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

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 965 by tim, Fri May 19 20:45:55 2006 UTC vs.
Revision 1564 by chuckv, Wed May 18 19:28:52 2011 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include "io/DumpWriter.hpp"
#	Line 46 | Line 46
46		#include "io/gzstream.hpp"
47		#include "io/Globals.hpp"
48
49	+
50		#ifdef IS_MPI
51		#include <mpi.h>
52		#endif //is_mpi
53
54	<	namespace oopse {
54	>	using namespace std;
55	>	namespace OpenMD {
56
57		DumpWriter::DumpWriter(SimInfo* info)
58		: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
#	Line 61 | Line 63 | namespace oopse {
63		createDumpFile_ = true;
64		#ifdef HAVE_LIBZ
65		if (needCompression_) {
66	<	filename_ += ".gz";
67	<	eorFilename_ += ".gz";
66	>	filename_ += ".gz";
67	>	eorFilename_ += ".gz";
68		}
69		#endif
70
71		#ifdef IS_MPI
72
73	<	if (worldRank == 0) {
73	>	if (worldRank == 0) {
74		#endif // is_mpi
73	–
75
76	<	dumpFile_ = createOStream(filename_);
76	>	dumpFile_ = createOStream(filename_);
77
78	<	if (!dumpFile_) {
79	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
80	<	filename_.c_str());
81	<	painCave.isFatal = 1;
82	<	simError();
83	<	}
78	>	if (!dumpFile_) {
79	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
80	>	filename_.c_str());
81	>	painCave.isFatal = 1;
82	>	simError();
83	>	}
84
85		#ifdef IS_MPI
86
87	<	}
87	>	}
88
88	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
89	–	MPIcheckPoint();
90	–
89		#endif // is_mpi
90
91	<	}
91	>	}
92
93
94		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
#	Line 104 | Line 102 | namespace oopse {
102		createDumpFile_ = true;
103		#ifdef HAVE_LIBZ
104		if (needCompression_) {
105	<	filename_ += ".gz";
106	<	eorFilename_ += ".gz";
105	>	filename_ += ".gz";
106	>	eorFilename_ += ".gz";
107		}
108		#endif
109
110		#ifdef IS_MPI
111
112	<	if (worldRank == 0) {
112	>	if (worldRank == 0) {
113		#endif // is_mpi
114
115
116	<	dumpFile_ = createOStream(filename_);
116	>	dumpFile_ = createOStream(filename_);
117
118	<	if (!dumpFile_) {
119	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
120	<	filename_.c_str());
121	<	painCave.isFatal = 1;
122	<	simError();
123	<	}
118	>	if (!dumpFile_) {
119	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
120	>	filename_.c_str());
121	>	painCave.isFatal = 1;
122	>	simError();
123	>	}
124
125		#ifdef IS_MPI
126
127	<	}
127	>	}
128
131	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
132	–	MPIcheckPoint();
133	–
129		#endif // is_mpi
130
131	<	}
131	>	}
132
133		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
134	<	: info_(info), filename_(filename){
134	>	: info_(info), filename_(filename){
135
136		Globals* simParams = info->getSimParams();
137		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
#	Line 170 | Line 165 | namespace oopse {
165		#ifdef IS_MPI
166
167		}
168	+
169
174	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
175	–	MPIcheckPoint();
176	–
170		#endif // is_mpi
171
172		}
180	–
181	–
182	–
183	–
184	–
173
174		DumpWriter::~DumpWriter() {
175
#	Line 190 | Line 178 | namespace oopse {
178		if (worldRank == 0) {
179		#endif // is_mpi
180		if (createDumpFile_){
181	+	writeClosing(*dumpFile_);
182		delete dumpFile_;
183		}
184		#ifdef IS_MPI
#	Line 200 | Line 189 | namespace oopse {
189
190		}
191
192	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
192	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
193
194	<	RealType currentTime;
206	<	Mat3x3d hmat;
207	<	RealType chi;
208	<	RealType 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";
194	>	char buffer[1024];
195
196	<	//write out additional parameters, such as chi and eta
196	>	os << "    <FrameData>\n";
197
198	<	os << chi << "\t" << integralOfChiDt << ";\t";
198	>	RealType currentTime = s->getTime();
199
200	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
201	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
202	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
203	<
204	<	os << "\n";
200	>	if (isinf(currentTime) || isnan(currentTime)) {
201	>	sprintf( painCave.errMsg,
202	>	"DumpWriter detected a numerical error writing the time");
203	>	painCave.isFatal = 1;
204	>	simError();
205	>	}
206	>
207	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
208	>	os << buffer;
209	>
210	>	Mat3x3d hmat;
211	>	hmat = s->getHmat();
212	>
213	>	for (unsigned int i = 0; i < 3; i++) {
214	>	for (unsigned int j = 0; j < 3; j++) {
215	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
216	>	sprintf( painCave.errMsg,
217	>	"DumpWriter detected a numerical error writing the box");
218	>	painCave.isFatal = 1;
219	>	simError();
220	>	}
221	>	}
222	>	}
223	>
224	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
225	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
226	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
227	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
228	>	os << buffer;
229	>
230	>	RealType chi = s->getChi();
231	>	RealType integralOfChiDt = s->getIntegralOfChiDt();
232	>	if (isinf(chi) || isnan(chi) ||
233	>	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
234	>	sprintf( painCave.errMsg,
235	>	"DumpWriter detected a numerical error writing the thermostat");
236	>	painCave.isFatal = 1;
237	>	simError();
238	>	}
239	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
240	>	os << buffer;
241	>
242	>	Mat3x3d eta;
243	>	eta = s->getEta();
244	>
245	>	for (unsigned int i = 0; i < 3; i++) {
246	>	for (unsigned int j = 0; j < 3; j++) {
247	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
248	>	sprintf( painCave.errMsg,
249	>	"DumpWriter detected a numerical error writing the barostat");
250	>	painCave.isFatal = 1;
251	>	simError();
252	>	}
253	>	}
254	>	}
255	>
256	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
257	>	eta(0, 0), eta(1, 0), eta(2, 0),
258	>	eta(0, 1), eta(1, 1), eta(2, 1),
259	>	eta(0, 2), eta(1, 2), eta(2, 2));
260	>	os << buffer;
261	>
262	>	os << "    </FrameData>\n";
263		}
264
265		void DumpWriter::writeFrame(std::ostream& os) {
234	–	const int BUFFERSIZE = 2000;
235	–	const int MINIBUFFERSIZE = 100;
266
267	<	char tempBuffer[BUFFERSIZE];
268	<	char writeLine[BUFFERSIZE];
267	>	#ifdef IS_MPI
268	>	MPI_Status istatus;
269	>	#endif
270
240	–	Quat4d q;
241	–	Vector3d ji;
242	–	Vector3d pos;
243	–	Vector3d vel;
244	–	Vector3d frc;
245	–	Vector3d trq;
246	–
271		Molecule* mol;
272		StuntDouble* integrableObject;
273		SimInfo::MoleculeIterator mi;
274		Molecule::IntegrableObjectIterator ii;
251	–
252	–	int nTotObjects;
253	–	nTotObjects = info_->getNGlobalIntegrableObjects();
275
276		#ifndef IS_MPI
277	+	os << "  <Snapshot>\n";
278	+
279	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
280
281	+	os << "    <StuntDoubles>\n";
282	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
283
284	<	os << nTotObjects << "\n";
285	<
286	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
284	>
285	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
286	>	integrableObject = mol->nextIntegrableObject(ii)) {
287	>	os << prepareDumpLine(integrableObject);
288	>
289	>	}
290	>	}
291	>	os << "    </StuntDoubles>\n";
292	>
293	>	os << "  </Snapshot>\n";
294
295	+	os.flush();
296	+	#else
297	+	//every node prepares the dump lines for integrable objects belong to itself
298	+	std::string buffer;
299		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
300
264	–	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
265	–	integrableObject = mol->nextIntegrableObject(ii)) {
266	–
301
302	<	pos = integrableObject->getPos();
303	<	vel = integrableObject->getVel();
304	<
271	<	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	<
302	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
303	>	integrableObject = mol->nextIntegrableObject(ii)) {
304	>	buffer += prepareDumpLine(integrableObject);
305		}
306		}
307	<
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	<	*********************************************************************/
307	>
308		const int masterNode = 0;
345	–
346	–	int * potatoes;
347	–	int myPotato;
309		int nProc;
310	<	int which_node;
311	<	RealType atomData[19];
312	<	int isDirectional;
313	<	char MPIatomTypeString[MINIBUFFERSIZE];
314	<	int msgLen; // the length of message actually recieved at master nodes
315	<	int haveError;
316	<	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);
310	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
311	>	if (worldRank == masterNode) {
312	>	os << "  <Snapshot>\n";
313	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
314	>	os << "    <StuntDoubles>\n";
315	>
316	>	os << buffer;
317
318	<	if (flag) {
319	<	MAXTAG = *tagub;
318	>
319	>	for (int i = 1; i < nProc; ++i) {
320	>
321	>	// receive the length of the string buffer that was
322	>	// prepared by processor i
323	>
324	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
325	>	int recvLength;
326	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
327	>	char* recvBuffer = new char[recvLength];
328	>	if (recvBuffer == NULL) {
329	>	} else {
330	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
331	>	os << recvBuffer;
332	>	delete [] recvBuffer;
333	>	}
334	>	}
335	>	os << "    </StuntDoubles>\n";
336	>
337	>	os << "  </Snapshot>\n";
338	>	os.flush();
339		} else {
340	<	MAXTAG = 32767;
340	>	int sendBufferLength = buffer.size() + 1;
341	>	int myturn = 0;
342	>	for (int i = 1; i < nProc; ++i){
343	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
344	>	if (myturn == worldRank){
345	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
346	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
347	>	}
348	>	}
349		}
350
351	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
351	>	#endif // is_mpi
352
353	<	// Node 0 needs a list of the magic potatoes for each processor;
353	>	}
354
355	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
356	<	potatoes = new int[nProc];
355	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
356	>
357	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
358	>	std::string type("pv");
359	>	std::string line;
360	>	char tempBuffer[4096];
361
362	<	//write out the comment lines
363	<	for(int i = 0; i < nProc; i++) {
364	<	potatoes[i] = 0;
380	<	}
362	>	Vector3d pos;
363	>	Vector3d vel;
364	>	pos = integrableObject->getPos();
365
366	+	if (isinf(pos[0]) || isnan(pos[0]) ||
367	+	isinf(pos[1]) || isnan(pos[1]) ||
368	+	isinf(pos[2]) || isnan(pos[2]) ) {
369	+	sprintf( painCave.errMsg,
370	+	"DumpWriter detected a numerical error writing the position"
371	+	" for object %d", index);
372	+	painCave.isFatal = 1;
373	+	simError();
374	+	}
375
376	<	os << nTotObjects << "\n";
384	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
376	>	vel = integrableObject->getVel();
377
378	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
378	>	if (isinf(vel[0]) || isnan(vel[0]) ||
379	>	isinf(vel[1]) || isnan(vel[1]) ||
380	>	isinf(vel[2]) || isnan(vel[2]) ) {
381	>	sprintf( painCave.errMsg,
382	>	"DumpWriter detected a numerical error writing the velocity"
383	>	" for object %d", index);
384	>	painCave.isFatal = 1;
385	>	simError();
386	>	}
387
388	<	// Get the Node number which has this atom;
388	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
389	>	pos[0], pos[1], pos[2],
390	>	vel[0], vel[1], vel[2]);
391	>	line += tempBuffer;
392
393	<	which_node = info_->getMolToProc(i);
393	>	if (integrableObject->isDirectional()) {
394	>	type += "qj";
395	>	Quat4d q;
396	>	Vector3d ji;
397	>	q = integrableObject->getQ();
398
399	<	if (which_node != masterNode) { //current molecule is in slave node
400	<	if (potatoes[which_node] + 1 >= MAXTAG) {
401	<	// The potato was going to exceed the maximum value,
402	<	// so wrap this processor potato back to 0:
399	>	if (isinf(q[0]) || isnan(q[0]) ||
400	>	isinf(q[1]) || isnan(q[1]) ||
401	>	isinf(q[2]) || isnan(q[2]) ||
402	>	isinf(q[3]) || isnan(q[3]) ) {
403	>	sprintf( painCave.errMsg,
404	>	"DumpWriter detected a numerical error writing the quaternion"
405	>	" for object %d", index);
406	>	painCave.isFatal = 1;
407	>	simError();
408	>	}
409
410	<	potatoes[which_node] = 0;
398	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
399	<	MPI_COMM_WORLD);
400	<	}
410	>	ji = integrableObject->getJ();
411
412	<	myPotato = potatoes[which_node];
413	<
414	<	//recieve the number of integrableObject in current molecule
415	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
416	<	MPI_COMM_WORLD, &istatus);
417	<	myPotato++;
412	>	if (isinf(ji[0]) || isnan(ji[0]) ||
413	>	isinf(ji[1]) || isnan(ji[1]) ||
414	>	isinf(ji[2]) || isnan(ji[2]) ) {
415	>	sprintf( painCave.errMsg,
416	>	"DumpWriter detected a numerical error writing the angular"
417	>	" momentum for object %d", index);
418	>	painCave.isFatal = 1;
419	>	simError();
420	>	}
421
422	<	for(int l = 0; l < nCurObj; l++) {
423	<	if (potatoes[which_node] + 2 >= MAXTAG) {
424	<	// The potato was going to exceed the maximum value,
425	<	// so wrap this processor potato back to 0:
422	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
423	>	q[0], q[1], q[2], q[3],
424	>	ji[0], ji[1], ji[2]);
425	>	line += tempBuffer;
426	>	}
427
428	<	potatoes[which_node] = 0;
429	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
430	<	0, MPI_COMM_WORLD);
417	<	}
428	>	if (needForceVector_) {
429	>	type += "f";
430	>	Vector3d frc;
431
432	<	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_REALTYPE, which_node, myPotato,
426	<	MPI_COMM_WORLD, &istatus);
427	<	myPotato++;
428	<
429	<	MPI_Get_count(&istatus, MPI_REALTYPE, &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	<	}
432	>	frc = integrableObject->getFrc();
433
434	<	os << writeLine << "\n";
435	<
436	<	} //end for(iter = integrableObject.begin())
437	<	}
438	<	} //end for(i = 0; i < mpiSim->getNmol())
439	<
440	<	os.flush();
441	<
617	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
618	<	MPIcheckPoint();
619	<
620	<	delete [] potatoes;
621	<	} else {
622	<
623	<	// worldRank != 0, so I'm a remote node.
624	<
625	<	// Set my magic potato to 0:
626	<
627	<	myPotato = 0;
628	<
629	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
630	<
631	<	// Am I the node which has this integrableObject?
632	<	int whichNode = info_->getMolToProc(i);
633	<	if (whichNode == worldRank) {
634	<	if (myPotato + 1 >= MAXTAG) {
635	<
636	<	// The potato was going to exceed the maximum value,
637	<	// so wrap this processor potato back to 0 (and block until
638	<	// node 0 says we can go:
639	<
640	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
641	<	&istatus);
642	<	}
643	<
644	<	mol = info_->getMoleculeByGlobalIndex(i);
645	<
646	<
647	<	nCurObj = mol->getNIntegrableObjects();
648	<
649	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
650	<	myPotato++;
651	<
652	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
653	<	integrableObject = mol->nextIntegrableObject(ii)) {
654	<
655	<	if (myPotato + 2 >= MAXTAG) {
656	<
657	<	// The potato was going to exceed the maximum value,
658	<	// so wrap this processor potato back to 0 (and block until
659	<	// node 0 says we can go:
660	<
661	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
662	<	&istatus);
663	<	}
664	<
665	<	pos = integrableObject->getPos();
666	<	vel = integrableObject->getVel();
667	<
668	<	atomData[0] = pos[0];
669	<	atomData[1] = pos[1];
670	<	atomData[2] = pos[2];
671	<
672	<	atomData[3] = vel[0];
673	<	atomData[4] = vel[1];
674	<	atomData[5] = vel[2];
675	<
676	<	isDirectional = 0;
677	<
678	<	if (integrableObject->isDirectional()) {
679	<	isDirectional = 1;
680	<
681	<	q = integrableObject->getQ();
682	<	ji = integrableObject->getJ();
683	<
684	<	atomData[6] = q[0];
685	<	atomData[7] = q[1];
686	<	atomData[8] = q[2];
687	<	atomData[9] = q[3];
688	<
689	<	atomData[10] = ji[0];
690	<	atomData[11] = ji[1];
691	<	atomData[12] = ji[2];
692	<	}
693	<
694	<	if (needForceVector_) {
695	<	frc = integrableObject->getFrc();
696	<	trq = integrableObject->getTrq();
697	<
698	<	if (!isDirectional) {
699	<	atomData[6] = frc[0];
700	<	atomData[7] = frc[1];
701	<	atomData[8] = frc[2];
702	<
703	<	atomData[9] = trq[0];
704	<	atomData[10] = trq[1];
705	<	atomData[11] = trq[2];
706	<	} else {
707	<	atomData[13] = frc[0];
708	<	atomData[14] = frc[1];
709	<	atomData[15] = frc[2];
710	<
711	<	atomData[16] = trq[0];
712	<	atomData[17] = trq[1];
713	<	atomData[18] = trq[2];
714	<	}
715	<	}
716	<
717	<	strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
718	<
719	<	// null terminate the  std::string before sending (just in case):
720	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
721	<
722	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
723	<	myPotato, MPI_COMM_WORLD);
724	<
725	<	myPotato++;
726	<
727	<	if (isDirectional && needForceVector_) {
728	<	MPI_Send(atomData, 19, MPI_REALTYPE, 0, myPotato,
729	<	MPI_COMM_WORLD);
730	<	} else if (isDirectional) {
731	<	MPI_Send(atomData, 13, MPI_REALTYPE, 0, myPotato,
732	<	MPI_COMM_WORLD);
733	<	} else if (needForceVector_) {
734	<	MPI_Send(atomData, 12, MPI_REALTYPE, 0, myPotato,
735	<	MPI_COMM_WORLD);
736	<	} else {
737	<	MPI_Send(atomData, 6, MPI_REALTYPE, 0, myPotato,
738	<	MPI_COMM_WORLD);
739	<	}
740	<
741	<	myPotato++;
742	<	}
743	<
744	<	}
745	<
434	>	if (isinf(frc[0]) || isnan(frc[0]) ||
435	>	isinf(frc[1]) || isnan(frc[1]) ||
436	>	isinf(frc[2]) || isnan(frc[2]) ) {
437	>	sprintf( painCave.errMsg,
438	>	"DumpWriter detected a numerical error writing the force"
439	>	" for object %d", index);
440	>	painCave.isFatal = 1;
441	>	simError();
442		}
443	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
444	<	MPIcheckPoint();
443	>	sprintf(tempBuffer, " %13e %13e %13e",
444	>	frc[0], frc[1], frc[2]);
445	>	line += tempBuffer;
446	>
447	>	if (integrableObject->isDirectional()) {
448	>	type += "t";
449	>	Vector3d trq;
450	>
451	>	trq = integrableObject->getTrq();
452	>
453	>	if (isinf(trq[0]) || isnan(trq[0]) ||
454	>	isinf(trq[1]) || isnan(trq[1]) ||
455	>	isinf(trq[2]) || isnan(trq[2]) ) {
456	>	sprintf( painCave.errMsg,
457	>	"DumpWriter detected a numerical error writing the torque"
458	>	" for object %d", index);
459	>	painCave.isFatal = 1;
460	>	simError();
461	>	}
462	>
463	>	sprintf(tempBuffer, " %13e %13e %13e",
464	>	trq[0], trq[1], trq[2]);
465	>	line += tempBuffer;
466	>	}
467		}
468	<
469	<	#endif // is_mpi
470	<
468	>
469	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
470	>	return std::string(tempBuffer);
471		}
472
473		void DumpWriter::writeDump() {
#	Line 774 | Line 492 | namespace oopse {
492		#ifdef IS_MPI
493		if (worldRank == 0) {
494		#endif // is_mpi
495	<	delete eorStream;
496	<
495	>	writeClosing(*eorStream);
496	>	delete eorStream;
497		#ifdef IS_MPI
498		}
499		#endif // is_mpi
#	Line 808 | Line 526 | namespace oopse {
526		#ifdef IS_MPI
527		if (worldRank == 0) {
528		#endif // is_mpi
529	<	delete eorStream;
530	<
529	>	writeClosing(*eorStream);
530	>	delete eorStream;
531		#ifdef IS_MPI
532		}
533		#endif // is_mpi
534
535		}
536
537	<	std::ostream* DumpWriter::createOStream(const std::string& filename) {
537	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
538
539		std::ostream* newOStream;
540		#ifdef HAVE_LIBZ
541		if (needCompression_) {
542	<	newOStream = new ogzstream(filename.c_str());
542	>	newOStream = new ogzstream(filename.c_str());
543		} else {
544	<	newOStream = new std::ofstream(filename.c_str());
544	>	newOStream = new std::ofstream(filename.c_str());
545		}
546		#else
547		newOStream = new std::ofstream(filename.c_str());
548		#endif
549	+	//write out MetaData first
550	+	(*newOStream) << "<OpenMD version=1>" << std::endl;
551	+	(*newOStream) << "  <MetaData>" << std::endl;
552	+	(*newOStream) << info_->getRawMetaData();
553	+	(*newOStream) << "  </MetaData>" << std::endl;
554		return newOStream;
555	<	}
555	>	}
556
557	<	}//end namespace oopse
557	>	void DumpWriter::writeClosing(std::ostream& os) {
558	>
559	>	os << "</OpenMD>\n";
560	>	os.flush();
561	>	}
562	>
563	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpWriter.cpp (property svn:keywords):
Revision 965 by tim, Fri May 19 20:45:55 2006 UTC vs.
Revision 1564 by chuckv, Wed May 18 19:28:52 2011 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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