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

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trunk/src/io/DumpWriter.cpp (file contents), Revision 965 by tim, Fri May 19 20:45:55 2006 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1764 by gezelter, Tue Jul 3 18:32:27 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
53	>	#endif
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
73	–
86
87	<	dumpFile_ = createOStream(filename_);
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	<	}
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
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_);
137	>	dumpFile_ = createOStream(filename_);
138
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	<	}
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
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	<	}
152	>	}
153
154		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
155	<	: info_(info), filename_(filename){
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	<
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";
#	Line 170 | Line 195 | namespace oopse {
195		#ifdef IS_MPI
196
197		}
198	+
199
174	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
175	–	MPIcheckPoint();
176	–
200		#endif // is_mpi
201
202		}
180	–
181	–
182	–
183	–
184	–
203
204		DumpWriter::~DumpWriter() {
205
#	Line 190 | Line 208 | namespace oopse {
208		if (worldRank == 0) {
209		#endif // is_mpi
210		if (createDumpFile_){
211	+	writeClosing(*dumpFile_);
212		delete dumpFile_;
213		}
214		#ifdef IS_MPI
#	Line 200 | 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	<	RealType currentTime;
225	<	Mat3x3d hmat;
226	<	RealType chi;
227	<	RealType 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	>	pair<RealType, RealType> thermostat = s->getThermostat();
261
262	<	os << chi << "\t" << integralOfChiDt << ";\t";
262	>	if (isinf(thermostat.first)  || isnan(thermostat.first) ||
263	>	isinf(thermostat.second) || isnan(thermostat.second)) {
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", thermostat.first,
270	>	thermostat.second);
271	>	os << buffer;
272
273	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
274	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
275	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
276	<
277	<	os << "\n";
273	>	Mat3x3d eta;
274	>	eta = s->getBarostat();
275	>
276	>	for (unsigned int i = 0; i < 3; i++) {
277	>	for (unsigned int j = 0; j < 3; j++) {
278	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
279	>	sprintf( painCave.errMsg,
280	>	"DumpWriter detected a numerical error writing the barostat");
281	>	painCave.isFatal = 1;
282	>	simError();
283	>	}
284	>	}
285	>	}
286	>
287	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
288	>	eta(0, 0), eta(1, 0), eta(2, 0),
289	>	eta(0, 1), eta(1, 1), eta(2, 1),
290	>	eta(0, 2), eta(1, 2), eta(2, 2));
291	>	os << buffer;
292	>
293	>	os << "    </FrameData>\n";
294		}
295
296		void DumpWriter::writeFrame(std::ostream& os) {
234	–	const int BUFFERSIZE = 2000;
235	–	const int MINIBUFFERSIZE = 100;
297
298	<	char tempBuffer[BUFFERSIZE];
299	<	char writeLine[BUFFERSIZE];
298	>	#ifdef IS_MPI
299	>	MPI_Status istatus;
300	>	#endif
301
240	–	Quat4d q;
241	–	Vector3d ji;
242	–	Vector3d pos;
243	–	Vector3d vel;
244	–	Vector3d frc;
245	–	Vector3d trq;
246	–
302		Molecule* mol;
303		StuntDouble* integrableObject;
304		SimInfo::MoleculeIterator mi;
305		Molecule::IntegrableObjectIterator ii;
306	<
307	<	int nTotObjects;
253	<	nTotObjects = info_->getNGlobalIntegrableObjects();
306	>	RigidBody::AtomIterator ai;
307	>	Atom* atom;
308
309		#ifndef IS_MPI
310	+	os << "  <Snapshot>\n";
311	+
312	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
313
314	+	os << "    <StuntDoubles>\n";
315	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
316
317	<	os << nTotObjects << "\n";
318	<
319	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
317	>
318	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
319	>	integrableObject = mol->nextIntegrableObject(ii)) {
320	>	os << prepareDumpLine(integrableObject);
321	>
322	>	}
323	>	}
324	>	os << "    </StuntDoubles>\n";
325
326	+	if (doSiteData_) {
327	+	os << "    <SiteData>\n";
328	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
329	+
330	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
331	+	integrableObject = mol->nextIntegrableObject(ii)) {
332	+
333	+	int ioIndex = integrableObject->getGlobalIntegrableObjectIndex();
334	+	// do one for the IO itself
335	+	os << prepareSiteLine(integrableObject, ioIndex, 0);
336	+
337	+	if (integrableObject->isRigidBody()) {
338	+
339	+	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
340	+	int siteIndex = 0;
341	+	for (atom = rb->beginAtom(ai); atom != NULL;
342	+	atom = rb->nextAtom(ai)) {
343	+	os << prepareSiteLine(atom, ioIndex, siteIndex);
344	+	siteIndex++;
345	+	}
346	+	}
347	+	}
348	+	}
349	+	os << "    </SiteData>\n";
350	+	}
351	+	os << "  </Snapshot>\n";
352	+
353	+	os.flush();
354	+	#else
355	+	//every node prepares the dump lines for integrable objects belong to itself
356	+	std::string buffer;
357		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
358
264	–	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
265	–	integrableObject = mol->nextIntegrableObject(ii)) {
266	–
359
360	<	pos = integrableObject->getPos();
361	<	vel = integrableObject->getVel();
362	<
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	<
360	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
361	>	integrableObject = mol->nextIntegrableObject(ii)) {
362	>	buffer += prepareDumpLine(integrableObject);
363		}
364		}
365	<
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	<	*********************************************************************/
365	>
366		const int masterNode = 0;
345	–
346	–	int * potatoes;
347	–	int myPotato;
367		int nProc;
368	<	int which_node;
369	<	RealType atomData[19];
370	<	int isDirectional;
371	<	char MPIatomTypeString[MINIBUFFERSIZE];
372	<	int msgLen; // the length of message actually recieved at master nodes
373	<	int haveError;
374	<	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);
368	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
369	>	if (worldRank == masterNode) {
370	>	os << "  <Snapshot>\n";
371	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
372	>	os << "    <StuntDoubles>\n";
373	>
374	>	os << buffer;
375
376	<	if (flag) {
377	<	MAXTAG = *tagub;
376	>	for (int i = 1; i < nProc; ++i) {
377	>
378	>	// receive the length of the string buffer that was
379	>	// prepared by processor i
380	>
381	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
382	>	int recvLength;
383	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
384	>	char* recvBuffer = new char[recvLength];
385	>	if (recvBuffer == NULL) {
386	>	} else {
387	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
388	>	os << recvBuffer;
389	>	delete [] recvBuffer;
390	>	}
391	>	}
392	>	os << "    </StuntDoubles>\n";
393	>
394	>	os << "  </Snapshot>\n";
395	>	os.flush();
396		} else {
397	<	MAXTAG = 32767;
397	>	int sendBufferLength = buffer.size() + 1;
398	>	int myturn = 0;
399	>	for (int i = 1; i < nProc; ++i){
400	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
401	>	if (myturn == worldRank){
402	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
403	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
404	>	}
405	>	}
406		}
407
408	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
408	>	#endif // is_mpi
409
410	<	// Node 0 needs a list of the magic potatoes for each processor;
410	>	}
411
412	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
413	<	potatoes = new int[nProc];
412	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
413	>
414	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
415	>	std::string type("pv");
416	>	std::string line;
417	>	char tempBuffer[4096];
418
419	<	//write out the comment lines
420	<	for(int i = 0; i < nProc; i++) {
421	<	potatoes[i] = 0;
380	<	}
419	>	Vector3d pos;
420	>	Vector3d vel;
421	>	pos = integrableObject->getPos();
422
423	+	if (isinf(pos[0]) || isnan(pos[0]) ||
424	+	isinf(pos[1]) || isnan(pos[1]) ||
425	+	isinf(pos[2]) || isnan(pos[2]) ) {
426	+	sprintf( painCave.errMsg,
427	+	"DumpWriter detected a numerical error writing the position"
428	+	" for object %d", index);
429	+	painCave.isFatal = 1;
430	+	simError();
431	+	}
432
433	<	os << nTotObjects << "\n";
384	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
433	>	vel = integrableObject->getVel();
434
435	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
435	>	if (isinf(vel[0]) || isnan(vel[0]) ||
436	>	isinf(vel[1]) || isnan(vel[1]) ||
437	>	isinf(vel[2]) || isnan(vel[2]) ) {
438	>	sprintf( painCave.errMsg,
439	>	"DumpWriter detected a numerical error writing the velocity"
440	>	" for object %d", index);
441	>	painCave.isFatal = 1;
442	>	simError();
443	>	}
444
445	<	// Get the Node number which has this atom;
445	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
446	>	pos[0], pos[1], pos[2],
447	>	vel[0], vel[1], vel[2]);
448	>	line += tempBuffer;
449
450	<	which_node = info_->getMolToProc(i);
450	>	if (integrableObject->isDirectional()) {
451	>	type += "qj";
452	>	Quat4d q;
453	>	Vector3d ji;
454	>	q = integrableObject->getQ();
455
456	<	if (which_node != masterNode) { //current molecule is in slave node
457	<	if (potatoes[which_node] + 1 >= MAXTAG) {
458	<	// The potato was going to exceed the maximum value,
459	<	// so wrap this processor potato back to 0:
456	>	if (isinf(q[0]) || isnan(q[0]) ||
457	>	isinf(q[1]) || isnan(q[1]) ||
458	>	isinf(q[2]) || isnan(q[2]) ||
459	>	isinf(q[3]) || isnan(q[3]) ) {
460	>	sprintf( painCave.errMsg,
461	>	"DumpWriter detected a numerical error writing the quaternion"
462	>	" for object %d", index);
463	>	painCave.isFatal = 1;
464	>	simError();
465	>	}
466
467	<	potatoes[which_node] = 0;
398	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
399	<	MPI_COMM_WORLD);
400	<	}
467	>	ji = integrableObject->getJ();
468
469	<	myPotato = potatoes[which_node];
469	>	if (isinf(ji[0]) || isnan(ji[0]) ||
470	>	isinf(ji[1]) || isnan(ji[1]) ||
471	>	isinf(ji[2]) || isnan(ji[2]) ) {
472	>	sprintf( painCave.errMsg,
473	>	"DumpWriter detected a numerical error writing the angular"
474	>	" momentum for object %d", index);
475	>	painCave.isFatal = 1;
476	>	simError();
477	>	}
478
479	<	//recieve the number of integrableObject in current molecule
480	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
481	<	MPI_COMM_WORLD, &istatus);
482	<	myPotato++;
479	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
480	>	q[0], q[1], q[2], q[3],
481	>	ji[0], ji[1], ji[2]);
482	>	line += tempBuffer;
483	>	}
484
485	<	for(int l = 0; l < nCurObj; l++) {
486	<	if (potatoes[which_node] + 2 >= MAXTAG) {
487	<	// The potato was going to exceed the maximum value,
488	<	// so wrap this processor potato back to 0:
485	>	if (needForceVector_) {
486	>	type += "f";
487	>	Vector3d frc = integrableObject->getFrc();
488	>	if (isinf(frc[0]) || isnan(frc[0]) ||
489	>	isinf(frc[1]) || isnan(frc[1]) ||
490	>	isinf(frc[2]) || isnan(frc[2]) ) {
491	>	sprintf( painCave.errMsg,
492	>	"DumpWriter detected a numerical error writing the force"
493	>	" for object %d", index);
494	>	painCave.isFatal = 1;
495	>	simError();
496	>	}
497	>	sprintf(tempBuffer, " %13e %13e %13e",
498	>	frc[0], frc[1], frc[2]);
499	>	line += tempBuffer;
500	>
501	>	if (integrableObject->isDirectional()) {
502	>	type += "t";
503	>	Vector3d trq = integrableObject->getTrq();
504	>	if (isinf(trq[0]) || isnan(trq[0]) ||
505	>	isinf(trq[1]) || isnan(trq[1]) ||
506	>	isinf(trq[2]) || isnan(trq[2]) ) {
507	>	sprintf( painCave.errMsg,
508	>	"DumpWriter detected a numerical error writing the torque"
509	>	" for object %d", index);
510	>	painCave.isFatal = 1;
511	>	simError();
512	>	}
513	>	sprintf(tempBuffer, " %13e %13e %13e",
514	>	trq[0], trq[1], trq[2]);
515	>	line += tempBuffer;
516	>	}
517	>	}
518
519	<	potatoes[which_node] = 0;
520	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
521	<	0, MPI_COMM_WORLD);
417	<	}
519	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
520	>	return std::string(tempBuffer);
521	>	}
522
523	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
524	<	which_node, myPotato, MPI_COMM_WORLD,
421	<	&istatus);
523	>	std::string DumpWriter::prepareSiteLine(StuntDouble* integrableObject, int ioIndex, int siteIndex) {
524	>
525
526	<	myPotato++;
526	>	std::string id;
527	>	std::string type;
528	>	std::string line;
529	>	char tempBuffer[4096];
530
531	<	MPI_Recv(atomData, 19, MPI_REALTYPE, which_node, myPotato,
532	<	MPI_COMM_WORLD, &istatus);
533	<	myPotato++;
531	>	if (integrableObject->isRigidBody()) {
532	>	sprintf(tempBuffer, "%10d           ", ioIndex);
533	>	id = std::string(tempBuffer);
534	>	} else {
535	>	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
536	>	id = std::string(tempBuffer);
537	>	}
538	>
539	>	if (needFlucQ_) {
540	>	type += "cw";
541	>	RealType fqPos = integrableObject->getFlucQPos();
542	>	if (isinf(fqPos) || isnan(fqPos) ) {
543	>	sprintf( painCave.errMsg,
544	>	"DumpWriter detected a numerical error writing the"
545	>	" fluctuating charge for object %s", id.c_str());
546	>	painCave.isFatal = 1;
547	>	simError();
548	>	}
549	>	sprintf(tempBuffer, " %13e ", fqPos);
550	>	line += tempBuffer;
551	>
552	>	RealType fqVel = integrableObject->getFlucQVel();
553	>	if (isinf(fqVel) || isnan(fqVel) ) {
554	>	sprintf( painCave.errMsg,
555	>	"DumpWriter detected a numerical error writing the"
556	>	" fluctuating charge velocity for object %s", id.c_str());
557	>	painCave.isFatal = 1;
558	>	simError();
559	>	}
560	>	sprintf(tempBuffer, " %13e ", fqVel);
561	>	line += tempBuffer;
562
563	<	MPI_Get_count(&istatus, MPI_REALTYPE, &msgLen);
563	>	if (needForceVector_) {
564	>	type += "g";
565	>	RealType fqFrc = integrableObject->getFlucQFrc();
566	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
567	>	sprintf( painCave.errMsg,
568	>	"DumpWriter detected a numerical error writing the"
569	>	" fluctuating charge force for object %s", id.c_str());
570	>	painCave.isFatal = 1;
571	>	simError();
572	>	}
573	>	sprintf(tempBuffer, " %13e ", fqFrc);
574	>	line += tempBuffer;
575	>	}
576	>	}
577
578	<	if (msgLen == 13 || msgLen == 19)
579	<	isDirectional = 1;
580	<	else
581	<	isDirectional = 0;
578	>	if (needElectricField_) {
579	>	type += "e";
580	>	Vector3d eField= integrableObject->getElectricField();
581	>	if (isinf(eField[0]) || isnan(eField[0]) ||
582	>	isinf(eField[1]) || isnan(eField[1]) ||
583	>	isinf(eField[2]) || isnan(eField[2]) ) {
584	>	sprintf( painCave.errMsg,
585	>	"DumpWriter detected a numerical error writing the electric"
586	>	" field for object %s", id.c_str());
587	>	painCave.isFatal = 1;
588	>	simError();
589	>	}
590	>	sprintf(tempBuffer, " %13e %13e %13e",
591	>	eField[0], eField[1], eField[2]);
592	>	line += tempBuffer;
593	>	}
594
436	–	// If we've survived to here, format the line:
595
596	<	if (!isDirectional) {
597	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
598	<	MPIatomTypeString, atomData[0],
599	<	atomData[1], atomData[2],
600	<	atomData[3], atomData[4],
601	<	atomData[5]);
596	>	if (needParticlePot_) {
597	>	type += "u";
598	>	RealType particlePot = integrableObject->getParticlePot();
599	>	if (isinf(particlePot) || isnan(particlePot)) {
600	>	sprintf( painCave.errMsg,
601	>	"DumpWriter detected a numerical error writing the particle "
602	>	" potential for object %s", id.c_str());
603	>	painCave.isFatal = 1;
604	>	simError();
605	>	}
606	>	sprintf(tempBuffer, " %13e", particlePot);
607	>	line += tempBuffer;
608	>	}
609	>
610
611	<	strcat(writeLine,
612	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
447	<	} else {
448	<	sprintf(writeLine,
449	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
450	<	MPIatomTypeString,
451	<	atomData[0],
452	<	atomData[1],
453	<	atomData[2],
454	<	atomData[3],
455	<	atomData[4],
456	<	atomData[5],
457	<	atomData[6],
458	<	atomData[7],
459	<	atomData[8],
460	<	atomData[9],
461	<	atomData[10],
462	<	atomData[11],
463	<	atomData[12]);
464	<	}
465	<
466	<	if (needForceVector_) {
467	<	if (!isDirectional) {
468	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
469	<	atomData[6],
470	<	atomData[7],
471	<	atomData[8],
472	<	atomData[9],
473	<	atomData[10],
474	<	atomData[11]);
475	<	} else {
476	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
477	<	atomData[13],
478	<	atomData[14],
479	<	atomData[15],
480	<	atomData[16],
481	<	atomData[17],
482	<	atomData[18]);
483	<	}
484	<	}
485	<
486	<	sprintf(writeLine, "\n");
487	<	os << writeLine;
488	<
489	<	} // end for(int l =0)
490	<
491	<	potatoes[which_node] = myPotato;
492	<	} else { //master node has current molecule
493	<
494	<	mol = info_->getMoleculeByGlobalIndex(i);
495	<
496	<	if (mol == NULL) {
497	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
498	<	painCave.isFatal = 1;
499	<	simError();
500	<	}
501	<
502	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
503	<	integrableObject = mol->nextIntegrableObject(ii)) {
504	<
505	<	pos = integrableObject->getPos();
506	<	vel = integrableObject->getVel();
507	<
508	<	atomData[0] = pos[0];
509	<	atomData[1] = pos[1];
510	<	atomData[2] = pos[2];
511	<
512	<	atomData[3] = vel[0];
513	<	atomData[4] = vel[1];
514	<	atomData[5] = vel[2];
515	<
516	<	isDirectional = 0;
517	<
518	<	if (integrableObject->isDirectional()) {
519	<	isDirectional = 1;
520	<
521	<	q = integrableObject->getQ();
522	<	ji = integrableObject->getJ();
523	<
524	<	for(int j = 0; j < 6; j++) {
525	<	atomData[j] = atomData[j];
526	<	}
527	<
528	<	atomData[6] = q[0];
529	<	atomData[7] = q[1];
530	<	atomData[8] = q[2];
531	<	atomData[9] = q[3];
532	<
533	<	atomData[10] = ji[0];
534	<	atomData[11] = ji[1];
535	<	atomData[12] = ji[2];
536	<	}
537	<
538	<	if (needForceVector_) {
539	<	frc = integrableObject->getFrc();
540	<	trq = integrableObject->getTrq();
541	<
542	<	if (!isDirectional) {
543	<	atomData[6] = frc[0];
544	<	atomData[7] = frc[1];
545	<	atomData[8] = frc[2];
546	<	atomData[9] = trq[0];
547	<	atomData[10] = trq[1];
548	<	atomData[11] = trq[2];
549	<	} else {
550	<	atomData[13] = frc[0];
551	<	atomData[14] = frc[1];
552	<	atomData[15] = frc[2];
553	<	atomData[16] = trq[0];
554	<	atomData[17] = trq[1];
555	<	atomData[18] = trq[2];
556	<	}
557	<	}
558	<
559	<	// If we've survived to here, format the line:
560	<
561	<	if (!isDirectional) {
562	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
563	<	integrableObject->getType().c_str(), atomData[0],
564	<	atomData[1], atomData[2],
565	<	atomData[3], atomData[4],
566	<	atomData[5]);
567	<
568	<	strcat(writeLine,
569	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
570	<	} else {
571	<	sprintf(writeLine,
572	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
573	<	integrableObject->getType().c_str(),
574	<	atomData[0],
575	<	atomData[1],
576	<	atomData[2],
577	<	atomData[3],
578	<	atomData[4],
579	<	atomData[5],
580	<	atomData[6],
581	<	atomData[7],
582	<	atomData[8],
583	<	atomData[9],
584	<	atomData[10],
585	<	atomData[11],
586	<	atomData[12]);
587	<	}
588	<
589	<	if (needForceVector_) {
590	<	if (!isDirectional) {
591	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
592	<	atomData[6],
593	<	atomData[7],
594	<	atomData[8],
595	<	atomData[9],
596	<	atomData[10],
597	<	atomData[11]);
598	<	} else {
599	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
600	<	atomData[13],
601	<	atomData[14],
602	<	atomData[15],
603	<	atomData[16],
604	<	atomData[17],
605	<	atomData[18]);
606	<	}
607	<	}
608	<
609	<	os << writeLine << "\n";
610	<
611	<	} //end for(iter = integrableObject.begin())
612	<	}
613	<	} //end for(i = 0; i < mpiSim->getNmol())
614	<
615	<	os.flush();
616	<
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	<
746	<	}
747	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
748	<	MPIcheckPoint();
749	<	}
750	<
751	<	#endif // is_mpi
752	<
611	>	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
612	>	return std::string(tempBuffer);
613		}
614
615		void DumpWriter::writeDump() {
#	Line 774 | Line 634 | namespace oopse {
634		#ifdef IS_MPI
635		if (worldRank == 0) {
636		#endif // is_mpi
637	<	delete eorStream;
638	<
637	>	writeClosing(*eorStream);
638	>	delete eorStream;
639		#ifdef IS_MPI
640		}
641		#endif // is_mpi
#	Line 808 | Line 668 | namespace oopse {
668		#ifdef IS_MPI
669		if (worldRank == 0) {
670		#endif // is_mpi
671	<	delete eorStream;
672	<
671	>	writeClosing(*eorStream);
672	>	delete eorStream;
673		#ifdef IS_MPI
674		}
675		#endif // is_mpi
676
677		}
678
679	<	std::ostream* DumpWriter::createOStream(const std::string& filename) {
679	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
680
681		std::ostream* newOStream;
682		#ifdef HAVE_LIBZ
683		if (needCompression_) {
684	<	newOStream = new ogzstream(filename.c_str());
684	>	newOStream = new ogzstream(filename.c_str());
685		} else {
686	<	newOStream = new std::ofstream(filename.c_str());
686	>	newOStream = new std::ofstream(filename.c_str());
687		}
688		#else
689		newOStream = new std::ofstream(filename.c_str());
690		#endif
691	+	//write out MetaData first
692	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
693	+	(*newOStream) << "  <MetaData>" << std::endl;
694	+	(*newOStream) << info_->getRawMetaData();
695	+	(*newOStream) << "  </MetaData>" << std::endl;
696		return newOStream;
697	<	}
697	>	}
698
699	<	}//end namespace oopse
699	>	void DumpWriter::writeClosing(std::ostream& os) {
700	>
701	>	os << "</OpenMD>\n";
702	>	os.flush();
703	>	}
704	>
705	>	}//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.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

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