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

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1564 by chuckv, Wed May 18 19:28:52 2011 UTC

#	Line 46 | Line 46
46		#include "io/gzstream.hpp"
47		#include "io/Globals.hpp"
48
49	+
50		#ifdef IS_MPI
51		#include <mpi.h>
52		#endif //is_mpi
53
54	+	using namespace std;
55		namespace OpenMD {
56
57		DumpWriter::DumpWriter(SimInfo* info)
#	Line 194 | Line 196 | namespace OpenMD {
196		os << "    <FrameData>\n";
197
198		RealType currentTime = s->getTime();
199	+
200	+	if (isinf(currentTime) || isnan(currentTime)) {
201	+	sprintf( painCave.errMsg,
202	+	"DumpWriter detected a numerical error writing the time");
203	+	painCave.isFatal = 1;
204	+	simError();
205	+	}
206	+
207		sprintf(buffer, "        Time: %.10g\n", currentTime);
208		os << buffer;
209
210		Mat3x3d hmat;
211		hmat = s->getHmat();
212	+
213	+	for (unsigned int i = 0; i < 3; i++) {
214	+	for (unsigned int j = 0; j < 3; j++) {
215	+	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
216	+	sprintf( painCave.errMsg,
217	+	"DumpWriter detected a numerical error writing the box");
218	+	painCave.isFatal = 1;
219	+	simError();
220	+	}
221	+	}
222	+	}
223	+
224		sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
225		hmat(0, 0), hmat(1, 0), hmat(2, 0),
226		hmat(0, 1), hmat(1, 1), hmat(2, 1),
#	Line 207 | Line 229 | namespace OpenMD {
229
230		RealType chi = s->getChi();
231		RealType integralOfChiDt = s->getIntegralOfChiDt();
232	+	if (isinf(chi) || isnan(chi) ||
233	+	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
234	+	sprintf( painCave.errMsg,
235	+	"DumpWriter detected a numerical error writing the thermostat");
236	+	painCave.isFatal = 1;
237	+	simError();
238	+	}
239		sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
240		os << buffer;
241
242		Mat3x3d eta;
243		eta = s->getEta();
244	+
245	+	for (unsigned int i = 0; i < 3; i++) {
246	+	for (unsigned int j = 0; j < 3; j++) {
247	+	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
248	+	sprintf( painCave.errMsg,
249	+	"DumpWriter detected a numerical error writing the barostat");
250	+	painCave.isFatal = 1;
251	+	simError();
252	+	}
253	+	}
254	+	}
255	+
256		sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
257		eta(0, 0), eta(1, 0), eta(2, 0),
258		eta(0, 1), eta(1, 1), eta(2, 1),
#	Line 265 | Line 306 | namespace OpenMD {
306		}
307
308		const int masterNode = 0;
309	<
309	>	int nProc;
310	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
311		if (worldRank == masterNode) {
312		os << "  <Snapshot>\n";
313		writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
#	Line 273 | Line 315 | namespace OpenMD {
315
316		os << buffer;
317
318	<	int nProc;
277	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
318	>
319		for (int i = 1; i < nProc; ++i) {
320
321		// receive the length of the string buffer that was
322		// prepared by processor i
323	<
323	>
324	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
325		int recvLength;
326		MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
327		char* recvBuffer = new char[recvLength];
#	Line 296 | Line 338 | namespace OpenMD {
338		os.flush();
339		} else {
340		int sendBufferLength = buffer.size() + 1;
341	<	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
342	<	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
341	>	int myturn = 0;
342	>	for (int i = 1; i < nProc; ++i){
343	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
344	>	if (myturn == worldRank){
345	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
346	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
347	>	}
348	>	}
349		}
350
351		#endif // is_mpi
#	Line 314 | Line 362 | namespace OpenMD {
362		Vector3d pos;
363		Vector3d vel;
364		pos = integrableObject->getPos();
365	+
366	+	if (isinf(pos[0]) || isnan(pos[0]) ||
367	+	isinf(pos[1]) || isnan(pos[1]) ||
368	+	isinf(pos[2]) || isnan(pos[2]) ) {
369	+	sprintf( painCave.errMsg,
370	+	"DumpWriter detected a numerical error writing the position"
371	+	" for object %d", index);
372	+	painCave.isFatal = 1;
373	+	simError();
374	+	}
375	+
376		vel = integrableObject->getVel();
377	+
378	+	if (isinf(vel[0]) || isnan(vel[0]) ||
379	+	isinf(vel[1]) || isnan(vel[1]) ||
380	+	isinf(vel[2]) || isnan(vel[2]) ) {
381	+	sprintf( painCave.errMsg,
382	+	"DumpWriter detected a numerical error writing the velocity"
383	+	" for object %d", index);
384	+	painCave.isFatal = 1;
385	+	simError();
386	+	}
387	+
388		sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
389		pos[0], pos[1], pos[2],
390		vel[0], vel[1], vel[2]);
#	Line 325 | Line 395 | namespace OpenMD {
395		Quat4d q;
396		Vector3d ji;
397		q = integrableObject->getQ();
398	+
399	+	if (isinf(q[0]) || isnan(q[0]) ||
400	+	isinf(q[1]) || isnan(q[1]) ||
401	+	isinf(q[2]) || isnan(q[2]) ||
402	+	isinf(q[3]) || isnan(q[3]) ) {
403	+	sprintf( painCave.errMsg,
404	+	"DumpWriter detected a numerical error writing the quaternion"
405	+	" for object %d", index);
406	+	painCave.isFatal = 1;
407	+	simError();
408	+	}
409	+
410		ji = integrableObject->getJ();
411	+
412	+	if (isinf(ji[0]) || isnan(ji[0]) ||
413	+	isinf(ji[1]) || isnan(ji[1]) ||
414	+	isinf(ji[2]) || isnan(ji[2]) ) {
415	+	sprintf( painCave.errMsg,
416	+	"DumpWriter detected a numerical error writing the angular"
417	+	" momentum for object %d", index);
418	+	painCave.isFatal = 1;
419	+	simError();
420	+	}
421	+
422		sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
423		q[0], q[1], q[2], q[3],
424		ji[0], ji[1], ji[2]);
#	Line 333 | Line 426 | namespace OpenMD {
426		}
427
428		if (needForceVector_) {
429	<	type += "ft";
429	>	type += "f";
430		Vector3d frc;
431	<	Vector3d trq;
431	>
432		frc = integrableObject->getFrc();
433	<	trq = integrableObject->getTrq();
434	<
435	<	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e",
436	<	frc[0], frc[1], frc[2],
437	<	trq[0], trq[1], trq[2]);
433	>
434	>	if (isinf(frc[0]) || isnan(frc[0]) ||
435	>	isinf(frc[1]) || isnan(frc[1]) ||
436	>	isinf(frc[2]) || isnan(frc[2]) ) {
437	>	sprintf( painCave.errMsg,
438	>	"DumpWriter detected a numerical error writing the force"
439	>	" for object %d", index);
440	>	painCave.isFatal = 1;
441	>	simError();
442	>	}
443	>	sprintf(tempBuffer, " %13e %13e %13e",
444	>	frc[0], frc[1], frc[2]);
445		line += tempBuffer;
446	+
447	+	if (integrableObject->isDirectional()) {
448	+	type += "t";
449	+	Vector3d trq;
450	+
451	+	trq = integrableObject->getTrq();
452	+
453	+	if (isinf(trq[0]) || isnan(trq[0]) ||
454	+	isinf(trq[1]) || isnan(trq[1]) ||
455	+	isinf(trq[2]) || isnan(trq[2]) ) {
456	+	sprintf( painCave.errMsg,
457	+	"DumpWriter detected a numerical error writing the torque"
458	+	" for object %d", index);
459	+	painCave.isFatal = 1;
460	+	simError();
461	+	}
462	+
463	+	sprintf(tempBuffer, " %13e %13e %13e",
464	+	trq[0], trq[1], trq[2]);
465	+	line += tempBuffer;
466	+	}
467		}
468	<
468	>
469		sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
470		return std::string(tempBuffer);
471		}

Comparing trunk/src/io/DumpWriter.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1564 by chuckv, Wed May 18 19:28:52 2011 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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