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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 1764 by gezelter, Tue Jul 3 18:32:27 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 49 | Line 50
50
51		#ifdef IS_MPI
52		#include <mpi.h>
53	<	#endif //is_mpi
53	>	#endif
54
55		using namespace std;
56		namespace OpenMD {
#	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 227 | Line 257 | namespace OpenMD {
257		hmat(0, 2), hmat(1, 2), hmat(2, 2));
258		os << buffer;
259
260	<	RealType chi = s->getChi();
261	<	RealType integralOfChiDt = s->getIntegralOfChiDt();
262	<	if (isinf(chi) || isnan(chi) ||
263	<	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
260	>	pair<RealType, RealType> thermostat = s->getThermostat();
261	>
262	>	if (isinf(thermostat.first)  || isnan(thermostat.first) ||
263	>	isinf(thermostat.second) || isnan(thermostat.second)) {
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);
269	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
270	>	thermostat.second);
271		os << buffer;
272
273		Mat3x3d eta;
274	<	eta = s->getEta();
274	>	eta = s->getBarostat();
275
276		for (unsigned int i = 0; i < 3; i++) {
277		for (unsigned int j = 0; j < 3; j++) {
#	Line 272 | Line 303 | namespace OpenMD {
303		StuntDouble* integrableObject;
304		SimInfo::MoleculeIterator mi;
305		Molecule::IntegrableObjectIterator ii;
306	+	RigidBody::AtomIterator ai;
307	+	Atom* atom;
308
309		#ifndef IS_MPI
310		os << "  <Snapshot>\n";
#	Line 289 | Line 322 | namespace OpenMD {
322		}
323		}
324		os << "    </StuntDoubles>\n";
325	<
325	>
326	>	if (doSiteData_) {
327	>	os << "    <SiteData>\n";
328	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
329	>
330	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
331	>	integrableObject = mol->nextIntegrableObject(ii)) {
332	>
333	>	int ioIndex = integrableObject->getGlobalIntegrableObjectIndex();
334	>	// do one for the IO itself
335	>	os << prepareSiteLine(integrableObject, ioIndex, 0);
336	>
337	>	if (integrableObject->isRigidBody()) {
338	>
339	>	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
340	>	int siteIndex = 0;
341	>	for (atom = rb->beginAtom(ai); atom != NULL;
342	>	atom = rb->nextAtom(ai)) {
343	>	os << prepareSiteLine(atom, ioIndex, siteIndex);
344	>	siteIndex++;
345	>	}
346	>	}
347	>	}
348	>	}
349	>	os << "    </SiteData>\n";
350	>	}
351		os << "  </Snapshot>\n";
352
353		os.flush();
#	Line 306 | Line 364 | namespace OpenMD {
364		}
365
366		const int masterNode = 0;
367	<
367	>	int nProc;
368	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
369		if (worldRank == masterNode) {
370		os << "  <Snapshot>\n";
371		writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
#	Line 314 | Line 373 | namespace OpenMD {
373
374		os << buffer;
375
317	–	int nProc;
318	–	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
376		for (int i = 1; i < nProc; ++i) {
377
378		// receive the length of the string buffer that was
379		// prepared by processor i
380
381	+	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
382		int recvLength;
383		MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
384		char* recvBuffer = new char[recvLength];
#	Line 337 | Line 395 | namespace OpenMD {
395		os.flush();
396		} else {
397		int sendBufferLength = buffer.size() + 1;
398	<	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
399	<	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
398	>	int myturn = 0;
399	>	for (int i = 1; i < nProc; ++i){
400	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
401	>	if (myturn == worldRank){
402	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
403	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
404	>	}
405	>	}
406		}
407
408		#endif // is_mpi
#	Line 420 | Line 484 | namespace OpenMD {
484
485		if (needForceVector_) {
486		type += "f";
487	<	Vector3d frc;
424	<
425	<	frc = integrableObject->getFrc();
426	<
487	>	Vector3d frc = integrableObject->getFrc();
488		if (isinf(frc[0]) || isnan(frc[0]) ||
489		isinf(frc[1]) || isnan(frc[1]) ||
490		isinf(frc[2]) || isnan(frc[2]) ) {
#	Line 439 | Line 500 | namespace OpenMD {
500
501		if (integrableObject->isDirectional()) {
502		type += "t";
503	<	Vector3d trq;
443	<
444	<	trq = integrableObject->getTrq();
445	<
503	>	Vector3d trq = integrableObject->getTrq();
504		if (isinf(trq[0]) || isnan(trq[0]) ||
505		isinf(trq[1]) || isnan(trq[1]) ||
506		isinf(trq[2]) || isnan(trq[2]) ) {
#	Line 451 | Line 509 | namespace OpenMD {
509		" for object %d", index);
510		painCave.isFatal = 1;
511		simError();
512	<	}
455	<
512	>	}
513		sprintf(tempBuffer, " %13e %13e %13e",
514		trq[0], trq[1], trq[2]);
515		line += tempBuffer;
516		}
517		}
518	<
518	>
519		sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
520		return std::string(tempBuffer);
521		}
522
523	+	std::string DumpWriter::prepareSiteLine(StuntDouble* integrableObject, int ioIndex, int siteIndex) {
524	+
525	+
526	+	std::string id;
527	+	std::string type;
528	+	std::string line;
529	+	char tempBuffer[4096];
530	+
531	+	if (integrableObject->isRigidBody()) {
532	+	sprintf(tempBuffer, "%10d           ", ioIndex);
533	+	id = std::string(tempBuffer);
534	+	} else {
535	+	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
536	+	id = std::string(tempBuffer);
537	+	}
538	+
539	+	if (needFlucQ_) {
540	+	type += "cw";
541	+	RealType fqPos = integrableObject->getFlucQPos();
542	+	if (isinf(fqPos) || isnan(fqPos) ) {
543	+	sprintf( painCave.errMsg,
544	+	"DumpWriter detected a numerical error writing the"
545	+	" fluctuating charge for object %s", id.c_str());
546	+	painCave.isFatal = 1;
547	+	simError();
548	+	}
549	+	sprintf(tempBuffer, " %13e ", fqPos);
550	+	line += tempBuffer;
551	+
552	+	RealType fqVel = integrableObject->getFlucQVel();
553	+	if (isinf(fqVel) || isnan(fqVel) ) {
554	+	sprintf( painCave.errMsg,
555	+	"DumpWriter detected a numerical error writing the"
556	+	" fluctuating charge velocity for object %s", id.c_str());
557	+	painCave.isFatal = 1;
558	+	simError();
559	+	}
560	+	sprintf(tempBuffer, " %13e ", fqVel);
561	+	line += tempBuffer;
562	+
563	+	if (needForceVector_) {
564	+	type += "g";
565	+	RealType fqFrc = integrableObject->getFlucQFrc();
566	+	if (isinf(fqFrc) || isnan(fqFrc) ) {
567	+	sprintf( painCave.errMsg,
568	+	"DumpWriter detected a numerical error writing the"
569	+	" fluctuating charge force for object %s", id.c_str());
570	+	painCave.isFatal = 1;
571	+	simError();
572	+	}
573	+	sprintf(tempBuffer, " %13e ", fqFrc);
574	+	line += tempBuffer;
575	+	}
576	+	}
577	+
578	+	if (needElectricField_) {
579	+	type += "e";
580	+	Vector3d eField= integrableObject->getElectricField();
581	+	if (isinf(eField[0]) || isnan(eField[0]) ||
582	+	isinf(eField[1]) || isnan(eField[1]) ||
583	+	isinf(eField[2]) || isnan(eField[2]) ) {
584	+	sprintf( painCave.errMsg,
585	+	"DumpWriter detected a numerical error writing the electric"
586	+	" field for object %s", id.c_str());
587	+	painCave.isFatal = 1;
588	+	simError();
589	+	}
590	+	sprintf(tempBuffer, " %13e %13e %13e",
591	+	eField[0], eField[1], eField[2]);
592	+	line += tempBuffer;
593	+	}
594	+
595	+
596	+	if (needParticlePot_) {
597	+	type += "u";
598	+	RealType particlePot = integrableObject->getParticlePot();
599	+	if (isinf(particlePot) || isnan(particlePot)) {
600	+	sprintf( painCave.errMsg,
601	+	"DumpWriter detected a numerical error writing the particle "
602	+	" potential for object %s", id.c_str());
603	+	painCave.isFatal = 1;
604	+	simError();
605	+	}
606	+	sprintf(tempBuffer, " %13e", particlePot);
607	+	line += tempBuffer;
608	+	}
609	+
610	+
611	+	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
612	+	return std::string(tempBuffer);
613	+	}
614	+
615		void DumpWriter::writeDump() {
616		writeFrame(*dumpFile_);
617		}
#	Line 540 | Line 689 | namespace OpenMD {
689		newOStream = new std::ofstream(filename.c_str());
690		#endif
691		//write out MetaData first
692	<	(*newOStream) << "<OpenMD version=1>" << std::endl;
692	>	(*newOStream) << "<OpenMD version=2>" << std::endl;
693		(*newOStream) << "  <MetaData>" << std::endl;
694		(*newOStream) << info_->getRawMetaData();
695		(*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 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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