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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 1752 by gezelter, Sun Jun 10 14:05:02 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	>	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	+
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),
#	Line 207 | Line 259 | namespace oopse {
259
260		RealType chi = s->getChi();
261		RealType integralOfChiDt = s->getIntegralOfChiDt();
262	+	if (isinf(chi) || isnan(chi) ||
263	+	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
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", chi, integralOfChiDt);
270		os << buffer;
271
272		Mat3x3d eta;
273		eta = s->getEta();
274	+
275	+	for (unsigned int i = 0; i < 3; i++) {
276	+	for (unsigned int j = 0; j < 3; j++) {
277	+	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
278	+	sprintf( painCave.errMsg,
279	+	"DumpWriter detected a numerical error writing the barostat");
280	+	painCave.isFatal = 1;
281	+	simError();
282	+	}
283	+	}
284	+	}
285	+
286		sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
287		eta(0, 0), eta(1, 0), eta(2, 0),
288		eta(0, 1), eta(1, 1), eta(2, 1),
#	Line 231 | Line 302 | namespace oopse {
302		StuntDouble* integrableObject;
303		SimInfo::MoleculeIterator mi;
304		Molecule::IntegrableObjectIterator ii;
305	+	RigidBody::AtomIterator ai;
306	+	Atom* atom;
307
308		#ifndef IS_MPI
309		os << "  <Snapshot>\n";
#	Line 240 | Line 313 | namespace oopse {
313		os << "    <StuntDoubles>\n";
314		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
315
316	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
316	>
317	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
318		integrableObject = mol->nextIntegrableObject(ii)) {
319	<	os << prepareDumpLine(integrableObject);
320	<
319	>	os << prepareDumpLine(integrableObject);
320	>
321		}
322		}
323		os << "    </StuntDoubles>\n";
324
325	+	if (doSiteData_) {
326	+	os << "    <SiteData>\n";
327	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
328	+
329	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
330	+	integrableObject = mol->nextIntegrableObject(ii)) {
331	+
332	+	int ioIndex = integrableObject->getGlobalIntegrableObjectIndex();
333	+	// do one for the IO itself
334	+	os << prepareSiteLine(integrableObject, ioIndex, 0);
335	+
336	+	if (integrableObject->isRigidBody()) {
337	+
338	+	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
339	+	int siteIndex = 0;
340	+	for (atom = rb->beginAtom(ai); atom != NULL;
341	+	atom = rb->nextAtom(ai)) {
342	+	os << prepareSiteLine(atom, ioIndex, siteIndex);
343	+	siteIndex++;
344	+	}
345	+	}
346	+	}
347	+	}
348	+	os << "    </SiteData>\n";
349	+	}
350		os << "  </Snapshot>\n";
351
352		os.flush();
#	Line 255 | Line 354 | namespace oopse {
354		//every node prepares the dump lines for integrable objects belong to itself
355		std::string buffer;
356		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
357	<
357	>
358	>
359		for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
360		integrableObject = mol->nextIntegrableObject(ii)) {
361	<	buffer += prepareDumpLine(integrableObject);
361	>	buffer += prepareDumpLine(integrableObject);
362		}
363		}
364
365		const int masterNode = 0;
366	<
366	>	int nProc;
367	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
368		if (worldRank == masterNode) {
369		os << "  <Snapshot>\n";
370		writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
#	Line 271 | Line 372 | namespace oopse {
372
373		os << buffer;
374
274	–	int nProc;
275	–	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
375		for (int i = 1; i < nProc; ++i) {
376
377		// receive the length of the string buffer that was
378		// prepared by processor i
379
380	+	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
381		int recvLength;
382		MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
383		char* recvBuffer = new char[recvLength];
#	Line 285 | Line 385 | namespace oopse {
385		} else {
386		MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
387		os << recvBuffer;
388	<	delete recvBuffer;
388	>	delete [] recvBuffer;
389		}
390		}
391		os << "    </StuntDoubles>\n";
#	Line 294 | Line 394 | namespace oopse {
394		os.flush();
395		} else {
396		int sendBufferLength = buffer.size() + 1;
397	<	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
398	<	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
397	>	int myturn = 0;
398	>	for (int i = 1; i < nProc; ++i){
399	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
400	>	if (myturn == worldRank){
401	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
402	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
403	>	}
404	>	}
405		}
406
407		#endif // is_mpi
#	Line 312 | Line 418 | namespace oopse {
418		Vector3d pos;
419		Vector3d vel;
420		pos = integrableObject->getPos();
421	+
422	+	if (isinf(pos[0]) || isnan(pos[0]) ||
423	+	isinf(pos[1]) || isnan(pos[1]) ||
424	+	isinf(pos[2]) || isnan(pos[2]) ) {
425	+	sprintf( painCave.errMsg,
426	+	"DumpWriter detected a numerical error writing the position"
427	+	" for object %d", index);
428	+	painCave.isFatal = 1;
429	+	simError();
430	+	}
431	+
432		vel = integrableObject->getVel();
433	+
434	+	if (isinf(vel[0]) || isnan(vel[0]) ||
435	+	isinf(vel[1]) || isnan(vel[1]) ||
436	+	isinf(vel[2]) || isnan(vel[2]) ) {
437	+	sprintf( painCave.errMsg,
438	+	"DumpWriter detected a numerical error writing the velocity"
439	+	" for object %d", index);
440	+	painCave.isFatal = 1;
441	+	simError();
442	+	}
443	+
444		sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
445		pos[0], pos[1], pos[2],
446		vel[0], vel[1], vel[2]);
#	Line 323 | Line 451 | namespace oopse {
451		Quat4d q;
452		Vector3d ji;
453		q = integrableObject->getQ();
454	+
455	+	if (isinf(q[0]) || isnan(q[0]) ||
456	+	isinf(q[1]) || isnan(q[1]) ||
457	+	isinf(q[2]) || isnan(q[2]) ||
458	+	isinf(q[3]) || isnan(q[3]) ) {
459	+	sprintf( painCave.errMsg,
460	+	"DumpWriter detected a numerical error writing the quaternion"
461	+	" for object %d", index);
462	+	painCave.isFatal = 1;
463	+	simError();
464	+	}
465	+
466		ji = integrableObject->getJ();
467	+
468	+	if (isinf(ji[0]) || isnan(ji[0]) ||
469	+	isinf(ji[1]) || isnan(ji[1]) ||
470	+	isinf(ji[2]) || isnan(ji[2]) ) {
471	+	sprintf( painCave.errMsg,
472	+	"DumpWriter detected a numerical error writing the angular"
473	+	" momentum for object %d", index);
474	+	painCave.isFatal = 1;
475	+	simError();
476	+	}
477	+
478		sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
479		q[0], q[1], q[2], q[3],
480		ji[0], ji[1], ji[2]);
#	Line 331 | Line 482 | namespace oopse {
482		}
483
484		if (needForceVector_) {
485	<	type += "ft";
486	<	Vector3d frc;
487	<	Vector3d trq;
488	<	frc = integrableObject->getFrc();
489	<	trq = integrableObject->getTrq();
490	<
491	<	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e",
492	<	frc[0], frc[1], frc[2],
493	<	trq[0], trq[1], trq[2]);
485	>	type += "f";
486	>	Vector3d frc = integrableObject->getFrc();
487	>	if (isinf(frc[0]) || isnan(frc[0]) ||
488	>	isinf(frc[1]) || isnan(frc[1]) ||
489	>	isinf(frc[2]) || isnan(frc[2]) ) {
490	>	sprintf( painCave.errMsg,
491	>	"DumpWriter detected a numerical error writing the force"
492	>	" for object %d", index);
493	>	painCave.isFatal = 1;
494	>	simError();
495	>	}
496	>	sprintf(tempBuffer, " %13e %13e %13e",
497	>	frc[0], frc[1], frc[2]);
498		line += tempBuffer;
499	+
500	+	if (integrableObject->isDirectional()) {
501	+	type += "t";
502	+	Vector3d trq = integrableObject->getTrq();
503	+	if (isinf(trq[0]) || isnan(trq[0]) ||
504	+	isinf(trq[1]) || isnan(trq[1]) ||
505	+	isinf(trq[2]) || isnan(trq[2]) ) {
506	+	sprintf( painCave.errMsg,
507	+	"DumpWriter detected a numerical error writing the torque"
508	+	" for object %d", index);
509	+	painCave.isFatal = 1;
510	+	simError();
511	+	}
512	+	sprintf(tempBuffer, " %13e %13e %13e",
513	+	trq[0], trq[1], trq[2]);
514	+	line += tempBuffer;
515	+	}
516		}
517	<
517	>
518		sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
519		return std::string(tempBuffer);
520		}
521
522	+	std::string DumpWriter::prepareSiteLine(StuntDouble* integrableObject, int ioIndex, int siteIndex) {
523	+
524	+
525	+	std::string id;
526	+	std::string type;
527	+	std::string line;
528	+	char tempBuffer[4096];
529	+
530	+	if (integrableObject->isRigidBody()) {
531	+	sprintf(tempBuffer, "%10d           ", ioIndex);
532	+	id = std::string(tempBuffer);
533	+	} else {
534	+	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
535	+	id = std::string(tempBuffer);
536	+	}
537	+
538	+	if (needFlucQ_) {
539	+	type += "cw";
540	+	RealType fqPos = integrableObject->getFlucQPos();
541	+	if (isinf(fqPos) || isnan(fqPos) ) {
542	+	sprintf( painCave.errMsg,
543	+	"DumpWriter detected a numerical error writing the"
544	+	" fluctuating charge for object %s", id.c_str());
545	+	painCave.isFatal = 1;
546	+	simError();
547	+	}
548	+	sprintf(tempBuffer, " %13e ", fqPos);
549	+	line += tempBuffer;
550	+
551	+	RealType fqVel = integrableObject->getFlucQVel();
552	+	if (isinf(fqVel) || isnan(fqVel) ) {
553	+	sprintf( painCave.errMsg,
554	+	"DumpWriter detected a numerical error writing the"
555	+	" fluctuating charge velocity for object %s", id.c_str());
556	+	painCave.isFatal = 1;
557	+	simError();
558	+	}
559	+	sprintf(tempBuffer, " %13e ", fqVel);
560	+	line += tempBuffer;
561	+
562	+	if (needForceVector_) {
563	+	type += "g";
564	+	RealType fqFrc = integrableObject->getFlucQFrc();
565	+	if (isinf(fqFrc) || isnan(fqFrc) ) {
566	+	sprintf( painCave.errMsg,
567	+	"DumpWriter detected a numerical error writing the"
568	+	" fluctuating charge force for object %s", id.c_str());
569	+	painCave.isFatal = 1;
570	+	simError();
571	+	}
572	+	sprintf(tempBuffer, " %13e ", fqFrc);
573	+	line += tempBuffer;
574	+	}
575	+	}
576	+
577	+	if (needElectricField_) {
578	+	type += "e";
579	+	Vector3d eField= integrableObject->getElectricField();
580	+	if (isinf(eField[0]) || isnan(eField[0]) ||
581	+	isinf(eField[1]) || isnan(eField[1]) ||
582	+	isinf(eField[2]) || isnan(eField[2]) ) {
583	+	sprintf( painCave.errMsg,
584	+	"DumpWriter detected a numerical error writing the electric"
585	+	" field for object %s", id.c_str());
586	+	painCave.isFatal = 1;
587	+	simError();
588	+	}
589	+	sprintf(tempBuffer, " %13e %13e %13e",
590	+	eField[0], eField[1], eField[2]);
591	+	line += tempBuffer;
592	+	}
593	+
594	+
595	+	if (needParticlePot_) {
596	+	type += "u";
597	+	RealType particlePot = integrableObject->getParticlePot();
598	+	if (isinf(particlePot) || isnan(particlePot)) {
599	+	sprintf( painCave.errMsg,
600	+	"DumpWriter detected a numerical error writing the particle "
601	+	" potential for object %s", id.c_str());
602	+	painCave.isFatal = 1;
603	+	simError();
604	+	}
605	+	sprintf(tempBuffer, " %13e", particlePot);
606	+	line += tempBuffer;
607	+	}
608	+
609	+
610	+	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
611	+	return std::string(tempBuffer);
612	+	}
613	+
614		void DumpWriter::writeDump() {
615		writeFrame(*dumpFile_);
616		}
#	Line 424 | Line 688 | namespace oopse {
688		newOStream = new std::ofstream(filename.c_str());
689		#endif
690		//write out MetaData first
691	<	(*newOStream) << "<OOPSE version=4>" << std::endl;
691	>	(*newOStream) << "<OpenMD version=2>" << std::endl;
692		(*newOStream) << "  <MetaData>" << std::endl;
693		(*newOStream) << info_->getRawMetaData();
694		(*newOStream) << "  </MetaData>" << std::endl;
#	Line 433 | Line 697 | namespace oopse {
697
698		void DumpWriter::writeClosing(std::ostream& os) {
699
700	<	os << "</OOPSE>\n";
700	>	os << "</OpenMD>\n";
701		os.flush();
702		}
703
704	<	}//end namespace oopse
704	>	}//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 1752 by gezelter, Sun Jun 10 14:05:02 2012 UTC

#	Line 0 | Line 1
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