--- trunk/src/brains/ForceManager.cpp	2007/04/06 21:53:43	1126
+++ trunk/src/brains/ForceManager.cpp	2008/09/12 20:51:22	1292
@@ -50,11 +50,13 @@
 #include "brains/ForceManager.hpp"
 #include "primitives/Molecule.hpp"
 #include "UseTheForce/doForces_interface.h"
-#define __C
+#define __OOPSE_C
 #include "UseTheForce/DarkSide/fInteractionMap.h"
 #include "utils/simError.h"
+#include "primitives/Bond.hpp"
 #include "primitives/Bend.hpp"
-#include "primitives/Bend.hpp"
+#include "primitives/Torsion.hpp"
+#include "primitives/Inversion.hpp"
 namespace oopse {
 
   void ForceManager::calcForces(bool needPotential, bool needStress) {
@@ -83,18 +85,19 @@ namespace oopse {
     
     // forces are zeroed here, before any are accumulated.
     // NOTE: do not rezero the forces in Fortran.
-
+    
     for (mol = info_->beginMolecule(mi); mol != NULL; 
          mol = info_->nextMolecule(mi)) {
       for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
 	atom->zeroForcesAndTorques();
       }
-      
+          
       //change the positions of atoms which belong to the rigidbodies
       for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
            rb = mol->nextRigidBody(rbIter)) {
 	rb->zeroForcesAndTorques();
       }        
+          
     }
     
     // Zero out the stress tensor
@@ -108,14 +111,17 @@ namespace oopse {
     Bond* bond;
     Bend* bend;
     Torsion* torsion;
+    Inversion* inversion;
     SimInfo::MoleculeIterator mi;
     Molecule::RigidBodyIterator rbIter;
     Molecule::BondIterator bondIter;;
     Molecule::BendIterator  bendIter;
     Molecule::TorsionIterator  torsionIter;
+    Molecule::InversionIterator  inversionIter;
     RealType bondPotential = 0.0;
     RealType bendPotential = 0.0;
     RealType torsionPotential = 0.0;
+    RealType inversionPotential = 0.0;
 
     //calculate short range interactions    
     for (mol = info_->beginMolecule(mi); mol != NULL; 
@@ -175,6 +181,30 @@ namespace oopse {
           i->second.prev.potential = i->second.curr.potential;
           i->second.curr.angle = angle;
           i->second.curr.potential = currTorsionPot;
+          i->second.deltaV =  fabs(i->second.curr.potential -  
+                                   i->second.prev.potential);
+        }      
+      }      
+
+      for (inversion = mol->beginInversion(inversionIter); 
+	   inversion != NULL; 
+           inversion = mol->nextInversion(inversionIter)) {
+        RealType angle;
+        inversion->calcForce(angle);
+        RealType currInversionPot = inversion->getPotential();
+        inversionPotential += inversion->getPotential();
+        std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
+        if (i == inversionDataSets.end()) {
+          InversionDataSet dataSet;
+          dataSet.prev.angle = dataSet.curr.angle = angle;
+          dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
+          dataSet.deltaV = 0.0;
+          inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
+        }else {
+          i->second.prev.angle = i->second.curr.angle;
+          i->second.prev.potential = i->second.curr.potential;
+          i->second.curr.angle = angle;
+          i->second.curr.potential = currInversionPot;
           i->second.deltaV =  fabs(i->second.curr.potential -  
                                    i->second.prev.potential);
         }      
@@ -182,12 +212,13 @@ namespace oopse {
     }
     
     RealType  shortRangePotential = bondPotential + bendPotential + 
-      torsionPotential;    
+      torsionPotential +  inversionPotential;    
     Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
     curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
     curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
     curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
     curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
+    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
     
   }
   
@@ -201,6 +232,7 @@ namespace oopse {
     RealType* A;
     RealType* electroFrame;
     RealType* rc;
+    RealType* particlePot;
     
     //get current snapshot from SimInfo
     curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
@@ -212,6 +244,7 @@ namespace oopse {
     trq = config->getArrayPointer(DataStorage::dslTorque);
     A   = config->getArrayPointer(DataStorage::dslAmat);
     electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
+    particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
 
     //calculate the center of mass of cutoff group
     SimInfo::MoleculeIterator mi;
@@ -251,18 +284,19 @@ namespace oopse {
       longRangePotential[i]=0.0; //Initialize array
     }
     
-    doForceLoop( pos,
-		 rc,
-		 A,
-		 electroFrame,
-		 frc,
-		 trq,
-		 tau.getArrayPointer(),
-		 longRangePotential, 
-		 &passedCalcPot,
-		 &passedCalcStress,
-		 &isError );
-
+    doForceLoop(pos,
+                rc,
+                A,
+                electroFrame,
+                frc,
+                trq,
+	        tau.getArrayPointer(),
+                longRangePotential, 
+                particlePot,
+		&passedCalcPot,
+                &passedCalcStress,
+                &isError );
+    
     if( isError ){
       sprintf( painCave.errMsg,
 	       "Error returned from the fortran force calculation.\n" );