Changeset 34e0013 for src

Timestamp:

Oct 30, 2009, 4:09:29 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:

fa649a

Parents:

b21a64

Message:

BondGraph is initialized within config::Load(), as it has to happen after parsing options and before loading molecule. And various fixes.

• FIX: BondGraph::LoadBondLengthTable() - scans into TempContainer, which is later given over to BondLengthMatrix or NULL'd if parsing failed.
• BondGraph::ConstructBondGraph() adapted to above, uses both bonds functions depending on present BondLengthMatrix.
• FIX: BondGraph::GetBondLength() - checks whether BondLengthMatrix is NULL.
• config::Load() and ..LoadOld() get additionally the BondLengthFilename and allocates and parses BondGraph.
• builder.cpp ParseCommandLineOptions() has been adapted to above changes.
• FIX: molecule::CreateAdjacencyList() checks whether bonddistance is > 1. (otherwise quite useless and yielding too many cells).

Location:

src

Files:

• bondgraph.cpp (modified) (6 diffs)
• builder.cpp (modified) (3 diffs)
• config.cpp (modified) (5 diffs)
• config.hpp (modified) (1 diff)
• molecule_graph.cpp (modified) (1 diff)

src/bondgraph.cpp

@@ -32 +32 @@
 
 /** Parses the bond lengths in a given file and puts them int a matrix form.
- * Allocates \a MatrixContainer and uses MatrixContainer::ParseMatrix().
+ * Allocates \a MatrixContainer for BondGraph::BondLengthMatrix, using MatrixContainer::ParseMatrix(),
+ * but only if parsing is successfull. Otherwise variable is left as NULL.
  * \param *out output stream for debugging
  * \param filename file with bond lengths to parse
@@ -40 +41 @@
 {
   bool status = true;
+  MatrixContainer *TempContainer = NULL;
 
   // allocate MatrixContainer
@@ -46 +48 @@
     delete(BondLengthMatrix);
   }
-  BondLengthMatrix = new MatrixContainer;
+  TempContainer = new MatrixContainer;
 
   // parse in matrix
-  BondLengthMatrix->ParseMatrix(filename.c_str(), 0, 1, 0);
+  status = TempContainer->ParseMatrix(filename.c_str(), 0, 1, 0);
 
   // find greatest distance
   max_distance=0;
-  for(int i=0;i<BondLengthMatrix->RowCounter[0];i++)
-    for(int j=i;j<BondLengthMatrix->ColumnCounter[0];j++)
-      if (BondLengthMatrix->Matrix[0][i][j] > max_distance)
-        max_distance = BondLengthMatrix->Matrix[0][i][j];
+  if (status) {
+    for(int i=0;i<TempContainer->RowCounter[0];i++)
+      for(int j=i;j<TempContainer->ColumnCounter[0];j++)
+        if (TempContainer->Matrix[0][i][j] > max_distance)
+          max_distance = TempContainer->Matrix[0][i][j];
+  }
 
+  if (status) // set to not NULL only if matrix was parsed
+    BondLengthMatrix = TempContainer;
+  else {
+    BondLengthMatrix = NULL;
+    delete(TempContainer);
+  }
   return status;
 };
@@ -70 +80 @@
   bool status = true;
 
-  if (BondLengthMatrix == NULL)
-   return false;
-  mol->CreateAdjacencyList(out, max_distance, IsAngstroem, &BondGraph::BondLengthMatrixMinMaxDistance, this);
+  if (mol->start->next == mol->end) // only construct if molecule is not empty
+    return false;
+
+  if (BondLengthMatrix == NULL) // no bond length matrix parsed?
+    mol->CreateAdjacencyList(out, max_distance, IsAngstroem, &BondGraph::CovalentMinMaxDistance, this);
+  else
+    mol->CreateAdjacencyList(out, max_distance, IsAngstroem, &BondGraph::BondLengthMatrixMinMaxDistance, this);
 
   return status;
@@ -84 +98 @@
 double BondGraph::GetBondLength(int firstZ, int secondZ)
 {
-  return (BondLengthMatrix->Matrix[0][firstZ][secondZ]);
+  if (BondLengthMatrix == NULL)
+    return( -1. );
+  else
+    return (BondLengthMatrix->Matrix[0][firstZ][secondZ]);
 };
 
@@ -113 +130 @@
 void BondGraph::BondLengthMatrixMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem)
 {
-  if (BondLengthMatrix->Matrix == NULL) {// safety measure if no matrix has been parsed yet
+  if (BondLengthMatrix == NULL) {// safety measure if no matrix has been parsed yet
     cerr << Verbose(1) << "WARNING:  BondLengthMatrixMinMaxDistance() called without having parsed the bond length matrix yet!" << endl;
     CovalentMinMaxDistance(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);

src/builder.cpp

@@ -1451 +1451 @@
       return 1;
     }
-    // 3b. Find config file name and parse if possible
+    // 3b. Find config file name and parse if possible, also BondGraphFileName
     if (argv[1][0] != '-') {
       // simply create a new molecule, wherein the config file is loaded and the manipulation takes place
@@ -1479 +1479 @@
           case 1:
             cout << "new syntax." << endl;
-            configuration.Load(ConfigFileName, periode, mol);
+            configuration.Load(ConfigFileName, BondGraphFileName, periode, mol);
             configPresent = present;
             break;
           case 0:
             cout << "old syntax." << endl;
-            configuration.LoadOld(ConfigFileName, periode, mol);
+            configuration.LoadOld(ConfigFileName, BondGraphFileName, periode, mol);
             configPresent = present;
             break;
@@ -1494 +1494 @@
     } else
       configPresent = absent;
-    // 3c. parse the bond graph file if given
-    configuration.BG = new BondGraph(configuration.GetIsAngstroem());
-    if (configuration.BG->LoadBondLengthTable((ofstream *)&cout, BondGraphFileName)) {
-      cout << Verbose(0) << "Bond length table loaded successfully." << endl;
-    } else {
-      cout << Verbose(0) << "Bond length table loading failed." << endl;
-      return 1;
-    }
     // 4. parse again through options, now for those depending on elements db and config presence
     argptr = 1;

src/config.cpp

@@ -831 +831 @@
 /** Initializes config file structure by loading elements from a give file.
  * \param *file input file stream being the opened config file
+ * \param BondGraphFileName file name of the bond length table file, if string is left blank, no table is parsed.
  * \param *periode pointer to a periodentafel class with all elements
  * \param *mol pointer to molecule containing all atoms of the molecule
  */
-void config::Load(const char * const filename, const periodentafel * const periode, molecule * const &mol)
+void config::Load(const char * const filename, const string &BondGraphFileName, const periodentafel * const periode, molecule * const &mol)
 {
   ifstream *file = new ifstream(filename);
@@ -860 +861 @@
   /* Namen einlesen */
 
+  // 1. parse in options
   ParseForParameter(verbose,FileBuffer, "mainname", 0, 1, 1, string_type, (config::mainname), 1, critical);
   ParseForParameter(verbose,FileBuffer, "defaultpath", 0, 1, 1, string_type, (config::defaultpath), 1, critical);
@@ -1040 +1042 @@
     config::StructOpt = 0;
 
+  // 2. parse the bond graph file if given
+  BG = new BondGraph(IsAngstroem);
+  if (BG->LoadBondLengthTable((ofstream *)&cout, BondGraphFileName)) {
+    cout << Verbose(0) << "Bond length table loaded successfully." << endl;
+  } else {
+    cout << Verbose(0) << "Bond length table loading failed." << endl;
+  }
+
+  // 3. parse the molecule in
   LoadMolecule(mol, FileBuffer, periode, FastParsing);
+
+  // 4. dissect the molecule into connected subgraphs
+  BG->ConstructBondGraph((ofstream *)&cout, mol);
 
   delete(FileBuffer);
@@ -1047 +1061 @@
 /** Initializes config file structure by loading elements from a give file with old pcp syntax.
  * \param *file input file stream being the opened config file with old pcp syntax
+ * \param BondGraphFileName file name of the bond length table file, if string is left blank, no table is parsed.
  * \param *periode pointer to a periodentafel class with all elements
  * \param *mol pointer to molecule containing all atoms of the molecule
  */
-void config::LoadOld(const char * const filename, const periodentafel * const periode, molecule * const &mol)
+void config::LoadOld(const char * const filename, const string &BondGraphFileName, const periodentafel * const periode, molecule * const &mol)
 {
   ifstream *file = new ifstream(filename);
@@ -1207 +1222 @@
   config::StructOpt = 0;
 
+
+  // 2. parse the bond graph file if given
+  BG = new BondGraph(IsAngstroem);
+  if (BG->LoadBondLengthTable((ofstream *)&cout, BondGraphFileName)) {
+    cout << Verbose(0) << "Bond length table loaded successfully." << endl;
+  } else {
+    cout << Verbose(0) << "Bond length table loading failed." << endl;
+  }
+
   // Routine from builder.cpp
-
 
   for (i=MAX_ELEMENTS;i--;)

src/config.hpp

@@ -135 +135 @@
 
   int TestSyntax(const char * const filename, const periodentafel * const periode, const molecule * const mol) const;
-  void Load(const char * const filename, const periodentafel * const periode, molecule * const &mol);
-  void LoadOld(const char * const filename, const periodentafel * const periode, molecule * const &mol);
+  void Load(const char * const filename, const string &BondGraphFileName, const periodentafel * const periode, molecule * const &mol);
+  void LoadOld(const char * const filename, const string &BondGraphFileName, const periodentafel * const periode, molecule * const &mol);
   void RetrieveConfigPathAndName(const string filename);
   bool Save(const char * const filename, const periodentafel * const periode, molecule * const mol) const;

src/molecule_graph.cpp

@@ -122 +122 @@
   *out << Verbose(1) << "AtomCount " << AtomCount << "." << endl;
 
-  if (AtomCount != 0) {
+  if ((AtomCount > 1) && (bonddistance > 1.)) {
     LC = new LinkedCell(this, bonddistance);