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root/OpenMD/branches/development/src/io/ZConsWriter.cpp

Comparing:
trunk/src/io/ZConsWriter.cpp (file contents), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/io/ZConsWriter.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 1 | Line 1
1	+	/*
2	+	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	+	*
4	+	* The University of Notre Dame grants you ("Licensee") a
5	+	* non-exclusive, royalty free, license to use, modify and
6	+	* redistribute this software in source and binary code form, provided
7	+	* that the following conditions are met:
8	+	*
9	+	* 1. Redistributions of source code must retain the above copyright
10	+	*    notice, this list of conditions and the following disclaimer.
11	+	*
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.
16	+	*
17	+	* This software is provided "AS IS," without a warranty of any
18	+	* kind. All express or implied conditions, representations and
19	+	* warranties, including any implied warranty of merchantability,
20	+	* fitness for a particular purpose or non-infringement, are hereby
21	+	* excluded.  The University of Notre Dame and its licensors shall not
22	+	* be liable for any damages suffered by licensee as a result of
23	+	* using, modifying or distributing the software or its
24	+	* derivatives. In no event will the University of Notre Dame or its
25	+	* licensors be liable for any lost revenue, profit or data, or for
26	+	* direct, indirect, special, consequential, incidental or punitive
27	+	* damages, however caused and regardless of the theory of liability,
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, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40	+	*/
41	+
42		#include <algorithm>
43		#include <iostream>
44		#include <vector>
4	–	//#include <pair>
5	–	#include "ZConsWriter.hpp"
6	–	#include "simError.h"
45
8	–	using namespace std;
46
47	<	ZConsWriter::ZConsWriter(const char* filename, vector<ZConsParaItem>* thePara)
48	<	{
12	<	//use master - slave mode, only master node writes to disk
47	>	#include "io/ZConsWriter.hpp"
48	>	#include "utils/simError.h"
49		#ifdef IS_MPI
50	<	if(worldRank == 0){
50	>	#include <mpi.h>
51		#endif
52
53	<	output.open(filename);
54	<
55	<	if(!output){
56	<	sprintf( painCave.errMsg,
57	<	"Could not open %s for z constrain output \n",
58	<	filename);
23	<	painCave.isFatal = 1;
24	<	simError();
25	<	}
26	<	output << "#number of z constrain molecules" << endl;
27	<	output << "#global Index of molecule\tzPos" << endl;
28	<	output << "#every frame will contain below data" <<endl;
29	<	output << "#time(fs)" << endl;
30	<	output << "#number of fixed z-constrain molecules" << endl;
31	<	output << "#global Index of molecule\tzconstrain force\tcurrentZPos" << endl;
53	>	namespace OpenMD {
54	>	ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) : info_(info) {
55	>	//use master - slave mode, only master node writes to disk
56	>	#ifdef IS_MPI
57	>	if(worldRank == 0){
58	>	#endif
59
60	<	parameters = thePara;
34	<	writeZPos();
60	>	output_.open(filename.c_str());
61
62	+	if(!output_){
63	+	sprintf( painCave.errMsg,
64	+	"Could not open %s for z constrain output_ \n", filename.c_str());
65	+	painCave.isFatal = 1;
66	+	simError();
67	+	}
68	+
69	+	output_ << "//time(fs)" << std::endl;
70	+	output_ << "//number of fixed z-constrain molecules" << std::endl;
71	+	output_ << "//global Index of molecule\tzconstrain force\tcurrentZPos" << std::endl;
72	+
73		#ifdef IS_MPI
74	<	}
74	>	}
75		#endif
76
77	<	}
77	>	}
78
79	<	ZConsWriter::~ZConsWriter()
80	<	{
79	>	ZConsWriter::~ZConsWriter()
80	>	{
81
82		#ifdef IS_MPI
83	<	if(worldRank == 0 ){
83	>	if(worldRank == 0 ){
84		#endif
85	<	output.close();
85	>	output_.close();
86		#ifdef IS_MPI
87	<	}
87	>	}
88		#endif
89	<	}
89	>	}
90
91	<	/**
55	<	*
56	<	*/
57	<	void ZConsWriter::writeFZ(double time, int num, int* index, double* fz, double* curZPos, double* zpos){
58	<
91	>	void ZConsWriter::writeFZ(const std::list<ZconstraintMol>& fixedZmols){
92		#ifndef IS_MPI
93	<	output << time << endl;
94	<	output << num << endl;
62	<
63	<	for(int i = 0; i < num; i++)
64	<	output << index[i] <<"\t" << fz[i] << "\t" << curZPos[i] << "\t" << zpos[i] <<endl;
93	>	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
94	>	output_ << fixedZmols.size() << std::endl;
95
96	+	std::list<ZconstraintMol>::const_iterator i;
97	+	for ( i = fixedZmols.begin(); i != fixedZmols.end(); ++i) {
98	+	output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos << "\t" << i->param.zTargetPos <<std::endl;
99	+	}
100		#else
101	<	int totalNum;
102	<	MPI_Allreduce(&num, &totalNum, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
103	<
104	<	if(worldRank == 0){
105	<	output << time << endl;
106	<	output << totalNum << endl;
107	<	}
74	<
75	<	int whichNode;
76	<	enum CommType { RequesPosAndForce, EndOfRequest} status;
77	<	double pos;
78	<	double force;
79	<	double zconsPos;
80	<	int localIndex;
81	<	MPI_Status ierr;
82	<	int tag = 0;
83	<
84	<	if(worldRank == 0){
101	>	int nproc;
102	>	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
103	>	const int masterNode = 0;
104	>	int myNode = worldRank;
105	>	std::vector<int> tmpNFixedZmols(nproc, 0);
106	>	std::vector<int> nFixedZmolsInProc(nproc, 0);
107	>	tmpNFixedZmols[myNode] = fixedZmols.size();
108
109	<	int globalIndexOfCurMol;
110	<	int *MolToProcMap;
111	<	MolToProcMap = mpiSim->getMolToProcMap();
89	<
90	<	for(int i = 0; i < (int)(parameters->size()); i++){
91	<
92	<	globalIndexOfCurMol = (*parameters)[i].zconsIndex;
93	<	whichNode = MolToProcMap[globalIndexOfCurMol];
94	<
95	<	if(whichNode == 0){
96	<
97	<	for(int j = 0; j < num; j++)
98	<	if(index[j] == globalIndexOfCurMol){
99	<	localIndex = j;
100	<	break;
101	<	}
109	>	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
110	>	MPI_Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0], nproc, MPI_INT,
111	>	MPI_SUM, MPI_COMM_WORLD);
112
113	<	force = fz[localIndex];
114	<	pos = curZPos[localIndex];
115	<
106	<	}
107	<	else{
108	<	status = RequesPosAndForce;
109	<	MPI_Send(&status, 1, MPI_INT, whichNode, tag, MPI_COMM_WORLD);
110	<	MPI_Send(&globalIndexOfCurMol, 1, MPI_INT, whichNode, tag, MPI_COMM_WORLD);
111	<	MPI_Recv(&force, 1, MPI_DOUBLE, whichNode, tag, MPI_COMM_WORLD, &ierr);
112	<	MPI_Recv(&pos, 1, MPI_DOUBLE, whichNode, tag, MPI_COMM_WORLD, &ierr);
113	<	MPI_Recv(&zconsPos, 1, MPI_DOUBLE, whichNode, tag, MPI_COMM_WORLD, &ierr);
114	<	}
115	<
116	<	output << globalIndexOfCurMol << "\t" << force << "\t" << pos << "\t"<<  zconsPos << endl;
117	<
118	<	} //End of Request Loop
113	>	MPI_Status ierr;
114	>	int zmolIndex;
115	>	RealType data[3];
116
117	<	//Send ending request message to slave nodes
121	<	status = EndOfRequest;
122	<	for(int i =1; i < mpiSim->getNProcessors(); i++)
123	<	MPI_Send(&status, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
124	<
125	<	}
126	<	else{
127	<
128	<	int whichMol;
129	<	bool done = false;
117	>	if (masterNode == 0) {
118
119	<	while (!done){
120	<
121	<	MPI_Recv(&status, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &ierr);
122	<
123	<	switch (status){
124	<
125	<	case RequesPosAndForce :
126	<
127	<	MPI_Recv(&whichMol, 1, MPI_INT, 0, tag, MPI_COMM_WORLD,&ierr);
128	<
129	<	for(int i = 0; i < num; i++)
130	<	if(index[i] == whichMol){
131	<	localIndex = i;
132	<	break;
133	<	}
134	<
135	<	MPI_Send(&fz[localIndex], 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD);
136	<	MPI_Send(&curZPos[localIndex], 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD);
137	<	MPI_Send(&zpos[localIndex], 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD);
138	<	break;
139	<
140	<	case EndOfRequest :
141	<
142	<	done = true;
143	<	break;
119	>	std::vector<ZconsData> zconsData;
120	>	ZconsData tmpData;
121	>	for(int i =0 ; i < nproc; ++i) {
122	>	if (i == masterNode) {
123	>	std::list<ZconstraintMol>::const_iterator j;
124	>	for ( j = fixedZmols.begin(); j != fixedZmols.end(); ++j) {
125	>	tmpData.zmolIndex = j->mol->getGlobalIndex() ;
126	>	tmpData.zforce= j->fz;
127	>	tmpData.zpos = j->zpos;
128	>	tmpData.zconsPos = j->param.zTargetPos;
129	>	zconsData.push_back(tmpData);
130	>	}
131	>
132	>	} else {
133	>	for(int k =0 ; k < nFixedZmolsInProc[i]; ++k) {
134	>	MPI_Recv(&zmolIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr);
135	>	MPI_Recv(data, 3, MPI_REALTYPE, i, 0, MPI_COMM_WORLD,&ierr);
136	>	tmpData.zmolIndex = zmolIndex;
137	>	tmpData.zforce= data[0];
138	>	tmpData.zpos = data[1];
139	>	tmpData.zconsPos = data[2];
140	>	zconsData.push_back(tmpData);
141	>	}
142	>	}
143	>
144		}
157	–
158	–	}
159	–
160	–	}
145
162	–	#endif
146
147	<	}
147	>	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
148	>	output_ << zconsData.size() << std::endl;
149
150	<	/*
151	<	*
152	<	*/
153	<	void ZConsWriter::writeZPos(){
150	>	std::vector<ZconsData>::iterator l;
151	>	for (l = zconsData.begin(); l != zconsData.end(); ++l) {
152	>	output_ << l->zmolIndex << "\t" << l->zforce << "\t" << l->zpos << "\t" <<  l->zconsPos << std::endl;
153	>	}
154	>
155	>	} else {
156
157	<	#ifdef IS_MPI
158	<	if(worldRank == 0){
157	>	std::list<ZconstraintMol>::const_iterator j;
158	>	for (j = fixedZmols.begin(); j != fixedZmols.end(); ++j) {
159	>	zmolIndex = j->mol->getGlobalIndex();
160	>	data[0] = j->fz;
161	>	data[1] = j->zpos;
162	>	data[2] = j->param.zTargetPos;
163	>	MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
164	>	MPI_Send(data, 3, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD);
165	>
166	>	}
167	>	}
168		#endif
174	–
175	–	output << parameters->size() << endl;
176	–
177	–	for(int i =0 ; i < (int)(parameters->size()); i++)
178	–	output << (*parameters)[i].zconsIndex << "\t" <<  (*parameters)[i].zPos << endl;
179	–
180	–	#ifdef IS_MPI
169		}
170	<	#endif
170	>
171		}

Comparing:
trunk/src/io/ZConsWriter.cpp (property svn:keywords), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/io/ZConsWriter.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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