--- trunk/src/applications/hydrodynamics/RoughShell.cpp	2006/03/15 15:51:44	898
+++ trunk/src/applications/hydrodynamics/RoughShell.cpp	2006/03/29 18:09:26	921
@@ -40,16 +40,17 @@
  */
 
 #include "applications/hydrodynamics/RoughShell.hpp"
-
+#include "applications/hydrodynamics/ShapeBuilder.hpp"
+#include "brains/SimInfo.hpp"
 namespace oopse {
 
-RoughShell::RoughShell(StuntDouble* sd, const DynamicProperty& extraParams) : HydrodynamicsModel(sd, extraParams), sdShape_(sd){
-    DynamicProperty::const_iterator iter = extraParams.find("Sigma");
-    if (iter != extraParams.end()) {
-        boost::any param = iter->second;
-        sigma_ = boost::any_cast<double>(param);
+RoughShell::RoughShell(StuntDouble* sd, SimInfo* info) : ApproximationModel(sd, info){
+    shape_=ShapeBuilder::createShape(sd);
+    Globals* simParams = info->getSimParams();
+    if (simParams->haveBeadSize()) {
+        sigma_ = simParams->getBeadSize();
     }else {
-        std::cout << "RoughShell Model Error\n" ;
+
     }
 }
 
@@ -75,9 +76,11 @@ bool RoughShell::createBeads(std::vector<BeadParam>& b
 
 };
 bool RoughShell::createBeads(std::vector<BeadParam>& beads) {
-    std::pair<Vector3d, Vector3d> boxBoundary = sdShape_.getBox();
-    double len = boxBoundary.second[0] - boxBoundary.first[0];
-    int numLattices = static_cast<int>(len/sigma_) + 1;
+    std::pair<Vector3d, Vector3d> boxBoundary = shape_->getBox();
+    double firstMin = std::min(std::min(boxBoundary.first[0], boxBoundary.first[1]), boxBoundary.first[2]);
+    double secondMax = std::max(std::max(boxBoundary.second[0], boxBoundary.second[1]), boxBoundary.second[2]);
+    double len = secondMax - firstMin;
+    int numLattices = static_cast<int>(len/sigma_) + 2;
     Grid3D<BeadLattice>  grid(numLattices, numLattices, numLattices);
 
     //fill beads
@@ -85,9 +88,9 @@ bool RoughShell::createBeads(std::vector<BeadParam>& b
         for (int j = 0; j < numLattices; ++j) {
             for (int k = 0; k < numLattices; ++k) {
                 BeadLattice& currentBead = grid(i, j, k);
-                currentBead.origin = Vector3d(i*sigma_ + boxBoundary.first[0], j *sigma_ + boxBoundary.first[1], k*sigma_+ boxBoundary.first[2]);
+                currentBead.origin = Vector3d((i-1)*sigma_ + boxBoundary.first[0], (j-1) *sigma_ + boxBoundary.first[1], (k-1)*sigma_+ boxBoundary.first[2]);
                 currentBead.radius = sigma_;
-                currentBead.interior = sdShape_.isInterior(grid(i, j, k).origin);                
+                currentBead.interior = shape_->isInterior(grid(i, j, k).origin);                
             }
         }
     }
@@ -99,17 +102,26 @@ bool RoughShell::createBeads(std::vector<BeadParam>& b
                  std::vector<BeadLattice> neighborCells = grid.getAllNeighbors(i, j, k);
                  //if one of its neighbor cells is exterior, current cell is on the surface
 
-                 std::vector<BeadLattice>::iterator ei = std::find_if(neighborCells.begin(), neighborCells.end(), ExteriorFunctor());                
-                 std::vector<BeadLattice>::iterator ii = std::find_if(neighborCells.begin(), neighborCells.end(), InteriorFunctor());                
-                 
-                  if (ei != neighborCells.end() && ii != neighborCells.end()) {
+                 if (grid(i, j, k).interior){
+
+                    bool allNeighBorIsInterior = true;
+                    for (std::vector<BeadLattice>::iterator l = neighborCells.begin(); l != neighborCells.end(); ++l) {
+                        if (!l->interior) {
+                            allNeighBorIsInterior = false;
+                            break;
+                        }
+                    }
+
+                    if (allNeighBorIsInterior)
+                        continue;
+
                       BeadParam surfaceBead;
-                      surfaceBead.atomName = "Bead";
+                      surfaceBead.atomName = "H";
                       surfaceBead.pos = grid(i, j, k).origin;
                       surfaceBead.radius = grid(i, j, k).radius;
-                      beads.push_back(surfaceBead);
-                  }
+                      beads.push_back(surfaceBead);                    
 
+                 }
             }
         }
     }