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

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trunk/src/io/DumpWriter.cpp (file contents), Revision 966 by chrisfen, Fri May 19 21:26:41 2006 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1714 by gezelter, Sat May 19 18:12:46 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()){
60
61		Globals* simParams = info->getSimParams();
62	<	needCompression_ = simParams->getCompressDumpFile();
63	<	needForceVector_ = simParams->getOutputForceVector();
62	>	needCompression_   = simParams->getCompressDumpFile();
63	>	needForceVector_   = simParams->getOutputForceVector();
64	>	needParticlePot_   = simParams->getOutputParticlePotential();
65	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
66	>	needElectricField_ = simParams->getOutputElectricField();
67	>
68		createDumpFile_ = true;
69		#ifdef HAVE_LIBZ
70		if (needCompression_) {
71	<	filename_ += ".gz";
72	<	eorFilename_ += ".gz";
71	>	filename_ += ".gz";
72	>	eorFilename_ += ".gz";
73		}
74		#endif
75
76		#ifdef IS_MPI
77
78	<	if (worldRank == 0) {
78	>	if (worldRank == 0) {
79		#endif // is_mpi
73	–
80
81	<	dumpFile_ = createOStream(filename_);
81	>	dumpFile_ = createOStream(filename_);
82
83	<	if (!dumpFile_) {
84	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
85	<	filename_.c_str());
86	<	painCave.isFatal = 1;
87	<	simError();
88	<	}
83	>	if (!dumpFile_) {
84	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
85	>	filename_.c_str());
86	>	painCave.isFatal = 1;
87	>	simError();
88	>	}
89
90		#ifdef IS_MPI
91
92	<	}
92	>	}
93
88	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
89	–	MPIcheckPoint();
90	–
94		#endif // is_mpi
95
96	<	}
96	>	}
97
98
99		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
#	Line 99 | Line 102 | namespace oopse {
102		Globals* simParams = info->getSimParams();
103		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
104
105	<	needCompression_ = simParams->getCompressDumpFile();
106	<	needForceVector_ = simParams->getOutputForceVector();
105	>	needCompression_   = simParams->getCompressDumpFile();
106	>	needForceVector_   = simParams->getOutputForceVector();
107	>	needParticlePot_   = simParams->getOutputParticlePotential();
108	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
109	>	needElectricField_ = simParams->getOutputElectricField();
110	>
111		createDumpFile_ = true;
112		#ifdef HAVE_LIBZ
113		if (needCompression_) {
114	<	filename_ += ".gz";
115	<	eorFilename_ += ".gz";
114	>	filename_ += ".gz";
115	>	eorFilename_ += ".gz";
116		}
117		#endif
118
119		#ifdef IS_MPI
120
121	<	if (worldRank == 0) {
121	>	if (worldRank == 0) {
122		#endif // is_mpi
123
124
125	<	dumpFile_ = createOStream(filename_);
125	>	dumpFile_ = createOStream(filename_);
126
127	<	if (!dumpFile_) {
128	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
129	<	filename_.c_str());
130	<	painCave.isFatal = 1;
131	<	simError();
132	<	}
127	>	if (!dumpFile_) {
128	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
129	>	filename_.c_str());
130	>	painCave.isFatal = 1;
131	>	simError();
132	>	}
133
134		#ifdef IS_MPI
135
136	<	}
136	>	}
137
131	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
132	–	MPIcheckPoint();
133	–
138		#endif // is_mpi
139
140	<	}
140	>	}
141
142		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
143	<	: info_(info), filename_(filename){
143	>	: info_(info), filename_(filename){
144
145		Globals* simParams = info->getSimParams();
146		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
147
148	<	needCompression_ = simParams->getCompressDumpFile();
149	<	needForceVector_ = simParams->getOutputForceVector();
150	<
148	>	needCompression_   = simParams->getCompressDumpFile();
149	>	needForceVector_   = simParams->getOutputForceVector();
150	>	needParticlePot_   = simParams->getOutputParticlePotential();
151	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
152	>	needElectricField_ = simParams->getOutputElectricField();
153	>
154		#ifdef HAVE_LIBZ
155		if (needCompression_) {
156		filename_ += ".gz";
#	Line 170 | Line 177 | namespace oopse {
177		#ifdef IS_MPI
178
179		}
180	+
181
174	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
175	–	MPIcheckPoint();
176	–
182		#endif // is_mpi
183
184		}
180	–
181	–
182	–
183	–
184	–
185
186		DumpWriter::~DumpWriter() {
187
#	Line 190 | Line 190 | namespace oopse {
190		if (worldRank == 0) {
191		#endif // is_mpi
192		if (createDumpFile_){
193	+	writeClosing(*dumpFile_);
194		delete dumpFile_;
195		}
196		#ifdef IS_MPI
#	Line 200 | Line 201 | namespace oopse {
201
202		}
203
204	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
204	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
205
206	<	RealType currentTime;
207	<	Mat3x3d hmat;
208	<	RealType chi;
209	<	RealType integralOfChiDt;
210	<	Mat3x3d eta;
211	<
212	<	currentTime = s->getTime();
213	<	hmat = s->getHmat();
214	<	chi = s->getChi();
215	<	integralOfChiDt = s->getIntegralOfChiDt();
216	<	eta = s->getEta();
206	>	char buffer[1024];
207	>
208	>	os << "    <FrameData>\n";
209	>
210	>	RealType currentTime = s->getTime();
211	>
212	>	if (isinf(currentTime) || isnan(currentTime)) {
213	>	sprintf( painCave.errMsg,
214	>	"DumpWriter detected a numerical error writing the time");
215	>	painCave.isFatal = 1;
216	>	simError();
217	>	}
218
219	<	os << currentTime << ";\t"
220	<	<< 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";
219	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
220	>	os << buffer;
221
222	<	//write out additional parameters, such as chi and eta
222	>	Mat3x3d hmat;
223	>	hmat = s->getHmat();
224
225	<	os << chi << "\t" << integralOfChiDt << ";\t";
225	>	for (unsigned int i = 0; i < 3; i++) {
226	>	for (unsigned int j = 0; j < 3; j++) {
227	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
228	>	sprintf( painCave.errMsg,
229	>	"DumpWriter detected a numerical error writing the box");
230	>	painCave.isFatal = 1;
231	>	simError();
232	>	}
233	>	}
234	>	}
235	>
236	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
237	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
238	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
239	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
240	>	os << buffer;
241
242	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
243	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
244	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
245	<
246	<	os << "\n";
242	>	RealType chi = s->getChi();
243	>	RealType integralOfChiDt = s->getIntegralOfChiDt();
244	>	if (isinf(chi) || isnan(chi) ||
245	>	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
246	>	sprintf( painCave.errMsg,
247	>	"DumpWriter detected a numerical error writing the thermostat");
248	>	painCave.isFatal = 1;
249	>	simError();
250	>	}
251	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
252	>	os << buffer;
253	>
254	>	Mat3x3d eta;
255	>	eta = s->getEta();
256	>
257	>	for (unsigned int i = 0; i < 3; i++) {
258	>	for (unsigned int j = 0; j < 3; j++) {
259	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
260	>	sprintf( painCave.errMsg,
261	>	"DumpWriter detected a numerical error writing the barostat");
262	>	painCave.isFatal = 1;
263	>	simError();
264	>	}
265	>	}
266	>	}
267	>
268	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
269	>	eta(0, 0), eta(1, 0), eta(2, 0),
270	>	eta(0, 1), eta(1, 1), eta(2, 1),
271	>	eta(0, 2), eta(1, 2), eta(2, 2));
272	>	os << buffer;
273	>
274	>	os << "    </FrameData>\n";
275		}
276
277		void DumpWriter::writeFrame(std::ostream& os) {
234	–	const int BUFFERSIZE = 2000;
235	–	const int MINIBUFFERSIZE = 100;
278
279	<	char tempBuffer[BUFFERSIZE];
280	<	char writeLine[BUFFERSIZE];
279	>	#ifdef IS_MPI
280	>	MPI_Status istatus;
281	>	#endif
282
240	–	Quat4d q;
241	–	Vector3d ji;
242	–	Vector3d pos;
243	–	Vector3d vel;
244	–	Vector3d frc;
245	–	Vector3d trq;
246	–
283		Molecule* mol;
284		StuntDouble* integrableObject;
285		SimInfo::MoleculeIterator mi;
286		Molecule::IntegrableObjectIterator ii;
251	–
252	–	int nTotObjects;
253	–	nTotObjects = info_->getNGlobalIntegrableObjects();
287
288		#ifndef IS_MPI
289	+	os << "  <Snapshot>\n";
290	+
291	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
292
293	+	os << "    <StuntDoubles>\n";
294	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
295
296	<	os << nTotObjects << "\n";
297	<
298	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
296	>
297	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
298	>	integrableObject = mol->nextIntegrableObject(ii)) {
299	>	os << prepareDumpLine(integrableObject);
300	>
301	>	}
302	>	}
303	>	os << "    </StuntDoubles>\n";
304	>
305	>	os << "  </Snapshot>\n";
306
307	+	os.flush();
308	+	#else
309	+	//every node prepares the dump lines for integrable objects belong to itself
310	+	std::string buffer;
311		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
312
264	–	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
265	–	integrableObject = mol->nextIntegrableObject(ii)) {
266	–
313
314	<	pos = integrableObject->getPos();
315	<	vel = integrableObject->getVel();
316	<
317	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
272	<	integrableObject->getType().c_str(),
273	<	pos[0], pos[1], pos[2],
274	<	vel[0], vel[1], vel[2]);
275	<
276	<	strcpy(writeLine, tempBuffer);
277	<
278	<	if (integrableObject->isDirectional()) {
279	<	q = integrableObject->getQ();
280	<	ji = integrableObject->getJ();
281	<
282	<	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	<	}
289	<
290	<	if (needForceVector_) {
291	<	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;
302	<
303	<	}
314	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
315	>	integrableObject = mol->nextIntegrableObject(ii)) {
316	>	buffer += prepareDumpLine(integrableObject);
317	>	}
318		}
319	<
306	<	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	<	*********************************************************************/
319	>
320		const int masterNode = 0;
345	–
346	–	int * potatoes;
347	–	int myPotato;
321		int nProc;
322	<	int which_node;
323	<	RealType atomData[19];
324	<	int isDirectional;
325	<	char MPIatomTypeString[MINIBUFFERSIZE];
326	<	int msgLen; // the length of message actually recieved at master nodes
327	<	int haveError;
328	<	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);
322	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
323	>	if (worldRank == masterNode) {
324	>	os << "  <Snapshot>\n";
325	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
326	>	os << "    <StuntDoubles>\n";
327	>
328	>	os << buffer;
329
330	<	if (flag) {
365	<	MAXTAG = *tagub;
366	<	} else {
367	<	MAXTAG = 32767;
368	<	}
330	>	for (int i = 1; i < nProc; ++i) {
331
332	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
332	>	// receive the length of the string buffer that was
333	>	// prepared by processor i
334
335	<	// Node 0 needs a list of the magic potatoes for each processor;
336	<
337	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
338	<	potatoes = new int[nProc];
339	<
340	<	//write out the comment lines
341	<	for(int i = 0; i < nProc; i++) {
342	<	potatoes[i] = 0;
335	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
336	>	int recvLength;
337	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
338	>	char* recvBuffer = new char[recvLength];
339	>	if (recvBuffer == NULL) {
340	>	} else {
341	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
342	>	os << recvBuffer;
343	>	delete [] recvBuffer;
344	>	}
345	>	}
346	>	os << "    </StuntDoubles>\n";
347	>
348	>	os << "  </Snapshot>\n";
349	>	os.flush();
350	>	} else {
351	>	int sendBufferLength = buffer.size() + 1;
352	>	int myturn = 0;
353	>	for (int i = 1; i < nProc; ++i){
354	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
355	>	if (myturn == worldRank){
356	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
357	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
358	>	}
359		}
360	+	}
361
362	+	#endif // is_mpi
363
364	<	os << nTotObjects << "\n";
384	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
364	>	}
365
366	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
366	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
367	>
368	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
369	>	std::string type("pv");
370	>	std::string line;
371	>	char tempBuffer[4096];
372
373	<	// Get the Node number which has this atom;
373	>	Vector3d pos;
374	>	Vector3d vel;
375	>	pos = integrableObject->getPos();
376
377	<	which_node = info_->getMolToProc(i);
377	>	if (isinf(pos[0]) || isnan(pos[0]) ||
378	>	isinf(pos[1]) || isnan(pos[1]) ||
379	>	isinf(pos[2]) || isnan(pos[2]) ) {
380	>	sprintf( painCave.errMsg,
381	>	"DumpWriter detected a numerical error writing the position"
382	>	" for object %d", index);
383	>	painCave.isFatal = 1;
384	>	simError();
385	>	}
386
387	<	if (which_node != masterNode) { //current molecule is in slave node
393	<	if (potatoes[which_node] + 1 >= MAXTAG) {
394	<	// The potato was going to exceed the maximum value,
395	<	// so wrap this processor potato back to 0:
387	>	vel = integrableObject->getVel();
388
389	<	potatoes[which_node] = 0;
390	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
391	<	MPI_COMM_WORLD);
392	<	}
389	>	if (isinf(vel[0]) || isnan(vel[0]) ||
390	>	isinf(vel[1]) || isnan(vel[1]) ||
391	>	isinf(vel[2]) || isnan(vel[2]) ) {
392	>	sprintf( painCave.errMsg,
393	>	"DumpWriter detected a numerical error writing the velocity"
394	>	" for object %d", index);
395	>	painCave.isFatal = 1;
396	>	simError();
397	>	}
398
399	<	myPotato = potatoes[which_node];
399	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
400	>	pos[0], pos[1], pos[2],
401	>	vel[0], vel[1], vel[2]);
402	>	line += tempBuffer;
403
404	<	//recieve the number of integrableObject in current molecule
405	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
406	<	MPI_COMM_WORLD, &istatus);
407	<	myPotato++;
404	>	if (integrableObject->isDirectional()) {
405	>	type += "qj";
406	>	Quat4d q;
407	>	Vector3d ji;
408	>	q = integrableObject->getQ();
409
410	<	for(int l = 0; l < nCurObj; l++) {
411	<	if (potatoes[which_node] + 2 >= MAXTAG) {
412	<	// The potato was going to exceed the maximum value,
413	<	// so wrap this processor potato back to 0:
410	>	if (isinf(q[0]) || isnan(q[0]) ||
411	>	isinf(q[1]) || isnan(q[1]) ||
412	>	isinf(q[2]) || isnan(q[2]) ||
413	>	isinf(q[3]) || isnan(q[3]) ) {
414	>	sprintf( painCave.errMsg,
415	>	"DumpWriter detected a numerical error writing the quaternion"
416	>	" for object %d", index);
417	>	painCave.isFatal = 1;
418	>	simError();
419	>	}
420
421	<	potatoes[which_node] = 0;
415	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
416	<	0, MPI_COMM_WORLD);
417	<	}
421	>	ji = integrableObject->getJ();
422
423	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
424	<	which_node, myPotato, MPI_COMM_WORLD,
425	<	&istatus);
426	<
427	<	myPotato++;
423	>	if (isinf(ji[0]) || isnan(ji[0]) ||
424	>	isinf(ji[1]) || isnan(ji[1]) ||
425	>	isinf(ji[2]) || isnan(ji[2]) ) {
426	>	sprintf( painCave.errMsg,
427	>	"DumpWriter detected a numerical error writing the angular"
428	>	" momentum for object %d", index);
429	>	painCave.isFatal = 1;
430	>	simError();
431	>	}
432
433	<	MPI_Recv(atomData, 19, MPI_REALTYPE, which_node, myPotato,
434	<	MPI_COMM_WORLD, &istatus);
435	<	myPotato++;
433	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
434	>	q[0], q[1], q[2], q[3],
435	>	ji[0], ji[1], ji[2]);
436	>	line += tempBuffer;
437	>	}
438
439	<	MPI_Get_count(&istatus, MPI_REALTYPE, &msgLen);
439	>	if (needForceVector_) {
440	>	type += "f";
441	>	Vector3d frc = integrableObject->getFrc();
442	>	if (isinf(frc[0]) || isnan(frc[0]) ||
443	>	isinf(frc[1]) || isnan(frc[1]) ||
444	>	isinf(frc[2]) || isnan(frc[2]) ) {
445	>	sprintf( painCave.errMsg,
446	>	"DumpWriter detected a numerical error writing the force"
447	>	" for object %d", index);
448	>	painCave.isFatal = 1;
449	>	simError();
450	>	}
451	>	sprintf(tempBuffer, " %13e %13e %13e",
452	>	frc[0], frc[1], frc[2]);
453	>	line += tempBuffer;
454	>
455	>	if (integrableObject->isDirectional()) {
456	>	type += "t";
457	>	Vector3d trq = integrableObject->getTrq();
458	>	if (isinf(trq[0]) || isnan(trq[0]) ||
459	>	isinf(trq[1]) || isnan(trq[1]) ||
460	>	isinf(trq[2]) || isnan(trq[2]) ) {
461	>	sprintf( painCave.errMsg,
462	>	"DumpWriter detected a numerical error writing the torque"
463	>	" for object %d", index);
464	>	painCave.isFatal = 1;
465	>	simError();
466	>	}
467	>	sprintf(tempBuffer, " %13e %13e %13e",
468	>	trq[0], trq[1], trq[2]);
469	>	line += tempBuffer;
470	>	}
471	>	}
472
473	<	if (msgLen == 13 || msgLen == 19)
474	<	isDirectional = 1;
475	<	else
476	<	isDirectional = 0;
473	>	if (needParticlePot_) {
474	>	type += "u";
475	>	RealType particlePot = integrableObject->getParticlePot();
476	>	if (isinf(particlePot) || isnan(particlePot)) {
477	>	sprintf( painCave.errMsg,
478	>	"DumpWriter detected a numerical error writing the particle "
479	>	" potential for object %d", index);
480	>	painCave.isFatal = 1;
481	>	simError();
482	>	}
483	>	sprintf(tempBuffer, " %13e", particlePot);
484	>	line += tempBuffer;
485	>	}
486	>
487	>	if (needFlucQ_) {
488	>	type += "cw";
489	>	RealType fqPos = integrableObject->getFlucQPos();
490	>	if (isinf(fqPos) || isnan(fqPos) ) {
491	>	sprintf( painCave.errMsg,
492	>	"DumpWriter detected a numerical error writing the"
493	>	" fluctuating charge for object %d", index);
494	>	painCave.isFatal = 1;
495	>	simError();
496	>	}
497	>	sprintf(tempBuffer, " %13e ", fqPos);
498	>	line += tempBuffer;
499	>
500	>	RealType fqVel = integrableObject->getFlucQVel();
501	>	if (isinf(fqVel) || isnan(fqVel) ) {
502	>	sprintf( painCave.errMsg,
503	>	"DumpWriter detected a numerical error writing the"
504	>	" fluctuating charge velocity for object %d", index);
505	>	painCave.isFatal = 1;
506	>	simError();
507	>	}
508	>	sprintf(tempBuffer, " %13e ", fqVel);
509	>	line += tempBuffer;
510
511	<	// If we've survived to here, format the line:
512	<
513	<	if (!isDirectional) {
514	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
515	<	MPIatomTypeString, atomData[0],
516	<	atomData[1], atomData[2],
517	<	atomData[3], atomData[4],
518	<	atomData[5]);
519	<
520	<	strcat(writeLine,
521	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
522	<	} else {
523	<	sprintf(writeLine,
524	<	"%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	<	os << writeLine << "\n";
487	<
488	<	} // end for(int l =0)
489	<
490	<	potatoes[which_node] = myPotato;
491	<	} else { //master node has current molecule
492	<
493	<	mol = info_->getMoleculeByGlobalIndex(i);
494	<
495	<	if (mol == NULL) {
496	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
497	<	painCave.isFatal = 1;
498	<	simError();
499	<	}
500	<
501	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
502	<	integrableObject = mol->nextIntegrableObject(ii)) {
503	<
504	<	pos = integrableObject->getPos();
505	<	vel = integrableObject->getVel();
506	<
507	<	atomData[0] = pos[0];
508	<	atomData[1] = pos[1];
509	<	atomData[2] = pos[2];
510	<
511	<	atomData[3] = vel[0];
512	<	atomData[4] = vel[1];
513	<	atomData[5] = vel[2];
514	<
515	<	isDirectional = 0;
516	<
517	<	if (integrableObject->isDirectional()) {
518	<	isDirectional = 1;
519	<
520	<	q = integrableObject->getQ();
521	<	ji = integrableObject->getJ();
522	<
523	<	for(int j = 0; j < 6; j++) {
524	<	atomData[j] = atomData[j];
525	<	}
526	<
527	<	atomData[6] = q[0];
528	<	atomData[7] = q[1];
529	<	atomData[8] = q[2];
530	<	atomData[9] = q[3];
531	<
532	<	atomData[10] = ji[0];
533	<	atomData[11] = ji[1];
534	<	atomData[12] = ji[2];
535	<	}
536	<
537	<	if (needForceVector_) {
538	<	frc = integrableObject->getFrc();
539	<	trq = integrableObject->getTrq();
540	<
541	<	if (!isDirectional) {
542	<	atomData[6] = frc[0];
543	<	atomData[7] = frc[1];
544	<	atomData[8] = frc[2];
545	<	atomData[9] = trq[0];
546	<	atomData[10] = trq[1];
547	<	atomData[11] = trq[2];
548	<	} else {
549	<	atomData[13] = frc[0];
550	<	atomData[14] = frc[1];
551	<	atomData[15] = frc[2];
552	<	atomData[16] = trq[0];
553	<	atomData[17] = trq[1];
554	<	atomData[18] = trq[2];
555	<	}
556	<	}
557	<
558	<	// If we've survived to here, format the line:
559	<
560	<	if (!isDirectional) {
561	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
562	<	integrableObject->getType().c_str(), atomData[0],
563	<	atomData[1], atomData[2],
564	<	atomData[3], atomData[4],
565	<	atomData[5]);
511	>	if (needForceVector_) {
512	>	type += "g";
513	>	RealType fqFrc = integrableObject->getFlucQFrc();
514	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
515	>	sprintf( painCave.errMsg,
516	>	"DumpWriter detected a numerical error writing the"
517	>	" fluctuating charge force for object %d", index);
518	>	painCave.isFatal = 1;
519	>	simError();
520	>	}
521	>	sprintf(tempBuffer, " %13e ", fqFrc);
522	>	line += tempBuffer;
523	>	}
524	>	}
525
526	<	strcat(writeLine,
527	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
528	<	} else {
529	<	sprintf(writeLine,
530	<	"%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",
531	<	integrableObject->getType().c_str(),
532	<	atomData[0],
533	<	atomData[1],
534	<	atomData[2],
535	<	atomData[3],
536	<	atomData[4],
578	<	atomData[5],
579	<	atomData[6],
580	<	atomData[7],
581	<	atomData[8],
582	<	atomData[9],
583	<	atomData[10],
584	<	atomData[11],
585	<	atomData[12]);
586	<	}
587	<
588	<	if (needForceVector_) {
589	<	if (!isDirectional) {
590	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
591	<	atomData[6],
592	<	atomData[7],
593	<	atomData[8],
594	<	atomData[9],
595	<	atomData[10],
596	<	atomData[11]);
597	<	} else {
598	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
599	<	atomData[13],
600	<	atomData[14],
601	<	atomData[15],
602	<	atomData[16],
603	<	atomData[17],
604	<	atomData[18]);
605	<	}
606	<	}
607	<
608	<	os << writeLine << "\n";
609	<
610	<	} //end for(iter = integrableObject.begin())
611	<	}
612	<	} //end for(i = 0; i < mpiSim->getNmol())
613	<
614	<	os.flush();
615	<
616	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
617	<	MPIcheckPoint();
618	<
619	<	delete [] potatoes;
620	<	} else {
621	<
622	<	// worldRank != 0, so I'm a remote node.
623	<
624	<	// Set my magic potato to 0:
625	<
626	<	myPotato = 0;
627	<
628	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
629	<
630	<	// Am I the node which has this integrableObject?
631	<	int whichNode = info_->getMolToProc(i);
632	<	if (whichNode == worldRank) {
633	<	if (myPotato + 1 >= MAXTAG) {
634	<
635	<	// The potato was going to exceed the maximum value,
636	<	// so wrap this processor potato back to 0 (and block until
637	<	// node 0 says we can go:
638	<
639	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
640	<	&istatus);
641	<	}
642	<
643	<	mol = info_->getMoleculeByGlobalIndex(i);
644	<
645	<
646	<	nCurObj = mol->getNIntegrableObjects();
647	<
648	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
649	<	myPotato++;
650	<
651	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
652	<	integrableObject = mol->nextIntegrableObject(ii)) {
653	<
654	<	if (myPotato + 2 >= MAXTAG) {
655	<
656	<	// The potato was going to exceed the maximum value,
657	<	// so wrap this processor potato back to 0 (and block until
658	<	// node 0 says we can go:
659	<
660	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
661	<	&istatus);
662	<	}
663	<
664	<	pos = integrableObject->getPos();
665	<	vel = integrableObject->getVel();
666	<
667	<	atomData[0] = pos[0];
668	<	atomData[1] = pos[1];
669	<	atomData[2] = pos[2];
670	<
671	<	atomData[3] = vel[0];
672	<	atomData[4] = vel[1];
673	<	atomData[5] = vel[2];
674	<
675	<	isDirectional = 0;
676	<
677	<	if (integrableObject->isDirectional()) {
678	<	isDirectional = 1;
679	<
680	<	q = integrableObject->getQ();
681	<	ji = integrableObject->getJ();
682	<
683	<	atomData[6] = q[0];
684	<	atomData[7] = q[1];
685	<	atomData[8] = q[2];
686	<	atomData[9] = q[3];
687	<
688	<	atomData[10] = ji[0];
689	<	atomData[11] = ji[1];
690	<	atomData[12] = ji[2];
691	<	}
692	<
693	<	if (needForceVector_) {
694	<	frc = integrableObject->getFrc();
695	<	trq = integrableObject->getTrq();
696	<
697	<	if (!isDirectional) {
698	<	atomData[6] = frc[0];
699	<	atomData[7] = frc[1];
700	<	atomData[8] = frc[2];
701	<
702	<	atomData[9] = trq[0];
703	<	atomData[10] = trq[1];
704	<	atomData[11] = trq[2];
705	<	} else {
706	<	atomData[13] = frc[0];
707	<	atomData[14] = frc[1];
708	<	atomData[15] = frc[2];
709	<
710	<	atomData[16] = trq[0];
711	<	atomData[17] = trq[1];
712	<	atomData[18] = trq[2];
713	<	}
714	<	}
715	<
716	<	strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
717	<
718	<	// null terminate the  std::string before sending (just in case):
719	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
720	<
721	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
722	<	myPotato, MPI_COMM_WORLD);
723	<
724	<	myPotato++;
725	<
726	<	if (isDirectional && needForceVector_) {
727	<	MPI_Send(atomData, 19, MPI_REALTYPE, 0, myPotato,
728	<	MPI_COMM_WORLD);
729	<	} else if (isDirectional) {
730	<	MPI_Send(atomData, 13, MPI_REALTYPE, 0, myPotato,
731	<	MPI_COMM_WORLD);
732	<	} else if (needForceVector_) {
733	<	MPI_Send(atomData, 12, MPI_REALTYPE, 0, myPotato,
734	<	MPI_COMM_WORLD);
735	<	} else {
736	<	MPI_Send(atomData, 6, MPI_REALTYPE, 0, myPotato,
737	<	MPI_COMM_WORLD);
738	<	}
739	<
740	<	myPotato++;
741	<	}
742	<
743	<	}
744	<
526	>	if (needElectricField_) {
527	>	type += "e";
528	>	Vector3d eField= integrableObject->getElectricField();
529	>	if (isinf(eField[0]) || isnan(eField[0]) ||
530	>	isinf(eField[1]) || isnan(eField[1]) ||
531	>	isinf(eField[2]) || isnan(eField[2]) ) {
532	>	sprintf( painCave.errMsg,
533	>	"DumpWriter detected a numerical error writing the electric"
534	>	" field for object %d", index);
535	>	painCave.isFatal = 1;
536	>	simError();
537		}
538	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
539	<	MPIcheckPoint();
538	>	sprintf(tempBuffer, " %13e %13e %13e",
539	>	eField[0], eField[1], eField[2]);
540	>	line += tempBuffer;
541		}
542
543	<	#endif // is_mpi
544	<
543	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
544	>	return std::string(tempBuffer);
545		}
546
547		void DumpWriter::writeDump() {
#	Line 773 | Line 566 | namespace oopse {
566		#ifdef IS_MPI
567		if (worldRank == 0) {
568		#endif // is_mpi
569	<	delete eorStream;
570	<
569	>	writeClosing(*eorStream);
570	>	delete eorStream;
571		#ifdef IS_MPI
572		}
573		#endif // is_mpi
#	Line 807 | Line 600 | namespace oopse {
600		#ifdef IS_MPI
601		if (worldRank == 0) {
602		#endif // is_mpi
603	<	delete eorStream;
604	<
603	>	writeClosing(*eorStream);
604	>	delete eorStream;
605		#ifdef IS_MPI
606		}
607		#endif // is_mpi
608
609		}
610
611	<	std::ostream* DumpWriter::createOStream(const std::string& filename) {
611	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
612
613		std::ostream* newOStream;
614		#ifdef HAVE_LIBZ
615		if (needCompression_) {
616	<	newOStream = new ogzstream(filename.c_str());
616	>	newOStream = new ogzstream(filename.c_str());
617		} else {
618	<	newOStream = new std::ofstream(filename.c_str());
618	>	newOStream = new std::ofstream(filename.c_str());
619		}
620		#else
621		newOStream = new std::ofstream(filename.c_str());
622		#endif
623	+	//write out MetaData first
624	+	(*newOStream) << "<OpenMD version=1>" << std::endl;
625	+	(*newOStream) << "  <MetaData>" << std::endl;
626	+	(*newOStream) << info_->getRawMetaData();
627	+	(*newOStream) << "  </MetaData>" << std::endl;
628		return newOStream;
629	<	}
629	>	}
630
631	<	}//end namespace oopse
631	>	void DumpWriter::writeClosing(std::ostream& os) {
632	>
633	>	os << "</OpenMD>\n";
634	>	os.flush();
635	>	}
636	>
637	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 966 by chrisfen, Fri May 19 21:26:41 2006 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1714 by gezelter, Sat May 19 18:12:46 2012 UTC

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