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

Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 1037 by gezelter, Fri Sep 8 16:13:21 2006 UTC vs.
Revision 1793 by gezelter, Fri Aug 31 21:16:10 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) {
71	>	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
72
73		#ifdef IS_MPI
74
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 142 | Line 141 | namespace oopse {
141		prevPos = currPos;
142		bool foundOpenSnapshotTag = false;
143		bool foundClosedSnapshotTag = false;
144	+
145		while(inFile_->getline(buffer, bufferSize)) {
146		++lineNo;
147
#	Line 240 | Line 240 | namespace oopse {
240		}
241
242		readSet(whichFrame);
243	+
244	+	if (needCOMprops_) {
245	+	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
246	+	Thermo thermo(info_);
247	+	Vector3d com;
248	+
249	+	if (needPos_ && needVel_) {
250	+	Vector3d comvel;
251	+	Vector3d comw;
252	+	thermo.getComAll(com, comvel);
253	+	comw = thermo.getAngularMomentum();
254	+	} else {
255	+	com = thermo.getCom();
256	+	}
257	+	}
258		}
259
260		void DumpReader::readSet(int whichFrame) {
261		std::string line;
262
263		#ifndef IS_MPI
249	–
264		inFile_->clear();
265		inFile_->seekg(framePos_[whichFrame]);
266
#	Line 280 | Line 294 | namespace oopse {
294		int sendBufferSize;
295		MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
296		char * recvBuffer = new char[sendBufferSize+1];
297	+	assert(recvBuffer);
298	+	recvBuffer[sendBufferSize] = '\0';
299		MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
300		sstream.str(recvBuffer);
301	+	delete [] recvBuffer;
302		}
303
304		std::istream& inputStream = sstream;
#	Line 305 | Line 322 | namespace oopse {
322
323		inputStream.getline(buffer, bufferSize);
324		line = buffer;
325	<	if (line.find("</Snapshot>") == std::string::npos) {
326	<	sprintf(painCave.errMsg,
327	<	"DumpReader Error: can not find </Snapshot>\n");
328	<	painCave.isFatal = 1;
329	<	simError();
330	<	}
331	<
325	>
326	>	if (line.find("<SiteData>") != std::string::npos) {
327	>	//read SiteData
328	>	readSiteData(inputStream);
329	>	} else {
330	>	if (line.find("</Snapshot>") == std::string::npos) {
331	>	sprintf(painCave.errMsg,
332	>	"DumpReader Error: can not find </Snapshot>\n");
333	>	painCave.isFatal = 1;
334	>	simError();
335	>	}
336	>	}
337		}
338
339		void DumpReader::parseDumpLine(const std::string& line) {
#	Line 322 | Line 344 | namespace oopse {
344
345		nTokens = tokenizer.countTokens();
346
347	<	if (nTokens < 2) {
347	>	if (nTokens < 2) {
348		sprintf(painCave.errMsg,
349		"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
350		painCave.isFatal = 1;
#	Line 331 | Line 353 | namespace oopse {
353
354		int index = tokenizer.nextTokenAsInt();
355
356	<	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
356	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
357
358	<	if (integrableObject == NULL) {
358	>	if (sd == NULL) {
359		return;
360		}
361		std::string type = tokenizer.nextToken();
362		int size = type.size();
363
364	+	size_t found;
365	+
366	+	if (needPos_) {
367	+	found = type.find("p");
368	+	if (found == std::string::npos) {
369	+	sprintf(painCave.errMsg,
370	+	"DumpReader Error: StuntDouble %d has no Position\n"
371	+	"\tField (\"p\") specified.\n%s\n", index,
372	+	line.c_str());
373	+	painCave.isFatal = 1;
374	+	simError();
375	+	}
376	+	}
377	+
378	+	if (sd->isDirectional()) {
379	+	if (needQuaternion_) {
380	+	found = type.find("q");
381	+	if (found == std::string::npos) {
382	+	sprintf(painCave.errMsg,
383	+	"DumpReader Error: Directional StuntDouble %d has no\n"
384	+	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
385	+	line.c_str());
386	+	painCave.isFatal = 1;
387	+	simError();
388	+	}
389	+	}
390	+	}
391	+
392		for(int i = 0; i < size; ++i) {
393		switch(type[i]) {
394
#	Line 348 | Line 398 | namespace oopse {
398		pos[1] = tokenizer.nextTokenAsDouble();
399		pos[2] = tokenizer.nextTokenAsDouble();
400		if (needPos_) {
401	<	integrableObject->setPos(pos);
401	>	sd->setPos(pos);
402		}
403		break;
404		}
#	Line 358 | Line 408 | namespace oopse {
408		vel[1] = tokenizer.nextTokenAsDouble();
409		vel[2] = tokenizer.nextTokenAsDouble();
410		if (needVel_) {
411	<	integrableObject->setVel(vel);
411	>	sd->setVel(vel);
412		}
413		break;
414		}
415
416		case 'q' : {
417		Quat4d q;
418	<	if (integrableObject->isDirectional()) {
418	>	if (sd->isDirectional()) {
419
420		q[0] = tokenizer.nextTokenAsDouble();
421		q[1] = tokenizer.nextTokenAsDouble();
#	Line 373 | Line 423 | namespace oopse {
423		q[3] = tokenizer.nextTokenAsDouble();
424
425		RealType qlen = q.length();
426	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
426	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
427
428		sprintf(painCave.errMsg,
429		"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
#	Line 384 | Line 434 | namespace oopse {
434
435		q.normalize();
436		if (needQuaternion_) {
437	<	integrableObject->setQ(q);
437	>	sd->setQ(q);
438		}
439		}
440		break;
441		}
442		case 'j' : {
443		Vector3d ji;
444	<	if (integrableObject->isDirectional()) {
444	>	if (sd->isDirectional()) {
445		ji[0] = tokenizer.nextTokenAsDouble();
446		ji[1] = tokenizer.nextTokenAsDouble();
447		ji[2] = tokenizer.nextTokenAsDouble();
448		if (needAngMom_) {
449	<	integrableObject->setJ(ji);
449	>	sd->setJ(ji);
450		}
451		}
452		break;
#	Line 407 | Line 457 | namespace oopse {
457		force[0] = tokenizer.nextTokenAsDouble();
458		force[1] = tokenizer.nextTokenAsDouble();
459		force[2] = tokenizer.nextTokenAsDouble();
460	<	integrableObject->setFrc(force);
460	>	sd->setFrc(force);
461		break;
462		}
463		case 't' : {
#	Line 416 | Line 466 | namespace oopse {
466		torque[0] = tokenizer.nextTokenAsDouble();
467		torque[1] = tokenizer.nextTokenAsDouble();
468		torque[2] = tokenizer.nextTokenAsDouble();
469	<	integrableObject->setTrq(torque);
469	>	sd->setTrq(torque);
470		break;
471		}
472	+	case 'u' : {
473	+
474	+	RealType particlePot;
475	+	particlePot = tokenizer.nextTokenAsDouble();
476	+	sd->setParticlePot(particlePot);
477	+	break;
478	+	}
479	+	case 'c' : {
480	+
481	+	RealType flucQPos;
482	+	flucQPos = tokenizer.nextTokenAsDouble();
483	+	sd->setFlucQPos(flucQPos);
484	+	break;
485	+	}
486	+	case 'w' : {
487	+
488	+	RealType flucQVel;
489	+	flucQVel = tokenizer.nextTokenAsDouble();
490	+	sd->setFlucQVel(flucQVel);
491	+	break;
492	+	}
493	+	case 'g' : {
494	+
495	+	RealType flucQFrc;
496	+	flucQFrc = tokenizer.nextTokenAsDouble();
497	+	sd->setFlucQFrc(flucQFrc);
498	+	break;
499	+	}
500	+	case 'e' : {
501	+
502	+	Vector3d eField;
503	+	eField[0] = tokenizer.nextTokenAsDouble();
504	+	eField[1] = tokenizer.nextTokenAsDouble();
505	+	eField[2] = tokenizer.nextTokenAsDouble();
506	+	sd->setElectricField(eField);
507	+	break;
508	+	}
509		default: {
510		sprintf(painCave.errMsg,
511		"DumpReader Error: %s is an unrecognized type\n", type.c_str());
#	Line 433 | Line 520 | namespace oopse {
520		}
521
522
523	<	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
523	>	void DumpReader::parseSiteLine(const std::string& line) {
524
525	+	StringTokenizer tokenizer(line);
526	+	int nTokens;
527	+
528	+	nTokens = tokenizer.countTokens();
529	+
530	+	if (nTokens < 2) {
531	+	sprintf(painCave.errMsg,
532	+	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
533	+	painCave.isFatal = 1;
534	+	simError();
535	+	}
536	+
537	+	/**
538	+	* The first token is the global integrable object index.
539	+	*/
540	+
541	+	int index = tokenizer.nextTokenAsInt();
542	+	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
543	+	if (sd == NULL) {
544	+	return;
545	+	}
546	+
547	+	/**
548	+	* Test to see if the next token is an integer or not.  If not,
549	+	* we've got data on the integrable object itself.  If there is an
550	+	* integer, we're parsing data for a site on a rigid body.
551	+	*/
552	+
553	+	std::string indexTest = tokenizer.peekNextToken();
554	+	std::istringstream i(indexTest);
555	+	int siteIndex;
556	+	if (i >> siteIndex) {
557	+	// chew up this token and parse as an int:
558	+	siteIndex = tokenizer.nextTokenAsInt();
559	+	RigidBody* rb = static_cast<RigidBody*>(sd);
560	+	sd = rb->getAtoms()[siteIndex];
561	+	}
562	+
563	+	/**
564	+	* The next token contains information on what follows.
565	+	*/
566	+	std::string type = tokenizer.nextToken();
567	+	int size = type.size();
568	+
569	+	for(int i = 0; i < size; ++i) {
570	+	switch(type[i]) {
571	+
572	+	case 'u' : {
573	+
574	+	RealType particlePot;
575	+	particlePot = tokenizer.nextTokenAsDouble();
576	+	sd->setParticlePot(particlePot);
577	+	break;
578	+	}
579	+	case 'c' : {
580	+
581	+	RealType flucQPos;
582	+	flucQPos = tokenizer.nextTokenAsDouble();
583	+	sd->setFlucQPos(flucQPos);
584	+	break;
585	+	}
586	+	case 'w' : {
587	+
588	+	RealType flucQVel;
589	+	flucQVel = tokenizer.nextTokenAsDouble();
590	+	sd->setFlucQVel(flucQVel);
591	+	break;
592	+	}
593	+	case 'g' : {
594	+
595	+	RealType flucQFrc;
596	+	flucQFrc = tokenizer.nextTokenAsDouble();
597	+	sd->setFlucQFrc(flucQFrc);
598	+	break;
599	+	}
600	+	case 'e' : {
601	+
602	+	Vector3d eField;
603	+	eField[0] = tokenizer.nextTokenAsDouble();
604	+	eField[1] = tokenizer.nextTokenAsDouble();
605	+	eField[2] = tokenizer.nextTokenAsDouble();
606	+	sd->setElectricField(eField);
607	+	break;
608	+	}
609	+	default: {
610	+	sprintf(painCave.errMsg,
611	+	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
612	+	painCave.isFatal = 1;
613	+	simError();
614	+	break;
615	+	}
616	+	}
617	+	}
618	+	}
619	+
620	+
621	+	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
622	+
623		inputStream.getline(buffer, bufferSize);
624		std::string line(buffer);
625
#	Line 457 | Line 642 | namespace oopse {
642
643		}
644
645	+	void  DumpReader::readSiteData(std::istream& inputStream) {
646	+
647	+	inputStream.getline(buffer, bufferSize);
648	+	std::string line(buffer);
649	+
650	+	if (line.find("<SiteData>") == std::string::npos) {
651	+	// site data isn't required for a simulation, so skip
652	+	return;
653	+	}
654	+
655	+	while(inputStream.getline(buffer, bufferSize)) {
656	+	line = buffer;
657	+
658	+	if(line.find("</SiteData>") != std::string::npos) {
659	+	break;
660	+	}
661	+
662	+	parseSiteLine(line);
663	+	}
664	+
665	+	}
666	+
667		void DumpReader::readFrameProperties(std::istream& inputStream) {
668
669		Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
#	Line 502 | Line 709 | namespace oopse {
709		hmat(2, 2) = tokenizer.nextTokenAsDouble();
710		s->setHmat(hmat);
711		} else if (propertyName == "Thermostat") {
712	<	RealType chi = tokenizer.nextTokenAsDouble();
713	<	RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
714	<	s->setChi(chi);
715	<	s->setIntegralOfChiDt(integralOfChiDt);
712	>	pair<RealType, RealType> thermostat;
713	>	thermostat.first = tokenizer.nextTokenAsDouble();
714	>	thermostat.second = tokenizer.nextTokenAsDouble();
715	>	s->setThermostat(thermostat);
716		} else if (propertyName == "Barostat") {
717		Mat3x3d eta;
718		eta(0, 0) = tokenizer.nextTokenAsDouble();
#	Line 517 | Line 724 | namespace oopse {
724		eta(2, 0) = tokenizer.nextTokenAsDouble();
725		eta(2, 1) = tokenizer.nextTokenAsDouble();
726		eta(2, 2) = tokenizer.nextTokenAsDouble();
727	<	s->setEta(eta);
727	>	s->setBarostat(eta);
728		} else {
729		sprintf(painCave.errMsg,
730		"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
#	Line 530 | Line 737 | namespace oopse {
737		}
738
739
740	<	}//end namespace oopse
740	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpReader.cpp (property svn:keywords):
Revision 1037 by gezelter, Fri Sep 8 16:13:21 2006 UTC vs.
Revision 1793 by gezelter, Fri Aug 31 21:16:10 2012 UTC

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

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
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