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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 1714 by gezelter, Sat May 19 18:12:46 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
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		createDumpFile_ = true;
69		#ifdef HAVE_LIBZ
70		if (needCompression_) {
#	Line 95 | Line 102 | namespace oopse {
102		Globals* simParams = info->getSimParams();
103		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
104
105	<	needCompression_ = simParams->getCompressDumpFile();
106	<	needForceVector_ = simParams->getOutputForceVector();
105	>	needCompression_   = simParams->getCompressDumpFile();
106	>	needForceVector_   = simParams->getOutputForceVector();
107	>	needParticlePot_   = simParams->getOutputParticlePotential();
108	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
109	>	needElectricField_ = simParams->getOutputElectricField();
110	>
111		createDumpFile_ = true;
112		#ifdef HAVE_LIBZ
113		if (needCompression_) {
#	Line 134 | Line 145 | namespace oopse {
145		Globals* simParams = info->getSimParams();
146		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
147
148	<	needCompression_ = simParams->getCompressDumpFile();
149	<	needForceVector_ = simParams->getOutputForceVector();
150	<
148	>	needCompression_   = simParams->getCompressDumpFile();
149	>	needForceVector_   = simParams->getOutputForceVector();
150	>	needParticlePot_   = simParams->getOutputParticlePotential();
151	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
152	>	needElectricField_ = simParams->getOutputElectricField();
153	>
154		#ifdef HAVE_LIBZ
155		if (needCompression_) {
156		filename_ += ".gz";
#	Line 194 | Line 208 | namespace oopse {
208		os << "    <FrameData>\n";
209
210		RealType currentTime = s->getTime();
211	+
212	+	if (isinf(currentTime) || isnan(currentTime)) {
213	+	sprintf( painCave.errMsg,
214	+	"DumpWriter detected a numerical error writing the time");
215	+	painCave.isFatal = 1;
216	+	simError();
217	+	}
218	+
219		sprintf(buffer, "        Time: %.10g\n", currentTime);
220		os << buffer;
221
222		Mat3x3d hmat;
223		hmat = s->getHmat();
224	+
225	+	for (unsigned int i = 0; i < 3; i++) {
226	+	for (unsigned int j = 0; j < 3; j++) {
227	+	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
228	+	sprintf( painCave.errMsg,
229	+	"DumpWriter detected a numerical error writing the box");
230	+	painCave.isFatal = 1;
231	+	simError();
232	+	}
233	+	}
234	+	}
235	+
236		sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
237		hmat(0, 0), hmat(1, 0), hmat(2, 0),
238		hmat(0, 1), hmat(1, 1), hmat(2, 1),
#	Line 207 | Line 241 | namespace oopse {
241
242		RealType chi = s->getChi();
243		RealType integralOfChiDt = s->getIntegralOfChiDt();
244	+	if (isinf(chi) || isnan(chi) ||
245	+	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
246	+	sprintf( painCave.errMsg,
247	+	"DumpWriter detected a numerical error writing the thermostat");
248	+	painCave.isFatal = 1;
249	+	simError();
250	+	}
251		sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
252		os << buffer;
253
254		Mat3x3d eta;
255		eta = s->getEta();
256	+
257	+	for (unsigned int i = 0; i < 3; i++) {
258	+	for (unsigned int j = 0; j < 3; j++) {
259	+	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
260	+	sprintf( painCave.errMsg,
261	+	"DumpWriter detected a numerical error writing the barostat");
262	+	painCave.isFatal = 1;
263	+	simError();
264	+	}
265	+	}
266	+	}
267	+
268		sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
269		eta(0, 0), eta(1, 0), eta(2, 0),
270		eta(0, 1), eta(1, 1), eta(2, 1),
#	Line 240 | Line 293 | namespace oopse {
293		os << "    <StuntDoubles>\n";
294		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
295
296	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
296	>
297	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
298		integrableObject = mol->nextIntegrableObject(ii)) {
299	<	os << prepareDumpLine(integrableObject);
300	<
299	>	os << prepareDumpLine(integrableObject);
300	>
301		}
302		}
303		os << "    </StuntDoubles>\n";
304	<
304	>
305		os << "  </Snapshot>\n";
306
307		os.flush();
#	Line 255 | Line 309 | namespace oopse {
309		//every node prepares the dump lines for integrable objects belong to itself
310		std::string buffer;
311		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
312	<
312	>
313	>
314		for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
315		integrableObject = mol->nextIntegrableObject(ii)) {
316	<	buffer += prepareDumpLine(integrableObject);
316	>	buffer += prepareDumpLine(integrableObject);
317		}
318		}
319
320		const int masterNode = 0;
321	<
321	>	int nProc;
322	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
323		if (worldRank == masterNode) {
324		os << "  <Snapshot>\n";
325		writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
#	Line 271 | Line 327 | namespace oopse {
327
328		os << buffer;
329
274	–	int nProc;
275	–	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
330		for (int i = 1; i < nProc; ++i) {
331
332		// receive the length of the string buffer that was
333		// prepared by processor i
334
335	+	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
336		int recvLength;
337		MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
338		char* recvBuffer = new char[recvLength];
#	Line 285 | Line 340 | namespace oopse {
340		} else {
341		MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
342		os << recvBuffer;
343	<	delete recvBuffer;
343	>	delete [] recvBuffer;
344		}
345		}
346		os << "    </StuntDoubles>\n";
#	Line 294 | Line 349 | namespace oopse {
349		os.flush();
350		} else {
351		int sendBufferLength = buffer.size() + 1;
352	<	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
353	<	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
352	>	int myturn = 0;
353	>	for (int i = 1; i < nProc; ++i){
354	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
355	>	if (myturn == worldRank){
356	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
357	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
358	>	}
359	>	}
360		}
361
362		#endif // is_mpi
#	Line 312 | Line 373 | namespace oopse {
373		Vector3d pos;
374		Vector3d vel;
375		pos = integrableObject->getPos();
376	+
377	+	if (isinf(pos[0]) || isnan(pos[0]) ||
378	+	isinf(pos[1]) || isnan(pos[1]) ||
379	+	isinf(pos[2]) || isnan(pos[2]) ) {
380	+	sprintf( painCave.errMsg,
381	+	"DumpWriter detected a numerical error writing the position"
382	+	" for object %d", index);
383	+	painCave.isFatal = 1;
384	+	simError();
385	+	}
386	+
387		vel = integrableObject->getVel();
388	+
389	+	if (isinf(vel[0]) || isnan(vel[0]) ||
390	+	isinf(vel[1]) || isnan(vel[1]) ||
391	+	isinf(vel[2]) || isnan(vel[2]) ) {
392	+	sprintf( painCave.errMsg,
393	+	"DumpWriter detected a numerical error writing the velocity"
394	+	" for object %d", index);
395	+	painCave.isFatal = 1;
396	+	simError();
397	+	}
398	+
399		sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
400		pos[0], pos[1], pos[2],
401		vel[0], vel[1], vel[2]);
#	Line 323 | Line 406 | namespace oopse {
406		Quat4d q;
407		Vector3d ji;
408		q = integrableObject->getQ();
409	+
410	+	if (isinf(q[0]) || isnan(q[0]) ||
411	+	isinf(q[1]) || isnan(q[1]) ||
412	+	isinf(q[2]) || isnan(q[2]) ||
413	+	isinf(q[3]) || isnan(q[3]) ) {
414	+	sprintf( painCave.errMsg,
415	+	"DumpWriter detected a numerical error writing the quaternion"
416	+	" for object %d", index);
417	+	painCave.isFatal = 1;
418	+	simError();
419	+	}
420	+
421		ji = integrableObject->getJ();
422	+
423	+	if (isinf(ji[0]) || isnan(ji[0]) ||
424	+	isinf(ji[1]) || isnan(ji[1]) ||
425	+	isinf(ji[2]) || isnan(ji[2]) ) {
426	+	sprintf( painCave.errMsg,
427	+	"DumpWriter detected a numerical error writing the angular"
428	+	" momentum for object %d", index);
429	+	painCave.isFatal = 1;
430	+	simError();
431	+	}
432	+
433		sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
434		q[0], q[1], q[2], q[3],
435		ji[0], ji[1], ji[2]);
#	Line 331 | Line 437 | namespace oopse {
437		}
438
439		if (needForceVector_) {
440	<	type += "ft";
441	<	Vector3d frc;
442	<	Vector3d trq;
443	<	frc = integrableObject->getFrc();
444	<	trq = integrableObject->getTrq();
445	<
446	<	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e",
447	<	frc[0], frc[1], frc[2],
448	<	trq[0], trq[1], trq[2]);
440	>	type += "f";
441	>	Vector3d frc = integrableObject->getFrc();
442	>	if (isinf(frc[0]) || isnan(frc[0]) ||
443	>	isinf(frc[1]) || isnan(frc[1]) ||
444	>	isinf(frc[2]) || isnan(frc[2]) ) {
445	>	sprintf( painCave.errMsg,
446	>	"DumpWriter detected a numerical error writing the force"
447	>	" for object %d", index);
448	>	painCave.isFatal = 1;
449	>	simError();
450	>	}
451	>	sprintf(tempBuffer, " %13e %13e %13e",
452	>	frc[0], frc[1], frc[2]);
453		line += tempBuffer;
454	+
455	+	if (integrableObject->isDirectional()) {
456	+	type += "t";
457	+	Vector3d trq = integrableObject->getTrq();
458	+	if (isinf(trq[0]) || isnan(trq[0]) ||
459	+	isinf(trq[1]) || isnan(trq[1]) ||
460	+	isinf(trq[2]) || isnan(trq[2]) ) {
461	+	sprintf( painCave.errMsg,
462	+	"DumpWriter detected a numerical error writing the torque"
463	+	" for object %d", index);
464	+	painCave.isFatal = 1;
465	+	simError();
466	+	}
467	+	sprintf(tempBuffer, " %13e %13e %13e",
468	+	trq[0], trq[1], trq[2]);
469	+	line += tempBuffer;
470	+	}
471		}
472	<
472	>
473	>	if (needParticlePot_) {
474	>	type += "u";
475	>	RealType particlePot = integrableObject->getParticlePot();
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	>	if (needFlucQ_) {
488	>	type += "cw";
489	>	RealType fqPos = integrableObject->getFlucQPos();
490	>	if (isinf(fqPos) || isnan(fqPos) ) {
491	>	sprintf( painCave.errMsg,
492	>	"DumpWriter detected a numerical error writing the"
493	>	" fluctuating charge for object %d", index);
494	>	painCave.isFatal = 1;
495	>	simError();
496	>	}
497	>	sprintf(tempBuffer, " %13e ", fqPos);
498	>	line += tempBuffer;
499	>
500	>	RealType fqVel = integrableObject->getFlucQVel();
501	>	if (isinf(fqVel) || isnan(fqVel) ) {
502	>	sprintf( painCave.errMsg,
503	>	"DumpWriter detected a numerical error writing the"
504	>	" fluctuating charge velocity for object %d", index);
505	>	painCave.isFatal = 1;
506	>	simError();
507	>	}
508	>	sprintf(tempBuffer, " %13e ", fqVel);
509	>	line += tempBuffer;
510	>
511	>	if (needForceVector_) {
512	>	type += "g";
513	>	RealType fqFrc = integrableObject->getFlucQFrc();
514	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
515	>	sprintf( painCave.errMsg,
516	>	"DumpWriter detected a numerical error writing the"
517	>	" fluctuating charge force for object %d", index);
518	>	painCave.isFatal = 1;
519	>	simError();
520	>	}
521	>	sprintf(tempBuffer, " %13e ", fqFrc);
522	>	line += tempBuffer;
523	>	}
524	>	}
525	>
526	>	if (needElectricField_) {
527	>	type += "e";
528	>	Vector3d eField= integrableObject->getElectricField();
529	>	if (isinf(eField[0]) || isnan(eField[0]) ||
530	>	isinf(eField[1]) || isnan(eField[1]) ||
531	>	isinf(eField[2]) || isnan(eField[2]) ) {
532	>	sprintf( painCave.errMsg,
533	>	"DumpWriter detected a numerical error writing the electric"
534	>	" field for object %d", index);
535	>	painCave.isFatal = 1;
536	>	simError();
537	>	}
538	>	sprintf(tempBuffer, " %13e %13e %13e",
539	>	eField[0], eField[1], eField[2]);
540	>	line += tempBuffer;
541	>	}
542	>
543		sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
544		return std::string(tempBuffer);
545		}
#	Line 424 | Line 621 | namespace oopse {
621		newOStream = new std::ofstream(filename.c_str());
622		#endif
623		//write out MetaData first
624	<	(*newOStream) << "<OOPSE version=4>" << std::endl;
624	>	(*newOStream) << "<OpenMD version=1>" << std::endl;
625		(*newOStream) << "  <MetaData>" << std::endl;
626		(*newOStream) << info_->getRawMetaData();
627		(*newOStream) << "  </MetaData>" << std::endl;
#	Line 433 | Line 630 | namespace oopse {
630
631		void DumpWriter::writeClosing(std::ostream& os) {
632
633	<	os << "</OOPSE>\n";
633	>	os << "</OpenMD>\n";
634		os.flush();
635		}
636
637	<	}//end namespace oopse
637	>	}//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 1714 by gezelter, Sat May 19 18:12:46 2012 UTC

#	Line 0 | Line 1
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