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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 1794 by gezelter, Thu Sep 6 19:44:06 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 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 297 | Line 296 | namespace oopse {
296		int sendBufferSize;
297		MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
298		char * recvBuffer = new char[sendBufferSize+1];
299	+	assert(recvBuffer);
300	+	recvBuffer[sendBufferSize] = '\0';
301		MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
302		sstream.str(recvBuffer);
303	+	delete [] recvBuffer;
304		}
305
306		std::istream& inputStream = sstream;
#	Line 322 | Line 324 | namespace oopse {
324
325		inputStream.getline(buffer, bufferSize);
326		line = buffer;
327	<	if (line.find("</Snapshot>") == std::string::npos) {
328	<	sprintf(painCave.errMsg,
329	<	"DumpReader Error: can not find </Snapshot>\n");
330	<	painCave.isFatal = 1;
331	<	simError();
332	<	}
333	<
327	>
328	>	if (line.find("<SiteData>") != std::string::npos) {
329	>	//read SiteData
330	>	readSiteData(inputStream);
331	>	} else {
332	>	if (line.find("</Snapshot>") == std::string::npos) {
333	>	sprintf(painCave.errMsg,
334	>	"DumpReader Error: can not find </Snapshot>\n");
335	>	painCave.isFatal = 1;
336	>	simError();
337	>	}
338	>	}
339		}
340
341		void DumpReader::parseDumpLine(const std::string& line) {
#	Line 339 | Line 346 | namespace oopse {
346
347		nTokens = tokenizer.countTokens();
348
349	<	if (nTokens < 2) {
349	>	if (nTokens < 2) {
350		sprintf(painCave.errMsg,
351		"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
352		painCave.isFatal = 1;
#	Line 348 | Line 355 | namespace oopse {
355
356		int index = tokenizer.nextTokenAsInt();
357
358	<	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
358	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
359
360	<	if (integrableObject == NULL) {
360	>	if (sd == NULL) {
361		return;
362		}
363		std::string type = tokenizer.nextToken();
364		int size = type.size();
365
366	+	size_t found;
367	+
368	+	if (needPos_) {
369	+	found = type.find("p");
370	+	if (found == std::string::npos) {
371	+	sprintf(painCave.errMsg,
372	+	"DumpReader Error: StuntDouble %d has no Position\n"
373	+	"\tField (\"p\") specified.\n%s\n", index,
374	+	line.c_str());
375	+	painCave.isFatal = 1;
376	+	simError();
377	+	}
378	+	}
379	+
380	+	if (sd->isDirectional()) {
381	+	if (needQuaternion_) {
382	+	found = type.find("q");
383	+	if (found == std::string::npos) {
384	+	sprintf(painCave.errMsg,
385	+	"DumpReader Error: Directional StuntDouble %d has no\n"
386	+	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
387	+	line.c_str());
388	+	painCave.isFatal = 1;
389	+	simError();
390	+	}
391	+	}
392	+	}
393	+
394		for(int i = 0; i < size; ++i) {
395		switch(type[i]) {
396
#	Line 365 | Line 400 | namespace oopse {
400		pos[1] = tokenizer.nextTokenAsDouble();
401		pos[2] = tokenizer.nextTokenAsDouble();
402		if (needPos_) {
403	<	integrableObject->setPos(pos);
403	>	sd->setPos(pos);
404		}
405		break;
406		}
#	Line 375 | Line 410 | namespace oopse {
410		vel[1] = tokenizer.nextTokenAsDouble();
411		vel[2] = tokenizer.nextTokenAsDouble();
412		if (needVel_) {
413	<	integrableObject->setVel(vel);
413	>	sd->setVel(vel);
414		}
415		break;
416		}
417
418		case 'q' : {
419		Quat4d q;
420	<	if (integrableObject->isDirectional()) {
420	>	if (sd->isDirectional()) {
421
422		q[0] = tokenizer.nextTokenAsDouble();
423		q[1] = tokenizer.nextTokenAsDouble();
#	Line 390 | Line 425 | namespace oopse {
425		q[3] = tokenizer.nextTokenAsDouble();
426
427		RealType qlen = q.length();
428	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
428	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
429
430		sprintf(painCave.errMsg,
431		"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
#	Line 401 | Line 436 | namespace oopse {
436
437		q.normalize();
438		if (needQuaternion_) {
439	<	integrableObject->setQ(q);
439	>	sd->setQ(q);
440		}
441		}
442		break;
443		}
444		case 'j' : {
445		Vector3d ji;
446	<	if (integrableObject->isDirectional()) {
446	>	if (sd->isDirectional()) {
447		ji[0] = tokenizer.nextTokenAsDouble();
448		ji[1] = tokenizer.nextTokenAsDouble();
449		ji[2] = tokenizer.nextTokenAsDouble();
450		if (needAngMom_) {
451	<	integrableObject->setJ(ji);
451	>	sd->setJ(ji);
452		}
453		}
454		break;
#	Line 424 | Line 459 | namespace oopse {
459		force[0] = tokenizer.nextTokenAsDouble();
460		force[1] = tokenizer.nextTokenAsDouble();
461		force[2] = tokenizer.nextTokenAsDouble();
462	<	integrableObject->setFrc(force);
462	>	sd->setFrc(force);
463		break;
464		}
465		case 't' : {
#	Line 433 | Line 468 | namespace oopse {
468		torque[0] = tokenizer.nextTokenAsDouble();
469		torque[1] = tokenizer.nextTokenAsDouble();
470		torque[2] = tokenizer.nextTokenAsDouble();
471	<	integrableObject->setTrq(torque);
471	>	sd->setTrq(torque);
472		break;
473		}
474	+	case 'u' : {
475	+
476	+	RealType particlePot;
477	+	particlePot = tokenizer.nextTokenAsDouble();
478	+	sd->setParticlePot(particlePot);
479	+	break;
480	+	}
481	+	case 'c' : {
482	+
483	+	RealType flucQPos;
484	+	flucQPos = tokenizer.nextTokenAsDouble();
485	+	sd->setFlucQPos(flucQPos);
486	+	break;
487	+	}
488	+	case 'w' : {
489	+
490	+	RealType flucQVel;
491	+	flucQVel = tokenizer.nextTokenAsDouble();
492	+	sd->setFlucQVel(flucQVel);
493	+	break;
494	+	}
495	+	case 'g' : {
496	+
497	+	RealType flucQFrc;
498	+	flucQFrc = tokenizer.nextTokenAsDouble();
499	+	sd->setFlucQFrc(flucQFrc);
500	+	break;
501	+	}
502	+	case 'e' : {
503	+
504	+	Vector3d eField;
505	+	eField[0] = tokenizer.nextTokenAsDouble();
506	+	eField[1] = tokenizer.nextTokenAsDouble();
507	+	eField[2] = tokenizer.nextTokenAsDouble();
508	+	sd->setElectricField(eField);
509	+	break;
510	+	}
511		default: {
512		sprintf(painCave.errMsg,
513		"DumpReader Error: %s is an unrecognized type\n", type.c_str());
#	Line 450 | Line 522 | namespace oopse {
522		}
523
524
525	<	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
525	>	void DumpReader::parseSiteLine(const std::string& line) {
526
527	+	StringTokenizer tokenizer(line);
528	+	int nTokens;
529	+
530	+	nTokens = tokenizer.countTokens();
531	+
532	+	if (nTokens < 2) {
533	+	sprintf(painCave.errMsg,
534	+	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
535	+	painCave.isFatal = 1;
536	+	simError();
537	+	}
538	+
539	+	/**
540	+	* The first token is the global integrable object index.
541	+	*/
542	+
543	+	int index = tokenizer.nextTokenAsInt();
544	+	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
545	+	if (sd == NULL) {
546	+	return;
547	+	}
548	+
549	+	/**
550	+	* Test to see if the next token is an integer or not.  If not,
551	+	* we've got data on the integrable object itself.  If there is an
552	+	* integer, we're parsing data for a site on a rigid body.
553	+	*/
554	+
555	+	std::string indexTest = tokenizer.peekNextToken();
556	+	std::istringstream i(indexTest);
557	+	int siteIndex;
558	+	if (i >> siteIndex) {
559	+	// chew up this token and parse as an int:
560	+	siteIndex = tokenizer.nextTokenAsInt();
561	+	RigidBody* rb = static_cast<RigidBody*>(sd);
562	+	sd = rb->getAtoms()[siteIndex];
563	+	}
564	+
565	+	/**
566	+	* The next token contains information on what follows.
567	+	*/
568	+	std::string type = tokenizer.nextToken();
569	+	int size = type.size();
570	+
571	+	for(int i = 0; i < size; ++i) {
572	+	switch(type[i]) {
573	+
574	+	case 'u' : {
575	+
576	+	RealType particlePot;
577	+	particlePot = tokenizer.nextTokenAsDouble();
578	+	sd->setParticlePot(particlePot);
579	+	break;
580	+	}
581	+	case 'c' : {
582	+
583	+	RealType flucQPos;
584	+	flucQPos = tokenizer.nextTokenAsDouble();
585	+	sd->setFlucQPos(flucQPos);
586	+	break;
587	+	}
588	+	case 'w' : {
589	+
590	+	RealType flucQVel;
591	+	flucQVel = tokenizer.nextTokenAsDouble();
592	+	sd->setFlucQVel(flucQVel);
593	+	break;
594	+	}
595	+	case 'g' : {
596	+
597	+	RealType flucQFrc;
598	+	flucQFrc = tokenizer.nextTokenAsDouble();
599	+	sd->setFlucQFrc(flucQFrc);
600	+	break;
601	+	}
602	+	case 'e' : {
603	+
604	+	Vector3d eField;
605	+	eField[0] = tokenizer.nextTokenAsDouble();
606	+	eField[1] = tokenizer.nextTokenAsDouble();
607	+	eField[2] = tokenizer.nextTokenAsDouble();
608	+	sd->setElectricField(eField);
609	+	break;
610	+	}
611	+	default: {
612	+	sprintf(painCave.errMsg,
613	+	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
614	+	painCave.isFatal = 1;
615	+	simError();
616	+	break;
617	+	}
618	+	}
619	+	}
620	+	}
621	+
622	+
623	+	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
624	+
625		inputStream.getline(buffer, bufferSize);
626		std::string line(buffer);
627
#	Line 474 | Line 644 | namespace oopse {
644
645		}
646
647	+	void  DumpReader::readSiteData(std::istream& inputStream) {
648	+
649	+	inputStream.getline(buffer, bufferSize);
650	+	std::string line(buffer);
651	+
652	+	if (line.find("<SiteData>") == std::string::npos) {
653	+	// site data isn't required for a simulation, so skip
654	+	return;
655	+	}
656	+
657	+	while(inputStream.getline(buffer, bufferSize)) {
658	+	line = buffer;
659	+
660	+	if(line.find("</SiteData>") != std::string::npos) {
661	+	break;
662	+	}
663	+
664	+	parseSiteLine(line);
665	+	}
666	+
667	+	}
668	+
669		void DumpReader::readFrameProperties(std::istream& inputStream) {
670
671		Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
#	Line 519 | Line 711 | namespace oopse {
711		hmat(2, 2) = tokenizer.nextTokenAsDouble();
712		s->setHmat(hmat);
713		} else if (propertyName == "Thermostat") {
714	<	RealType chi = tokenizer.nextTokenAsDouble();
715	<	RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
716	<	s->setChi(chi);
717	<	s->setIntegralOfChiDt(integralOfChiDt);
714	>	pair<RealType, RealType> thermostat;
715	>	thermostat.first = tokenizer.nextTokenAsDouble();
716	>	thermostat.second = tokenizer.nextTokenAsDouble();
717	>	s->setThermostat(thermostat);
718		} else if (propertyName == "Barostat") {
719		Mat3x3d eta;
720		eta(0, 0) = tokenizer.nextTokenAsDouble();
#	Line 534 | Line 726 | namespace oopse {
726		eta(2, 0) = tokenizer.nextTokenAsDouble();
727		eta(2, 1) = tokenizer.nextTokenAsDouble();
728		eta(2, 2) = tokenizer.nextTokenAsDouble();
729	<	s->setEta(eta);
729	>	s->setBarostat(eta);
730		} else {
731		sprintf(painCave.errMsg,
732		"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
#	Line 547 | Line 739 | namespace oopse {
739		}
740
741
742	<	}//end namespace oopse
742	>	}//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 1794 by gezelter, Thu Sep 6 19:44:06 2012 UTC

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

Diff Legend

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