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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 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

#	Line 35 | Line 35
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]  Vardeman & Gezelter, in progress (2009).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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
#	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 67 | Line 68 | namespace OpenMD {
68		namespace OpenMD {
69
70		void RestReader::scanFile(){
71	<	int lineNo = 0;
71	>
72		std::streampos prevPos;
73		std::streampos  currPos;
74
#	Line 81 | Line 82 | namespace OpenMD {
82		prevPos = currPos;
83
84		bool foundOpenSnapshotTag = false;
85	<
85	>	int lineNo = 0;
86		while(!foundOpenSnapshotTag && inFile_->getline(buffer, bufferSize)) {
87		++lineNo;
88
#	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");
369	<	ObjectRestraint* oRest;
370	>	GenericData* data = sd->getPropertyByName("Restraint");
371
372		if (data != NULL) {
373		// make sure we can reinterpret the generic data as restraint data:
#	Line 374 | Line 375 | namespace OpenMD {
375		if (restData != NULL) {
376		// make sure we can reinterpet the restraint data as a pointer to
377		// an ObjectRestraint:
378	<	oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
378	>	ObjectRestraint* 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 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

#	Line 0 | Line 1
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