--- trunk/src/brains/ForceManager.cpp	2008/05/27 16:39:06	1245
+++ trunk/src/brains/ForceManager.cpp	2010/06/17 14:58:49	1448
@@ -6,19 +6,10 @@
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the
  *    distribution.
@@ -37,6 +28,15 @@
  * arising out of the use of or inability to use software, even if the
  * University of Notre Dame has been advised of the possibility of
  * such damages.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
+ * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
+ * [4]  Vardeman & Gezelter, in progress (2009).                        
  */
  
 /**
@@ -50,12 +50,14 @@
 #include "brains/ForceManager.hpp"
 #include "primitives/Molecule.hpp"
 #include "UseTheForce/doForces_interface.h"
-#define __C
+#define __OPENMD_C
 #include "UseTheForce/DarkSide/fInteractionMap.h"
 #include "utils/simError.h"
 #include "primitives/Bond.hpp"
 #include "primitives/Bend.hpp"
-namespace oopse {
+#include "primitives/Torsion.hpp"
+#include "primitives/Inversion.hpp"
+namespace OpenMD {
 
   void ForceManager::calcForces(bool needPotential, bool needStress) {
     
@@ -109,14 +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; 
@@ -140,6 +145,7 @@ namespace oopse {
         RealType angle;
         bend->calcForce(angle);
         RealType currBendPot = bend->getPotential();          
+         
         bendPotential += bend->getPotential();
         std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
         if (i == bendDataSets.end()) {
@@ -180,15 +186,40 @@ namespace oopse {
                                    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);
+        }      
+      }      
     }
     
     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;
     
   }
   
@@ -325,4 +356,4 @@ namespace oopse {
     } 
   }
 
-} //end namespace oopse
+} //end namespace OpenMD