--- trunk/src/io/ZConsWriter.cpp	2008/04/25 15:14:47	1241
+++ branches/development/src/io/ZConsWriter.cpp	2013/02/20 15:39:39	1850
@@ -6,19 +6,10 @@
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the
  *    distribution.
@@ -37,6 +28,16 @@
  * arising out of the use of or inability to use software, even if the
  * University of Notre Dame has been advised of the possibility of
  * such damages.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [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, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 #include <algorithm>
@@ -50,7 +51,7 @@
 #include <mpi.h>
 #endif
 
-namespace oopse {
+namespace OpenMD {
   ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) : info_(info) {
     //use master - slave mode, only master node writes to disk
 #ifdef IS_MPI
@@ -98,19 +99,19 @@ namespace oopse {
       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);
+    int nproc = MPI::COMM_WORLD.Get_size();
     const int masterNode = 0;
     int myNode = worldRank;
     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);
+    //do MPI_ALLREDUCE to exchange the total number of atoms,
+    //rigidbodies and cutoff groups
+    MPI::COMM_WORLD.Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0], 
+                              nproc, MPI::INT, MPI::SUM);
 
-    MPI_Status ierr;
+    MPI::Status ierr;
     int zmolIndex;
     RealType data[3];
     
@@ -131,8 +132,8 @@ namespace oopse {
 
 	} 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::COMM_WORLD.Recv(&zmolIndex, 1, MPI::INT, i, 0, ierr);
+            MPI::COMM_WORLD.Recv(data, 3, MPI::REALTYPE, i, 0, ierr);
 	    tmpData.zmolIndex = zmolIndex;
 	    tmpData.zforce= data[0];
 	    tmpData.zpos = data[1];
@@ -160,8 +161,8 @@ namespace oopse {
 	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::COMM_WORLD.Send(&zmolIndex, 1, MPI::INT, masterNode, 0);
+        MPI::COMM_WORLD.Send(data, 3, MPI::REALTYPE, masterNode, 0);
             
       }
     }