Changeset bd6bfa

Timestamp:

Jun 1, 2010, 7:28:15 AM (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:

acf800

Parents:

1b9321

Message:

Fixes after first,last removal.

• BUGFIX: molecule::OutputGraphInfoPerBond() - had removal loop, not go-through-each-loop.
• BUGFIX: MoleculeListClass::~MoleculeListClass() - did falsely destroy molecules too although this is done by World.
• new function MoleculeListClass::erase() - handles signing off molecule as observer and removes from list.
• FIX: MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs()
  • all molecules are removed from MoleculeListClass and also from World.
  • all bonds are removed, by going through all atoms of World.
  • molecule::getAtomCount() - calls doCountAtoms() which re-numbers and -labels atoms. This confused stuff.
• TESTFIX: Molecules/6 and Molecules/7 had wrong (old) ordering in their test.conf

Files:

• src/bondgraph.cpp (modified) (1 diff)
• src/molecule.hpp (modified) (1 diff)
• src/molecule_graph.cpp (modified) (2 diffs)
• src/moleculelist.cpp (modified) (5 diffs)
• tests/regression/Molecules/6/post/test.conf (modified) (1 diff)
• tests/regression/Molecules/7/post/test.conf (modified) (1 diff)

src/bondgraph.cpp

@@ -88 +88 @@
 {
   Info FunctionInfo(__func__);
-bool status = true;
+  bool status = true;
 
   if (mol->empty()) // only construct if molecule is not empty

src/molecule.hpp

@@ -380 +380 @@
   bool StoreForcesFile(char *path, int *SortIndex);
   void insert(molecule *mol);
+  void erase(molecule *mol);
   molecule * ReturnIndex(int index);
   bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);

src/molecule_graph.cpp

@@ -67 +67 @@
     performCriticalExit();
   };
+  doCountAtoms();
 
   // skip header
@@ -632 +633 @@
   DoLog(1) && (Log() << Verbose(1) << "Final graph info for each bond is:" << endl);
   for(molecule::const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner)
-    for(BondList::const_iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); !(*AtomRunner)->ListOfBonds.empty(); BondRunner = (*AtomRunner)->ListOfBonds.begin())
+    for(BondList::const_iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); BondRunner != (*AtomRunner)->ListOfBonds.end(); ++BondRunner)
       if ((*BondRunner)->leftatom == *AtomRunner) {
         Binder = *BondRunner;

src/moleculelist.cpp

@@ -40 +40 @@
 MoleculeListClass::~MoleculeListClass()
 {
-  DoLog(3) && (Log() << Verbose(3) << this << ": Freeing ListOfMolcules." << endl);
-  for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
-    DoLog(4) && (Log() << Verbose(4) << "ListOfMolecules: Freeing " << *ListRunner << "." << endl);
-    world->destroyMolecule(*ListRunner);
-  }
-  DoLog(4) && (Log() << Verbose(4) << "Freeing ListOfMolecules." << endl);
+  DoLog(4) && (Log() << Verbose(4) << "Clearing ListOfMolecules." << endl);
+  for(MoleculeList::iterator MolRunner = ListOfMolecules.begin(); MolRunner != ListOfMolecules.end(); ++MolRunner)
+    (*MolRunner)->signOff(this);
   ListOfMolecules.clear(); // empty list
 };
@@ -51 +48 @@
 /** Insert a new molecule into the list and set its number.
  * \param *mol molecule to add to list.
- * \return true - add successful
  */
 void MoleculeListClass::insert(molecule *mol)
@@ -59 +55 @@
   ListOfMolecules.push_back(mol);
   mol->signOn(this);
+};
+
+/** Erases a molecule from the list.
+ * \param *mol molecule to add to list.
+ */
+void MoleculeListClass::erase(molecule *mol)
+{
+  OBSERVE;
+  mol->signOff(this);
+  ListOfMolecules.remove(mol);
 };
 
@@ -742 +748 @@
 void MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration)
 {
+  // 0a. remove all present molecules
+  vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
+  for (vector<molecule *>::iterator MolRunner = allmolecules.begin(); MolRunner != allmolecules.end(); ++MolRunner) {
+    erase(*MolRunner);
+    World::getInstance().destroyMolecule(*MolRunner);
+  }
+  // 0b. remove all bonds
   molecule *mol = World::getInstance().createMolecule();
-  bond *Binder = NULL;
-  // 0. gather all atoms into single molecule
-  for (MoleculeList::iterator MolRunner = ListOfMolecules.begin(); !ListOfMolecules.empty(); MolRunner = ListOfMolecules.begin()) {
-    // shift all atoms to new molecule
-    for (molecule::iterator iter = (*MolRunner)->begin(); (*MolRunner)->empty(); iter = (*MolRunner)->begin()) {
-      DoLog(3) && (Log() << Verbose(3) << "Re-linking " << (*iter) << "..." << endl);
-      (*iter)->father = (*iter);
-      mol->AddAtom((*iter));    // counting starts at 1
-      (*MolRunner)->erase(iter);
-    }
-    // remove all bonds
-    for(molecule::iterator AtomRunner = (*MolRunner)->begin(); AtomRunner != (*MolRunner)->end(); ++AtomRunner)
-      for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); !(*AtomRunner)->ListOfBonds.empty(); BondRunner = (*AtomRunner)->ListOfBonds.begin())
-        delete(*BondRunner);
-    // remove the molecule
-    World::getInstance().destroyMolecule(*MolRunner);
-    ListOfMolecules.erase(MolRunner);
+  vector <atom *> allatoms = World::getInstance().getAllAtoms();
+  for(vector<atom *>::iterator AtomRunner = allatoms.begin(); AtomRunner != allatoms.end(); ++AtomRunner) {
+    for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); !(*AtomRunner)->ListOfBonds.empty(); BondRunner = (*AtomRunner)->ListOfBonds.begin())
+      delete(*BondRunner);
+    mol->AddAtom(*AtomRunner);
   }
 
@@ -816 +817 @@
   // 4c. relocate atoms to new molecules and remove from Leafs
   for (molecule::iterator iter = mol->begin(); !mol->empty(); iter = mol->begin()) {
-    if (((*iter)->nr <0) || ((*iter)->nr >= mol->getAtomCount())) {
-      DoeLog(0) && (eLog()<< Verbose(0) << "Index of atom " << **iter << " is invalid!" << endl);
+    const int count = mol->getAtomCount();
+    if (((*iter)->nr <0) || ((*iter)->nr >= count)) {
+      DoeLog(0) && (eLog()<< Verbose(0) << "Index " << (*iter)->nr << " of atom " << **iter << " in molecule of " << count << " atoms is invalid!" << endl);
       performCriticalExit();
     }
-    FragmentCounter = MolMap[(*iter)->nr];
-    if (FragmentCounter != 0) {
+    const int Index = MolMap[(*iter)->nr];
+    if (Index != 0) {
       DoLog(3) && (Log() << Verbose(3) << "Re-linking " << **iter << "..." << endl);
-      molecules[FragmentCounter-1]->AddAtom((*iter));    // counting starts at 1
+      molecules[Index-1]->AddAtom((*iter));    // counting starts at 1
       mol->erase(iter);
     } else {

tests/regression/Molecules/6/post/test.conf

@@ -71 +71 @@
 Ion_Type2       3       6       1.0     3       3       12.01100000000  Carbon  C
 #Ion_TypeNr._Nr.R[0]    R[1]    R[2]    MoveType (0 MoveIon, 1 FixedIon)
-Ion_Type2_1     10.782085945    4.275186040     4.535886037     0 # molecule nr 0
-Ion_Type2_2     9.532785963     5.158586027     4.535886037     0 # molecule nr 1
-Ion_Type2_3     8.283585982     4.275186040     4.535886037     0 # molecule nr 2
-Ion_Type1_1     10.782085945    3.645886050     3.645886050     0 # molecule nr 3
-Ion_Type1_2     10.782085945    3.645886050     5.425886024     0 # molecule nr 4
-Ion_Type1_3     11.672039608    4.904536878     4.535886037     0 # molecule nr 5
-Ion_Type1_4     9.532785963     5.787886018     3.645886050     0 # molecule nr 6
-Ion_Type1_5     9.532785963     5.787886018     5.425886024     0 # molecule nr 7
-Ion_Type1_6     7.393632318     4.904536877     4.535886037     0 # molecule nr 8
-Ion_Type1_7     8.283585982     3.645886050     3.645886050     0 # molecule nr 9
-Ion_Type1_8     8.283585982     3.645886050     5.425886024     0 # molecule nr 10
+Ion_Type1_1     10.782085945    3.645886050     3.645886050     0 # molecule nr 0
+Ion_Type1_2     10.782085945    3.645886050     5.425886024     0 # molecule nr 1
+Ion_Type1_3     11.672039608    4.904536878     4.535886037     0 # molecule nr 2
+Ion_Type1_4     9.532785963     5.787886018     3.645886050     0 # molecule nr 3
+Ion_Type1_5     9.532785963     5.787886018     5.425886024     0 # molecule nr 4
+Ion_Type1_6     7.393632318     4.904536877     4.535886037     0 # molecule nr 5
+Ion_Type1_7     8.283585982     3.645886050     3.645886050     0 # molecule nr 6
+Ion_Type1_8     8.283585982     3.645886050     5.425886024     0 # molecule nr 7
+Ion_Type2_1     10.782085945    4.275186040     4.535886037     0 # molecule nr 8
+Ion_Type2_2     9.532785963     5.158586027     4.535886037     0 # molecule nr 9
+Ion_Type2_3     8.283585982     4.275186040     4.535886037     0 # molecule nr 10

tests/regression/Molecules/7/post/test.conf

@@ -71 +71 @@
 Ion_Type2       3       6       1.0     3       3       12.01100000000  Carbon  C
 #Ion_TypeNr._Nr.R[0]    R[1]    R[2]    MoveType (0 MoveIon, 1 FixedIon)
-Ion_Type2_1     1.782085945     15.275186040    15.535886037    0 # molecule nr 0
-Ion_Type2_2     0.532785963     16.158586027    15.535886037    0 # molecule nr 1
-Ion_Type2_3     19.283585982    15.275186040    15.535886037    0 # molecule nr 2
-Ion_Type1_1     1.782085945     14.645886050    14.645886050    0 # molecule nr 3
-Ion_Type1_2     1.782085945     14.645886050    16.425886024    0 # molecule nr 4
-Ion_Type1_3     2.672039608     15.904536878    15.535886037    0 # molecule nr 5
-Ion_Type1_4     0.532785963     16.787886018    14.645886050    0 # molecule nr 6
-Ion_Type1_5     0.532785963     16.787886018    16.425886024    0 # molecule nr 7
-Ion_Type1_6     18.393632318    15.904536877    15.535886037    0 # molecule nr 8
-Ion_Type1_7     19.283585982    14.645886050    14.645886050    0 # molecule nr 9
-Ion_Type1_8     19.283585982    14.645886050    16.425886024    0 # molecule nr 10
+Ion_Type1_1     1.782085945     14.645886050    14.645886050    0 # molecule nr 0
+Ion_Type1_2     1.782085945     14.645886050    16.425886024    0 # molecule nr 1
+Ion_Type1_3     2.672039608     15.904536878    15.535886037    0 # molecule nr 2
+Ion_Type1_4     0.532785963     16.787886018    14.645886050    0 # molecule nr 3
+Ion_Type1_5     0.532785963     16.787886018    16.425886024    0 # molecule nr 4
+Ion_Type1_6     18.393632318    15.904536877    15.535886037    0 # molecule nr 5
+Ion_Type1_7     19.283585982    14.645886050    14.645886050    0 # molecule nr 6
+Ion_Type1_8     19.283585982    14.645886050    16.425886024    0 # molecule nr 7
+Ion_Type2_1     1.782085945     15.275186040    15.535886037    0 # molecule nr 8
+Ion_Type2_2     0.532785963     16.158586027    15.535886037    0 # molecule nr 9
+Ion_Type2_3     19.283585982    15.275186040    15.535886037    0 # molecule nr 10