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

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trunk/src/io/DumpWriter.cpp (file contents), Revision 1024 by tim, Wed Aug 30 18:42:29 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_) {
#	Line 95 | 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_) {
#	Line 134 | Line 157 | namespace oopse {
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 194 | Line 226 | namespace oopse {
226		os << "    <FrameData>\n";
227
228		RealType currentTime = s->getTime();
229	<	sprintf(buffer, "        Time: %.10g\n", time);
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	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
238		os << buffer;
239
240		Mat3x3d hmat;
241		hmat = s->getHmat();
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		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	<	RealType chi = s->getChi();
261	<	RealType integralOfChiDt = s->getIntegralOfChiDt();
262	<	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
260	>	pair<RealType, RealType> thermostat = s->getThermostat();
261	>
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		Mat3x3d eta;
274	<	eta = s->getEta();
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),
#	Line 231 | Line 303 | namespace oopse {
303		StuntDouble* integrableObject;
304		SimInfo::MoleculeIterator mi;
305		Molecule::IntegrableObjectIterator ii;
306	+	RigidBody::AtomIterator ai;
307	+	Atom* atom;
308
309		#ifndef IS_MPI
310		os << "  <Snapshot>\n";
311	<
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	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
317	>
318	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
319		integrableObject = mol->nextIntegrableObject(ii)) {
320	<	os << prepareDumpLine(integrableObject);
321	<
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();
#	Line 255 | Line 355 | namespace oopse {
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	<
358	>
359	>
360		for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
361		integrableObject = mol->nextIntegrableObject(ii)) {
362	<	buffer += prepareDumpLine(integrableObject);
362	>	buffer += prepareDumpLine(integrableObject);
363		}
364		}
365
366		const int masterNode = 0;
367	<
367	>	int nProc;
368	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
369		if (worldRank == masterNode) {
370		os << "  <Snapshot>\n";
371		writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
270	–	os << buffer;
372		os << "    <StuntDoubles>\n";
373
374	<	int nProc;
375	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
374	>	os << buffer;
375	>
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) {
284	–
386		} else {
387	<	MPI_Recv(&recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
387	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
388		os << recvBuffer;
389	<	delete recvBuffer;
389	>	delete [] recvBuffer;
390		}
290	–
391		}
392		os << "    </StuntDoubles>\n";
393
394		os << "  </Snapshot>\n";
395		os.flush();
396		} else {
397	<	int sendBufferLength = buffer.size();
398	<	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
399	<	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
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		#endif // is_mpi
#	Line 313 | Line 419 | namespace oopse {
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		vel = integrableObject->getVel();
434	<	sprintf(tempBuffer, "%18.10g\t%18.10g\t%18.10g\t%14.10g\t%14.10g\t%14.10g",
434	>
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	>	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;
#	Line 324 | Line 452 | namespace oopse {
452		Quat4d q;
453		Vector3d ji;
454		q = integrableObject->getQ();
455	+
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		ji = integrableObject->getJ();
468	<	sprintf(tempBuffer, "\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g",
468	>
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	>	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		if (needForceVector_) {
486	<	type += "ft";
487	<	Vector3d frc;
488	<	Vector3d trq;
489	<	frc = integrableObject->getFrc();
490	<	trq = integrableObject->getTrq();
491	<
492	<	sprintf(tempBuffer, "\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g",
493	<	frc[0], frc[1], frc[2],
494	<	trq[0], trq[1], trq[2]);
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	+	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
520	+	return std::string(tempBuffer);
521	+	}
522	+
523	+	std::string DumpWriter::prepareSiteLine(StuntDouble* integrableObject, int ioIndex, int siteIndex) {
524
525	<	sprintf(tempBuffer, "%d\t%s\t%s\n", index, type.c_str(), line.c_str());
525	>
526	>	std::string id;
527	>	std::string type;
528	>	std::string line;
529	>	char tempBuffer[4096];
530	>
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	>	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 (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	>
595	>
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	>	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
612		return std::string(tempBuffer);
613		}
614
#	Line 425 | Line 689 | namespace oopse {
689		newOStream = new std::ofstream(filename.c_str());
690		#endif
691		//write out MetaData first
692	<	(*newOStream) << "<OOPSE version=4>" << std::endl;
692	>	(*newOStream) << "<OpenMD version=2>" << std::endl;
693		(*newOStream) << "  <MetaData>" << std::endl;
694		(*newOStream) << info_->getRawMetaData();
695		(*newOStream) << "  </MetaData>" << std::endl;
#	Line 434 | Line 698 | namespace oopse {
698
699		void DumpWriter::writeClosing(std::ostream& os) {
700
701	<	os << "</OOPSE>\n";
701	>	os << "</OpenMD>\n";
702		os.flush();
703		}
704
705	<	}//end namespace oopse
705	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 1024 by tim, Wed Aug 30 18:42:29 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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