Changeset 20895b for molecuilder/src/analysis_correlation.cpp

Timestamp:

Nov 4, 2009, 5:34:05 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

5f1d021

Parents:

c1b76e

Message:

Extension to the periodic boundary case for analysis_correlation.cpp

• Distance() -> PeriodicDistance(): PairCorrelation(), CorrelationToPoint(), CorrelationToSurface()
• CorrelationToSurface() - goes through periodic cells given by a ranges variable and puts into map as well.
• const: ReturnFullMatrixforSymmetric() and InverseMatrix() now have const * const parameter
• InverseMatrix() shifted from class Vector into helpers.cpp
• adapted due to InverseMatrix(): molecule::CenterInBox(), molecule::BoundInBox(), molecule::TranslatePeriodically()
• new function: RDET3(), RDET2() (former #define's)
• FIX: molecule::CorrectBondDegree() would loop eternally, if bonds cannot be fully corrected.
• FIX for NULL return: Tesselation::FindClosestTrianglesToPoint(), Tesselation::GetCircleOfConnectedPoints()
• FIX: Vector::DistanceToPlane() - did not give correct sign before according to PlaneNormal orientation

other stuff:

• less output: BondedParticle::CorrectBondDegree(), molecule::CyclicStructureAnalysis()

File:

• molecuilder/src/analysis_correlation.cpp (modified) (5 diffs)

molecuilder/src/analysis_correlation.cpp

@@ -52 +52 @@
                 if (Walker->nr < OtherWalker->nr)
                   if ((type2 == NULL) || (OtherWalker->type == type2)) {
-                    distance = Walker->node->Distance(OtherWalker->node);
+                    distance = Walker->node->PeriodicDistance(OtherWalker->node, (*MolWalker)->cell_size);
                     //*out << Verbose(1) <<"Inserting " << *Walker << " and " << *OtherWalker << endl;
                     outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> (Walker, OtherWalker) ) );
@@ -90 +90 @@
         *out << Verbose(3) << "Current atom is " << *Walker << "." << endl;
         if ((type == NULL) || (Walker->type == type)) {
-          distance = Walker->node->Distance(point);
+          distance = Walker->node->PeriodicDistance(point, (*MolWalker)->cell_size);
           *out << Verbose(4) << "Current distance is " << distance << "." << endl;
           outmap->insert ( pair<double, pair<atom *, const Vector*> >(distance, pair<atom *, const Vector*> (Walker, point) ) );
@@ -111 +111 @@
 {
   CorrelationToSurfaceMap *outmap = NULL;
-  double distance = 0.;
+  double distance = 0;
   class BoundaryTriangleSet *triangle = NULL;
   Vector centroid;
+  int ranges[NDIM] = {1, 1, 1};
+  int n[NDIM];
+  Vector periodicX;
+  Vector checkX;
 
   if ((Surface == NULL) || (LC == NULL) || (molecules->ListOfMolecules.empty())) {
@@ -122 +126 @@
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
     if ((*MolWalker)->ActiveFlag) {
+      const double * const FullMatrix = ReturnFullMatrixforSymmetric((*MolWalker)->cell_size);
+      const double * const FullInverseMatrix = InverseMatrix(FullMatrix);
       *out << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl;
       atom *Walker = (*MolWalker)->start;
@@ -128 +134 @@
         *out << Verbose(3) << "Current atom is " << *Walker << "." << endl;
         if ((type == NULL) || (Walker->type == type)) {
-          triangle = Surface->FindClosestTriangleToPoint(out, Walker->node, LC );
-          if (triangle != NULL) {
-            distance = DistanceToTrianglePlane(out, Walker->node, triangle);
-            outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(distance, pair<atom *, BoundaryTriangleSet*> (Walker, triangle) ) );
+          periodicX.CopyVector(Walker->node);
+          periodicX.MatrixMultiplication(FullInverseMatrix);  // x now in [0,1)^3
+          // go through every range in xyz and get distance
+          for (n[0]=-ranges[0]; n[0] <= ranges[0]; n[0]++)
+            for (n[1]=-ranges[1]; n[1] <= ranges[1]; n[1]++)
+              for (n[2]=-ranges[2]; n[2] <= ranges[2]; n[2]++) {
+                checkX.Init(n[0], n[1], n[2]);
+                checkX.AddVector(&periodicX);
+                checkX.MatrixMultiplication(FullMatrix);
+                triangle = Surface->FindClosestTriangleToPoint(out, &checkX, LC );
+                if (triangle != NULL) {
+                  distance = DistanceToTrianglePlane(out, &checkX, triangle);
+                  outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(distance, pair<atom *, BoundaryTriangleSet*> (Walker, triangle) ) );
+                }
           }
         }