--- trunk/OOPSE/libmdtools/AtomVisitor.cpp	2004/04/19 17:44:48	1119
+++ trunk/OOPSE/libmdtools/AtomVisitor.cpp	2004/04/22 03:29:30	1129
@@ -44,6 +44,7 @@ void SSDAtomVisitor::visit(DirectionalAtom* datom){
   double ox[3] = {0.0, 0.0, -0.0654};
   double u[3] = {0, 0, 1};
   double rotMatrix[3][3];
+  double rotTrans[3][3];
   AtomInfo* atomInfo;
   double pos[3];
   double vel[3];
@@ -54,7 +55,7 @@ void SSDAtomVisitor::visit(DirectionalAtom* datom){
   bool haveAtomData;
   
   //if atom is not SSD atom, just skip it
-  if(!strcmp(datom->getType(), "SSD"))
+  if(strcmp(datom->getType(), "SSD"))
     return;
 
   data = datom->getProperty("ATOMDATA");
@@ -78,9 +79,12 @@ void SSDAtomVisitor::visit(DirectionalAtom* datom){
   datom->getPos(pos);
   datom->getQ(q);
   datom->getA(rotMatrix);
+
+  // We need A^T to convert from body-fixed to space-fixed:
+  transposeMat3(rotMatrix, rotTrans);
   
   //center of mass of the water molecule
-  matVecMul3(rotMatrix, u, newVec);
+  matVecMul3(rotTrans, u, newVec);
   atomInfo = new AtomInfo;
   atomInfo->AtomType = "X";
   atomInfo->pos[0] = pos[0];
@@ -93,7 +97,7 @@ void SSDAtomVisitor::visit(DirectionalAtom* datom){
   atomData->addAtomInfo(atomInfo);
 
   //oxygen
-  matVecMul3(rotMatrix, ox, newVec);
+  matVecMul3(rotTrans, ox, newVec);
   atomInfo = new AtomInfo;
   atomInfo->AtomType = "O";
   atomInfo->pos[0] = pos[0] + newVec[0];
@@ -106,7 +110,7 @@ void SSDAtomVisitor::visit(DirectionalAtom* datom){
 
 
   //hydrogen1
-    matVecMul3(rotMatrix, h1, newVec);
+    matVecMul3(rotTrans, h1, newVec);
   atomInfo = new AtomInfo;
   atomInfo->AtomType = "H";
   atomInfo->pos[0] = pos[0] + newVec[0];
@@ -118,7 +122,7 @@ void SSDAtomVisitor::visit(DirectionalAtom* datom){
   atomData->addAtomInfo(atomInfo);
 
   //hydrogen2
-  matVecMul3(rotMatrix, h2, newVec);
+  matVecMul3(rotTrans, h2, newVec);
   atomInfo = new AtomInfo;
   atomInfo->AtomType = "H";
   atomInfo->pos[0] = pos[0] + newVec[0];
@@ -140,6 +144,27 @@ void SSDAtomVisitor::visit(DirectionalAtom* datom){
 
 }
 
+const string SSDAtomVisitor::toString(){
+  char buffer[65535];
+  string result;
+  
+  sprintf(buffer ,"------------------------------------------------------------------\n");
+  result += buffer;
+
+  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
+  result += buffer;
+
+  sprintf(buffer , "Visitor Description: Convert SSD into 4 differnet atoms\n");
+  result += buffer;
+
+  sprintf(buffer ,"------------------------------------------------------------------\n");
+  result += buffer;
+
+  return result;
+}
+
+//----------------------------------------------------------------------------//
+
 void DefaultAtomVisitor::visit(Atom* atom){
   AtomData* atomData;
   AtomInfo* atomInfo;
@@ -199,4 +224,23 @@ void DefaultAtomVisitor::visit(DirectionalAtom* datom)
 
   setVisited(datom);
 }
-    
+
+
+const string DefaultAtomVisitor::toString(){
+  char buffer[65535];
+  string result;
+  
+  sprintf(buffer ,"------------------------------------------------------------------\n");
+  result += buffer;
+
+  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
+  result += buffer;
+
+  sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n");
+  result += buffer;
+
+  sprintf(buffer ,"------------------------------------------------------------------\n");
+  result += buffer;
+
+  return result;
+}