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

Comparing trunk/src/io/ZConsWriter.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 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"
53
54	<
55	<	namespace oopse {
56	<	ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) : info_(info) {
57	<	//use master - slave mode, only master node writes to disk
54	>	namespace OpenMD {
55	>	ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) :
56	>	info_(info) {
57	>	// use master - slave mode, only master node writes to disk
58		#ifdef IS_MPI
59		if(worldRank == 0){
60		#endif
57	–
61		output_.open(filename.c_str());
62
63		if(!output_){
64		sprintf( painCave.errMsg,
65	<	"Could not open %s for z constrain output_ \n", filename.c_str());
65	>	"Could not open %s for z constrain output_ \n",
66	>	filename.c_str());
67		painCave.isFatal = 1;
68		simError();
69		}
70
71		output_ << "//time(fs)" << std::endl;
72		output_ << "//number of fixed z-constrain molecules" << std::endl;
73	<	output_ << "//global Index of molecule\tzconstrain force\tcurrentZPos" << std::endl;
74	<
73	>	output_ << "//global Index of molecule\tzconstrain force\tcurrentZPos"
74	>	<< std::endl;
75		#ifdef IS_MPI
76		}
77	<	#endif
74	<
77	>	#endif
78		}
79	<
79	>
80		ZConsWriter::~ZConsWriter()
81		{
82	<
82	>
83		#ifdef IS_MPI
84		if(worldRank == 0 ){
85		#endif
#	Line 88 | Line 91 | namespace oopse {
91
92		void ZConsWriter::writeFZ(const std::list<ZconstraintMol>& fixedZmols){
93		#ifndef IS_MPI
94	<	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
94	>	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
95	>	<< std::endl;
96		output_ << fixedZmols.size() << std::endl;
97
98		std::list<ZconstraintMol>::const_iterator i;
99		for ( i = fixedZmols.begin(); i != fixedZmols.end(); ++i) {
100	<	output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos << "\t" << i->param.zTargetPos <<std::endl;
100	>	output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos
101	>	<< "\t" << i->param.zTargetPos <<std::endl;
102		}
103		#else
104	<	int nproc;
100	<	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
104	>
105		const int masterNode = 0;
106	<	int myNode = worldRank;
106	>	int nproc;
107	>	int myNode;
108	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
109	>	MPI_Comm_rank( MPI_COMM_WORLD, &myNode);
110	>
111		std::vector<int> tmpNFixedZmols(nproc, 0);
112		std::vector<int> nFixedZmolsInProc(nproc, 0);
113		tmpNFixedZmols[myNode] = fixedZmols.size();
114
115	<	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
116	<	MPI_Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0], nproc, MPI_INT,
117	<	MPI_SUM, MPI_COMM_WORLD);
118	<
119	<	MPI_Status ierr;
115	>	//do MPI_ALLREDUCE to exchange the total number of atoms,
116	>	//rigidbodies and cutoff groups
117	>	MPI_Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0],
118	>	nproc, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
119	>
120	>	MPI_Status* ierr = NULL;
121		int zmolIndex;
122		RealType data[3];
123
124	<	if (masterNode == 0) {
125	<
124	>	if (myNode == masterNode) {
125	>
126		std::vector<ZconsData> zconsData;
127		ZconsData tmpData;
128		for(int i =0 ; i < nproc; ++i) {
#	Line 126 | Line 135 | namespace oopse {
135		tmpData.zconsPos = j->param.zTargetPos;
136		zconsData.push_back(tmpData);
137		}
138	<
138	>
139		} else {
140		for(int k =0 ; k < nFixedZmolsInProc[i]; ++k) {
141	<	MPI_Recv(&zmolIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr);
142	<	MPI_Recv(data, 3, MPI_REALTYPE, i, 0, MPI_COMM_WORLD,&ierr);
141	>	MPI_Recv(&zmolIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD, ierr);
142	>	MPI_Recv(data, 3, MPI_REALTYPE, i, 0, MPI_COMM_WORLD, ierr);
143		tmpData.zmolIndex = zmolIndex;
144		tmpData.zforce= data[0];
145		tmpData.zpos = data[1];
146		tmpData.zconsPos = data[2];
147	<	zconsData.push_back(tmpData);
147	>	zconsData.push_back(tmpData);
148		}
149	<	}
141	<
149	>	}
150		}
151
152	<
153	<	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
152	>	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
153	>	<< std::endl;
154		output_ << zconsData.size() << std::endl;
155
156		std::vector<ZconsData>::iterator l;
157		for (l = zconsData.begin(); l != zconsData.end(); ++l) {
158	<	output_ << l->zmolIndex << "\t" << l->zforce << "\t" << l->zpos << "\t" <<  l->zconsPos << std::endl;
158	>	output_ << l->zmolIndex << "\t" << l->zforce << "\t" << l->zpos
159	>	<< "\t" <<  l->zconsPos << std::endl;
160		}
161	<
161	>
162		} else {
163	<
163	>
164		std::list<ZconstraintMol>::const_iterator j;
165		for (j = fixedZmols.begin(); j != fixedZmols.end(); ++j) {
166		zmolIndex = j->mol->getGlobalIndex();
167		data[0] = j->fz;
168		data[1] = j->zpos;
169		data[2] = j->param.zTargetPos;
170	<	MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
171	<	MPI_Send(data, 3, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD);
163	<
170	>	MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
171	>	MPI_Send(data, 3, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD);
172		}
173		}
174		#endif
175		}
168	–
176		}

Comparing trunk/src/io/ZConsWriter.cpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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