--- trunk/OOPSE/libmdtools/SimSetup.cpp	2004/06/03 20:02:25	1229
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2004/06/04 03:15:31	1234
@@ -11,8 +11,9 @@
 #include "simError.h"
 #include "RigidBody.hpp"
 #include "OOPSEMinimizer.hpp"
-//#include "ConstraintElement.hpp"
-//#include "ConstraintPair.hpp"
+#include "ConstraintElement.hpp"
+#include "ConstraintPair.hpp"
+#include "ConstraintManager.hpp"
 
 #ifdef IS_MPI
 #include "mpiBASS.h"
@@ -157,6 +158,10 @@ void SimSetup::createSim(void){
 
   initFortran();
 
+  //creat constraint manager
+  for(int i = 0; i < nInfo; i++)
+    info[i].consMan = new ConstraintManager(&info[i]);
+
   if (globals->haveMinimizer())
     // make minimizer
     makeMinimizer();
@@ -199,12 +204,13 @@ void SimSetup::makeMolecules(void){
   char* molName;
   char rbName[100];
 
-  //ConstraintPair* consPair; //constraint pair
-  //ConstraintElement* consElement1;  //first element of constraint pair
-  //ConstraintElement* consElement2;  //second element of constraint pair
-  //int whichRigidBody; 
-  //int consAtomIndex;  //index of constraint atom in rigid body's atom array
-  //vector<pair<int, int> > jointAtoms;
+  ConstraintPair* consPair; //constraint pair
+  ConstraintElement* consElement1;  //first element of constraint pair
+  ConstraintElement* consElement2;  //second element of constraint pair
+  int whichRigidBody; 
+  int consAtomIndex;  //index of constraint atom in rigid body's atom array
+  vector<pair<int, int> > jointAtoms;
+  double bondLength2;
   //init the forceField paramters
 
   the_ff->readParams();
@@ -599,37 +605,50 @@ void SimSetup::makeMolecules(void){
         info[k].integrableObjects.push_back(mySD);      
         molInfo.myIntegrableObjects.push_back(mySD);
       }
+         
+      // send the arrays off to the forceField for init.
+      
+      the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
+      the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
+      the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
+      the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
+                                 theTorsions);
 
 
-    /*
-
       //creat ConstraintPair.
-      molInfo.myConstraintPair.clear();
+      molInfo.myConstraintPairs.clear();
       
       for (j = 0; j < molInfo.nBonds; j++){
 
-        //if both atoms are in the same rigid body, just skip it
-        currentBond = comp_stamps[stampID]->getBond(j);
-        if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
-
-          tempI = currentBond->getA() + atomOffset;
-          if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
-            consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
-          else
-             consElement1 = new ConstraintAtom(info[k].atoms[tempI]);       
+        //if bond is constrained bond, add it into constraint pair
+        if(molInfo.myBonds[j]->is_constrained()){
 
-          tempJ =  currentBond->getB() + atomOffset;
-          if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
-            consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
-          else
-             consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);     
+          //if both atoms are in the same rigid body, just skip it
+          currentBond = comp_stamps[stampID]->getBond(j);
+          
+          if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
 
-          consPair = new DistanceConstraintPair(consElement1, consElement2);
-          molInfo.myConstraintPairs.push_back(consPair);
-        }
+            tempI = currentBond->getA() + atomOffset;
+            if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
+              consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
+            else
+               consElement1 = new ConstraintAtom(info[k].atoms[tempI]);       
+
+            tempJ =  currentBond->getB() + atomOffset;
+            if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
+              consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
+            else
+               consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);     
+
+            bondLength2 = molInfo.myBonds[j]->get_constraint()->get_dsqr();            
+            consPair = new DistanceConstraintPair(consElement1, consElement2, bondLength2);
+
+            molInfo.myConstraintPairs.push_back(consPair);
+          }
+        }//end if(molInfo.myBonds[j]->is_constrained())
       }  
       
-      //loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
+      //loop over rigid bodies, if two rigid bodies share same joint, creat a JointConstraintPair
       for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
         for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
           
@@ -645,15 +664,7 @@ void SimSetup::makeMolecules(void){
 
         }
       }
-      
-*/      
-      // send the arrays off to the forceField for init.
       
-      the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
-      the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
-      the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
-      the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
-                                 theTorsions);
 
       info[k].molecules[i].initialize(molInfo);