--- trunk/src/brains/ForceManager.cpp	2005/11/16 23:10:02	749
+++ trunk/src/brains/ForceManager.cpp	2006/05/17 21:51:42	963
@@ -57,6 +57,7 @@ namespace oopse {
 #include "primitives/Bend.hpp"
 namespace oopse {
 
+/*
   struct BendOrderStruct {
     Bend* bend;
     BendDataSet dataSet;
@@ -73,7 +74,7 @@ namespace oopse {
   bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
     return t1.dataSet.deltaV < t2.dataSet.deltaV;
   }
-  
+  */
   void ForceManager::calcForces(bool needPotential, bool needStress) {
 
     if (!info_->isFortranInitialized()) {
@@ -88,6 +89,7 @@ namespace oopse {
 
     postCalculation();
 
+/*
     std::vector<BendOrderStruct> bendOrderStruct;
     for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
         BendOrderStruct tmp;
@@ -106,19 +108,17 @@ namespace oopse {
     
     std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
     std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
-    std::cout << "bend" << std::endl;
     for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
         Bend* bend = k->bend;
-        std::cout << "atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
+        std::cout << "Bend: atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
         std::cout << "deltaV=" << k->dataSet.deltaV << ",p_theta=" << k->dataSet.prev.angle <<",p_pot=" << k->dataSet.prev.potential<< ",c_theta=" << k->dataSet.curr.angle << ", c_pot = " << k->dataSet.curr.potential <<std::endl;
     }
-    std::cout << "torsio" << std::endl;
     for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
         Torsion* torsion = l->torsion;
-        std::cout << "atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
+        std::cout << "Torsion: atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
         std::cout << "deltaV=" << l->dataSet.deltaV << ",p_theta=" << l->dataSet.prev.angle <<",p_pot=" << l->dataSet.prev.potential<< ",c_theta=" << l->dataSet.curr.angle << ", c_pot = " << l->dataSet.curr.potential <<std::endl;
     }
-    
+   */ 
   }
 
   void ForceManager::preCalculation() {
@@ -155,9 +155,9 @@ namespace oopse {
     Molecule::BondIterator bondIter;;
     Molecule::BendIterator  bendIter;
     Molecule::TorsionIterator  torsionIter;
-    double bondPotential = 0.0;
-    double bendPotential = 0.0;
-    double torsionPotential = 0.0;
+    RealType bondPotential = 0.0;
+    RealType bendPotential = 0.0;
+    RealType torsionPotential = 0.0;
 
     //calculate short range interactions    
     for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
@@ -172,12 +172,12 @@ namespace oopse {
         bondPotential += bond->getPotential();
       }
 
-      //int i =0;
+
       for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
-          //std::cout << i++ << "\t";
-          double angle;
+
+          RealType angle;
 	    bend->calcForce(angle);
-          double currBendPot = bend->getPotential();          
+          RealType currBendPot = bend->getPotential();          
   	    bendPotential += bend->getPotential();
           std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
           if (i == bendDataSets.end()) {
@@ -196,9 +196,9 @@ namespace oopse {
       }
 
       for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
-        double angle;
+        RealType angle;
   	  torsion->calcForce(angle);
-        double currTorsionPot = torsion->getPotential();
+        RealType currTorsionPot = torsion->getPotential();
 	  torsionPotential += torsion->getPotential();
           std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
           if (i == torsionDataSets.end()) {
@@ -218,7 +218,7 @@ namespace oopse {
 
     }
     
-    double  shortRangePotential = bondPotential + bendPotential + torsionPotential;    
+    RealType  shortRangePotential = bondPotential + bendPotential + torsionPotential;    
     Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
     curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
     curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
@@ -230,12 +230,12 @@ namespace oopse {
   void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
     Snapshot* curSnapshot;
     DataStorage* config;
-    double* frc;
-    double* pos;
-    double* trq;
-    double* A;
-    double* electroFrame;
-    double* rc;
+    RealType* frc;
+    RealType* pos;
+    RealType* trq;
+    RealType* A;
+    RealType* electroFrame;
+    RealType* rc;
     
     //get current snapshot from SimInfo
     curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
@@ -272,8 +272,8 @@ namespace oopse {
     }
   
     //initialize data before passing to fortran
-    double longRangePotential[LR_POT_TYPES];
-    double lrPot = 0.0;
+    RealType longRangePotential[LR_POT_TYPES];
+    RealType lrPot = 0.0;
     
     Mat3x3d tau;
     short int passedCalcPot = needPotential;