Changeset ee0032

Timestamp:

Mar 27, 2012, 3:53:36 PM (13 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:

bdf6c8

Parents:

64b197

git-author:

Frederik Heber <heber@…> (01/30/12 09:33:06)

git-committer:

Frederik Heber <heber@…> (03/27/12 15:53:36)

Message:

Extracted VolumeOfConvexEnvelope() from boundary and placed into class Tesselation.

• parameter config replaced by boolean IsAngstroem.

Location:

src

Files:

• Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) (1 diff)
• Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) (1 diff)
• Tesselation/boundary.cpp (modified) (5 diffs)
• Tesselation/boundary.hpp (modified) (1 diff)
• Tesselation/tesselation.cpp (modified) (1 diff)
• Tesselation/tesselation.hpp (modified) (1 diff)

src/Actions/AnalysisAction/MolecularVolumeAction.cpp

@@ -60 +60 @@
     //RemoveAllBoundaryPoints(TesselStruct, mol, argv[argptr]);
     double volumedifference = ConvexizeNonconvexEnvelope(TesselStruct, mol, NULL);
-    double clustervolume = VolumeOfConvexEnvelope(TesselStruct, configuration);
+    double clustervolume = TesselStruct->getVolumeOfConvexEnvelope(configuration->GetIsAngstroem());
     LOG(0, "The tesselated volume area is " << clustervolume << " " << (configuration->GetIsAngstroem() ? "angstrom" : "atomiclength") << "^3.");
     LOG(0, "The non-convex tesselated volume area is " << clustervolume-volumedifference << " " << (configuration->GetIsAngstroem() ? "angstrom" : "atomiclength") << "^3.");

src/Actions/TesselationAction/ConvexEnvelopeAction.cpp

@@ -63 +63 @@
     //RemoveAllBoundaryPoints(TesselStruct, mol, argv[argptr]);
     const double volumedifference = ConvexizeNonconvexEnvelope(TesselStruct, mol, params.filenameConvex.string().c_str());
-    const double clustervolume = VolumeOfConvexEnvelope(TesselStruct, configuration);
+    const double clustervolume = TesselStruct->getVolumeOfConvexEnvelope(configuration->GetIsAngstroem());
     LOG(0, "The tesselated volume area is " << clustervolume << " " << (configuration->GetIsAngstroem() ? "angstrom" : "atomiclength") << "^3.");
     LOG(0, "The non-convex tesselated volume area is " << clustervolume-volumedifference << " " << (configuration->GetIsAngstroem() ? "angstrom" : "atomiclength") << "^3.");

src/Tesselation/boundary.cpp

@@ -490 +490 @@
  *   -# if not, we mark an error and stop
  * Note: This routine - for free - calculates the difference in volume between convex and
- * non-convex envelope, as the former is easy to calculate - VolumeOfConvexEnvelope() - it
+ * non-convex envelope, as the former is easy to calculate - Tesselation::getVolumeOfConvexEnvelope() - it
  * can be used to compute volumes of arbitrary shapes.
  * \param *out output stream for debugging
@@ -605 +605 @@
 
 
-/** Determines the volume of a cluster.
- * Determines first the convex envelope, then tesselates it and calculates its volume.
- * \param *out output stream for debugging
- * \param *TesselStruct Tesselation filled with points, lines and triangles on boundary on return
- * \param *configuration needed for path to store convex envelope file
- * \return determined volume of the cluster in cubed config:GetIsAngstroem()
- */
-double VolumeOfConvexEnvelope(class Tesselation *TesselStruct, class config *configuration)
-{
-        Info FunctionInfo(__func__);
-  bool IsAngstroem = configuration->GetIsAngstroem();
-  double volume = 0.;
-  Vector x;
-  Vector y;
-
-  // 6a. Every triangle forms a pyramid with the center of gravity as its peak, sum up the volumes
-  for (TriangleMap::iterator runner = TesselStruct->TrianglesOnBoundary.begin(); runner != TesselStruct->TrianglesOnBoundary.end(); runner++)
-    { // go through every triangle, calculate volume of its pyramid with CoG as peak
-      x = runner->second->getEndpoint(0) - runner->second->getEndpoint(1);
-      y = runner->second->getEndpoint(0) - runner->second->getEndpoint(2);
-      const double a = x.Norm();
-      const double b = y.Norm();
-      const double c = runner->second->getEndpoint(2).distance(runner->second->getEndpoint(1));
-      const double G = sqrt(((a + b + c) * (a + b + c) - 2 * (a * a + b * b + c * c)) / 16.); // area of tesselated triangle
-      x = runner->second->getPlane().getNormal();
-      x.Scale(runner->second->getEndpoint(1).ScalarProduct(x));
-      const double h = x.Norm(); // distance of CoG to triangle
-      const double PyramidVolume = (1. / 3.) * G * h; // this formula holds for _all_ pyramids (independent of n-edge base or (not) centered peak)
-      LOG(1, "INFO: Area of triangle is " << setprecision(10) << G << " "
-          << (IsAngstroem ? "angstrom" : "atomiclength") << "^2, height is "
-          << h << " and the volume is " << PyramidVolume << " "
-          << (IsAngstroem ? "angstrom" : "atomiclength") << "^3.");
-      volume += PyramidVolume;
-    }
-  LOG(0, "RESULT: The summed volume is " << setprecision(6)
-      << volume << " " << (IsAngstroem ? "angstrom" : "atomiclength") << "^3.");
-
-  return volume;
-};
-
 /** Stores triangles to file.
  * \param *out output stream for debugging
@@ -680 +640 @@
 
 /** Creates multiples of the by \a *mol given cluster and suspends them in water with a given final density.
- * We get cluster volume by VolumeOfConvexEnvelope() and its diameters by GetDiametersOfCluster()
+ * We get cluster volume by Tesselation::getVolumeOfConvexEnvelope() and its diameters by GetDiametersOfCluster()
  * TODO: Here, we need a VolumeOfGeneralEnvelope (i.e. non-convex one)
  * \param *out output stream for debugging
@@ -686 +646 @@
  * \param *mol molecule structure representing the cluster
  * \param *&TesselStruct Tesselation structure with triangles on return
- * \param ClusterVolume guesstimated cluster volume, if equal 0 we used VolumeOfConvexEnvelope() instead.
+ * \param ClusterVolume guesstimated cluster volume, if equal 0 we used Tesselation::getVolumeOfConvexEnvelope() instead.
  * \param celldensity desired average density in final cell
  */
@@ -719 +679 @@
   // some preparations beforehand
   if (ClusterVolume == 0)
-    clustervolume = VolumeOfConvexEnvelope(TesselStruct, configuration);
+    clustervolume = TesselStruct->getVolumeOfConvexEnvelope(configuration->GetIsAngstroem());
   else
     clustervolume = ClusterVolume;

src/Tesselation/boundary.hpp

@@ -50 +50 @@
 bool RemoveAllBoundaryPoints(class Tesselation *&TesselStruct, const molecule * const mol, const char * const filename);
 void StoreTrianglesinFile(const molecule * const mol, const Tesselation * const TesselStruct, const char *filename, const char *extraSuffix);
-double VolumeOfConvexEnvelope(class Tesselation *TesselStruct, class config *configuration);
 
 

src/Tesselation/tesselation.cpp

@@ -87 +87 @@
   }
   LOG(0, "This envelope was written to file " << TriangleFilesWritten << " times(s).");
+}
+
+/** Determines the volume of a tesselated convex envelope.
+ *
+ * @param IsAngstroem unit of length is angstroem or bohr radii
+ * \return determined volume of envelope assumed being convex
+ */
+double Tesselation::getVolumeOfConvexEnvelope(const bool IsAngstroem) const
+{
+  double volume = 0.;
+  Vector x;
+  Vector y;
+
+  // 6a. Every triangle forms a pyramid with the center of gravity as its peak, sum up the volumes
+  for (TriangleMap::const_iterator runner = TrianglesOnBoundary.begin(); runner != TrianglesOnBoundary.end(); runner++)
+    { // go through every triangle, calculate volume of its pyramid with CoG as peak
+      x = runner->second->getEndpoint(0) - runner->second->getEndpoint(1);
+      const double G = runner->second->getArea();
+      x = runner->second->getPlane().getNormal();
+      x.Scale(runner->second->getEndpoint(1).ScalarProduct(x));
+      const double h = x.Norm(); // distance of CoG to triangle
+      const double PyramidVolume = (1. / 3.) * G * h; // this formula holds for _all_ pyramids (independent of n-edge base or (not) centered peak)
+      LOG(1, "INFO: Area of triangle is " << setprecision(10) << G << " "
+          << (IsAngstroem ? "angstrom" : "atomiclength") << "^2, height is "
+          << h << " and the volume is " << PyramidVolume << " "
+          << (IsAngstroem ? "angstrom" : "atomiclength") << "^3.");
+      volume += PyramidVolume;
+    }
+  LOG(0, "RESULT: The summed volume is " << setprecision(6)
+      << volume << " " << (IsAngstroem ? "angstrom" : "atomiclength") << "^3.");
+
+  return volume;
 }
 

src/Tesselation/tesselation.hpp

@@ -69 +69 @@
     Tesselation();
     virtual ~Tesselation();
+
+    double getVolumeOfConvexEnvelope(const bool IsAngstroem) const;
 
     void AddTesselationPoint(TesselPoint* Candidate, const int n);