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root/OpenMD/trunk/src/io/DumpReader.cpp

Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 1104 by gezelter, Fri Dec 29 21:43:18 2006 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 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
19	<	*    notice, this list of conditions and the following disclaimer.
20	<	*
21	<	* 3. Redistributions in binary form must reproduce the above copyright
22	<	*    notice, this list of conditions and the following disclaimer in the
23	<	*    documentation and/or other materials provided with the
24	<	*    distribution.
25	<	*
26	<	* This software is provided "AS IS," without a warranty of any
27	<	* kind. All express or implied conditions, representations and
28	<	* warranties, including any implied warranty of merchantability,
29	<	* fitness for a particular purpose or non-infringement, are hereby
30	<	* excluded.  The University of Notre Dame and its licensors shall not
31	<	* be liable for any damages suffered by licensee as a result of
32	<	* using, modifying or distributing the software or its
33	<	* derivatives. In no event will the University of Notre Dame or its
34	<	* licensors be liable for any lost revenue, profit or data, or for
35	<	* direct, indirect, special, consequential, incidental or punitive
36	<	* damages, however caused and regardless of the theory of liability,
37	<	* arising out of the use of or inability to use software, even if the
38	<	* University of Notre Dame has been advised of the possibility of
39	<	* such damages.
40	<	*/
1	>	/*
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. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
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.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
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, 234107 (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		#define _LARGEFILE_SOURCE64
44		#define _FILE_OFFSET_BITS 64
45
46	+	#ifdef IS_MPI
47	+	#include <mpi.h>
48	+	#endif
49	+
50		#include <sys/types.h>
51		#include <sys/stat.h>
52
#	Line 57 | Line 62
62		#include "utils/simError.h"
63		#include "utils/MemoryUtils.hpp"
64		#include "utils/StringTokenizer.hpp"
65	+	#include "brains/Thermo.hpp"
66
61	–	#ifdef IS_MPI
67
68	<	#include <mpi.h>
64	<	#define TAKE_THIS_TAG_CHAR 0
65	<	#define TAKE_THIS_TAG_INT 1
66	<
67	<	#endif // is_mpi
68	<
69	<
70	<	namespace oopse {
68	>	namespace OpenMD {
69
70		DumpReader::DumpReader(SimInfo* info, const std::string& filename)
71		: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
#	Line 77 | Line 75 | namespace oopse {
75		if (worldRank == 0) {
76		#endif
77
78	<	inFile_ = new std::ifstream(filename_.c_str());
78	>	inFile_ = new std::ifstream(filename_.c_str(),
79	>	ifstream::in | ifstream::binary);
80
81		if (inFile_->fail()) {
82		sprintf(painCave.errMsg,
#	Line 92 | Line 91 | namespace oopse {
91		}
92
93		strcpy(checkPointMsg, "Dump file opened for reading successfully.");
94	<	MPIcheckPoint();
94	>	errorCheckPoint();
95
96		#endif
97
#	Line 113 | Line 112 | namespace oopse {
112		}
113
114		strcpy(checkPointMsg, "Dump file closed successfully.");
115	<	MPIcheckPoint();
115	>	errorCheckPoint();
116
117		#endif
118
#	Line 129 | Line 128 | namespace oopse {
128		}
129
130		void DumpReader::scanFile(void) {
131	<	int lineNo = 0;
131	>
132		std::streampos prevPos;
133		std::streampos  currPos;
134
#	Line 142 | Line 141 | namespace oopse {
141		prevPos = currPos;
142		bool foundOpenSnapshotTag = false;
143		bool foundClosedSnapshotTag = false;
144	+
145	+	int lineNo = 0;
146		while(inFile_->getline(buffer, bufferSize)) {
147		++lineNo;
148
#	Line 227 | Line 228 | namespace oopse {
228		needVel_ = false;
229		}
230
231	<	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
231	>	if (storageLayout & DataStorage::dslAmat ||
232	>	storageLayout & DataStorage::dslDipole ||
233	>	storageLayout & DataStorage::dslQuadrupole) {
234		needQuaternion_ = true;
235		} else {
236		needQuaternion_ = false;
#	Line 243 | Line 246 | namespace oopse {
246
247		if (needCOMprops_) {
248		Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
249	+	Thermo thermo(info_);
250		Vector3d com;
247	–	Vector3d comvel;
248	–	Vector3d comw;
249	–	info_->getComAll(com, comvel);
250	–	comw = info_->getAngularMomentum();
251	–	s->setCOMprops(com, comvel, comw);
252	–	}
251
252	+	if (needPos_ && needVel_) {
253	+	Vector3d comvel;
254	+	Vector3d comw;
255	+	thermo.getComAll(com, comvel);
256	+	comw = thermo.getAngularMomentum();
257	+	} else {
258	+	com = thermo.getCom();
259	+	}
260	+	}
261		}
262
263		void DumpReader::readSet(int whichFrame) {
264		std::string line;
265
266		#ifndef IS_MPI
260	–
267		inFile_->clear();
268		inFile_->seekg(framePos_[whichFrame]);
269
#	Line 284 | Line 290 | namespace oopse {
290
291		int sendBufferSize = sendBuffer.size();
292		MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
293	<	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
293	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize,
294	>	MPI_CHAR, masterNode, MPI_COMM_WORLD);
295
296		sstream.str(sendBuffer);
297		} else {
298		int sendBufferSize;
299	<	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
299	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
300		char * recvBuffer = new char[sendBufferSize+1];
301	<	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
301	>	assert(recvBuffer);
302	>	recvBuffer[sendBufferSize] = '\0';
303	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
304		sstream.str(recvBuffer);
305	+	delete [] recvBuffer;
306		}
307
308		std::istream& inputStream = sstream;
#	Line 316 | Line 326 | namespace oopse {
326
327		inputStream.getline(buffer, bufferSize);
328		line = buffer;
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	<
329	>
330	>	if (line.find("<SiteData>") != std::string::npos) {
331	>	//read SiteData
332	>	readSiteData(inputStream);
333	>	} else {
334	>	if (line.find("</Snapshot>") == std::string::npos) {
335	>	sprintf(painCave.errMsg,
336	>	"DumpReader Error: can not find </Snapshot>\n");
337	>	painCave.isFatal = 1;
338	>	simError();
339	>	}
340	>	}
341		}
342
343		void DumpReader::parseDumpLine(const std::string& line) {
#	Line 333 | Line 348 | namespace oopse {
348
349		nTokens = tokenizer.countTokens();
350
351	<	if (nTokens < 2) {
351	>	if (nTokens < 2) {
352		sprintf(painCave.errMsg,
353		"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
354		painCave.isFatal = 1;
#	Line 342 | Line 357 | namespace oopse {
357
358		int index = tokenizer.nextTokenAsInt();
359
360	<	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
360	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
361
362	<	if (integrableObject == NULL) {
362	>	if (sd == NULL) {
363		return;
364		}
365		std::string type = tokenizer.nextToken();
366		int size = type.size();
367
368	+	size_t found;
369	+
370	+	if (needPos_) {
371	+	found = type.find("p");
372	+	if (found == std::string::npos) {
373	+	sprintf(painCave.errMsg,
374	+	"DumpReader Error: StuntDouble %d has no Position\n"
375	+	"\tField (\"p\") specified.\n%s\n", index,
376	+	line.c_str());
377	+	painCave.isFatal = 1;
378	+	simError();
379	+	}
380	+	}
381	+
382	+	if (sd->isDirectional()) {
383	+	if (needQuaternion_) {
384	+	found = type.find("q");
385	+	if (found == std::string::npos) {
386	+	sprintf(painCave.errMsg,
387	+	"DumpReader Error: Directional StuntDouble %d has no\n"
388	+	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
389	+	line.c_str());
390	+	painCave.isFatal = 1;
391	+	simError();
392	+	}
393	+	}
394	+	}
395	+
396		for(int i = 0; i < size; ++i) {
397		switch(type[i]) {
398
#	Line 359 | Line 402 | namespace oopse {
402		pos[1] = tokenizer.nextTokenAsDouble();
403		pos[2] = tokenizer.nextTokenAsDouble();
404		if (needPos_) {
405	<	integrableObject->setPos(pos);
405	>	sd->setPos(pos);
406		}
407		break;
408		}
#	Line 369 | Line 412 | namespace oopse {
412		vel[1] = tokenizer.nextTokenAsDouble();
413		vel[2] = tokenizer.nextTokenAsDouble();
414		if (needVel_) {
415	<	integrableObject->setVel(vel);
415	>	sd->setVel(vel);
416		}
417		break;
418		}
419
420		case 'q' : {
421		Quat4d q;
422	<	if (integrableObject->isDirectional()) {
422	>	if (sd->isDirectional()) {
423
424		q[0] = tokenizer.nextTokenAsDouble();
425		q[1] = tokenizer.nextTokenAsDouble();
#	Line 384 | Line 427 | namespace oopse {
427		q[3] = tokenizer.nextTokenAsDouble();
428
429		RealType qlen = q.length();
430	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
430	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
431
432		sprintf(painCave.errMsg,
433		"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
#	Line 395 | Line 438 | namespace oopse {
438
439		q.normalize();
440		if (needQuaternion_) {
441	<	integrableObject->setQ(q);
441	>	sd->setQ(q);
442		}
443		}
444		break;
445		}
446		case 'j' : {
447		Vector3d ji;
448	<	if (integrableObject->isDirectional()) {
448	>	if (sd->isDirectional()) {
449		ji[0] = tokenizer.nextTokenAsDouble();
450		ji[1] = tokenizer.nextTokenAsDouble();
451		ji[2] = tokenizer.nextTokenAsDouble();
452		if (needAngMom_) {
453	<	integrableObject->setJ(ji);
453	>	sd->setJ(ji);
454		}
455		}
456		break;
#	Line 418 | Line 461 | namespace oopse {
461		force[0] = tokenizer.nextTokenAsDouble();
462		force[1] = tokenizer.nextTokenAsDouble();
463		force[2] = tokenizer.nextTokenAsDouble();
464	<	integrableObject->setFrc(force);
464	>	sd->setFrc(force);
465		break;
466		}
467		case 't' : {
#	Line 427 | Line 470 | namespace oopse {
470		torque[0] = tokenizer.nextTokenAsDouble();
471		torque[1] = tokenizer.nextTokenAsDouble();
472		torque[2] = tokenizer.nextTokenAsDouble();
473	<	integrableObject->setTrq(torque);
473	>	sd->setTrq(torque);
474		break;
475		}
476	+	case 'u' : {
477	+
478	+	RealType particlePot;
479	+	particlePot = tokenizer.nextTokenAsDouble();
480	+	sd->setParticlePot(particlePot);
481	+	break;
482	+	}
483	+	case 'c' : {
484	+
485	+	RealType flucQPos;
486	+	flucQPos = tokenizer.nextTokenAsDouble();
487	+	sd->setFlucQPos(flucQPos);
488	+	break;
489	+	}
490	+	case 'w' : {
491	+
492	+	RealType flucQVel;
493	+	flucQVel = tokenizer.nextTokenAsDouble();
494	+	sd->setFlucQVel(flucQVel);
495	+	break;
496	+	}
497	+	case 'g' : {
498	+
499	+	RealType flucQFrc;
500	+	flucQFrc = tokenizer.nextTokenAsDouble();
501	+	sd->setFlucQFrc(flucQFrc);
502	+	break;
503	+	}
504	+	case 'e' : {
505	+
506	+	Vector3d eField;
507	+	eField[0] = tokenizer.nextTokenAsDouble();
508	+	eField[1] = tokenizer.nextTokenAsDouble();
509	+	eField[2] = tokenizer.nextTokenAsDouble();
510	+	sd->setElectricField(eField);
511	+	break;
512	+	}
513	+	case 's' : {
514	+
515	+	RealType sPot;
516	+	sPot = tokenizer.nextTokenAsDouble();
517	+	sd->setSitePotential(sPot);
518	+	break;
519	+	}
520		default: {
521		sprintf(painCave.errMsg,
522		"DumpReader Error: %s is an unrecognized type\n", type.c_str());
#	Line 440 | Line 527 | namespace oopse {
527
528		}
529		}
443	–
530		}
531
532
533	<	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
533	>	void DumpReader::parseSiteLine(const std::string& line) {
534
535	+	StringTokenizer tokenizer(line);
536	+	int nTokens;
537	+
538	+	nTokens = tokenizer.countTokens();
539	+
540	+	if (nTokens < 2) {
541	+	sprintf(painCave.errMsg,
542	+	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
543	+	painCave.isFatal = 1;
544	+	simError();
545	+	}
546	+
547	+	/**
548	+	* The first token is the global integrable object index.
549	+	*/
550	+
551	+	int index = tokenizer.nextTokenAsInt();
552	+	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
553	+	if (sd == NULL) {
554	+	return;
555	+	}
556	+
557	+	/**
558	+	* Test to see if the next token is an integer or not.  If not,
559	+	* we've got data on the integrable object itself.  If there is an
560	+	* integer, we're parsing data for a site on a rigid body.
561	+	*/
562	+
563	+	std::string indexTest = tokenizer.peekNextToken();
564	+	std::istringstream i(indexTest);
565	+	int siteIndex;
566	+	if (i >> siteIndex) {
567	+	// chew up this token and parse as an int:
568	+	siteIndex = tokenizer.nextTokenAsInt();
569	+
570	+	if (sd->isRigidBody()) {
571	+	RigidBody* rb = static_cast<RigidBody*>(sd);
572	+	sd = rb->getAtoms()[siteIndex];
573	+	}
574	+	}
575	+
576	+	/**
577	+	* The next token contains information on what follows.
578	+	*/
579	+	std::string type = tokenizer.nextToken();
580	+	int size = type.size();
581	+
582	+	for(int i = 0; i < size; ++i) {
583	+	switch(type[i]) {
584	+
585	+	case 'u' : {
586	+
587	+	RealType particlePot;
588	+	particlePot = tokenizer.nextTokenAsDouble();
589	+	sd->setParticlePot(particlePot);
590	+	break;
591	+	}
592	+	case 'c' : {
593	+
594	+	RealType flucQPos;
595	+	flucQPos = tokenizer.nextTokenAsDouble();
596	+	sd->setFlucQPos(flucQPos);
597	+	break;
598	+	}
599	+	case 'w' : {
600	+
601	+	RealType flucQVel;
602	+	flucQVel = tokenizer.nextTokenAsDouble();
603	+	sd->setFlucQVel(flucQVel);
604	+	break;
605	+	}
606	+	case 'g' : {
607	+
608	+	RealType flucQFrc;
609	+	flucQFrc = tokenizer.nextTokenAsDouble();
610	+	sd->setFlucQFrc(flucQFrc);
611	+	break;
612	+	}
613	+	case 'e' : {
614	+
615	+	Vector3d eField;
616	+	eField[0] = tokenizer.nextTokenAsDouble();
617	+	eField[1] = tokenizer.nextTokenAsDouble();
618	+	eField[2] = tokenizer.nextTokenAsDouble();
619	+	sd->setElectricField(eField);
620	+	break;
621	+	}
622	+	case 's' : {
623	+
624	+	RealType sPot;
625	+	sPot = tokenizer.nextTokenAsDouble();
626	+	sd->setSitePotential(sPot);
627	+	break;
628	+	}
629	+	default: {
630	+	sprintf(painCave.errMsg,
631	+	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
632	+	painCave.isFatal = 1;
633	+	simError();
634	+	break;
635	+	}
636	+	}
637	+	}
638	+	}
639	+
640	+
641	+	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
642	+
643		inputStream.getline(buffer, bufferSize);
644		std::string line(buffer);
645
#	Line 468 | Line 662 | namespace oopse {
662
663		}
664
665	+	void  DumpReader::readSiteData(std::istream& inputStream) {
666	+
667	+	std::string line(buffer);
668	+
669	+	// We already found the starting <SiteData> tag or we wouldn't be
670	+	// here, so just start parsing until we get to the ending
671	+	// </SiteData> tag:
672	+
673	+	while(inputStream.getline(buffer, bufferSize)) {
674	+	line = buffer;
675	+
676	+	if(line.find("</SiteData>") != std::string::npos) {
677	+	break;
678	+	}
679	+
680	+	parseSiteLine(line);
681	+	}
682	+
683	+	}
684	+
685		void DumpReader::readFrameProperties(std::istream& inputStream) {
686
687		Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
#	Line 513 | Line 727 | namespace oopse {
727		hmat(2, 2) = tokenizer.nextTokenAsDouble();
728		s->setHmat(hmat);
729		} else if (propertyName == "Thermostat") {
730	<	RealType chi = tokenizer.nextTokenAsDouble();
731	<	RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
732	<	s->setChi(chi);
733	<	s->setIntegralOfChiDt(integralOfChiDt);
730	>	pair<RealType, RealType> thermostat;
731	>	thermostat.first = tokenizer.nextTokenAsDouble();
732	>	thermostat.second = tokenizer.nextTokenAsDouble();
733	>	s->setThermostat(thermostat);
734		} else if (propertyName == "Barostat") {
735		Mat3x3d eta;
736		eta(0, 0) = tokenizer.nextTokenAsDouble();
#	Line 528 | Line 742 | namespace oopse {
742		eta(2, 0) = tokenizer.nextTokenAsDouble();
743		eta(2, 1) = tokenizer.nextTokenAsDouble();
744		eta(2, 2) = tokenizer.nextTokenAsDouble();
745	<	s->setEta(eta);
745	>	s->setBarostat(eta);
746		} else {
747		sprintf(painCave.errMsg,
748		"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
#	Line 541 | Line 755 | namespace oopse {
755		}
756
757
758	<	}//end namespace oopse
758	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpReader.cpp (property svn:keywords):
Revision 1104 by gezelter, Fri Dec 29 21:43:18 2006 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

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