--- trunk/src/io/RestWriter.cpp	2005/03/10 15:10:24	417
+++ trunk/src/io/RestWriter.cpp	2009/10/07 20:49:50	1364
@@ -1,5 +1,5 @@
- /*
- * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
+/*
+ * Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
  * non-exclusive, royalty free, license to use, modify and
@@ -38,150 +38,94 @@
  * University of Notre Dame has been advised of the possibility of
  * such damages.
  */
- 
-#include <algorithm>
+
+
 #include <iostream>
-#include <map>
 
-#include "primitives/Molecule.hpp"
 #include "io/RestWriter.hpp"
 #include "utils/simError.h"
+#include "brains/SnapshotManager.hpp"
+#ifdef IS_MPI
+#include <mpi.h>
+#endif
 
-
 namespace oopse {
-  RestWriter::RestWriter(SimInfo* info) : 
-  info_(info) {
-    
-    //we use master - slave mode, only master node writes to disk
-    outName = info_->getRestFileName();
-  }
-  
-  RestWriter::~RestWriter() {}
-  
-  void RestWriter::writeZangle(){
-    const int BUFFERSIZE = 2000;
-    char tempBuffer[BUFFERSIZE];
-    char writeLine[BUFFERSIZE];
-    
-    std::ofstream finalOut;
-    
-    Molecule* mol;
-    StuntDouble* integrableObject;
-    SimInfo::MoleculeIterator mi;
-    Molecule::IntegrableObjectIterator ii;
-    
+  RestWriter::RestWriter(SimInfo* info, const std::string& filename, 
+                         std::vector<Restraint*> restraints ) : 
+    info_(info){
+
+    //use master - slave mode, only master node writes to disk
 #ifdef IS_MPI
-    if(worldRank == 0 ){
-#endif    
-      finalOut.open( outName.c_str(), std::ios::out | std::ios::trunc );
-      if( !finalOut ){
+    if(worldRank == 0){
+#endif
+      
+      output_.open(filename.c_str());
+      
+      if(!output_){
         sprintf( painCave.errMsg,
-                 "Could not open \"%s\" for zAngle output.\n",
-                 outName );
+                 "Could not open %s for restraint output.\n", 
+                 filename.c_str());
         painCave.isFatal = 1;
         simError();
       }
-#ifdef IS_MPI
-    }
-#endif // is_mpi
-    
-#ifndef IS_MPI
-    // first we do output for the single processor version
-    finalOut
-      << info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
-      << " : omega values at this time\n";
-    
-    for (mol = info_->beginMolecule(mi); mol != NULL; 
-         mol = info_->nextMolecule(mi)) {
+
+      output_ << "#time\t";
       
-      for (integrableObject = mol->beginIntegrableObject(ii); 
-           integrableObject != NULL; 
-           integrableObject = mol->nextIntegrableObject(ii)) {    
-        
-        sprintf( tempBuffer,
-                 "%14.10lf\n",
-                 integrableObject->getZangle());
-        strcpy( writeLine, tempBuffer );
-        
-        finalOut << writeLine;      
-      }
-      
-    }
-    
-#else
-    int nproc;
-    MPI_Comm_size(MPI_COMM_WORLD, &nproc);
-    const int masterNode = 0;
-    int myNode = worldRank;
-    std::vector<int> tmpNIntObjects(nproc, 0);
-    std::vector<int> nIntObjectsInProc(nproc, 0);
-    tmpNIntObjects[myNode] = info_->getNGlobalIntegrableObjects();
-    
-    //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
-    MPI_Allreduce(&tmpNIntObjects[0], &nIntObjectsInProc[0], nproc, MPI_INT,
-                  MPI_SUM, MPI_COMM_WORLD);
-    
-    MPI_Status ierr;
-    int intObIndex;
-    double zAngle;
-    
-    if (masterNode == 0) {
-      std::map<int, double> zAngData;
-      for(int i = 0 ; i < nproc; ++i) {
-        if (i == masterNode) {
-          for (mol = info_->beginMolecule(mi); mol != NULL; 
-               mol = info_->nextMolecule(mi)) {
-            
-            for (integrableObject = mol->beginIntegrableObject(ii); 
-                 integrableObject != NULL; 
-                 integrableObject = mol->nextIntegrableObject(ii)) { 
-              
-              intObIndex = integrableObject->getGlobalIndex() ;
-              zAngle = integrableObject->getZangle();
-              zAngData.insert(pair<int, double>(intObIndex, zAngle));
-            }      
-          }
+      // TODO:  get Restraint info from slave nodes:
+      std::vector<Restraint*>::const_iterator resti;
+      for(resti=restraints.begin(); resti != restraints.end(); ++resti){
+
+        if ((*resti)->getPrintRestraint()) {
+          std::string myName = (*resti)->getRestraintName();
+          int myType = (*resti)->getRestraintType();
           
-        } else {
-          for(int k = 0; k < nIntObjectsInProc[i]; ++k) {
-            MPI_Recv(&intObIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr);
-            MPI_Recv(&zAngle, 1, MPI_DOUBLE, i, 0, MPI_COMM_WORLD,&ierr);
-            zAngData.insert(pair<int, double>(intObIndex, zAngle));
-          }
+          output_ << myName << ":";
+          
+          if (myType & Restraint::rtDisplacement)
+            output_ << "\tPosition(angstroms)\tEnergy(kcal/mol)";
+          
+          if (myType & Restraint::rtTwist)
+            output_ << "\tTwistAngle(radians)\tEnergy(kcal/mol)";
+          
+          if (myType & Restraint::rtSwingX)
+            output_ << "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
+          
+          if (myType & Restraint::rtSwingY)
+            output_ << "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
+          
         }
-        
       }
-      
-      finalOut
-        << info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
-        << " : omega values at this time\n";
-      
-      std::map<int, double>::iterator l;
-      for (l = zAngData.begin(); l != zAngData.end(); ++l) {
-        finalOut << l->second << "\n";
-      }
-      
-    } else {
-      
-      for (mol = info_->beginMolecule(mi); mol != NULL; 
-           mol = info_->nextMolecule(mi)) {
-        
-        for (integrableObject = mol->beginIntegrableObject(ii); 
-             integrableObject != NULL; 
-             integrableObject = mol->nextIntegrableObject(ii)) { 
-          intObIndex = integrableObject->getGlobalIndex();            
-          zAngle = integrableObject->getZangle();
-          MPI_Send(&intObIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
-          MPI_Send(&zAngle, 1, MPI_DOUBLE, masterNode, 0, MPI_COMM_WORLD);
-        }
-      }
+      output_ << "\n";
+#ifdef IS_MPI
     }
-#endif
-    
+#endif      
+  }
+  
+  RestWriter::~RestWriter() {
 #ifdef IS_MPI
-    finalOut.close();
+    if(worldRank == 0 ){
+#endif  
+      output_.close();  
+#ifdef IS_MPI  
+    }
 #endif
+  }
+  
+  void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo){
+      
     
+    output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
+        
+    // output some information about the molecules
+    std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
+    std::map<int, Restraint::RealPair>::const_iterator j;
+    for( i = restInfo.begin(); i != restInfo.end(); ++i){
+      for(j = (*i).begin(); j != (*i).end(); ++j){                
+        output_ << "\t" << (j->second).first << "\t" << (j->second).second;
+      }
+      output_ << std::endl;
+    }
   }
   
-}
+}// end oopse
+