Assert::Abort);
-    molecule *mol = NULL;
     Vector x, y, z, n;
     ifstream test;

src/config.cpp

@@ -1784 +1784 @@
   char filename[MAXSTRINGSIZE];
   ofstream output;
-  molecule *mol = World::getInstance().createMolecule();
-  mol->SetNameFromFilename(ConfigFileName);
+  molecule *mol = NULL;
 
   if (!strcmp(configpath, GetDefaultPath())) {
@@ -1816 +1815 @@
   // translate each to its center and merge all molecules in MoleculeListClass into this molecule
   int N = molecules->ListOfMolecules.size();
-  int *src = new int[N];
-  N=0;
-  for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
-    src[N++] = (*ListRunner)->IndexNr;
-    (*ListRunner)->Translate(&(*ListRunner)->Center);
-  }
-  molecules->SimpleMultiAdd(mol, src, N);
-  delete[](src);
-
-  // ... and translate back
-  for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
-    (*ListRunner)->Center.Scale(-1.);
-    (*ListRunner)->Translate(&(*ListRunner)->Center);
-    (*ListRunner)->Center.Scale(-1.);
+  if (N != 1) { // don't do anything in case of only one molecule (shifts mol ids otherwise)
+    int *src = new int[N];
+    N=0;
+    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->doCountAtoms();
+    mol->CountElements();
+    mol->CalculateOrbitals(*this);
+    delete[](src);
+  } else {
+    if (!molecules->ListOfMolecules.empty()) {
+      mol = *(molecules->ListOfMolecules.begin());
+      mol->doCountAtoms();
+      mol->CalculateOrbitals(*this);
+    } else {
+      DoeLog(1) && (eLog() << Verbose(1) << "There are no molecules to save!" << endl);
+    }
   }
 
   Log() << Verbose(0) << "Storing configuration ... " << endl;
   // get correct valence orbitals
-  mol->CalculateOrbitals(*this);
-  InitMaxMinStopStep = MaxMinStopStep = MaxPsiDouble;
   if (ConfigFileName != NULL) { // test the file name
     strcpy(filename, ConfigFileName);
@@ -1895 +1900 @@
   }
 
-  World::getInstance().destroyMolecule(mol);
+  // don't destroy molecule as it contains all our atoms
+  //World::getInstance().destroyMolecule(mol);
 };
 

src/molecule.cpp

@@ -42 +42 @@
   NoCyclicBonds(0), BondDistance(0.),  ActiveFlag(false), IndexNr(-1),
   formula(this,boost::bind(&molecule::calcFormula,this),"formula"),
-  AtomCount(this,boost::bind(&molecule::doCountAtoms,this),"AtomCount"), last_atom(0),  InternalPointer(begin())
+  AtomCount(this,boost::bind(&molecule::doCountAtoms,this),"AtomCount"), last_atom(0),  InternalPointer(atoms.begin())
 {
 
@@ -146 +146 @@
   iter--;
   atom* atom = *loc;
-  atoms.erase( loc );
+  atomIds.erase( atom->getId() );
+  atoms.remove( atom );
   atom->removeFromMolecule();
   return iter;
@@ -156 +157 @@
   molecule::const_iterator iter = find(key);
   if (iter != end()){
-    atoms.erase( iter++ );
+    atomIds.erase( key->getId() );
+    atoms.remove( key );
     key->removeFromMolecule();
   }
@@ -164 +166 @@
 molecule::const_iterator molecule::find ( atom * key ) const
 {
-  return atoms.find( key );
+  molecule::const_iterator iter;
+  for (molecule::const_iterator Runner = begin(); Runner != end(); ++Runner) {
+    if (*Runner == key)
+      return molecule::const_iterator(Runner);
+  }
+  return molecule::const_iterator(atoms.end());
 }
 
 pair<molecule::iterator,bool> molecule::insert ( atom * const key )
 {
-  pair<atomSet::iterator,bool> res = atoms.insert(key);
-  return pair<iterator,bool>(iterator(res.first,this),res.second);
+  pair<atomIdSet::iterator,bool> res = atomIds.insert(key->getId());
+  if (res.second) { // push atom if went well
+    atoms.push_back(key);
+    return pair<iterator,bool>(molecule::iterator(--end()),res.second);
+  } else {
+    return pair<iterator,bool>(molecule::iterator(end()),res.second);
+  }
 }
 
 bool molecule::containsAtom(atom* key){
-  return atoms.count(key);
+  return (find(key) != end());
 }
 
@@ -790 +802 @@
   for (molecule::iterator iter = begin(); !empty(); iter = begin())
       erase(iter);
+  return empty();
 };
 
@@ -1010 +1023 @@
   configuration.MaxPsiDouble /= 2;
   configuration.PsiType = (configuration.PsiMaxNoDown == configuration.PsiMaxNoUp) ? 0 : 1;
-  if ((configuration.PsiType == 1) && (configuration.ProcPEPsi < 2)) {
+  if ((configuration.PsiType == 1) && (configuration.ProcPEPsi < 2) && ((configuration.PsiMaxNoDown != 1) || (configuration.PsiMaxNoUp != 0))) {
     configuration.ProcPEGamma /= 2;
     configuration.ProcPEPsi *= 2;
@@ -1017 +1030 @@
     configuration.ProcPEPsi = 1;
   }
-  configuration.InitMaxMinStopStep = configuration.MaxMinStopStep = configuration.MaxPsiDouble;
+  cout << configuration.PsiMaxNoDown << ">" << configuration.PsiMaxNoUp << endl;
+  if (configuration.PsiMaxNoDown > configuration.PsiMaxNoUp) {
+    configuration.InitMaxMinStopStep = configuration.MaxMinStopStep = configuration.PsiMaxNoDown;
+    cout << configuration.PsiMaxNoDown << " " << configuration.InitMaxMinStopStep << endl;
+  } else {
+    configuration.InitMaxMinStopStep = configuration.MaxMinStopStep = configuration.PsiMaxNoUp;
+    cout << configuration.PsiMaxNoUp << " " << configuration.InitMaxMinStopStep << endl;
+  }
 };
 

src/molecule.hpp

@@ -93 +93 @@
 
   public:
-    typedef std::set<atom*> atomSet;
+    typedef std::list<atom*> atomSet;
+    typedef std::set<atomId_t> atomIdSet;
     typedef ObservedIterator<atomSet> iterator;
     typedef atomSet::const_iterator const_iterator;
@@ -121 +122 @@
     Cacheable<int>    AtomCount;
     moleculeId_t id;
-    atomSet atoms; //<!set of atoms
+    atomSet atoms; //<!list of atoms
+    atomIdSet atomIds; //<!set of atomic ids to check uniqueness of atoms
   protected:
     //void CountAtoms();

src/molecule_pointcloud.cpp

@@ -57 +57 @@
 void molecule::GoToFirst() const
 {
-  InternalPointer = atoms.begin();
+  // evil hack necessary because
+  // -# although InternalPointer is mutable
+  // -# only const_iterator begin() is called due to const in the function declaration above
+  // -# and there is no cast from const_iterator to const iterator
+  atomSet::const_iterator test = begin();
+  InternalPointer = *(reinterpret_cast<atomSet::iterator *>(&test));
 };
 

src/moleculelist.cpp

@@ -212 +212 @@
 
   // put all molecules of src into mol
-  molecule::iterator runner;
-  for (molecule::iterator iter = srcmol->begin(); iter != srcmol->end(); ++iter) {
-    runner = iter++;
-    srcmol->UnlinkAtom((*runner));
-    mol->AddAtom((*runner));
+  for (molecule::iterator iter = srcmol->begin(); !srcmol->empty(); iter=srcmol->begin()) {
+    atom * const Walker = *iter;
+    srcmol->UnlinkAtom(Walker);
+    mol->AddAtom(Walker);
   }
 
@@ -259 +258 @@
     status = status && SimpleMerge(mol, srcmol);
   }
+  insert(mol);
   return status;
 };

src/orbitals.db

@@ +1 @@
+# atomicnumber numberoforbitals
 1       1
 2       0

src/periodentafel.cpp

@@ -373 +373 @@
       (*input) >> elements[Z]->Valence;
       (*input) >> ws;
-      //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->Valence << " valence electrons." << endl;
+      //Log() << Verbose(3) << "Element " << Z << " has " << FindElement(Z)->Valence << " valence electrons." << endl;
     }
     return true;
@@ -396 +396 @@
       (*input) >> elements[Z]->NoValenceOrbitals;
       (*input) >> ws;
-      //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->NoValenceOrbitals << " number of singly occupied valence orbitals." << endl;
+      //Log() << Verbose(3) << "Element " << Z << " has " << FindElement(Z)->NoValenceOrbitals << " number of singly occupied valence orbitals." << endl;
     }
     return true;

src/valence.db

@@ +1 @@
+#atomicnumber numberofvalenceorbitals
 1       0.10000000000000E+01
 2       0.20000000000000E+01