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root/OpenMD/trunk/src/io/ZConsWriter.cpp

Comparing trunk/src/io/ZConsWriter.cpp (file contents):
Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
Revision 1981 by gezelter, Mon Apr 14 18:32:51 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
122	<	if (masterNode == 0) {
122	>	if (myNode == masterNode) {
123
124		std::vector<ZconsData> zconsData;
125		ZconsData tmpData;
#	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 1981 by gezelter, Mon Apr 14 18:32:51 2014 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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