--- branches/development/src/flucq/FluctuatingChargePropagator.cpp	2012/07/05 17:08:25	1766
+++ trunk/src/flucq/FluctuatingChargePropagator.cpp	2015/03/07 21:41:51	2071
@@ -35,7 +35,7 @@
  *                                                                      
  * [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).          
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
  * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
  * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
@@ -56,11 +56,13 @@ namespace OpenMD {
 namespace OpenMD {
 
   FluctuatingChargePropagator::FluctuatingChargePropagator(SimInfo* info) : 
-    info_(info), hasFlucQ_(false), forceMan_(NULL) {
+    info_(info), forceMan_(NULL), hasFlucQ_(false), initialized_(false) {
     
     Globals* simParams = info_->getSimParams();
-    fqParams_ = simParams->getFluctuatingChargeParameters();
+    fqParams_ = simParams->getFluctuatingChargeParameters();    
+  }
 
+  FluctuatingChargePropagator::~FluctuatingChargePropagator() {
   }
 
   void FluctuatingChargePropagator::setForceManager(ForceManager* forceMan) {
@@ -68,46 +70,57 @@ namespace OpenMD {
   }
 
   void FluctuatingChargePropagator::initialize() {
-
     if (info_->usesFluctuatingCharges()) {
       if (info_->getNFluctuatingCharges() > 0) {
         hasFlucQ_ = true;
-	fqConstraints_ = new FluctuatingChargeConstraints(info_);        
+	fqConstraints_ = new FluctuatingChargeConstraints(info_);
+	fqConstraints_->setConstrainRegions(fqParams_->getConstrainRegions());
       }
     }
-
-    if (!hasFlucQ_) return;
-
-    SimInfo::MoleculeIterator i;
-    Molecule::FluctuatingChargeIterator  j;
-    Molecule* mol;
-    Atom* atom;
     
-    for (mol = info_->beginMolecule(i); mol != NULL; 
-         mol = info_->nextMolecule(i)) {
-      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
-           atom = mol->nextFluctuatingCharge(j)) {
-        atom->setFlucQPos(0.0);
-        atom->setFlucQVel(0.0);
-      }
+    if (!hasFlucQ_) {
+      initialized_ = true;
+      return;
     }
+
+    // SimInfo::MoleculeIterator i;
+    // Molecule::FluctuatingChargeIterator  j;
+    // Molecule* mol;
+    // Atom* atom;
+    //  
+    // For single-minima flucq, this ensures a net neutral system, but
+    // for multiple minima, this is no longer the right thing to do:
+    //
+    // for (mol = info_->beginMolecule(i); mol != NULL; 
+    //      mol = info_->nextMolecule(i)) {
+    //   for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
+    //        atom = mol->nextFluctuatingCharge(j)) {
+    //     atom->setFlucQPos(0.0);
+    //     atom->setFlucQVel(0.0);
+    //   }
+    // }
     
-    fqConstraints_ = new FluctuatingChargeConstraints(info_);
-    FluctuatingChargeObjectiveFunction flucQobjf(info_, forceMan_, fqConstraints_);    
+    FluctuatingChargeObjectiveFunction flucQobjf(info_, forceMan_, 
+                                                 fqConstraints_);
+
     DynamicVector<RealType> initCoords = flucQobjf.setInitialCoords();
-    Problem problem(flucQobjf, *(new NoConstraint()), *(new NoStatus()), initCoords);
+    Problem problem(flucQobjf, *(new NoConstraint()), *(new NoStatus()), 
+                    initCoords);
+
     EndCriteria endCriteria(1000, 100, 1e-5, 1e-5, 1e-5);       
+
     OptimizationMethod* minim = OptimizationFactory::getInstance()->createOptimization("SD", info_);
 
-    DumpStatusFunction dsf(info_);  // we want a dump file written every iteration
-
+    DumpStatusFunction dsf(info_);  // we want a dump file written
+                                    // every iteration
     minim->minimize(problem, endCriteria);
-
+    cerr << "back from minim\n";
+    initialized_ = true;
   }
 
   void FluctuatingChargePropagator::applyConstraints() {
+    if (!initialized_) initialize();
     if (!hasFlucQ_) return;
-
     fqConstraints_->applyConstraints();
   }
 }