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

Comparing:
trunk/src/io/DumpWriter.cpp (file contents), Revision 1437 by gezelter, Wed Apr 21 14:59:18 2010 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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		#include "io/DumpWriter.hpp"
#	Line 60 | Line 61 | namespace OpenMD {
61		Globals* simParams = info->getSimParams();
62		needCompression_ = simParams->getCompressDumpFile();
63		needForceVector_ = simParams->getOutputForceVector();
64	+	needParticlePot_ = simParams->getOutputParticlePotential();
65		createDumpFile_ = true;
66		#ifdef HAVE_LIBZ
67		if (needCompression_) {
#	Line 138 | Line 140 | namespace OpenMD {
140
141		needCompression_ = simParams->getCompressDumpFile();
142		needForceVector_ = simParams->getOutputForceVector();
143	+	needParticlePot_ = simParams->getOutputParticlePotential();
144
145		#ifdef HAVE_LIBZ
146		if (needCompression_) {
#	Line 306 | Line 309 | namespace OpenMD {
309		}
310
311		const int masterNode = 0;
312	<
312	>	int nProc;
313	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
314		if (worldRank == masterNode) {
315		os << "  <Snapshot>\n";
316		writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
#	Line 314 | Line 318 | namespace OpenMD {
318
319		os << buffer;
320
317	–	int nProc;
318	–	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
321		for (int i = 1; i < nProc; ++i) {
322
323		// receive the length of the string buffer that was
324		// prepared by processor i
325
326	+	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
327		int recvLength;
328		MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
329		char* recvBuffer = new char[recvLength];
#	Line 337 | Line 340 | namespace OpenMD {
340		os.flush();
341		} else {
342		int sendBufferLength = buffer.size() + 1;
343	<	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
344	<	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
343	>	int myturn = 0;
344	>	for (int i = 1; i < nProc; ++i){
345	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
346	>	if (myturn == worldRank){
347	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
348	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
349	>	}
350	>	}
351		}
352
353		#endif // is_mpi
#	Line 458 | Line 467 | namespace OpenMD {
467		line += tempBuffer;
468		}
469		}
470	+	if (needParticlePot_) {
471	+	type += "u";
472	+	RealType particlePot;
473	+
474	+	particlePot = integrableObject->getParticlePot();
475	+
476	+	if (isinf(particlePot) || isnan(particlePot)) {
477	+	sprintf( painCave.errMsg,
478	+	"DumpWriter detected a numerical error writing the particle "
479	+	" potential for object %d", index);
480	+	painCave.isFatal = 1;
481	+	simError();
482	+	}
483	+	sprintf(tempBuffer, " %13e", particlePot);
484	+	line += tempBuffer;
485	+	}
486
487		sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
488		return std::string(tempBuffer);

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 1437 by gezelter, Wed Apr 21 14:59:18 2010 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 0 | Line 1
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