Changeset afa056 for molecuilder/src

Timestamp:

Jan 11, 2010, 9:35:52 AM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

49d3e1e

Parents:

91b1e79

Message:

Removed unnecessary epsilon parameter.

• epsilon before was used as a threshold parameter but is not needed anymore.
• removed as parameter in case 'F' in builder.cpp
• removed from Tesselation::IsInnerPoint()
• removed from FillBoxWithMolecul() in boundary.?pp

Location:

molecuilder/src

Files:

• boundary.cpp (modified) (2 diffs)
• boundary.hpp (modified) (1 diff)
• builder.cpp (modified) (3 diffs)
• tesselation.cpp (modified) (1 diff)
• tesselation.hpp (modified) (1 diff)

molecuilder/src/boundary.cpp

@@ -795 +795 @@
  * \return *mol pointer to new molecule with filled atoms
  */
-molecule * FillBoxWithMolecule(MoleculeListClass *List, molecule *filler, config &configuration, const double distance[NDIM], const double epsilon, const double RandomAtomDisplacement, const double RandomMolDisplacement, const bool DoRandomRotation)
+molecule * FillBoxWithMolecule(MoleculeListClass *List, molecule *filler, config &configuration, const double distance[NDIM], const double RandomAtomDisplacement, const double RandomMolDisplacement, const bool DoRandomRotation)
 {
         Info FunctionInfo(__func__);
@@ -856 +856 @@
             FillIt = false;
           } else {
-            const bool FillResult = (!TesselStruct[i]->IsInnerPoint(CurrentPosition, LCList[i], epsilon));
+            const bool FillResult = (!TesselStruct[i]->IsInnerPoint(CurrentPosition, LCList[i]));
             FillIt = FillIt && FillResult;
             if (FillResult) {

molecuilder/src/boundary.hpp

@@ -49 +49 @@
 
 double ConvexizeNonconvexEnvelope(class Tesselation *&TesselStruct, const molecule * const mol, const char * const filename);
-molecule * FillBoxWithMolecule(MoleculeListClass *List, molecule *filler, config &configuration, const double distance[NDIM], const double epsilon, const double RandomAtomDisplacement, const double RandomMolDisplacement, const bool DoRandomRotation);
+molecule * FillBoxWithMolecule(MoleculeListClass *List, molecule *filler, config &configuration, const double distance[NDIM], const double RandomAtomDisplacement, const double RandomMolDisplacement, const bool DoRandomRotation);
 void FindConvexBorder(const molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *LCList, const char *filename);
 Vector* FindEmbeddingHole(MoleculeListClass *mols, molecule *srcmol);

molecuilder/src/builder.cpp

@@ -1417 +1417 @@
             Log() << Verbose(0) << "\t-e <file>\tSets the databases path to be parsed (default: ./)." << endl;
             Log() << Verbose(0) << "\t-E <id> <Z>\tChange atom <id>'s element to <Z>, <id> begins at 0." << endl;
-            Log() << Verbose(0) << "\t-f/F <dist> <order>\tFragments the molecule in BOSSANOVA manner (with/out rings compressed) and stores config files in same dir as config (return code 0 - fragmented, 2 - no fragmentation necessary)." << endl;
-            Log() << Verbose(0) << "\t-F\tFilling Box with water molecules." << endl;
+            Log() << Verbose(0) << "\t-f <dist> <order>\tFragments the molecule in BOSSANOVA manner (with/out rings compressed) and stores config files in same dir as config (return code 0 - fragmented, 2 - no fragmentation necessary)." << endl;
+            Log() << Verbose(0) << "\t-F <dist_x> <dist_y> <dist_z> <epsilon> <randatom> <randmol> <DoRotate>\tFilling Box with water molecules." << endl;
             Log() << Verbose(0) << "\t-g <file>\tParses a bond length table from the given file." << endl;
             Log() << Verbose(0) << "\t-h/-H/-?\tGive this help screen." << endl;
@@ -1738 +1738 @@
               if (argptr+6 >=argc) {
                 ExitFlag = 255;
-                eLog() << Verbose(0) << "Not enough or invalid arguments given for filling box with water: -F <dist_x> <dist_y> <dist_z> <epsilon> <randatom> <randmol> <DoRotate>" << endl;
+                eLog() << Verbose(0) << "Not enough or invalid arguments given for filling box with water: -F <dist_x> <dist_y> <dist_z> <randatom> <randmol> <DoRotate>" << endl;
                 performCriticalExit();
               } else {
@@ -1769 +1769 @@
                 for (int i=0;i<NDIM;i++)
                   distance[i] = atof(argv[argptr+i]);
-                Filling = FillBoxWithMolecule(molecules, filler, configuration, distance, atof(argv[argptr+3]), atof(argv[argptr+4]), atof(argv[argptr+5]), atoi(argv[argptr+6]));
+                Filling = FillBoxWithMolecule(molecules, filler, configuration, distance, atof(argv[argptr+3]), atof(argv[argptr+4]), atoi(argv[argptr+5]));
                 if (Filling != NULL) {
                   Filling->ActiveFlag = false;

molecuilder/src/tesselation.cpp

@@ -3247 +3247 @@
  * @param point of which to check the position
  * @param *LC LinkedCell structure
- * @param epsilon Distance of \a &Point to Center of triangle (of point outwards) is tested less against this value (standard: -MYEPSILON)
  *
  * @return true if the point is inside the tesselation structure, false otherwise
  */
-bool Tesselation::IsInnerPoint(const Vector &Point, const LinkedCell* const LC, const double epsilon) const
+bool Tesselation::IsInnerPoint(const Vector &Point, const LinkedCell* const LC) const
 {
   Info FunctionInfo(__func__);

molecuilder/src/tesselation.hpp

@@ -312 +312 @@
     list<BoundaryTriangleSet*> * FindClosestTrianglesToPoint(const Vector *x, const LinkedCell* LC) const;
     class BoundaryTriangleSet * FindClosestTriangleToPoint(const Vector *x, const LinkedCell* LC) const;
-    bool IsInnerPoint(const Vector &Point, const LinkedCell* const LC, const double epsilon = -MYEPSILON) const;
+    bool IsInnerPoint(const Vector &Point, const LinkedCell* const LC) const;
     bool AddBoundaryPoint(TesselPoint * Walker, const int n);
     DistanceToPointMap * FindClosestBoundaryPointsToVector(const Vector *x, const LinkedCell* LC) const;