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

Comparing:
trunk/src/io/DumpReader.cpp (file contents), Revision 1313 by gezelter, Wed Oct 22 20:01:49 2008 UTC vs.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1714 by gezelter, Sat May 19 18:12:46 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 341 | Line 342 | namespace oopse {
342
343		nTokens = tokenizer.countTokens();
344
345	<	if (nTokens < 2) {
345	>	if (nTokens < 2) {
346		sprintf(painCave.errMsg,
347		"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
348		painCave.isFatal = 1;
#	Line 357 | Line 358 | namespace oopse {
358		}
359		std::string type = tokenizer.nextToken();
360		int size = type.size();
361	+
362	+	size_t found;
363	+
364	+	if (needPos_) {
365	+	found = type.find("p");
366	+	if (found == std::string::npos) {
367	+	sprintf(painCave.errMsg,
368	+	"DumpReader Error: StuntDouble %d has no Position\n"
369	+	"\tField (\"p\") specified.\n%s\n", index,
370	+	line.c_str());
371	+	painCave.isFatal = 1;
372	+	simError();
373	+	}
374	+	}
375	+
376	+	if (integrableObject->isDirectional()) {
377	+	if (needQuaternion_) {
378	+	found = type.find("q");
379	+	if (found == std::string::npos) {
380	+	sprintf(painCave.errMsg,
381	+	"DumpReader Error: Directional StuntDouble %d has no\n"
382	+	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
383	+	line.c_str());
384	+	painCave.isFatal = 1;
385	+	simError();
386	+	}
387	+	}
388	+	}
389
390		for(int i = 0; i < size; ++i) {
391		switch(type[i]) {
#	Line 392 | Line 421 | namespace oopse {
421		q[3] = tokenizer.nextTokenAsDouble();
422
423		RealType qlen = q.length();
424	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
424	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
425
426		sprintf(painCave.errMsg,
427		"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
#	Line 436 | Line 465 | namespace oopse {
465		torque[1] = tokenizer.nextTokenAsDouble();
466		torque[2] = tokenizer.nextTokenAsDouble();
467		integrableObject->setTrq(torque);
468	+	break;
469	+	}
470	+	case 'u' : {
471	+
472	+	RealType particlePot;
473	+	particlePot = tokenizer.nextTokenAsDouble();
474	+	integrableObject->setParticlePot(particlePot);
475		break;
476		}
477	+	case 'c' : {
478	+
479	+	RealType flucQPos;
480	+	flucQPos = tokenizer.nextTokenAsDouble();
481	+	integrableObject->setFlucQPos(flucQPos);
482	+	break;
483	+	}
484	+	case 'w' : {
485	+
486	+	RealType flucQVel;
487	+	flucQVel = tokenizer.nextTokenAsDouble();
488	+	integrableObject->setFlucQVel(flucQVel);
489	+	break;
490	+	}
491	+	case 'g' : {
492	+
493	+	RealType flucQFrc;
494	+	flucQFrc = tokenizer.nextTokenAsDouble();
495	+	integrableObject->setFlucQFrc(flucQFrc);
496	+	break;
497	+	}
498	+	case 'e' : {
499	+
500	+	Vector3d eField;
501	+	eField[0] = tokenizer.nextTokenAsDouble();
502	+	eField[1] = tokenizer.nextTokenAsDouble();
503	+	eField[2] = tokenizer.nextTokenAsDouble();
504	+	integrableObject->setElectricField(eField);
505	+	break;
506	+	}
507		default: {
508		sprintf(painCave.errMsg,
509		"DumpReader Error: %s is an unrecognized type\n", type.c_str());
#	Line 549 | Line 615 | namespace oopse {
615		}
616
617
618	<	}//end namespace oopse
618	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpReader.cpp (property svn:keywords), Revision 1313 by gezelter, Wed Oct 22 20:01:49 2008 UTC vs.
branches/development/src/io/DumpReader.cpp (property svn:keywords), Revision 1714 by gezelter, Sat May 19 18:12:46 2012 UTC

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