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root/OpenMD/trunk/src/io/RestReader.cpp

Comparing trunk/src/io/RestReader.cpp (file contents):
Revision 1409 by gezelter, Fri Jan 22 21:31:12 2010 UTC vs.
Revision 1796 by gezelter, Mon Sep 10 18:38:44 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 96 | Line 97 | namespace OpenMD {
97
98		#ifdef IS_MPI
99		}
100	<	MPI_Bcast(&framePos_, 1, MPI_INT, 0, MPI_COMM_WORLD);
100	>	MPI::COMM_WORLD.Bcast(&framePos_, 1, MPI::INT, 0);
101		#endif // is_mpi
102		}
103
#	Line 131 | Line 132 | namespace OpenMD {
132		}
133
134		int sendBufferSize = sendBuffer.size();
135	<	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
136	<	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
135	>	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
136	>	MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize,
137	>	MPI::CHAR, masterNode);
138
139		sstream.str(sendBuffer);
140		} else {
141		int sendBufferSize;
142	<	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
142	>	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
143		char * recvBuffer = new char[sendBufferSize+1];
144		assert(recvBuffer);
145		recvBuffer[sendBufferSize] = '\0';
146	<	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
146	>	MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
147		sstream.str(recvBuffer);
148		delete [] recvBuffer;
149		}
#	Line 279 | Line 281 | namespace OpenMD {
281
282		int index = tokenizer.nextTokenAsInt();
283
284	<	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
284	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
285
286	<	if (integrableObject == NULL) {
286	>	if (sd == NULL) {
287		return;
288		}
289
#	Line 309 | Line 311 | namespace OpenMD {
311		}
312
313		case 'q' : {
314	<	if (integrableObject->isDirectional()) {
314	>	if (sd->isDirectional()) {
315
316		q[0] = tokenizer.nextTokenAsDouble();
317		q[1] = tokenizer.nextTokenAsDouble();
#	Line 331 | Line 333 | namespace OpenMD {
333		}
334		case 'j' : {
335		Vector3d ji;
336	<	if (integrableObject->isDirectional()) {
336	>	if (sd->isDirectional()) {
337		ji[0] = tokenizer.nextTokenAsDouble();
338		ji[1] = tokenizer.nextTokenAsDouble();
339		ji[2] = tokenizer.nextTokenAsDouble();
#	Line 365 | Line 367 | namespace OpenMD {
367		all_pos_[index] = pos;
368
369		// is this io restrained?
370	<	GenericData* data = integrableObject->getPropertyByName("Restraint");
370	>	GenericData* data = sd->getPropertyByName("Restraint");
371		ObjectRestraint* oRest;
372
373		if (data != NULL) {
#	Line 376 | Line 378 | namespace OpenMD {
378		// an ObjectRestraint:
379		oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
380		if (oRest != NULL) {
381	<	if (integrableObject->isDirectional()) {
381	>	if (sd->isDirectional()) {
382		oRest->setReferenceStructure(pos, q.toRotationMatrix3());
383		} else {
384		oRest->setReferenceStructure(pos);

Comparing trunk/src/io/RestReader.cpp (property svn:keywords):
Revision 1409 by gezelter, Fri Jan 22 21:31:12 2010 UTC vs.
Revision 1796 by gezelter, Mon Sep 10 18:38:44 2012 UTC

#	Line 0 | Line 1
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