Changeset 450d63

Timestamp:

Oct 18, 2008, 2:03:57 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, 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:

51695c, 5621c3, 674220, 85d278

Parents:

65de9b

Message:

VolumeOfConvexEnvelope() has new parameter with tecplot ofstream and the file is stored there and not in Tesselation::Tesselation().

+ BUGFIX: As we shift the molecule to the center of gravity for the "projection onto axis planes" method to work, we forgot about shifting it back before storing nodes and triangles in the tecplot file. Now, we store the data to file in VolumeOfConvexEnvelope(), where the molecule has been shifted back already.
+ VolumeOfConvexEnvelope() now gets an additional parameter with the tecplot ofstream, so that the name of the tecplot file may be chosen on the command line (with checks whether the argument was given or not)

Location:

src

Files:

• boundary.cpp (modified) (5 diffs)
• boundary.hpp (modified) (1 diff)
• builder.cpp (modified) (2 diffs)

src/boundary.cpp

@@ -456 +456 @@
  * Determines first the convex envelope, then tesselates it and calculates its volume.
  * \param *out output stream for debugging
+ * \param *tecplot output stream for tecplot data
  * \param *configuration needed for path to store convex envelope file
  * \param *BoundaryPoints NDIM set of boundary points on the projected plane per axis, on return if desired
  * \param *mol molecule structure representing the cluster
+ * \return determined volume of the cluster in cubed config:GetIsAngstroem() 
  */
-double VolumeOfConvexEnvelope(ofstream *out, config *configuration, Boundaries *BoundaryPtr, molecule *mol) 
+double VolumeOfConvexEnvelope(ofstream *out, ofstream *tecplot, config *configuration, Boundaries *BoundaryPtr, molecule *mol) 
 {
   bool IsAngstroem = configuration->GetIsAngstroem();
@@ -501 +503 @@
   *out << Verbose(2) << "I found " << TesselStruct->PointsOnBoundaryCount << " points on the convex boundary." << endl;
   // now we have the whole set of edge points in the BoundaryList
-
 
   // listing for debugging
@@ -547 +548 @@
     Walker->x.Translate(CenterOfGravity);
   }
+  
+  // 8. Store triangles in tecplot file
+  if (tecplot != NULL) {
+    *tecplot << "TITLE = \"3D CONVEX SHELL\"" << endl;
+    *tecplot << "VARIABLES = \"X\" \"Y\" \"Z\"" << endl;
+    *tecplot << "ZONE T=\"TRIANGLES\", N=" <<  TesselStruct->PointsOnBoundaryCount << ", E=" <<  TesselStruct->TrianglesOnBoundaryCount << ", DATAPACKING=POINT, ZONETYPE=FETRIANGLE" << endl;
+    int *LookupList = new int[mol->AtomCount];
+    for (int i=0;i<mol->AtomCount;i++)
+      LookupList[i] = -1;
+    
+    // print atom coordinates
+    *out << Verbose(2) << "The following triangles were created:";
+    int Counter = 1;
+    atom *Walker = NULL;
+    for (PointMap::iterator target =  TesselStruct->PointsOnBoundary.begin(); target !=  TesselStruct->PointsOnBoundary.end(); target++) {
+      Walker = target->second->node;
+      LookupList[Walker->nr] = Counter++;
+      *tecplot << Walker->x.x[0] << " " << Walker->x.x[1] << " " << Walker->x.x[2] << " " << endl;
+    }
+    *tecplot << endl;
+      // print connectivity
+    for (TriangleMap::iterator runner =  TesselStruct->TrianglesOnBoundary.begin(); runner !=  TesselStruct->TrianglesOnBoundary.end(); runner++) {
+      *out << " " << runner->second->endpoints[0]->node->Name << "<->" << runner->second->endpoints[1]->node->Name << "<->" << runner->second->endpoints[2]->node->Name;
+      *tecplot << LookupList[runner->second->endpoints[0]->node->nr] << " " << LookupList[runner->second->endpoints[1]->node->nr] << " " << LookupList[runner->second->endpoints[2]->node->nr] << endl; 
+    }
+    delete[](LookupList);
+    *out << endl;
+  }
 
   // free reference lists
@@ -574 +603 @@
   double clustervolume;
   if (ClusterVolume == 0)
-    clustervolume = VolumeOfConvexEnvelope(out, configuration, BoundaryPoints, mol);
+    clustervolume = VolumeOfConvexEnvelope(out, NULL, configuration, BoundaryPoints, mol);
   else 
     clustervolume = ClusterVolume;
@@ -952 +981 @@
   } while (flag);
   
-  stringstream line;
-  line << configuration->configpath << "/" << CONVEXENVELOPE;
-  *out << Verbose(1) << "Storing convex envelope in tecplot data file " << line.str() << "." << endl;
-  ofstream output(line.str().c_str());
-  output << "TITLE = \"3D CONVEX SHELL\"" << endl;
-  output << "VARIABLES = \"X\" \"Y\" \"Z\"" << endl;
-  output << "ZONE T=\"TRIANGLES\", N=" << PointsOnBoundaryCount << ", E=" << TrianglesOnBoundaryCount << ", DATAPACKING=POINT, ZONETYPE=FETRIANGLE" << endl;
-  int *LookupList = new int[mol->AtomCount];
-  for (int i=0;i<mol->AtomCount;i++)
-    LookupList[i] = -1;
-  
-  // print atom coordinates
-  *out << Verbose(2) << "The following triangles were created:";
-  int Counter = 1;
-  atom *Walker = NULL;
-  for (PointMap::iterator target = PointsOnBoundary.begin(); target != PointsOnBoundary.end(); target++) {
-    Walker = target->second->node;
-    LookupList[Walker->nr] = Counter++;
-    output << Walker->x.x[0] << " " << Walker->x.x[1] << " " << Walker->x.x[2] << " " << endl;
-  }
-  output << endl;
-    // print connectivity
-  for (TriangleMap::iterator runner = TrianglesOnBoundary.begin(); runner != TrianglesOnBoundary.end(); runner++) {
-    *out << " " << runner->second->endpoints[0]->node->Name << "<->" << runner->second->endpoints[1]->node->Name << "<->" << runner->second->endpoints[2]->node->Name;
-    output << LookupList[runner->second->endpoints[0]->node->nr] << " " << LookupList[runner->second->endpoints[1]->node->nr] << " " << LookupList[runner->second->endpoints[2]->node->nr] << endl; 
-  }
-  output.close();
-  delete[](LookupList);
-  *out << endl;
 };
 

src/boundary.hpp

@@ -99 +99 @@
 
 
-double VolumeOfConvexEnvelope(ofstream *out, config *configuration, Boundaries *BoundaryPoints, molecule *mol);
+double VolumeOfConvexEnvelope(ofstream *out, ofstream *tecplot, config *configuration, Boundaries *BoundaryPoints, molecule *mol);
 double * GetDiametersOfCluster(ofstream *out, Boundaries *BoundaryPtr, molecule *mol, bool IsAngstroem);
 void PrepareClustersinWater(ofstream *out, config *configuration, molecule *mol, double ClusterVolume, double celldensity);

src/builder.cpp

@@ -569 +569 @@
     case 'e':
         cout << Verbose(0) << "Evaluating volume of the convex envelope.";
-        VolumeOfConvexEnvelope((ofstream *)&cout, configuration, NULL, mol);
+        VolumeOfConvexEnvelope((ofstream *)&cout, NULL, configuration, NULL, mol);
         break;
     case 'f':
@@ -1168 +1168 @@
             case 'o':
               ExitFlag = 1;
-              SaveFlag = true;
-              cout << Verbose(0) << "Evaluating volume of the convex envelope.";
-              VolumeOfConvexEnvelope((ofstream *)&cout, &configuration, NULL, mol);
+              if ((argptr >= argc) || (argv[argptr][0] == '-')) {
+                ExitFlag = 255;
+                cerr << "Not enough or invalid arguments given for convex envelope: -o <tecplot output file>" << endl;
+              } else {
+                cout << Verbose(0) << "Evaluating volume of the convex envelope.";
+                cout << Verbose(1) << "Storing tecplot data in " << argv[argptr] << "." << endl;
+                ofstream *output = new ofstream(argv[argptr], ios::trunc);
+                VolumeOfConvexEnvelope((ofstream *)&cout, output, &configuration, NULL, mol);
+                output->close();
+                delete(output);
+                argptr+=1;
+              }
               break;
             case 'U':