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

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 966 by chrisfen, Fri May 19 21:26:41 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_) {
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) {
237	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
238
239	<	RealType currentTime;
240	<	Mat3x3d hmat;
241	<	RealType chi;
242	<	RealType integralOfChiDt;
243	<	Mat3x3d eta;
239	>	char buffer[1024];
240	>
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	<	currentTime = s->getTime();
252	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
253	>	os << buffer;
254	>
255	>	Mat3x3d hmat;
256		hmat = s->getHmat();
257	<	chi = s->getChi();
258	<	integralOfChiDt = s->getIntegralOfChiDt();
259	<	eta = s->getEta();
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	<	os << currentTime << ";\t"
270	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
271	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
272	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
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	<	//write out additional parameters, such as chi and eta
275	>	pair<RealType, RealType> thermostat = s->getThermostat();
276
277	<	os << chi << "\t" << integralOfChiDt << ";\t";
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	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
289	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
290	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
291	<
292	<	os << "\n";
288	>	Mat3x3d eta;
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),
305	>	eta(0, 2), eta(1, 2), eta(2, 2));
306	>	os << buffer;
307	>
308	>	os << "    </FrameData>\n";
309		}
310
311		void DumpWriter::writeFrame(std::ostream& os) {
234	–	const int BUFFERSIZE = 2000;
235	–	const int MINIBUFFERSIZE = 100;
312
313	<	char tempBuffer[BUFFERSIZE];
314	<	char writeLine[BUFFERSIZE];
313	>	#ifdef IS_MPI
314	>	MPI_Status istatus;
315	>	#endif
316
240	–	Quat4d q;
241	–	Vector3d ji;
242	–	Vector3d pos;
243	–	Vector3d vel;
244	–	Vector3d frc;
245	–	Vector3d trq;
246	–
317		Molecule* mol;
318	<	StuntDouble* integrableObject;
318	>	StuntDouble* sd;
319		SimInfo::MoleculeIterator mi;
320		Molecule::IntegrableObjectIterator ii;
321	<
252	<	int nTotObjects;
253	<	nTotObjects = info_->getNGlobalIntegrableObjects();
321	>	RigidBody::AtomIterator ai;
322
323		#ifndef IS_MPI
324	+	os << "  <Snapshot>\n";
325	+
326	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
327
328	<
329	<	os << nTotObjects << "\n";
330	<
331	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
332	<
333	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
334	<
335	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
265	<	integrableObject = mol->nextIntegrableObject(ii)) {
266	<
267	<
268	<	pos = integrableObject->getPos();
269	<	vel = integrableObject->getVel();
270	<
271	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
272	<	integrableObject->getType().c_str(),
273	<	pos[0], pos[1], pos[2],
274	<	vel[0], vel[1], vel[2]);
275	<
276	<	strcpy(writeLine, tempBuffer);
277	<
278	<	if (integrableObject->isDirectional()) {
279	<	q = integrableObject->getQ();
280	<	ji = integrableObject->getJ();
281	<
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;
302	<
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;
374	<	int which_node;
375	<	RealType atomData[19];
376	<	int isDirectional;
377	<	char MPIatomTypeString[MINIBUFFERSIZE];
378	<	int msgLen; // the length of message actually recieved at master nodes
379	<	int haveError;
380	<	MPI_Status istatus;
381	<	int nCurObj;
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;
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	<	// code to find maximum tag value
397	<	int * tagub;
398	<	int flag;
399	<	int MAXTAG;
400	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
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
402	<	if (flag) {
403	<	MAXTAG = *tagub;
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, 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	>	// 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	>	// get rid of the receive buffer:
420	>	delete [] recvBuffer;
421	>	}
422	>	}
423		} else {
424	<	MAXTAG = 32767;
425	<	}
424	>	int sendBufferLength = buffer.size() + 1;
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	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
432	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
433
434	<	// Node 0 needs a list of the magic potatoes for each processor;
434	>	// send our buffer:
435	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
436	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
437
438	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
439	<	potatoes = new int[nProc];
438	>	}
439	>	}
440	>	}
441	>
442	>	if (worldRank == masterNode) {
443	>	os << "    </StuntDoubles>\n";
444	>	}
445
446	<	//write out the comment lines
447	<	for(int i = 0; i < nProc; i++) {
448	<	potatoes[i] = 0;
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	+	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	<	os << nTotObjects << "\n";
475	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
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	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
531	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
532	>
533	>	int index = sd->getGlobalIntegrableObjectIndex();
534	>	std::string type("pv");
535	>	std::string line;
536	>	char tempBuffer[4096];
537
538	<	// Get the Node number which has this atom;
538	>	Vector3d pos;
539	>	Vector3d vel;
540	>	pos = sd->getPos();
541
542	<	which_node = info_->getMolToProc(i);
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	<	if (which_node != masterNode) { //current molecule is in slave node
393	<	if (potatoes[which_node] + 1 >= MAXTAG) {
394	<	// The potato was going to exceed the maximum value,
395	<	// so wrap this processor potato back to 0:
552	>	vel = sd->getVel();
553
554	<	potatoes[which_node] = 0;
555	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
556	<	MPI_COMM_WORLD);
557	<	}
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	<	myPotato = potatoes[which_node];
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	<	//recieve the number of integrableObject in current molecule
570	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
571	<	MPI_COMM_WORLD, &istatus);
572	<	myPotato++;
569	>	if (sd->isDirectional()) {
570	>	type += "qj";
571	>	Quat4d q;
572	>	Vector3d ji;
573	>	q = sd->getQ();
574
575	<	for(int l = 0; l < nCurObj; l++) {
576	<	if (potatoes[which_node] + 2 >= MAXTAG) {
577	<	// The potato was going to exceed the maximum value,
578	<	// so wrap this processor potato back to 0:
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	<	potatoes[which_node] = 0;
415	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
416	<	0, MPI_COMM_WORLD);
417	<	}
586	>	ji = sd->getJ();
587
588	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
589	<	which_node, myPotato, MPI_COMM_WORLD,
590	<	&istatus);
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	<	myPotato++;
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]);
601	>	line += tempBuffer;
602	>	}
603
604	<	MPI_Recv(atomData, 19, MPI_REALTYPE, which_node, myPotato,
605	<	MPI_COMM_WORLD, &istatus);
606	<	myPotato++;
604	>	if (needForceVector_) {
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
638	<	MPI_Get_count(&istatus, MPI_REALTYPE, &msgLen);
638	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
639	>	return std::string(tempBuffer);
640	>	}
641
642	<	if (msgLen == 13 || msgLen == 19)
643	<	isDirectional = 1;
433	<	else
434	<	isDirectional = 0;
642	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
643	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
644
645	<	// If we've survived to here, format the line:
645	>	std::string id;
646	>	std::string type;
647	>	std::string line;
648	>	char tempBuffer[4096];
649
650	<	if (!isDirectional) {
651	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
652	<	MPIatomTypeString, atomData[0],
653	<	atomData[1], atomData[2],
654	<	atomData[3], atomData[4],
655	<	atomData[5]);
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	<	strcat(writeLine,
674	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
675	<	} else {
676	<	sprintf(writeLine,
677	<	"%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",
678	<	MPIatomTypeString,
679	<	atomData[0],
680	<	atomData[1],
681	<	atomData[2],
682	<	atomData[3],
683	<	atomData[4],
684	<	atomData[5],
685	<	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	<	}
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	<	os << writeLine << "\n";
688	<
689	<	} // end for(int l =0)
690	<
691	<	potatoes[which_node] = myPotato;
692	<	} else { //master node has current molecule
693	<
694	<	mol = info_->getMoleculeByGlobalIndex(i);
695	<
696	<	if (mol == NULL) {
697	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
698	<	painCave.isFatal = 1;
699	<	simError();
700	<	}
500	<
501	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
502	<	integrableObject = mol->nextIntegrableObject(ii)) {
503	<
504	<	pos = integrableObject->getPos();
505	<	vel = integrableObject->getVel();
506	<
507	<	atomData[0] = pos[0];
508	<	atomData[1] = pos[1];
509	<	atomData[2] = pos[2];
510	<
511	<	atomData[3] = vel[0];
512	<	atomData[4] = vel[1];
513	<	atomData[5] = vel[2];
514	<
515	<	isDirectional = 0;
516	<
517	<	if (integrableObject->isDirectional()) {
518	<	isDirectional = 1;
519	<
520	<	q = integrableObject->getQ();
521	<	ji = integrableObject->getJ();
522	<
523	<	for(int j = 0; j < 6; j++) {
524	<	atomData[j] = atomData[j];
525	<	}
526	<
527	<	atomData[6] = q[0];
528	<	atomData[7] = q[1];
529	<	atomData[8] = q[2];
530	<	atomData[9] = q[3];
531	<
532	<	atomData[10] = ji[0];
533	<	atomData[11] = ji[1];
534	<	atomData[12] = ji[2];
535	<	}
536	<
537	<	if (needForceVector_) {
538	<	frc = integrableObject->getFrc();
539	<	trq = integrableObject->getTrq();
540	<
541	<	if (!isDirectional) {
542	<	atomData[6] = frc[0];
543	<	atomData[7] = frc[1];
544	<	atomData[8] = frc[2];
545	<	atomData[9] = trq[0];
546	<	atomData[10] = trq[1];
547	<	atomData[11] = trq[2];
548	<	} else {
549	<	atomData[13] = frc[0];
550	<	atomData[14] = frc[1];
551	<	atomData[15] = frc[2];
552	<	atomData[16] = trq[0];
553	<	atomData[17] = trq[1];
554	<	atomData[18] = trq[2];
555	<	}
556	<	}
557	<
558	<	// If we've survived to here, format the line:
559	<
560	<	if (!isDirectional) {
561	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
562	<	integrableObject->getType().c_str(), atomData[0],
563	<	atomData[1], atomData[2],
564	<	atomData[3], atomData[4],
565	<	atomData[5]);
566	<
567	<	strcat(writeLine,
568	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0");
569	<	} else {
570	<	sprintf(writeLine,
571	<	"%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",
572	<	integrableObject->getType().c_str(),
573	<	atomData[0],
574	<	atomData[1],
575	<	atomData[2],
576	<	atomData[3],
577	<	atomData[4],
578	<	atomData[5],
579	<	atomData[6],
580	<	atomData[7],
581	<	atomData[8],
582	<	atomData[9],
583	<	atomData[10],
584	<	atomData[11],
585	<	atomData[12]);
586	<	}
587	<
588	<	if (needForceVector_) {
589	<	if (!isDirectional) {
590	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
591	<	atomData[6],
592	<	atomData[7],
593	<	atomData[8],
594	<	atomData[9],
595	<	atomData[10],
596	<	atomData[11]);
597	<	} else {
598	<	sprintf(writeLine, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
599	<	atomData[13],
600	<	atomData[14],
601	<	atomData[15],
602	<	atomData[16],
603	<	atomData[17],
604	<	atomData[18]);
605	<	}
606	<	}
607	<
608	<	os << writeLine << "\n";
609	<
610	<	} //end for(iter = integrableObject.begin())
611	<	}
612	<	} //end for(i = 0; i < mpiSim->getNmol())
613	<
614	<	os.flush();
615	<
616	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
617	<	MPIcheckPoint();
618	<
619	<	delete [] potatoes;
620	<	} else {
621	<
622	<	// worldRank != 0, so I'm a remote node.
623	<
624	<	// Set my magic potato to 0:
625	<
626	<	myPotato = 0;
627	<
628	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
629	<
630	<	// Am I the node which has this integrableObject?
631	<	int whichNode = info_->getMolToProc(i);
632	<	if (whichNode == worldRank) {
633	<	if (myPotato + 1 >= MAXTAG) {
634	<
635	<	// The potato was going to exceed the maximum value,
636	<	// so wrap this processor potato back to 0 (and block until
637	<	// node 0 says we can go:
638	<
639	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
640	<	&istatus);
641	<	}
642	<
643	<	mol = info_->getMoleculeByGlobalIndex(i);
644	<
645	<
646	<	nCurObj = mol->getNIntegrableObjects();
647	<
648	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
649	<	myPotato++;
650	<
651	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
652	<	integrableObject = mol->nextIntegrableObject(ii)) {
653	<
654	<	if (myPotato + 2 >= MAXTAG) {
655	<
656	<	// The potato was going to exceed the maximum value,
657	<	// so wrap this processor potato back to 0 (and block until
658	<	// node 0 says we can go:
659	<
660	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
661	<	&istatus);
662	<	}
663	<
664	<	pos = integrableObject->getPos();
665	<	vel = integrableObject->getVel();
666	<
667	<	atomData[0] = pos[0];
668	<	atomData[1] = pos[1];
669	<	atomData[2] = pos[2];
670	<
671	<	atomData[3] = vel[0];
672	<	atomData[4] = vel[1];
673	<	atomData[5] = vel[2];
674	<
675	<	isDirectional = 0;
676	<
677	<	if (integrableObject->isDirectional()) {
678	<	isDirectional = 1;
679	<
680	<	q = integrableObject->getQ();
681	<	ji = integrableObject->getJ();
682	<
683	<	atomData[6] = q[0];
684	<	atomData[7] = q[1];
685	<	atomData[8] = q[2];
686	<	atomData[9] = q[3];
687	<
688	<	atomData[10] = ji[0];
689	<	atomData[11] = ji[1];
690	<	atomData[12] = ji[2];
691	<	}
692	<
693	<	if (needForceVector_) {
694	<	frc = integrableObject->getFrc();
695	<	trq = integrableObject->getTrq();
696	<
697	<	if (!isDirectional) {
698	<	atomData[6] = frc[0];
699	<	atomData[7] = frc[1];
700	<	atomData[8] = frc[2];
701	<
702	<	atomData[9] = trq[0];
703	<	atomData[10] = trq[1];
704	<	atomData[11] = trq[2];
705	<	} else {
706	<	atomData[13] = frc[0];
707	<	atomData[14] = frc[1];
708	<	atomData[15] = frc[2];
709	<
710	<	atomData[16] = trq[0];
711	<	atomData[17] = trq[1];
712	<	atomData[18] = trq[2];
713	<	}
714	<	}
715	<
716	<	strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
717	<
718	<	// null terminate the  std::string before sending (just in case):
719	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
720	<
721	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
722	<	myPotato, MPI_COMM_WORLD);
723	<
724	<	myPotato++;
725	<
726	<	if (isDirectional && needForceVector_) {
727	<	MPI_Send(atomData, 19, MPI_REALTYPE, 0, myPotato,
728	<	MPI_COMM_WORLD);
729	<	} else if (isDirectional) {
730	<	MPI_Send(atomData, 13, MPI_REALTYPE, 0, myPotato,
731	<	MPI_COMM_WORLD);
732	<	} else if (needForceVector_) {
733	<	MPI_Send(atomData, 12, MPI_REALTYPE, 0, myPotato,
734	<	MPI_COMM_WORLD);
735	<	} else {
736	<	MPI_Send(atomData, 6, MPI_REALTYPE, 0, myPotato,
737	<	MPI_COMM_WORLD);
738	<	}
739	<
740	<	myPotato++;
741	<	}
742	<
743	<	}
744	<
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		}
746	–	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
747	–	MPIcheckPoint();
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	<	#endif // is_mpi
724	<
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() {
#	Line 756 | Line 761 | namespace oopse {
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
782	<	delete eorStream;
783	<
781	>	#endif
782	>
783	>	writeClosing(*eorStream);
784	>	delete eorStream;
785	>
786		#ifdef IS_MPI
787		}
788		#endif // is_mpi
#	Line 788 | Line 796 | namespace oopse {
796		#ifdef IS_MPI
797		if (worldRank == 0) {
798		#endif // is_mpi
791	–
799		buffers.push_back(dumpFile_->rdbuf());
793	–
800		eorStream = createOStream(eorFilename_);
795	–
801		buffers.push_back(eorStream->rdbuf());
797	–
802		#ifdef IS_MPI
803		}
804		#endif // is_mpi
805
806		TeeBuf tbuf(buffers.begin(), buffers.end());
807		std::ostream os(&tbuf);
804	–
808		writeFrame(os);
809
810		#ifdef IS_MPI
811		if (worldRank == 0) {
812		#endif // is_mpi
813	<	delete eorStream;
814	<
813	>	writeClosing(*eorStream);
814	>	delete eorStream;
815		#ifdef IS_MPI
816		}
817	<	#endif // is_mpi
815	<
817	>	#endif // is_mpi
818		}
819
820	<	std::ostream* DumpWriter::createOStream(const std::string& filename) {
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());
825	>	newOStream = new ogzstream(filename.c_str());
826		} else {
827	<	newOStream = new std::ofstream(filename.c_str());
827	>	newOStream = new std::ofstream(filename.c_str());
828		}
829		#else
830		newOStream = new std::ofstream(filename.c_str());
831		#endif
832	+	//write out MetaData first
833	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
834	+	(*newOStream) << "  <MetaData>" << std::endl;
835	+	(*newOStream) << info_->getRawMetaData();
836	+	(*newOStream) << "  </MetaData>" << std::endl;
837		return newOStream;
838	<	}
838	>	}
839
840	<	}//end namespace oopse
840	>	void DumpWriter::writeClosing(std::ostream& os) {
841	>
842	>	os << "</OpenMD>\n";
843	>	os.flush();
844	>	}
845	>
846	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpWriter.cpp (property svn:keywords):
Revision 966 by chrisfen, Fri May 19 21:26:41 2006 UTC vs.
Revision 2020 by gezelter, Mon Sep 22 19:18:35 2014 UTC

#	Line 0 | Line 1
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