Changeset 3c349b

Timestamp:

Nov 3, 2009, 4:34:31 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:

f4e1f5

Parents:

ae38fb

Message:

"not working parsed molecule into subgraph splitting"-BUG fixed, BugFinder branch can be closed.

• config::Load() - atoms were not in the right order for MaxOrder-test (12). Hence, the BondFragmentAdjacency could not be parsed. Now, we just take the subgraphs as the association of each atom to a molecule, i.e. we make a list and then re-link each atom to its new connected subgraph molecule, which is returned as the MoleculeListClass.

other fixes:

• BondGraph::SetMaxDistanceToMaxOfCovalentRadii() - parses the molecule and set to max of covalent radii of elements found therein
• BondGraph::ConstructBondGraph() - SetMaxDistanceToMaxOfCovalentRadii() called before CreateAdjacencyList() to have current max_distance
• BUGFIX: molecule::CreateAdjacencyList() - BondCount was not set to zero after cleaning of list
• FIX: CreateFatherLookupTable() - as we use Calloc(), initialization to NULL was unnecessary

Location:

src

Files:

• bondgraph.cpp (modified) (2 diffs)
• bondgraph.hpp (modified) (1 diff)
• boundary.cpp (modified) (1 diff)
• config.cpp (modified) (2 diffs)
• helpers.hpp (modified) (2 diffs)
• molecule_fragmentation.cpp (modified) (1 diff)
• molecule_graph.cpp (modified) (1 diff)

src/bondgraph.cpp ¶

@@ -84 +84 @@
     return false;
 
-  if (BondLengthMatrix == NULL) // no bond length matrix parsed?
+  if (BondLengthMatrix == NULL) { // no bond length matrix parsed?
+    SetMaxDistanceToMaxOfCovalentRadii(out, mol);
     mol->CreateAdjacencyList(out, max_distance, IsAngstroem, &BondGraph::CovalentMinMaxDistance, this);
-  else
+  } else
     mol->CreateAdjacencyList(out, max_distance, IsAngstroem, &BondGraph::BondLengthMatrixMinMaxDistance, this);
 
@@ -105 +106 @@
 };
 
-/** Determines the maximum of all element::CovalentRadius.
+/** Determines the maximum of all element::CovalentRadius for elements present in \a *mol.
  * \param *out output stream for debugging
- * \param *periode periodentafel with all elements.
+ * \param *mol molecule with all atoms and their respective elements.
  */
-double BondGraph::SetMaxDistanceToMaxOfCovalentRadii(ofstream * const out, const periodentafel * const periode)
+double BondGraph::SetMaxDistanceToMaxOfCovalentRadii(ofstream * const out, const molecule * const mol)
 {
   max_distance = 0.;
 
-  element * Runner = periode->start;
-  while (Runner->next != periode->end) {
+  atom *Runner = mol->start;
+  while (Runner->next != mol->end) {
     Runner = Runner->next;
-    if (Runner->CovalentRadius > max_distance)
-      max_distance = Runner->CovalentRadius;
+    if (Runner->type->CovalentRadius > max_distance)
+      max_distance = Runner->type->CovalentRadius;
   }
   max_distance *= 2.;

src/bondgraph.hpp ¶

@@ -38 +38 @@
   bool ConstructBondGraph(ofstream * const out, molecule * const mol);
   double GetBondLength(int firstelement, int secondelement);
-  double SetMaxDistanceToMaxOfCovalentRadii(ofstream * const out, const periodentafel * const periode);
+  double SetMaxDistanceToMaxOfCovalentRadii(ofstream * const out, const molecule * const mol);
 
   void BondLengthMatrixMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem);

src/boundary.cpp ¶

@@ -655 +655 @@
       volume += PyramidVolume;
     }
-  *out << Verbose(0) << "RESULT: The summed volume is " << setprecision(8)
+  *out << Verbose(0) << "RESULT: The summed volume is " << setprecision(6)
       << volume << " " << (IsAngstroem ? "angstrom" : "atomiclength") << "^3."
       << endl;

src/config.cpp ¶

@@ -1051 +1051 @@
   } else {
     cout << Verbose(0) << "Bond length table loading failed." << endl;
-    BG->SetMaxDistanceToMaxOfCovalentRadii((ofstream *)&cout, periode);
   }
 
@@ -1068 +1067 @@
   delete(BackEdgeStack);
 
-  // 6. dissect
-  atom ***ListOfLocalAtoms = NULL;
+  // 6. dissect (the following construct is needed to have the atoms not in the order of the DFS, but in
+  // the original one as parsed in)
+  // TODO: Optimize this, when molecules just contain pointer list of global atoms!
+
+  // 6a. create array of molecules to fill
+  const int MolCount = Subgraphs->Count();
+  molecule **molecules = Malloc<molecule *>(MolCount, "config::Load() - **molecules");
+  for (int i=0;i<MolCount;i++) {
+    molecules[i] = (molecule*) new molecule(periode);
+    molecules[i]->ActiveFlag = true;
+    MolList->insert(molecules[i]);
+  }
+
+  // 6b. create and fill map of which atom is associated to which connected molecule (note, counting starts at 1)
   int FragmentCounter = 0;
+  int *MolMap = Calloc<int>(mol->AtomCount, "config::Load() - *MolMap");
   MoleculeLeafClass *MolecularWalker = Subgraphs;
   atom *Walker = NULL;
   while (MolecularWalker->next != NULL) {
     MolecularWalker = MolecularWalker->next;
-    // fill the bond structure of the individually stored subgraphs (goes through whole chained list by itself)
-    MolecularWalker->FillBondStructureFromReference((ofstream *)&cout, mol, FragmentCounter, ListOfLocalAtoms, false);  // we don't want to keep the created ListOfLocalAtoms
-    FragmentCounter++;
-    MolecularWalker->Leaf->ActiveFlag = true;
     Walker = MolecularWalker->Leaf->start;
     while (Walker->next != MolecularWalker->Leaf->end) {
       Walker = Walker->next;
-      Walker->father = Walker;
+      MolMap[Walker->GetTrueFather()->nr] = FragmentCounter+1;
     }
-    MolList->insert(MolecularWalker->Leaf);
-    MolecularWalker->Leaf = NULL; // don't remove molecule when deleting MolecularWalker
+    FragmentCounter++;
+  }
+
+  // 6c. relocate atoms to new molecules and remove from Leafs
+  Walker = mol->start;
+  while (mol->start->next != mol->end) {
+    Walker = mol->start->next;
+    if ((Walker->nr <0) || (Walker->nr >= mol->AtomCount)) {
+      cerr << "Index of atom " << *Walker << " is invalid!" << endl;
+      performCriticalExit();
+    }
+    FragmentCounter = MolMap[Walker->nr];
+    if (FragmentCounter != 0) {
+      cout << Verbose(3) << "Re-linking " << *Walker << "..." << endl;
+      unlink(Walker);
+      molecules[FragmentCounter-1]->AddAtom(Walker);    // counting starts at 1
+    } else {
+      cerr << "Atom " << *Walker << " not associated to molecule!" << endl;
+      performCriticalExit();
+    }
+  }
+  // 6d. we don't need to redo bonds, as they are connected subgraphs and still maintained their ListOfBonds
+  // 6e. free Leafs
+  MolecularWalker = Subgraphs;
+  while (MolecularWalker->next != NULL) {
+    MolecularWalker = MolecularWalker->next;
     delete(MolecularWalker->previous);
   }
   delete(MolecularWalker);
-  for (int i=0;i<FragmentCounter;i++)
-    Free(&ListOfLocalAtoms[i]);
-  Free(&ListOfLocalAtoms);
+  delete(mol);
+  Free(&MolMap);
+  Free(&molecules);
   cout << Verbose(1) << "I scanned " << FragmentCounter << " molecules." << endl;
-
-  // 6. free parsed in molecule
-  delete(mol);
 
   delete(FileBuffer);

src/helpers.hpp ¶

@@ -71 +71 @@
  * \paran *end end of chain list
  * \param **Lookuptable pointer to return allocated lookup table (should be NULL on start)
- * \param count optional predetermined count for table (otherwise we set the count to highest true father id)
+ * \param count optional predetermined size for table (otherwise we set the count to highest true father id)
  * \return true - success, false - failure
  */
@@ -104 +104 @@
     status = false;
   } else {
-    for (int i=0;i<count;i++)
-      LookupTable[i] = NULL;
     Walker = start;
     while (Walker->next != end) { // create a lookup table (Atom::nr -> atom) used as a marker table lateron

src/molecule_fragmentation.cpp ¶

@@ -641 +641 @@
     }
   }
+  *out << Verbose(2) << "CheckOrder is " << CheckOrder << "." << endl;
   delete[](RootStack);
   delete[](AtomMask);

src/molecule_graph.cpp ¶

@@ -121 +121 @@
     removewithoutcheck(Binder);
   }
+  BondCount = 0;
 
   // count atoms in molecule = dimension of matrix (also give each unique name and continuous numbering)