Changeset 71b20e for src/boundary.cpp

Timestamp:

Dec 19, 2009, 7:32:24 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, 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:

c15ca2

Parents:

3930eb

Message:

Attempt to fix the embedding.

Basically it would be working, but there was some failures with the FindClosestTriangleToPoint() routines.
We get triangles wrong if we start looking for the closest point. Actually, we should really look at each
triangle and check the distance. Now, we look at least at each line, but code is unfinished and crashes at the end
unexplainedly.

File:

• src/boundary.cpp (modified) (7 diffs)

src/boundary.cpp

@@ -654 +654 @@
  * \param *out output stream for debugging
  * \param *mol molecule with atoms and bonds
- * \param *&TesselStruct Tesselation with boundary triangles
+ * \param *TesselStruct Tesselation with boundary triangles
  * \param *filename prefix of filename
  * \param *extraSuffix intermediate suffix
  */
-void StoreTrianglesinFile(const molecule * const mol, const Tesselation *&TesselStruct, const char *filename, const char *extraSuffix)
+void StoreTrianglesinFile(const molecule * const mol, const Tesselation * const TesselStruct, const char *filename, const char *extraSuffix)
 {
         Info FunctionInfo(__func__);
@@ -789 +789 @@
  * \param configuration contains box dimensions
  * \param distance[NDIM] distance between filling molecules in each direction
+ * \param epsilon distance to surface which is not filled
  * \param RandAtomDisplacement maximum distance for random displacement per atom
  * \param RandMolDisplacement maximum distance for random displacement per filler molecule
@@ -794 +795 @@
  * \return *mol pointer to new molecule with filled atoms
  */
-molecule * FillBoxWithMolecule(MoleculeListClass *List, molecule *filler, config &configuration, double distance[NDIM], double RandomAtomDisplacement, double RandomMolDisplacement, bool DoRandomRotation)
+molecule * FillBoxWithMolecule(MoleculeListClass *List, molecule *filler, config &configuration, const double distance[NDIM], const double epsilon, const double RandomAtomDisplacement, const double RandomMolDisplacement, const bool DoRandomRotation)
 {
         Info FunctionInfo(__func__);
@@ -817 +818 @@
   for (MoleculeList::iterator ListRunner = List->ListOfMolecules.begin(); ListRunner != List->ListOfMolecules.end(); ListRunner++) {
     Log() << Verbose(1) << "Pre-creating linked cell lists for molecule " << *ListRunner << "." << endl;
-    LCList[i] = new LinkedCell((*ListRunner), 5.); // get linked cell list
-    if (TesselStruct[i] == NULL) {
-      Log() << Verbose(1) << "Pre-creating tesselation for molecule " << *ListRunner << "." << endl;
-      FindNonConvexBorder((*ListRunner), TesselStruct[i], (const LinkedCell *&)LCList[i], 5., NULL);
-    }
+    LCList[i] = new LinkedCell((*ListRunner), 10.); // get linked cell list
+    Log() << Verbose(1) << "Pre-creating tesselation for molecule " << *ListRunner << "." << endl;
+    TesselStruct[i] = NULL;
+    FindNonConvexBorder((*ListRunner), TesselStruct[i], (const LinkedCell *&)LCList[i], 5., NULL);
     i++;
   }
@@ -835 +835 @@
   FillerDistance.Init(distance[0], distance[1], distance[2]);
   FillerDistance.InverseMatrixMultiplication(M);
-  Log() << Verbose(1) << "INFO: Grid steps are ";
-  for(int i=0;i<NDIM;i++) {
+  for(int i=0;i<NDIM;i++)
     N[i] = (int) ceil(1./FillerDistance.x[i]);
-    Log() << Verbose(1) << N[i];
-    if (i != NDIM-1)
-      Log() << Verbose(1)<< ", ";
-    else
-      Log() << Verbose(1) << "." << endl;
-  }
+  Log() << Verbose(1) << "INFO: Grid steps are " << N[0] << ", " << N[1] << ", " << N[2] << "." << endl;
 
   // go over [0,1]^3 filler grid
@@ -862 +856 @@
             FillIt = false;
           } else {
-            FillIt = FillIt && (!TesselStruct[i]->IsInnerPoint(CurrentPosition, LCList[i]));
+            const bool FillResult = (!TesselStruct[i]->IsInnerPoint(CurrentPosition, LCList[i], epsilon));
+            FillIt = FillIt && FillResult;
+            if (FillResult) {
+              Log() << Verbose(1) << "INFO: Position at " << CurrentPosition << " is outer point." << endl;
+            } else {
+              Log() << Verbose(1) << "INFO: Position at " << CurrentPosition << " is inner point." << endl;
+            }
             i++;
           }
         }
 
-        if (FillIt) {
+        if (!FillIt) {
           // fill in Filler
           Log() << Verbose(2) << "Space at " << CurrentPosition << " is unoccupied by any molecule, filling in." << endl;
@@ -931 +931 @@
       }
   Free(&M);
+
+  // output to file
+  TesselStruct[0]->LastTriangle = NULL;
+  StoreTrianglesinFile(Filling, TesselStruct[0], "Tesselated", ".dat");
+
   for (size_t i=0;i<List->ListOfMolecules.size();i++) {
         delete(LCList[i]);