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root/OpenMD/trunk/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.
Revision 1796 by gezelter, Mon Sep 10 18:38:44 2012 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	+	*/
42	+
43		#include <algorithm>
44		#include <iostream>
45		#include <vector>
4	–	//#include <pair>
5	–	#include "ZConsWriter.hpp"
6	–	#include "simError.h"
46
8	–	using namespace std;
47
48	<	ZConsWriter::ZConsWriter(const char* filename, vector<ZConsParaItem>* thePara)
49	<	{
12	<	//use master - slave mode, only master node writes to disk
48	>	#include "io/ZConsWriter.hpp"
49	>	#include "utils/simError.h"
50		#ifdef IS_MPI
51	<	if(worldRank == 0){
51	>	#include <mpi.h>
52		#endif
53
54	<	output.open(filename);
55	<
56	<	if(!output){
57	<	sprintf( painCave.errMsg,
58	<	"Could not open %s for z constrain output \n",
59	<	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;
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
58	>	if(worldRank == 0){
59	>	#endif
60
61	<	parameters = thePara;
34	<	writeZPos();
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());
66	+	painCave.isFatal = 1;
67	+	simError();
68	+	}
69	+
70	+	output_ << "//time(fs)" << std::endl;
71	+	output_ << "//number of fixed z-constrain molecules" << std::endl;
72	+	output_ << "//global Index of molecule\tzconstrain force\tcurrentZPos" << std::endl;
73	+
74		#ifdef IS_MPI
75	<	}
75	>	}
76		#endif
77
78	<	}
78	>	}
79
80	<	ZConsWriter::~ZConsWriter()
81	<	{
80	>	ZConsWriter::~ZConsWriter()
81	>	{
82
83		#ifdef IS_MPI
84	<	if(worldRank == 0 ){
84	>	if(worldRank == 0 ){
85		#endif
86	<	output.close();
86	>	output_.close();
87		#ifdef IS_MPI
88	<	}
88	>	}
89		#endif
90	<	}
90	>	}
91
92	<	/**
55	<	*
56	<	*/
57	<	void ZConsWriter::writeFZ(double time, int num, int* index, double* fz, double* curZPos, double* zpos){
58	<
92	>	void ZConsWriter::writeFZ(const std::list<ZconstraintMol>& fixedZmols){
93		#ifndef IS_MPI
94	<	output << time << endl;
95	<	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;
94	>	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
95	>	output_ << fixedZmols.size() << std::endl;
96
97	+	std::list<ZconstraintMol>::const_iterator i;
98	+	for ( i = fixedZmols.begin(); i != fixedZmols.end(); ++i) {
99	+	output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos << "\t" << i->param.zTargetPos <<std::endl;
100	+	}
101		#else
102	<	int totalNum;
103	<	MPI_Allreduce(&num, &totalNum, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
104	<
105	<	if(worldRank == 0){
106	<	output << time << endl;
107	<	output << totalNum << endl;
73	<	}
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){
102	>	int nproc = MPI::COMM_WORLD.Get_size();
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();
112	<
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,
110	>	//rigidbodies and cutoff groups
111	>	MPI::COMM_WORLD.Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0],
112	>	nproc, MPI::INT, MPI::SUM);
113
114	<	force = fz[localIndex];
115	<	pos = curZPos[localIndex];
116	<
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
114	>	MPI::Status ierr;
115	>	int zmolIndex;
116	>	RealType data[3];
117
118	<	//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;
118	>	if (masterNode == 0) {
119
120	<	while (!done){
121	<
122	<	MPI_Recv(&status, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &ierr);
123	<
124	<	switch (status){
125	<
126	<	case RequesPosAndForce :
127	<
128	<	MPI_Recv(&whichMol, 1, MPI_INT, 0, tag, MPI_COMM_WORLD,&ierr);
129	<
130	<	for(int i = 0; i < num; i++)
131	<	if(index[i] == whichMol){
132	<	localIndex = i;
133	<	break;
134	<	}
135	<
136	<	MPI_Send(&fz[localIndex], 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD);
137	<	MPI_Send(&curZPos[localIndex], 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD);
138	<	MPI_Send(&zpos[localIndex], 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD);
139	<	break;
140	<
141	<	case EndOfRequest :
142	<
143	<	done = true;
144	<	break;
120	>	std::vector<ZconsData> zconsData;
121	>	ZconsData tmpData;
122	>	for(int i =0 ; i < nproc; ++i) {
123	>	if (i == masterNode) {
124	>	std::list<ZconstraintMol>::const_iterator j;
125	>	for ( j = fixedZmols.begin(); j != fixedZmols.end(); ++j) {
126	>	tmpData.zmolIndex = j->mol->getGlobalIndex() ;
127	>	tmpData.zforce= j->fz;
128	>	tmpData.zpos = j->zpos;
129	>	tmpData.zconsPos = j->param.zTargetPos;
130	>	zconsData.push_back(tmpData);
131	>	}
132	>
133	>	} else {
134	>	for(int k =0 ; k < nFixedZmolsInProc[i]; ++k) {
135	>	MPI::COMM_WORLD.Recv(&zmolIndex, 1, MPI::INT, i, 0, ierr);
136	>	MPI::COMM_WORLD.Recv(data, 3, MPI::REALTYPE, i, 0, ierr);
137	>	tmpData.zmolIndex = zmolIndex;
138	>	tmpData.zforce= data[0];
139	>	tmpData.zpos = data[1];
140	>	tmpData.zconsPos = data[2];
141	>	zconsData.push_back(tmpData);
142	>	}
143	>	}
144	>
145		}
157	–
158	–	}
159	–
160	–	}
146
162	–	#endif
147
148	<	}
148	>	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
149	>	output_ << zconsData.size() << std::endl;
150
151	<	/*
152	<	*
153	<	*/
154	<	void ZConsWriter::writeZPos(){
151	>	std::vector<ZconsData>::iterator l;
152	>	for (l = zconsData.begin(); l != zconsData.end(); ++l) {
153	>	output_ << l->zmolIndex << "\t" << l->zforce << "\t" << l->zpos << "\t" <<  l->zconsPos << std::endl;
154	>	}
155	>
156	>	} else {
157
158	<	#ifdef IS_MPI
159	<	if(worldRank == 0){
158	>	std::list<ZconstraintMol>::const_iterator j;
159	>	for (j = fixedZmols.begin(); j != fixedZmols.end(); ++j) {
160	>	zmolIndex = j->mol->getGlobalIndex();
161	>	data[0] = j->fz;
162	>	data[1] = j->zpos;
163	>	data[2] = j->param.zTargetPos;
164	>	MPI::COMM_WORLD.Send(&zmolIndex, 1, MPI::INT, masterNode, 0);
165	>	MPI::COMM_WORLD.Send(data, 3, MPI::REALTYPE, masterNode, 0);
166	>
167	>	}
168	>	}
169		#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
170		}
171	<	#endif
171	>
172		}

Comparing trunk/src/io/ZConsWriter.cpp (property svn:keywords):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1796 by gezelter, Mon Sep 10 18:38:44 2012 UTC

#	Line 0 | Line 1
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