--- branches/development/src/parallel/ForceDecomposition.cpp	2011/01/14 22:31:31	1539
+++ branches/development/src/parallel/ForceDecomposition.cpp	2011/03/18 19:31:52	1544
@@ -39,28 +39,71 @@
  * [4]  Vardeman & Gezelter, in progress (2009).                        
  */
 #include "parallel/ForceDecomposition.hpp"
-#include "parallel/Communicator.hpp"
 #include "math/SquareMatrix3.hpp"
+#include "nonbonded/NonBondedInteraction.hpp"
+#include "brains/SnapshotManager.hpp"
 
+using namespace std;
 namespace OpenMD {
 
+  /**
+   * distributeInitialData is essentially a copy of the older fortran 
+   * SimulationSetup
+   */
+  
   void ForceDecomposition::distributeInitialData() {
-#ifdef IS_MPI
+#ifdef IS_MPI    
+    Snapshot* snap = sman_->getCurrentSnapshot();
+    int nLocal = snap->getNumberOfAtoms();
+    int nGroups = snap->getNumberOfCutoffGroups();
 
-    int nAtoms;
-    int nGroups;
+    AtomCommIntI = new Communicator<Row,int>(nLocal);
+    AtomCommRealI = new Communicator<Row,RealType>(nLocal);
+    AtomCommVectorI = new Communicator<Row,Vector3d>(nLocal);
+    AtomCommMatrixI = new Communicator<Row,Mat3x3d>(nLocal);
 
-    AtomCommRealI = new Comm<I,RealType>(nAtoms);
-    AtomCommVectorI = new Comm<I,Vector3d>(nAtoms);
-    AtomCommMatrixI = new Comm<I,Mat3x3d>(nAtoms);
+    AtomCommIntJ = new Communicator<Column,int>(nLocal);
+    AtomCommRealJ = new Communicator<Column,RealType>(nLocal);
+    AtomCommVectorJ = new Communicator<Column,Vector3d>(nLocal);
+    AtomCommMatrixJ = new Communicator<Column,Mat3x3d>(nLocal);
 
-    AtomCommRealJ = new Comm<J,RealType>(nAtoms);
-    AtomCommVectorJ = new Comm<J,Vector3d>(nAtoms);
-    AtomCommMatrixJ = new Comm<J,Mat3x3d>(nAtoms);
+    cgCommIntI = new Communicator<Row,int>(nGroups);
+    cgCommVectorI = new Communicator<Row,Vector3d>(nGroups);
+    cgCommIntJ = new Communicator<Column,int>(nGroups);
+    cgCommVectorJ = new Communicator<Column,Vector3d>(nGroups);
 
-    cgCommVectorI = new Comm<I,Vector3d>(nGroups);
-    cgCommVectorJ = new Comm<J,Vector3d>(nGroups);
-    // more to come
+    int nAtomsInRow = AtomCommIntI->getSize();
+    int nAtomsInCol = AtomCommIntJ->getSize();
+    int nGroupsInRow = cgCommIntI->getSize();
+    int nGroupsInCol = cgCommIntJ->getSize();
+
+    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES, 
+                                      vector<RealType> (nAtomsInRow, 0.0));
+    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
+                                      vector<RealType> (nAtomsInCol, 0.0));
+    
+    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
+
+    // gather the information for atomtype IDs (atids):
+    AtomCommIntI->gather(info_->getIdentArray(), identsRow);
+    AtomCommIntJ->gather(info_->getIdentArray(), identsCol);
+
+    AtomLocalToGlobal = info_->getLocalToGlobalAtomIndex();
+    AtomCommIntI->gather(AtomLocalToGlobal, AtomRowToGlobal);
+    AtomCommIntJ->gather(AtomLocalToGlobal, AtomColToGlobal);
+
+    cgLocalToGlobal = info_->getLocalToGlobalCutoffGroupIndex();
+    cgCommIntI->gather(cgLocalToGlobal, cgRowToGlobal);
+    cgCommIntJ->gather(cgLocalToGlobal, cgColToGlobal);
+
+      
+      
+
+
+
+    // still need:
+    // topoDist
+    // exclude
 #endif
   }
     
@@ -69,33 +112,33 @@ namespace OpenMD {
   void ForceDecomposition::distributeData()  {
 #ifdef IS_MPI
     Snapshot* snap = sman_->getCurrentSnapshot();
-
+    
     // gather up the atomic positions
     AtomCommVectorI->gather(snap->atomData.position, 
                             snap->atomIData.position);
     AtomCommVectorJ->gather(snap->atomData.position, 
-                           snap->atomJData.position);
+                            snap->atomJData.position);
     
     // gather up the cutoff group positions
     cgCommVectorI->gather(snap->cgData.position, 
-                         snap->cgIData.position);
+                          snap->cgIData.position);
     cgCommVectorJ->gather(snap->cgData.position, 
-                         snap->cgJData.position);
+                          snap->cgJData.position);
     
     // if needed, gather the atomic rotation matrices
     if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
       AtomCommMatrixI->gather(snap->atomData.aMat, 
-                             snap->atomIData.aMat);
+                              snap->atomIData.aMat);
       AtomCommMatrixJ->gather(snap->atomData.aMat, 
-                             snap->atomJData.aMat);
+                              snap->atomJData.aMat);
     }
     
     // if needed, gather the atomic eletrostatic frames
     if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
       AtomCommMatrixI->gather(snap->atomData.electroFrame, 
-                             snap->atomIData.electroFrame);
+                              snap->atomIData.electroFrame);
       AtomCommMatrixJ->gather(snap->atomData.electroFrame, 
-                             snap->atomJData.electroFrame);
+                              snap->atomJData.electroFrame);
     }
 #endif      
   }
@@ -103,14 +146,14 @@ namespace OpenMD {
   void ForceDecomposition::collectIntermediateData() {
 #ifdef IS_MPI
     Snapshot* snap = sman_->getCurrentSnapshot();
-    // gather up the atomic positions
     
     if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
+
       AtomCommRealI->scatter(snap->atomIData.density, 
-                            snap->atomData.density);
-      std::vector<RealType> rho_tmp;
-      int n = snap->getNumberOfAtoms();
-      rho_tmp.reserve( n );
+                             snap->atomData.density);
+
+      int n = snap->atomData.density.size();
+      std::vector<RealType> rho_tmp(n, 0.0);
       AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
       for (int i = 0; i < n; i++)
         snap->atomData.density[i] += rho_tmp[i];
@@ -123,16 +166,16 @@ namespace OpenMD {
     Snapshot* snap = sman_->getCurrentSnapshot();
     if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
       AtomCommRealI->gather(snap->atomData.functional, 
-                           snap->atomIData.functional);
+                            snap->atomIData.functional);
       AtomCommRealJ->gather(snap->atomData.functional, 
-                           snap->atomJData.functional);
+                            snap->atomJData.functional);
     }
     
     if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
       AtomCommRealI->gather(snap->atomData.functionalDerivative, 
-                           snap->atomIData.functionalDerivative);
+                            snap->atomIData.functionalDerivative);
       AtomCommRealJ->gather(snap->atomData.functionalDerivative, 
-                           snap->atomJData.functionalDerivative);
+                            snap->atomJData.functionalDerivative);
     }
 #endif
   }
@@ -140,6 +183,49 @@ namespace OpenMD {
   
   void ForceDecomposition::collectData() {
 #ifdef IS_MPI
+    Snapshot* snap = sman_->getCurrentSnapshot();
+    
+    int n = snap->atomData.force.size();
+    vector<Vector3d> frc_tmp(n, V3Zero);
+    
+    AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp);
+    for (int i = 0; i < n; i++) {
+      snap->atomData.force[i] += frc_tmp[i];
+      frc_tmp[i] = 0.0;
+    }
+    
+    AtomCommVectorJ->scatter(snap->atomJData.force, frc_tmp);
+    for (int i = 0; i < n; i++)
+      snap->atomData.force[i] += frc_tmp[i];
+    
+    
+    if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) {
+
+      int nt = snap->atomData.force.size();
+      vector<Vector3d> trq_tmp(nt, V3Zero);
+
+      AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp);
+      for (int i = 0; i < n; i++) {
+        snap->atomData.torque[i] += trq_tmp[i];
+        trq_tmp[i] = 0.0;
+      }
+      
+      AtomCommVectorJ->scatter(snap->atomJData.torque, trq_tmp);
+      for (int i = 0; i < n; i++)
+        snap->atomData.torque[i] += trq_tmp[i];
+    }
+    
+    int nLocal = snap->getNumberOfAtoms();
+
+    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES, 
+                                       vector<RealType> (nLocal, 0.0));
+    
+    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
+      AtomCommRealI->scatter(pot_row[i], pot_temp[i]);
+      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
+        pot_local[i] += pot_temp[i][ii];
+      }
+    }
 #endif
   }