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

Comparing:
trunk/src/io/DumpWriter.cpp (file contents), Revision 1025 by gezelter, Wed Aug 30 20:33:44 2006 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 1 | Line 1
1		/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
2	>	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include "io/DumpWriter.hpp"
#	Line 46 | Line 46
46		#include "io/gzstream.hpp"
47		#include "io/Globals.hpp"
48
49	+
50		#ifdef IS_MPI
51		#include <mpi.h>
52		#endif //is_mpi
53
54	<	namespace oopse {
54	>	using namespace std;
55	>	namespace OpenMD {
56
57		DumpWriter::DumpWriter(SimInfo* info)
58		: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
#	Line 194 | Line 196 | namespace oopse {
196		os << "    <FrameData>\n";
197
198		RealType currentTime = s->getTime();
199	+
200	+	if (isinf(currentTime) || isnan(currentTime)) {
201	+	sprintf( painCave.errMsg,
202	+	"DumpWriter detected a numerical error writing the time");
203	+	painCave.isFatal = 1;
204	+	simError();
205	+	}
206	+
207		sprintf(buffer, "        Time: %.10g\n", currentTime);
208		os << buffer;
209
210		Mat3x3d hmat;
211		hmat = s->getHmat();
212	+
213	+	for (unsigned int i = 0; i < 3; i++) {
214	+	for (unsigned int j = 0; j < 3; j++) {
215	+	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
216	+	sprintf( painCave.errMsg,
217	+	"DumpWriter detected a numerical error writing the box");
218	+	painCave.isFatal = 1;
219	+	simError();
220	+	}
221	+	}
222	+	}
223	+
224		sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
225		hmat(0, 0), hmat(1, 0), hmat(2, 0),
226		hmat(0, 1), hmat(1, 1), hmat(2, 1),
#	Line 207 | Line 229 | namespace oopse {
229
230		RealType chi = s->getChi();
231		RealType integralOfChiDt = s->getIntegralOfChiDt();
232	+	if (isinf(chi) || isnan(chi) ||
233	+	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
234	+	sprintf( painCave.errMsg,
235	+	"DumpWriter detected a numerical error writing the thermostat");
236	+	painCave.isFatal = 1;
237	+	simError();
238	+	}
239		sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
240		os << buffer;
241
242		Mat3x3d eta;
243		eta = s->getEta();
244	+
245	+	for (unsigned int i = 0; i < 3; i++) {
246	+	for (unsigned int j = 0; j < 3; j++) {
247	+	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
248	+	sprintf( painCave.errMsg,
249	+	"DumpWriter detected a numerical error writing the barostat");
250	+	painCave.isFatal = 1;
251	+	simError();
252	+	}
253	+	}
254	+	}
255	+
256		sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
257		eta(0, 0), eta(1, 0), eta(2, 0),
258		eta(0, 1), eta(1, 1), eta(2, 1),
#	Line 240 | Line 281 | namespace oopse {
281		os << "    <StuntDoubles>\n";
282		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
283
284	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
284	>
285	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
286		integrableObject = mol->nextIntegrableObject(ii)) {
287	<	os << prepareDumpLine(integrableObject);
288	<
287	>	os << prepareDumpLine(integrableObject);
288	>
289		}
290		}
291		os << "    </StuntDoubles>\n";
292	<
292	>
293		os << "  </Snapshot>\n";
294
295		os.flush();
#	Line 255 | Line 297 | namespace oopse {
297		//every node prepares the dump lines for integrable objects belong to itself
298		std::string buffer;
299		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
300	<
300	>
301	>
302		for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
303		integrableObject = mol->nextIntegrableObject(ii)) {
304	<	buffer += prepareDumpLine(integrableObject);
304	>	buffer += prepareDumpLine(integrableObject);
305		}
306		}
307
#	Line 285 | Line 328 | namespace oopse {
328		} else {
329		MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
330		os << recvBuffer;
331	<	delete recvBuffer;
331	>	delete [] recvBuffer;
332		}
333		}
334		os << "    </StuntDoubles>\n";
#	Line 312 | Line 355 | namespace oopse {
355		Vector3d pos;
356		Vector3d vel;
357		pos = integrableObject->getPos();
358	+
359	+	if (isinf(pos[0]) || isnan(pos[0]) ||
360	+	isinf(pos[1]) || isnan(pos[1]) ||
361	+	isinf(pos[2]) || isnan(pos[2]) ) {
362	+	sprintf( painCave.errMsg,
363	+	"DumpWriter detected a numerical error writing the position"
364	+	" for object %d", index);
365	+	painCave.isFatal = 1;
366	+	simError();
367	+	}
368	+
369		vel = integrableObject->getVel();
370	+
371	+	if (isinf(vel[0]) || isnan(vel[0]) ||
372	+	isinf(vel[1]) || isnan(vel[1]) ||
373	+	isinf(vel[2]) || isnan(vel[2]) ) {
374	+	sprintf( painCave.errMsg,
375	+	"DumpWriter detected a numerical error writing the velocity"
376	+	" for object %d", index);
377	+	painCave.isFatal = 1;
378	+	simError();
379	+	}
380	+
381		sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
382		pos[0], pos[1], pos[2],
383		vel[0], vel[1], vel[2]);
#	Line 323 | Line 388 | namespace oopse {
388		Quat4d q;
389		Vector3d ji;
390		q = integrableObject->getQ();
391	+
392	+	if (isinf(q[0]) || isnan(q[0]) ||
393	+	isinf(q[1]) || isnan(q[1]) ||
394	+	isinf(q[2]) || isnan(q[2]) ||
395	+	isinf(q[3]) || isnan(q[3]) ) {
396	+	sprintf( painCave.errMsg,
397	+	"DumpWriter detected a numerical error writing the quaternion"
398	+	" for object %d", index);
399	+	painCave.isFatal = 1;
400	+	simError();
401	+	}
402	+
403		ji = integrableObject->getJ();
404	+
405	+	if (isinf(ji[0]) || isnan(ji[0]) ||
406	+	isinf(ji[1]) || isnan(ji[1]) ||
407	+	isinf(ji[2]) || isnan(ji[2]) ) {
408	+	sprintf( painCave.errMsg,
409	+	"DumpWriter detected a numerical error writing the angular"
410	+	" momentum for object %d", index);
411	+	painCave.isFatal = 1;
412	+	simError();
413	+	}
414	+
415		sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
416		q[0], q[1], q[2], q[3],
417		ji[0], ji[1], ji[2]);
#	Line 331 | Line 419 | namespace oopse {
419		}
420
421		if (needForceVector_) {
422	<	type += "ft";
422	>	type += "f";
423		Vector3d frc;
424	<	Vector3d trq;
424	>
425		frc = integrableObject->getFrc();
426	<	trq = integrableObject->getTrq();
427	<
428	<	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e",
429	<	frc[0], frc[1], frc[2],
430	<	trq[0], trq[1], trq[2]);
426	>
427	>	if (isinf(frc[0]) || isnan(frc[0]) ||
428	>	isinf(frc[1]) || isnan(frc[1]) ||
429	>	isinf(frc[2]) || isnan(frc[2]) ) {
430	>	sprintf( painCave.errMsg,
431	>	"DumpWriter detected a numerical error writing the force"
432	>	" for object %d", index);
433	>	painCave.isFatal = 1;
434	>	simError();
435	>	}
436	>	sprintf(tempBuffer, " %13e %13e %13e",
437	>	frc[0], frc[1], frc[2]);
438		line += tempBuffer;
439	+
440	+	if (integrableObject->isDirectional()) {
441	+	type += "t";
442	+	Vector3d trq;
443	+
444	+	trq = integrableObject->getTrq();
445	+
446	+	if (isinf(trq[0]) || isnan(trq[0]) ||
447	+	isinf(trq[1]) || isnan(trq[1]) ||
448	+	isinf(trq[2]) || isnan(trq[2]) ) {
449	+	sprintf( painCave.errMsg,
450	+	"DumpWriter detected a numerical error writing the torque"
451	+	" for object %d", index);
452	+	painCave.isFatal = 1;
453	+	simError();
454	+	}
455	+
456	+	sprintf(tempBuffer, " %13e %13e %13e",
457	+	trq[0], trq[1], trq[2]);
458	+	line += tempBuffer;
459	+	}
460		}
461	<
461	>
462		sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
463		return std::string(tempBuffer);
464		}
#	Line 424 | Line 540 | namespace oopse {
540		newOStream = new std::ofstream(filename.c_str());
541		#endif
542		//write out MetaData first
543	<	(*newOStream) << "<OOPSE version=4>" << std::endl;
543	>	(*newOStream) << "<OpenMD version=1>" << std::endl;
544		(*newOStream) << "  <MetaData>" << std::endl;
545		(*newOStream) << info_->getRawMetaData();
546		(*newOStream) << "  </MetaData>" << std::endl;
#	Line 433 | Line 549 | namespace oopse {
549
550		void DumpWriter::writeClosing(std::ostream& os) {
551
552	<	os << "</OOPSE>\n";
552	>	os << "</OpenMD>\n";
553		os.flush();
554		}
555
556	<	}//end namespace oopse
556	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 1025 by gezelter, Wed Aug 30 20:33:44 2006 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 0 | Line 1
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