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root/OpenMD/trunk/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.
Revision 2020 by gezelter, Mon Sep 22 19:18:35 2014 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, 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	+	#include "config.h"
44	+
45	+	#ifdef IS_MPI
46	+	#include <mpi.h>
47	+	#endif
48
49		#include "io/DumpWriter.hpp"
50		#include "primitives/Molecule.hpp"
51		#include "utils/simError.h"
52		#include "io/basic_teebuf.hpp"
53	+	#ifdef HAVE_ZLIB
54		#include "io/gzstream.hpp"
55	+	#endif
56		#include "io/Globals.hpp"
57
58	<	#ifdef IS_MPI
59	<	#include <mpi.h>
60	<	#endif //is_mpi
58	>	#ifdef _MSC_VER
59	>	#define isnan(x) _isnan((x))
60	>	#define isinf(x) (!_finite(x) && !_isnan(x))
61	>	#endif
62
63	<	namespace oopse {
63	>	using namespace std;
64	>	namespace OpenMD {
65
66		DumpWriter::DumpWriter(SimInfo* info)
67	<	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
67	>	: info_(info), filename_(info->getDumpFileName()),
68	>	eorFilename_(info->getFinalConfigFileName()){
69
70		Globals* simParams = info->getSimParams();
71	<	needCompression_ = simParams->getCompressDumpFile();
72	<	needForceVector_ = simParams->getOutputForceVector();
71	>	needCompression_   = simParams->getCompressDumpFile();
72	>	needForceVector_   = simParams->getOutputForceVector();
73	>	needParticlePot_   = simParams->getOutputParticlePotential();
74	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
75	>	needElectricField_ = simParams->getOutputElectricField();
76	>	needSitePotential_ = simParams->getOutputSitePotential();
77	>
78	>	if (needParticlePot_ || needFlucQ_ || needElectricField_ ||
79	>	needSitePotential_) {
80	>	doSiteData_ = true;
81	>	} else {
82	>	doSiteData_ = false;
83	>	}
84	>
85		createDumpFile_ = true;
86		#ifdef HAVE_LIBZ
87		if (needCompression_) {
#	Line 95 | Line 119 | namespace oopse {
119		Globals* simParams = info->getSimParams();
120		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
121
122	<	needCompression_ = simParams->getCompressDumpFile();
123	<	needForceVector_ = simParams->getOutputForceVector();
122	>	needCompression_   = simParams->getCompressDumpFile();
123	>	needForceVector_   = simParams->getOutputForceVector();
124	>	needParticlePot_   = simParams->getOutputParticlePotential();
125	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
126	>	needElectricField_ = simParams->getOutputElectricField();
127	>	needSitePotential_ = simParams->getOutputSitePotential();
128	>
129	>	if (needParticlePot_ || needFlucQ_ || needElectricField_ ||
130	>	needSitePotential_) {
131	>	doSiteData_ = true;
132	>	} else {
133	>	doSiteData_ = false;
134	>	}
135	>
136		createDumpFile_ = true;
137		#ifdef HAVE_LIBZ
138		if (needCompression_) {
#	Line 134 | Line 170 | namespace oopse {
170		Globals* simParams = info->getSimParams();
171		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
172
173	<	needCompression_ = simParams->getCompressDumpFile();
174	<	needForceVector_ = simParams->getOutputForceVector();
175	<
173	>	needCompression_   = simParams->getCompressDumpFile();
174	>	needForceVector_   = simParams->getOutputForceVector();
175	>	needParticlePot_   = simParams->getOutputParticlePotential();
176	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
177	>	needElectricField_ = simParams->getOutputElectricField();
178	>	needSitePotential_ = simParams->getOutputSitePotential();
179	>
180	>	if (needParticlePot_ || needFlucQ_ || needElectricField_ ||
181	>	needSitePotential_) {
182	>	doSiteData_ = true;
183	>	} else {
184	>	doSiteData_ = false;
185	>	}
186	>
187		#ifdef HAVE_LIBZ
188		if (needCompression_) {
189		filename_ += ".gz";
#	Line 194 | Line 241 | namespace oopse {
241		os << "    <FrameData>\n";
242
243		RealType currentTime = s->getTime();
244	+
245	+	if (isinf(currentTime) || isnan(currentTime)) {
246	+	sprintf( painCave.errMsg,
247	+	"DumpWriter detected a numerical error writing the time");
248	+	painCave.isFatal = 1;
249	+	simError();
250	+	}
251	+
252		sprintf(buffer, "        Time: %.10g\n", currentTime);
253		os << buffer;
254
255		Mat3x3d hmat;
256		hmat = s->getHmat();
257	+
258	+	for (unsigned int i = 0; i < 3; i++) {
259	+	for (unsigned int j = 0; j < 3; j++) {
260	+	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
261	+	sprintf( painCave.errMsg,
262	+	"DumpWriter detected a numerical error writing the box");
263	+	painCave.isFatal = 1;
264	+	simError();
265	+	}
266	+	}
267	+	}
268	+
269		sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
270		hmat(0, 0), hmat(1, 0), hmat(2, 0),
271		hmat(0, 1), hmat(1, 1), hmat(2, 1),
272		hmat(0, 2), hmat(1, 2), hmat(2, 2));
273		os << buffer;
274
275	<	RealType chi = s->getChi();
276	<	RealType integralOfChiDt = s->getIntegralOfChiDt();
277	<	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
275	>	pair<RealType, RealType> thermostat = s->getThermostat();
276	>
277	>	if (isinf(thermostat.first)  || isnan(thermostat.first) ||
278	>	isinf(thermostat.second) || isnan(thermostat.second)) {
279	>	sprintf( painCave.errMsg,
280	>	"DumpWriter detected a numerical error writing the thermostat");
281	>	painCave.isFatal = 1;
282	>	simError();
283	>	}
284	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
285	>	thermostat.second);
286		os << buffer;
287
288		Mat3x3d eta;
289	<	eta = s->getEta();
289	>	eta = s->getBarostat();
290	>
291	>	for (unsigned int i = 0; i < 3; i++) {
292	>	for (unsigned int j = 0; j < 3; j++) {
293	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
294	>	sprintf( painCave.errMsg,
295	>	"DumpWriter detected a numerical error writing the barostat");
296	>	painCave.isFatal = 1;
297	>	simError();
298	>	}
299	>	}
300	>	}
301	>
302		sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
303		eta(0, 0), eta(1, 0), eta(2, 0),
304		eta(0, 1), eta(1, 1), eta(2, 1),
#	Line 228 | Line 315 | namespace oopse {
315		#endif
316
317		Molecule* mol;
318	<	StuntDouble* integrableObject;
318	>	StuntDouble* sd;
319		SimInfo::MoleculeIterator mi;
320		Molecule::IntegrableObjectIterator ii;
321	+	RigidBody::AtomIterator ai;
322
323		#ifndef IS_MPI
324		os << "  <Snapshot>\n";
#	Line 238 | Line 326 | namespace oopse {
326		writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
327
328		os << "    <StuntDoubles>\n";
329	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
330	<
331	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
332	<	integrableObject = mol->nextIntegrableObject(ii)) {
333	<	os << prepareDumpLine(integrableObject);
334	<
329	>	for (mol = info_->beginMolecule(mi); mol != NULL;
330	>	mol = info_->nextMolecule(mi)) {
331	>
332	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
333	>	sd = mol->nextIntegrableObject(ii)) {
334	>	os << prepareDumpLine(sd);
335	>
336		}
337		}
338		os << "    </StuntDoubles>\n";
339
340	+	if (doSiteData_) {
341	+	os << "    <SiteData>\n";
342	+	for (mol = info_->beginMolecule(mi); mol != NULL;
343	+	mol = info_->nextMolecule(mi)) {
344	+
345	+	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
346	+	sd = mol->nextIntegrableObject(ii)) {
347	+
348	+	int ioIndex = sd->getGlobalIntegrableObjectIndex();
349	+	// do one for the IO itself
350	+	os << prepareSiteLine(sd, ioIndex, 0);
351	+
352	+	if (sd->isRigidBody()) {
353	+
354	+	RigidBody* rb = static_cast<RigidBody*>(sd);
355	+	int siteIndex = 0;
356	+	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
357	+	atom = rb->nextAtom(ai)) {
358	+	os << prepareSiteLine(atom, ioIndex, siteIndex);
359	+	siteIndex++;
360	+	}
361	+	}
362	+	}
363	+	}
364	+	os << "    </SiteData>\n";
365	+	}
366		os << "  </Snapshot>\n";
367
368		os.flush();
369		#else
370	+
371	+	const int masterNode = 0;
372	+	int worldRank;
373	+	int nProc;
374	+
375	+	MPI_Comm_size( MPI_COMM_WORLD, &nProc);
376	+	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
377	+
378	+
379	+	if (worldRank == masterNode) {
380	+	os << "  <Snapshot>\n";
381	+	writeFrameProperties(os,
382	+	info_->getSnapshotManager()->getCurrentSnapshot());
383	+	os << "    <StuntDoubles>\n";
384	+	}
385	+
386		//every node prepares the dump lines for integrable objects belong to itself
387		std::string buffer;
388	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
389	<
390	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
391	<	integrableObject = mol->nextIntegrableObject(ii)) {
392	<	buffer += prepareDumpLine(integrableObject);
388	>	for (mol = info_->beginMolecule(mi); mol != NULL;
389	>	mol = info_->nextMolecule(mi)) {
390	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
391	>	sd = mol->nextIntegrableObject(ii)) {
392	>	buffer += prepareDumpLine(sd);
393		}
394		}
395
265	–	const int masterNode = 0;
266	–
396		if (worldRank == masterNode) {
268	–	os << "  <Snapshot>\n";
269	–	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
270	–	os << "    <StuntDoubles>\n";
271	–
397		os << buffer;
398	<
274	<	int nProc;
275	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
398	>
399		for (int i = 1; i < nProc; ++i) {
400	+	// tell processor i to start sending us data:
401
402	<	// receive the length of the string buffer that was
279	<	// prepared by processor i
402	>	MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
403
404	+	// receive the length of the string buffer that was
405	+	// prepared by processor i:
406		int recvLength;
407	<	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
407	>	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
408	>	&istatus);
409	>
410	>	// create a buffer to receive the data
411		char* recvBuffer = new char[recvLength];
412		if (recvBuffer == NULL) {
413		} else {
414	<	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
414	>	// receive the data:
415	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
416	>	MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
417	>	// send it to the file:
418		os << recvBuffer;
419	<	delete recvBuffer;
419	>	// get rid of the receive buffer:
420	>	delete [] recvBuffer;
421		}
422		}
291	–	os << "    </StuntDoubles>\n";
292	–
293	–	os << "  </Snapshot>\n";
294	–	os.flush();
423		} else {
424		int sendBufferLength = buffer.size() + 1;
425	<	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
426	<	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
425	>	int myturn = 0;
426	>	for (int i = 1; i < nProc; ++i){
427	>	// wait for the master node to call our number:
428	>	MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
429	>	if (myturn == worldRank){
430	>	// send the length of our buffer:
431	>
432	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
433	>
434	>	// send our buffer:
435	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
436	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
437	>
438	>	}
439	>	}
440		}
441	+
442	+	if (worldRank == masterNode) {
443	+	os << "    </StuntDoubles>\n";
444	+	}
445
446	<	#endif // is_mpi
446	>	if (doSiteData_) {
447	>	if (worldRank == masterNode) {
448	>	os << "    <SiteData>\n";
449	>	}
450	>	buffer.clear();
451	>	for (mol = info_->beginMolecule(mi); mol != NULL;
452	>	mol = info_->nextMolecule(mi)) {
453	>
454	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
455	>	sd = mol->nextIntegrableObject(ii)) {
456	>
457	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
458	>	// do one for the IO itself
459	>	buffer += prepareSiteLine(sd, ioIndex, 0);
460
461	<	}
461	>	if (sd->isRigidBody()) {
462	>
463	>	RigidBody* rb = static_cast<RigidBody*>(sd);
464	>	int siteIndex = 0;
465	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
466	>	atom = rb->nextAtom(ai)) {
467	>	buffer += prepareSiteLine(atom, ioIndex, siteIndex);
468	>	siteIndex++;
469	>	}
470	>	}
471	>	}
472	>	}
473
474	<	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
474	>	if (worldRank == masterNode) {
475	>	os << buffer;
476	>
477	>	for (int i = 1; i < nProc; ++i) {
478	>
479	>	// tell processor i to start sending us data:
480	>	MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
481	>
482	>	// receive the length of the string buffer that was
483	>	// prepared by processor i:
484	>	int recvLength;
485	>	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
486	>	&istatus);
487	>
488	>	// create a buffer to receive the data
489	>	char* recvBuffer = new char[recvLength];
490	>	if (recvBuffer == NULL) {
491	>	} else {
492	>	// receive the data:
493	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
494	>	MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
495	>	// send it to the file:
496	>	os << recvBuffer;
497	>	// get rid of the receive buffer:
498	>	delete [] recvBuffer;
499	>	}
500	>	}
501	>	} else {
502	>	int sendBufferLength = buffer.size() + 1;
503	>	int myturn = 0;
504	>	for (int i = 1; i < nProc; ++i){
505	>	// wait for the master node to call our number:
506	>	MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
507	>	if (myturn == worldRank){
508	>	// send the length of our buffer:
509	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
510	>	// send our buffer:
511	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
512	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
513	>	}
514	>	}
515	>	}
516	>
517	>	if (worldRank == masterNode) {
518	>	os << "    </SiteData>\n";
519	>	}
520	>	}
521	>
522	>	if (worldRank == masterNode) {
523	>	os << "  </Snapshot>\n";
524	>	os.flush();
525	>	}
526	>
527	>	#endif // is_mpi
528	>
529	>	}
530	>
531	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
532
533	<	int index = integrableObject->getGlobalIntegrableObjectIndex();
533	>	int index = sd->getGlobalIntegrableObjectIndex();
534		std::string type("pv");
535		std::string line;
536		char tempBuffer[4096];
537
538		Vector3d pos;
539		Vector3d vel;
540	<	pos = integrableObject->getPos();
541	<	vel = integrableObject->getVel();
540	>	pos = sd->getPos();
541	>
542	>	if (isinf(pos[0]) || isnan(pos[0]) ||
543	>	isinf(pos[1]) || isnan(pos[1]) ||
544	>	isinf(pos[2]) || isnan(pos[2]) ) {
545	>	sprintf( painCave.errMsg,
546	>	"DumpWriter detected a numerical error writing the position"
547	>	" for object %d", index);
548	>	painCave.isFatal = 1;
549	>	simError();
550	>	}
551	>
552	>	vel = sd->getVel();
553	>
554	>	if (isinf(vel[0]) || isnan(vel[0]) ||
555	>	isinf(vel[1]) || isnan(vel[1]) ||
556	>	isinf(vel[2]) || isnan(vel[2]) ) {
557	>	sprintf( painCave.errMsg,
558	>	"DumpWriter detected a numerical error writing the velocity"
559	>	" for object %d", index);
560	>	painCave.isFatal = 1;
561	>	simError();
562	>	}
563	>
564		sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
565		pos[0], pos[1], pos[2],
566		vel[0], vel[1], vel[2]);
567		line += tempBuffer;
568
569	<	if (integrableObject->isDirectional()) {
569	>	if (sd->isDirectional()) {
570		type += "qj";
571		Quat4d q;
572		Vector3d ji;
573	<	q = integrableObject->getQ();
574	<	ji = integrableObject->getJ();
573	>	q = sd->getQ();
574	>
575	>	if (isinf(q[0]) || isnan(q[0]) ||
576	>	isinf(q[1]) || isnan(q[1]) ||
577	>	isinf(q[2]) || isnan(q[2]) ||
578	>	isinf(q[3]) || isnan(q[3]) ) {
579	>	sprintf( painCave.errMsg,
580	>	"DumpWriter detected a numerical error writing the quaternion"
581	>	" for object %d", index);
582	>	painCave.isFatal = 1;
583	>	simError();
584	>	}
585	>
586	>	ji = sd->getJ();
587	>
588	>	if (isinf(ji[0]) || isnan(ji[0]) ||
589	>	isinf(ji[1]) || isnan(ji[1]) ||
590	>	isinf(ji[2]) || isnan(ji[2]) ) {
591	>	sprintf( painCave.errMsg,
592	>	"DumpWriter detected a numerical error writing the angular"
593	>	" momentum for object %d", index);
594	>	painCave.isFatal = 1;
595	>	simError();
596	>	}
597	>
598		sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
599		q[0], q[1], q[2], q[3],
600		ji[0], ji[1], ji[2]);
#	Line 331 | Line 602 | namespace oopse {
602		}
603
604		if (needForceVector_) {
605	<	type += "ft";
606	<	Vector3d frc;
607	<	Vector3d trq;
608	<	frc = integrableObject->getFrc();
609	<	trq = integrableObject->getTrq();
610	<
611	<	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e",
612	<	frc[0], frc[1], frc[2],
613	<	trq[0], trq[1], trq[2]);
605	>	type += "f";
606	>	Vector3d frc = sd->getFrc();
607	>	if (isinf(frc[0]) || isnan(frc[0]) ||
608	>	isinf(frc[1]) || isnan(frc[1]) ||
609	>	isinf(frc[2]) || isnan(frc[2]) ) {
610	>	sprintf( painCave.errMsg,
611	>	"DumpWriter detected a numerical error writing the force"
612	>	" for object %d", index);
613	>	painCave.isFatal = 1;
614	>	simError();
615	>	}
616	>	sprintf(tempBuffer, " %13e %13e %13e",
617	>	frc[0], frc[1], frc[2]);
618		line += tempBuffer;
619	+
620	+	if (sd->isDirectional()) {
621	+	type += "t";
622	+	Vector3d trq = sd->getTrq();
623	+	if (isinf(trq[0]) || isnan(trq[0]) ||
624	+	isinf(trq[1]) || isnan(trq[1]) ||
625	+	isinf(trq[2]) || isnan(trq[2]) ) {
626	+	sprintf( painCave.errMsg,
627	+	"DumpWriter detected a numerical error writing the torque"
628	+	" for object %d", index);
629	+	painCave.isFatal = 1;
630	+	simError();
631	+	}
632	+	sprintf(tempBuffer, " %13e %13e %13e",
633	+	trq[0], trq[1], trq[2]);
634	+	line += tempBuffer;
635	+	}
636		}
637	<
637	>
638		sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
639		return std::string(tempBuffer);
640		}
641
642	+	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
643	+	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
644	+
645	+	std::string id;
646	+	std::string type;
647	+	std::string line;
648	+	char tempBuffer[4096];
649	+
650	+	if (sd->isRigidBody()) {
651	+	sprintf(tempBuffer, "%10d           ", ioIndex);
652	+	id = std::string(tempBuffer);
653	+	} else {
654	+	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
655	+	id = std::string(tempBuffer);
656	+	}
657	+
658	+	if (needFlucQ_) {
659	+	if (storageLayout & DataStorage::dslFlucQPosition) {
660	+	type += "c";
661	+	RealType fqPos = sd->getFlucQPos();
662	+	if (isinf(fqPos) || isnan(fqPos) ) {
663	+	sprintf( painCave.errMsg,
664	+	"DumpWriter detected a numerical error writing the"
665	+	" fluctuating charge for object %s", id.c_str());
666	+	painCave.isFatal = 1;
667	+	simError();
668	+	}
669	+	sprintf(tempBuffer, " %13e ", fqPos);
670	+	line += tempBuffer;
671	+	}
672	+
673	+	if (storageLayout & DataStorage::dslFlucQVelocity) {
674	+	type += "w";
675	+	RealType fqVel = sd->getFlucQVel();
676	+	if (isinf(fqVel) || isnan(fqVel) ) {
677	+	sprintf( painCave.errMsg,
678	+	"DumpWriter detected a numerical error writing the"
679	+	" fluctuating charge velocity for object %s", id.c_str());
680	+	painCave.isFatal = 1;
681	+	simError();
682	+	}
683	+	sprintf(tempBuffer, " %13e ", fqVel);
684	+	line += tempBuffer;
685	+	}
686	+
687	+	if (needForceVector_) {
688	+	if (storageLayout & DataStorage::dslFlucQForce) {
689	+	type += "g";
690	+	RealType fqFrc = sd->getFlucQFrc();
691	+	if (isinf(fqFrc) || isnan(fqFrc) ) {
692	+	sprintf( painCave.errMsg,
693	+	"DumpWriter detected a numerical error writing the"
694	+	" fluctuating charge force for object %s", id.c_str());
695	+	painCave.isFatal = 1;
696	+	simError();
697	+	}
698	+	sprintf(tempBuffer, " %13e ", fqFrc);
699	+	line += tempBuffer;
700	+	}
701	+	}
702	+	}
703	+
704	+	if (needElectricField_) {
705	+	if (storageLayout & DataStorage::dslElectricField) {
706	+	type += "e";
707	+	Vector3d eField= sd->getElectricField();
708	+	if (isinf(eField[0]) || isnan(eField[0]) ||
709	+	isinf(eField[1]) || isnan(eField[1]) ||
710	+	isinf(eField[2]) || isnan(eField[2]) ) {
711	+	sprintf( painCave.errMsg,
712	+	"DumpWriter detected a numerical error writing the electric"
713	+	" field for object %s", id.c_str());
714	+	painCave.isFatal = 1;
715	+	simError();
716	+	}
717	+	sprintf(tempBuffer, " %13e %13e %13e",
718	+	eField[0], eField[1], eField[2]);
719	+	line += tempBuffer;
720	+	}
721	+	}
722	+
723	+	if (needSitePotential_) {
724	+	if (storageLayout & DataStorage::dslSitePotential) {
725	+	type += "s";
726	+	RealType sPot = sd->getSitePotential();
727	+	if (isinf(sPot) || isnan(sPot) ) {
728	+	sprintf( painCave.errMsg,
729	+	"DumpWriter detected a numerical error writing the"
730	+	" site potential for object %s", id.c_str());
731	+	painCave.isFatal = 1;
732	+	simError();
733	+	}
734	+	sprintf(tempBuffer, " %13e ", sPot);
735	+	line += tempBuffer;
736	+	}
737	+	}
738	+
739	+	if (needParticlePot_) {
740	+	if (storageLayout & DataStorage::dslParticlePot) {
741	+	type += "u";
742	+	RealType particlePot = sd->getParticlePot();
743	+	if (isinf(particlePot) || isnan(particlePot)) {
744	+	sprintf( painCave.errMsg,
745	+	"DumpWriter detected a numerical error writing the particle "
746	+	" potential for object %s", id.c_str());
747	+	painCave.isFatal = 1;
748	+	simError();
749	+	}
750	+	sprintf(tempBuffer, " %13e", particlePot);
751	+	line += tempBuffer;
752	+	}
753	+	}
754	+
755	+	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
756	+	return std::string(tempBuffer);
757	+	}
758	+
759		void DumpWriter::writeDump() {
760		writeFrame(*dumpFile_);
761		}
762
763		void DumpWriter::writeEor() {
764	<	std::ostream* eorStream;
765	<
764	>
765	>	std::ostream* eorStream = NULL;
766	>
767		#ifdef IS_MPI
768		if (worldRank == 0) {
769		#endif // is_mpi
770	<
770	>
771		eorStream = createOStream(eorFilename_);
772
773		#ifdef IS_MPI
774		}
775	<	#endif // is_mpi
776	<
775	>	#endif
776	>
777		writeFrame(*eorStream);
778	<
778	>
779		#ifdef IS_MPI
780		if (worldRank == 0) {
781	<	#endif // is_mpi
781	>	#endif
782	>
783		writeClosing(*eorStream);
784		delete eorStream;
785	+
786		#ifdef IS_MPI
787		}
788		#endif // is_mpi
#	Line 384 | Line 796 | namespace oopse {
796		#ifdef IS_MPI
797		if (worldRank == 0) {
798		#endif // is_mpi
387	–
799		buffers.push_back(dumpFile_->rdbuf());
389	–
800		eorStream = createOStream(eorFilename_);
391	–
801		buffers.push_back(eorStream->rdbuf());
393	–
802		#ifdef IS_MPI
803		}
804		#endif // is_mpi
805
806		TeeBuf tbuf(buffers.begin(), buffers.end());
807		std::ostream os(&tbuf);
400	–
808		writeFrame(os);
809
810		#ifdef IS_MPI
#	Line 407 | Line 814 | namespace oopse {
814		delete eorStream;
815		#ifdef IS_MPI
816		}
817	<	#endif // is_mpi
411	<
817	>	#endif // is_mpi
818		}
819
820		std::ostream* DumpWriter::createOStream(const std::string& filename) {
821
822		std::ostream* newOStream;
823	<	#ifdef HAVE_LIBZ
823	>	#ifdef HAVE_ZLIB
824		if (needCompression_) {
825		newOStream = new ogzstream(filename.c_str());
826		} else {
#	Line 424 | Line 830 | namespace oopse {
830		newOStream = new std::ofstream(filename.c_str());
831		#endif
832		//write out MetaData first
833	<	(*newOStream) << "<OOPSE version=4>" << std::endl;
833	>	(*newOStream) << "<OpenMD version=2>" << std::endl;
834		(*newOStream) << "  <MetaData>" << std::endl;
835		(*newOStream) << info_->getRawMetaData();
836		(*newOStream) << "  </MetaData>" << std::endl;
#	Line 433 | Line 839 | namespace oopse {
839
840		void DumpWriter::writeClosing(std::ostream& os) {
841
842	<	os << "</OOPSE>\n";
842	>	os << "</OpenMD>\n";
843		os.flush();
844		}
845
846	<	}//end namespace oopse
846	>	}//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.
Revision 2020 by gezelter, Mon Sep 22 19:18:35 2014 UTC

#	Line 0 | Line 1
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