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

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 965 by tim, Fri May 19 20:45:55 2006 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 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_) {
88	<	filename_ += ".gz";
89	<	eorFilename_ += ".gz";
88	>	filename_ += ".gz";
89	>	eorFilename_ += ".gz";
90		}
91		#endif
92
93		#ifdef IS_MPI
94
95	<	if (worldRank == 0) {
95	>	if (worldRank == 0) {
96		#endif // is_mpi
73	–
97
98	<	dumpFile_ = createOStream(filename_);
98	>	dumpFile_ = createOStream(filename_);
99
100	<	if (!dumpFile_) {
101	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
102	<	filename_.c_str());
103	<	painCave.isFatal = 1;
104	<	simError();
105	<	}
100	>	if (!dumpFile_) {
101	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
102	>	filename_.c_str());
103	>	painCave.isFatal = 1;
104	>	simError();
105	>	}
106
107		#ifdef IS_MPI
108
109	<	}
109	>	}
110
88	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
89	–	MPIcheckPoint();
90	–
111		#endif // is_mpi
112
113	<	}
113	>	}
114
115
116		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
#	Line 99 | 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_) {
139	<	filename_ += ".gz";
140	<	eorFilename_ += ".gz";
139	>	filename_ += ".gz";
140	>	eorFilename_ += ".gz";
141		}
142		#endif
143
144		#ifdef IS_MPI
145
146	<	if (worldRank == 0) {
146	>	if (worldRank == 0) {
147		#endif // is_mpi
148
149
150	<	dumpFile_ = createOStream(filename_);
150	>	dumpFile_ = createOStream(filename_);
151
152	<	if (!dumpFile_) {
153	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
154	<	filename_.c_str());
155	<	painCave.isFatal = 1;
156	<	simError();
157	<	}
152	>	if (!dumpFile_) {
153	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
154	>	filename_.c_str());
155	>	painCave.isFatal = 1;
156	>	simError();
157	>	}
158
159		#ifdef IS_MPI
160
161	<	}
161	>	}
162
131	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
132	–	MPIcheckPoint();
133	–
163		#endif // is_mpi
164
165	<	}
165	>	}
166
167		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
168	<	: info_(info), filename_(filename){
168	>	: info_(info), filename_(filename){
169
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 170 | Line 210 | namespace oopse {
210		#ifdef IS_MPI
211
212		}
213	+
214
174	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
175	–	MPIcheckPoint();
176	–
215		#endif // is_mpi
216
217		}
180	–
181	–
182	–
183	–
184	–
218
219		DumpWriter::~DumpWriter() {
220
#	Line 190 | Line 223 | namespace oopse {
223		if (worldRank == 0) {
224		#endif // is_mpi
225		if (createDumpFile_){
226	+	writeClosing(*dumpFile_);
227		delete dumpFile_;
228		}
229		#ifdef IS_MPI
#	Line 200 | Line 234 | namespace oopse {
234
235		}
236
237	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
204	<
205	<	RealType currentTime;
206	<	Mat3x3d hmat;
207	<	RealType chi;
208	<	RealType integralOfChiDt;
209	<	Mat3x3d eta;
210	<
211	<	currentTime = s->getTime();
212	<	hmat = s->getHmat();
213	<	chi = s->getChi();
214	<	integralOfChiDt = s->getIntegralOfChiDt();
215	<	eta = s->getEta();
216	<
217	<	os << currentTime << ";\t"
218	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
219	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
220	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
237	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
238
239	<	//write out additional parameters, such as chi and eta
239	>	char buffer[1024];
240
241	<	os << chi << "\t" << integralOfChiDt << ";\t";
241	>	os << "    <FrameData>\n";
242
243	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
227	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
228	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
229	<
230	<	os << "\n";
231	<	}
243	>	RealType currentTime = s->getTime();
244
245	<	void DumpWriter::writeFrame(std::ostream& os) {
246	<	const int BUFFERSIZE = 2000;
247	<	const int MINIBUFFERSIZE = 100;
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	<	char tempBuffer[BUFFERSIZE];
256	<	char writeLine[BUFFERSIZE];
255	>	Mat3x3d hmat;
256	>	hmat = s->getHmat();
257
258	<	Quat4d q;
259	<	Vector3d ji;
260	<	Vector3d pos;
261	<	Vector3d vel;
262	<	Vector3d frc;
263	<	Vector3d trq;
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	<	Molecule* mol;
248	<	StuntDouble* integrableObject;
249	<	SimInfo::MoleculeIterator mi;
250	<	Molecule::IntegrableObjectIterator ii;
251	<
252	<	int nTotObjects;
253	<	nTotObjects = info_->getNGlobalIntegrableObjects();
275	>	pair<RealType, RealType> thermostat = s->getThermostat();
276
277	<	#ifndef IS_MPI
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->getBarostat();
290
291	<	os << nTotObjects << "\n";
292	<
293	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
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	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
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),
305	>	eta(0, 2), eta(1, 2), eta(2, 2));
306	>	os << buffer;
307
308	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
309	<	integrableObject = mol->nextIntegrableObject(ii)) {
266	<
308	>	os << "    </FrameData>\n";
309	>	}
310
311	<	pos = integrableObject->getPos();
269	<	vel = integrableObject->getVel();
311	>	void DumpWriter::writeFrame(std::ostream& os) {
312
313	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
314	<	integrableObject->getType().c_str(),
315	<	pos[0], pos[1], pos[2],
274	<	vel[0], vel[1], vel[2]);
313	>	#ifdef IS_MPI
314	>	MPI_Status istatus;
315	>	#endif
316
317	<	strcpy(writeLine, tempBuffer);
317	>	Molecule* mol;
318	>	StuntDouble* sd;
319	>	SimInfo::MoleculeIterator mi;
320	>	Molecule::IntegrableObjectIterator ii;
321	>	RigidBody::AtomIterator ai;
322
323	<	if (integrableObject->isDirectional()) {
324	<	q = integrableObject->getQ();
325	<	ji = integrableObject->getJ();
326	<
282	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
283	<	q[0], q[1], q[2], q[3],
284	<	ji[0], ji[1], ji[2]);
285	<	strcat(writeLine, tempBuffer);
286	<	} else {
287	<	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
288	<	}
289	<
290	<	if (needForceVector_) {
291	<	frc = integrableObject->getFrc();
292	<	trq = integrableObject->getTrq();
293	<
294	<	sprintf(tempBuffer, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
295	<	frc[0], frc[1], frc[2],
296	<	trq[0], trq[1], trq[2]);
297	<	strcat(writeLine, tempBuffer);
298	<	}
299	<
300	<	strcat(writeLine, "\n");
301	<	os << writeLine;
323	>	#ifndef IS_MPI
324	>	os << "  <Snapshot>\n";
325	>
326	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
327
328	+	os << "    <StuntDoubles>\n";
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 // is_mpi
308	<	/*********************************************************************
309	<	* Documentation?  You want DOCUMENTATION?
310	<	*
311	<	* Why all the potatoes below?
312	<	*
313	<	* To make a long story short, the original version of DumpWriter
314	<	* worked in the most inefficient way possible.  Node 0 would
315	<	* poke each of the node for an individual atom's formatted data
316	<	* as node 0 worked its way down the global index. This was particularly
317	<	* inefficient since the method blocked all processors at every atom
318	<	* (and did it twice!).
319	<	*
320	<	* An intermediate version of DumpWriter could be described from Node
321	<	* zero's perspective as follows:
322	<	*
323	<	*  1) Have 100 of your friends stand in a circle.
324	<	*  2) When you say go, have all of them start tossing potatoes at
325	<	*     you (one at a time).
326	<	*  3) Catch the potatoes.
327	<	*
328	<	* It was an improvement, but MPI has buffers and caches that could
329	<	* best be described in this analogy as "potato nets", so there's no
330	<	* need to block the processors atom-by-atom.
331	<	*
332	<	* This new and improved DumpWriter works in an even more efficient
333	<	* way:
334	<	*
335	<	*  1) Have 100 of your friend stand in a circle.
336	<	*  2) When you say go, have them start tossing 5-pound bags of
337	<	*     potatoes at you.
338	<	*  3) Once you've caught a friend's bag of potatoes,
339	<	*     toss them a spud to let them know they can toss another bag.
340	<	*
341	<	* How's THAT for documentation?
342	<	*
343	<	*********************************************************************/
344	<	const int masterNode = 0;
369	>	#else
370
371	<	int * potatoes;
372	<	int myPotato;
371	>	const int masterNode = 0;
372	>	int worldRank;
373		int nProc;
349	–	int which_node;
350	–	RealType atomData[19];
351	–	int isDirectional;
352	–	char MPIatomTypeString[MINIBUFFERSIZE];
353	–	int msgLen; // the length of message actually recieved at master nodes
354	–	int haveError;
355	–	MPI_Status istatus;
356	–	int nCurObj;
357	–
358	–	// code to find maximum tag value
359	–	int * tagub;
360	–	int flag;
361	–	int MAXTAG;
362	–	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
374
375	<	if (flag) {
376	<	MAXTAG = *tagub;
377	<	} else {
378	<	MAXTAG = 32767;
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	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
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;
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	>
396	>	if (worldRank == masterNode) {
397	>	os << buffer;
398	>
399	>	for (int i = 1; i < nProc; ++i) {
400	>	// tell processor i to start sending us data:
401	>	MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
402
403	<	// Node 0 needs a list of the magic potatoes for each processor;
403	>	// receive the length of the string buffer that was
404	>	// prepared by processor i:
405	>	int recvLength;
406	>	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
407	>	&istatus);
408
409	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
410	<	potatoes = new int[nProc];
409	>	// create a buffer to receive the data
410	>	char* recvBuffer = new char[recvLength];
411	>	if (recvBuffer == NULL) {
412	>	} else {
413	>	// receive the data:
414	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
415	>	MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
416	>	// send it to the file:
417	>	os << recvBuffer;
418	>	// get rid of the receive buffer:
419	>	delete [] recvBuffer;
420	>	}
421	>	}
422	>	} else {
423	>	int sendBufferLength = buffer.size() + 1;
424	>	int myturn = 0;
425	>	for (int i = 1; i < nProc; ++i){
426	>	// wait for the master node to call our number:
427	>	MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
428	>	if (myturn == worldRank){
429	>	// send the length of our buffer:
430	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
431
432	<	//write out the comment lines
433	<	for(int i = 0; i < nProc; i++) {
434	<	potatoes[i] = 0;
432	>	// send our buffer:
433	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
434	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
435	>
436	>	}
437		}
438	+	}
439	+
440	+	if (worldRank == masterNode) {
441	+	os << "    </StuntDoubles>\n";
442	+	}
443
444	+	if (doSiteData_) {
445	+	if (worldRank == masterNode) {
446	+	os << "    <SiteData>\n";
447	+	}
448	+	buffer.clear();
449	+	for (mol = info_->beginMolecule(mi); mol != NULL;
450	+	mol = info_->nextMolecule(mi)) {
451	+
452	+	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
453	+	sd = mol->nextIntegrableObject(ii)) {
454	+
455	+	int ioIndex = sd->getGlobalIntegrableObjectIndex();
456	+	// do one for the IO itself
457	+	buffer += prepareSiteLine(sd, ioIndex, 0);
458
459	<	os << nTotObjects << "\n";
460	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
459	>	if (sd->isRigidBody()) {
460	>
461	>	RigidBody* rb = static_cast<RigidBody*>(sd);
462	>	int siteIndex = 0;
463	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
464	>	atom = rb->nextAtom(ai)) {
465	>	buffer += prepareSiteLine(atom, ioIndex, siteIndex);
466	>	siteIndex++;
467	>	}
468	>	}
469	>	}
470	>	}
471
472	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
472	>	if (worldRank == masterNode) {
473	>	os << buffer;
474	>
475	>	for (int i = 1; i < nProc; ++i) {
476	>
477	>	// tell processor i to start sending us data:
478	>	MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
479	>
480	>	// receive the length of the string buffer that was
481	>	// prepared by processor i:
482	>	int recvLength;
483	>	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
484	>	&istatus);
485	>
486	>	// create a buffer to receive the data
487	>	char* recvBuffer = new char[recvLength];
488	>	if (recvBuffer == NULL) {
489	>	} else {
490	>	// receive the data:
491	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
492	>	MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
493	>	// send it to the file:
494	>	os << recvBuffer;
495	>	// get rid of the receive buffer:
496	>	delete [] recvBuffer;
497	>	}
498	>	}
499	>	} else {
500	>	int sendBufferLength = buffer.size() + 1;
501	>	int myturn = 0;
502	>	for (int i = 1; i < nProc; ++i){
503	>	// wait for the master node to call our number:
504	>	MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
505	>	if (myturn == worldRank){
506	>	// send the length of our buffer:
507	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
508	>	// send our buffer:
509	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
510	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
511	>	}
512	>	}
513	>	}
514	>
515	>	if (worldRank == masterNode) {
516	>	os << "    </SiteData>\n";
517	>	}
518	>	}
519	>
520	>	if (worldRank == masterNode) {
521	>	os << "  </Snapshot>\n";
522	>	os.flush();
523	>	}
524	>
525	>	#endif // is_mpi
526	>
527	>	}
528
529	<	// Get the Node number which has this atom;
529	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
530	>
531	>	int index = sd->getGlobalIntegrableObjectIndex();
532	>	std::string type("pv");
533	>	std::string line;
534	>	char tempBuffer[4096];
535
536	<	which_node = info_->getMolToProc(i);
536	>	Vector3d pos;
537	>	Vector3d vel;
538	>	pos = sd->getPos();
539
540	<	if (which_node != masterNode) { //current molecule is in slave node
541	<	if (potatoes[which_node] + 1 >= MAXTAG) {
542	<	// The potato was going to exceed the maximum value,
543	<	// so wrap this processor potato back to 0:
540	>	if (isinf(pos[0]) || isnan(pos[0]) ||
541	>	isinf(pos[1]) || isnan(pos[1]) ||
542	>	isinf(pos[2]) || isnan(pos[2]) ) {
543	>	sprintf( painCave.errMsg,
544	>	"DumpWriter detected a numerical error writing the position"
545	>	" for object %d", index);
546	>	painCave.isFatal = 1;
547	>	simError();
548	>	}
549
550	<	potatoes[which_node] = 0;
398	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
399	<	MPI_COMM_WORLD);
400	<	}
550	>	vel = sd->getVel();
551
552	<	myPotato = potatoes[which_node];
552	>	if (isinf(vel[0]) || isnan(vel[0]) ||
553	>	isinf(vel[1]) || isnan(vel[1]) ||
554	>	isinf(vel[2]) || isnan(vel[2]) ) {
555	>	sprintf( painCave.errMsg,
556	>	"DumpWriter detected a numerical error writing the velocity"
557	>	" for object %d", index);
558	>	painCave.isFatal = 1;
559	>	simError();
560	>	}
561	>
562	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
563	>	pos[0], pos[1], pos[2],
564	>	vel[0], vel[1], vel[2]);
565	>	line += tempBuffer;
566
567	<	//recieve the number of integrableObject in current molecule
568	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
569	<	MPI_COMM_WORLD, &istatus);
570	<	myPotato++;
567	>	if (sd->isDirectional()) {
568	>	type += "qj";
569	>	Quat4d q;
570	>	Vector3d ji;
571	>	q = sd->getQ();
572
573	<	for(int l = 0; l < nCurObj; l++) {
574	<	if (potatoes[which_node] + 2 >= MAXTAG) {
575	<	// The potato was going to exceed the maximum value,
576	<	// so wrap this processor potato back to 0:
573	>	if (isinf(q[0]) || isnan(q[0]) ||
574	>	isinf(q[1]) || isnan(q[1]) ||
575	>	isinf(q[2]) || isnan(q[2]) ||
576	>	isinf(q[3]) || isnan(q[3]) ) {
577	>	sprintf( painCave.errMsg,
578	>	"DumpWriter detected a numerical error writing the quaternion"
579	>	" for object %d", index);
580	>	painCave.isFatal = 1;
581	>	simError();
582	>	}
583
584	<	potatoes[which_node] = 0;
415	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
416	<	0, MPI_COMM_WORLD);
417	<	}
584	>	ji = sd->getJ();
585
586	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
587	<	which_node, myPotato, MPI_COMM_WORLD,
588	<	&istatus);
586	>	if (isinf(ji[0]) || isnan(ji[0]) ||
587	>	isinf(ji[1]) || isnan(ji[1]) ||
588	>	isinf(ji[2]) || isnan(ji[2]) ) {
589	>	sprintf( painCave.errMsg,
590	>	"DumpWriter detected a numerical error writing the angular"
591	>	" momentum for object %d", index);
592	>	painCave.isFatal = 1;
593	>	simError();
594	>	}
595
596	<	myPotato++;
596	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
597	>	q[0], q[1], q[2], q[3],
598	>	ji[0], ji[1], ji[2]);
599	>	line += tempBuffer;
600	>	}
601
602	<	MPI_Recv(atomData, 19, MPI_REALTYPE, which_node, myPotato,
603	<	MPI_COMM_WORLD, &istatus);
604	<	myPotato++;
602	>	if (needForceVector_) {
603	>	type += "f";
604	>	Vector3d frc = sd->getFrc();
605	>	if (isinf(frc[0]) || isnan(frc[0]) ||
606	>	isinf(frc[1]) || isnan(frc[1]) ||
607	>	isinf(frc[2]) || isnan(frc[2]) ) {
608	>	sprintf( painCave.errMsg,
609	>	"DumpWriter detected a numerical error writing the force"
610	>	" for object %d", index);
611	>	painCave.isFatal = 1;
612	>	simError();
613	>	}
614	>	sprintf(tempBuffer, " %13e %13e %13e",
615	>	frc[0], frc[1], frc[2]);
616	>	line += tempBuffer;
617	>
618	>	if (sd->isDirectional()) {
619	>	type += "t";
620	>	Vector3d trq = sd->getTrq();
621	>	if (isinf(trq[0]) || isnan(trq[0]) ||
622	>	isinf(trq[1]) || isnan(trq[1]) ||
623	>	isinf(trq[2]) || isnan(trq[2]) ) {
624	>	sprintf( painCave.errMsg,
625	>	"DumpWriter detected a numerical error writing the torque"
626	>	" for object %d", index);
627	>	painCave.isFatal = 1;
628	>	simError();
629	>	}
630	>	sprintf(tempBuffer, " %13e %13e %13e",
631	>	trq[0], trq[1], trq[2]);
632	>	line += tempBuffer;
633	>	}
634	>	}
635
636	<	MPI_Get_count(&istatus, MPI_REALTYPE, &msgLen);
636	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
637	>	return std::string(tempBuffer);
638	>	}
639
640	<	if (msgLen == 13 || msgLen == 19)
641	<	isDirectional = 1;
433	<	else
434	<	isDirectional = 0;
640	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
641	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
642
643	<	// If we've survived to here, format the line:
643	>	std::string id;
644	>	std::string type;
645	>	std::string line;
646	>	char tempBuffer[4096];
647
648	<	if (!isDirectional) {
649	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
650	<	MPIatomTypeString, atomData[0],
651	<	atomData[1], atomData[2],
652	<	atomData[3], atomData[4],
653	<	atomData[5]);
648	>	if (sd->isRigidBody()) {
649	>	sprintf(tempBuffer, "%10d           ", ioIndex);
650	>	id = std::string(tempBuffer);
651	>	} else {
652	>	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
653	>	id = std::string(tempBuffer);
654	>	}
655	>
656	>	if (needFlucQ_) {
657	>	if (storageLayout & DataStorage::dslFlucQPosition) {
658	>	type += "c";
659	>	RealType fqPos = sd->getFlucQPos();
660	>	if (isinf(fqPos) || isnan(fqPos) ) {
661	>	sprintf( painCave.errMsg,
662	>	"DumpWriter detected a numerical error writing the"
663	>	" fluctuating charge for object %s", id.c_str());
664	>	painCave.isFatal = 1;
665	>	simError();
666	>	}
667	>	sprintf(tempBuffer, " %13e ", fqPos);
668	>	line += tempBuffer;
669	>	}
670
671	<	strcat(writeLine,
672	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
673	<	} else {
674	<	sprintf(writeLine,
675	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
676	<	MPIatomTypeString,
677	<	atomData[0],
678	<	atomData[1],
679	<	atomData[2],
680	<	atomData[3],
681	<	atomData[4],
682	<	atomData[5],
683	<	atomData[6],
458	<	atomData[7],
459	<	atomData[8],
460	<	atomData[9],
461	<	atomData[10],
462	<	atomData[11],
463	<	atomData[12]);
464	<	}
465	<
466	<	if (needForceVector_) {
467	<	if (!isDirectional) {
468	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
469	<	atomData[6],
470	<	atomData[7],
471	<	atomData[8],
472	<	atomData[9],
473	<	atomData[10],
474	<	atomData[11]);
475	<	} else {
476	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
477	<	atomData[13],
478	<	atomData[14],
479	<	atomData[15],
480	<	atomData[16],
481	<	atomData[17],
482	<	atomData[18]);
483	<	}
484	<	}
671	>	if (storageLayout & DataStorage::dslFlucQVelocity) {
672	>	type += "w";
673	>	RealType fqVel = sd->getFlucQVel();
674	>	if (isinf(fqVel) || isnan(fqVel) ) {
675	>	sprintf( painCave.errMsg,
676	>	"DumpWriter detected a numerical error writing the"
677	>	" fluctuating charge velocity for object %s", id.c_str());
678	>	painCave.isFatal = 1;
679	>	simError();
680	>	}
681	>	sprintf(tempBuffer, " %13e ", fqVel);
682	>	line += tempBuffer;
683	>	}
684
685	<	sprintf(writeLine, "\n");
686	<	os << writeLine;
687	<
688	<	} // end for(int l =0)
689	<
690	<	potatoes[which_node] = myPotato;
691	<	} else { //master node has current molecule
692	<
693	<	mol = info_->getMoleculeByGlobalIndex(i);
694	<
695	<	if (mol == NULL) {
696	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
697	<	painCave.isFatal = 1;
698	<	simError();
500	<	}
501	<
502	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
503	<	integrableObject = mol->nextIntegrableObject(ii)) {
504	<
505	<	pos = integrableObject->getPos();
506	<	vel = integrableObject->getVel();
507	<
508	<	atomData[0] = pos[0];
509	<	atomData[1] = pos[1];
510	<	atomData[2] = pos[2];
511	<
512	<	atomData[3] = vel[0];
513	<	atomData[4] = vel[1];
514	<	atomData[5] = vel[2];
515	<
516	<	isDirectional = 0;
517	<
518	<	if (integrableObject->isDirectional()) {
519	<	isDirectional = 1;
520	<
521	<	q = integrableObject->getQ();
522	<	ji = integrableObject->getJ();
523	<
524	<	for(int j = 0; j < 6; j++) {
525	<	atomData[j] = atomData[j];
526	<	}
527	<
528	<	atomData[6] = q[0];
529	<	atomData[7] = q[1];
530	<	atomData[8] = q[2];
531	<	atomData[9] = q[3];
532	<
533	<	atomData[10] = ji[0];
534	<	atomData[11] = ji[1];
535	<	atomData[12] = ji[2];
536	<	}
537	<
538	<	if (needForceVector_) {
539	<	frc = integrableObject->getFrc();
540	<	trq = integrableObject->getTrq();
541	<
542	<	if (!isDirectional) {
543	<	atomData[6] = frc[0];
544	<	atomData[7] = frc[1];
545	<	atomData[8] = frc[2];
546	<	atomData[9] = trq[0];
547	<	atomData[10] = trq[1];
548	<	atomData[11] = trq[2];
549	<	} else {
550	<	atomData[13] = frc[0];
551	<	atomData[14] = frc[1];
552	<	atomData[15] = frc[2];
553	<	atomData[16] = trq[0];
554	<	atomData[17] = trq[1];
555	<	atomData[18] = trq[2];
556	<	}
557	<	}
558	<
559	<	// If we've survived to here, format the line:
560	<
561	<	if (!isDirectional) {
562	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
563	<	integrableObject->getType().c_str(), atomData[0],
564	<	atomData[1], atomData[2],
565	<	atomData[3], atomData[4],
566	<	atomData[5]);
567	<
568	<	strcat(writeLine,
569	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
570	<	} else {
571	<	sprintf(writeLine,
572	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
573	<	integrableObject->getType().c_str(),
574	<	atomData[0],
575	<	atomData[1],
576	<	atomData[2],
577	<	atomData[3],
578	<	atomData[4],
579	<	atomData[5],
580	<	atomData[6],
581	<	atomData[7],
582	<	atomData[8],
583	<	atomData[9],
584	<	atomData[10],
585	<	atomData[11],
586	<	atomData[12]);
587	<	}
588	<
589	<	if (needForceVector_) {
590	<	if (!isDirectional) {
591	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
592	<	atomData[6],
593	<	atomData[7],
594	<	atomData[8],
595	<	atomData[9],
596	<	atomData[10],
597	<	atomData[11]);
598	<	} else {
599	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
600	<	atomData[13],
601	<	atomData[14],
602	<	atomData[15],
603	<	atomData[16],
604	<	atomData[17],
605	<	atomData[18]);
606	<	}
607	<	}
608	<
609	<	os << writeLine << "\n";
610	<
611	<	} //end for(iter = integrableObject.begin())
612	<	}
613	<	} //end for(i = 0; i < mpiSim->getNmol())
614	<
615	<	os.flush();
616	<
617	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
618	<	MPIcheckPoint();
619	<
620	<	delete [] potatoes;
621	<	} else {
622	<
623	<	// worldRank != 0, so I'm a remote node.
624	<
625	<	// Set my magic potato to 0:
626	<
627	<	myPotato = 0;
628	<
629	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
630	<
631	<	// Am I the node which has this integrableObject?
632	<	int whichNode = info_->getMolToProc(i);
633	<	if (whichNode == worldRank) {
634	<	if (myPotato + 1 >= MAXTAG) {
635	<
636	<	// The potato was going to exceed the maximum value,
637	<	// so wrap this processor potato back to 0 (and block until
638	<	// node 0 says we can go:
639	<
640	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
641	<	&istatus);
642	<	}
643	<
644	<	mol = info_->getMoleculeByGlobalIndex(i);
645	<
646	<
647	<	nCurObj = mol->getNIntegrableObjects();
648	<
649	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
650	<	myPotato++;
651	<
652	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
653	<	integrableObject = mol->nextIntegrableObject(ii)) {
654	<
655	<	if (myPotato + 2 >= MAXTAG) {
656	<
657	<	// The potato was going to exceed the maximum value,
658	<	// so wrap this processor potato back to 0 (and block until
659	<	// node 0 says we can go:
660	<
661	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
662	<	&istatus);
663	<	}
664	<
665	<	pos = integrableObject->getPos();
666	<	vel = integrableObject->getVel();
667	<
668	<	atomData[0] = pos[0];
669	<	atomData[1] = pos[1];
670	<	atomData[2] = pos[2];
671	<
672	<	atomData[3] = vel[0];
673	<	atomData[4] = vel[1];
674	<	atomData[5] = vel[2];
675	<
676	<	isDirectional = 0;
677	<
678	<	if (integrableObject->isDirectional()) {
679	<	isDirectional = 1;
680	<
681	<	q = integrableObject->getQ();
682	<	ji = integrableObject->getJ();
683	<
684	<	atomData[6] = q[0];
685	<	atomData[7] = q[1];
686	<	atomData[8] = q[2];
687	<	atomData[9] = q[3];
688	<
689	<	atomData[10] = ji[0];
690	<	atomData[11] = ji[1];
691	<	atomData[12] = ji[2];
692	<	}
693	<
694	<	if (needForceVector_) {
695	<	frc = integrableObject->getFrc();
696	<	trq = integrableObject->getTrq();
697	<
698	<	if (!isDirectional) {
699	<	atomData[6] = frc[0];
700	<	atomData[7] = frc[1];
701	<	atomData[8] = frc[2];
702	<
703	<	atomData[9] = trq[0];
704	<	atomData[10] = trq[1];
705	<	atomData[11] = trq[2];
706	<	} else {
707	<	atomData[13] = frc[0];
708	<	atomData[14] = frc[1];
709	<	atomData[15] = frc[2];
710	<
711	<	atomData[16] = trq[0];
712	<	atomData[17] = trq[1];
713	<	atomData[18] = trq[2];
714	<	}
715	<	}
716	<
717	<	strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
718	<
719	<	// null terminate the  std::string before sending (just in case):
720	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
721	<
722	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
723	<	myPotato, MPI_COMM_WORLD);
724	<
725	<	myPotato++;
726	<
727	<	if (isDirectional && needForceVector_) {
728	<	MPI_Send(atomData, 19, MPI_REALTYPE, 0, myPotato,
729	<	MPI_COMM_WORLD);
730	<	} else if (isDirectional) {
731	<	MPI_Send(atomData, 13, MPI_REALTYPE, 0, myPotato,
732	<	MPI_COMM_WORLD);
733	<	} else if (needForceVector_) {
734	<	MPI_Send(atomData, 12, MPI_REALTYPE, 0, myPotato,
735	<	MPI_COMM_WORLD);
736	<	} else {
737	<	MPI_Send(atomData, 6, MPI_REALTYPE, 0, myPotato,
738	<	MPI_COMM_WORLD);
739	<	}
740	<
741	<	myPotato++;
742	<	}
743	<
744	<	}
745	<
685	>	if (needForceVector_) {
686	>	if (storageLayout & DataStorage::dslFlucQForce) {
687	>	type += "g";
688	>	RealType fqFrc = sd->getFlucQFrc();
689	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
690	>	sprintf( painCave.errMsg,
691	>	"DumpWriter detected a numerical error writing the"
692	>	" fluctuating charge force for object %s", id.c_str());
693	>	painCave.isFatal = 1;
694	>	simError();
695	>	}
696	>	sprintf(tempBuffer, " %13e ", fqFrc);
697	>	line += tempBuffer;
698	>	}
699		}
747	–	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
748	–	MPIcheckPoint();
700		}
701	+
702	+	if (needElectricField_) {
703	+	if (storageLayout & DataStorage::dslElectricField) {
704	+	type += "e";
705	+	Vector3d eField= sd->getElectricField();
706	+	if (isinf(eField[0]) || isnan(eField[0]) ||
707	+	isinf(eField[1]) || isnan(eField[1]) ||
708	+	isinf(eField[2]) || isnan(eField[2]) ) {
709	+	sprintf( painCave.errMsg,
710	+	"DumpWriter detected a numerical error writing the electric"
711	+	" field for object %s", id.c_str());
712	+	painCave.isFatal = 1;
713	+	simError();
714	+	}
715	+	sprintf(tempBuffer, " %13e %13e %13e",
716	+	eField[0], eField[1], eField[2]);
717	+	line += tempBuffer;
718	+	}
719	+	}
720
721	<	#endif // is_mpi
722	<
721	>	if (needSitePotential_) {
722	>	if (storageLayout & DataStorage::dslSitePotential) {
723	>	type += "s";
724	>	RealType sPot = sd->getSitePotential();
725	>	if (isinf(sPot) || isnan(sPot) ) {
726	>	sprintf( painCave.errMsg,
727	>	"DumpWriter detected a numerical error writing the"
728	>	" site potential for object %s", id.c_str());
729	>	painCave.isFatal = 1;
730	>	simError();
731	>	}
732	>	sprintf(tempBuffer, " %13e ", sPot);
733	>	line += tempBuffer;
734	>	}
735	>	}
736	>
737	>	if (needParticlePot_) {
738	>	if (storageLayout & DataStorage::dslParticlePot) {
739	>	type += "u";
740	>	RealType particlePot = sd->getParticlePot();
741	>	if (isinf(particlePot) || isnan(particlePot)) {
742	>	sprintf( painCave.errMsg,
743	>	"DumpWriter detected a numerical error writing the particle "
744	>	" potential for object %s", id.c_str());
745	>	painCave.isFatal = 1;
746	>	simError();
747	>	}
748	>	sprintf(tempBuffer, " %13e", particlePot);
749	>	line += tempBuffer;
750	>	}
751	>	}
752	>
753	>	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
754	>	return std::string(tempBuffer);
755		}
756
757		void DumpWriter::writeDump() {
#	Line 757 | Line 759 | namespace oopse {
759		}
760
761		void DumpWriter::writeEor() {
762	<	std::ostream* eorStream;
763	<
762	>
763	>	std::ostream* eorStream = NULL;
764	>
765		#ifdef IS_MPI
766		if (worldRank == 0) {
767		#endif // is_mpi
768	<
768	>
769		eorStream = createOStream(eorFilename_);
770
771		#ifdef IS_MPI
772		}
773	<	#endif // is_mpi
774	<
773	>	#endif
774	>
775		writeFrame(*eorStream);
776	<
776	>
777		#ifdef IS_MPI
778		if (worldRank == 0) {
779	<	#endif // is_mpi
780	<	delete eorStream;
781	<
779	>	#endif
780	>
781	>	writeClosing(*eorStream);
782	>	delete eorStream;
783	>
784		#ifdef IS_MPI
785		}
786		#endif // is_mpi
#	Line 789 | Line 794 | namespace oopse {
794		#ifdef IS_MPI
795		if (worldRank == 0) {
796		#endif // is_mpi
792	–
797		buffers.push_back(dumpFile_->rdbuf());
794	–
798		eorStream = createOStream(eorFilename_);
796	–
799		buffers.push_back(eorStream->rdbuf());
798	–
800		#ifdef IS_MPI
801		}
802		#endif // is_mpi
803
804		TeeBuf tbuf(buffers.begin(), buffers.end());
805		std::ostream os(&tbuf);
805	–
806		writeFrame(os);
807
808		#ifdef IS_MPI
809		if (worldRank == 0) {
810		#endif // is_mpi
811	<	delete eorStream;
812	<
811	>	writeClosing(*eorStream);
812	>	delete eorStream;
813		#ifdef IS_MPI
814		}
815	<	#endif // is_mpi
816	<
815	>	#endif // is_mpi
816		}
817
818	<	std::ostream* DumpWriter::createOStream(const std::string& filename) {
818	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
819
820		std::ostream* newOStream;
821	<	#ifdef HAVE_LIBZ
821	>	#ifdef HAVE_ZLIB
822		if (needCompression_) {
823	<	newOStream = new ogzstream(filename.c_str());
823	>	newOStream = new ogzstream(filename.c_str());
824		} else {
825	<	newOStream = new std::ofstream(filename.c_str());
825	>	newOStream = new std::ofstream(filename.c_str());
826		}
827		#else
828		newOStream = new std::ofstream(filename.c_str());
829		#endif
830	+	//write out MetaData first
831	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
832	+	(*newOStream) << "  <MetaData>" << std::endl;
833	+	(*newOStream) << info_->getRawMetaData();
834	+	(*newOStream) << "  </MetaData>" << std::endl;
835		return newOStream;
836	<	}
836	>	}
837
838	<	}//end namespace oopse
838	>	void DumpWriter::writeClosing(std::ostream& os) {
839	>
840	>	os << "</OpenMD>\n";
841	>	os.flush();
842	>	}
843	>
844	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpWriter.cpp (property svn:keywords):
Revision 965 by tim, Fri May 19 20:45:55 2006 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

#	Line 0 | Line 1
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