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

Comparing:
trunk/src/io/DumpWriter.cpp (file contents), Revision 376 by tim, Thu Feb 24 20:55:07 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1711 by gezelter, Sat May 19 02:58:35 2012 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
1	>	/*
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		#include "io/DumpWriter.hpp"
44		#include "primitives/Molecule.hpp"
45		#include "utils/simError.h"
46		#include "io/basic_teebuf.hpp"
47	+	#include "io/gzstream.hpp"
48	+	#include "io/Globals.hpp"
49	+
50	+
51		#ifdef IS_MPI
52		#include <mpi.h>
53		#endif //is_mpi
54
55	<	namespace oopse {
55	>	using namespace std;
56	>	namespace OpenMD {
57
58	<	DumpWriter::DumpWriter(SimInfo* info)
59	<	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
58	>	DumpWriter::DumpWriter(SimInfo* info)
59	>	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
60	>
61	>	Globals* simParams = info->getSimParams();
62	>	needCompression_ = simParams->getCompressDumpFile();
63	>	needForceVector_ = simParams->getOutputForceVector();
64	>	needParticlePot_ = simParams->getOutputParticlePotential();
65	>	cerr << "DW npp = " << needParticlePot_ << "\n";
66	>	createDumpFile_ = true;
67	>	#ifdef HAVE_LIBZ
68	>	if (needCompression_) {
69	>	filename_ += ".gz";
70	>	eorFilename_ += ".gz";
71	>	}
72	>	#endif
73	>
74		#ifdef IS_MPI
75
76		if (worldRank == 0) {
77		#endif // is_mpi
78	+
79	+	dumpFile_ = createOStream(filename_);
80
81	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
81	>	if (!dumpFile_) {
82	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
83	>	filename_.c_str());
84	>	painCave.isFatal = 1;
85	>	simError();
86	>	}
87
61	–	if (!dumpFile_) {
62	–	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
63	–	filename_.c_str());
64	–	painCave.isFatal = 1;
65	–	simError();
66	–	}
67	–
88		#ifdef IS_MPI
89
90		}
91
72	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73	–	MPIcheckPoint();
74	–
92		#endif // is_mpi
93
94	<	}
94	>	}
95
96
97	<	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
98	<	: info_(info), filename_(filename){
97	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
98	>	: info_(info), filename_(filename){
99	>
100	>	Globals* simParams = info->getSimParams();
101	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
102	>
103	>	needCompression_ = simParams->getCompressDumpFile();
104	>	needForceVector_ = simParams->getOutputForceVector();
105	>	createDumpFile_ = true;
106	>	#ifdef HAVE_LIBZ
107	>	if (needCompression_) {
108	>	filename_ += ".gz";
109	>	eorFilename_ += ".gz";
110	>	}
111	>	#endif
112	>
113		#ifdef IS_MPI
114
115		if (worldRank == 0) {
116		#endif // is_mpi
117
118	<	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
119	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
118	>
119	>	dumpFile_ = createOStream(filename_);
120
121	<	if (!dumpFile_) {
122	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
123	<	filename_.c_str());
124	<	painCave.isFatal = 1;
125	<	simError();
126	<	}
121	>	if (!dumpFile_) {
122	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
123	>	filename_.c_str());
124	>	painCave.isFatal = 1;
125	>	simError();
126	>	}
127
128		#ifdef IS_MPI
129
130		}
131
132	<	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
102	<	MPIcheckPoint();
132	>	#endif // is_mpi
133
134	+	}
135	+
136	+	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
137	+	: info_(info), filename_(filename){
138	+
139	+	Globals* simParams = info->getSimParams();
140	+	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
141	+
142	+	needCompression_ = simParams->getCompressDumpFile();
143	+	needForceVector_ = simParams->getOutputForceVector();
144	+	needParticlePot_ = simParams->getOutputParticlePotential();
145	+
146	+	#ifdef HAVE_LIBZ
147	+	if (needCompression_) {
148	+	filename_ += ".gz";
149	+	eorFilename_ += ".gz";
150	+	}
151	+	#endif
152	+
153	+	#ifdef IS_MPI
154	+
155	+	if (worldRank == 0) {
156		#endif // is_mpi
157	+
158	+	createDumpFile_ = writeDumpFile;
159	+	if (createDumpFile_) {
160	+	dumpFile_ = createOStream(filename_);
161	+
162	+	if (!dumpFile_) {
163	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
164	+	filename_.c_str());
165	+	painCave.isFatal = 1;
166	+	simError();
167	+	}
168	+	}
169	+	#ifdef IS_MPI
170	+
171	+	}
172
173	<	}
173	>
174	>	#endif // is_mpi
175	>
176	>	}
177
178	<	DumpWriter::~DumpWriter() {
178	>	DumpWriter::~DumpWriter() {
179
180		#ifdef IS_MPI
181
182		if (worldRank == 0) {
183		#endif // is_mpi
184	<
185	<	dumpFile_.close();
186	<
184	>	if (createDumpFile_){
185	>	writeClosing(*dumpFile_);
186	>	delete dumpFile_;
187	>	}
188		#ifdef IS_MPI
189
190		}
191
192		#endif // is_mpi
193
194	<	}
194	>	}
195
196	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
196	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
197
198	<	double currentTime;
199	<	Mat3x3d hmat;
200	<	double chi;
201	<	double integralOfChiDt;
202	<	Mat3x3d eta;
198	>	char buffer[1024];
199	>
200	>	os << "    <FrameData>\n";
201	>
202	>	RealType currentTime = s->getTime();
203	>
204	>	if (isinf(currentTime) || isnan(currentTime)) {
205	>	sprintf( painCave.errMsg,
206	>	"DumpWriter detected a numerical error writing the time");
207	>	painCave.isFatal = 1;
208	>	simError();
209	>	}
210
211	<	currentTime = s->getTime();
211	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
212	>	os << buffer;
213	>
214	>	Mat3x3d hmat;
215		hmat = s->getHmat();
216	<	chi = s->getChi();
217	<	integralOfChiDt = s->getIntegralOfChiDt();
218	<	eta = s->getEta();
216	>
217	>	for (unsigned int i = 0; i < 3; i++) {
218	>	for (unsigned int j = 0; j < 3; j++) {
219	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
220	>	sprintf( painCave.errMsg,
221	>	"DumpWriter detected a numerical error writing the box");
222	>	painCave.isFatal = 1;
223	>	simError();
224	>	}
225	>	}
226	>	}
227
228	<	os << currentTime << ";\t"
229	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
230	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
231	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
228	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
229	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
230	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
231	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
232	>	os << buffer;
233
234	<	//write out additional parameters, such as chi and eta
234	>	RealType chi = s->getChi();
235	>	RealType integralOfChiDt = s->getIntegralOfChiDt();
236	>	if (isinf(chi) || isnan(chi) ||
237	>	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
238	>	sprintf( painCave.errMsg,
239	>	"DumpWriter detected a numerical error writing the thermostat");
240	>	painCave.isFatal = 1;
241	>	simError();
242	>	}
243	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
244	>	os << buffer;
245
246	<	os << chi << "\t" << integralOfChiDt << "\t;";
246	>	Mat3x3d eta;
247	>	eta = s->getEta();
248
249	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
250	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
251	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
252	<
253	<	os << "\n";
254	<	}
249	>	for (unsigned int i = 0; i < 3; i++) {
250	>	for (unsigned int j = 0; j < 3; j++) {
251	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
252	>	sprintf( painCave.errMsg,
253	>	"DumpWriter detected a numerical error writing the barostat");
254	>	painCave.isFatal = 1;
255	>	simError();
256	>	}
257	>	}
258	>	}
259
260	<	void DumpWriter::writeFrame(std::ostream& os) {
261	<	const int BUFFERSIZE = 2000;
262	<	const int MINIBUFFERSIZE = 100;
260	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
261	>	eta(0, 0), eta(1, 0), eta(2, 0),
262	>	eta(0, 1), eta(1, 1), eta(2, 1),
263	>	eta(0, 2), eta(1, 2), eta(2, 2));
264	>	os << buffer;
265
266	<	char tempBuffer[BUFFERSIZE];
267	<	char writeLine[BUFFERSIZE];
266	>	os << "    </FrameData>\n";
267	>	}
268
269	<	Quat4d q;
163	<	Vector3d ji;
164	<	Vector3d pos;
165	<	Vector3d vel;
269	>	void DumpWriter::writeFrame(std::ostream& os) {
270
271	+	#ifdef IS_MPI
272	+	MPI_Status istatus;
273	+	#endif
274	+
275		Molecule* mol;
276		StuntDouble* integrableObject;
277		SimInfo::MoleculeIterator mi;
278		Molecule::IntegrableObjectIterator ii;
171	–
172	–	int nTotObjects;
173	–	nTotObjects = info_->getNGlobalIntegrableObjects();
279
280		#ifndef IS_MPI
281	+	os << "  <Snapshot>\n";
282	+
283	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
284
285	+	os << "    <StuntDoubles>\n";
286	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
287
288	<	os << nTotObjects << "\n";
289	<
290	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
288	>
289	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
290	>	integrableObject = mol->nextIntegrableObject(ii)) {
291	>	os << prepareDumpLine(integrableObject);
292	>
293	>	}
294	>	}
295	>	os << "    </StuntDoubles>\n";
296	>
297	>	os << "  </Snapshot>\n";
298
299	+	os.flush();
300	+	#else
301	+	//every node prepares the dump lines for integrable objects belong to itself
302	+	std::string buffer;
303		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
304
184	–	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
185	–	integrableObject = mol->nextIntegrableObject(ii)) {
186	–
305
306	<	pos = integrableObject->getPos();
307	<	vel = integrableObject->getVel();
306	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
307	>	integrableObject = mol->nextIntegrableObject(ii)) {
308	>	buffer += prepareDumpLine(integrableObject);
309	>	}
310	>	}
311	>
312	>	const int masterNode = 0;
313	>	int nProc;
314	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
315	>	if (worldRank == masterNode) {
316	>	os << "  <Snapshot>\n";
317	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
318	>	os << "    <StuntDoubles>\n";
319	>
320	>	os << buffer;
321
322	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
192	<	integrableObject->getType().c_str(),
193	<	pos[0], pos[1], pos[2],
194	<	vel[0], vel[1], vel[2]);
322	>	for (int i = 1; i < nProc; ++i) {
323
324	<	strcpy(writeLine, tempBuffer);
324	>	// receive the length of the string buffer that was
325	>	// prepared by processor i
326
327	<	if (integrableObject->isDirectional()) {
328	<	q = integrableObject->getQ();
329	<	ji = integrableObject->getJ();
327	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
328	>	int recvLength;
329	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
330	>	char* recvBuffer = new char[recvLength];
331	>	if (recvBuffer == NULL) {
332	>	} else {
333	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
334	>	os << recvBuffer;
335	>	delete [] recvBuffer;
336	>	}
337	>	}
338	>	os << "    </StuntDoubles>\n";
339	>
340	>	os << "  </Snapshot>\n";
341	>	os.flush();
342	>	} else {
343	>	int sendBufferLength = buffer.size() + 1;
344	>	int myturn = 0;
345	>	for (int i = 1; i < nProc; ++i){
346	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
347	>	if (myturn == worldRank){
348	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
349	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
350	>	}
351	>	}
352	>	}
353
354	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
203	<	q[0], q[1], q[2], q[3],
204	<	ji[0], ji[1], ji[2]);
205	<	strcat(writeLine, tempBuffer);
206	<	} else {
207	<	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
208	<	}
354	>	#endif // is_mpi
355
356	<	os << writeLine;
356	>	}
357
358	<	}
359	<	}
358	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
359	>
360	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
361	>	std::string type("pv");
362	>	std::string line;
363	>	char tempBuffer[4096];
364
365	<	os.flush();
366	<	#else // is_mpi
367	<	/*********************************************************************
218	<	* Documentation?  You want DOCUMENTATION?
219	<	*
220	<	* Why all the potatoes below?
221	<	*
222	<	* To make a long story short, the original version of DumpWriter
223	<	* worked in the most inefficient way possible.  Node 0 would
224	<	* poke each of the node for an individual atom's formatted data
225	<	* as node 0 worked its way down the global index. This was particularly
226	<	* inefficient since the method blocked all processors at every atom
227	<	* (and did it twice!).
228	<	*
229	<	* An intermediate version of DumpWriter could be described from Node
230	<	* zero's perspective as follows:
231	<	*
232	<	*  1) Have 100 of your friends stand in a circle.
233	<	*  2) When you say go, have all of them start tossing potatoes at
234	<	*     you (one at a time).
235	<	*  3) Catch the potatoes.
236	<	*
237	<	* It was an improvement, but MPI has buffers and caches that could
238	<	* best be described in this analogy as "potato nets", so there's no
239	<	* need to block the processors atom-by-atom.
240	<	*
241	<	* This new and improved DumpWriter works in an even more efficient
242	<	* way:
243	<	*
244	<	*  1) Have 100 of your friend stand in a circle.
245	<	*  2) When you say go, have them start tossing 5-pound bags of
246	<	*     potatoes at you.
247	<	*  3) Once you've caught a friend's bag of potatoes,
248	<	*     toss them a spud to let them know they can toss another bag.
249	<	*
250	<	* How's THAT for documentation?
251	<	*
252	<	*********************************************************************/
253	<	const int masterNode = 0;
365	>	Vector3d pos;
366	>	Vector3d vel;
367	>	pos = integrableObject->getPos();
368
369	<	int * potatoes;
370	<	int myPotato;
371	<	int nProc;
372	<	int which_node;
373	<	double atomData[13];
374	<	int isDirectional;
375	<	const char * atomTypeString;
376	<	char MPIatomTypeString[MINIBUFFERSIZE];
377	<	int msgLen; // the length of message actually recieved at master nodes
264	<	int haveError;
265	<	MPI_Status istatus;
266	<	int nCurObj;
267	<
268	<	// code to find maximum tag value
269	<	int * tagub;
270	<	int flag;
271	<	int MAXTAG;
272	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
369	>	if (isinf(pos[0]) || isnan(pos[0]) ||
370	>	isinf(pos[1]) || isnan(pos[1]) ||
371	>	isinf(pos[2]) || isnan(pos[2]) ) {
372	>	sprintf( painCave.errMsg,
373	>	"DumpWriter detected a numerical error writing the position"
374	>	" for object %d", index);
375	>	painCave.isFatal = 1;
376	>	simError();
377	>	}
378
379	<	if (flag) {
380	<	MAXTAG = *tagub;
381	<	} else {
382	<	MAXTAG = 32767;
379	>	vel = integrableObject->getVel();
380	>
381	>	if (isinf(vel[0]) || isnan(vel[0]) ||
382	>	isinf(vel[1]) || isnan(vel[1]) ||
383	>	isinf(vel[2]) || isnan(vel[2]) ) {
384	>	sprintf( painCave.errMsg,
385	>	"DumpWriter detected a numerical error writing the velocity"
386	>	" for object %d", index);
387	>	painCave.isFatal = 1;
388	>	simError();
389		}
390
391	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
391	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
392	>	pos[0], pos[1], pos[2],
393	>	vel[0], vel[1], vel[2]);
394	>	line += tempBuffer;
395
396	<	// Node 0 needs a list of the magic potatoes for each processor;
396	>	if (integrableObject->isDirectional()) {
397	>	type += "qj";
398	>	Quat4d q;
399	>	Vector3d ji;
400	>	q = integrableObject->getQ();
401
402	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
403	<	potatoes = new int[nProc];
402	>	if (isinf(q[0]) || isnan(q[0]) ||
403	>	isinf(q[1]) || isnan(q[1]) ||
404	>	isinf(q[2]) || isnan(q[2]) ||
405	>	isinf(q[3]) || isnan(q[3]) ) {
406	>	sprintf( painCave.errMsg,
407	>	"DumpWriter detected a numerical error writing the quaternion"
408	>	" for object %d", index);
409	>	painCave.isFatal = 1;
410	>	simError();
411	>	}
412
413	<	//write out the comment lines
288	<	for(int i = 0; i < nProc; i++) {
289	<	potatoes[i] = 0;
290	<	}
413	>	ji = integrableObject->getJ();
414
415	+	if (isinf(ji[0]) || isnan(ji[0]) ||
416	+	isinf(ji[1]) || isnan(ji[1]) ||
417	+	isinf(ji[2]) || isnan(ji[2]) ) {
418	+	sprintf( painCave.errMsg,
419	+	"DumpWriter detected a numerical error writing the angular"
420	+	" momentum for object %d", index);
421	+	painCave.isFatal = 1;
422	+	simError();
423	+	}
424
425	<	os << nTotObjects << "\n";
426	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
425	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
426	>	q[0], q[1], q[2], q[3],
427	>	ji[0], ji[1], ji[2]);
428	>	line += tempBuffer;
429	>	}
430
431	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
431	>	if (needForceVector_) {
432	>	type += "f";
433	>	Vector3d frc;
434
435	<	// Get the Node number which has this atom;
435	>	frc = integrableObject->getFrc();
436
437	<	which_node = info_->getMolToProc(i);
437	>	if (isinf(frc[0]) || isnan(frc[0]) ||
438	>	isinf(frc[1]) || isnan(frc[1]) ||
439	>	isinf(frc[2]) || isnan(frc[2]) ) {
440	>	sprintf( painCave.errMsg,
441	>	"DumpWriter detected a numerical error writing the force"
442	>	" for object %d", index);
443	>	painCave.isFatal = 1;
444	>	simError();
445	>	}
446	>	sprintf(tempBuffer, " %13e %13e %13e",
447	>	frc[0], frc[1], frc[2]);
448	>	line += tempBuffer;
449	>
450	>	if (integrableObject->isDirectional()) {
451	>	type += "t";
452	>	Vector3d trq;
453	>
454	>	trq = integrableObject->getTrq();
455	>
456	>	if (isinf(trq[0]) || isnan(trq[0]) ||
457	>	isinf(trq[1]) || isnan(trq[1]) ||
458	>	isinf(trq[2]) || isnan(trq[2]) ) {
459	>	sprintf( painCave.errMsg,
460	>	"DumpWriter detected a numerical error writing the torque"
461	>	" for object %d", index);
462	>	painCave.isFatal = 1;
463	>	simError();
464	>	}
465	>
466	>	sprintf(tempBuffer, " %13e %13e %13e",
467	>	trq[0], trq[1], trq[2]);
468	>	line += tempBuffer;
469	>	}
470	>	}
471	>	if (needParticlePot_) {
472	>	type += "u";
473	>	RealType particlePot;
474
475	<	if (which_node != masterNode) { //current molecule is in slave node
303	<	if (potatoes[which_node] + 1 >= MAXTAG) {
304	<	// The potato was going to exceed the maximum value,
305	<	// so wrap this processor potato back to 0:
475	>	particlePot = integrableObject->getParticlePot();
476
477	<	potatoes[which_node] = 0;
478	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
479	<	MPI_COMM_WORLD);
480	<	}
481	<
482	<	myPotato = potatoes[which_node];
483	<
484	<	//recieve the number of integrableObject in current molecule
485	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
316	<	MPI_COMM_WORLD, &istatus);
317	<	myPotato++;
318	<
319	<	for(int l = 0; l < nCurObj; l++) {
320	<	if (potatoes[which_node] + 2 >= MAXTAG) {
321	<	// The potato was going to exceed the maximum value,
322	<	// so wrap this processor potato back to 0:
323	<
324	<	potatoes[which_node] = 0;
325	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
326	<	0, MPI_COMM_WORLD);
327	<	}
328	<
329	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
330	<	which_node, myPotato, MPI_COMM_WORLD,
331	<	&istatus);
332	<
333	<	atomTypeString = MPIatomTypeString;
334	<
335	<	myPotato++;
336	<
337	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
338	<	MPI_COMM_WORLD, &istatus);
339	<	myPotato++;
340	<
341	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
342	<
343	<	if (msgLen == 13)
344	<	isDirectional = 1;
345	<	else
346	<	isDirectional = 0;
347	<
348	<	// If we've survived to here, format the line:
349	<
350	<	if (!isDirectional) {
351	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
352	<	atomTypeString, atomData[0],
353	<	atomData[1], atomData[2],
354	<	atomData[3], atomData[4],
355	<	atomData[5]);
356	<
357	<	strcat(writeLine,
358	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
359	<	} else {
360	<	sprintf(writeLine,
361	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
362	<	atomTypeString,
363	<	atomData[0],
364	<	atomData[1],
365	<	atomData[2],
366	<	atomData[3],
367	<	atomData[4],
368	<	atomData[5],
369	<	atomData[6],
370	<	atomData[7],
371	<	atomData[8],
372	<	atomData[9],
373	<	atomData[10],
374	<	atomData[11],
375	<	atomData[12]);
376	<	}
377	<
378	<	os << writeLine;
379	<
380	<	} // end for(int l =0)
381	<
382	<	potatoes[which_node] = myPotato;
383	<	} else { //master node has current molecule
384	<
385	<	mol = info_->getMoleculeByGlobalIndex(i);
386	<
387	<	if (mol == NULL) {
388	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
389	<	painCave.isFatal = 1;
390	<	simError();
391	<	}
392	<
393	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
394	<	integrableObject = mol->nextIntegrableObject(ii)) {
395	<
396	<	atomTypeString = integrableObject->getType().c_str();
397	<
398	<	pos = integrableObject->getPos();
399	<	vel = integrableObject->getVel();
400	<
401	<	atomData[0] = pos[0];
402	<	atomData[1] = pos[1];
403	<	atomData[2] = pos[2];
404	<
405	<	atomData[3] = vel[0];
406	<	atomData[4] = vel[1];
407	<	atomData[5] = vel[2];
408	<
409	<	isDirectional = 0;
410	<
411	<	if (integrableObject->isDirectional()) {
412	<	isDirectional = 1;
413	<
414	<	q = integrableObject->getQ();
415	<	ji = integrableObject->getJ();
416	<
417	<	for(int j = 0; j < 6; j++) {
418	<	atomData[j] = atomData[j];
419	<	}
420	<
421	<	atomData[6] = q[0];
422	<	atomData[7] = q[1];
423	<	atomData[8] = q[2];
424	<	atomData[9] = q[3];
425	<
426	<	atomData[10] = ji[0];
427	<	atomData[11] = ji[1];
428	<	atomData[12] = ji[2];
429	<	}
430	<
431	<	// If we've survived to here, format the line:
432	<
433	<	if (!isDirectional) {
434	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
435	<	atomTypeString, atomData[0],
436	<	atomData[1], atomData[2],
437	<	atomData[3], atomData[4],
438	<	atomData[5]);
439	<
440	<	strcat(writeLine,
441	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
442	<	} else {
443	<	sprintf(writeLine,
444	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
445	<	atomTypeString,
446	<	atomData[0],
447	<	atomData[1],
448	<	atomData[2],
449	<	atomData[3],
450	<	atomData[4],
451	<	atomData[5],
452	<	atomData[6],
453	<	atomData[7],
454	<	atomData[8],
455	<	atomData[9],
456	<	atomData[10],
457	<	atomData[11],
458	<	atomData[12]);
459	<	}
460	<
461	<
462	<	os << writeLine;
463	<
464	<	} //end for(iter = integrableObject.begin())
465	<	}
466	<	} //end for(i = 0; i < mpiSim->getNmol())
467	<
468	<	os.flush();
469	<
470	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
471	<	MPIcheckPoint();
472	<
473	<	delete [] potatoes;
474	<	} else {
475	<
476	<	// worldRank != 0, so I'm a remote node.
477	<
478	<	// Set my magic potato to 0:
479	<
480	<	myPotato = 0;
481	<
482	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
483	<
484	<	// Am I the node which has this integrableObject?
485	<	int whichNode = info_->getMolToProc(i);
486	<	if (whichNode == worldRank) {
487	<	if (myPotato + 1 >= MAXTAG) {
488	<
489	<	// The potato was going to exceed the maximum value,
490	<	// so wrap this processor potato back to 0 (and block until
491	<	// node 0 says we can go:
492	<
493	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
494	<	&istatus);
495	<	}
496	<
497	<	mol = info_->getMoleculeByGlobalIndex(i);
498	<
499	<
500	<	nCurObj = mol->getNIntegrableObjects();
501	<
502	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
503	<	myPotato++;
504	<
505	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
506	<	integrableObject = mol->nextIntegrableObject(ii)) {
507	<
508	<	if (myPotato + 2 >= MAXTAG) {
509	<
510	<	// The potato was going to exceed the maximum value,
511	<	// so wrap this processor potato back to 0 (and block until
512	<	// node 0 says we can go:
513	<
514	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
515	<	&istatus);
516	<	}
517	<
518	<	atomTypeString = integrableObject->getType().c_str();
519	<
520	<	pos = integrableObject->getPos();
521	<	vel = integrableObject->getVel();
522	<
523	<	atomData[0] = pos[0];
524	<	atomData[1] = pos[1];
525	<	atomData[2] = pos[2];
526	<
527	<	atomData[3] = vel[0];
528	<	atomData[4] = vel[1];
529	<	atomData[5] = vel[2];
530	<
531	<	isDirectional = 0;
532	<
533	<	if (integrableObject->isDirectional()) {
534	<	isDirectional = 1;
535	<
536	<	q = integrableObject->getQ();
537	<	ji = integrableObject->getJ();
538	<
539	<	atomData[6] = q[0];
540	<	atomData[7] = q[1];
541	<	atomData[8] = q[2];
542	<	atomData[9] = q[3];
543	<
544	<	atomData[10] = ji[0];
545	<	atomData[11] = ji[1];
546	<	atomData[12] = ji[2];
547	<	}
548	<
549	<	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
550	<
551	<	// null terminate the  std::string before sending (just in case):
552	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
553	<
554	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
555	<	myPotato, MPI_COMM_WORLD);
556	<
557	<	myPotato++;
558	<
559	<	if (isDirectional) {
560	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
561	<	MPI_COMM_WORLD);
562	<	} else {
563	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
564	<	MPI_COMM_WORLD);
565	<	}
566	<
567	<	myPotato++;
568	<	}
569	<
570	<	}
571	<
572	<	}
573	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
574	<	MPIcheckPoint();
477	>	if (isinf(particlePot) || isnan(particlePot)) {
478	>	sprintf( painCave.errMsg,
479	>	"DumpWriter detected a numerical error writing the particle "
480	>	" potential for object %d", index);
481	>	painCave.isFatal = 1;
482	>	simError();
483	>	}
484	>	sprintf(tempBuffer, " %13e", particlePot);
485	>	line += tempBuffer;
486		}
487	+
488	+	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
489	+	return std::string(tempBuffer);
490	+	}
491
492	<	#endif // is_mpi
492	>	void DumpWriter::writeDump() {
493	>	writeFrame(*dumpFile_);
494	>	}
495
496	<	}
497	<
581	<	void DumpWriter::writeDump() {
582	<	writeFrame(dumpFile_);
583	<
584	<	}
585	<
586	<	void DumpWriter::writeEor() {
587	<	std::ofstream eorStream;
496	>	void DumpWriter::writeEor() {
497	>	std::ostream* eorStream;
498
499		#ifdef IS_MPI
500		if (worldRank == 0) {
501		#endif // is_mpi
502
503	<	eorStream.open(eorFilename_.c_str());
594	<	if (!eorStream.is_open()) {
595	<	sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n",
596	<	eorFilename_.c_str());
597	<	painCave.isFatal = 1;
598	<	simError();
599	<	}
503	>	eorStream = createOStream(eorFilename_);
504
505		#ifdef IS_MPI
506		}
507		#endif // is_mpi
508
509	<	writeFrame(eorStream);
606	<	}
509	>	writeFrame(*eorStream);
510
511	+	#ifdef IS_MPI
512	+	if (worldRank == 0) {
513	+	#endif // is_mpi
514	+	writeClosing(*eorStream);
515	+	delete eorStream;
516	+	#ifdef IS_MPI
517	+	}
518	+	#endif // is_mpi
519
520	<	void DumpWriter::writeDumpAndEor() {
521	<	std::ofstream eorStream;
520	>	}
521	>
522	>
523	>	void DumpWriter::writeDumpAndEor() {
524		std::vector<std::streambuf*> buffers;
525	+	std::ostream* eorStream;
526		#ifdef IS_MPI
527		if (worldRank == 0) {
528		#endif // is_mpi
529
530	<	buffers.push_back(dumpFile_.rdbuf());
530	>	buffers.push_back(dumpFile_->rdbuf());
531
532	<	eorStream.open(eorFilename_.c_str());
619	<	if (!eorStream.is_open()) {
620	<	sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n",
621	<	eorFilename_.c_str());
622	<	painCave.isFatal = 1;
623	<	simError();
624	<	}
532	>	eorStream = createOStream(eorFilename_);
533
534	<	buffers.push_back(eorStream.rdbuf());
534	>	buffers.push_back(eorStream->rdbuf());
535
536		#ifdef IS_MPI
537		}
#	Line 633 | Line 541 | void DumpWriter::writeDumpAndEor() {
541		std::ostream os(&tbuf);
542
543		writeFrame(os);
544	+
545	+	#ifdef IS_MPI
546	+	if (worldRank == 0) {
547	+	#endif // is_mpi
548	+	writeClosing(*eorStream);
549	+	delete eorStream;
550	+	#ifdef IS_MPI
551	+	}
552	+	#endif // is_mpi
553
554	<	}
554	>	}
555
556	+	std::ostream* DumpWriter::createOStream(const std::string& filename) {
557
558	+	std::ostream* newOStream;
559	+	#ifdef HAVE_LIBZ
560	+	if (needCompression_) {
561	+	newOStream = new ogzstream(filename.c_str());
562	+	} else {
563	+	newOStream = new std::ofstream(filename.c_str());
564	+	}
565	+	#else
566	+	newOStream = new std::ofstream(filename.c_str());
567	+	#endif
568	+	//write out MetaData first
569	+	(*newOStream) << "<OpenMD version=1>" << std::endl;
570	+	(*newOStream) << "  <MetaData>" << std::endl;
571	+	(*newOStream) << info_->getRawMetaData();
572	+	(*newOStream) << "  </MetaData>" << std::endl;
573	+	return newOStream;
574	+	}
575
576	<	}//end namespace oopse
576	>	void DumpWriter::writeClosing(std::ostream& os) {
577	>
578	>	os << "</OpenMD>\n";
579	>	os.flush();
580	>	}
581	>
582	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 376 by tim, Thu Feb 24 20:55:07 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1711 by gezelter, Sat May 19 02:58:35 2012 UTC

#	Line 0 | Line 1
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