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

Comparing:
trunk/src/io/RestWriter.cpp (file contents), Revision 990 by chrisfen, Mon Jun 19 01:36:06 2006 UTC vs.
branches/development/src/io/RestWriter.cpp (file contents), Revision 1850 by gezelter, Wed Feb 20 15:39:39 2013 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	>
44	>	#include <string>
45	>	#include <sstream>
46		#include <iostream>
44	–	#include <map>
47
46	–	#include "primitives/Molecule.hpp"
48		#include "io/RestWriter.hpp"
49		#include "utils/simError.h"
50	<
50	<
51	<	namespace oopse {
52	<	RestWriter::RestWriter(SimInfo* info) :
53	<	info_(info) {
54	<
55	<	// only the master node writes to the disk
50	>	#include "brains/SnapshotManager.hpp"
51		#ifdef IS_MPI
52	<	if (worldRank == 0) {
53	<	#endif // is_mpi
52	>	#include <mpi.h>
53	>	#endif
54
55	<	outName = info_->getRestFileName();
56	<
57	<	#ifdef IS_MPI
58	<	}
59	<	#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];
55	>	namespace OpenMD {
56	>	RestWriter::RestWriter(SimInfo* info, const std::string& filename,
57	>	std::vector<Restraint*> restraints ) :
58	>	info_(info){
59	>	createRestFile_ = true;
60
74	–	std::ofstream finalOut;
75	–
76	–	Molecule* mol;
77	–	StuntDouble* integrableObject;
78	–	SimInfo::MoleculeIterator mi;
79	–	Molecule::IntegrableObjectIterator ii;
80	–
61		#ifdef IS_MPI
62	<	if(worldRank == 0 ){
63	<	#endif
64	<	finalOut.open( outName.c_str(), std::ios::out | std::ios::trunc );
65	<	if( !finalOut ){
62	>	if(worldRank == 0){
63	>	#endif
64	>
65	>	output_ = new std::ofstream(filename.c_str());
66	>
67	>	if(!output_){
68		sprintf( painCave.errMsg,
69	<	"Could not open \"%s\" for zAngle output.\n",
70	<	outName.c_str() );
69	>	"Could not open %s for restraint output.\n",
70	>	filename.c_str());
71		painCave.isFatal = 1;
72		simError();
73		}
74	+
75		#ifdef IS_MPI
76		}
77		#endif // is_mpi
78	+
79	+
80	+	#ifdef IS_MPI
81	+	MPI::Status istatus;
82	+	#endif
83
84		#ifndef IS_MPI
85	<	// first we do output for the single processor version
86	<	finalOut
87	<	<< info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
88	<	<< " : omega values at this time\n";
89	<
90	<	for (mol = info_->beginMolecule(mi); mol != NULL;
91	<	mol = info_->nextMolecule(mi)) {
104	<
105	<	for (integrableObject = mol->beginIntegrableObject(ii);
106	<	integrableObject != NULL;
107	<	integrableObject = mol->nextIntegrableObject(ii)) {
85	>
86	>	(*output_) << "#time\t";
87	>
88	>	std::vector<Restraint*>::const_iterator resti;
89	>
90	>	for(resti=restraints.begin(); resti != restraints.end(); ++resti){
91	>	if ((*resti)->getPrintRestraint()) {
92
93	<	sprintf( tempBuffer,
94	<	"%14.10lf\n",
111	<	integrableObject->getZangle());
112	<	strcpy( writeLine, tempBuffer );
93	>	std::string myName = (*resti)->getRestraintName();
94	>	int myType = (*resti)->getRestraintType();
95
96	<	finalOut << writeLine;
96	>	(*output_) << myName << ":";
97	>
98	>	if (myType & Restraint::rtDisplacement)
99	>	(*output_) << "\tPosition(angstroms)\tEnergy(kcal/mol)";
100	>
101	>	if (myType & Restraint::rtTwist)
102	>	(*output_) << "\tTwistAngle(radians)\tEnergy(kcal/mol)";
103	>
104	>	if (myType & Restraint::rtSwingX)
105	>	(*output_) << "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
106	>
107	>	if (myType & Restraint::rtSwingY)
108	>	(*output_) << "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
109		}
116	–
110		}
111	+
112	+	(*output_) << "\n";
113	+	(*output_).flush();
114
115		#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();
116
117	<	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
118	<	MPI_Allreduce(&tmpNIntObjects[0], &nIntObjectsInProc[0], nproc, MPI_INT,
119	<	MPI_SUM, MPI_COMM_WORLD);
117	>	std::string buffer;
118	>
119	>	std::vector<Restraint*>::const_iterator resti;
120	>
121	>	for(resti=restraints.begin(); resti != restraints.end(); ++resti){
122	>	if ((*resti)->getPrintRestraint()) {
123	>
124	>	std::string myName = (*resti)->getRestraintName();
125	>	int myType = (*resti)->getRestraintType();
126	>
127	>	buffer += (myName + ":");
128	>
129	>	if (myType & Restraint::rtDisplacement)
130	>	buffer += "\tPosition(angstroms)\tEnergy(kcal/mol)";
131	>
132	>	if (myType & Restraint::rtTwist)
133	>	buffer += "\tTwistAngle(radians)\tEnergy(kcal/mol)";
134	>
135	>	if (myType & Restraint::rtSwingX)
136	>	buffer += "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
137	>
138	>	if (myType & Restraint::rtSwingY)
139	>	buffer += "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
140	>
141	>	buffer += "\n";
142	>	}
143	>	}
144
145	<	MPI_Status ierr;
146	<	int intObIndex;
134	<	RealType zAngle;
135	<
145	>	const int masterNode = 0;
146	>
147		if (worldRank == masterNode) {
148	<	std::map<int, RealType> zAngData;
149	<	for(int i = 0 ; i < nproc; ++i) {
150	<	if (i == masterNode) {
151	<	for (mol = info_->beginMolecule(mi); mol != NULL;
152	<	mol = info_->nextMolecule(mi)) {
153	<
154	<	for (integrableObject = mol->beginIntegrableObject(ii);
155	<	integrableObject != NULL;
156	<	integrableObject = mol->nextIntegrableObject(ii)) {
157	<
158	<	intObIndex = integrableObject->getGlobalIndex();
159	<
160	<	zAngle = integrableObject->getZangle();
150	<	zAngData.insert(std::pair<int, RealType>(intObIndex, zAngle));
151	<	}
152	<	}
148	>	(*output_) << "#time\t";
149	>	(*output_) << buffer;
150	>
151	>	int nProc = MPI::COMM_WORLD.Get_size();
152	>	for (int i = 1; i < nProc; ++i) {
153	>
154	>	// receive the length of the string buffer that was
155	>	// prepared by processor i
156	>
157	>	int recvLength;
158	>	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, 0, istatus);
159	>	char* recvBuffer = new char[recvLength];
160	>	if (recvBuffer == NULL) {
161		} else {
162	<	for (mol = info_->beginMolecule(mi); mol != NULL;
163	<	mol = info_->nextMolecule(mi)) {
164	<
165	<	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	<	}
162	>	MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i, 0,
163	>	istatus);
164	>	(*output_) << recvBuffer;
165	>	delete [] recvBuffer;
166		}
167	+	}
168	+	(*output_).flush();
169	+	} else {
170	+	int sendBufferLength = buffer.size() + 1;
171	+	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
172	+	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength, MPI::CHAR,
173	+	masterNode, 0);
174	+	}
175	+
176	+	#endif // is_mpi
177	+
178	+	}
179	+
180	+	void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo) {
181	+
182	+	#ifdef IS_MPI
183	+	MPI::Status istatus;
184	+	#endif
185	+
186	+	#ifndef IS_MPI
187	+	(*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
188	+
189	+	// output some information about the molecules
190	+	std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
191	+	std::map<int, Restraint::RealPair>::const_iterator j;
192	+
193	+	for( i = restInfo.begin(); i != restInfo.end(); ++i){
194	+	for(j = (*i).begin(); j != (*i).end(); ++j){
195	+	(*output_) << "\t" << (j->second).first << "\t" << (j->second).second;
196		}
197	<
198	<	finalOut
199	<	<< info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
200	<	<< " : omega values at this time\n";
201	<
202	<	std::map<int, RealType>::iterator l;
203	<	for (l = zAngData.begin(); l != zAngData.end(); ++l) {
204	<	sprintf( tempBuffer,
205	<	"%14.10lf\n",
206	<	l->second);
207	<	strcpy( writeLine, tempBuffer );
208	<
209	<	finalOut << writeLine;
197	>	(*output_) << std::endl;
198	>	}
199	>	(*output_).flush();
200	>	#else
201	>	std::string buffer, first, second;
202	>	std::stringstream ss;
203	>
204	>	std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
205	>	std::map<int, Restraint::RealPair>::const_iterator j;
206	>
207	>	for( i = restInfo.begin(); i != restInfo.end(); ++i){
208	>	for(j = (*i).begin(); j != (*i).end(); ++j){
209	>	ss.clear();
210	>	ss << (j->second).first;
211	>	ss >> first;
212	>	ss.clear();
213	>	ss << (j->second).second;
214	>	ss >> second;
215	>	buffer += ("\t" + first + "\t" + second);
216		}
217	<
218	<	finalOut.close();
217	>	buffer += "\n";
218	>	}
219	>
220	>	const int masterNode = 0;
221	>
222	>	if (worldRank == masterNode) {
223	>	(*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
224	>	(*output_) << buffer;
225
226	+	int nProc;
227	+	nProc = MPI::COMM_WORLD.Get_size();
228	+	for (int i = 1; i < nProc; ++i) {
229	+
230	+	// receive the length of the string buffer that was
231	+	// prepared by processor i
232	+
233	+	int recvLength;
234	+	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, 0, istatus);
235	+	char* recvBuffer = new char[recvLength];
236	+	if (recvBuffer == NULL) {
237	+	} else {
238	+	MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i, 0,
239	+	istatus);
240	+	(*output_) << recvBuffer;
241	+
242	+	delete [] recvBuffer;
243	+	}
244	+	}
245	+	(*output_).flush();
246		} else {
247	<	for(int j = 1; j < nproc; ++j) {
248	<	for (mol = info_->beginMolecule(mi); mol != NULL;
249	<	mol = info_->nextMolecule(mi)) {
250	<
251	<	for (integrableObject = mol->beginIntegrableObject(ii);
252	<	integrableObject != NULL;
253	<	integrableObject = mol->nextIntegrableObject(ii)) {
254	<	intObIndex = integrableObject->getGlobalIndex();
255	<	zAngle = integrableObject->getZangle();
256	<
257	<	MPI_Send(&intObIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
258	<	MPI_Send(&zAngle, 1, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD);
259	<	}
260	<	}
247	>	int sendBufferLength = buffer.size() + 1;
248	>	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
249	>	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
250	>	MPI::CHAR, masterNode, 0);
251	>	}
252	>	#endif // is_mpi
253	>	}
254	>
255	>
256	>	RestWriter::~RestWriter() {
257	>
258	>	#ifdef IS_MPI
259	>
260	>	if (worldRank == 0) {
261	>	#endif // is_mpi
262	>	if (createRestFile_){
263	>	writeClosing(*output_);
264	>	delete output_;
265		}
266	+	#ifdef IS_MPI
267		}
268	<
203	<	#endif
268	>	#endif // is_mpi
269		}
270
271	<	}
271	>	void RestWriter::writeClosing(std::ostream& os) {
272	>	os.flush();
273	>	}
274	>
275	>	}// end namespace OpenMD
276	>

Comparing:
trunk/src/io/RestWriter.cpp (property svn:keywords), Revision 990 by chrisfen, Mon Jun 19 01:36:06 2006 UTC vs.
branches/development/src/io/RestWriter.cpp (property svn:keywords), Revision 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC

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