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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 1665 by gezelter, Tue Nov 22 20:38:56 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]  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()){
#	Line 58 | Line 61 | namespace oopse {
61		Globals* simParams = info->getSimParams();
62		needCompression_ = simParams->getCompressDumpFile();
63		needForceVector_ = simParams->getOutputForceVector();
64	+	needParticlePot_ = simParams->getOutputParticlePotential();
65		createDumpFile_ = true;
66		#ifdef HAVE_LIBZ
67		if (needCompression_) {
#	Line 136 | Line 140 | namespace oopse {
140
141		needCompression_ = simParams->getCompressDumpFile();
142		needForceVector_ = simParams->getOutputForceVector();
143	+	needParticlePot_ = simParams->getOutputParticlePotential();
144
145		#ifdef HAVE_LIBZ
146		if (needCompression_) {
#	Line 194 | Line 199 | namespace oopse {
199		os << "    <FrameData>\n";
200
201		RealType currentTime = s->getTime();
202	+
203	+	if (isinf(currentTime) || isnan(currentTime)) {
204	+	sprintf( painCave.errMsg,
205	+	"DumpWriter detected a numerical error writing the time");
206	+	painCave.isFatal = 1;
207	+	simError();
208	+	}
209	+
210		sprintf(buffer, "        Time: %.10g\n", currentTime);
211		os << buffer;
212
213		Mat3x3d hmat;
214		hmat = s->getHmat();
215	+
216	+	for (unsigned int i = 0; i < 3; i++) {
217	+	for (unsigned int j = 0; j < 3; j++) {
218	+	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
219	+	sprintf( painCave.errMsg,
220	+	"DumpWriter detected a numerical error writing the box");
221	+	painCave.isFatal = 1;
222	+	simError();
223	+	}
224	+	}
225	+	}
226	+
227		sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
228		hmat(0, 0), hmat(1, 0), hmat(2, 0),
229		hmat(0, 1), hmat(1, 1), hmat(2, 1),
#	Line 207 | Line 232 | namespace oopse {
232
233		RealType chi = s->getChi();
234		RealType integralOfChiDt = s->getIntegralOfChiDt();
235	+	if (isinf(chi) || isnan(chi) ||
236	+	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
237	+	sprintf( painCave.errMsg,
238	+	"DumpWriter detected a numerical error writing the thermostat");
239	+	painCave.isFatal = 1;
240	+	simError();
241	+	}
242		sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
243		os << buffer;
244
245		Mat3x3d eta;
246		eta = s->getEta();
247	+
248	+	for (unsigned int i = 0; i < 3; i++) {
249	+	for (unsigned int j = 0; j < 3; j++) {
250	+	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
251	+	sprintf( painCave.errMsg,
252	+	"DumpWriter detected a numerical error writing the barostat");
253	+	painCave.isFatal = 1;
254	+	simError();
255	+	}
256	+	}
257	+	}
258	+
259		sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
260		eta(0, 0), eta(1, 0), eta(2, 0),
261		eta(0, 1), eta(1, 1), eta(2, 1),
#	Line 240 | Line 284 | namespace oopse {
284		os << "    <StuntDoubles>\n";
285		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
286
287	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
287	>
288	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
289		integrableObject = mol->nextIntegrableObject(ii)) {
290	<	os << prepareDumpLine(integrableObject);
291	<
290	>	os << prepareDumpLine(integrableObject);
291	>
292		}
293		}
294		os << "    </StuntDoubles>\n";
295	<
295	>
296		os << "  </Snapshot>\n";
297
298		os.flush();
#	Line 255 | Line 300 | namespace oopse {
300		//every node prepares the dump lines for integrable objects belong to itself
301		std::string buffer;
302		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
303	<
303	>
304	>
305		for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
306		integrableObject = mol->nextIntegrableObject(ii)) {
307	<	buffer += prepareDumpLine(integrableObject);
307	>	buffer += prepareDumpLine(integrableObject);
308		}
309		}
310
311		const int masterNode = 0;
312	<
312	>	int nProc;
313	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
314		if (worldRank == masterNode) {
315		os << "  <Snapshot>\n";
316		writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
#	Line 271 | Line 318 | namespace oopse {
318
319		os << buffer;
320
274	–	int nProc;
275	–	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
321		for (int i = 1; i < nProc; ++i) {
322
323		// receive the length of the string buffer that was
324		// prepared by processor i
325
326	+	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
327		int recvLength;
328		MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
329		char* recvBuffer = new char[recvLength];
#	Line 285 | Line 331 | namespace oopse {
331		} else {
332		MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
333		os << recvBuffer;
334	<	delete recvBuffer;
334	>	delete [] recvBuffer;
335		}
336		}
337		os << "    </StuntDoubles>\n";
#	Line 294 | Line 340 | namespace oopse {
340		os.flush();
341		} else {
342		int sendBufferLength = buffer.size() + 1;
343	<	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
344	<	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
343	>	int myturn = 0;
344	>	for (int i = 1; i < nProc; ++i){
345	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
346	>	if (myturn == worldRank){
347	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
348	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
349	>	}
350	>	}
351		}
352
353		#endif // is_mpi
#	Line 312 | Line 364 | namespace oopse {
364		Vector3d pos;
365		Vector3d vel;
366		pos = integrableObject->getPos();
367	+
368	+	if (isinf(pos[0]) || isnan(pos[0]) ||
369	+	isinf(pos[1]) || isnan(pos[1]) ||
370	+	isinf(pos[2]) || isnan(pos[2]) ) {
371	+	sprintf( painCave.errMsg,
372	+	"DumpWriter detected a numerical error writing the position"
373	+	" for object %d", index);
374	+	painCave.isFatal = 1;
375	+	simError();
376	+	}
377	+
378		vel = integrableObject->getVel();
379	+
380	+	if (isinf(vel[0]) || isnan(vel[0]) ||
381	+	isinf(vel[1]) || isnan(vel[1]) ||
382	+	isinf(vel[2]) || isnan(vel[2]) ) {
383	+	sprintf( painCave.errMsg,
384	+	"DumpWriter detected a numerical error writing the velocity"
385	+	" for object %d", index);
386	+	painCave.isFatal = 1;
387	+	simError();
388	+	}
389	+
390		sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
391		pos[0], pos[1], pos[2],
392		vel[0], vel[1], vel[2]);
#	Line 323 | Line 397 | namespace oopse {
397		Quat4d q;
398		Vector3d ji;
399		q = integrableObject->getQ();
400	+
401	+	if (isinf(q[0]) || isnan(q[0]) ||
402	+	isinf(q[1]) || isnan(q[1]) ||
403	+	isinf(q[2]) || isnan(q[2]) ||
404	+	isinf(q[3]) || isnan(q[3]) ) {
405	+	sprintf( painCave.errMsg,
406	+	"DumpWriter detected a numerical error writing the quaternion"
407	+	" for object %d", index);
408	+	painCave.isFatal = 1;
409	+	simError();
410	+	}
411	+
412		ji = integrableObject->getJ();
413	+
414	+	if (isinf(ji[0]) || isnan(ji[0]) ||
415	+	isinf(ji[1]) || isnan(ji[1]) ||
416	+	isinf(ji[2]) || isnan(ji[2]) ) {
417	+	sprintf( painCave.errMsg,
418	+	"DumpWriter detected a numerical error writing the angular"
419	+	" momentum for object %d", index);
420	+	painCave.isFatal = 1;
421	+	simError();
422	+	}
423	+
424		sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
425		q[0], q[1], q[2], q[3],
426		ji[0], ji[1], ji[2]);
#	Line 331 | Line 428 | namespace oopse {
428		}
429
430		if (needForceVector_) {
431	<	type += "ft";
431	>	type += "f";
432		Vector3d frc;
433	<	Vector3d trq;
433	>
434		frc = integrableObject->getFrc();
435	<	trq = integrableObject->getTrq();
436	<
437	<	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e",
438	<	frc[0], frc[1], frc[2],
439	<	trq[0], trq[1], trq[2]);
435	>
436	>	if (isinf(frc[0]) || isnan(frc[0]) ||
437	>	isinf(frc[1]) || isnan(frc[1]) ||
438	>	isinf(frc[2]) || isnan(frc[2]) ) {
439	>	sprintf( painCave.errMsg,
440	>	"DumpWriter detected a numerical error writing the force"
441	>	" for object %d", index);
442	>	painCave.isFatal = 1;
443	>	simError();
444	>	}
445	>	sprintf(tempBuffer, " %13e %13e %13e",
446	>	frc[0], frc[1], frc[2]);
447		line += tempBuffer;
448	+
449	+	if (integrableObject->isDirectional()) {
450	+	type += "t";
451	+	Vector3d trq;
452	+
453	+	trq = integrableObject->getTrq();
454	+
455	+	if (isinf(trq[0]) || isnan(trq[0]) ||
456	+	isinf(trq[1]) || isnan(trq[1]) ||
457	+	isinf(trq[2]) || isnan(trq[2]) ) {
458	+	sprintf( painCave.errMsg,
459	+	"DumpWriter detected a numerical error writing the torque"
460	+	" for object %d", index);
461	+	painCave.isFatal = 1;
462	+	simError();
463	+	}
464	+
465	+	sprintf(tempBuffer, " %13e %13e %13e",
466	+	trq[0], trq[1], trq[2]);
467	+	line += tempBuffer;
468	+	}
469		}
470	<
470	>	if (needParticlePot_) {
471	>	type += "u";
472	>	RealType particlePot;
473	>
474	>	particlePot = integrableObject->getParticlePot();
475	>
476	>	if (isinf(particlePot) || isnan(particlePot)) {
477	>	sprintf( painCave.errMsg,
478	>	"DumpWriter detected a numerical error writing the particle "
479	>	" potential for object %d", index);
480	>	painCave.isFatal = 1;
481	>	simError();
482	>	}
483	>	sprintf(tempBuffer, " %13e", particlePot);
484	>	line += tempBuffer;
485	>	}
486	>
487		sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
488		return std::string(tempBuffer);
489		}
#	Line 424 | Line 565 | namespace oopse {
565		newOStream = new std::ofstream(filename.c_str());
566		#endif
567		//write out MetaData first
568	<	(*newOStream) << "<OOPSE version=4>" << std::endl;
568	>	(*newOStream) << "<OpenMD version=1>" << std::endl;
569		(*newOStream) << "  <MetaData>" << std::endl;
570		(*newOStream) << info_->getRawMetaData();
571		(*newOStream) << "  </MetaData>" << std::endl;
#	Line 433 | Line 574 | namespace oopse {
574
575		void DumpWriter::writeClosing(std::ostream& os) {
576
577	<	os << "</OOPSE>\n";
577	>	os << "</OpenMD>\n";
578		os.flush();
579		}
580
581	<	}//end namespace oopse
581	>	}//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 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 0 | Line 1
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