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root/OpenMD/branches/development/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.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1787 by gezelter, Wed Aug 29 18:13:11 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) {
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 227 | Line 226 | namespace oopse {
226		needVel_ = false;
227		}
228
229	<	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
229	>	if (storageLayout & DataStorage::dslAmat ||
230	>	storageLayout & DataStorage::dslDipole ||
231	>	storageLayout & DataStorage::dslQuadrupole) {
232		needQuaternion_ = true;
233		} else {
234		needQuaternion_ = false;
#	Line 240 | Line 241 | namespace oopse {
241		}
242
243		readSet(whichFrame);
244	+
245	+	if (needCOMprops_) {
246	+	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
247	+	Thermo thermo(info_);
248	+	Vector3d com;
249	+
250	+	if (needPos_ && needVel_) {
251	+	Vector3d comvel;
252	+	Vector3d comw;
253	+	thermo.getComAll(com, comvel);
254	+	comw = thermo.getAngularMomentum();
255	+	} else {
256	+	com = thermo.getCom();
257	+	}
258	+	}
259		}
260
261		void DumpReader::readSet(int whichFrame) {
262		std::string line;
263
264		#ifndef IS_MPI
249	–
265		inFile_->clear();
266		inFile_->seekg(framePos_[whichFrame]);
267
#	Line 280 | Line 295 | namespace oopse {
295		int sendBufferSize;
296		MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
297		char * recvBuffer = new char[sendBufferSize+1];
298	+	assert(recvBuffer);
299	+	recvBuffer[sendBufferSize] = '\0';
300		MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
301		sstream.str(recvBuffer);
302	+	delete [] recvBuffer;
303		}
304
305		std::istream& inputStream = sstream;
#	Line 305 | Line 323 | namespace oopse {
323
324		inputStream.getline(buffer, bufferSize);
325		line = buffer;
326	<	if (line.find("</Snapshot>") == std::string::npos) {
327	<	sprintf(painCave.errMsg,
328	<	"DumpReader Error: can not find </Snapshot>\n");
329	<	painCave.isFatal = 1;
330	<	simError();
331	<	}
332	<
326	>
327	>	if (line.find("<SiteData>") != std::string::npos) {
328	>	//read SiteData
329	>	readSiteData(inputStream);
330	>	} else {
331	>	if (line.find("</Snapshot>") == std::string::npos) {
332	>	sprintf(painCave.errMsg,
333	>	"DumpReader Error: can not find </Snapshot>\n");
334	>	painCave.isFatal = 1;
335	>	simError();
336	>	}
337	>	}
338		}
339
340		void DumpReader::parseDumpLine(const std::string& line) {
#	Line 322 | Line 345 | namespace oopse {
345
346		nTokens = tokenizer.countTokens();
347
348	<	if (nTokens < 2) {
348	>	if (nTokens < 2) {
349		sprintf(painCave.errMsg,
350		"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
351		painCave.isFatal = 1;
#	Line 331 | Line 354 | namespace oopse {
354
355		int index = tokenizer.nextTokenAsInt();
356
357	<	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
357	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
358
359	<	if (integrableObject == NULL) {
359	>	if (sd == NULL) {
360		return;
361		}
362		std::string type = tokenizer.nextToken();
363		int size = type.size();
364
365	+	size_t found;
366	+
367	+	if (needPos_) {
368	+	found = type.find("p");
369	+	if (found == std::string::npos) {
370	+	sprintf(painCave.errMsg,
371	+	"DumpReader Error: StuntDouble %d has no Position\n"
372	+	"\tField (\"p\") specified.\n%s\n", index,
373	+	line.c_str());
374	+	painCave.isFatal = 1;
375	+	simError();
376	+	}
377	+	}
378	+
379	+	if (sd->isDirectional()) {
380	+	if (needQuaternion_) {
381	+	found = type.find("q");
382	+	if (found == std::string::npos) {
383	+	sprintf(painCave.errMsg,
384	+	"DumpReader Error: Directional StuntDouble %d has no\n"
385	+	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
386	+	line.c_str());
387	+	painCave.isFatal = 1;
388	+	simError();
389	+	}
390	+	}
391	+	}
392	+
393		for(int i = 0; i < size; ++i) {
394		switch(type[i]) {
395
#	Line 348 | Line 399 | namespace oopse {
399		pos[1] = tokenizer.nextTokenAsDouble();
400		pos[2] = tokenizer.nextTokenAsDouble();
401		if (needPos_) {
402	<	integrableObject->setPos(pos);
402	>	sd->setPos(pos);
403		}
404		break;
405		}
#	Line 358 | Line 409 | namespace oopse {
409		vel[1] = tokenizer.nextTokenAsDouble();
410		vel[2] = tokenizer.nextTokenAsDouble();
411		if (needVel_) {
412	<	integrableObject->setVel(vel);
412	>	sd->setVel(vel);
413		}
414		break;
415		}
416
417		case 'q' : {
418		Quat4d q;
419	<	if (integrableObject->isDirectional()) {
419	>	if (sd->isDirectional()) {
420
421		q[0] = tokenizer.nextTokenAsDouble();
422		q[1] = tokenizer.nextTokenAsDouble();
#	Line 373 | Line 424 | namespace oopse {
424		q[3] = tokenizer.nextTokenAsDouble();
425
426		RealType qlen = q.length();
427	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
427	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
428
429		sprintf(painCave.errMsg,
430		"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
#	Line 384 | Line 435 | namespace oopse {
435
436		q.normalize();
437		if (needQuaternion_) {
438	<	integrableObject->setQ(q);
438	>	sd->setQ(q);
439		}
440		}
441		break;
442		}
443		case 'j' : {
444		Vector3d ji;
445	<	if (integrableObject->isDirectional()) {
445	>	if (sd->isDirectional()) {
446		ji[0] = tokenizer.nextTokenAsDouble();
447		ji[1] = tokenizer.nextTokenAsDouble();
448		ji[2] = tokenizer.nextTokenAsDouble();
449		if (needAngMom_) {
450	<	integrableObject->setJ(ji);
450	>	sd->setJ(ji);
451		}
452		}
453		break;
#	Line 407 | Line 458 | namespace oopse {
458		force[0] = tokenizer.nextTokenAsDouble();
459		force[1] = tokenizer.nextTokenAsDouble();
460		force[2] = tokenizer.nextTokenAsDouble();
461	<	integrableObject->setFrc(force);
461	>	sd->setFrc(force);
462		break;
463		}
464		case 't' : {
#	Line 416 | Line 467 | namespace oopse {
467		torque[0] = tokenizer.nextTokenAsDouble();
468		torque[1] = tokenizer.nextTokenAsDouble();
469		torque[2] = tokenizer.nextTokenAsDouble();
470	<	integrableObject->setTrq(torque);
470	>	sd->setTrq(torque);
471		break;
472		}
473	+	case 'u' : {
474	+
475	+	RealType particlePot;
476	+	particlePot = tokenizer.nextTokenAsDouble();
477	+	sd->setParticlePot(particlePot);
478	+	break;
479	+	}
480	+	case 'c' : {
481	+
482	+	RealType flucQPos;
483	+	flucQPos = tokenizer.nextTokenAsDouble();
484	+	sd->setFlucQPos(flucQPos);
485	+	break;
486	+	}
487	+	case 'w' : {
488	+
489	+	RealType flucQVel;
490	+	flucQVel = tokenizer.nextTokenAsDouble();
491	+	sd->setFlucQVel(flucQVel);
492	+	break;
493	+	}
494	+	case 'g' : {
495	+
496	+	RealType flucQFrc;
497	+	flucQFrc = tokenizer.nextTokenAsDouble();
498	+	sd->setFlucQFrc(flucQFrc);
499	+	break;
500	+	}
501	+	case 'e' : {
502	+
503	+	Vector3d eField;
504	+	eField[0] = tokenizer.nextTokenAsDouble();
505	+	eField[1] = tokenizer.nextTokenAsDouble();
506	+	eField[2] = tokenizer.nextTokenAsDouble();
507	+	sd->setElectricField(eField);
508	+	break;
509	+	}
510		default: {
511		sprintf(painCave.errMsg,
512		"DumpReader Error: %s is an unrecognized type\n", type.c_str());
#	Line 433 | Line 521 | namespace oopse {
521		}
522
523
524	<	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
524	>	void DumpReader::parseSiteLine(const std::string& line) {
525
526	+	StringTokenizer tokenizer(line);
527	+	int nTokens;
528	+
529	+	nTokens = tokenizer.countTokens();
530	+
531	+	if (nTokens < 2) {
532	+	sprintf(painCave.errMsg,
533	+	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
534	+	painCave.isFatal = 1;
535	+	simError();
536	+	}
537	+
538	+	/**
539	+	* The first token is the global integrable object index.
540	+	*/
541	+
542	+	int index = tokenizer.nextTokenAsInt();
543	+	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
544	+	if (sd == NULL) {
545	+	return;
546	+	}
547	+
548	+	/**
549	+	* Test to see if the next token is an integer or not.  If not,
550	+	* we've got data on the integrable object itself.  If there is an
551	+	* integer, we're parsing data for a site on a rigid body.
552	+	*/
553	+
554	+	std::string indexTest = tokenizer.peekNextToken();
555	+	std::istringstream i(indexTest);
556	+	int siteIndex;
557	+	if (i >> siteIndex) {
558	+	// chew up this token and parse as an int:
559	+	siteIndex = tokenizer.nextTokenAsInt();
560	+	RigidBody* rb = static_cast<RigidBody*>(sd);
561	+	sd = rb->getAtoms()[siteIndex];
562	+	}
563	+
564	+	/**
565	+	* The next token contains information on what follows.
566	+	*/
567	+	std::string type = tokenizer.nextToken();
568	+	int size = type.size();
569	+
570	+	for(int i = 0; i < size; ++i) {
571	+	switch(type[i]) {
572	+
573	+	case 'u' : {
574	+
575	+	RealType particlePot;
576	+	particlePot = tokenizer.nextTokenAsDouble();
577	+	sd->setParticlePot(particlePot);
578	+	break;
579	+	}
580	+	case 'c' : {
581	+
582	+	RealType flucQPos;
583	+	flucQPos = tokenizer.nextTokenAsDouble();
584	+	sd->setFlucQPos(flucQPos);
585	+	break;
586	+	}
587	+	case 'w' : {
588	+
589	+	RealType flucQVel;
590	+	flucQVel = tokenizer.nextTokenAsDouble();
591	+	sd->setFlucQVel(flucQVel);
592	+	break;
593	+	}
594	+	case 'g' : {
595	+
596	+	RealType flucQFrc;
597	+	flucQFrc = tokenizer.nextTokenAsDouble();
598	+	sd->setFlucQFrc(flucQFrc);
599	+	break;
600	+	}
601	+	case 'e' : {
602	+
603	+	Vector3d eField;
604	+	eField[0] = tokenizer.nextTokenAsDouble();
605	+	eField[1] = tokenizer.nextTokenAsDouble();
606	+	eField[2] = tokenizer.nextTokenAsDouble();
607	+	sd->setElectricField(eField);
608	+	break;
609	+	}
610	+	default: {
611	+	sprintf(painCave.errMsg,
612	+	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
613	+	painCave.isFatal = 1;
614	+	simError();
615	+	break;
616	+	}
617	+	}
618	+	}
619	+	}
620	+
621	+
622	+	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
623	+
624		inputStream.getline(buffer, bufferSize);
625		std::string line(buffer);
626
#	Line 457 | Line 643 | namespace oopse {
643
644		}
645
646	+	void  DumpReader::readSiteData(std::istream& inputStream) {
647	+
648	+	inputStream.getline(buffer, bufferSize);
649	+	std::string line(buffer);
650	+
651	+	if (line.find("<SiteData>") == std::string::npos) {
652	+	// site data isn't required for a simulation, so skip
653	+	return;
654	+	}
655	+
656	+	while(inputStream.getline(buffer, bufferSize)) {
657	+	line = buffer;
658	+
659	+	if(line.find("</SiteData>") != std::string::npos) {
660	+	break;
661	+	}
662	+
663	+	parseSiteLine(line);
664	+	}
665	+
666	+	}
667	+
668		void DumpReader::readFrameProperties(std::istream& inputStream) {
669
670		Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
#	Line 502 | Line 710 | namespace oopse {
710		hmat(2, 2) = tokenizer.nextTokenAsDouble();
711		s->setHmat(hmat);
712		} else if (propertyName == "Thermostat") {
713	<	RealType chi = tokenizer.nextTokenAsDouble();
714	<	RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
715	<	s->setChi(chi);
716	<	s->setIntegralOfChiDt(integralOfChiDt);
713	>	pair<RealType, RealType> thermostat;
714	>	thermostat.first = tokenizer.nextTokenAsDouble();
715	>	thermostat.second = tokenizer.nextTokenAsDouble();
716	>	s->setThermostat(thermostat);
717		} else if (propertyName == "Barostat") {
718		Mat3x3d eta;
719		eta(0, 0) = tokenizer.nextTokenAsDouble();
#	Line 517 | Line 725 | namespace oopse {
725		eta(2, 0) = tokenizer.nextTokenAsDouble();
726		eta(2, 1) = tokenizer.nextTokenAsDouble();
727		eta(2, 2) = tokenizer.nextTokenAsDouble();
728	<	s->setEta(eta);
728	>	s->setBarostat(eta);
729		} else {
730		sprintf(painCave.errMsg,
731		"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
#	Line 530 | Line 738 | namespace oopse {
738		}
739
740
741	<	}//end namespace oopse
741	>	}//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.
branches/development/src/io/DumpReader.cpp (property svn:keywords), Revision 1787 by gezelter, Wed Aug 29 18:13:11 2012 UTC

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

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+	Added lines
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>	Changed lines