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

Comparing:
trunk/src/io/DumpWriter.cpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 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 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
53	>	#endif
54
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 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 134 | 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 194 | Line 226 | namespace OpenMD {
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),
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	<	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, 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", 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++) {
278	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
279	>	sprintf( painCave.errMsg,
280	>	"DumpWriter detected a numerical error writing the barostat");
281	>	painCave.isFatal = 1;
282	>	simError();
283	>	}
284	>	}
285	>	}
286	>
287		sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
288		eta(0, 0), eta(1, 0), eta(2, 0),
289		eta(0, 1), eta(1, 1), eta(2, 1),
#	Line 231 | 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 248 | 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 265 | 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 273 | Line 373 | namespace OpenMD {
373
374		os << buffer;
375
276	–	int nProc;
277	–	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 296 | 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 314 | Line 419 | namespace OpenMD {
419		Vector3d pos;
420		Vector3d vel;
421		pos = integrableObject->getPos();
422	+
423	+	if (isinf(pos[0]) || isnan(pos[0]) ||
424	+	isinf(pos[1]) || isnan(pos[1]) ||
425	+	isinf(pos[2]) || isnan(pos[2]) ) {
426	+	sprintf( painCave.errMsg,
427	+	"DumpWriter detected a numerical error writing the position"
428	+	" for object %d", index);
429	+	painCave.isFatal = 1;
430	+	simError();
431	+	}
432	+
433		vel = integrableObject->getVel();
434	+
435	+	if (isinf(vel[0]) || isnan(vel[0]) ||
436	+	isinf(vel[1]) || isnan(vel[1]) ||
437	+	isinf(vel[2]) || isnan(vel[2]) ) {
438	+	sprintf( painCave.errMsg,
439	+	"DumpWriter detected a numerical error writing the velocity"
440	+	" for object %d", index);
441	+	painCave.isFatal = 1;
442	+	simError();
443	+	}
444	+
445		sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
446		pos[0], pos[1], pos[2],
447		vel[0], vel[1], vel[2]);
#	Line 325 | Line 452 | namespace OpenMD {
452		Quat4d q;
453		Vector3d ji;
454		q = integrableObject->getQ();
455	+
456	+	if (isinf(q[0]) || isnan(q[0]) ||
457	+	isinf(q[1]) || isnan(q[1]) ||
458	+	isinf(q[2]) || isnan(q[2]) ||
459	+	isinf(q[3]) || isnan(q[3]) ) {
460	+	sprintf( painCave.errMsg,
461	+	"DumpWriter detected a numerical error writing the quaternion"
462	+	" for object %d", index);
463	+	painCave.isFatal = 1;
464	+	simError();
465	+	}
466	+
467		ji = integrableObject->getJ();
468	+
469	+	if (isinf(ji[0]) || isnan(ji[0]) ||
470	+	isinf(ji[1]) || isnan(ji[1]) ||
471	+	isinf(ji[2]) || isnan(ji[2]) ) {
472	+	sprintf( painCave.errMsg,
473	+	"DumpWriter detected a numerical error writing the angular"
474	+	" momentum for object %d", index);
475	+	painCave.isFatal = 1;
476	+	simError();
477	+	}
478	+
479		sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
480		q[0], q[1], q[2], q[3],
481		ji[0], ji[1], ji[2]);
#	Line 333 | Line 483 | namespace OpenMD {
483		}
484
485		if (needForceVector_) {
486	<	type += "ft";
487	<	Vector3d frc;
488	<	Vector3d trq;
489	<	frc = integrableObject->getFrc();
490	<	trq = integrableObject->getTrq();
491	<
492	<	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e",
493	<	frc[0], frc[1], frc[2],
494	<	trq[0], trq[1], trq[2]);
486	>	type += "f";
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]) ) {
491	>	sprintf( painCave.errMsg,
492	>	"DumpWriter detected a numerical error writing the force"
493	>	" for object %d", index);
494	>	painCave.isFatal = 1;
495	>	simError();
496	>	}
497	>	sprintf(tempBuffer, " %13e %13e %13e",
498	>	frc[0], frc[1], frc[2]);
499		line += tempBuffer;
500	+
501	+	if (integrableObject->isDirectional()) {
502	+	type += "t";
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]) ) {
507	+	sprintf( painCave.errMsg,
508	+	"DumpWriter detected a numerical error writing the torque"
509	+	" for object %d", index);
510	+	painCave.isFatal = 1;
511	+	simError();
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 426 | 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 1390 by gezelter, Wed Nov 25 20:02:06 2009 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
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