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

Comparing:
trunk/src/io/DumpReader.cpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1769 by gezelter, Mon Jul 9 14:15:52 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		#define _LARGEFILE_SOURCE64
#	Line 57 | Line 58
58		#include "utils/simError.h"
59		#include "utils/MemoryUtils.hpp"
60		#include "utils/StringTokenizer.hpp"
61	+	#include "brains/Thermo.hpp"
62
63		#ifdef IS_MPI
62	–
64		#include <mpi.h>
65	<	#define TAKE_THIS_TAG_CHAR 0
65	<	#define TAKE_THIS_TAG_INT 1
65	>	#endif
66
67	–	#endif // is_mpi
67
69	–
68		namespace OpenMD {
69
70		DumpReader::DumpReader(SimInfo* info, const std::string& filename)
#	Line 142 | Line 140 | namespace OpenMD {
140		prevPos = currPos;
141		bool foundOpenSnapshotTag = false;
142		bool foundClosedSnapshotTag = false;
143	+	bool foundOpenSiteDataTag = false;
144		while(inFile_->getline(buffer, bufferSize)) {
145		++lineNo;
146
#	Line 243 | Line 242 | namespace OpenMD {
242
243		if (needCOMprops_) {
244		Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
245	+	Thermo thermo(info_);
246		Vector3d com;
247	<	Vector3d comvel;
248	<	Vector3d comw;
249	<	if (needPos_ && needVel_){
250	<	info_->getComAll(com, comvel);
251	<	comw = info_->getAngularMomentum();
252	<	}else{
253	<	com = info_->getCom();
254	<	comvel = 0.0;
255	<	comw   = 0.0;
256	<	}
257	<	s->setCOMprops(com, comvel, comw);
247	>
248	>	if (needPos_ && needVel_) {
249	>	Vector3d comvel;
250	>	Vector3d comw;
251	>	thermo.getComAll(com, comvel);
252	>	comw = thermo.getAngularMomentum();
253	>	} else {
254	>	com = thermo.getCom();
255	>	}
256		}
259	–
257		}
258
259		void DumpReader::readSet(int whichFrame) {
#	Line 324 | Line 321 | namespace OpenMD {
321
322		inputStream.getline(buffer, bufferSize);
323		line = buffer;
324	<	if (line.find("</Snapshot>") == std::string::npos) {
325	<	sprintf(painCave.errMsg,
326	<	"DumpReader Error: can not find </Snapshot>\n");
327	<	painCave.isFatal = 1;
328	<	simError();
329	<	}
330	<
324	>
325	>	if (line.find("<SiteData>") != std::string::npos) {
326	>	//read SiteData
327	>	readSiteData(inputStream);
328	>	} else {
329	>	if (line.find("</Snapshot>") == std::string::npos) {
330	>	sprintf(painCave.errMsg,
331	>	"DumpReader Error: can not find </Snapshot>\n");
332	>	painCave.isFatal = 1;
333	>	simError();
334	>	}
335	>	}
336		}
337
338		void DumpReader::parseDumpLine(const std::string& line) {
#	Line 341 | Line 343 | namespace OpenMD {
343
344		nTokens = tokenizer.countTokens();
345
346	<	if (nTokens < 2) {
346	>	if (nTokens < 2) {
347		sprintf(painCave.errMsg,
348		"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
349		painCave.isFatal = 1;
#	Line 350 | Line 352 | namespace OpenMD {
352
353		int index = tokenizer.nextTokenAsInt();
354
355	<	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
355	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
356
357	<	if (integrableObject == NULL) {
357	>	if (sd == NULL) {
358		return;
359		}
360		std::string type = tokenizer.nextToken();
361		int size = type.size();
362
363	+	size_t found;
364	+
365	+	if (needPos_) {
366	+	found = type.find("p");
367	+	if (found == std::string::npos) {
368	+	sprintf(painCave.errMsg,
369	+	"DumpReader Error: StuntDouble %d has no Position\n"
370	+	"\tField (\"p\") specified.\n%s\n", index,
371	+	line.c_str());
372	+	painCave.isFatal = 1;
373	+	simError();
374	+	}
375	+	}
376	+
377	+	if (sd->isDirectional()) {
378	+	if (needQuaternion_) {
379	+	found = type.find("q");
380	+	if (found == std::string::npos) {
381	+	sprintf(painCave.errMsg,
382	+	"DumpReader Error: Directional StuntDouble %d has no\n"
383	+	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
384	+	line.c_str());
385	+	painCave.isFatal = 1;
386	+	simError();
387	+	}
388	+	}
389	+	}
390	+
391		for(int i = 0; i < size; ++i) {
392		switch(type[i]) {
393
#	Line 367 | Line 397 | namespace OpenMD {
397		pos[1] = tokenizer.nextTokenAsDouble();
398		pos[2] = tokenizer.nextTokenAsDouble();
399		if (needPos_) {
400	<	integrableObject->setPos(pos);
400	>	sd->setPos(pos);
401		}
402		break;
403		}
#	Line 377 | Line 407 | namespace OpenMD {
407		vel[1] = tokenizer.nextTokenAsDouble();
408		vel[2] = tokenizer.nextTokenAsDouble();
409		if (needVel_) {
410	<	integrableObject->setVel(vel);
410	>	sd->setVel(vel);
411		}
412		break;
413		}
414
415		case 'q' : {
416		Quat4d q;
417	<	if (integrableObject->isDirectional()) {
417	>	if (sd->isDirectional()) {
418
419		q[0] = tokenizer.nextTokenAsDouble();
420		q[1] = tokenizer.nextTokenAsDouble();
#	Line 403 | Line 433 | namespace OpenMD {
433
434		q.normalize();
435		if (needQuaternion_) {
436	<	integrableObject->setQ(q);
436	>	sd->setQ(q);
437		}
438		}
439		break;
440		}
441		case 'j' : {
442		Vector3d ji;
443	<	if (integrableObject->isDirectional()) {
443	>	if (sd->isDirectional()) {
444		ji[0] = tokenizer.nextTokenAsDouble();
445		ji[1] = tokenizer.nextTokenAsDouble();
446		ji[2] = tokenizer.nextTokenAsDouble();
447		if (needAngMom_) {
448	<	integrableObject->setJ(ji);
448	>	sd->setJ(ji);
449		}
450		}
451		break;
#	Line 426 | Line 456 | namespace OpenMD {
456		force[0] = tokenizer.nextTokenAsDouble();
457		force[1] = tokenizer.nextTokenAsDouble();
458		force[2] = tokenizer.nextTokenAsDouble();
459	<	integrableObject->setFrc(force);
459	>	sd->setFrc(force);
460		break;
461		}
462		case 't' : {
#	Line 435 | Line 465 | namespace OpenMD {
465		torque[0] = tokenizer.nextTokenAsDouble();
466		torque[1] = tokenizer.nextTokenAsDouble();
467		torque[2] = tokenizer.nextTokenAsDouble();
468	<	integrableObject->setTrq(torque);
468	>	sd->setTrq(torque);
469		break;
470		}
471	+	case 'u' : {
472	+
473	+	RealType particlePot;
474	+	particlePot = tokenizer.nextTokenAsDouble();
475	+	sd->setParticlePot(particlePot);
476	+	break;
477	+	}
478	+	case 'c' : {
479	+
480	+	RealType flucQPos;
481	+	flucQPos = tokenizer.nextTokenAsDouble();
482	+	sd->setFlucQPos(flucQPos);
483	+	break;
484	+	}
485	+	case 'w' : {
486	+
487	+	RealType flucQVel;
488	+	flucQVel = tokenizer.nextTokenAsDouble();
489	+	sd->setFlucQVel(flucQVel);
490	+	break;
491	+	}
492	+	case 'g' : {
493	+
494	+	RealType flucQFrc;
495	+	flucQFrc = tokenizer.nextTokenAsDouble();
496	+	sd->setFlucQFrc(flucQFrc);
497	+	break;
498	+	}
499	+	case 'e' : {
500	+
501	+	Vector3d eField;
502	+	eField[0] = tokenizer.nextTokenAsDouble();
503	+	eField[1] = tokenizer.nextTokenAsDouble();
504	+	eField[2] = tokenizer.nextTokenAsDouble();
505	+	sd->setElectricField(eField);
506	+	break;
507	+	}
508		default: {
509		sprintf(painCave.errMsg,
510		"DumpReader Error: %s is an unrecognized type\n", type.c_str());
#	Line 452 | Line 519 | namespace OpenMD {
519		}
520
521
522	<	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
522	>	void DumpReader::parseSiteLine(const std::string& line) {
523
524	+	StringTokenizer tokenizer(line);
525	+	int nTokens;
526	+
527	+	nTokens = tokenizer.countTokens();
528	+
529	+	if (nTokens < 2) {
530	+	sprintf(painCave.errMsg,
531	+	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
532	+	painCave.isFatal = 1;
533	+	simError();
534	+	}
535	+
536	+	/**
537	+	* The first token is the global integrable object index.
538	+	*/
539	+
540	+	int index = tokenizer.nextTokenAsInt();
541	+	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
542	+	if (sd == NULL) {
543	+	return;
544	+	}
545	+
546	+	/**
547	+	* Test to see if the next token is an integer or not.  If not,
548	+	* we've got data on the integrable object itself.  If there is an
549	+	* integer, we're parsing data for a site on a rigid body.
550	+	*/
551	+
552	+	std::string indexTest = tokenizer.peekNextToken();
553	+	std::istringstream i(indexTest);
554	+	int siteIndex;
555	+	if (i >> siteIndex) {
556	+	// chew up this token and parse as an int:
557	+	siteIndex = tokenizer.nextTokenAsInt();
558	+	RigidBody* rb = static_cast<RigidBody*>(sd);
559	+	sd = rb->getAtoms()[siteIndex];
560	+	}
561	+
562	+	/**
563	+	* The next token contains information on what follows.
564	+	*/
565	+	std::string type = tokenizer.nextToken();
566	+	int size = type.size();
567	+
568	+	for(int i = 0; i < size; ++i) {
569	+	switch(type[i]) {
570	+
571	+	case 'u' : {
572	+
573	+	RealType particlePot;
574	+	particlePot = tokenizer.nextTokenAsDouble();
575	+	sd->setParticlePot(particlePot);
576	+	break;
577	+	}
578	+	case 'c' : {
579	+
580	+	RealType flucQPos;
581	+	flucQPos = tokenizer.nextTokenAsDouble();
582	+	sd->setFlucQPos(flucQPos);
583	+	break;
584	+	}
585	+	case 'w' : {
586	+
587	+	RealType flucQVel;
588	+	flucQVel = tokenizer.nextTokenAsDouble();
589	+	sd->setFlucQVel(flucQVel);
590	+	break;
591	+	}
592	+	case 'g' : {
593	+
594	+	RealType flucQFrc;
595	+	flucQFrc = tokenizer.nextTokenAsDouble();
596	+	sd->setFlucQFrc(flucQFrc);
597	+	break;
598	+	}
599	+	case 'e' : {
600	+
601	+	Vector3d eField;
602	+	eField[0] = tokenizer.nextTokenAsDouble();
603	+	eField[1] = tokenizer.nextTokenAsDouble();
604	+	eField[2] = tokenizer.nextTokenAsDouble();
605	+	sd->setElectricField(eField);
606	+	break;
607	+	}
608	+	default: {
609	+	sprintf(painCave.errMsg,
610	+	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
611	+	painCave.isFatal = 1;
612	+	simError();
613	+	break;
614	+	}
615	+	}
616	+	}
617	+	}
618	+
619	+
620	+	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
621	+
622		inputStream.getline(buffer, bufferSize);
623		std::string line(buffer);
624
#	Line 476 | Line 641 | namespace OpenMD {
641
642		}
643
644	+	void  DumpReader::readSiteData(std::istream& inputStream) {
645	+
646	+	inputStream.getline(buffer, bufferSize);
647	+	std::string line(buffer);
648	+
649	+	if (line.find("<SiteData>") == std::string::npos) {
650	+	// site data isn't required for a simulation, so skip
651	+	return;
652	+	}
653	+
654	+	while(inputStream.getline(buffer, bufferSize)) {
655	+	line = buffer;
656	+
657	+	if(line.find("</SiteData>") != std::string::npos) {
658	+	break;
659	+	}
660	+
661	+	parseSiteLine(line);
662	+	}
663	+
664	+	}
665	+
666		void DumpReader::readFrameProperties(std::istream& inputStream) {
667
668		Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
#	Line 521 | Line 708 | namespace OpenMD {
708		hmat(2, 2) = tokenizer.nextTokenAsDouble();
709		s->setHmat(hmat);
710		} else if (propertyName == "Thermostat") {
711	<	RealType chi = tokenizer.nextTokenAsDouble();
712	<	RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
713	<	s->setChi(chi);
714	<	s->setIntegralOfChiDt(integralOfChiDt);
711	>	pair<RealType, RealType> thermostat;
712	>	thermostat.first = tokenizer.nextTokenAsDouble();
713	>	thermostat.second = tokenizer.nextTokenAsDouble();
714	>	s->setThermostat(thermostat);
715		} else if (propertyName == "Barostat") {
716		Mat3x3d eta;
717		eta(0, 0) = tokenizer.nextTokenAsDouble();
#	Line 536 | Line 723 | namespace OpenMD {
723		eta(2, 0) = tokenizer.nextTokenAsDouble();
724		eta(2, 1) = tokenizer.nextTokenAsDouble();
725		eta(2, 2) = tokenizer.nextTokenAsDouble();
726	<	s->setEta(eta);
726	>	s->setBarostat(eta);
727		} else {
728		sprintf(painCave.errMsg,
729		"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());

Comparing:
trunk/src/io/DumpReader.cpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/io/DumpReader.cpp (property svn:keywords), Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

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

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+	Added lines
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>	Changed lines