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

Comparing:
trunk/src/io/RestReader.cpp (file contents), Revision 1408 by gezelter, Fri Jan 22 21:26:29 2010 UTC vs.
branches/development/src/io/RestReader.cpp (file contents), Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

#	Line 36 | Line 36
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]  Vardeman & Gezelter, in progress (2009).
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
#	Line 55 | Line 56
56		#include "primitives/Molecule.hpp"
57		#include "utils/simError.h"
58		#include "utils/MemoryUtils.hpp"
59	<	#include "utils/StringTokenizer.hpp"the
59	>	#include "utils/StringTokenizer.hpp"
60		#include "restraints/ObjectRestraint.hpp"
61		#include "restraints/MolecularRestraint.hpp"
62
#	Line 279 | Line 280 | namespace OpenMD {
280
281		int index = tokenizer.nextTokenAsInt();
282
283	<	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
283	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
284
285	<	if (integrableObject == NULL) {
285	>	if (sd == NULL) {
286		return;
287		}
288
#	Line 309 | Line 310 | namespace OpenMD {
310		}
311
312		case 'q' : {
313	<	if (integrableObject->isDirectional()) {
313	>	if (sd->isDirectional()) {
314
315		q[0] = tokenizer.nextTokenAsDouble();
316		q[1] = tokenizer.nextTokenAsDouble();
#	Line 331 | Line 332 | namespace OpenMD {
332		}
333		case 'j' : {
334		Vector3d ji;
335	<	if (integrableObject->isDirectional()) {
335	>	if (sd->isDirectional()) {
336		ji[0] = tokenizer.nextTokenAsDouble();
337		ji[1] = tokenizer.nextTokenAsDouble();
338		ji[2] = tokenizer.nextTokenAsDouble();
#	Line 365 | Line 366 | namespace OpenMD {
366		all_pos_[index] = pos;
367
368		// is this io restrained?
369	<	GenericData* data = integrableObject->getPropertyByName("Restraint");
369	>	GenericData* data = sd->getPropertyByName("Restraint");
370		ObjectRestraint* oRest;
371
372		if (data != NULL) {
#	Line 376 | Line 377 | namespace OpenMD {
377		// an ObjectRestraint:
378		oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
379		if (oRest != NULL) {
380	<	if (integrableObject->isDirectional()) {
380	>	if (sd->isDirectional()) {
381		oRest->setReferenceStructure(pos, q.toRotationMatrix3());
382		} else {
383		oRest->setReferenceStructure(pos);

Comparing:
trunk/src/io/RestReader.cpp (property svn:keywords), Revision 1408 by gezelter, Fri Jan 22 21:26:29 2010 UTC vs.
branches/development/src/io/RestReader.cpp (property svn:keywords), Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

#	Line 0 | Line 1
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