--- branches/development/src/flucq/FluctuatingChargePropagator.cpp	2012/05/31 12:25:30	1731
+++ trunk/src/flucq/FluctuatingChargePropagator.cpp	2014/04/14 18:32:51	1981
@@ -35,73 +35,92 @@
  *                                                                      
  * [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).
  */
  
-#include "FluctuatingChargePropagator.hpp"
-#include "primitives/Molecule.hpp"
-#include "utils/simError.h"
-#include "utils/PhysicalConstants.hpp"
+#include "flucq/FluctuatingChargePropagator.hpp"
+#include "flucq/FluctuatingChargeObjectiveFunction.hpp"
+#include "optimization/Constraint.hpp"
+#include "optimization/Problem.hpp"
+#include "optimization/EndCriteria.hpp"
+#include "optimization/StatusFunction.hpp"
+#include "optimization/OptimizationFactory.hpp"
+
 #ifdef IS_MPI
 #include <mpi.h>
 #endif
 
+using namespace QuantLib;
 namespace OpenMD {
 
-  void FluctuatingChargePropagator::applyConstraints() {
-    if (!hasFlucQ_) return;
+  FluctuatingChargePropagator::FluctuatingChargePropagator(SimInfo* info) : 
+    info_(info), hasFlucQ_(false), forceMan_(NULL), initialized_(false) {
+    
+    Globals* simParams = info_->getSimParams();
+    fqParams_ = simParams->getFluctuatingChargeParameters();    
+  }
 
+  FluctuatingChargePropagator::~FluctuatingChargePropagator() {
+  }
+
+  void FluctuatingChargePropagator::setForceManager(ForceManager* forceMan) {
+    forceMan_ = forceMan;
+  }
+
+  void FluctuatingChargePropagator::initialize() {
+    if (info_->usesFluctuatingCharges()) {
+      if (info_->getNFluctuatingCharges() > 0) {
+        hasFlucQ_ = true;
+	fqConstraints_ = new FluctuatingChargeConstraints(info_);
+	fqConstraints_->setConstrainRegions(fqParams_->getConstrainRegions());
+      }
+    }
+    
+    if (!hasFlucQ_) {
+      initialized_ = true;
+      return;
+    }
+
     SimInfo::MoleculeIterator i;
     Molecule::FluctuatingChargeIterator  j;
     Molecule* mol;
     Atom* atom;
     
-    RealType totalFrc, totalMolFrc, constrainedFrc;
+    // 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);
+    //   }
+    // }
+    
+    FluctuatingChargeObjectiveFunction flucQobjf(info_, forceMan_, 
+                                                 fqConstraints_);
 
-    // accumulate the total system fluctuating charge forces
-    totalFrc = 0.0;
+    DynamicVector<RealType> initCoords = flucQobjf.setInitialCoords();
+    Problem problem(flucQobjf, *(new NoConstraint()), *(new NoStatus()), 
+                    initCoords);
 
-    for (mol = info_->beginMolecule(i); mol != NULL; 
-         mol = info_->nextMolecule(i)) {
+    EndCriteria endCriteria(1000, 100, 1e-5, 1e-5, 1e-5);       
 
-      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
-           atom = mol->nextFluctuatingCharge(j)) {
-        totalFrc += atom->getFlucQFrc();
-      }
+    OptimizationMethod* minim = OptimizationFactory::getInstance()->createOptimization("SD", info_);
 
-    }
+    DumpStatusFunction dsf(info_);  // we want a dump file written
+                                    // every iteration
+    minim->minimize(problem, endCriteria);
+    cerr << "back from minim\n";
+    initialized_ = true;
+  }
 
-#ifdef IS_MPI
-    // in parallel, we need to add up the contributions from all
-    // processors:
-    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalFrc, 1, MPI::REALTYPE, 
-                              MPI::SUM);
-#endif
- 
-    // divide by the total number of fluctuating charges:
-    totalFrc /= info_->getNFluctuatingCharges();
-
-    for (mol = info_->beginMolecule(i); mol != NULL; 
-         mol = info_->nextMolecule(i)) {     
-      
-      totalMolFrc = 0.0;
-
-      // molecular constraints can be done with a second loop.
-      if (mol->constrainTotalCharge()) {
-        for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
-             atom = mol->nextFluctuatingCharge(j)) {
-          totalMolFrc += atom->getFlucQFrc();
-        }
-        totalMolFrc /= mol->getNFluctuatingCharges();
-      }
-
-      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
-           atom = mol->nextFluctuatingCharge(j)) {
-        constrainedFrc = atom->getFlucQFrc() - totalFrc - totalMolFrc;
-        atom->setFlucQFrc(constrainedFrc);
-      }      
-    }
+  void FluctuatingChargePropagator::applyConstraints() {
+    if (!initialized_) initialize();
+    if (!hasFlucQ_) return;
+    fqConstraints_->applyConstraints();
   }
 }