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Comparing trunk/src/io/RestWriter.cpp (file contents):
Revision 990 by chrisfen, Mon Jun 19 01:36:06 2006 UTC vs.
Revision 2020 by gezelter, Mon Sep 22 19:18:35 2014 UTC

#	Line 1 | Line 1
1		/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
2	>	* Copyright (c) 2009 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. 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	<	#include <algorithm>
42	>
43	>	#ifdef IS_MPI
44	>	#include <mpi.h>
45	>	#endif
46	>
47	>	#include <string>
48	>	#include <sstream>
49		#include <iostream>
44	–	#include <map>
50
46	–	#include "primitives/Molecule.hpp"
51		#include "io/RestWriter.hpp"
52		#include "utils/simError.h"
53	+	#include "brains/SnapshotManager.hpp"
54
55	+	namespace OpenMD {
56	+	RestWriter::RestWriter(SimInfo* info, const std::string& filename,
57	+	std::vector<Restraint*> restraints ) :
58	+	info_(info){
59
60	<	namespace oopse {
52	<	RestWriter::RestWriter(SimInfo* info) :
53	<	info_(info) {
60	>	std::vector<Restraint*>::const_iterator resti;
61
62	<	// only the master node writes to the disk
56	<	#ifdef IS_MPI
57	<	if (worldRank == 0) {
58	<	#endif // is_mpi
62	>	createRestFile_ = false;
63
64	<	outName = info_->getRestFileName();
65	<
66	<	#ifdef IS_MPI
64	>	#ifdef IS_MPI
65	>	MPI_Status* istatus;
66	>	#endif
67	>
68	>	int printAny = 0;
69	>	for(resti=restraints.begin(); resti != restraints.end(); ++resti){
70	>	if ((*resti)->getPrintRestraint()) {
71	>	printAny = 1;
72	>	}
73		}
64	–	#endif // is_mpi
65	–	}
66	–
67	–	RestWriter::~RestWriter() {}
68	–
69	–	void RestWriter::writeZangle(){
70	–	const int BUFFERSIZE = 2000;
71	–	char tempBuffer[BUFFERSIZE];
72	–	char writeLine[BUFFERSIZE];
74
75	<	std::ofstream finalOut;
76	<
77	<	Molecule* mol;
78	<	StuntDouble* integrableObject;
78	<	SimInfo::MoleculeIterator mi;
79	<	Molecule::IntegrableObjectIterator ii;
75	>	#ifdef IS_MPI
76	>	MPI_Allreduce(MPI_IN_PLACE, &printAny, 1, MPI_INT, MPI_SUM,
77	>	MPI_COMM_WORLD);
78	>	#endif
79
80	+	if (printAny) createRestFile_ = true;
81	+
82		#ifdef IS_MPI
83	<	if(worldRank == 0 ){
84	<	#endif
85	<	finalOut.open( outName.c_str(), std::ios::out | std::ios::trunc );
86	<	if( !finalOut ){
87	<	sprintf( painCave.errMsg,
88	<	"Could not open \"%s\" for zAngle output.\n",
89	<	outName.c_str() );
90	<	painCave.isFatal = 1;
91	<	simError();
83	>	if(worldRank == 0){
84	>	#endif
85	>
86	>	if (createRestFile_) {
87	>	output_ = new std::ofstream(filename.c_str());
88	>
89	>	if(!output_){
90	>	sprintf( painCave.errMsg,
91	>	"Could not open %s for restraint output.\n",
92	>	filename.c_str());
93	>	painCave.isFatal = 1;
94	>	simError();
95	>	}
96		}
97	+
98		#ifdef IS_MPI
99		}
100		#endif // is_mpi
101	<
101	>
102	>
103		#ifndef IS_MPI
104	<	// first we do output for the single processor version
105	<	finalOut
106	<	<< info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
107	<	<< " : omega values at this time\n";
108	<
109	<	for (mol = info_->beginMolecule(mi); mol != NULL;
110	<	mol = info_->nextMolecule(mi)) {
104	<
105	<	for (integrableObject = mol->beginIntegrableObject(ii);
106	<	integrableObject != NULL;
107	<	integrableObject = mol->nextIntegrableObject(ii)) {
104	>
105	>	if (createRestFile_) (*output_) << "#time\t";
106	>
107	>	for(resti=restraints.begin(); resti != restraints.end(); ++resti){
108	>	if ((*resti)->getPrintRestraint()) {
109	>	std::string myName = (*resti)->getRestraintName();
110	>	int myType = (*resti)->getRestraintType();
111
112	<	sprintf( tempBuffer,
110	<	"%14.10lf\n",
111	<	integrableObject->getZangle());
112	<	strcpy( writeLine, tempBuffer );
112	>	(*output_) << myName << ":";
113
114	<	finalOut << writeLine;
114	>	if (myType & Restraint::rtDisplacement)
115	>	(*output_) << "\tPosition(angstroms)\tEnergy(kcal/mol)";
116	>
117	>	if (myType & Restraint::rtTwist)
118	>	(*output_) << "\tTwistAngle(radians)\tEnergy(kcal/mol)";
119	>
120	>	if (myType & Restraint::rtSwingX)
121	>	(*output_) << "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
122	>
123	>	if (myType & Restraint::rtSwingY)
124	>	(*output_) << "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
125		}
116	–
126		}
127	+
128	+	if (createRestFile_) (*output_) << "\n";
129	+	if (createRestFile_) (*output_).flush();
130
131		#else
120	–	int nproc;
121	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
122	–	const int masterNode = 0;
123	–	int myNode = worldRank;
124	–	std::vector<int> tmpNIntObjects(nproc, 0);
125	–	std::vector<int> nIntObjectsInProc(nproc, 0);
126	–	tmpNIntObjects[myNode] = info_->getNGlobalIntegrableObjects();
132
133	<	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
134	<	MPI_Allreduce(&tmpNIntObjects[0], &nIntObjectsInProc[0], nproc, MPI_INT,
135	<	MPI_SUM, MPI_COMM_WORLD);
133	>	std::string buffer;
134	>
135	>	for(resti=restraints.begin(); resti != restraints.end(); ++resti){
136	>	if ((*resti)->getPrintRestraint()) {
137	>	std::string myName = (*resti)->getRestraintName();
138	>	int myType = (*resti)->getRestraintType();
139	>
140	>	buffer += (myName + ":");
141	>
142	>	if (myType & Restraint::rtDisplacement)
143	>	buffer += "\tPosition(angstroms)\tEnergy(kcal/mol)";
144	>
145	>	if (myType & Restraint::rtTwist)
146	>	buffer += "\tTwistAngle(radians)\tEnergy(kcal/mol)";
147	>
148	>	if (myType & Restraint::rtSwingX)
149	>	buffer += "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
150	>
151	>	if (myType & Restraint::rtSwingY)
152	>	buffer += "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
153	>
154	>	buffer += "\n";
155	>	}
156	>	}
157
158	<	MPI_Status ierr;
159	<	int intObIndex;
134	<	RealType zAngle;
135	<
158	>	const int masterNode = 0;
159	>
160		if (worldRank == masterNode) {
161	<	std::map<int, RealType> zAngData;
162	<	for(int i = 0 ; i < nproc; ++i) {
163	<	if (i == masterNode) {
164	<	for (mol = info_->beginMolecule(mi); mol != NULL;
165	<	mol = info_->nextMolecule(mi)) {
142	<
143	<	for (integrableObject = mol->beginIntegrableObject(ii);
144	<	integrableObject != NULL;
145	<	integrableObject = mol->nextIntegrableObject(ii)) {
146	<
147	<	intObIndex = integrableObject->getGlobalIndex();
161	>	if (createRestFile_) (*output_) << "#time\t";
162	>	if (createRestFile_) (*output_) << buffer;
163	>
164	>	int nProc;
165	>	MPI_Comm_size( MPI_COMM_WORLD, &nProc);
166
167	<	zAngle = integrableObject->getZangle();
168	<	zAngData.insert(std::pair<int, RealType>(intObIndex, zAngle));
169	<	}
170	<	}
167	>	for (int i = 1; i < nProc; ++i) {
168	>
169	>	// receive the length of the string buffer that was
170	>	// prepared by processor i
171	>
172	>	int recvLength;
173	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, istatus);
174	>	char* recvBuffer = new char[recvLength];
175	>	if (recvBuffer == NULL) {
176		} else {
177	<	for (mol = info_->beginMolecule(mi); mol != NULL;
178	<	mol = info_->nextMolecule(mi)) {
179	<
180	<	for (integrableObject = mol->beginIntegrableObject(ii);
158	<	integrableObject != NULL;
159	<	integrableObject = mol->nextIntegrableObject(ii)) {
160	<
161	<	MPI_Recv(&intObIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr);
162	<	MPI_Recv(&zAngle, 1, MPI_REALTYPE, i, 0, MPI_COMM_WORLD,&ierr);
163	<	zAngData.insert(std::pair<int, RealType>(intObIndex, zAngle));
164	<	}
165	<	}
177	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
178	>	istatus);
179	>	if (createRestFile_) (*output_) << recvBuffer;
180	>	delete [] recvBuffer;
181		}
182	<	}
182	>	}
183	>	if (createRestFile_) (*output_).flush();
184	>	} else {
185	>	int sendBufferLength = buffer.size() + 1;
186	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
187	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR,
188	>	masterNode, 0, MPI_COMM_WORLD);
189	>	}
190	>
191	>	#endif // is_mpi
192	>
193	>	}
194	>
195	>	void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo) {
196	>
197	>	#ifdef IS_MPI
198	>	MPI_Status* istatus;
199	>	#endif
200	>
201	>	#ifndef IS_MPI
202	>	if (createRestFile_)  (*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
203	>
204	>	// output some information about the molecules
205	>	std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
206	>	std::map<int, Restraint::RealPair>::const_iterator j;
207	>
208	>	cerr << "risize = " << restInfo.size() << "\n";
209	>
210	>	if ( createRestFile_ ) {
211
212	<	finalOut
213	<	<< info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
214	<	<< " : omega values at this time\n";
215	<
216	<	std::map<int, RealType>::iterator l;
217	<	for (l = zAngData.begin(); l != zAngData.end(); ++l) {
218	<	sprintf( tempBuffer,
219	<	"%14.10lf\n",
220	<	l->second);
221	<	strcpy( writeLine, tempBuffer );
212	>	for( i = restInfo.begin(); i != restInfo.end(); ++i){
213	>	for(j = (*i).begin(); j != (*i).end(); ++j){
214	>	(*output_) << "\t" << (j->second).first << "\t" << (j->second).second;
215	>	}
216	>	(*output_) << std::endl;
217	>	}
218	>	(*output_).flush();
219	>	}
220	>	#else
221	>	std::string buffer, first, second;
222	>	std::stringstream ss;
223	>
224	>	std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
225	>	std::map<int, Restraint::RealPair>::const_iterator j;
226	>
227	>	if ( createRestFile_ ) {
228	>	for( i = restInfo.begin(); i != restInfo.end(); ++i){
229
230	<	finalOut << writeLine;
230	>	for(j = (*i).begin(); j != (*i).end(); ++j){
231	>	ss.clear();
232	>	ss << (j->second).first;
233	>	ss >> first;
234	>	ss.clear();
235	>	ss << (j->second).second;
236	>	ss >> second;
237	>	buffer += ("\t" + first + "\t" + second);
238	>	}
239	>	buffer += "\n";
240		}
241	<
242	<	finalOut.close();
241	>	}
242	>
243	>	const int masterNode = 0;
244	>
245	>	if (createRestFile_) {
246	>	if (worldRank == masterNode) {
247	>
248	>	(*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
249	>	(*output_) << buffer;
250
251	<	} else {
252	<	for(int j = 1; j < nproc; ++j) {
253	<	for (mol = info_->beginMolecule(mi); mol != NULL;
254	<	mol = info_->nextMolecule(mi)) {
255	<
256	<	for (integrableObject = mol->beginIntegrableObject(ii);
257	<	integrableObject != NULL;
258	<	integrableObject = mol->nextIntegrableObject(ii)) {
259	<	intObIndex = integrableObject->getGlobalIndex();
260	<	zAngle = integrableObject->getZangle();
261	<
262	<	MPI_Send(&intObIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
263	<	MPI_Send(&zAngle, 1, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD);
264	<	}
265	<	}
251	>	int nProc;
252	>	MPI_Comm_size( MPI_COMM_WORLD, &nProc);
253	>	for (int i = 1; i < nProc; ++i) {
254	>
255	>	// receive the length of the string buffer that was
256	>	// prepared by processor i
257	>
258	>	int recvLength;
259	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, istatus);
260	>	char* recvBuffer = new char[recvLength];
261	>	if (recvBuffer == NULL) {
262	>	} else {
263	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
264	>	istatus);
265	>	if (createRestFile_) (*output_) << recvBuffer;
266	>
267	>	delete [] recvBuffer;
268	>	}
269	>	}
270	>	(*output_).flush();
271	>	} else {
272	>	int sendBufferLength = buffer.size() + 1;
273	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
274	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
275	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
276		}
277		}
278	<
203	<	#endif
278	>	#endif // is_mpi
279		}
280
281	<	}
281	>
282	>	RestWriter::~RestWriter() {
283	>
284	>	#ifdef IS_MPI
285	>
286	>	if (worldRank == 0) {
287	>	#endif // is_mpi
288	>	if (createRestFile_){
289	>	writeClosing(*output_);
290	>	delete output_;
291	>	}
292	>	#ifdef IS_MPI
293	>	}
294	>	#endif // is_mpi
295	>	}
296	>
297	>	void RestWriter::writeClosing(std::ostream& os) {
298	>	os.flush();
299	>	}
300	>
301	>	}// end namespace OpenMD
302	>

Comparing trunk/src/io/RestWriter.cpp (property svn:keywords):
Revision 990 by chrisfen, Mon Jun 19 01:36:06 2006 UTC vs.
Revision 2020 by gezelter, Mon Sep 22 19:18:35 2014 UTC

#	Line 0 | Line 1
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