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

Comparing:
trunk/src/io/DumpReader.cpp (file contents), Revision 1025 by gezelter, Wed Aug 30 20:33:44 2006 UTC vs.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1769 by gezelter, Mon Jul 9 14:15:52 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
#	Line 92 | Line 90 | namespace oopse {
90		}
91
92		strcpy(checkPointMsg, "Dump file opened for reading successfully.");
93	<	MPIcheckPoint();
93	>	errorCheckPoint();
94
95		#endif
96
#	Line 113 | Line 111 | namespace oopse {
111		}
112
113		strcpy(checkPointMsg, "Dump file closed successfully.");
114	<	MPIcheckPoint();
114	>	errorCheckPoint();
115
116		#endif
117
#	Line 142 | Line 140 | namespace oopse {
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 240 | Line 239 | namespace oopse {
239		}
240
241		readSet(whichFrame);
242	+
243	+	if (needCOMprops_) {
244	+	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
245	+	Thermo thermo(info_);
246	+	Vector3d com;
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	+	}
257		}
258
259		void DumpReader::readSet(int whichFrame) {
260		std::string line;
261
262		#ifndef IS_MPI
249	–
263		inFile_->clear();
264		inFile_->seekg(framePos_[whichFrame]);
265
#	Line 280 | Line 293 | namespace oopse {
293		int sendBufferSize;
294		MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
295		char * recvBuffer = new char[sendBufferSize+1];
296	+	assert(recvBuffer);
297	+	recvBuffer[sendBufferSize] = '\0';
298		MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
299		sstream.str(recvBuffer);
300	+	delete [] recvBuffer;
301		}
302
303		std::istream& inputStream = sstream;
#	Line 305 | Line 321 | namespace oopse {
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 322 | Line 343 | namespace oopse {
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 331 | Line 352 | namespace oopse {
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 347 | Line 397 | namespace oopse {
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 357 | Line 407 | namespace oopse {
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 372 | Line 422 | namespace oopse {
422		q[3] = tokenizer.nextTokenAsDouble();
423
424		RealType qlen = q.length();
425	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
425	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
426
427		sprintf(painCave.errMsg,
428		"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
#	Line 383 | Line 433 | namespace oopse {
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;
452		}
453		case 'f': {
454
#	Line 405 | Line 456 | namespace oopse {
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 414 | Line 465 | namespace oopse {
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 431 | Line 519 | namespace oopse {
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 455 | Line 641 | namespace oopse {
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 500 | Line 708 | namespace oopse {
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 515 | Line 723 | namespace oopse {
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());
#	Line 528 | Line 736 | namespace oopse {
736		}
737
738
739	<	}//end namespace oopse
739	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpReader.cpp (property svn:keywords), Revision 1025 by gezelter, Wed Aug 30 20:33:44 2006 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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