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

Comparing:
trunk/src/io/DumpWriter.cpp (file contents), Revision 1437 by gezelter, Wed Apr 21 14:59:18 2010 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1752 by gezelter, Sun Jun 10 14:05:02 2012 UTC

#	Line 36 | Line 36
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).
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 58 | Line 59 | namespace OpenMD {
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 97 | Line 108 | namespace OpenMD {
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 136 | Line 157 | namespace OpenMD {
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 272 | Line 302 | namespace OpenMD {
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 289 | Line 321 | namespace OpenMD {
321		}
322		}
323		os << "    </StuntDoubles>\n";
324	<
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 306 | Line 363 | namespace OpenMD {
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 314 | Line 372 | namespace OpenMD {
372
373		os << buffer;
374
317	–	int nProc;
318	–	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 337 | Line 394 | namespace OpenMD {
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 420 | Line 483 | namespace OpenMD {
483
484		if (needForceVector_) {
485		type += "f";
486	<	Vector3d frc;
424	<
425	<	frc = integrableObject->getFrc();
426	<
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]) ) {
#	Line 439 | Line 499 | namespace OpenMD {
499
500		if (integrableObject->isDirectional()) {
501		type += "t";
502	<	Vector3d trq;
443	<
444	<	trq = integrableObject->getTrq();
445	<
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]) ) {
#	Line 451 | Line 508 | namespace OpenMD {
508		" for object %d", index);
509		painCave.isFatal = 1;
510		simError();
511	<	}
455	<
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 540 | Line 688 | namespace OpenMD {
688		newOStream = new std::ofstream(filename.c_str());
689		#endif
690		//write out MetaData first
691	<	(*newOStream) << "<OpenMD version=1>" << std::endl;
691	>	(*newOStream) << "<OpenMD version=2>" << std::endl;
692		(*newOStream) << "  <MetaData>" << std::endl;
693		(*newOStream) << info_->getRawMetaData();
694		(*newOStream) << "  </MetaData>" << std::endl;

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 1437 by gezelter, Wed Apr 21 14:59:18 2010 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
1	+	Author Id Revision Date

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