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

Comparing:
trunk/src/io/DumpWriter.cpp (file contents), Revision 1217 by xsun, Wed Jan 23 21:23:02 2008 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 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 58 | Line 60 | namespace oopse {
60		Globals* simParams = info->getSimParams();
61		needCompression_ = simParams->getCompressDumpFile();
62		needForceVector_ = simParams->getOutputForceVector();
63	+	needParticlePot_ = simParams->getOutputParticlePotential();
64		createDumpFile_ = true;
65		#ifdef HAVE_LIBZ
66		if (needCompression_) {
#	Line 136 | Line 139 | namespace oopse {
139
140		needCompression_ = simParams->getCompressDumpFile();
141		needForceVector_ = simParams->getOutputForceVector();
142	+	needParticlePot_ = simParams->getOutputParticlePotential();
143
144		#ifdef HAVE_LIBZ
145		if (needCompression_) {
#	Line 194 | Line 198 | namespace oopse {
198		os << "    <FrameData>\n";
199
200		RealType currentTime = s->getTime();
201	+
202	+	if (isinf(currentTime) || isnan(currentTime)) {
203	+	sprintf( painCave.errMsg,
204	+	"DumpWriter detected a numerical error writing the time");
205	+	painCave.isFatal = 1;
206	+	simError();
207	+	}
208	+
209		sprintf(buffer, "        Time: %.10g\n", currentTime);
210		os << buffer;
211
212		Mat3x3d hmat;
213		hmat = s->getHmat();
214	+
215	+	for (unsigned int i = 0; i < 3; i++) {
216	+	for (unsigned int j = 0; j < 3; j++) {
217	+	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
218	+	sprintf( painCave.errMsg,
219	+	"DumpWriter detected a numerical error writing the box");
220	+	painCave.isFatal = 1;
221	+	simError();
222	+	}
223	+	}
224	+	}
225	+
226		sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
227		hmat(0, 0), hmat(1, 0), hmat(2, 0),
228		hmat(0, 1), hmat(1, 1), hmat(2, 1),
#	Line 207 | Line 231 | namespace oopse {
231
232		RealType chi = s->getChi();
233		RealType integralOfChiDt = s->getIntegralOfChiDt();
234	+	if (isinf(chi) || isnan(chi) ||
235	+	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
236	+	sprintf( painCave.errMsg,
237	+	"DumpWriter detected a numerical error writing the thermostat");
238	+	painCave.isFatal = 1;
239	+	simError();
240	+	}
241		sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
242		os << buffer;
243
244		Mat3x3d eta;
245		eta = s->getEta();
246	+
247	+	for (unsigned int i = 0; i < 3; i++) {
248	+	for (unsigned int j = 0; j < 3; j++) {
249	+	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
250	+	sprintf( painCave.errMsg,
251	+	"DumpWriter detected a numerical error writing the barostat");
252	+	painCave.isFatal = 1;
253	+	simError();
254	+	}
255	+	}
256	+	}
257	+
258		sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
259		eta(0, 0), eta(1, 0), eta(2, 0),
260		eta(0, 1), eta(1, 1), eta(2, 1),
#	Line 265 | Line 308 | namespace oopse {
308		}
309
310		const int masterNode = 0;
311	<
311	>	int nProc;
312	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
313		if (worldRank == masterNode) {
314		os << "  <Snapshot>\n";
315		writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
#	Line 273 | Line 317 | namespace oopse {
317
318		os << buffer;
319
276	–	int nProc;
277	–	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
320		for (int i = 1; i < nProc; ++i) {
321
322		// receive the length of the string buffer that was
323		// prepared by processor i
324
325	+	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
326		int recvLength;
327		MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
328		char* recvBuffer = new char[recvLength];
#	Line 287 | Line 330 | namespace oopse {
330		} else {
331		MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
332		os << recvBuffer;
333	<	delete recvBuffer;
333	>	delete [] recvBuffer;
334		}
335		}
336		os << "    </StuntDoubles>\n";
#	Line 296 | Line 339 | namespace oopse {
339		os.flush();
340		} else {
341		int sendBufferLength = buffer.size() + 1;
342	<	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
343	<	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
342	>	int myturn = 0;
343	>	for (int i = 1; i < nProc; ++i){
344	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
345	>	if (myturn == worldRank){
346	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
347	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
348	>	}
349	>	}
350		}
351
352		#endif // is_mpi
#	Line 314 | Line 363 | namespace oopse {
363		Vector3d pos;
364		Vector3d vel;
365		pos = integrableObject->getPos();
366	+
367	+	if (isinf(pos[0]) || isnan(pos[0]) ||
368	+	isinf(pos[1]) || isnan(pos[1]) ||
369	+	isinf(pos[2]) || isnan(pos[2]) ) {
370	+	sprintf( painCave.errMsg,
371	+	"DumpWriter detected a numerical error writing the position"
372	+	" for object %d", index);
373	+	painCave.isFatal = 1;
374	+	simError();
375	+	}
376	+
377		vel = integrableObject->getVel();
378	+
379	+	if (isinf(vel[0]) || isnan(vel[0]) ||
380	+	isinf(vel[1]) || isnan(vel[1]) ||
381	+	isinf(vel[2]) || isnan(vel[2]) ) {
382	+	sprintf( painCave.errMsg,
383	+	"DumpWriter detected a numerical error writing the velocity"
384	+	" for object %d", index);
385	+	painCave.isFatal = 1;
386	+	simError();
387	+	}
388	+
389		sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
390		pos[0], pos[1], pos[2],
391		vel[0], vel[1], vel[2]);
#	Line 325 | Line 396 | namespace oopse {
396		Quat4d q;
397		Vector3d ji;
398		q = integrableObject->getQ();
399	+
400	+	if (isinf(q[0]) || isnan(q[0]) ||
401	+	isinf(q[1]) || isnan(q[1]) ||
402	+	isinf(q[2]) || isnan(q[2]) ||
403	+	isinf(q[3]) || isnan(q[3]) ) {
404	+	sprintf( painCave.errMsg,
405	+	"DumpWriter detected a numerical error writing the quaternion"
406	+	" for object %d", index);
407	+	painCave.isFatal = 1;
408	+	simError();
409	+	}
410	+
411		ji = integrableObject->getJ();
412	+
413	+	if (isinf(ji[0]) || isnan(ji[0]) ||
414	+	isinf(ji[1]) || isnan(ji[1]) ||
415	+	isinf(ji[2]) || isnan(ji[2]) ) {
416	+	sprintf( painCave.errMsg,
417	+	"DumpWriter detected a numerical error writing the angular"
418	+	" momentum for object %d", index);
419	+	painCave.isFatal = 1;
420	+	simError();
421	+	}
422	+
423		sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
424		q[0], q[1], q[2], q[3],
425		ji[0], ji[1], ji[2]);
#	Line 333 | Line 427 | namespace oopse {
427		}
428
429		if (needForceVector_) {
430	<	type += "ft";
430	>	type += "f";
431		Vector3d frc;
432	<	Vector3d trq;
432	>
433		frc = integrableObject->getFrc();
434	<	trq = integrableObject->getTrq();
435	<
436	<	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e",
437	<	frc[0], frc[1], frc[2],
438	<	trq[0], trq[1], trq[2]);
434	>
435	>	if (isinf(frc[0]) || isnan(frc[0]) ||
436	>	isinf(frc[1]) || isnan(frc[1]) ||
437	>	isinf(frc[2]) || isnan(frc[2]) ) {
438	>	sprintf( painCave.errMsg,
439	>	"DumpWriter detected a numerical error writing the force"
440	>	" for object %d", index);
441	>	painCave.isFatal = 1;
442	>	simError();
443	>	}
444	>	sprintf(tempBuffer, " %13e %13e %13e",
445	>	frc[0], frc[1], frc[2]);
446		line += tempBuffer;
447	+
448	+	if (integrableObject->isDirectional()) {
449	+	type += "t";
450	+	Vector3d trq;
451	+
452	+	trq = integrableObject->getTrq();
453	+
454	+	if (isinf(trq[0]) || isnan(trq[0]) ||
455	+	isinf(trq[1]) || isnan(trq[1]) ||
456	+	isinf(trq[2]) || isnan(trq[2]) ) {
457	+	sprintf( painCave.errMsg,
458	+	"DumpWriter detected a numerical error writing the torque"
459	+	" for object %d", index);
460	+	painCave.isFatal = 1;
461	+	simError();
462	+	}
463	+
464	+	sprintf(tempBuffer, " %13e %13e %13e",
465	+	trq[0], trq[1], trq[2]);
466	+	line += tempBuffer;
467	+	}
468		}
469	<
469	>	if (needParticlePot_) {
470	>	type += "u";
471	>	RealType particlePot;
472	>
473	>	particlePot = integrableObject->getParticlePot();
474	>
475	>	if (isinf(particlePot) || isnan(particlePot)) {
476	>	sprintf( painCave.errMsg,
477	>	"DumpWriter detected a numerical error writing the particle "
478	>	" potential for object %d", index);
479	>	painCave.isFatal = 1;
480	>	simError();
481	>	}
482	>	sprintf(tempBuffer, " %13e", particlePot);
483	>	line += tempBuffer;
484	>	}
485	>
486		sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
487		return std::string(tempBuffer);
488		}
#	Line 426 | Line 564 | namespace oopse {
564		newOStream = new std::ofstream(filename.c_str());
565		#endif
566		//write out MetaData first
567	<	(*newOStream) << "<OOPSE version=4>" << std::endl;
567	>	(*newOStream) << "<OpenMD version=1>" << std::endl;
568		(*newOStream) << "  <MetaData>" << std::endl;
569		(*newOStream) << info_->getRawMetaData();
570		(*newOStream) << "  </MetaData>" << std::endl;
#	Line 435 | Line 573 | namespace oopse {
573
574		void DumpWriter::writeClosing(std::ostream& os) {
575
576	<	os << "</OOPSE>\n";
576	>	os << "</OpenMD>\n";
577		os.flush();
578		}
579
580	<	}//end namespace oopse
580	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 1217 by xsun, Wed Jan 23 21:23:02 2008 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC

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