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

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trunk/src/io/DumpWriter.cpp (file contents), Revision 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1752 by gezelter, Sun Jun 10 14:05:02 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	+	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
69	+	doSiteData_ = true;
70	+	} else {
71	+	doSiteData_ = false;
72	+	}
73	+
74	+	createDumpFile_ = true;
75		#ifdef HAVE_LIBZ
76		if (needCompression_) {
77	<	filename_ += ".gz";
78	<	eorFilename_ += ".gz";
77	>	filename_ += ".gz";
78	>	eorFilename_ += ".gz";
79		}
80		#endif
81
82		#ifdef IS_MPI
83
84	<	if (worldRank == 0) {
84	>	if (worldRank == 0) {
85		#endif // is_mpi
86	+
87	+	dumpFile_ = createOStream(filename_);
88
89	+	if (!dumpFile_) {
90	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
91	+	filename_.c_str());
92	+	painCave.isFatal = 1;
93	+	simError();
94	+	}
95
75	–	dumpFile_ = createOStream(filename_);
76	–
77	–	if (!dumpFile_) {
78	–	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
79	–	filename_.c_str());
80	–	painCave.isFatal = 1;
81	–	simError();
82	–	}
83	–
96		#ifdef IS_MPI
97
98	<	}
98	>	}
99
88	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
89	–	MPIcheckPoint();
90	–
100		#endif // is_mpi
101
102	<	}
102	>	}
103
104
105		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
#	Line 99 | Line 108 | namespace oopse {
108		Globals* simParams = info->getSimParams();
109		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
110
111	<	needCompression_ = simParams->getCompressDumpFile();
112	<	needForceVector_ = simParams->getOutputForceVector();
111	>	needCompression_   = simParams->getCompressDumpFile();
112	>	needForceVector_   = simParams->getOutputForceVector();
113	>	needParticlePot_   = simParams->getOutputParticlePotential();
114	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
115	>	needElectricField_ = simParams->getOutputElectricField();
116
117	+	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
118	+	doSiteData_ = true;
119	+	} else {
120	+	doSiteData_ = false;
121	+	}
122	+
123	+	createDumpFile_ = true;
124		#ifdef HAVE_LIBZ
125		if (needCompression_) {
126	<	filename_ += ".gz";
127	<	eorFilename_ += ".gz";
126	>	filename_ += ".gz";
127	>	eorFilename_ += ".gz";
128		}
129		#endif
130
131		#ifdef IS_MPI
132
133	<	if (worldRank == 0) {
133	>	if (worldRank == 0) {
134		#endif // is_mpi
135
136	+
137	+	dumpFile_ = createOStream(filename_);
138
139	<	dumpFile_ = createOStream(filename_);
139	>	if (!dumpFile_) {
140	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
141	>	filename_.c_str());
142	>	painCave.isFatal = 1;
143	>	simError();
144	>	}
145
120	–	if (!dumpFile_) {
121	–	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
122	–	filename_.c_str());
123	–	painCave.isFatal = 1;
124	–	simError();
125	–	}
126	–
146		#ifdef IS_MPI
147
148	<	}
148	>	}
149
131	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
132	–	MPIcheckPoint();
133	–
150		#endif // is_mpi
151
152	+	}
153	+
154	+	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
155	+	: info_(info), filename_(filename){
156	+
157	+	Globals* simParams = info->getSimParams();
158	+	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
159	+
160	+	needCompression_   = simParams->getCompressDumpFile();
161	+	needForceVector_   = simParams->getOutputForceVector();
162	+	needParticlePot_   = simParams->getOutputParticlePotential();
163	+	needFlucQ_         = simParams->getOutputFluctuatingCharges();
164	+	needElectricField_ = simParams->getOutputElectricField();
165	+
166	+	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
167	+	doSiteData_ = true;
168	+	} else {
169	+	doSiteData_ = false;
170	+	}
171	+
172	+	#ifdef HAVE_LIBZ
173	+	if (needCompression_) {
174	+	filename_ += ".gz";
175	+	eorFilename_ += ".gz";
176	+	}
177	+	#endif
178	+
179	+	#ifdef IS_MPI
180	+
181	+	if (worldRank == 0) {
182	+	#endif // is_mpi
183	+
184	+	createDumpFile_ = writeDumpFile;
185	+	if (createDumpFile_) {
186	+	dumpFile_ = createOStream(filename_);
187	+
188	+	if (!dumpFile_) {
189	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
190	+	filename_.c_str());
191	+	painCave.isFatal = 1;
192	+	simError();
193	+	}
194	+	}
195	+	#ifdef IS_MPI
196	+
197		}
198
199	+
200	+	#endif // is_mpi
201	+
202	+	}
203	+
204		DumpWriter::~DumpWriter() {
205
206		#ifdef IS_MPI
207
208		if (worldRank == 0) {
209		#endif // is_mpi
210	<
211	<	delete dumpFile_;
212	<
210	>	if (createDumpFile_){
211	>	writeClosing(*dumpFile_);
212	>	delete dumpFile_;
213	>	}
214		#ifdef IS_MPI
215
216		}
#	Line 152 | Line 219 | namespace oopse {
219
220		}
221
222	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
222	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
223
224	<	double currentTime;
225	<	Mat3x3d hmat;
226	<	double chi;
227	<	double integralOfChiDt;
228	<	Mat3x3d eta;
224	>	char buffer[1024];
225	>
226	>	os << "    <FrameData>\n";
227	>
228	>	RealType currentTime = s->getTime();
229	>
230	>	if (isinf(currentTime) || isnan(currentTime)) {
231	>	sprintf( painCave.errMsg,
232	>	"DumpWriter detected a numerical error writing the time");
233	>	painCave.isFatal = 1;
234	>	simError();
235	>	}
236
237	<	currentTime = s->getTime();
237	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
238	>	os << buffer;
239	>
240	>	Mat3x3d hmat;
241		hmat = s->getHmat();
242	<	chi = s->getChi();
243	<	integralOfChiDt = s->getIntegralOfChiDt();
244	<	eta = s->getEta();
242	>
243	>	for (unsigned int i = 0; i < 3; i++) {
244	>	for (unsigned int j = 0; j < 3; j++) {
245	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
246	>	sprintf( painCave.errMsg,
247	>	"DumpWriter detected a numerical error writing the box");
248	>	painCave.isFatal = 1;
249	>	simError();
250	>	}
251	>	}
252	>	}
253
254	<	os << currentTime << ";\t"
255	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
256	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
257	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
254	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
255	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
256	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
257	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
258	>	os << buffer;
259
260	<	//write out additional parameters, such as chi and eta
260	>	RealType chi = s->getChi();
261	>	RealType integralOfChiDt = s->getIntegralOfChiDt();
262	>	if (isinf(chi) || isnan(chi) ||
263	>	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
264	>	sprintf( painCave.errMsg,
265	>	"DumpWriter detected a numerical error writing the thermostat");
266	>	painCave.isFatal = 1;
267	>	simError();
268	>	}
269	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
270	>	os << buffer;
271
272	<	os << chi << "\t" << integralOfChiDt << "\t;";
272	>	Mat3x3d eta;
273	>	eta = s->getEta();
274
275	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
276	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
277	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
278	<
279	<	os << "\n";
275	>	for (unsigned int i = 0; i < 3; i++) {
276	>	for (unsigned int j = 0; j < 3; j++) {
277	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
278	>	sprintf( painCave.errMsg,
279	>	"DumpWriter detected a numerical error writing the barostat");
280	>	painCave.isFatal = 1;
281	>	simError();
282	>	}
283	>	}
284	>	}
285	>
286	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
287	>	eta(0, 0), eta(1, 0), eta(2, 0),
288	>	eta(0, 1), eta(1, 1), eta(2, 1),
289	>	eta(0, 2), eta(1, 2), eta(2, 2));
290	>	os << buffer;
291	>
292	>	os << "    </FrameData>\n";
293		}
294
295		void DumpWriter::writeFrame(std::ostream& os) {
186	–	const int BUFFERSIZE = 2000;
187	–	const int MINIBUFFERSIZE = 100;
296
297	<	char tempBuffer[BUFFERSIZE];
298	<	char writeLine[BUFFERSIZE];
297	>	#ifdef IS_MPI
298	>	MPI_Status istatus;
299	>	#endif
300
192	–	Quat4d q;
193	–	Vector3d ji;
194	–	Vector3d pos;
195	–	Vector3d vel;
196	–	Vector3d frc;
197	–	Vector3d trq;
198	–
301		Molecule* mol;
302		StuntDouble* integrableObject;
303		SimInfo::MoleculeIterator mi;
304		Molecule::IntegrableObjectIterator ii;
305	<
306	<	int nTotObjects;
205	<	nTotObjects = info_->getNGlobalIntegrableObjects();
305	>	RigidBody::AtomIterator ai;
306	>	Atom* atom;
307
308		#ifndef IS_MPI
309	+	os << "  <Snapshot>\n";
310	+
311	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
312
313	<
210	<	os << nTotObjects << "\n";
211	<
212	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
213	<
313	>	os << "    <StuntDoubles>\n";
314		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
315
316	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
317	<	integrableObject = mol->nextIntegrableObject(ii)) {
318	<
316	>
317	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
318	>	integrableObject = mol->nextIntegrableObject(ii)) {
319	>	os << prepareDumpLine(integrableObject);
320	>
321	>	}
322	>	}
323	>	os << "    </StuntDoubles>\n";
324
325	<	pos = integrableObject->getPos();
326	<	vel = integrableObject->getVel();
325	>	if (doSiteData_) {
326	>	os << "    <SiteData>\n";
327	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
328	>
329	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
330	>	integrableObject = mol->nextIntegrableObject(ii)) {
331
332	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
333	<	integrableObject->getType().c_str(),
334	<	pos[0], pos[1], pos[2],
226	<	vel[0], vel[1], vel[2]);
332	>	int ioIndex = integrableObject->getGlobalIntegrableObjectIndex();
333	>	// do one for the IO itself
334	>	os << prepareSiteLine(integrableObject, ioIndex, 0);
335
336	<	strcpy(writeLine, tempBuffer);
336	>	if (integrableObject->isRigidBody()) {
337	>
338	>	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
339	>	int siteIndex = 0;
340	>	for (atom = rb->beginAtom(ai); atom != NULL;
341	>	atom = rb->nextAtom(ai)) {
342	>	os << prepareSiteLine(atom, ioIndex, siteIndex);
343	>	siteIndex++;
344	>	}
345	>	}
346	>	}
347	>	}
348	>	os << "    </SiteData>\n";
349	>	}
350	>	os << "  </Snapshot>\n";
351
352	<	if (integrableObject->isDirectional()) {
353	<	q = integrableObject->getQ();
354	<	ji = integrableObject->getJ();
352	>	os.flush();
353	>	#else
354	>	//every node prepares the dump lines for integrable objects belong to itself
355	>	std::string buffer;
356	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
357
234	–	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
235	–	q[0], q[1], q[2], q[3],
236	–	ji[0], ji[1], ji[2]);
237	–	strcat(writeLine, tempBuffer);
238	–	} else {
239	–	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
240	–	}
358
359	<	if (needForceVector_) {
360	<	frc = integrableObject->getFrc();
361	<	trq = integrableObject->getTrq();
245	<
246	<	sprintf(tempBuffer, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
247	<	frc[0], frc[1], frc[2],
248	<	trq[0], trq[1], trq[2]);
249	<	strcat(writeLine, tempBuffer);
250	<	}
251	<
252	<	strcat(writeLine, "\n");
253	<	os << writeLine;
254	<
359	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
360	>	integrableObject = mol->nextIntegrableObject(ii)) {
361	>	buffer += prepareDumpLine(integrableObject);
362		}
363		}
364	<
258	<	os.flush();
259	<	#else // is_mpi
260	<	/*********************************************************************
261	<	* Documentation?  You want DOCUMENTATION?
262	<	*
263	<	* Why all the potatoes below?
264	<	*
265	<	* To make a long story short, the original version of DumpWriter
266	<	* worked in the most inefficient way possible.  Node 0 would
267	<	* poke each of the node for an individual atom's formatted data
268	<	* as node 0 worked its way down the global index. This was particularly
269	<	* inefficient since the method blocked all processors at every atom
270	<	* (and did it twice!).
271	<	*
272	<	* An intermediate version of DumpWriter could be described from Node
273	<	* zero's perspective as follows:
274	<	*
275	<	*  1) Have 100 of your friends stand in a circle.
276	<	*  2) When you say go, have all of them start tossing potatoes at
277	<	*     you (one at a time).
278	<	*  3) Catch the potatoes.
279	<	*
280	<	* It was an improvement, but MPI has buffers and caches that could
281	<	* best be described in this analogy as "potato nets", so there's no
282	<	* need to block the processors atom-by-atom.
283	<	*
284	<	* This new and improved DumpWriter works in an even more efficient
285	<	* way:
286	<	*
287	<	*  1) Have 100 of your friend stand in a circle.
288	<	*  2) When you say go, have them start tossing 5-pound bags of
289	<	*     potatoes at you.
290	<	*  3) Once you've caught a friend's bag of potatoes,
291	<	*     toss them a spud to let them know they can toss another bag.
292	<	*
293	<	* How's THAT for documentation?
294	<	*
295	<	*********************************************************************/
364	>
365		const int masterNode = 0;
297	–
298	–	int * potatoes;
299	–	int myPotato;
366		int nProc;
367	<	int which_node;
368	<	double atomData[19];
369	<	int isDirectional;
370	<	char MPIatomTypeString[MINIBUFFERSIZE];
371	<	int msgLen; // the length of message actually recieved at master nodes
372	<	int haveError;
373	<	MPI_Status istatus;
308	<	int nCurObj;
309	<
310	<	// code to find maximum tag value
311	<	int * tagub;
312	<	int flag;
313	<	int MAXTAG;
314	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
367	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
368	>	if (worldRank == masterNode) {
369	>	os << "  <Snapshot>\n";
370	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
371	>	os << "    <StuntDoubles>\n";
372	>
373	>	os << buffer;
374
375	<	if (flag) {
376	<	MAXTAG = *tagub;
375	>	for (int i = 1; i < nProc; ++i) {
376	>
377	>	// receive the length of the string buffer that was
378	>	// prepared by processor i
379	>
380	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
381	>	int recvLength;
382	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
383	>	char* recvBuffer = new char[recvLength];
384	>	if (recvBuffer == NULL) {
385	>	} else {
386	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
387	>	os << recvBuffer;
388	>	delete [] recvBuffer;
389	>	}
390	>	}
391	>	os << "    </StuntDoubles>\n";
392	>
393	>	os << "  </Snapshot>\n";
394	>	os.flush();
395		} else {
396	<	MAXTAG = 32767;
396	>	int sendBufferLength = buffer.size() + 1;
397	>	int myturn = 0;
398	>	for (int i = 1; i < nProc; ++i){
399	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
400	>	if (myturn == worldRank){
401	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
402	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
403	>	}
404	>	}
405		}
406
407	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
407	>	#endif // is_mpi
408
409	<	// Node 0 needs a list of the magic potatoes for each processor;
409	>	}
410
411	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
412	<	potatoes = new int[nProc];
411	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
412	>
413	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
414	>	std::string type("pv");
415	>	std::string line;
416	>	char tempBuffer[4096];
417
418	<	//write out the comment lines
419	<	for(int i = 0; i < nProc; i++) {
420	<	potatoes[i] = 0;
332	<	}
418	>	Vector3d pos;
419	>	Vector3d vel;
420	>	pos = integrableObject->getPos();
421
422	+	if (isinf(pos[0]) || isnan(pos[0]) ||
423	+	isinf(pos[1]) || isnan(pos[1]) ||
424	+	isinf(pos[2]) || isnan(pos[2]) ) {
425	+	sprintf( painCave.errMsg,
426	+	"DumpWriter detected a numerical error writing the position"
427	+	" for object %d", index);
428	+	painCave.isFatal = 1;
429	+	simError();
430	+	}
431
432	<	os << nTotObjects << "\n";
336	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
432	>	vel = integrableObject->getVel();
433
434	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
434	>	if (isinf(vel[0]) || isnan(vel[0]) ||
435	>	isinf(vel[1]) || isnan(vel[1]) ||
436	>	isinf(vel[2]) || isnan(vel[2]) ) {
437	>	sprintf( painCave.errMsg,
438	>	"DumpWriter detected a numerical error writing the velocity"
439	>	" for object %d", index);
440	>	painCave.isFatal = 1;
441	>	simError();
442	>	}
443
444	<	// Get the Node number which has this atom;
444	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
445	>	pos[0], pos[1], pos[2],
446	>	vel[0], vel[1], vel[2]);
447	>	line += tempBuffer;
448
449	<	which_node = info_->getMolToProc(i);
449	>	if (integrableObject->isDirectional()) {
450	>	type += "qj";
451	>	Quat4d q;
452	>	Vector3d ji;
453	>	q = integrableObject->getQ();
454
455	<	if (which_node != masterNode) { //current molecule is in slave node
456	<	if (potatoes[which_node] + 1 >= MAXTAG) {
457	<	// The potato was going to exceed the maximum value,
458	<	// so wrap this processor potato back to 0:
455	>	if (isinf(q[0]) || isnan(q[0]) ||
456	>	isinf(q[1]) || isnan(q[1]) ||
457	>	isinf(q[2]) || isnan(q[2]) ||
458	>	isinf(q[3]) || isnan(q[3]) ) {
459	>	sprintf( painCave.errMsg,
460	>	"DumpWriter detected a numerical error writing the quaternion"
461	>	" for object %d", index);
462	>	painCave.isFatal = 1;
463	>	simError();
464	>	}
465
466	<	potatoes[which_node] = 0;
350	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
351	<	MPI_COMM_WORLD);
352	<	}
466	>	ji = integrableObject->getJ();
467
468	<	myPotato = potatoes[which_node];
468	>	if (isinf(ji[0]) || isnan(ji[0]) ||
469	>	isinf(ji[1]) || isnan(ji[1]) ||
470	>	isinf(ji[2]) || isnan(ji[2]) ) {
471	>	sprintf( painCave.errMsg,
472	>	"DumpWriter detected a numerical error writing the angular"
473	>	" momentum for object %d", index);
474	>	painCave.isFatal = 1;
475	>	simError();
476	>	}
477
478	<	//recieve the number of integrableObject in current molecule
479	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
480	<	MPI_COMM_WORLD, &istatus);
481	<	myPotato++;
478	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
479	>	q[0], q[1], q[2], q[3],
480	>	ji[0], ji[1], ji[2]);
481	>	line += tempBuffer;
482	>	}
483
484	<	for(int l = 0; l < nCurObj; l++) {
485	<	if (potatoes[which_node] + 2 >= MAXTAG) {
486	<	// The potato was going to exceed the maximum value,
487	<	// so wrap this processor potato back to 0:
484	>	if (needForceVector_) {
485	>	type += "f";
486	>	Vector3d frc = integrableObject->getFrc();
487	>	if (isinf(frc[0]) || isnan(frc[0]) ||
488	>	isinf(frc[1]) || isnan(frc[1]) ||
489	>	isinf(frc[2]) || isnan(frc[2]) ) {
490	>	sprintf( painCave.errMsg,
491	>	"DumpWriter detected a numerical error writing the force"
492	>	" for object %d", index);
493	>	painCave.isFatal = 1;
494	>	simError();
495	>	}
496	>	sprintf(tempBuffer, " %13e %13e %13e",
497	>	frc[0], frc[1], frc[2]);
498	>	line += tempBuffer;
499	>
500	>	if (integrableObject->isDirectional()) {
501	>	type += "t";
502	>	Vector3d trq = integrableObject->getTrq();
503	>	if (isinf(trq[0]) || isnan(trq[0]) ||
504	>	isinf(trq[1]) || isnan(trq[1]) ||
505	>	isinf(trq[2]) || isnan(trq[2]) ) {
506	>	sprintf( painCave.errMsg,
507	>	"DumpWriter detected a numerical error writing the torque"
508	>	" for object %d", index);
509	>	painCave.isFatal = 1;
510	>	simError();
511	>	}
512	>	sprintf(tempBuffer, " %13e %13e %13e",
513	>	trq[0], trq[1], trq[2]);
514	>	line += tempBuffer;
515	>	}
516	>	}
517
518	<	potatoes[which_node] = 0;
519	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
520	<	0, MPI_COMM_WORLD);
369	<	}
518	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
519	>	return std::string(tempBuffer);
520	>	}
521
522	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
523	<	which_node, myPotato, MPI_COMM_WORLD,
373	<	&istatus);
522	>	std::string DumpWriter::prepareSiteLine(StuntDouble* integrableObject, int ioIndex, int siteIndex) {
523	>
524
525	<	myPotato++;
525	>	std::string id;
526	>	std::string type;
527	>	std::string line;
528	>	char tempBuffer[4096];
529
530	<	MPI_Recv(atomData, 19, MPI_DOUBLE, which_node, myPotato,
531	<	MPI_COMM_WORLD, &istatus);
532	<	myPotato++;
530	>	if (integrableObject->isRigidBody()) {
531	>	sprintf(tempBuffer, "%10d           ", ioIndex);
532	>	id = std::string(tempBuffer);
533	>	} else {
534	>	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
535	>	id = std::string(tempBuffer);
536	>	}
537	>
538	>	if (needFlucQ_) {
539	>	type += "cw";
540	>	RealType fqPos = integrableObject->getFlucQPos();
541	>	if (isinf(fqPos) || isnan(fqPos) ) {
542	>	sprintf( painCave.errMsg,
543	>	"DumpWriter detected a numerical error writing the"
544	>	" fluctuating charge for object %s", id.c_str());
545	>	painCave.isFatal = 1;
546	>	simError();
547	>	}
548	>	sprintf(tempBuffer, " %13e ", fqPos);
549	>	line += tempBuffer;
550	>
551	>	RealType fqVel = integrableObject->getFlucQVel();
552	>	if (isinf(fqVel) || isnan(fqVel) ) {
553	>	sprintf( painCave.errMsg,
554	>	"DumpWriter detected a numerical error writing the"
555	>	" fluctuating charge velocity for object %s", id.c_str());
556	>	painCave.isFatal = 1;
557	>	simError();
558	>	}
559	>	sprintf(tempBuffer, " %13e ", fqVel);
560	>	line += tempBuffer;
561
562	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
562	>	if (needForceVector_) {
563	>	type += "g";
564	>	RealType fqFrc = integrableObject->getFlucQFrc();
565	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
566	>	sprintf( painCave.errMsg,
567	>	"DumpWriter detected a numerical error writing the"
568	>	" fluctuating charge force for object %s", id.c_str());
569	>	painCave.isFatal = 1;
570	>	simError();
571	>	}
572	>	sprintf(tempBuffer, " %13e ", fqFrc);
573	>	line += tempBuffer;
574	>	}
575	>	}
576
577	<	if (msgLen == 13 || msgLen == 19)
578	<	isDirectional = 1;
579	<	else
580	<	isDirectional = 0;
577	>	if (needElectricField_) {
578	>	type += "e";
579	>	Vector3d eField= integrableObject->getElectricField();
580	>	if (isinf(eField[0]) || isnan(eField[0]) ||
581	>	isinf(eField[1]) || isnan(eField[1]) ||
582	>	isinf(eField[2]) || isnan(eField[2]) ) {
583	>	sprintf( painCave.errMsg,
584	>	"DumpWriter detected a numerical error writing the electric"
585	>	" field for object %s", id.c_str());
586	>	painCave.isFatal = 1;
587	>	simError();
588	>	}
589	>	sprintf(tempBuffer, " %13e %13e %13e",
590	>	eField[0], eField[1], eField[2]);
591	>	line += tempBuffer;
592	>	}
593
388	–	// If we've survived to here, format the line:
594
595	<	if (!isDirectional) {
596	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
597	<	MPIatomTypeString, atomData[0],
598	<	atomData[1], atomData[2],
599	<	atomData[3], atomData[4],
600	<	atomData[5]);
601	<
602	<	strcat(writeLine,
603	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
399	<	} else {
400	<	sprintf(writeLine,
401	<	"%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",
402	<	MPIatomTypeString,
403	<	atomData[0],
404	<	atomData[1],
405	<	atomData[2],
406	<	atomData[3],
407	<	atomData[4],
408	<	atomData[5],
409	<	atomData[6],
410	<	atomData[7],
411	<	atomData[8],
412	<	atomData[9],
413	<	atomData[10],
414	<	atomData[11],
415	<	atomData[12]);
416	<	}
417	<
418	<	if (needForceVector_) {
419	<	if (!isDirectional) {
420	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
421	<	atomData[6],
422	<	atomData[7],
423	<	atomData[8],
424	<	atomData[9],
425	<	atomData[10],
426	<	atomData[11]);
427	<	} else {
428	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
429	<	atomData[13],
430	<	atomData[14],
431	<	atomData[15],
432	<	atomData[16],
433	<	atomData[17],
434	<	atomData[18]);
435	<	}
436	<	}
437	<
438	<	sprintf(writeLine, "\n");
439	<	os << writeLine;
440	<
441	<	} // end for(int l =0)
442	<
443	<	potatoes[which_node] = myPotato;
444	<	} else { //master node has current molecule
445	<
446	<	mol = info_->getMoleculeByGlobalIndex(i);
447	<
448	<	if (mol == NULL) {
449	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
450	<	painCave.isFatal = 1;
451	<	simError();
452	<	}
453	<
454	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
455	<	integrableObject = mol->nextIntegrableObject(ii)) {
456	<
457	<	pos = integrableObject->getPos();
458	<	vel = integrableObject->getVel();
459	<
460	<	atomData[0] = pos[0];
461	<	atomData[1] = pos[1];
462	<	atomData[2] = pos[2];
463	<
464	<	atomData[3] = vel[0];
465	<	atomData[4] = vel[1];
466	<	atomData[5] = vel[2];
467	<
468	<	isDirectional = 0;
469	<
470	<	if (integrableObject->isDirectional()) {
471	<	isDirectional = 1;
472	<
473	<	q = integrableObject->getQ();
474	<	ji = integrableObject->getJ();
475	<
476	<	for(int j = 0; j < 6; j++) {
477	<	atomData[j] = atomData[j];
478	<	}
479	<
480	<	atomData[6] = q[0];
481	<	atomData[7] = q[1];
482	<	atomData[8] = q[2];
483	<	atomData[9] = q[3];
484	<
485	<	atomData[10] = ji[0];
486	<	atomData[11] = ji[1];
487	<	atomData[12] = ji[2];
488	<	}
489	<
490	<	if (needForceVector_) {
491	<	frc = integrableObject->getFrc();
492	<	trq = integrableObject->getTrq();
493	<
494	<	if (!isDirectional) {
495	<	atomData[6] = frc[0];
496	<	atomData[7] = frc[1];
497	<	atomData[8] = frc[2];
498	<	atomData[9] = trq[0];
499	<	atomData[10] = trq[1];
500	<	atomData[11] = trq[2];
501	<	} else {
502	<	atomData[13] = frc[0];
503	<	atomData[14] = frc[1];
504	<	atomData[15] = frc[2];
505	<	atomData[16] = trq[0];
506	<	atomData[17] = trq[1];
507	<	atomData[18] = trq[2];
508	<	}
509	<	}
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	<	integrableObject->getType().c_str(), 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",
525	<	integrableObject->getType().c_str(),
526	<	atomData[0],
527	<	atomData[1],
528	<	atomData[2],
529	<	atomData[3],
530	<	atomData[4],
531	<	atomData[5],
532	<	atomData[6],
533	<	atomData[7],
534	<	atomData[8],
535	<	atomData[9],
536	<	atomData[10],
537	<	atomData[11],
538	<	atomData[12]);
539	<	}
540	<
541	<	if (needForceVector_) {
542	<	if (!isDirectional) {
543	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
544	<	atomData[6],
545	<	atomData[7],
546	<	atomData[8],
547	<	atomData[9],
548	<	atomData[10],
549	<	atomData[11]);
550	<	} else {
551	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
552	<	atomData[13],
553	<	atomData[14],
554	<	atomData[15],
555	<	atomData[16],
556	<	atomData[17],
557	<	atomData[18]);
558	<	}
559	<	}
560	<
561	<	sprintf(writeLine, "\n");
562	<	os << writeLine;
563	<
564	<	} //end for(iter = integrableObject.begin())
565	<	}
566	<	} //end for(i = 0; i < mpiSim->getNmol())
567	<
568	<	os.flush();
569	<
570	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
571	<	MPIcheckPoint();
572	<
573	<	delete [] potatoes;
574	<	} else {
575	<
576	<	// worldRank != 0, so I'm a remote node.
577	<
578	<	// Set my magic potato to 0:
579	<
580	<	myPotato = 0;
581	<
582	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
583	<
584	<	// Am I the node which has this integrableObject?
585	<	int whichNode = info_->getMolToProc(i);
586	<	if (whichNode == worldRank) {
587	<	if (myPotato + 1 >= MAXTAG) {
588	<
589	<	// The potato was going to exceed the maximum value,
590	<	// so wrap this processor potato back to 0 (and block until
591	<	// node 0 says we can go:
592	<
593	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
594	<	&istatus);
595	<	}
596	<
597	<	mol = info_->getMoleculeByGlobalIndex(i);
598	<
599	<
600	<	nCurObj = mol->getNIntegrableObjects();
601	<
602	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
603	<	myPotato++;
604	<
605	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
606	<	integrableObject = mol->nextIntegrableObject(ii)) {
607	<
608	<	if (myPotato + 2 >= MAXTAG) {
609	<
610	<	// The potato was going to exceed the maximum value,
611	<	// so wrap this processor potato back to 0 (and block until
612	<	// node 0 says we can go:
613	<
614	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
615	<	&istatus);
616	<	}
617	<
618	<	pos = integrableObject->getPos();
619	<	vel = integrableObject->getVel();
620	<
621	<	atomData[0] = pos[0];
622	<	atomData[1] = pos[1];
623	<	atomData[2] = pos[2];
624	<
625	<	atomData[3] = vel[0];
626	<	atomData[4] = vel[1];
627	<	atomData[5] = vel[2];
628	<
629	<	isDirectional = 0;
630	<
631	<	if (integrableObject->isDirectional()) {
632	<	isDirectional = 1;
633	<
634	<	q = integrableObject->getQ();
635	<	ji = integrableObject->getJ();
636	<
637	<	atomData[6] = q[0];
638	<	atomData[7] = q[1];
639	<	atomData[8] = q[2];
640	<	atomData[9] = q[3];
641	<
642	<	atomData[10] = ji[0];
643	<	atomData[11] = ji[1];
644	<	atomData[12] = ji[2];
645	<	}
646	<
647	<	if (needForceVector_) {
648	<	frc = integrableObject->getFrc();
649	<	trq = integrableObject->getTrq();
650	<
651	<	if (!isDirectional) {
652	<	atomData[6] = frc[0];
653	<	atomData[7] = frc[1];
654	<	atomData[8] = frc[2];
655	<
656	<	atomData[9] = trq[0];
657	<	atomData[10] = trq[1];
658	<	atomData[11] = trq[2];
659	<	} else {
660	<	atomData[13] = frc[0];
661	<	atomData[14] = frc[1];
662	<	atomData[15] = frc[2];
663	<
664	<	atomData[16] = trq[0];
665	<	atomData[17] = trq[1];
666	<	atomData[18] = trq[2];
667	<	}
668	<	}
669	<
670	<	strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
671	<
672	<	// null terminate the  std::string before sending (just in case):
673	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
674	<
675	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
676	<	myPotato, MPI_COMM_WORLD);
677	<
678	<	myPotato++;
679	<
680	<	if (isDirectional && needForceVector_) {
681	<	MPI_Send(atomData, 19, MPI_DOUBLE, 0, myPotato,
682	<	MPI_COMM_WORLD);
683	<	} else if (isDirectional) {
684	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
685	<	MPI_COMM_WORLD);
686	<	} else if (needForceVector_) {
687	<	MPI_Send(atomData, 12, MPI_DOUBLE, 0, myPotato,
688	<	MPI_COMM_WORLD);
689	<	} else {
690	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
691	<	MPI_COMM_WORLD);
692	<	}
693	<
694	<	myPotato++;
695	<	}
696	<
697	<	}
698	<
595	>	if (needParticlePot_) {
596	>	type += "u";
597	>	RealType particlePot = integrableObject->getParticlePot();
598	>	if (isinf(particlePot) || isnan(particlePot)) {
599	>	sprintf( painCave.errMsg,
600	>	"DumpWriter detected a numerical error writing the particle "
601	>	" potential for object %s", id.c_str());
602	>	painCave.isFatal = 1;
603	>	simError();
604		}
605	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
606	<	MPIcheckPoint();
605	>	sprintf(tempBuffer, " %13e", particlePot);
606	>	line += tempBuffer;
607		}
608	+
609
610	<	#endif // is_mpi
611	<
610	>	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
611	>	return std::string(tempBuffer);
612		}
613
614		void DumpWriter::writeDump() {
#	Line 727 | Line 633 | namespace oopse {
633		#ifdef IS_MPI
634		if (worldRank == 0) {
635		#endif // is_mpi
636	<	delete eorStream;
637	<
636	>	writeClosing(*eorStream);
637	>	delete eorStream;
638		#ifdef IS_MPI
639		}
640		#endif // is_mpi
#	Line 761 | Line 667 | namespace oopse {
667		#ifdef IS_MPI
668		if (worldRank == 0) {
669		#endif // is_mpi
670	<	delete eorStream;
671	<
670	>	writeClosing(*eorStream);
671	>	delete eorStream;
672		#ifdef IS_MPI
673		}
674		#endif // is_mpi
675
676		}
677
678	<	std::ostream* DumpWriter::createOStream(const std::string& filename) {
678	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
679
680		std::ostream* newOStream;
681		#ifdef HAVE_LIBZ
682		if (needCompression_) {
683	<	newOStream = new ogzstream(filename.c_str());
683	>	newOStream = new ogzstream(filename.c_str());
684		} else {
685	<	newOStream = new std::ofstream(filename.c_str());
685	>	newOStream = new std::ofstream(filename.c_str());
686		}
687		#else
688		newOStream = new std::ofstream(filename.c_str());
689		#endif
690	+	//write out MetaData first
691	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
692	+	(*newOStream) << "  <MetaData>" << std::endl;
693	+	(*newOStream) << info_->getRawMetaData();
694	+	(*newOStream) << "  </MetaData>" << std::endl;
695		return newOStream;
696	<	}
696	>	}
697
698	<	}//end namespace oopse
698	>	void DumpWriter::writeClosing(std::ostream& os) {
699	>
700	>	os << "</OpenMD>\n";
701	>	os.flush();
702	>	}
703	>
704	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1752 by gezelter, Sun Jun 10 14:05:02 2012 UTC

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