ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing:
trunk/src/io/DumpWriter.cpp (file contents), Revision 1025 by gezelter, Wed Aug 30 20:33:44 2006 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1712 by gezelter, Sat May 19 13:30:21 2012 UTC

#	Line 1 | Line 1
1		/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
2	>	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
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]  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 46 | Line 47
47		#include "io/gzstream.hpp"
48		#include "io/Globals.hpp"
49
50	+
51		#ifdef IS_MPI
52		#include <mpi.h>
53		#endif //is_mpi
54
55	<	namespace oopse {
55	>	using namespace std;
56	>	namespace OpenMD {
57
58		DumpWriter::DumpWriter(SimInfo* info)
59		: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
#	Line 58 | Line 61 | namespace oopse {
61		Globals* simParams = info->getSimParams();
62		needCompression_ = simParams->getCompressDumpFile();
63		needForceVector_ = simParams->getOutputForceVector();
64	+	needParticlePot_ = simParams->getOutputParticlePotential();
65	+	cerr << "DW npp = " << needParticlePot_ << "\n";
66		createDumpFile_ = true;
67		#ifdef HAVE_LIBZ
68		if (needCompression_) {
#	Line 97 | Line 102 | namespace oopse {
102
103		needCompression_ = simParams->getCompressDumpFile();
104		needForceVector_ = simParams->getOutputForceVector();
105	+	needParticlePot_ = simParams->getOutputParticlePotential();
106		createDumpFile_ = true;
107		#ifdef HAVE_LIBZ
108		if (needCompression_) {
#	Line 136 | Line 142 | namespace oopse {
142
143		needCompression_ = simParams->getCompressDumpFile();
144		needForceVector_ = simParams->getOutputForceVector();
145	+	needParticlePot_ = simParams->getOutputParticlePotential();
146
147		#ifdef HAVE_LIBZ
148		if (needCompression_) {
#	Line 194 | Line 201 | namespace oopse {
201		os << "    <FrameData>\n";
202
203		RealType currentTime = s->getTime();
204	+
205	+	if (isinf(currentTime) || isnan(currentTime)) {
206	+	sprintf( painCave.errMsg,
207	+	"DumpWriter detected a numerical error writing the time");
208	+	painCave.isFatal = 1;
209	+	simError();
210	+	}
211	+
212		sprintf(buffer, "        Time: %.10g\n", currentTime);
213		os << buffer;
214
215		Mat3x3d hmat;
216		hmat = s->getHmat();
217	+
218	+	for (unsigned int i = 0; i < 3; i++) {
219	+	for (unsigned int j = 0; j < 3; j++) {
220	+	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
221	+	sprintf( painCave.errMsg,
222	+	"DumpWriter detected a numerical error writing the box");
223	+	painCave.isFatal = 1;
224	+	simError();
225	+	}
226	+	}
227	+	}
228	+
229		sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
230		hmat(0, 0), hmat(1, 0), hmat(2, 0),
231		hmat(0, 1), hmat(1, 1), hmat(2, 1),
#	Line 207 | Line 234 | namespace oopse {
234
235		RealType chi = s->getChi();
236		RealType integralOfChiDt = s->getIntegralOfChiDt();
237	+	if (isinf(chi) || isnan(chi) ||
238	+	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
239	+	sprintf( painCave.errMsg,
240	+	"DumpWriter detected a numerical error writing the thermostat");
241	+	painCave.isFatal = 1;
242	+	simError();
243	+	}
244		sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
245		os << buffer;
246
247		Mat3x3d eta;
248		eta = s->getEta();
249	+
250	+	for (unsigned int i = 0; i < 3; i++) {
251	+	for (unsigned int j = 0; j < 3; j++) {
252	+	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
253	+	sprintf( painCave.errMsg,
254	+	"DumpWriter detected a numerical error writing the barostat");
255	+	painCave.isFatal = 1;
256	+	simError();
257	+	}
258	+	}
259	+	}
260	+
261		sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
262		eta(0, 0), eta(1, 0), eta(2, 0),
263		eta(0, 1), eta(1, 1), eta(2, 1),
#	Line 240 | Line 286 | namespace oopse {
286		os << "    <StuntDoubles>\n";
287		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
288
289	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
289	>
290	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
291		integrableObject = mol->nextIntegrableObject(ii)) {
292	<	os << prepareDumpLine(integrableObject);
293	<
292	>	os << prepareDumpLine(integrableObject);
293	>
294		}
295		}
296		os << "    </StuntDoubles>\n";
297	<
297	>
298		os << "  </Snapshot>\n";
299
300		os.flush();
#	Line 255 | Line 302 | namespace oopse {
302		//every node prepares the dump lines for integrable objects belong to itself
303		std::string buffer;
304		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
305	<
305	>
306	>
307		for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
308		integrableObject = mol->nextIntegrableObject(ii)) {
309	<	buffer += prepareDumpLine(integrableObject);
309	>	buffer += prepareDumpLine(integrableObject);
310		}
311		}
312
313		const int masterNode = 0;
314	<
314	>	int nProc;
315	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
316		if (worldRank == masterNode) {
317		os << "  <Snapshot>\n";
318		writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
#	Line 271 | Line 320 | namespace oopse {
320
321		os << buffer;
322
274	–	int nProc;
275	–	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
323		for (int i = 1; i < nProc; ++i) {
324
325		// receive the length of the string buffer that was
326		// prepared by processor i
327
328	+	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
329		int recvLength;
330		MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
331		char* recvBuffer = new char[recvLength];
#	Line 285 | Line 333 | namespace oopse {
333		} else {
334		MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
335		os << recvBuffer;
336	<	delete recvBuffer;
336	>	delete [] recvBuffer;
337		}
338		}
339		os << "    </StuntDoubles>\n";
#	Line 294 | Line 342 | namespace oopse {
342		os.flush();
343		} else {
344		int sendBufferLength = buffer.size() + 1;
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);
345	>	int myturn = 0;
346	>	for (int i = 1; i < nProc; ++i){
347	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
348	>	if (myturn == worldRank){
349	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
350	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
351	>	}
352	>	}
353		}
354
355		#endif // is_mpi
#	Line 312 | Line 366 | namespace oopse {
366		Vector3d pos;
367		Vector3d vel;
368		pos = integrableObject->getPos();
369	+
370	+	if (isinf(pos[0]) || isnan(pos[0]) ||
371	+	isinf(pos[1]) || isnan(pos[1]) ||
372	+	isinf(pos[2]) || isnan(pos[2]) ) {
373	+	sprintf( painCave.errMsg,
374	+	"DumpWriter detected a numerical error writing the position"
375	+	" for object %d", index);
376	+	painCave.isFatal = 1;
377	+	simError();
378	+	}
379	+
380		vel = integrableObject->getVel();
381	+
382	+	if (isinf(vel[0]) || isnan(vel[0]) ||
383	+	isinf(vel[1]) || isnan(vel[1]) ||
384	+	isinf(vel[2]) || isnan(vel[2]) ) {
385	+	sprintf( painCave.errMsg,
386	+	"DumpWriter detected a numerical error writing the velocity"
387	+	" for object %d", index);
388	+	painCave.isFatal = 1;
389	+	simError();
390	+	}
391	+
392		sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
393		pos[0], pos[1], pos[2],
394		vel[0], vel[1], vel[2]);
#	Line 323 | Line 399 | namespace oopse {
399		Quat4d q;
400		Vector3d ji;
401		q = integrableObject->getQ();
402	+
403	+	if (isinf(q[0]) || isnan(q[0]) ||
404	+	isinf(q[1]) || isnan(q[1]) ||
405	+	isinf(q[2]) || isnan(q[2]) ||
406	+	isinf(q[3]) || isnan(q[3]) ) {
407	+	sprintf( painCave.errMsg,
408	+	"DumpWriter detected a numerical error writing the quaternion"
409	+	" for object %d", index);
410	+	painCave.isFatal = 1;
411	+	simError();
412	+	}
413	+
414		ji = integrableObject->getJ();
415	+
416	+	if (isinf(ji[0]) || isnan(ji[0]) ||
417	+	isinf(ji[1]) || isnan(ji[1]) ||
418	+	isinf(ji[2]) || isnan(ji[2]) ) {
419	+	sprintf( painCave.errMsg,
420	+	"DumpWriter detected a numerical error writing the angular"
421	+	" momentum for object %d", index);
422	+	painCave.isFatal = 1;
423	+	simError();
424	+	}
425	+
426		sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
427		q[0], q[1], q[2], q[3],
428		ji[0], ji[1], ji[2]);
#	Line 331 | Line 430 | namespace oopse {
430		}
431
432		if (needForceVector_) {
433	<	type += "ft";
433	>	type += "f";
434		Vector3d frc;
435	<	Vector3d trq;
435	>
436		frc = integrableObject->getFrc();
437	<	trq = integrableObject->getTrq();
438	<
439	<	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e",
440	<	frc[0], frc[1], frc[2],
441	<	trq[0], trq[1], trq[2]);
437	>
438	>	if (isinf(frc[0]) || isnan(frc[0]) ||
439	>	isinf(frc[1]) || isnan(frc[1]) ||
440	>	isinf(frc[2]) || isnan(frc[2]) ) {
441	>	sprintf( painCave.errMsg,
442	>	"DumpWriter detected a numerical error writing the force"
443	>	" for object %d", index);
444	>	painCave.isFatal = 1;
445	>	simError();
446	>	}
447	>	sprintf(tempBuffer, " %13e %13e %13e",
448	>	frc[0], frc[1], frc[2]);
449		line += tempBuffer;
450	+
451	+	if (integrableObject->isDirectional()) {
452	+	type += "t";
453	+	Vector3d trq;
454	+
455	+	trq = integrableObject->getTrq();
456	+
457	+	if (isinf(trq[0]) || isnan(trq[0]) ||
458	+	isinf(trq[1]) || isnan(trq[1]) ||
459	+	isinf(trq[2]) || isnan(trq[2]) ) {
460	+	sprintf( painCave.errMsg,
461	+	"DumpWriter detected a numerical error writing the torque"
462	+	" for object %d", index);
463	+	painCave.isFatal = 1;
464	+	simError();
465	+	}
466	+
467	+	sprintf(tempBuffer, " %13e %13e %13e",
468	+	trq[0], trq[1], trq[2]);
469	+	line += tempBuffer;
470	+	}
471		}
472	<
472	>	if (needParticlePot_) {
473	>	type += "u";
474	>	RealType particlePot;
475	>
476	>	particlePot = integrableObject->getParticlePot();
477	>
478	>	if (isinf(particlePot) || isnan(particlePot)) {
479	>	sprintf( painCave.errMsg,
480	>	"DumpWriter detected a numerical error writing the particle "
481	>	" potential for object %d", index);
482	>	painCave.isFatal = 1;
483	>	simError();
484	>	}
485	>	sprintf(tempBuffer, " %13e", particlePot);
486	>	line += tempBuffer;
487	>	}
488	>
489		sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
490		return std::string(tempBuffer);
491		}
#	Line 424 | Line 567 | namespace oopse {
567		newOStream = new std::ofstream(filename.c_str());
568		#endif
569		//write out MetaData first
570	<	(*newOStream) << "<OOPSE version=4>" << std::endl;
570	>	(*newOStream) << "<OpenMD version=1>" << std::endl;
571		(*newOStream) << "  <MetaData>" << std::endl;
572		(*newOStream) << info_->getRawMetaData();
573		(*newOStream) << "  </MetaData>" << std::endl;
#	Line 433 | Line 576 | namespace oopse {
576
577		void DumpWriter::writeClosing(std::ostream& os) {
578
579	<	os << "</OOPSE>\n";
579	>	os << "</OpenMD>\n";
580		os.flush();
581		}
582
583	<	}//end namespace oopse
583	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 1025 by gezelter, Wed Aug 30 20:33:44 2006 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1712 by gezelter, Sat May 19 13:30:21 2012 UTC

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

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines