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Comparing trunk/src/io/RestWriter.cpp (file contents):
Revision 1030 by chrisfen, Fri Sep 1 14:15:05 2006 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 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, 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	+
44	+	#include <string>
45	+	#include <sstream>
46	+	#include <iostream>
47	+
48		#include "io/RestWriter.hpp"
43	–	#include "primitives/Molecule.hpp"
49		#include "utils/simError.h"
50	<	#include "io/basic_teebuf.hpp"
46	<
50	>	#include "brains/SnapshotManager.hpp"
51		#ifdef IS_MPI
52		#include <mpi.h>
53	<	#define TAKE_THIS_TAG_INT 1
50	<	#define TAKE_THIS_TAG_REAL 2
51	<	#endif //is_mpi
53	>	#endif
54
55	<	namespace oopse {
56	<	RestWriter::RestWriter(SimInfo* info) :
57	<	info_(info), outName_(info_->getRestFileName()) {
58	<	}
59	<
58	<	RestWriter::~RestWriter() {}
59	<
60	<	void RestWriter::writeZAngFile() {
61	<	std::ostream* zangStream;
55	>	namespace OpenMD {
56	>	RestWriter::RestWriter(SimInfo* info, const std::string& filename,
57	>	std::vector<Restraint*> restraints ) :
58	>	info_(info){
59	>	createRestFile_ = true;
60
61		#ifdef IS_MPI
62	<	if (worldRank == 0) {
63	<	#endif // is_mpi
64	<
65	<	zangStream = new std::ofstream(outName_.c_str());
66	<
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 restraint output.\n",
70	>	filename.c_str());
71	>	painCave.isFatal = 1;
72	>	simError();
73	>	}
74	>
75		#ifdef IS_MPI
76		}
71	–	#endif // is_mpi
72	–
73	–	writeZangle(*zangStream);
74	–
75	–	#ifdef IS_MPI
76	–	if (worldRank == 0) {
77		#endif // is_mpi
78	<	delete zangStream;
79	<
78	>
79	>
80		#ifdef IS_MPI
81	<	}
82	<	#endif // is_mpi
81	>	MPI_Status istatus;
82	>	#endif
83
84	<	}
84	>	#ifndef IS_MPI
85	>
86	>	(*output_) << "#time\t";
87
88	<	void RestWriter::writeZangle(std::ostream& finalOut){
89	<	const int BUFFERSIZE = 2000;
90	<	char tempBuffer[BUFFERSIZE];
91	<	char writeLine[BUFFERSIZE];
88	>	std::vector<Restraint*>::const_iterator resti;
89	>
90	>	for(resti=restraints.begin(); resti != restraints.end(); ++resti){
91	>	if ((*resti)->getPrintRestraint()) {
92	>
93	>	std::string myName = (*resti)->getRestraintName();
94	>	int myType = (*resti)->getRestraintType();
95	>
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	>	}
110	>	}
111	>
112	>	(*output_) << "\n";
113	>	(*output_).flush();
114
115	<	Molecule* mol;
92	<	StuntDouble* integrableObject;
93	<	SimInfo::MoleculeIterator mi;
94	<	Molecule::IntegrableObjectIterator ii;
115	>	#else
116
117	<	#ifndef IS_MPI
118	<	// first we do output for the single processor version
119	<	finalOut
120	<	<< info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
121	<	<< " : omega values at this time\n";
122	<
102	<	for (mol = info_->beginMolecule(mi); mol != NULL;
103	<	mol = info_->nextMolecule(mi)) {
104	<
105	<	for (integrableObject = mol->beginIntegrableObject(ii);
106	<	integrableObject != NULL;
107	<	integrableObject = mol->nextIntegrableObject(ii)) {
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	<	sprintf( tempBuffer,
125	<	"%14.10lf\n",
111	<	integrableObject->getZangle());
112	<	strcpy( writeLine, tempBuffer );
113	<
114	<	finalOut << writeLine;
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
119	–	#else
120	–	int nproc;
121	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
145		const int masterNode = 0;
146
124	–	MPI_Status ierr;
125	–	int intObIndex;
126	–	int vecLength;
127	–	RealType zAngle;
128	–	std::vector<int> gIndex;
129	–	std::vector<RealType> zValues;
130	–
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->getGlobalIntegrableObjectIndex();
159	<
160	<	zAngle = integrableObject->getZangle();
161	<	zAngData.insert(std::pair<int, RealType>(intObIndex, zAngle));
146	<	}
147	<	}
148	>	(*output_) << "#time\t";
149	>	(*output_) << buffer;
150	>
151	>	int nProc;
152	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
153	>	for (int i = 1; i < nProc; ++i) {
154	>
155	>	// receive the length of the string buffer that was
156	>	// prepared by processor i
157	>
158	>	int recvLength;
159	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
160	>	char* recvBuffer = new char[recvLength];
161	>	if (recvBuffer == NULL) {
162		} else {
163	<	MPI_Recv(&vecLength, 1, MPI_INT, i,
164	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &ierr);
165	<	// make sure the vectors are the right size for the incoming data
166	<	gIndex.resize(vecLength);
153	<	zValues.resize(vecLength);
154	<
155	<	MPI_Recv(&gIndex[0], vecLength, MPI_INT, i,
156	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &ierr);
157	<	MPI_Recv(&zValues[0], vecLength, MPI_REALTYPE, i,
158	<	TAKE_THIS_TAG_REAL, MPI_COMM_WORLD, &ierr);
159	<
160	<	for (int k = 0; k < vecLength; k++){
161	<	zAngData.insert(std::pair<int, RealType>(gIndex[k], zValues[k]));
162	<	}
163	<	gIndex.clear();
164	<	zValues.clear();
163	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
164	>	&istatus);
165	>	(*output_) << recvBuffer;
166	>	delete [] recvBuffer;
167		}
168	+	}
169	+	(*output_).flush();
170	+	} else {
171	+	int sendBufferLength = buffer.size() + 1;
172	+	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
173	+	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode,
174	+	0, MPI_COMM_WORLD);
175	+	}
176	+
177	+	#endif // is_mpi
178	+
179	+	}
180	+
181	+	void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo) {
182	+
183	+	#ifdef IS_MPI
184	+	MPI_Status istatus;
185	+	#endif
186	+
187	+	#ifndef IS_MPI
188	+	(*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
189	+
190	+	// output some information about the molecules
191	+	std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
192	+	std::map<int, Restraint::RealPair>::const_iterator j;
193	+
194	+	for( i = restInfo.begin(); i != restInfo.end(); ++i){
195	+	for(j = (*i).begin(); j != (*i).end(); ++j){
196	+	(*output_) << "\t" << (j->second).first << "\t" << (j->second).second;
197		}
198	<
199	<	finalOut << 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	<
205	<	sprintf( tempBuffer,
206	<	"%14.10lf\n",
207	<	l->second);
208	<	strcpy( writeLine, tempBuffer );
209	<
210	<	finalOut << writeLine;
198	>	(*output_) << std::endl;
199	>	}
200	>	(*output_).flush();
201	>	#else
202	>	std::string buffer, first, second;
203	>	std::stringstream ss;
204	>
205	>	std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
206	>	std::map<int, Restraint::RealPair>::const_iterator j;
207	>
208	>	for( i = restInfo.begin(); i != restInfo.end(); ++i){
209	>	for(j = (*i).begin(); j != (*i).end(); ++j){
210	>	ss.clear();
211	>	ss << (j->second).first;
212	>	ss >> first;
213	>	ss.clear();
214	>	ss << (j->second).second;
215	>	ss >> second;
216	>	buffer += ("\t" + first + "\t" + second);
217		}
218	+	buffer += "\n";
219	+	}
220	+
221	+	const int masterNode = 0;
222	+
223	+	if (worldRank == masterNode) {
224	+	(*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
225	+	(*output_) << buffer;
226
227	+	int nProc;
228	+	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
229	+	for (int i = 1; i < nProc; ++i) {
230	+
231	+	// receive the length of the string buffer that was
232	+	// prepared by processor i
233	+
234	+	int recvLength;
235	+	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
236	+	char* recvBuffer = new char[recvLength];
237	+	if (recvBuffer == NULL) {
238	+	} else {
239	+	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
240	+	&istatus);
241	+	(*output_) << recvBuffer;
242	+
243	+	delete [] recvBuffer;
244	+	}
245	+	}
246	+	(*output_).flush();
247		} else {
248	<	// pack up and send the appropriate info to the master node
249	<	for(int j = 1; j < nproc; ++j) {
250	<	if (worldRank == j) {
251	<	for (mol = info_->beginMolecule(mi); mol != NULL;
252	<	mol = info_->nextMolecule(mi)) {
253	<
254	<	for (integrableObject = mol->beginIntegrableObject(ii);
255	<	integrableObject != NULL;
256	<	integrableObject = mol->nextIntegrableObject(ii)) {
257	<
258	<	// build a vector of the indicies
259	<	intObIndex = integrableObject->getGlobalIntegrableObjectIndex();
260	<	gIndex.push_back(intObIndex);
261	<
262	<	// build a vector of the zAngle values
263	<	zAngle = integrableObject->getZangle();
264	<	zValues.push_back(zAngle);
265	<
201	<	}
202	<	}
203	<
204	<	// let's send these vectors to the master node so that it
205	<	// can sort them and write to the disk
206	<	vecLength = gIndex.size();
207	<
208	<	MPI_Send(&vecLength, 1, MPI_INT, masterNode,
209	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
210	<	MPI_Send(&gIndex[0], vecLength, MPI_INT, masterNode,
211	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
212	<	MPI_Send(&zValues[0], vecLength, MPI_REALTYPE, masterNode,
213	<	TAKE_THIS_TAG_REAL, MPI_COMM_WORLD);
214	<
215	<	}
248	>	int sendBufferLength = buffer.size() + 1;
249	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
250	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode,
251	>	0, MPI_COMM_WORLD);
252	>	}
253	>	#endif // is_mpi
254	>	}
255	>
256	>
257	>	RestWriter::~RestWriter() {
258	>
259	>	#ifdef IS_MPI
260	>
261	>	if (worldRank == 0) {
262	>	#endif // is_mpi
263	>	if (createRestFile_){
264	>	writeClosing(*output_);
265	>	delete output_;
266		}
267	+	#ifdef IS_MPI
268		}
269	<
219	<	#endif
269	>	#endif // is_mpi
270		}
271
272	<	}
272	>	void RestWriter::writeClosing(std::ostream& os) {
273	>	os.flush();
274	>	}
275	>
276	>	}// end namespace OpenMD
277	>

Comparing trunk/src/io/RestWriter.cpp (property svn:keywords):
Revision 1030 by chrisfen, Fri Sep 1 14:15:05 2006 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

#	Line 0 | Line 1
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