--- branches/development/src/flucq/FluctuatingChargePropagator.cpp	2012/06/13 14:45:59	1754
+++ trunk/src/flucq/FluctuatingChargePropagator.cpp	2013/07/31 19:30:46	1920
@@ -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).
  */
@@ -48,8 +48,6 @@
 #include "optimization/StatusFunction.hpp"
 #include "optimization/OptimizationFactory.hpp"
 
-
-
 #ifdef IS_MPI
 #include <mpi.h>
 #endif
@@ -57,26 +55,35 @@ namespace OpenMD {
 using namespace QuantLib;
 namespace OpenMD {
 
-  FluctuatingChargePropagator::FluctuatingChargePropagator(SimInfo* info, 
-                                                           ForceManager* fm) : 
-    info_(info), forceMan_(fm), hasFlucQ_(false) {
+  FluctuatingChargePropagator::FluctuatingChargePropagator(SimInfo* info) : 
+    info_(info), hasFlucQ_(false), forceMan_(NULL), initialized_(false) {
     
+    Globals* simParams = info_->getSimParams();
+    fqParams_ = simParams->getFluctuatingChargeParameters();    
+  }
+
+  FluctuatingChargePropagator::~FluctuatingChargePropagator() {
+    if (fqConstraints_ != NULL) delete fqConstraints_;
+  }
+
+  void FluctuatingChargePropagator::setForceManager(ForceManager* forceMan) {
+    forceMan_ = forceMan;
+  }
+
+  void FluctuatingChargePropagator::initialize() {
     if (info_->usesFluctuatingCharges()) {
       if (info_->getNFluctuatingCharges() > 0) {
-        
         hasFlucQ_ = true;
-        Globals* simParams = info_->getSimParams();
-        fqParams_ = simParams->getFluctuatingChargeParameters();
 	fqConstraints_ = new FluctuatingChargeConstraints(info_);
-        
+	fqConstraints_->setConstrainRegions(fqParams_->getConstrainRegions());
       }
     }
-  }
+    
+    if (!hasFlucQ_) {
+      initialized_ = true;
+      return;
+    }
 
-  void FluctuatingChargePropagator::initialize() {
-
-    if (!hasFlucQ_) return;
-
     SimInfo::MoleculeIterator i;
     Molecule::FluctuatingChargeIterator  j;
     Molecule* mol;
@@ -90,33 +97,27 @@ namespace OpenMD {
         atom->setFlucQVel(0.0);
       }
     }
-
-    std::cerr << "doing a minimization\n";
     
-    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 << "Finished minimization\n";
-    for (mol = info_->beginMolecule(i); mol != NULL; 
-         mol = info_->nextMolecule(i)) {
-      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
-           atom = mol->nextFluctuatingCharge(j)) {
-	cerr << atom->getType() << "\tQ Pos: " << atom->getFlucQPos() << "\n";
-      }
-    }
+    initialized_ = true;
   }
 
-
   void FluctuatingChargePropagator::applyConstraints() {
+    if (!initialized_) initialize();
     if (!hasFlucQ_) return;
-
     fqConstraints_->applyConstraints();
   }
 }