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root/OpenMD/trunk/src/io/ZConsWriter.cpp
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Comparing trunk/src/io/ZConsWriter.cpp (file contents):
Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39 + * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 + * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43 + #ifdef IS_MPI
44 + #include <mpi.h>
45 + #endif
46 +
47   #include <algorithm>
48   #include <iostream>
49   #include <vector>
50  
46 –
51   #include "io/ZConsWriter.hpp"
52   #include "utils/simError.h"
49 – #ifdef IS_MPI
50 – #include <mpi.h>
51 – #endif
53  
54 < namespace oopse {
54 > namespace OpenMD {
55    ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) : info_(info) {
56      //use master - slave mode, only master node writes to disk
57   #ifdef IS_MPI
# Line 98 | Line 99 | namespace oopse {
99        output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos << "\t" << i->param.zTargetPos <<std::endl;
100      }
101   #else
102 <    int nproc;
102 <    MPI_Comm_size(MPI_COMM_WORLD, &nproc);
102 >  
103      const int masterNode = 0;
104 <    int myNode = worldRank;
104 >    int nproc;
105 >    int myNode;      
106 >    MPI_Comm_size( MPI_COMM_WORLD, &nproc);
107 >    MPI_Comm_rank( MPI_COMM_WORLD, &myNode);
108 >
109      std::vector<int> tmpNFixedZmols(nproc, 0);
110      std::vector<int> nFixedZmolsInProc(nproc, 0);
111      tmpNFixedZmols[myNode] = fixedZmols.size();
112      
113 <    //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
114 <    MPI_Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0], nproc, MPI_INT,
115 <                  MPI_SUM, MPI_COMM_WORLD);
113 >    //do MPI_ALLREDUCE to exchange the total number of atoms,
114 >    //rigidbodies and cutoff groups
115 >    MPI_Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0],
116 >                  nproc, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
117  
118 <    MPI_Status ierr;
118 >    MPI_Status* ierr;
119      int zmolIndex;
120      RealType data[3];
121      
# Line 131 | Line 136 | namespace oopse {
136  
137          } else {
138            for(int k =0 ; k < nFixedZmolsInProc[i]; ++k) {
139 <            MPI_Recv(&zmolIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr);
140 <            MPI_Recv(data, 3, MPI_REALTYPE, i, 0, MPI_COMM_WORLD,&ierr);
139 >            MPI_Recv(&zmolIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD, ierr);
140 >            MPI_Recv(data, 3, MPI_REALTYPE, i, 0, MPI_COMM_WORLD, ierr);
141              tmpData.zmolIndex = zmolIndex;
142              tmpData.zforce= data[0];
143              tmpData.zpos = data[1];
# Line 160 | Line 165 | namespace oopse {
165          data[0] = j->fz;
166          data[1] = j->zpos;
167          data[2] = j->param.zTargetPos;
168 <        MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
169 <        MPI_Send(data, 3, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD);
168 >        MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
169 >        MPI_Send(data, 3, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD);
170              
171        }
172      }

Comparing trunk/src/io/ZConsWriter.cpp (property svn:keywords):
Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

# Line 0 | Line 1
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