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root/OpenMD/trunk/src/io/RestWriter.cpp

Comparing trunk/src/io/RestWriter.cpp (file contents):
Revision 1030 by chrisfen, Fri Sep 1 14:15:05 2006 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 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	+	#ifdef IS_MPI
44	+	#include <mpi.h>
45	+	#endif
46	+
47	+	#include <string>
48	+	#include <sstream>
49	+	#include <iostream>
50	+
51		#include "io/RestWriter.hpp"
43	–	#include "primitives/Molecule.hpp"
52		#include "utils/simError.h"
53	<	#include "io/basic_teebuf.hpp"
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	+	createRestFile_ = true;
60	+
61		#ifdef IS_MPI
62	<	#include <mpi.h>
63	<	#define TAKE_THIS_TAG_INT 1
50	<	#define TAKE_THIS_TAG_REAL 2
51	<	#endif //is_mpi
52	<
53	<	namespace oopse {
54	<	RestWriter::RestWriter(SimInfo* info) :
55	<	info_(info), outName_(info_->getRestFileName()) {
56	<	}
62	>	if(worldRank == 0){
63	>	#endif
64
65	<	RestWriter::~RestWriter() {}
66	<
67	<	void RestWriter::writeZAngFile() {
68	<	std::ostream* zangStream;
69	<
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
64	–	if (worldRank == 0) {
65	–	#endif // is_mpi
66	–
67	–	zangStream = new std::ofstream(outName_.c_str());
68	–
69	–	#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)) {
137	<
138	<	for (integrableObject = mol->beginIntegrableObject(ii);
139	<	integrableObject != NULL;
140	<	integrableObject = mol->nextIntegrableObject(ii)) {
141	<
142	<	intObIndex = integrableObject->getGlobalIntegrableObjectIndex();
148	>	(*output_) << "#time\t";
149	>	(*output_) << buffer;
150	>
151	>	int nProc;
152	>	MPI_Comm_size( MPI_COMM_WORLD, &nProc);
153
154	<	zAngle = integrableObject->getZangle();
155	<	zAngData.insert(std::pair<int, RealType>(intObIndex, zAngle));
156	<	}
157	<	}
154	>	for (int i = 1; i < nProc; ++i) {
155	>
156	>	// receive the length of the string buffer that was
157	>	// prepared by processor i
158	>
159	>	int recvLength;
160	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, istatus);
161	>	char* recvBuffer = new char[recvLength];
162	>	if (recvBuffer == NULL) {
163		} else {
164	<	MPI_Recv(&vecLength, 1, MPI_INT, i,
165	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &ierr);
166	<	// make sure the vectors are the right size for the incoming data
167	<	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();
164	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
165	>	istatus);
166	>	(*output_) << recvBuffer;
167	>	delete [] recvBuffer;
168		}
169	+	}
170	+	(*output_).flush();
171	+	} else {
172	+	int sendBufferLength = buffer.size() + 1;
173	+	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
174	+	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR,
175	+	masterNode, 0, MPI_COMM_WORLD);
176	+	}
177	+
178	+	#endif // is_mpi
179	+
180	+	}
181	+
182	+	void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo) {
183	+
184	+	#ifdef IS_MPI
185	+	MPI_Status* istatus;
186	+	#endif
187	+
188	+	#ifndef IS_MPI
189	+	(*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
190	+
191	+	// output some information about the molecules
192	+	std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
193	+	std::map<int, Restraint::RealPair>::const_iterator j;
194	+
195	+	for( i = restInfo.begin(); i != restInfo.end(); ++i){
196	+	for(j = (*i).begin(); j != (*i).end(); ++j){
197	+	(*output_) << "\t" << (j->second).first << "\t" << (j->second).second;
198		}
199	<
200	<	finalOut << info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
201	<	<< " : omega values at this time\n";
202	<
203	<	std::map<int, RealType>::iterator l;
204	<	for (l = zAngData.begin(); l != zAngData.end(); ++l) {
205	<
206	<	sprintf( tempBuffer,
207	<	"%14.10lf\n",
208	<	l->second);
209	<	strcpy( writeLine, tempBuffer );
210	<
211	<	finalOut << writeLine;
199	>	(*output_) << std::endl;
200	>	}
201	>	(*output_).flush();
202	>	#else
203	>	std::string buffer, first, second;
204	>	std::stringstream ss;
205	>
206	>	std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
207	>	std::map<int, Restraint::RealPair>::const_iterator j;
208	>
209	>	for( i = restInfo.begin(); i != restInfo.end(); ++i){
210	>	for(j = (*i).begin(); j != (*i).end(); ++j){
211	>	ss.clear();
212	>	ss << (j->second).first;
213	>	ss >> first;
214	>	ss.clear();
215	>	ss << (j->second).second;
216	>	ss >> second;
217	>	buffer += ("\t" + first + "\t" + second);
218		}
219	+	buffer += "\n";
220	+	}
221	+
222	+	const int masterNode = 0;
223	+
224	+	if (worldRank == masterNode) {
225	+	(*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
226	+	(*output_) << buffer;
227
228	+	int nProc;
229	+	MPI_Comm_size( MPI_COMM_WORLD, &nProc);
230	+	for (int i = 1; i < nProc; ++i) {
231	+
232	+	// receive the length of the string buffer that was
233	+	// prepared by processor i
234	+
235	+	int recvLength;
236	+	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, istatus);
237	+	char* recvBuffer = new char[recvLength];
238	+	if (recvBuffer == NULL) {
239	+	} else {
240	+	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
241	+	istatus);
242	+	(*output_) << recvBuffer;
243	+
244	+	delete [] recvBuffer;
245	+	}
246	+	}
247	+	(*output_).flush();
248		} else {
249	<	// pack up and send the appropriate info to the master node
250	<	for(int j = 1; j < nproc; ++j) {
251	<	if (worldRank == j) {
252	<	for (mol = info_->beginMolecule(mi); mol != NULL;
253	<	mol = info_->nextMolecule(mi)) {
254	<
255	<	for (integrableObject = mol->beginIntegrableObject(ii);
256	<	integrableObject != NULL;
257	<	integrableObject = mol->nextIntegrableObject(ii)) {
258	<
259	<	// build a vector of the indicies
260	<	intObIndex = integrableObject->getGlobalIntegrableObjectIndex();
261	<	gIndex.push_back(intObIndex);
262	<
263	<	// build a vector of the zAngle values
264	<	zAngle = integrableObject->getZangle();
265	<	zValues.push_back(zAngle);
266	<
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	<	}
249	>	int sendBufferLength = buffer.size() + 1;
250	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
251	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
252	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
253	>	}
254	>	#endif // is_mpi
255	>	}
256	>
257	>
258	>	RestWriter::~RestWriter() {
259	>
260	>	#ifdef IS_MPI
261	>
262	>	if (worldRank == 0) {
263	>	#endif // is_mpi
264	>	if (createRestFile_){
265	>	writeClosing(*output_);
266	>	delete output_;
267		}
268	+	#ifdef IS_MPI
269		}
270	<
219	<	#endif
270	>	#endif // is_mpi
271		}
272
273	<	}
273	>	void RestWriter::writeClosing(std::ostream& os) {
274	>	os.flush();
275	>	}
276	>
277	>	}// end namespace OpenMD
278	>

Comparing trunk/src/io/RestWriter.cpp (property svn:keywords):
Revision 1030 by chrisfen, Fri Sep 1 14:15:05 2006 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

#	Line 0 | Line 1
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