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

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trunk/src/io/DumpWriter.cpp (file contents), Revision 791 by chuckv, Tue Dec 6 17:52:45 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1712 by gezelter, Sat May 19 13:30:21 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		#include "io/DumpWriter.hpp"
#	Line 46 | Line 47
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()){
#	Line 58 | Line 61 | namespace oopse {
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";
69	>	filename_ += ".gz";
70	>	eorFilename_ += ".gz";
71		}
72		#endif
73
74		#ifdef IS_MPI
75
76	<	if (worldRank == 0) {
76	>	if (worldRank == 0) {
77		#endif // is_mpi
73	–
78
79	<	dumpFile_ = createOStream(filename_);
79	>	dumpFile_ = createOStream(filename_);
80
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	<	}
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
88		#ifdef IS_MPI
89
90	<	}
90	>	}
91
88	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
89	–	MPIcheckPoint();
90	–
92		#endif // is_mpi
93
94	<	}
94	>	}
95
96
97		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
#	Line 101 | Line 102 | namespace oopse {
102
103		needCompression_ = simParams->getCompressDumpFile();
104		needForceVector_ = simParams->getOutputForceVector();
105	+	needParticlePot_ = simParams->getOutputParticlePotential();
106		createDumpFile_ = true;
107		#ifdef HAVE_LIBZ
108		if (needCompression_) {
109	<	filename_ += ".gz";
110	<	eorFilename_ += ".gz";
109	>	filename_ += ".gz";
110	>	eorFilename_ += ".gz";
111		}
112		#endif
113
114		#ifdef IS_MPI
115
116	<	if (worldRank == 0) {
116	>	if (worldRank == 0) {
117		#endif // is_mpi
118
119
120	<	dumpFile_ = createOStream(filename_);
120	>	dumpFile_ = createOStream(filename_);
121
122	<	if (!dumpFile_) {
123	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
124	<	filename_.c_str());
125	<	painCave.isFatal = 1;
126	<	simError();
127	<	}
122	>	if (!dumpFile_) {
123	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
124	>	filename_.c_str());
125	>	painCave.isFatal = 1;
126	>	simError();
127	>	}
128
129		#ifdef IS_MPI
130
131	<	}
131	>	}
132
131	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
132	–	MPIcheckPoint();
133	–
133		#endif // is_mpi
134
135	<	}
135	>	}
136
137		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
138	<	: info_(info), filename_(filename){
138	>	: info_(info), filename_(filename){
139
140		Globals* simParams = info->getSimParams();
141		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
142
143		needCompression_ = simParams->getCompressDumpFile();
144		needForceVector_ = simParams->getOutputForceVector();
145	+	needParticlePot_ = simParams->getOutputParticlePotential();
146
147		#ifdef HAVE_LIBZ
148		if (needCompression_) {
#	Line 170 | Line 170 | namespace oopse {
170		#ifdef IS_MPI
171
172		}
173	+
174
174	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
175	–	MPIcheckPoint();
176	–
175		#endif // is_mpi
176
177		}
180	–
181	–
182	–
183	–
184	–
178
179		DumpWriter::~DumpWriter() {
180
#	Line 190 | Line 183 | namespace oopse {
183		if (worldRank == 0) {
184		#endif // is_mpi
185		if (createDumpFile_){
186	+	writeClosing(*dumpFile_);
187		delete dumpFile_;
188		}
189		#ifdef IS_MPI
#	Line 200 | Line 194 | namespace oopse {
194
195		}
196
197	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
197	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
198
199	<	double currentTime;
206	<	Mat3x3d hmat;
207	<	double chi;
208	<	double integralOfChiDt;
209	<	Mat3x3d eta;
210	<
211	<	currentTime = s->getTime();
212	<	hmat = s->getHmat();
213	<	chi = s->getChi();
214	<	integralOfChiDt = s->getIntegralOfChiDt();
215	<	eta = s->getEta();
216	<
217	<	os << currentTime << ";\t"
218	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
219	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
220	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
199	>	char buffer[1024];
200
201	<	//write out additional parameters, such as chi and eta
201	>	os << "    <FrameData>\n";
202
203	<	os << chi << "\t" << integralOfChiDt << "\t;";
203	>	RealType currentTime = s->getTime();
204
205	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
206	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
207	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
208	<
209	<	os << "\n";
205	>	if (isinf(currentTime) || isnan(currentTime)) {
206	>	sprintf( painCave.errMsg,
207	>	"DumpWriter detected a numerical error writing the time");
208	>	painCave.isFatal = 1;
209	>	simError();
210	>	}
211	>
212	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
213	>	os << buffer;
214	>
215	>	Mat3x3d hmat;
216	>	hmat = s->getHmat();
217	>
218	>	for (unsigned int i = 0; i < 3; i++) {
219	>	for (unsigned int j = 0; j < 3; j++) {
220	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
221	>	sprintf( painCave.errMsg,
222	>	"DumpWriter detected a numerical error writing the box");
223	>	painCave.isFatal = 1;
224	>	simError();
225	>	}
226	>	}
227	>	}
228	>
229	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
230	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
231	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
232	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
233	>	os << buffer;
234	>
235	>	RealType chi = s->getChi();
236	>	RealType integralOfChiDt = s->getIntegralOfChiDt();
237	>	if (isinf(chi) || isnan(chi) ||
238	>	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
239	>	sprintf( painCave.errMsg,
240	>	"DumpWriter detected a numerical error writing the thermostat");
241	>	painCave.isFatal = 1;
242	>	simError();
243	>	}
244	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
245	>	os << buffer;
246	>
247	>	Mat3x3d eta;
248	>	eta = s->getEta();
249	>
250	>	for (unsigned int i = 0; i < 3; i++) {
251	>	for (unsigned int j = 0; j < 3; j++) {
252	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
253	>	sprintf( painCave.errMsg,
254	>	"DumpWriter detected a numerical error writing the barostat");
255	>	painCave.isFatal = 1;
256	>	simError();
257	>	}
258	>	}
259	>	}
260	>
261	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
262	>	eta(0, 0), eta(1, 0), eta(2, 0),
263	>	eta(0, 1), eta(1, 1), eta(2, 1),
264	>	eta(0, 2), eta(1, 2), eta(2, 2));
265	>	os << buffer;
266	>
267	>	os << "    </FrameData>\n";
268		}
269
270		void DumpWriter::writeFrame(std::ostream& os) {
234	–	const int BUFFERSIZE = 2000;
235	–	const int MINIBUFFERSIZE = 100;
271
272	<	char tempBuffer[BUFFERSIZE];
273	<	char writeLine[BUFFERSIZE];
272	>	#ifdef IS_MPI
273	>	MPI_Status istatus;
274	>	#endif
275
240	–	Quat4d q;
241	–	Vector3d ji;
242	–	Vector3d pos;
243	–	Vector3d vel;
244	–	Vector3d frc;
245	–	Vector3d trq;
246	–
276		Molecule* mol;
277		StuntDouble* integrableObject;
278		SimInfo::MoleculeIterator mi;
279		Molecule::IntegrableObjectIterator ii;
251	–
252	–	int nTotObjects;
253	–	nTotObjects = info_->getNGlobalIntegrableObjects();
280
281		#ifndef IS_MPI
282	+	os << "  <Snapshot>\n";
283	+
284	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
285
286	+	os << "    <StuntDoubles>\n";
287	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
288
289	<	os << nTotObjects << "\n";
290	<
291	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
289	>
290	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
291	>	integrableObject = mol->nextIntegrableObject(ii)) {
292	>	os << prepareDumpLine(integrableObject);
293	>
294	>	}
295	>	}
296	>	os << "    </StuntDoubles>\n";
297	>
298	>	os << "  </Snapshot>\n";
299
300	+	os.flush();
301	+	#else
302	+	//every node prepares the dump lines for integrable objects belong to itself
303	+	std::string buffer;
304		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
305
264	–	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
265	–	integrableObject = mol->nextIntegrableObject(ii)) {
266	–
306
307	<	pos = integrableObject->getPos();
308	<	vel = integrableObject->getVel();
309	<
310	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
311	<	integrableObject->getType().c_str(),
312	<	pos[0], pos[1], pos[2],
313	<	vel[0], vel[1], vel[2]);
314	<
315	<	strcpy(writeLine, tempBuffer);
316	<
317	<	if (integrableObject->isDirectional()) {
318	<	q = integrableObject->getQ();
319	<	ji = integrableObject->getJ();
307	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
308	>	integrableObject = mol->nextIntegrableObject(ii)) {
309	>	buffer += prepareDumpLine(integrableObject);
310	>	}
311	>	}
312	>
313	>	const int masterNode = 0;
314	>	int nProc;
315	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
316	>	if (worldRank == masterNode) {
317	>	os << "  <Snapshot>\n";
318	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
319	>	os << "    <StuntDoubles>\n";
320	>
321	>	os << buffer;
322
323	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
283	<	q[0], q[1], q[2], q[3],
284	<	ji[0], ji[1], ji[2]);
285	<	strcat(writeLine, tempBuffer);
286	<	} else {
287	<	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
288	<	}
323	>	for (int i = 1; i < nProc; ++i) {
324
325	<	if (needForceVector_) {
326	<	frc = integrableObject->getFrc();
292	<	trq = integrableObject->getTrq();
293	<
294	<	sprintf(tempBuffer, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
295	<	frc[0], frc[1], frc[2],
296	<	trq[0], trq[1], trq[2]);
297	<	strcat(writeLine, tempBuffer);
298	<	}
299	<
300	<	strcat(writeLine, "\n");
301	<	os << writeLine;
325	>	// receive the length of the string buffer that was
326	>	// prepared by processor i
327
328	+	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
329	+	int recvLength;
330	+	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
331	+	char* recvBuffer = new char[recvLength];
332	+	if (recvBuffer == NULL) {
333	+	} else {
334	+	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
335	+	os << recvBuffer;
336	+	delete [] recvBuffer;
337	+	}
338	+	}
339	+	os << "    </StuntDoubles>\n";
340	+
341	+	os << "  </Snapshot>\n";
342	+	os.flush();
343	+	} else {
344	+	int sendBufferLength = buffer.size() + 1;
345	+	int myturn = 0;
346	+	for (int i = 1; i < nProc; ++i){
347	+	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
348	+	if (myturn == worldRank){
349	+	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
350	+	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
351	+	}
352		}
353		}
354
355	<	os.flush();
307	<	#else // is_mpi
308	<	/*********************************************************************
309	<	* Documentation?  You want DOCUMENTATION?
310	<	*
311	<	* Why all the potatoes below?
312	<	*
313	<	* To make a long story short, the original version of DumpWriter
314	<	* worked in the most inefficient way possible.  Node 0 would
315	<	* poke each of the node for an individual atom's formatted data
316	<	* as node 0 worked its way down the global index. This was particularly
317	<	* inefficient since the method blocked all processors at every atom
318	<	* (and did it twice!).
319	<	*
320	<	* An intermediate version of DumpWriter could be described from Node
321	<	* zero's perspective as follows:
322	<	*
323	<	*  1) Have 100 of your friends stand in a circle.
324	<	*  2) When you say go, have all of them start tossing potatoes at
325	<	*     you (one at a time).
326	<	*  3) Catch the potatoes.
327	<	*
328	<	* It was an improvement, but MPI has buffers and caches that could
329	<	* best be described in this analogy as "potato nets", so there's no
330	<	* need to block the processors atom-by-atom.
331	<	*
332	<	* This new and improved DumpWriter works in an even more efficient
333	<	* way:
334	<	*
335	<	*  1) Have 100 of your friend stand in a circle.
336	<	*  2) When you say go, have them start tossing 5-pound bags of
337	<	*     potatoes at you.
338	<	*  3) Once you've caught a friend's bag of potatoes,
339	<	*     toss them a spud to let them know they can toss another bag.
340	<	*
341	<	* How's THAT for documentation?
342	<	*
343	<	*********************************************************************/
344	<	const int masterNode = 0;
355	>	#endif // is_mpi
356
357	<	int * potatoes;
347	<	int myPotato;
348	<	int nProc;
349	<	int which_node;
350	<	double atomData[19];
351	<	int isDirectional;
352	<	char MPIatomTypeString[MINIBUFFERSIZE];
353	<	int msgLen; // the length of message actually recieved at master nodes
354	<	int haveError;
355	<	MPI_Status istatus;
356	<	int nCurObj;
357	<
358	<	// code to find maximum tag value
359	<	int * tagub;
360	<	int flag;
361	<	int MAXTAG;
362	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
357	>	}
358
359	<	if (flag) {
360	<	MAXTAG = *tagub;
361	<	} else {
362	<	MAXTAG = 32767;
359	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
360	>
361	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
362	>	std::string type("pv");
363	>	std::string line;
364	>	char tempBuffer[4096];
365	>
366	>	Vector3d pos;
367	>	Vector3d vel;
368	>	pos = integrableObject->getPos();
369	>
370	>	if (isinf(pos[0]) || isnan(pos[0]) ||
371	>	isinf(pos[1]) || isnan(pos[1]) ||
372	>	isinf(pos[2]) || isnan(pos[2]) ) {
373	>	sprintf( painCave.errMsg,
374	>	"DumpWriter detected a numerical error writing the position"
375	>	" for object %d", index);
376	>	painCave.isFatal = 1;
377	>	simError();
378		}
379
380	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
380	>	vel = integrableObject->getVel();
381
382	<	// Node 0 needs a list of the magic potatoes for each processor;
382	>	if (isinf(vel[0]) || isnan(vel[0]) ||
383	>	isinf(vel[1]) || isnan(vel[1]) ||
384	>	isinf(vel[2]) || isnan(vel[2]) ) {
385	>	sprintf( painCave.errMsg,
386	>	"DumpWriter detected a numerical error writing the velocity"
387	>	" for object %d", index);
388	>	painCave.isFatal = 1;
389	>	simError();
390	>	}
391
392	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
393	<	potatoes = new int[nProc];
392	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
393	>	pos[0], pos[1], pos[2],
394	>	vel[0], vel[1], vel[2]);
395	>	line += tempBuffer;
396
397	<	//write out the comment lines
398	<	for(int i = 0; i < nProc; i++) {
399	<	potatoes[i] = 0;
397	>	if (integrableObject->isDirectional()) {
398	>	type += "qj";
399	>	Quat4d q;
400	>	Vector3d ji;
401	>	q = integrableObject->getQ();
402	>
403	>	if (isinf(q[0]) || isnan(q[0]) ||
404	>	isinf(q[1]) || isnan(q[1]) ||
405	>	isinf(q[2]) || isnan(q[2]) ||
406	>	isinf(q[3]) || isnan(q[3]) ) {
407	>	sprintf( painCave.errMsg,
408	>	"DumpWriter detected a numerical error writing the quaternion"
409	>	" for object %d", index);
410	>	painCave.isFatal = 1;
411	>	simError();
412		}
413
414	+	ji = integrableObject->getJ();
415
416	<	os << nTotObjects << "\n";
417	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
416	>	if (isinf(ji[0]) || isnan(ji[0]) ||
417	>	isinf(ji[1]) || isnan(ji[1]) ||
418	>	isinf(ji[2]) || isnan(ji[2]) ) {
419	>	sprintf( painCave.errMsg,
420	>	"DumpWriter detected a numerical error writing the angular"
421	>	" momentum for object %d", index);
422	>	painCave.isFatal = 1;
423	>	simError();
424	>	}
425
426	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
426	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
427	>	q[0], q[1], q[2], q[3],
428	>	ji[0], ji[1], ji[2]);
429	>	line += tempBuffer;
430	>	}
431
432	<	// Get the Node number which has this atom;
432	>	if (needForceVector_) {
433	>	type += "f";
434	>	Vector3d frc;
435
436	<	which_node = info_->getMolToProc(i);
436	>	frc = integrableObject->getFrc();
437
438	<	if (which_node != masterNode) { //current molecule is in slave node
439	<	if (potatoes[which_node] + 1 >= MAXTAG) {
440	<	// The potato was going to exceed the maximum value,
441	<	// so wrap this processor potato back to 0:
438	>	if (isinf(frc[0]) || isnan(frc[0]) ||
439	>	isinf(frc[1]) || isnan(frc[1]) ||
440	>	isinf(frc[2]) || isnan(frc[2]) ) {
441	>	sprintf( painCave.errMsg,
442	>	"DumpWriter detected a numerical error writing the force"
443	>	" for object %d", index);
444	>	painCave.isFatal = 1;
445	>	simError();
446	>	}
447	>	sprintf(tempBuffer, " %13e %13e %13e",
448	>	frc[0], frc[1], frc[2]);
449	>	line += tempBuffer;
450	>
451	>	if (integrableObject->isDirectional()) {
452	>	type += "t";
453	>	Vector3d trq;
454	>
455	>	trq = integrableObject->getTrq();
456	>
457	>	if (isinf(trq[0]) || isnan(trq[0]) ||
458	>	isinf(trq[1]) || isnan(trq[1]) ||
459	>	isinf(trq[2]) || isnan(trq[2]) ) {
460	>	sprintf( painCave.errMsg,
461	>	"DumpWriter detected a numerical error writing the torque"
462	>	" for object %d", index);
463	>	painCave.isFatal = 1;
464	>	simError();
465	>	}
466	>
467	>	sprintf(tempBuffer, " %13e %13e %13e",
468	>	trq[0], trq[1], trq[2]);
469	>	line += tempBuffer;
470	>	}
471	>	}
472	>	if (needParticlePot_) {
473	>	type += "u";
474	>	RealType particlePot;
475
476	<	potatoes[which_node] = 0;
398	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
399	<	MPI_COMM_WORLD);
400	<	}
476	>	particlePot = integrableObject->getParticlePot();
477
478	<	myPotato = potatoes[which_node];
479	<
480	<	//recieve the number of integrableObject in current molecule
481	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
482	<	MPI_COMM_WORLD, &istatus);
483	<	myPotato++;
408	<
409	<	for(int l = 0; l < nCurObj; l++) {
410	<	if (potatoes[which_node] + 2 >= MAXTAG) {
411	<	// The potato was going to exceed the maximum value,
412	<	// so wrap this processor potato back to 0:
413	<
414	<	potatoes[which_node] = 0;
415	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
416	<	0, MPI_COMM_WORLD);
417	<	}
418	<
419	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
420	<	which_node, myPotato, MPI_COMM_WORLD,
421	<	&istatus);
422	<
423	<	myPotato++;
424	<
425	<	MPI_Recv(atomData, 19, MPI_DOUBLE, which_node, myPotato,
426	<	MPI_COMM_WORLD, &istatus);
427	<	myPotato++;
428	<
429	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
430	<
431	<	if (msgLen == 13 || msgLen == 19)
432	<	isDirectional = 1;
433	<	else
434	<	isDirectional = 0;
435	<
436	<	// If we've survived to here, format the line:
437	<
438	<	if (!isDirectional) {
439	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
440	<	MPIatomTypeString, atomData[0],
441	<	atomData[1], atomData[2],
442	<	atomData[3], atomData[4],
443	<	atomData[5]);
444	<
445	<	strcat(writeLine,
446	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
447	<	} else {
448	<	sprintf(writeLine,
449	<	"%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",
450	<	MPIatomTypeString,
451	<	atomData[0],
452	<	atomData[1],
453	<	atomData[2],
454	<	atomData[3],
455	<	atomData[4],
456	<	atomData[5],
457	<	atomData[6],
458	<	atomData[7],
459	<	atomData[8],
460	<	atomData[9],
461	<	atomData[10],
462	<	atomData[11],
463	<	atomData[12]);
464	<	}
465	<
466	<	if (needForceVector_) {
467	<	if (!isDirectional) {
468	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
469	<	atomData[6],
470	<	atomData[7],
471	<	atomData[8],
472	<	atomData[9],
473	<	atomData[10],
474	<	atomData[11]);
475	<	} else {
476	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
477	<	atomData[13],
478	<	atomData[14],
479	<	atomData[15],
480	<	atomData[16],
481	<	atomData[17],
482	<	atomData[18]);
483	<	}
484	<	}
485	<
486	<	sprintf(writeLine, "\n");
487	<	os << writeLine;
488	<
489	<	} // end for(int l =0)
490	<
491	<	potatoes[which_node] = myPotato;
492	<	} else { //master node has current molecule
493	<
494	<	mol = info_->getMoleculeByGlobalIndex(i);
495	<
496	<	if (mol == NULL) {
497	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
498	<	painCave.isFatal = 1;
499	<	simError();
500	<	}
501	<
502	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
503	<	integrableObject = mol->nextIntegrableObject(ii)) {
504	<
505	<	pos = integrableObject->getPos();
506	<	vel = integrableObject->getVel();
507	<
508	<	atomData[0] = pos[0];
509	<	atomData[1] = pos[1];
510	<	atomData[2] = pos[2];
511	<
512	<	atomData[3] = vel[0];
513	<	atomData[4] = vel[1];
514	<	atomData[5] = vel[2];
515	<
516	<	isDirectional = 0;
517	<
518	<	if (integrableObject->isDirectional()) {
519	<	isDirectional = 1;
520	<
521	<	q = integrableObject->getQ();
522	<	ji = integrableObject->getJ();
523	<
524	<	for(int j = 0; j < 6; j++) {
525	<	atomData[j] = atomData[j];
526	<	}
527	<
528	<	atomData[6] = q[0];
529	<	atomData[7] = q[1];
530	<	atomData[8] = q[2];
531	<	atomData[9] = q[3];
532	<
533	<	atomData[10] = ji[0];
534	<	atomData[11] = ji[1];
535	<	atomData[12] = ji[2];
536	<	}
537	<
538	<	if (needForceVector_) {
539	<	frc = integrableObject->getFrc();
540	<	trq = integrableObject->getTrq();
541	<
542	<	if (!isDirectional) {
543	<	atomData[6] = frc[0];
544	<	atomData[7] = frc[1];
545	<	atomData[8] = frc[2];
546	<	atomData[9] = trq[0];
547	<	atomData[10] = trq[1];
548	<	atomData[11] = trq[2];
549	<	} else {
550	<	atomData[13] = frc[0];
551	<	atomData[14] = frc[1];
552	<	atomData[15] = frc[2];
553	<	atomData[16] = trq[0];
554	<	atomData[17] = trq[1];
555	<	atomData[18] = trq[2];
556	<	}
557	<	}
558	<
559	<	// If we've survived to here, format the line:
560	<
561	<	if (!isDirectional) {
562	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
563	<	integrableObject->getType().c_str(), atomData[0],
564	<	atomData[1], atomData[2],
565	<	atomData[3], atomData[4],
566	<	atomData[5]);
567	<
568	<	strcat(writeLine,
569	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
570	<	} else {
571	<	sprintf(writeLine,
572	<	"%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",
573	<	integrableObject->getType().c_str(),
574	<	atomData[0],
575	<	atomData[1],
576	<	atomData[2],
577	<	atomData[3],
578	<	atomData[4],
579	<	atomData[5],
580	<	atomData[6],
581	<	atomData[7],
582	<	atomData[8],
583	<	atomData[9],
584	<	atomData[10],
585	<	atomData[11],
586	<	atomData[12]);
587	<	}
588	<
589	<	if (needForceVector_) {
590	<	if (!isDirectional) {
591	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
592	<	atomData[6],
593	<	atomData[7],
594	<	atomData[8],
595	<	atomData[9],
596	<	atomData[10],
597	<	atomData[11]);
598	<	} else {
599	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
600	<	atomData[13],
601	<	atomData[14],
602	<	atomData[15],
603	<	atomData[16],
604	<	atomData[17],
605	<	atomData[18]);
606	<	}
607	<	}
608	<
609	<	sprintf(writeLine, "\n");
610	<	os << writeLine;
611	<
612	<	} //end for(iter = integrableObject.begin())
613	<	}
614	<	} //end for(i = 0; i < mpiSim->getNmol())
615	<
616	<	os.flush();
617	<
618	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
619	<	MPIcheckPoint();
620	<
621	<	delete [] potatoes;
622	<	} else {
623	<
624	<	// worldRank != 0, so I'm a remote node.
625	<
626	<	// Set my magic potato to 0:
627	<
628	<	myPotato = 0;
629	<
630	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
631	<
632	<	// Am I the node which has this integrableObject?
633	<	int whichNode = info_->getMolToProc(i);
634	<	if (whichNode == worldRank) {
635	<	if (myPotato + 1 >= MAXTAG) {
636	<
637	<	// The potato was going to exceed the maximum value,
638	<	// so wrap this processor potato back to 0 (and block until
639	<	// node 0 says we can go:
640	<
641	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
642	<	&istatus);
643	<	}
644	<
645	<	mol = info_->getMoleculeByGlobalIndex(i);
646	<
647	<
648	<	nCurObj = mol->getNIntegrableObjects();
649	<
650	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
651	<	myPotato++;
652	<
653	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
654	<	integrableObject = mol->nextIntegrableObject(ii)) {
655	<
656	<	if (myPotato + 2 >= MAXTAG) {
657	<
658	<	// The potato was going to exceed the maximum value,
659	<	// so wrap this processor potato back to 0 (and block until
660	<	// node 0 says we can go:
661	<
662	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
663	<	&istatus);
664	<	}
665	<
666	<	pos = integrableObject->getPos();
667	<	vel = integrableObject->getVel();
668	<
669	<	atomData[0] = pos[0];
670	<	atomData[1] = pos[1];
671	<	atomData[2] = pos[2];
672	<
673	<	atomData[3] = vel[0];
674	<	atomData[4] = vel[1];
675	<	atomData[5] = vel[2];
676	<
677	<	isDirectional = 0;
678	<
679	<	if (integrableObject->isDirectional()) {
680	<	isDirectional = 1;
681	<
682	<	q = integrableObject->getQ();
683	<	ji = integrableObject->getJ();
684	<
685	<	atomData[6] = q[0];
686	<	atomData[7] = q[1];
687	<	atomData[8] = q[2];
688	<	atomData[9] = q[3];
689	<
690	<	atomData[10] = ji[0];
691	<	atomData[11] = ji[1];
692	<	atomData[12] = ji[2];
693	<	}
694	<
695	<	if (needForceVector_) {
696	<	frc = integrableObject->getFrc();
697	<	trq = integrableObject->getTrq();
698	<
699	<	if (!isDirectional) {
700	<	atomData[6] = frc[0];
701	<	atomData[7] = frc[1];
702	<	atomData[8] = frc[2];
703	<
704	<	atomData[9] = trq[0];
705	<	atomData[10] = trq[1];
706	<	atomData[11] = trq[2];
707	<	} else {
708	<	atomData[13] = frc[0];
709	<	atomData[14] = frc[1];
710	<	atomData[15] = frc[2];
711	<
712	<	atomData[16] = trq[0];
713	<	atomData[17] = trq[1];
714	<	atomData[18] = trq[2];
715	<	}
716	<	}
717	<
718	<	strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
719	<
720	<	// null terminate the  std::string before sending (just in case):
721	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
722	<
723	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
724	<	myPotato, MPI_COMM_WORLD);
725	<
726	<	myPotato++;
727	<
728	<	if (isDirectional && needForceVector_) {
729	<	MPI_Send(atomData, 19, MPI_DOUBLE, 0, myPotato,
730	<	MPI_COMM_WORLD);
731	<	} else if (isDirectional) {
732	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
733	<	MPI_COMM_WORLD);
734	<	} else if (needForceVector_) {
735	<	MPI_Send(atomData, 12, MPI_DOUBLE, 0, myPotato,
736	<	MPI_COMM_WORLD);
737	<	} else {
738	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
739	<	MPI_COMM_WORLD);
740	<	}
741	<
742	<	myPotato++;
743	<	}
744	<
745	<	}
746	<
478	>	if (isinf(particlePot) || isnan(particlePot)) {
479	>	sprintf( painCave.errMsg,
480	>	"DumpWriter detected a numerical error writing the particle "
481	>	" potential for object %d", index);
482	>	painCave.isFatal = 1;
483	>	simError();
484		}
485	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
486	<	MPIcheckPoint();
485	>	sprintf(tempBuffer, " %13e", particlePot);
486	>	line += tempBuffer;
487		}
488	<
489	<	#endif // is_mpi
490	<
488	>
489	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
490	>	return std::string(tempBuffer);
491		}
492
493		void DumpWriter::writeDump() {
#	Line 775 | Line 512 | namespace oopse {
512		#ifdef IS_MPI
513		if (worldRank == 0) {
514		#endif // is_mpi
515	<	delete eorStream;
516	<
515	>	writeClosing(*eorStream);
516	>	delete eorStream;
517		#ifdef IS_MPI
518		}
519		#endif // is_mpi
#	Line 809 | Line 546 | namespace oopse {
546		#ifdef IS_MPI
547		if (worldRank == 0) {
548		#endif // is_mpi
549	<	delete eorStream;
550	<
549	>	writeClosing(*eorStream);
550	>	delete eorStream;
551		#ifdef IS_MPI
552		}
553		#endif // is_mpi
554
555		}
556
557	<	std::ostream* DumpWriter::createOStream(const std::string& filename) {
557	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
558
559		std::ostream* newOStream;
560		#ifdef HAVE_LIBZ
561		if (needCompression_) {
562	<	newOStream = new ogzstream(filename.c_str());
562	>	newOStream = new ogzstream(filename.c_str());
563		} else {
564	<	newOStream = new std::ofstream(filename.c_str());
564	>	newOStream = new std::ofstream(filename.c_str());
565		}
566		#else
567		newOStream = new std::ofstream(filename.c_str());
568		#endif
569	+	//write out MetaData first
570	+	(*newOStream) << "<OpenMD version=1>" << std::endl;
571	+	(*newOStream) << "  <MetaData>" << std::endl;
572	+	(*newOStream) << info_->getRawMetaData();
573	+	(*newOStream) << "  </MetaData>" << std::endl;
574		return newOStream;
575	<	}
575	>	}
576
577	<	}//end namespace oopse
577	>	void DumpWriter::writeClosing(std::ostream& os) {
578	>
579	>	os << "</OpenMD>\n";
580	>	os.flush();
581	>	}
582	>
583	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 791 by chuckv, Tue Dec 6 17:52:45 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1712 by gezelter, Sat May 19 13:30:21 2012 UTC

#	Line 0 | Line 1
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