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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 1769 by gezelter, Mon Jul 9 14:15:52 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"
44		#include "primitives/Molecule.hpp"
45		#include "utils/simError.h"
46		#include "io/basic_teebuf.hpp"
47	+	#ifdef HAVE_ZLIB
48		#include "io/gzstream.hpp"
49	+	#endif
50		#include "io/Globals.hpp"
51
52	+	#ifdef _MSC_VER
53	+	#define isnan(x) _isnan((x))
54	+	#define isinf(x) (!_finite(x) && !_isnan(x))
55	+	#endif
56	+
57		#ifdef IS_MPI
58		#include <mpi.h>
59	<	#endif //is_mpi
59	>	#endif
60
61	<	namespace oopse {
61	>	using namespace std;
62	>	namespace OpenMD {
63
64		DumpWriter::DumpWriter(SimInfo* info)
65		: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
66
67		Globals* simParams = info->getSimParams();
68	<	needCompression_ = simParams->getCompressDumpFile();
69	<	needForceVector_ = simParams->getOutputForceVector();
68	>	needCompression_   = simParams->getCompressDumpFile();
69	>	needForceVector_   = simParams->getOutputForceVector();
70	>	needParticlePot_   = simParams->getOutputParticlePotential();
71	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
72	>	needElectricField_ = simParams->getOutputElectricField();
73	>
74	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
75	>	doSiteData_ = true;
76	>	} else {
77	>	doSiteData_ = false;
78	>	}
79	>
80		createDumpFile_ = true;
81		#ifdef HAVE_LIBZ
82		if (needCompression_) {
83	<	filename_ += ".gz";
84	<	eorFilename_ += ".gz";
83	>	filename_ += ".gz";
84	>	eorFilename_ += ".gz";
85		}
86		#endif
87
88		#ifdef IS_MPI
89
90	<	if (worldRank == 0) {
90	>	if (worldRank == 0) {
91		#endif // is_mpi
73	–
92
93	<	dumpFile_ = createOStream(filename_);
93	>	dumpFile_ = createOStream(filename_);
94
95	<	if (!dumpFile_) {
96	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
97	<	filename_.c_str());
98	<	painCave.isFatal = 1;
99	<	simError();
100	<	}
95	>	if (!dumpFile_) {
96	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
97	>	filename_.c_str());
98	>	painCave.isFatal = 1;
99	>	simError();
100	>	}
101
102		#ifdef IS_MPI
103
104	<	}
104	>	}
105
88	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
89	–	MPIcheckPoint();
90	–
106		#endif // is_mpi
107
108	<	}
108	>	}
109
110
111		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
#	Line 99 | Line 114 | namespace oopse {
114		Globals* simParams = info->getSimParams();
115		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
116
117	<	needCompression_ = simParams->getCompressDumpFile();
118	<	needForceVector_ = simParams->getOutputForceVector();
117	>	needCompression_   = simParams->getCompressDumpFile();
118	>	needForceVector_   = simParams->getOutputForceVector();
119	>	needParticlePot_   = simParams->getOutputParticlePotential();
120	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
121	>	needElectricField_ = simParams->getOutputElectricField();
122	>
123	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
124	>	doSiteData_ = true;
125	>	} else {
126	>	doSiteData_ = false;
127	>	}
128	>
129		createDumpFile_ = true;
130		#ifdef HAVE_LIBZ
131		if (needCompression_) {
132	<	filename_ += ".gz";
133	<	eorFilename_ += ".gz";
132	>	filename_ += ".gz";
133	>	eorFilename_ += ".gz";
134		}
135		#endif
136
137		#ifdef IS_MPI
138
139	<	if (worldRank == 0) {
139	>	if (worldRank == 0) {
140		#endif // is_mpi
141
142
143	<	dumpFile_ = createOStream(filename_);
143	>	dumpFile_ = createOStream(filename_);
144
145	<	if (!dumpFile_) {
146	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
147	<	filename_.c_str());
148	<	painCave.isFatal = 1;
149	<	simError();
150	<	}
145	>	if (!dumpFile_) {
146	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
147	>	filename_.c_str());
148	>	painCave.isFatal = 1;
149	>	simError();
150	>	}
151
152		#ifdef IS_MPI
153
154	<	}
154	>	}
155
131	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
132	–	MPIcheckPoint();
133	–
156		#endif // is_mpi
157
158	<	}
158	>	}
159
160		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
161	<	: info_(info), filename_(filename){
161	>	: info_(info), filename_(filename){
162
163		Globals* simParams = info->getSimParams();
164		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
165
166	<	needCompression_ = simParams->getCompressDumpFile();
167	<	needForceVector_ = simParams->getOutputForceVector();
168	<
166	>	needCompression_   = simParams->getCompressDumpFile();
167	>	needForceVector_   = simParams->getOutputForceVector();
168	>	needParticlePot_   = simParams->getOutputParticlePotential();
169	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
170	>	needElectricField_ = simParams->getOutputElectricField();
171	>
172	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
173	>	doSiteData_ = true;
174	>	} else {
175	>	doSiteData_ = false;
176	>	}
177	>
178		#ifdef HAVE_LIBZ
179		if (needCompression_) {
180		filename_ += ".gz";
#	Line 170 | Line 201 | namespace oopse {
201		#ifdef IS_MPI
202
203		}
204	+
205
174	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
175	–	MPIcheckPoint();
176	–
206		#endif // is_mpi
207
208		}
180	–
181	–
182	–
183	–
184	–
209
210		DumpWriter::~DumpWriter() {
211
#	Line 190 | Line 214 | namespace oopse {
214		if (worldRank == 0) {
215		#endif // is_mpi
216		if (createDumpFile_){
217	+	writeClosing(*dumpFile_);
218		delete dumpFile_;
219		}
220		#ifdef IS_MPI
#	Line 200 | Line 225 | namespace oopse {
225
226		}
227
228	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
228	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
229
230	<	RealType currentTime;
231	<	Mat3x3d hmat;
232	<	RealType chi;
233	<	RealType integralOfChiDt;
234	<	Mat3x3d eta;
230	>	char buffer[1024];
231	>
232	>	os << "    <FrameData>\n";
233	>
234	>	RealType currentTime = s->getTime();
235	>
236	>	if (isinf(currentTime) || isnan(currentTime)) {
237	>	sprintf( painCave.errMsg,
238	>	"DumpWriter detected a numerical error writing the time");
239	>	painCave.isFatal = 1;
240	>	simError();
241	>	}
242
243	<	currentTime = s->getTime();
243	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
244	>	os << buffer;
245	>
246	>	Mat3x3d hmat;
247		hmat = s->getHmat();
248	<	chi = s->getChi();
249	<	integralOfChiDt = s->getIntegralOfChiDt();
250	<	eta = s->getEta();
248	>
249	>	for (unsigned int i = 0; i < 3; i++) {
250	>	for (unsigned int j = 0; j < 3; j++) {
251	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
252	>	sprintf( painCave.errMsg,
253	>	"DumpWriter detected a numerical error writing the box");
254	>	painCave.isFatal = 1;
255	>	simError();
256	>	}
257	>	}
258	>	}
259
260	<	os << currentTime << ";\t"
261	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
262	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
263	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
260	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
261	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
262	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
263	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
264	>	os << buffer;
265
266	<	//write out additional parameters, such as chi and eta
266	>	pair<RealType, RealType> thermostat = s->getThermostat();
267
268	<	os << chi << "\t" << integralOfChiDt << ";\t";
268	>	if (isinf(thermostat.first)  || isnan(thermostat.first) ||
269	>	isinf(thermostat.second) || isnan(thermostat.second)) {
270	>	sprintf( painCave.errMsg,
271	>	"DumpWriter detected a numerical error writing the thermostat");
272	>	painCave.isFatal = 1;
273	>	simError();
274	>	}
275	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
276	>	thermostat.second);
277	>	os << buffer;
278
279	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
280	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
281	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
282	<
283	<	os << "\n";
279	>	Mat3x3d eta;
280	>	eta = s->getBarostat();
281	>
282	>	for (unsigned int i = 0; i < 3; i++) {
283	>	for (unsigned int j = 0; j < 3; j++) {
284	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
285	>	sprintf( painCave.errMsg,
286	>	"DumpWriter detected a numerical error writing the barostat");
287	>	painCave.isFatal = 1;
288	>	simError();
289	>	}
290	>	}
291	>	}
292	>
293	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
294	>	eta(0, 0), eta(1, 0), eta(2, 0),
295	>	eta(0, 1), eta(1, 1), eta(2, 1),
296	>	eta(0, 2), eta(1, 2), eta(2, 2));
297	>	os << buffer;
298	>
299	>	os << "    </FrameData>\n";
300		}
301
302		void DumpWriter::writeFrame(std::ostream& os) {
234	–	const int BUFFERSIZE = 2000;
235	–	const int MINIBUFFERSIZE = 100;
303
304	<	char tempBuffer[BUFFERSIZE];
305	<	char writeLine[BUFFERSIZE];
304	>	#ifdef IS_MPI
305	>	MPI_Status istatus;
306	>	#endif
307
240	–	Quat4d q;
241	–	Vector3d ji;
242	–	Vector3d pos;
243	–	Vector3d vel;
244	–	Vector3d frc;
245	–	Vector3d trq;
246	–
308		Molecule* mol;
309	<	StuntDouble* integrableObject;
309	>	StuntDouble* sd;
310		SimInfo::MoleculeIterator mi;
311		Molecule::IntegrableObjectIterator ii;
312	<
313	<	int nTotObjects;
253	<	nTotObjects = info_->getNGlobalIntegrableObjects();
312	>	RigidBody::AtomIterator ai;
313	>	Atom* atom;
314
315		#ifndef IS_MPI
316	+	os << "  <Snapshot>\n";
317	+
318	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
319
320	<
258	<	os << nTotObjects << "\n";
259	<
260	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
261	<
320	>	os << "    <StuntDoubles>\n";
321		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
322
323	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
324	<	integrableObject = mol->nextIntegrableObject(ii)) {
325	<
323	>
324	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
325	>	sd = mol->nextIntegrableObject(ii)) {
326	>	os << prepareDumpLine(sd);
327	>
328	>	}
329	>	}
330	>	os << "    </StuntDoubles>\n";
331
332	<	pos = integrableObject->getPos();
333	<	vel = integrableObject->getVel();
332	>	if (doSiteData_) {
333	>	os << "    <SiteData>\n";
334	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
335	>
336	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
337	>	sd = mol->nextIntegrableObject(ii)) {
338
339	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
340	<	integrableObject->getType().c_str(),
341	<	pos[0], pos[1], pos[2],
274	<	vel[0], vel[1], vel[2]);
339	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
340	>	// do one for the IO itself
341	>	os << prepareSiteLine(sd, ioIndex, 0);
342
343	<	strcpy(writeLine, tempBuffer);
343	>	if (sd->isRigidBody()) {
344	>
345	>	RigidBody* rb = static_cast<RigidBody*>(sd);
346	>	int siteIndex = 0;
347	>	for (atom = rb->beginAtom(ai); atom != NULL;
348	>	atom = rb->nextAtom(ai)) {
349	>	os << prepareSiteLine(atom, ioIndex, siteIndex);
350	>	siteIndex++;
351	>	}
352	>	}
353	>	}
354	>	}
355	>	os << "    </SiteData>\n";
356	>	}
357	>	os << "  </Snapshot>\n";
358
359	<	if (integrableObject->isDirectional()) {
360	<	q = integrableObject->getQ();
361	<	ji = integrableObject->getJ();
359	>	os.flush();
360	>	#else
361	>	//every node prepares the dump lines for integrable objects belong to itself
362	>	std::string buffer;
363	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
364
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	–	}
365
366	<	if (needForceVector_) {
367	<	frc = integrableObject->getFrc();
368	<	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	<
366	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
367	>	sd = mol->nextIntegrableObject(ii)) {
368	>	buffer += prepareDumpLine(sd);
369		}
370		}
371	<
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	<	*********************************************************************/
371	>
372		const int masterNode = 0;
345	–
346	–	int * potatoes;
347	–	int myPotato;
373		int nProc;
374	<	int which_node;
375	<	RealType atomData[19];
376	<	int isDirectional;
377	<	char MPIatomTypeString[MINIBUFFERSIZE];
378	<	int msgLen; // the length of message actually recieved at master nodes
379	<	int haveError;
380	<	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);
374	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
375	>	if (worldRank == masterNode) {
376	>	os << "  <Snapshot>\n";
377	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
378	>	os << "    <StuntDoubles>\n";
379	>
380	>	os << buffer;
381
382	<	if (flag) {
383	<	MAXTAG = *tagub;
382	>	for (int i = 1; i < nProc; ++i) {
383	>
384	>	// receive the length of the string buffer that was
385	>	// prepared by processor i
386	>
387	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
388	>	int recvLength;
389	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
390	>	char* recvBuffer = new char[recvLength];
391	>	if (recvBuffer == NULL) {
392	>	} else {
393	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
394	>	os << recvBuffer;
395	>	delete [] recvBuffer;
396	>	}
397	>	}
398	>	os << "    </StuntDoubles>\n";
399	>
400	>	os << "  </Snapshot>\n";
401	>	os.flush();
402		} else {
403	<	MAXTAG = 32767;
403	>	int sendBufferLength = buffer.size() + 1;
404	>	int myturn = 0;
405	>	for (int i = 1; i < nProc; ++i){
406	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
407	>	if (myturn == worldRank){
408	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
409	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
410	>	}
411	>	}
412		}
413
414	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
414	>	#endif // is_mpi
415
416	<	// Node 0 needs a list of the magic potatoes for each processor;
416	>	}
417
418	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
419	<	potatoes = new int[nProc];
418	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
419	>
420	>	int index = sd->getGlobalIntegrableObjectIndex();
421	>	std::string type("pv");
422	>	std::string line;
423	>	char tempBuffer[4096];
424
425	<	//write out the comment lines
426	<	for(int i = 0; i < nProc; i++) {
427	<	potatoes[i] = 0;
380	<	}
425	>	Vector3d pos;
426	>	Vector3d vel;
427	>	pos = sd->getPos();
428
429	+	if (isinf(pos[0]) || isnan(pos[0]) ||
430	+	isinf(pos[1]) || isnan(pos[1]) ||
431	+	isinf(pos[2]) || isnan(pos[2]) ) {
432	+	sprintf( painCave.errMsg,
433	+	"DumpWriter detected a numerical error writing the position"
434	+	" for object %d", index);
435	+	painCave.isFatal = 1;
436	+	simError();
437	+	}
438
439	<	os << nTotObjects << "\n";
384	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
439	>	vel = sd->getVel();
440
441	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
441	>	if (isinf(vel[0]) || isnan(vel[0]) ||
442	>	isinf(vel[1]) || isnan(vel[1]) ||
443	>	isinf(vel[2]) || isnan(vel[2]) ) {
444	>	sprintf( painCave.errMsg,
445	>	"DumpWriter detected a numerical error writing the velocity"
446	>	" for object %d", index);
447	>	painCave.isFatal = 1;
448	>	simError();
449	>	}
450
451	<	// Get the Node number which has this atom;
451	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
452	>	pos[0], pos[1], pos[2],
453	>	vel[0], vel[1], vel[2]);
454	>	line += tempBuffer;
455
456	<	which_node = info_->getMolToProc(i);
456	>	if (sd->isDirectional()) {
457	>	type += "qj";
458	>	Quat4d q;
459	>	Vector3d ji;
460	>	q = sd->getQ();
461
462	<	if (which_node != masterNode) { //current molecule is in slave node
463	<	if (potatoes[which_node] + 1 >= MAXTAG) {
464	<	// The potato was going to exceed the maximum value,
465	<	// so wrap this processor potato back to 0:
462	>	if (isinf(q[0]) || isnan(q[0]) ||
463	>	isinf(q[1]) || isnan(q[1]) ||
464	>	isinf(q[2]) || isnan(q[2]) ||
465	>	isinf(q[3]) || isnan(q[3]) ) {
466	>	sprintf( painCave.errMsg,
467	>	"DumpWriter detected a numerical error writing the quaternion"
468	>	" for object %d", index);
469	>	painCave.isFatal = 1;
470	>	simError();
471	>	}
472
473	<	potatoes[which_node] = 0;
398	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
399	<	MPI_COMM_WORLD);
400	<	}
473	>	ji = sd->getJ();
474
475	<	myPotato = potatoes[which_node];
476	<
477	<	//recieve the number of integrableObject in current molecule
478	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
479	<	MPI_COMM_WORLD, &istatus);
480	<	myPotato++;
481	<
482	<	for(int l = 0; l < nCurObj; l++) {
483	<	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:
475	>	if (isinf(ji[0]) || isnan(ji[0]) ||
476	>	isinf(ji[1]) || isnan(ji[1]) ||
477	>	isinf(ji[2]) || isnan(ji[2]) ) {
478	>	sprintf( painCave.errMsg,
479	>	"DumpWriter detected a numerical error writing the angular"
480	>	" momentum for object %d", index);
481	>	painCave.isFatal = 1;
482	>	simError();
483	>	}
484
485	<	potatoes[which_node] = 0;
486	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
487	<	0, MPI_COMM_WORLD);
488	<	}
485	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
486	>	q[0], q[1], q[2], q[3],
487	>	ji[0], ji[1], ji[2]);
488	>	line += tempBuffer;
489	>	}
490
491	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
492	<	which_node, myPotato, MPI_COMM_WORLD,
493	<	&istatus);
491	>	if (needForceVector_) {
492	>	type += "f";
493	>	Vector3d frc = sd->getFrc();
494	>	if (isinf(frc[0]) || isnan(frc[0]) ||
495	>	isinf(frc[1]) || isnan(frc[1]) ||
496	>	isinf(frc[2]) || isnan(frc[2]) ) {
497	>	sprintf( painCave.errMsg,
498	>	"DumpWriter detected a numerical error writing the force"
499	>	" for object %d", index);
500	>	painCave.isFatal = 1;
501	>	simError();
502	>	}
503	>	sprintf(tempBuffer, " %13e %13e %13e",
504	>	frc[0], frc[1], frc[2]);
505	>	line += tempBuffer;
506	>
507	>	if (sd->isDirectional()) {
508	>	type += "t";
509	>	Vector3d trq = sd->getTrq();
510	>	if (isinf(trq[0]) || isnan(trq[0]) ||
511	>	isinf(trq[1]) || isnan(trq[1]) ||
512	>	isinf(trq[2]) || isnan(trq[2]) ) {
513	>	sprintf( painCave.errMsg,
514	>	"DumpWriter detected a numerical error writing the torque"
515	>	" for object %d", index);
516	>	painCave.isFatal = 1;
517	>	simError();
518	>	}
519	>	sprintf(tempBuffer, " %13e %13e %13e",
520	>	trq[0], trq[1], trq[2]);
521	>	line += tempBuffer;
522	>	}
523	>	}
524
525	<	myPotato++;
525	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
526	>	return std::string(tempBuffer);
527	>	}
528
529	<	MPI_Recv(atomData, 19, MPI_REALTYPE, which_node, myPotato,
530	<	MPI_COMM_WORLD, &istatus);
427	<	myPotato++;
529	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
530	>
531
532	<	MPI_Get_count(&istatus, MPI_REALTYPE, &msgLen);
532	>	std::string id;
533	>	std::string type;
534	>	std::string line;
535	>	char tempBuffer[4096];
536
537	<	if (msgLen == 13 || msgLen == 19)
538	<	isDirectional = 1;
539	<	else
540	<	isDirectional = 0;
537	>	if (sd->isRigidBody()) {
538	>	sprintf(tempBuffer, "%10d           ", ioIndex);
539	>	id = std::string(tempBuffer);
540	>	} else {
541	>	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
542	>	id = std::string(tempBuffer);
543	>	}
544	>
545	>	if (needFlucQ_) {
546	>	type += "cw";
547	>	RealType fqPos = sd->getFlucQPos();
548	>	if (isinf(fqPos) || isnan(fqPos) ) {
549	>	sprintf( painCave.errMsg,
550	>	"DumpWriter detected a numerical error writing the"
551	>	" fluctuating charge for object %s", id.c_str());
552	>	painCave.isFatal = 1;
553	>	simError();
554	>	}
555	>	sprintf(tempBuffer, " %13e ", fqPos);
556	>	line += tempBuffer;
557	>
558	>	RealType fqVel = sd->getFlucQVel();
559	>	if (isinf(fqVel) || isnan(fqVel) ) {
560	>	sprintf( painCave.errMsg,
561	>	"DumpWriter detected a numerical error writing the"
562	>	" fluctuating charge velocity for object %s", id.c_str());
563	>	painCave.isFatal = 1;
564	>	simError();
565	>	}
566	>	sprintf(tempBuffer, " %13e ", fqVel);
567	>	line += tempBuffer;
568
569	<	// If we've survived to here, format the line:
569	>	if (needForceVector_) {
570	>	type += "g";
571	>	RealType fqFrc = sd->getFlucQFrc();
572	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
573	>	sprintf( painCave.errMsg,
574	>	"DumpWriter detected a numerical error writing the"
575	>	" fluctuating charge force for object %s", id.c_str());
576	>	painCave.isFatal = 1;
577	>	simError();
578	>	}
579	>	sprintf(tempBuffer, " %13e ", fqFrc);
580	>	line += tempBuffer;
581	>	}
582	>	}
583
584	<	if (!isDirectional) {
585	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
586	<	MPIatomTypeString, atomData[0],
587	<	atomData[1], atomData[2],
588	<	atomData[3], atomData[4],
589	<	atomData[5]);
584	>	if (needElectricField_) {
585	>	type += "e";
586	>	Vector3d eField= sd->getElectricField();
587	>	if (isinf(eField[0]) || isnan(eField[0]) ||
588	>	isinf(eField[1]) || isnan(eField[1]) ||
589	>	isinf(eField[2]) || isnan(eField[2]) ) {
590	>	sprintf( painCave.errMsg,
591	>	"DumpWriter detected a numerical error writing the electric"
592	>	" field for object %s", id.c_str());
593	>	painCave.isFatal = 1;
594	>	simError();
595	>	}
596	>	sprintf(tempBuffer, " %13e %13e %13e",
597	>	eField[0], eField[1], eField[2]);
598	>	line += tempBuffer;
599	>	}
600
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	–	}
601
602	<	os << writeLine << "\n";
603	<
604	<	} // end for(int l =0)
605	<
606	<	potatoes[which_node] = myPotato;
607	<	} else { //master node has current molecule
608	<
609	<	mol = info_->getMoleculeByGlobalIndex(i);
610	<
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]);
566	<
567	<	strcat(writeLine,
568	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
569	<	} else {
570	<	sprintf(writeLine,
571	<	"%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",
572	<	integrableObject->getType().c_str(),
573	<	atomData[0],
574	<	atomData[1],
575	<	atomData[2],
576	<	atomData[3],
577	<	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	<
602	>	if (needParticlePot_) {
603	>	type += "u";
604	>	RealType particlePot = sd->getParticlePot();
605	>	if (isinf(particlePot) || isnan(particlePot)) {
606	>	sprintf( painCave.errMsg,
607	>	"DumpWriter detected a numerical error writing the particle "
608	>	" potential for object %s", id.c_str());
609	>	painCave.isFatal = 1;
610	>	simError();
611		}
612	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
613	<	MPIcheckPoint();
612	>	sprintf(tempBuffer, " %13e", particlePot);
613	>	line += tempBuffer;
614		}
615	+
616
617	<	#endif // is_mpi
618	<
617	>	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
618	>	return std::string(tempBuffer);
619		}
620
621		void DumpWriter::writeDump() {
#	Line 773 | Line 640 | namespace oopse {
640		#ifdef IS_MPI
641		if (worldRank == 0) {
642		#endif // is_mpi
643	<	delete eorStream;
644	<
643	>	writeClosing(*eorStream);
644	>	delete eorStream;
645		#ifdef IS_MPI
646		}
647		#endif // is_mpi
#	Line 807 | Line 674 | namespace oopse {
674		#ifdef IS_MPI
675		if (worldRank == 0) {
676		#endif // is_mpi
677	<	delete eorStream;
678	<
677	>	writeClosing(*eorStream);
678	>	delete eorStream;
679		#ifdef IS_MPI
680		}
681		#endif // is_mpi
682
683		}
684
685	<	std::ostream* DumpWriter::createOStream(const std::string& filename) {
685	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
686
687		std::ostream* newOStream;
688	<	#ifdef HAVE_LIBZ
688	>	#ifdef HAVE_ZLIB
689		if (needCompression_) {
690	<	newOStream = new ogzstream(filename.c_str());
690	>	newOStream = new ogzstream(filename.c_str());
691		} else {
692	<	newOStream = new std::ofstream(filename.c_str());
692	>	newOStream = new std::ofstream(filename.c_str());
693		}
694		#else
695		newOStream = new std::ofstream(filename.c_str());
696		#endif
697	+	//write out MetaData first
698	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
699	+	(*newOStream) << "  <MetaData>" << std::endl;
700	+	(*newOStream) << info_->getRawMetaData();
701	+	(*newOStream) << "  </MetaData>" << std::endl;
702		return newOStream;
703	<	}
703	>	}
704
705	<	}//end namespace oopse
705	>	void DumpWriter::writeClosing(std::ostream& os) {
706	>
707	>	os << "</OpenMD>\n";
708	>	os.flush();
709	>	}
710	>
711	>	}//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 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

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