--- trunk/src/io/ZConsWriter.cpp	2009/11/25 20:02:06	1390
+++ trunk/src/io/ZConsWriter.cpp	2015/03/07 21:41:51	2071
@@ -35,50 +35,51 @@
  *                                                                      
  * [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).          
- * [4]  Vardeman & Gezelter, in progress (2009).                        
+ * [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).
  */
  
+#ifdef IS_MPI
+#include <mpi.h>
+#endif
+
 #include <algorithm>
 #include <iostream>
 #include <vector>
 
-
 #include "io/ZConsWriter.hpp"
 #include "utils/simError.h"
-#ifdef IS_MPI
-#include <mpi.h>
-#endif
 
 namespace OpenMD {
-  ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) : info_(info) {
-    //use master - slave mode, only master node writes to disk
+  ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) : 
+    info_(info) {
+    // use master - slave mode, only master node writes to disk
 #ifdef IS_MPI
     if(worldRank == 0){
 #endif
-
       output_.open(filename.c_str());
 
       if(!output_){
 	sprintf( painCave.errMsg,
-		 "Could not open %s for z constrain output_ \n", filename.c_str());
+		 "Could not open %s for z constrain output_ \n", 
+		 filename.c_str());
 	painCave.isFatal = 1;
 	simError();
       }
 
       output_ << "//time(fs)" << std::endl;
       output_ << "//number of fixed z-constrain molecules" << std::endl;
-      output_ << "//global Index of molecule\tzconstrain force\tcurrentZPos" << std::endl;
-
+      output_ << "//global Index of molecule\tzconstrain force\tcurrentZPos" 
+	      << std::endl;
 #ifdef IS_MPI
     }
-#endif  
-
+#endif      
   }
-
+  
   ZConsWriter::~ZConsWriter()
   {
-
+    
 #ifdef IS_MPI
     if(worldRank == 0 ){
 #endif  
@@ -90,32 +91,38 @@ namespace OpenMD {
 
   void ZConsWriter::writeFZ(const std::list<ZconstraintMol>& fixedZmols){
 #ifndef IS_MPI
-    output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
+    output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() 
+	    << std::endl;
     output_ << fixedZmols.size() << std::endl;
 
     std::list<ZconstraintMol>::const_iterator i;
     for ( i = fixedZmols.begin(); i != fixedZmols.end(); ++i) {
-      output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos << "\t" << i->param.zTargetPos <<std::endl;
+      output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos 
+	      << "\t" << i->param.zTargetPos <<std::endl;
     }
 #else
-    int nproc;
-    MPI_Comm_size(MPI_COMM_WORLD, &nproc);
+    
     const int masterNode = 0;
-    int myNode = worldRank;
+    int nproc;
+    int myNode;      
+    MPI_Comm_size( MPI_COMM_WORLD, &nproc);
+    MPI_Comm_rank( MPI_COMM_WORLD, &myNode);
+    
     std::vector<int> tmpNFixedZmols(nproc, 0);
     std::vector<int> nFixedZmolsInProc(nproc, 0);
     tmpNFixedZmols[myNode] = fixedZmols.size();
     
-    //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
-    MPI_Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0], nproc, MPI_INT,
-                  MPI_SUM, MPI_COMM_WORLD);
-
-    MPI_Status ierr;
+    //do MPI_ALLREDUCE to exchange the total number of atoms,
+    //rigidbodies and cutoff groups
+    MPI_Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0], 
+                  nproc, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
+    
+    MPI_Status* ierr = NULL;
     int zmolIndex;
     RealType data[3];
     
-    if (masterNode == 0) {
-
+    if (myNode == masterNode) {
+      
       std::vector<ZconsData> zconsData;
       ZconsData tmpData;       
       for(int i =0 ; i < nproc; ++i) {
@@ -128,44 +135,42 @@ namespace OpenMD {
 	    tmpData.zconsPos = j->param.zTargetPos;
 	    zconsData.push_back(tmpData);
 	  }                
-
+	  
 	} else {
 	  for(int k =0 ; k < nFixedZmolsInProc[i]; ++k) {
-	    MPI_Recv(&zmolIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr);
-	    MPI_Recv(data, 3, MPI_REALTYPE, i, 0, MPI_COMM_WORLD,&ierr);
+            MPI_Recv(&zmolIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD, ierr);
+            MPI_Recv(data, 3, MPI_REALTYPE, i, 0, MPI_COMM_WORLD, ierr);
 	    tmpData.zmolIndex = zmolIndex;
 	    tmpData.zforce= data[0];
 	    tmpData.zpos = data[1];
 	    tmpData.zconsPos = data[2];
-	    zconsData.push_back(tmpData);                                        
+	    zconsData.push_back(tmpData);
 	  }
-	}
-            
+	}	
       }
 
-
-      output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
+      output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() 
+	      << std::endl;
       output_ << zconsData.size() << std::endl;
 
       std::vector<ZconsData>::iterator l;
       for (l = zconsData.begin(); l != zconsData.end(); ++l) {
-	output_ << l->zmolIndex << "\t" << l->zforce << "\t" << l->zpos << "\t" <<  l->zconsPos << std::endl;
+	output_ << l->zmolIndex << "\t" << l->zforce << "\t" << l->zpos 
+		<< "\t" <<  l->zconsPos << std::endl;
       }
-        
+      
     } else {
-
+      
       std::list<ZconstraintMol>::const_iterator j;
       for (j = fixedZmols.begin(); j != fixedZmols.end(); ++j) {
 	zmolIndex = j->mol->getGlobalIndex();            
 	data[0] = j->fz;
 	data[1] = j->zpos;
 	data[2] = j->param.zTargetPos;
-	MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
-	MPI_Send(data, 3, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD);
-            
+        MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
+        MPI_Send(data, 3, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD);
       }
     }
 #endif
   }
-
 }