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

Comparing:
trunk/src/io/DumpReader.cpp (file contents), Revision 1249 by gezelter, Mon Jun 2 02:42:50 2008 UTC vs.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1752 by gezelter, Sun Jun 10 14:05:02 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 67 | Line 68
68		#endif // is_mpi
69
70
71	<	namespace oopse {
71	>	namespace OpenMD {
72
73		DumpReader::DumpReader(SimInfo* info, const std::string& filename)
74		: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
#	Line 142 | Line 143 | namespace oopse {
143		prevPos = currPos;
144		bool foundOpenSnapshotTag = false;
145		bool foundClosedSnapshotTag = false;
146	+	bool foundOpenSiteDataTag = false;
147		while(inFile_->getline(buffer, bufferSize)) {
148		++lineNo;
149
#	Line 296 | Line 298 | namespace oopse {
298		int sendBufferSize;
299		MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
300		char * recvBuffer = new char[sendBufferSize+1];
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 321 | 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 338 | 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 354 | Line 364 | namespace oopse {
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 (integrableObject->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]) {
#	Line 389 | 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 433 | Line 471 | namespace oopse {
471		torque[1] = tokenizer.nextTokenAsDouble();
472		torque[2] = tokenizer.nextTokenAsDouble();
473		integrableObject->setTrq(torque);
474	+	break;
475	+	}
476	+	case 'u' : {
477	+
478	+	RealType particlePot;
479	+	particlePot = tokenizer.nextTokenAsDouble();
480	+	integrableObject->setParticlePot(particlePot);
481	+	break;
482	+	}
483	+	case 'c' : {
484	+
485	+	RealType flucQPos;
486	+	flucQPos = tokenizer.nextTokenAsDouble();
487	+	integrableObject->setFlucQPos(flucQPos);
488		break;
489		}
490	+	case 'w' : {
491	+
492	+	RealType flucQVel;
493	+	flucQVel = tokenizer.nextTokenAsDouble();
494	+	integrableObject->setFlucQVel(flucQVel);
495	+	break;
496	+	}
497	+	case 'g' : {
498	+
499	+	RealType flucQFrc;
500	+	flucQFrc = tokenizer.nextTokenAsDouble();
501	+	integrableObject->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	+	integrableObject->setElectricField(eField);
511	+	break;
512	+	}
513		default: {
514		sprintf(painCave.errMsg,
515		"DumpReader Error: %s is an unrecognized type\n", type.c_str());
#	Line 449 | Line 524 | namespace oopse {
524		}
525
526
527	<	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
527	>	void DumpReader::parseSiteLine(const std::string& line) {
528
529	+	StringTokenizer tokenizer(line);
530	+	int nTokens;
531	+
532	+	nTokens = tokenizer.countTokens();
533	+
534	+	if (nTokens < 2) {
535	+	sprintf(painCave.errMsg,
536	+	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
537	+	painCave.isFatal = 1;
538	+	simError();
539	+	}
540	+
541	+	/**
542	+	* The first token is the global integrable object index.
543	+	*/
544	+
545	+	int index = tokenizer.nextTokenAsInt();
546	+	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
547	+	if (integrableObject == NULL) {
548	+	return;
549	+	}
550	+	StuntDouble* sd = integrableObject;
551	+
552	+	/**
553	+	* Test to see if the next token is an integer or not.  If not,
554	+	* we've got data on the integrable object itself.  If there is an
555	+	* integer, we're parsing data for a site on a rigid body.
556	+	*/
557	+
558	+	std::string indexTest = tokenizer.peekNextToken();
559	+	std::istringstream i(indexTest);
560	+	int siteIndex;
561	+	if (i >> siteIndex) {
562	+	// chew up this token and parse as an int:
563	+	siteIndex = tokenizer.nextTokenAsInt();
564	+	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
565	+	sd = rb->getAtoms()[siteIndex];
566	+	}
567	+
568	+	/**
569	+	* The next token contains information on what follows.
570	+	*/
571	+	std::string type = tokenizer.nextToken();
572	+	int size = type.size();
573	+
574	+	for(int i = 0; i < size; ++i) {
575	+	switch(type[i]) {
576	+
577	+	case 'u' : {
578	+
579	+	RealType particlePot;
580	+	particlePot = tokenizer.nextTokenAsDouble();
581	+	sd->setParticlePot(particlePot);
582	+	break;
583	+	}
584	+	case 'c' : {
585	+
586	+	RealType flucQPos;
587	+	flucQPos = tokenizer.nextTokenAsDouble();
588	+	sd->setFlucQPos(flucQPos);
589	+	break;
590	+	}
591	+	case 'w' : {
592	+
593	+	RealType flucQVel;
594	+	flucQVel = tokenizer.nextTokenAsDouble();
595	+	sd->setFlucQVel(flucQVel);
596	+	break;
597	+	}
598	+	case 'g' : {
599	+
600	+	RealType flucQFrc;
601	+	flucQFrc = tokenizer.nextTokenAsDouble();
602	+	sd->setFlucQFrc(flucQFrc);
603	+	break;
604	+	}
605	+	case 'e' : {
606	+
607	+	Vector3d eField;
608	+	eField[0] = tokenizer.nextTokenAsDouble();
609	+	eField[1] = tokenizer.nextTokenAsDouble();
610	+	eField[2] = tokenizer.nextTokenAsDouble();
611	+	sd->setElectricField(eField);
612	+	break;
613	+	}
614	+	default: {
615	+	sprintf(painCave.errMsg,
616	+	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
617	+	painCave.isFatal = 1;
618	+	simError();
619	+	break;
620	+	}
621	+	}
622	+	}
623	+	}
624	+
625	+
626	+	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
627	+
628		inputStream.getline(buffer, bufferSize);
629		std::string line(buffer);
630
#	Line 473 | Line 647 | namespace oopse {
647
648		}
649
650	+	void  DumpReader::readSiteData(std::istream& inputStream) {
651	+
652	+	inputStream.getline(buffer, bufferSize);
653	+	std::string line(buffer);
654	+
655	+	if (line.find("<SiteData>") == std::string::npos) {
656	+	// site data isn't required for a simulation, so skip
657	+	return;
658	+	}
659	+
660	+	while(inputStream.getline(buffer, bufferSize)) {
661	+	line = buffer;
662	+
663	+	if(line.find("</SiteData>") != std::string::npos) {
664	+	break;
665	+	}
666	+
667	+	parseSiteLine(line);
668	+	}
669	+
670	+	}
671	+
672		void DumpReader::readFrameProperties(std::istream& inputStream) {
673
674		Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
#	Line 546 | Line 742 | namespace oopse {
742		}
743
744
745	<	}//end namespace oopse
745	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpReader.cpp (property svn:keywords), Revision 1249 by gezelter, Mon Jun 2 02:42:50 2008 UTC vs.
branches/development/src/io/DumpReader.cpp (property svn:keywords), Revision 1752 by gezelter, Sun Jun 10 14:05:02 2012 UTC

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