--- branches/development/src/nonbonded/InteractionManager.cpp	2011/06/08 16:05:07	1576
+++ branches/development/src/nonbonded/InteractionManager.cpp	2012/05/18 21:44:02	1710
@@ -36,7 +36,8 @@
  * [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).                        
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 #include "nonbonded/InteractionManager.hpp"
@@ -51,6 +52,7 @@ namespace OpenMD {
     gb_ = new GB();
     sticky_ = new Sticky();
     morse_ = new Morse();
+    repulsivePower_ = new RepulsivePower();
     eam_ = new EAM();
     sc_ = new SC();
     electrostatic_ = new Electrostatic();
@@ -67,8 +69,10 @@ namespace OpenMD {
     eam_->setForceField(forceField_);
     sc_->setForceField(forceField_);
     morse_->setForceField(forceField_);
+    electrostatic_->setSimInfo(info_);
     electrostatic_->setForceField(forceField_);
     maw_->setForceField(forceField_);
+    repulsivePower_->setForceField(forceField_);
 
     ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
     ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
@@ -81,14 +85,13 @@ namespace OpenMD {
          atype1 = atomTypes->nextType(i1)) {
       
       // add it to the map:
-      AtomTypeProperties atp = atype1->getATP();    
       
       pair<map<int,AtomType*>::iterator,bool> ret;    
-      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
+      ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) );
       if (ret.second == false) {
         sprintf( painCave.errMsg,
                  "InteractionManager already had a previous entry with ident %d\n",
-                 atp.ident);
+                 atype1->getIdent());
         painCave.severity = OPENMD_INFO;
         painCave.isFatal = 0;
         simError();                 
@@ -175,9 +178,33 @@ namespace OpenMD {
               if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
             }
             interactions_[key].insert(morse_);
+            vdwExplicit = true;
+          }
+
+          if (nbiType->isRepulsivePower()) {
+            if (vdwExplicit) {
+              sprintf( painCave.errMsg,
+                       "InteractionManager::initialize found more than one "
+                       "explicit \n"
+                       "\tvan der Waals interaction for atom types %s - %s\n",
+                       atype1->getName().c_str(), atype2->getName().c_str());
+              painCave.severity = OPENMD_ERROR;
+              painCave.isFatal = 1;
+              simError();
+            }
+            // We found an explicit RepulsivePower interaction.  
+            // override all other vdw entries for this pair of atom types:
+            set<NonBondedInteraction*>::iterator it;
+            for (it = interactions_[key].begin(); 
+                 it != interactions_[key].end(); ++it) {
+              InteractionFamily ifam = (*it)->getFamily();
+              if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
+            }
+            interactions_[key].insert(repulsivePower_);
             vdwExplicit = true;
           }
           
+          
           if (nbiType->isEAM()) {
             // We found an explicit EAM interaction.  
             // override all other metallic entries for this pair of atom types:
@@ -241,24 +268,26 @@ namespace OpenMD {
     }
     
     
-    // make sure every pair of atom types in this simulation has a
-    // non-bonded interaction:
+    // Make sure every pair of atom types in this simulation has a
+    // non-bonded interaction.  If not, just inform the user.
 
     set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
     set<AtomType*>::iterator it, jt;
+
     for (it = simTypes.begin(); it != simTypes.end(); ++it) {
       atype1 = (*it);
-      for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) {
+      for (jt = it; jt != simTypes.end(); ++jt) {
         atype2 = (*jt);
         key = make_pair(atype1, atype2);
         
         if (interactions_[key].size() == 0) {
           sprintf( painCave.errMsg,
-                   "InteractionManager unable to find an appropriate non-bonded\n"
-                   "\tinteraction for atom types %s - %s\n",
+                   "InteractionManager could not find a matching non-bonded\n"
+                   "\tinteraction for atom types %s - %s\n"
+                   "\tProceeding without this interaction.\n",
                    atype1->getName().c_str(), atype2->getName().c_str());
           painCave.severity = OPENMD_INFO;
-          painCave.isFatal = 1;
+          painCave.isFatal = 0;
           simError();
         }
       }
@@ -266,11 +295,24 @@ namespace OpenMD {
 
     initialized_ = true;
   }
+
+  void InteractionManager::setCutoffRadius(RealType rcut) {
+    
+    electrostatic_->setCutoffRadius(rcut);
+    eam_->setCutoffRadius(rcut);
+  }
+
+  void InteractionManager::setSwitchingRadius(RealType rswitch) {
+    electrostatic_->setSwitchingRadius(rswitch);
+  }
   
   void InteractionManager::doPrePair(InteractionData idat){
     
     if (!initialized_) initialize();
 	 
+    // excluded interaction, so just return
+    if (idat.excluded) return;
+
     set<NonBondedInteraction*>::iterator it;
 
     for (it = interactions_[ idat.atypes ].begin(); 
@@ -302,26 +344,17 @@ namespace OpenMD {
   void InteractionManager::doPair(InteractionData idat){
     
     if (!initialized_) initialize();
-   
+
     set<NonBondedInteraction*>::iterator it;
 
     for (it = interactions_[ idat.atypes ].begin(); 
-         it != interactions_[ idat.atypes ].end(); ++it)
-      (*it)->calcForce(idat);
-    
-    return;    
-  }
+         it != interactions_[ idat.atypes ].end(); ++it) {
 
-  void InteractionManager::doSkipCorrection(InteractionData idat){
+      // electrostatics still has to worry about indirect
+      // contributions from excluded pairs of atoms:
 
-    if (!initialized_) initialize();  
-    
-    set<NonBondedInteraction*>::iterator it;
-
-    for (it = interactions_[ idat.atypes ].begin(); 
-         it != interactions_[ idat.atypes ].end(); ++it){
-      if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
-        dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat);
+      if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
+        (*it)->calcForce(idat);
       }
     }