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

Comparing:
trunk/src/io/DumpReader.cpp (file contents), Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1798 by gezelter, Thu Sep 13 14:10:11 2012 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, 24107 (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
#	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
68	<
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 142 | Line 141 | namespace oopse {
141		prevPos = currPos;
142		bool foundOpenSnapshotTag = false;
143		bool foundClosedSnapshotTag = false;
144	+	bool foundOpenSiteDataTag = false;
145		while(inFile_->getline(buffer, bufferSize)) {
146		++lineNo;
147
#	Line 202 | Line 202 | namespace oopse {
202		#ifdef IS_MPI
203		}
204
205	<	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
205	>	MPI::COMM_WORLD.Bcast(&nframes_, 1, MPI::INT, 0);
206
207		#endif // is_mpi
208
#	Line 227 | Line 227 | namespace oopse {
227		needVel_ = false;
228		}
229
230	<	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
230	>	if (storageLayout & DataStorage::dslAmat ||
231	>	storageLayout & DataStorage::dslDipole ||
232	>	storageLayout & DataStorage::dslQuadrupole) {
233		needQuaternion_ = true;
234		} else {
235		needQuaternion_ = false;
#	Line 243 | Line 245 | namespace oopse {
245
246		if (needCOMprops_) {
247		Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
248	+	Thermo thermo(info_);
249		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);
258	–	}
250
251	+	if (needPos_ && needVel_) {
252	+	Vector3d comvel;
253	+	Vector3d comw;
254	+	thermo.getComAll(com, comvel);
255	+	comw = thermo.getAngularMomentum();
256	+	} else {
257	+	com = thermo.getCom();
258	+	}
259	+	}
260		}
261
262		void DumpReader::readSet(int whichFrame) {
263		std::string line;
264
265		#ifndef IS_MPI
266	–
266		inFile_->clear();
267		inFile_->seekg(framePos_[whichFrame]);
268
#	Line 289 | Line 288 | namespace oopse {
288		}
289
290		int sendBufferSize = sendBuffer.size();
291	<	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
292	<	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
291	>	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
292	>	MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize,
293	>	MPI::CHAR, masterNode);
294
295		sstream.str(sendBuffer);
296		} else {
297		int sendBufferSize;
298	<	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
298	>	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
299		char * recvBuffer = new char[sendBufferSize+1];
300	<	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
300	>	assert(recvBuffer);
301	>	recvBuffer[sendBufferSize] = '\0';
302	>	MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
303		sstream.str(recvBuffer);
304	+	delete [] recvBuffer;
305		}
306
307		std::istream& inputStream = sstream;
#	Line 322 | Line 325 | namespace oopse {
325
326		inputStream.getline(buffer, bufferSize);
327		line = buffer;
328	<	if (line.find("</Snapshot>") == std::string::npos) {
329	<	sprintf(painCave.errMsg,
330	<	"DumpReader Error: can not find </Snapshot>\n");
331	<	painCave.isFatal = 1;
332	<	simError();
333	<	}
334	<
328	>
329	>	if (line.find("<SiteData>") != std::string::npos) {
330	>	//read SiteData
331	>	readSiteData(inputStream);
332	>	} else {
333	>	if (line.find("</Snapshot>") == std::string::npos) {
334	>	sprintf(painCave.errMsg,
335	>	"DumpReader Error: can not find </Snapshot>\n");
336	>	painCave.isFatal = 1;
337	>	simError();
338	>	}
339	>	}
340		}
341
342		void DumpReader::parseDumpLine(const std::string& line) {
#	Line 339 | Line 347 | namespace oopse {
347
348		nTokens = tokenizer.countTokens();
349
350	<	if (nTokens < 2) {
350	>	if (nTokens < 2) {
351		sprintf(painCave.errMsg,
352		"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
353		painCave.isFatal = 1;
#	Line 348 | Line 356 | namespace oopse {
356
357		int index = tokenizer.nextTokenAsInt();
358
359	<	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
359	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
360
361	<	if (integrableObject == NULL) {
361	>	if (sd == NULL) {
362		return;
363		}
364		std::string type = tokenizer.nextToken();
365		int size = type.size();
366
367	+	size_t found;
368	+
369	+	if (needPos_) {
370	+	found = type.find("p");
371	+	if (found == std::string::npos) {
372	+	sprintf(painCave.errMsg,
373	+	"DumpReader Error: StuntDouble %d has no Position\n"
374	+	"\tField (\"p\") specified.\n%s\n", index,
375	+	line.c_str());
376	+	painCave.isFatal = 1;
377	+	simError();
378	+	}
379	+	}
380	+
381	+	if (sd->isDirectional()) {
382	+	if (needQuaternion_) {
383	+	found = type.find("q");
384	+	if (found == std::string::npos) {
385	+	sprintf(painCave.errMsg,
386	+	"DumpReader Error: Directional StuntDouble %d has no\n"
387	+	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
388	+	line.c_str());
389	+	painCave.isFatal = 1;
390	+	simError();
391	+	}
392	+	}
393	+	}
394	+
395		for(int i = 0; i < size; ++i) {
396		switch(type[i]) {
397
#	Line 365 | Line 401 | namespace oopse {
401		pos[1] = tokenizer.nextTokenAsDouble();
402		pos[2] = tokenizer.nextTokenAsDouble();
403		if (needPos_) {
404	<	integrableObject->setPos(pos);
404	>	sd->setPos(pos);
405		}
406		break;
407		}
#	Line 375 | Line 411 | namespace oopse {
411		vel[1] = tokenizer.nextTokenAsDouble();
412		vel[2] = tokenizer.nextTokenAsDouble();
413		if (needVel_) {
414	<	integrableObject->setVel(vel);
414	>	sd->setVel(vel);
415		}
416		break;
417		}
418
419		case 'q' : {
420		Quat4d q;
421	<	if (integrableObject->isDirectional()) {
421	>	if (sd->isDirectional()) {
422
423		q[0] = tokenizer.nextTokenAsDouble();
424		q[1] = tokenizer.nextTokenAsDouble();
#	Line 390 | Line 426 | namespace oopse {
426		q[3] = tokenizer.nextTokenAsDouble();
427
428		RealType qlen = q.length();
429	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
429	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
430
431		sprintf(painCave.errMsg,
432		"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
#	Line 401 | Line 437 | namespace oopse {
437
438		q.normalize();
439		if (needQuaternion_) {
440	<	integrableObject->setQ(q);
440	>	sd->setQ(q);
441		}
442		}
443		break;
444		}
445		case 'j' : {
446		Vector3d ji;
447	<	if (integrableObject->isDirectional()) {
447	>	if (sd->isDirectional()) {
448		ji[0] = tokenizer.nextTokenAsDouble();
449		ji[1] = tokenizer.nextTokenAsDouble();
450		ji[2] = tokenizer.nextTokenAsDouble();
451		if (needAngMom_) {
452	<	integrableObject->setJ(ji);
452	>	sd->setJ(ji);
453		}
454		}
455		break;
#	Line 424 | Line 460 | namespace oopse {
460		force[0] = tokenizer.nextTokenAsDouble();
461		force[1] = tokenizer.nextTokenAsDouble();
462		force[2] = tokenizer.nextTokenAsDouble();
463	<	integrableObject->setFrc(force);
463	>	sd->setFrc(force);
464		break;
465		}
466		case 't' : {
#	Line 433 | Line 469 | namespace oopse {
469		torque[0] = tokenizer.nextTokenAsDouble();
470		torque[1] = tokenizer.nextTokenAsDouble();
471		torque[2] = tokenizer.nextTokenAsDouble();
472	<	integrableObject->setTrq(torque);
472	>	sd->setTrq(torque);
473		break;
474		}
475	+	case 'u' : {
476	+
477	+	RealType particlePot;
478	+	particlePot = tokenizer.nextTokenAsDouble();
479	+	sd->setParticlePot(particlePot);
480	+	break;
481	+	}
482	+	case 'c' : {
483	+
484	+	RealType flucQPos;
485	+	flucQPos = tokenizer.nextTokenAsDouble();
486	+	sd->setFlucQPos(flucQPos);
487	+	break;
488	+	}
489	+	case 'w' : {
490	+
491	+	RealType flucQVel;
492	+	flucQVel = tokenizer.nextTokenAsDouble();
493	+	sd->setFlucQVel(flucQVel);
494	+	break;
495	+	}
496	+	case 'g' : {
497	+
498	+	RealType flucQFrc;
499	+	flucQFrc = tokenizer.nextTokenAsDouble();
500	+	sd->setFlucQFrc(flucQFrc);
501	+	break;
502	+	}
503	+	case 'e' : {
504	+
505	+	Vector3d eField;
506	+	eField[0] = tokenizer.nextTokenAsDouble();
507	+	eField[1] = tokenizer.nextTokenAsDouble();
508	+	eField[2] = tokenizer.nextTokenAsDouble();
509	+	sd->setElectricField(eField);
510	+	break;
511	+	}
512		default: {
513		sprintf(painCave.errMsg,
514		"DumpReader Error: %s is an unrecognized type\n", type.c_str());
#	Line 450 | Line 523 | namespace oopse {
523		}
524
525
526	<	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
526	>	void DumpReader::parseSiteLine(const std::string& line) {
527	>
528	>	StringTokenizer tokenizer(line);
529	>	int nTokens;
530	>
531	>	nTokens = tokenizer.countTokens();
532	>
533	>	if (nTokens < 2) {
534	>	sprintf(painCave.errMsg,
535	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
536	>	painCave.isFatal = 1;
537	>	simError();
538	>	}
539	>
540	>	/**
541	>	* The first token is the global integrable object index.
542	>	*/
543	>
544	>	int index = tokenizer.nextTokenAsInt();
545	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
546	>	if (sd == NULL) {
547	>	return;
548	>	}
549	>
550	>	/**
551	>	* Test to see if the next token is an integer or not.  If not,
552	>	* we've got data on the integrable object itself.  If there is an
553	>	* integer, we're parsing data for a site on a rigid body.
554	>	*/
555	>
556	>	std::string indexTest = tokenizer.peekNextToken();
557	>	std::istringstream i(indexTest);
558	>	int siteIndex;
559	>	if (i >> siteIndex) {
560	>	// chew up this token and parse as an int:
561	>	siteIndex = tokenizer.nextTokenAsInt();
562	>	RigidBody* rb = static_cast<RigidBody*>(sd);
563	>	sd = rb->getAtoms()[siteIndex];
564	>	}
565
566	+	/**
567	+	* The next token contains information on what follows.
568	+	*/
569	+	std::string type = tokenizer.nextToken();
570	+	int size = type.size();
571	+
572	+	for(int i = 0; i < size; ++i) {
573	+	switch(type[i]) {
574	+
575	+	case 'u' : {
576	+
577	+	RealType particlePot;
578	+	particlePot = tokenizer.nextTokenAsDouble();
579	+	sd->setParticlePot(particlePot);
580	+	break;
581	+	}
582	+	case 'c' : {
583	+
584	+	RealType flucQPos;
585	+	flucQPos = tokenizer.nextTokenAsDouble();
586	+	sd->setFlucQPos(flucQPos);
587	+	break;
588	+	}
589	+	case 'w' : {
590	+
591	+	RealType flucQVel;
592	+	flucQVel = tokenizer.nextTokenAsDouble();
593	+	sd->setFlucQVel(flucQVel);
594	+	break;
595	+	}
596	+	case 'g' : {
597	+
598	+	RealType flucQFrc;
599	+	flucQFrc = tokenizer.nextTokenAsDouble();
600	+	sd->setFlucQFrc(flucQFrc);
601	+	break;
602	+	}
603	+	case 'e' : {
604	+
605	+	Vector3d eField;
606	+	eField[0] = tokenizer.nextTokenAsDouble();
607	+	eField[1] = tokenizer.nextTokenAsDouble();
608	+	eField[2] = tokenizer.nextTokenAsDouble();
609	+	sd->setElectricField(eField);
610	+	break;
611	+	}
612	+	default: {
613	+	sprintf(painCave.errMsg,
614	+	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
615	+	painCave.isFatal = 1;
616	+	simError();
617	+	break;
618	+	}
619	+	}
620	+	}
621	+	}
622	+
623	+
624	+	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
625	+
626		inputStream.getline(buffer, bufferSize);
627		std::string line(buffer);
628
#	Line 474 | Line 645 | namespace oopse {
645
646		}
647
648	+	void  DumpReader::readSiteData(std::istream& inputStream) {
649	+
650	+	inputStream.getline(buffer, bufferSize);
651	+	std::string line(buffer);
652	+
653	+	if (line.find("<SiteData>") == std::string::npos) {
654	+	// site data isn't required for a simulation, so skip
655	+	return;
656	+	}
657	+
658	+	while(inputStream.getline(buffer, bufferSize)) {
659	+	line = buffer;
660	+
661	+	if(line.find("</SiteData>") != std::string::npos) {
662	+	break;
663	+	}
664	+
665	+	parseSiteLine(line);
666	+	}
667	+
668	+	}
669	+
670		void DumpReader::readFrameProperties(std::istream& inputStream) {
671
672		Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
#	Line 519 | Line 712 | namespace oopse {
712		hmat(2, 2) = tokenizer.nextTokenAsDouble();
713		s->setHmat(hmat);
714		} else if (propertyName == "Thermostat") {
715	<	RealType chi = tokenizer.nextTokenAsDouble();
716	<	RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
717	<	s->setChi(chi);
718	<	s->setIntegralOfChiDt(integralOfChiDt);
715	>	pair<RealType, RealType> thermostat;
716	>	thermostat.first = tokenizer.nextTokenAsDouble();
717	>	thermostat.second = tokenizer.nextTokenAsDouble();
718	>	s->setThermostat(thermostat);
719		} else if (propertyName == "Barostat") {
720		Mat3x3d eta;
721		eta(0, 0) = tokenizer.nextTokenAsDouble();
#	Line 534 | Line 727 | namespace oopse {
727		eta(2, 0) = tokenizer.nextTokenAsDouble();
728		eta(2, 1) = tokenizer.nextTokenAsDouble();
729		eta(2, 2) = tokenizer.nextTokenAsDouble();
730	<	s->setEta(eta);
730	>	s->setBarostat(eta);
731		} else {
732		sprintf(painCave.errMsg,
733		"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
#	Line 547 | Line 740 | namespace oopse {
740		}
741
742
743	<	}//end namespace oopse
743	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpReader.cpp (property svn:keywords), Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
branches/development/src/io/DumpReader.cpp (property svn:keywords), Revision 1798 by gezelter, Thu Sep 13 14:10:11 2012 UTC

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

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–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines