Changeset 6a7f78c for src

Timestamp:

Nov 24, 2009, 3:34:49 PM (16 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, Candidate_v1.7.0, Candidate_v1.7.1, 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:

791138

Parents:

c5f836

Message:

Fixes and naming of final Tecplot output file is now molecule name.

• FIXES to builder.cpp:
  • case 'p' would not dissect the molecule into connected subgraphs
  • if done so, the BondGraph was not yet initialised
  • if done so, we need to check whether BondGraphFileName has been set
  • BondGraphFileName.empty() could not be used as a check, as was set to "" instead of "\n"
  • if (finally) done so, we have to remove the empty molecule that we parsed in
  • ... and then pick the newly added molecule for mol to point at
  • SaveConfig() did not set the merged molecule name correctly.
  • if empty config is given, the empty molecule now receives the ConfigFileName as name

• FIXES to config.cpp
  • Load() did not set the name of the molecule

• changes to tesselationhelper.cpp and tesselation.cpp
  • WriteTecplotFile() uses N == -1 to make clear, that we are writing the final not a temporary tecplot file and then uses the molecule's name instead of the last triangle's endpoints
  • FindNextSuitableTriangle(): HasOtherBaselineBetterCandidate() was commented out for the moment (as it is not yet final and makes all the test fail)
  • IncludeSphereinRaster3D() did not check whether LastTriangle was NULL or not

• MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() names the subgraphs with suffixes "..-1", "..-2", ...

• changes to PointCloud and molecule
  • new virtual function PointCloud::GetName() returns "unknown"
  • new function molecule::GetName() returns pointer to name of molecule
  • IsEmpty() and IsEnd() now return true by default

• all .dat files in the "Tesselations" tests were changed accordingly (i.e. have now the name in the second line)
• benzene was added as a new test for an absolutely flat molecule. So far, it fails horribly.
• 13 of 17 tests run fine

Signed-off-by: Frederik Heber <heber@…>

Location:

src

Files:

• boundary.cpp (modified) (1 diff)
• builder.cpp (modified) (4 diffs)
• config.cpp (modified) (1 diff)
• molecule.hpp (modified) (1 diff)
• molecule_pointcloud.cpp (modified) (1 diff)
• moleculelist.cpp (modified) (2 diffs)
• tesselation.cpp (modified) (2 diffs)
• tesselation.hpp (modified) (2 diffs)
• tesselationhelpers.cpp (modified) (2 diffs)

src/boundary.cpp

@@ -671 +671 @@
       OutputName.append(TecplotSuffix);
       ofstream *tecplot = new ofstream(OutputName.c_str());
-      WriteTecplotFile(tecplot, TesselStruct, mol, 0);
+      WriteTecplotFile(tecplot, TesselStruct, mol, -1);
       tecplot->close();
       delete(tecplot);

src/builder.cpp

@@ -1247 +1247 @@
   ofstream output;
   molecule *mol = new molecule(periode);
+  mol->SetNameFromFilename(ConfigFileName);
 
   if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
@@ -1385 +1386 @@
   int argptr;
   molecule *mol = NULL;
-  string BondGraphFileName("");
+  string BondGraphFileName("\n");
   int verbosity = 0;
   strncpy(configuration.databasepath, LocalPath, MAXSTRINGSIZE-1);
@@ -1539 +1540 @@
        mol = new molecule(periode);
        mol->ActiveFlag = true;
+       if (ConfigFileName != NULL)
+         mol->SetNameFromFilename(ConfigFileName);
        molecules->insert(mol);
+     }
+     if (configuration.BG == NULL) {
+       configuration.BG = new BondGraph(configuration.GetIsAngstroem());
+       if ((BondGraphFileName.empty()) && (configuration.BG->LoadBondLengthTable(BondGraphFileName))) {
+         Log() << Verbose(0) << "Bond length table loaded successfully." << endl;
+       } else {
+         eLog() << Verbose(1) << "Bond length table loading failed." << endl;
+       }
      }
 
@@ -1563 +1574 @@
                 else {
                   Log() << Verbose(2) << "File found and parsed." << endl;
+                  mol->SetNameFromFilename(argv[argptr]);
+                  molecules->ListOfMolecules.remove(mol);
+                  molecules->DissectMoleculeIntoConnectedSubgraphs(mol,&configuration);
+                  if (molecules->ListOfMolecules.size() != 0) {
+                    for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
+                      if ((*ListRunner)->ActiveFlag) {
+                        mol = *ListRunner;
+                        break;
+                      }
+                  }
                   configPresent = present;
                 }

src/config.cpp

@@ -1056 +1056 @@
 
   // 2. parse the bond graph file if given
-  BG = new BondGraph(IsAngstroem);
-  if (BG->LoadBondLengthTable(BondGraphFileName)) {
-    Log() << Verbose(0) << "Bond length table loaded successfully." << endl;
-  } else {
-    eLog() << Verbose(1) << "Bond length table loading failed." << endl;
+  if (BG == NULL) {
+    BG = new BondGraph(IsAngstroem);
+    if (BG->LoadBondLengthTable(BondGraphFileName)) {
+      Log() << Verbose(0) << "Bond length table loaded successfully." << endl;
+    } else {
+      eLog() << Verbose(1) << "Bond length table loading failed." << endl;
+    }
   }
 
   // 3. parse the molecule in
   LoadMolecule(mol, FileBuffer, periode, FastParsing);
+  mol->SetNameFromFilename(filename);
   mol->ActiveFlag = true;
 

src/molecule.hpp

@@ -106 +106 @@
 
   // re-definition of virtual functions from PointCloud
+  const char * const GetName() const;
   Vector *GetCenter() const ;
   TesselPoint *GetPoint() const ;

src/molecule_pointcloud.cpp

@@ -13 +13 @@
 /************************************* Functions for class molecule *********************************/
 
+/** Returns a name for this point cloud, here the molecule's name.
+ * \return name of point cloud
+ */
+const char * const molecule::GetName() const
+{
+  return name;
+};
 
 /** Determine center of all atoms.

src/moleculelist.cpp

@@ -760 +760 @@
   // 4a. create array of molecules to fill
   const int MolCount = Subgraphs->next->Count();
+  char number[MAXSTRINGSIZE];
   molecule **molecules = Malloc<molecule *>(MolCount, "config::Load() - **molecules");
   for (int i=0;i<MolCount;i++) {
     molecules[i] = (molecule*) new molecule(mol->elemente);
     molecules[i]->ActiveFlag = true;
+    strncpy(molecules[i]->name, mol->name, MAXSTRINGSIZE);
+    if (MolCount > 1) {
+      sprintf(number, "-%d", i+1);
+      strncat(molecules[i]->name, number, MAXSTRINGSIZE - strlen(mol->name) - 1);
+    }
+    cout << "MolName is " << molecules[i]->name << endl;
     insert(molecules[i]);
   }
@@ -800 +807 @@
     }
   }
-  // 4d. we don't need to redo bonds, as they are connected subgraphs and still maintained their ListOfBonds, but we have to remove them from first..last list
+  // 4d. we don't need to redo bonds, as they are connected subgraphs and still maintain their ListOfBonds, but we have to remove them from first..last list
   bond *Binder = mol->first;
   while (mol->first->next != mol->last) {

src/tesselation.cpp

@@ -1957 +1957 @@
     BTS = NULL;
     // check for present edges and whether we reach better candidates from them
-    if (HasOtherBaselineBetterCandidate(BaseRay, (*it)->point, ShortestAngle, RADIUS, LC) ) {
+    //if (HasOtherBaselineBetterCandidate(BaseRay, (*it)->point, ShortestAngle, RADIUS, LC) ) {
+    if (0) {
       result = false;
       break;
@@ -3584 +3585 @@
   }
   delete(DegeneratedTriangles);
+  if (count > 0)
+    LastTriangle = NULL;
 
   Log() << Verbose(1) << "RemoveDegeneratedTriangles() removed " << count << " triangles:" << endl;

src/tesselation.hpp

@@ -170 +170 @@
   virtual ~PointCloud();
 
+  virtual const char * const GetName() const { return "unknown"; };
   virtual Vector *GetCenter() const { return NULL; };
   virtual TesselPoint *GetPoint() const { return NULL; };
@@ -177 +178 @@
   virtual void GoToFirst() const {};
   virtual void GoToLast() const {};
-  virtual bool IsEmpty() const { return false; };
-  virtual bool IsEnd() const { return false; };
+  virtual bool IsEmpty() const { return true; };
+  virtual bool IsEnd() const { return true; };
 };
 

src/tesselationhelpers.cpp

@@ -756 +756 @@
 {
   Vector helper;
-  // include the current position of the virtual sphere in the temporary raster3d file
-  Vector *center = cloud->GetCenter();
-  // make the circumsphere's center absolute again
-  helper.CopyVector(Tess->LastTriangle->endpoints[0]->node->node);
-  helper.AddVector(Tess->LastTriangle->endpoints[1]->node->node);
-  helper.AddVector(Tess->LastTriangle->endpoints[2]->node->node);
-  helper.Scale(1./3.);
-  helper.SubtractVector(center);
-  // and add to file plus translucency object
-  *rasterfile << "# current virtual sphere\n";
-  *rasterfile << "8\n  25.0    0.6     -1.0 -1.0 -1.0     0.2        0 0 0 0\n";
-  *rasterfile << "2\n  " << helper.x[0] << " " << helper.x[1] << " " << helper.x[2] << "\t" << 5. << "\t1 0 0\n";
-  *rasterfile << "9\n  terminating special property\n";
-  delete(center);
+
+  if (Tess->LastTriangle != NULL) {
+    // include the current position of the virtual sphere in the temporary raster3d file
+    Vector *center = cloud->GetCenter();
+    // make the circumsphere's center absolute again
+    helper.CopyVector(Tess->LastTriangle->endpoints[0]->node->node);
+    helper.AddVector(Tess->LastTriangle->endpoints[1]->node->node);
+    helper.AddVector(Tess->LastTriangle->endpoints[2]->node->node);
+    helper.Scale(1./3.);
+    helper.SubtractVector(center);
+    // and add to file plus translucency object
+    *rasterfile << "# current virtual sphere\n";
+    *rasterfile << "8\n  25.0    0.6     -1.0 -1.0 -1.0     0.2        0 0 0 0\n";
+    *rasterfile << "2\n  " << helper.x[0] << " " << helper.x[1] << " " << helper.x[2] << "\t" << 5. << "\t1 0 0\n";
+    *rasterfile << "9\n  terminating special property\n";
+    delete(center);
+  }
 };
 
@@ -829 +832 @@
     *tecplot << "TITLE = \"3D CONVEX SHELL\"" << endl;
     *tecplot << "VARIABLES = \"X\" \"Y\" \"Z\" \"U\"" << endl;
-    *tecplot << "ZONE T=\"" << N << "-";
-    for (int i=0;i<3;i++)
-      *tecplot << (i==0 ? "" : "_") << TesselStruct->LastTriangle->endpoints[i]->node->Name;
+    *tecplot << "ZONE T=\"";
+    if (N < 0) {
+      *tecplot << cloud->GetName();
+    } else {
+      *tecplot << N << "-";
+      for (int i=0;i<3;i++)
+        *tecplot << (i==0 ? "" : "_") << TesselStruct->LastTriangle->endpoints[i]->node->Name;
+    }
     *tecplot << "\", N=" << TesselStruct->PointsOnBoundary.size() << ", E=" << TesselStruct->TrianglesOnBoundary.size() << ", DATAPACKING=POINT, ZONETYPE=FETRIANGLE" << endl;
     int i=0;