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

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trunk/src/io/DumpWriter.cpp (file contents), Revision 619 by tim, Wed Sep 21 20:59:31 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1875 by gezelter, Fri May 17 14:41:42 2013 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 "io/DumpWriter.hpp"
44		#include "primitives/Molecule.hpp"
45		#include "utils/simError.h"
46		#include "io/basic_teebuf.hpp"
47	+	#ifdef HAVE_ZLIB
48		#include "io/gzstream.hpp"
49	+	#endif
50		#include "io/Globals.hpp"
51
52	+	#ifdef _MSC_VER
53	+	#define isnan(x) _isnan((x))
54	+	#define isinf(x) (!_finite(x) && !_isnan(x))
55	+	#endif
56	+
57		#ifdef IS_MPI
58		#include <mpi.h>
59	<	#endif //is_mpi
59	>	#endif
60
61	<	namespace oopse {
61	>	using namespace std;
62	>	namespace OpenMD {
63
64		DumpWriter::DumpWriter(SimInfo* info)
65		: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
66
67		Globals* simParams = info->getSimParams();
68	<	needCompression_ = simParams->getCompressDumpFile();
68	>	needCompression_   = simParams->getCompressDumpFile();
69	>	needForceVector_   = simParams->getOutputForceVector();
70	>	needParticlePot_   = simParams->getOutputParticlePotential();
71	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
72	>	needElectricField_ = simParams->getOutputElectricField();
73
74	+	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
75	+	doSiteData_ = true;
76	+	} else {
77	+	doSiteData_ = false;
78	+	}
79	+
80	+	createDumpFile_ = true;
81		#ifdef HAVE_LIBZ
82		if (needCompression_) {
83	<	filename_ += ".gz";
84	<	eorFilename_ += ".gz";
83	>	filename_ += ".gz";
84	>	eorFilename_ += ".gz";
85		}
86		#endif
87
88		#ifdef IS_MPI
89
90	<	if (worldRank == 0) {
90	>	if (worldRank == 0) {
91		#endif // is_mpi
92	+
93	+	dumpFile_ = createOStream(filename_);
94
95	+	if (!dumpFile_) {
96	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
97	+	filename_.c_str());
98	+	painCave.isFatal = 1;
99	+	simError();
100	+	}
101
74	–	dumpFile_ = createOStream(filename_);
75	–
76	–	if (!dumpFile_) {
77	–	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
78	–	filename_.c_str());
79	–	painCave.isFatal = 1;
80	–	simError();
81	–	}
82	–
102		#ifdef IS_MPI
103
104	<	}
104	>	}
105
87	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
88	–	MPIcheckPoint();
89	–
106		#endif // is_mpi
107
108	<	}
108	>	}
109
110
111		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
#	Line 98 | Line 114 | namespace oopse {
114		Globals* simParams = info->getSimParams();
115		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
116
117	<	needCompression_ = simParams->getCompressDumpFile();
117	>	needCompression_   = simParams->getCompressDumpFile();
118	>	needForceVector_   = simParams->getOutputForceVector();
119	>	needParticlePot_   = simParams->getOutputParticlePotential();
120	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
121	>	needElectricField_ = simParams->getOutputElectricField();
122
123	+	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
124	+	doSiteData_ = true;
125	+	} else {
126	+	doSiteData_ = false;
127	+	}
128	+
129	+	createDumpFile_ = true;
130		#ifdef HAVE_LIBZ
131		if (needCompression_) {
132	<	filename_ += ".gz";
133	<	eorFilename_ += ".gz";
132	>	filename_ += ".gz";
133	>	eorFilename_ += ".gz";
134		}
135		#endif
136
137		#ifdef IS_MPI
138
139	<	if (worldRank == 0) {
139	>	if (worldRank == 0) {
140		#endif // is_mpi
141
142	+
143	+	dumpFile_ = createOStream(filename_);
144
145	<	dumpFile_ = createOStream(filename_);
145	>	if (!dumpFile_) {
146	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
147	>	filename_.c_str());
148	>	painCave.isFatal = 1;
149	>	simError();
150	>	}
151
118	–	if (!dumpFile_) {
119	–	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
120	–	filename_.c_str());
121	–	painCave.isFatal = 1;
122	–	simError();
123	–	}
124	–
152		#ifdef IS_MPI
153
154	<	}
154	>	}
155
129	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
130	–	MPIcheckPoint();
131	–
156		#endif // is_mpi
157
158	+	}
159	+
160	+	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
161	+	: info_(info), filename_(filename){
162	+
163	+	Globals* simParams = info->getSimParams();
164	+	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
165	+
166	+	needCompression_   = simParams->getCompressDumpFile();
167	+	needForceVector_   = simParams->getOutputForceVector();
168	+	needParticlePot_   = simParams->getOutputParticlePotential();
169	+	needFlucQ_         = simParams->getOutputFluctuatingCharges();
170	+	needElectricField_ = simParams->getOutputElectricField();
171	+
172	+	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
173	+	doSiteData_ = true;
174	+	} else {
175	+	doSiteData_ = false;
176		}
177
178	+	#ifdef HAVE_LIBZ
179	+	if (needCompression_) {
180	+	filename_ += ".gz";
181	+	eorFilename_ += ".gz";
182	+	}
183	+	#endif
184	+
185	+	#ifdef IS_MPI
186	+
187	+	if (worldRank == 0) {
188	+	#endif // is_mpi
189	+
190	+	createDumpFile_ = writeDumpFile;
191	+	if (createDumpFile_) {
192	+	dumpFile_ = createOStream(filename_);
193	+
194	+	if (!dumpFile_) {
195	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
196	+	filename_.c_str());
197	+	painCave.isFatal = 1;
198	+	simError();
199	+	}
200	+	}
201	+	#ifdef IS_MPI
202	+
203	+	}
204	+
205	+
206	+	#endif // is_mpi
207	+
208	+	}
209	+
210		DumpWriter::~DumpWriter() {
211
212		#ifdef IS_MPI
213
214		if (worldRank == 0) {
215		#endif // is_mpi
216	<
217	<	delete dumpFile_;
218	<
216	>	if (createDumpFile_){
217	>	writeClosing(*dumpFile_);
218	>	delete dumpFile_;
219	>	}
220		#ifdef IS_MPI
221
222		}
#	Line 150 | Line 225 | namespace oopse {
225
226		}
227
228	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
228	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
229
230	<	double currentTime;
231	<	Mat3x3d hmat;
232	<	double chi;
233	<	double integralOfChiDt;
234	<	Mat3x3d eta;
230	>	char buffer[1024];
231	>
232	>	os << "    <FrameData>\n";
233	>
234	>	RealType currentTime = s->getTime();
235	>
236	>	if (isinf(currentTime) || isnan(currentTime)) {
237	>	sprintf( painCave.errMsg,
238	>	"DumpWriter detected a numerical error writing the time");
239	>	painCave.isFatal = 1;
240	>	simError();
241	>	}
242
243	<	currentTime = s->getTime();
243	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
244	>	os << buffer;
245	>
246	>	Mat3x3d hmat;
247		hmat = s->getHmat();
248	<	chi = s->getChi();
249	<	integralOfChiDt = s->getIntegralOfChiDt();
250	<	eta = s->getEta();
248	>
249	>	for (unsigned int i = 0; i < 3; i++) {
250	>	for (unsigned int j = 0; j < 3; j++) {
251	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
252	>	sprintf( painCave.errMsg,
253	>	"DumpWriter detected a numerical error writing the box");
254	>	painCave.isFatal = 1;
255	>	simError();
256	>	}
257	>	}
258	>	}
259
260	<	os << currentTime << ";\t"
261	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
262	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
263	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
260	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
261	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
262	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
263	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
264	>	os << buffer;
265
266	<	//write out additional parameters, such as chi and eta
266	>	pair<RealType, RealType> thermostat = s->getThermostat();
267
268	<	os << chi << "\t" << integralOfChiDt << "\t;";
268	>	if (isinf(thermostat.first)  || isnan(thermostat.first) ||
269	>	isinf(thermostat.second) || isnan(thermostat.second)) {
270	>	sprintf( painCave.errMsg,
271	>	"DumpWriter detected a numerical error writing the thermostat");
272	>	painCave.isFatal = 1;
273	>	simError();
274	>	}
275	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
276	>	thermostat.second);
277	>	os << buffer;
278
279	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
280	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
281	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
282	<
283	<	os << "\n";
279	>	Mat3x3d eta;
280	>	eta = s->getBarostat();
281	>
282	>	for (unsigned int i = 0; i < 3; i++) {
283	>	for (unsigned int j = 0; j < 3; j++) {
284	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
285	>	sprintf( painCave.errMsg,
286	>	"DumpWriter detected a numerical error writing the barostat");
287	>	painCave.isFatal = 1;
288	>	simError();
289	>	}
290	>	}
291	>	}
292	>
293	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
294	>	eta(0, 0), eta(1, 0), eta(2, 0),
295	>	eta(0, 1), eta(1, 1), eta(2, 1),
296	>	eta(0, 2), eta(1, 2), eta(2, 2));
297	>	os << buffer;
298	>
299	>	os << "    </FrameData>\n";
300		}
301
302		void DumpWriter::writeFrame(std::ostream& os) {
184	–	const int BUFFERSIZE = 2000;
185	–	const int MINIBUFFERSIZE = 100;
303
304	<	char tempBuffer[BUFFERSIZE];
305	<	char writeLine[BUFFERSIZE];
304	>	#ifdef IS_MPI
305	>	MPI::Status istatus;
306	>	#endif
307
190	–	Quat4d q;
191	–	Vector3d ji;
192	–	Vector3d pos;
193	–	Vector3d vel;
194	–
308		Molecule* mol;
309	<	StuntDouble* integrableObject;
309	>	StuntDouble* sd;
310		SimInfo::MoleculeIterator mi;
311		Molecule::IntegrableObjectIterator ii;
312	<
200	<	int nTotObjects;
201	<	nTotObjects = info_->getNGlobalIntegrableObjects();
312	>	RigidBody::AtomIterator ai;
313
314		#ifndef IS_MPI
315	<
316	<
317	<	os << nTotObjects << "\n";
207	<
208	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
209	<
210	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
315	>	os << "  <Snapshot>\n";
316	>
317	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
318
319	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
320	<	integrableObject = mol->nextIntegrableObject(ii)) {
321	<
319	>	os << "    <StuntDoubles>\n";
320	>	for (mol = info_->beginMolecule(mi); mol != NULL;
321	>	mol = info_->nextMolecule(mi)) {
322	>
323	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
324	>	sd = mol->nextIntegrableObject(ii)) {
325	>	os << prepareDumpLine(sd);
326	>
327	>	}
328	>	}
329	>	os << "    </StuntDoubles>\n";
330
331	<	pos = integrableObject->getPos();
332	<	vel = integrableObject->getVel();
331	>	if (doSiteData_) {
332	>	os << "    <SiteData>\n";
333	>	for (mol = info_->beginMolecule(mi); mol != NULL;
334	>	mol = info_->nextMolecule(mi)) {
335	>
336	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
337	>	sd = mol->nextIntegrableObject(ii)) {
338
339	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
340	<	integrableObject->getType().c_str(),
341	<	pos[0], pos[1], pos[2],
222	<	vel[0], vel[1], vel[2]);
339	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
340	>	// do one for the IO itself
341	>	os << prepareSiteLine(sd, ioIndex, 0);
342
343	<	strcpy(writeLine, tempBuffer);
343	>	if (sd->isRigidBody()) {
344	>
345	>	RigidBody* rb = static_cast<RigidBody*>(sd);
346	>	int siteIndex = 0;
347	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
348	>	atom = rb->nextAtom(ai)) {
349	>	os << prepareSiteLine(atom, ioIndex, siteIndex);
350	>	siteIndex++;
351	>	}
352	>	}
353	>	}
354	>	}
355	>	os << "    </SiteData>\n";
356	>	}
357	>	os << "  </Snapshot>\n";
358
359	<	if (integrableObject->isDirectional()) {
360	<	q = integrableObject->getQ();
228	<	ji = integrableObject->getJ();
359	>	os.flush();
360	>	#else
361
362	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
363	<	q[0], q[1], q[2], q[3],
364	<	ji[0], ji[1], ji[2]);
233	<	strcat(writeLine, tempBuffer);
234	<	} else {
235	<	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
236	<	}
362	>	const int masterNode = 0;
363	>	int worldRank = MPI::COMM_WORLD.Get_rank();
364	>	int nProc = MPI::COMM_WORLD.Get_size();
365
366	<	os << writeLine;
366	>	if (worldRank == masterNode) {
367	>	os << "  <Snapshot>\n";
368	>	writeFrameProperties(os,
369	>	info_->getSnapshotManager()->getCurrentSnapshot());
370	>	os << "    <StuntDoubles>\n";
371	>	}
372
373	+	//every node prepares the dump lines for integrable objects belong to itself
374	+	std::string buffer;
375	+	for (mol = info_->beginMolecule(mi); mol != NULL;
376	+	mol = info_->nextMolecule(mi)) {
377	+	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
378	+	sd = mol->nextIntegrableObject(ii)) {
379	+	buffer += prepareDumpLine(sd);
380		}
381		}
242	–
243	–	os.flush();
244	–	#else // is_mpi
245	–	/*********************************************************************
246	–	* Documentation?  You want DOCUMENTATION?
247	–	*
248	–	* Why all the potatoes below?
249	–	*
250	–	* To make a long story short, the original version of DumpWriter
251	–	* worked in the most inefficient way possible.  Node 0 would
252	–	* poke each of the node for an individual atom's formatted data
253	–	* as node 0 worked its way down the global index. This was particularly
254	–	* inefficient since the method blocked all processors at every atom
255	–	* (and did it twice!).
256	–	*
257	–	* An intermediate version of DumpWriter could be described from Node
258	–	* zero's perspective as follows:
259	–	*
260	–	*  1) Have 100 of your friends stand in a circle.
261	–	*  2) When you say go, have all of them start tossing potatoes at
262	–	*     you (one at a time).
263	–	*  3) Catch the potatoes.
264	–	*
265	–	* It was an improvement, but MPI has buffers and caches that could
266	–	* best be described in this analogy as "potato nets", so there's no
267	–	* need to block the processors atom-by-atom.
268	–	*
269	–	* This new and improved DumpWriter works in an even more efficient
270	–	* way:
271	–	*
272	–	*  1) Have 100 of your friend stand in a circle.
273	–	*  2) When you say go, have them start tossing 5-pound bags of
274	–	*     potatoes at you.
275	–	*  3) Once you've caught a friend's bag of potatoes,
276	–	*     toss them a spud to let them know they can toss another bag.
277	–	*
278	–	* How's THAT for documentation?
279	–	*
280	–	*********************************************************************/
281	–	const int masterNode = 0;
282	–
283	–	int * potatoes;
284	–	int myPotato;
285	–	int nProc;
286	–	int which_node;
287	–	double atomData[13];
288	–	int isDirectional;
289	–	char MPIatomTypeString[MINIBUFFERSIZE];
290	–	int msgLen; // the length of message actually recieved at master nodes
291	–	int haveError;
292	–	MPI_Status istatus;
293	–	int nCurObj;
382
383	<	// code to find maximum tag value
384	<	int * tagub;
385	<	int flag;
386	<	int MAXTAG;
387	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
383	>	if (worldRank == masterNode) {
384	>	os << buffer;
385	>
386	>	for (int i = 1; i < nProc; ++i) {
387	>	// tell processor i to start sending us data:
388	>	MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
389
390	<	if (flag) {
391	<	MAXTAG = *tagub;
390	>	// receive the length of the string buffer that was
391	>	// prepared by processor i:
392	>	int recvLength;
393	>	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
394	>	istatus);
395	>
396	>	// create a buffer to receive the data
397	>	char* recvBuffer = new char[recvLength];
398	>	if (recvBuffer == NULL) {
399	>	} else {
400	>	// receive the data:
401	>	MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
402	>	MPI::ANY_TAG, istatus);
403	>	// send it to the file:
404	>	os << recvBuffer;
405	>	// get rid of the receive buffer:
406	>	delete [] recvBuffer;
407	>	}
408	>	}
409		} else {
410	<	MAXTAG = 32767;
410	>	int sendBufferLength = buffer.size() + 1;
411	>	int myturn = 0;
412	>	for (int i = 1; i < nProc; ++i){
413	>	// wait for the master node to call our number:
414	>	MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
415	>	if (myturn == worldRank){
416	>	// send the length of our buffer:
417	>	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
418	>
419	>	// send our buffer:
420	>	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
421	>	MPI::CHAR, masterNode, 0);
422	>	}
423	>	}
424		}
425	+
426	+	if (worldRank == masterNode) {
427	+	os << "    </StuntDoubles>\n";
428	+	}
429
430	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
430	>	if (doSiteData_) {
431	>	if (worldRank == masterNode) {
432	>	os << "    <SiteData>\n";
433	>	}
434	>	buffer.clear();
435	>	for (mol = info_->beginMolecule(mi); mol != NULL;
436	>	mol = info_->nextMolecule(mi)) {
437	>
438	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
439	>	sd = mol->nextIntegrableObject(ii)) {
440	>
441	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
442	>	// do one for the IO itself
443	>	buffer += prepareSiteLine(sd, ioIndex, 0);
444
445	<	// Node 0 needs a list of the magic potatoes for each processor;
445	>	if (sd->isRigidBody()) {
446	>
447	>	RigidBody* rb = static_cast<RigidBody*>(sd);
448	>	int siteIndex = 0;
449	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
450	>	atom = rb->nextAtom(ai)) {
451	>	buffer += prepareSiteLine(atom, ioIndex, siteIndex);
452	>	siteIndex++;
453	>	}
454	>	}
455	>	}
456	>	}
457
458	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
459	<	potatoes = new int[nProc];
460	<
461	<	//write out the comment lines
462	<	for(int i = 0; i < nProc; i++) {
463	<	potatoes[i] = 0;
458	>	if (worldRank == masterNode) {
459	>	os << buffer;
460	>
461	>	for (int i = 1; i < nProc; ++i) {
462	>
463	>	// tell processor i to start sending us data:
464	>	MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
465	>
466	>	// receive the length of the string buffer that was
467	>	// prepared by processor i:
468	>	int recvLength;
469	>	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
470	>	istatus);
471	>
472	>	// create a buffer to receive the data
473	>	char* recvBuffer = new char[recvLength];
474	>	if (recvBuffer == NULL) {
475	>	} else {
476	>	// receive the data:
477	>	MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
478	>	MPI::ANY_TAG, istatus);
479	>	// send it to the file:
480	>	os << recvBuffer;
481	>	// get rid of the receive buffer:
482	>	delete [] recvBuffer;
483	>	}
484	>	}
485	>	} else {
486	>	int sendBufferLength = buffer.size() + 1;
487	>	int myturn = 0;
488	>	for (int i = 1; i < nProc; ++i){
489	>	// wait for the master node to call our number:
490	>	MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
491	>	if (myturn == worldRank){
492	>	// send the length of our buffer:
493	>	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
494	>	// send our buffer:
495	>	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
496	>	MPI::CHAR, masterNode, 0);
497	>	}
498	>	}
499		}
500	+
501	+	if (worldRank == masterNode) {
502	+	os << "    </SiteData>\n";
503	+	}
504	+	}
505	+
506	+	if (worldRank == masterNode) {
507	+	os << "  </Snapshot>\n";
508	+	os.flush();
509	+	}
510	+
511	+	#endif // is_mpi
512	+
513	+	}
514
515	+	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
516	+
517	+	int index = sd->getGlobalIntegrableObjectIndex();
518	+	std::string type("pv");
519	+	std::string line;
520	+	char tempBuffer[4096];
521
522	<	os << nTotObjects << "\n";
523	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
522	>	Vector3d pos;
523	>	Vector3d vel;
524	>	pos = sd->getPos();
525
526	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
526	>	if (isinf(pos[0]) || isnan(pos[0]) ||
527	>	isinf(pos[1]) || isnan(pos[1]) ||
528	>	isinf(pos[2]) || isnan(pos[2]) ) {
529	>	sprintf( painCave.errMsg,
530	>	"DumpWriter detected a numerical error writing the position"
531	>	" for object %d", index);
532	>	painCave.isFatal = 1;
533	>	simError();
534	>	}
535
536	<	// Get the Node number which has this atom;
536	>	vel = sd->getVel();
537
538	<	which_node = info_->getMolToProc(i);
538	>	if (isinf(vel[0]) || isnan(vel[0]) ||
539	>	isinf(vel[1]) || isnan(vel[1]) ||
540	>	isinf(vel[2]) || isnan(vel[2]) ) {
541	>	sprintf( painCave.errMsg,
542	>	"DumpWriter detected a numerical error writing the velocity"
543	>	" for object %d", index);
544	>	painCave.isFatal = 1;
545	>	simError();
546	>	}
547
548	<	if (which_node != masterNode) { //current molecule is in slave node
549	<	if (potatoes[which_node] + 1 >= MAXTAG) {
550	<	// The potato was going to exceed the maximum value,
551	<	// so wrap this processor potato back to 0:
548	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
549	>	pos[0], pos[1], pos[2],
550	>	vel[0], vel[1], vel[2]);
551	>	line += tempBuffer;
552
553	<	potatoes[which_node] = 0;
554	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
555	<	MPI_COMM_WORLD);
556	<	}
553	>	if (sd->isDirectional()) {
554	>	type += "qj";
555	>	Quat4d q;
556	>	Vector3d ji;
557	>	q = sd->getQ();
558
559	<	myPotato = potatoes[which_node];
559	>	if (isinf(q[0]) || isnan(q[0]) ||
560	>	isinf(q[1]) || isnan(q[1]) ||
561	>	isinf(q[2]) || isnan(q[2]) ||
562	>	isinf(q[3]) || isnan(q[3]) ) {
563	>	sprintf( painCave.errMsg,
564	>	"DumpWriter detected a numerical error writing the quaternion"
565	>	" for object %d", index);
566	>	painCave.isFatal = 1;
567	>	simError();
568	>	}
569
570	<	//recieve the number of integrableObject in current molecule
342	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
343	<	MPI_COMM_WORLD, &istatus);
344	<	myPotato++;
570	>	ji = sd->getJ();
571
572	<	for(int l = 0; l < nCurObj; l++) {
573	<	if (potatoes[which_node] + 2 >= MAXTAG) {
574	<	// The potato was going to exceed the maximum value,
575	<	// so wrap this processor potato back to 0:
572	>	if (isinf(ji[0]) || isnan(ji[0]) ||
573	>	isinf(ji[1]) || isnan(ji[1]) ||
574	>	isinf(ji[2]) || isnan(ji[2]) ) {
575	>	sprintf( painCave.errMsg,
576	>	"DumpWriter detected a numerical error writing the angular"
577	>	" momentum for object %d", index);
578	>	painCave.isFatal = 1;
579	>	simError();
580	>	}
581
582	<	potatoes[which_node] = 0;
583	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
584	<	0, MPI_COMM_WORLD);
585	<	}
582	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
583	>	q[0], q[1], q[2], q[3],
584	>	ji[0], ji[1], ji[2]);
585	>	line += tempBuffer;
586	>	}
587
588	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
589	<	which_node, myPotato, MPI_COMM_WORLD,
590	<	&istatus);
588	>	if (needForceVector_) {
589	>	type += "f";
590	>	Vector3d frc = sd->getFrc();
591	>	if (isinf(frc[0]) || isnan(frc[0]) ||
592	>	isinf(frc[1]) || isnan(frc[1]) ||
593	>	isinf(frc[2]) || isnan(frc[2]) ) {
594	>	sprintf( painCave.errMsg,
595	>	"DumpWriter detected a numerical error writing the force"
596	>	" for object %d", index);
597	>	painCave.isFatal = 1;
598	>	simError();
599	>	}
600	>	sprintf(tempBuffer, " %13e %13e %13e",
601	>	frc[0], frc[1], frc[2]);
602	>	line += tempBuffer;
603	>
604	>	if (sd->isDirectional()) {
605	>	type += "t";
606	>	Vector3d trq = sd->getTrq();
607	>	if (isinf(trq[0]) || isnan(trq[0]) ||
608	>	isinf(trq[1]) || isnan(trq[1]) ||
609	>	isinf(trq[2]) || isnan(trq[2]) ) {
610	>	sprintf( painCave.errMsg,
611	>	"DumpWriter detected a numerical error writing the torque"
612	>	" for object %d", index);
613	>	painCave.isFatal = 1;
614	>	simError();
615	>	}
616	>	sprintf(tempBuffer, " %13e %13e %13e",
617	>	trq[0], trq[1], trq[2]);
618	>	line += tempBuffer;
619	>	}
620	>	}
621
622	<	myPotato++;
622	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
623	>	return std::string(tempBuffer);
624	>	}
625
626	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
627	<	MPI_COMM_WORLD, &istatus);
364	<	myPotato++;
626	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
627	>
628
629	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
629	>	std::string id;
630	>	std::string type;
631	>	std::string line;
632	>	char tempBuffer[4096];
633
634	<	if (msgLen == 13)
635	<	isDirectional = 1;
636	<	else
637	<	isDirectional = 0;
634	>	if (sd->isRigidBody()) {
635	>	sprintf(tempBuffer, "%10d           ", ioIndex);
636	>	id = std::string(tempBuffer);
637	>	} else {
638	>	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
639	>	id = std::string(tempBuffer);
640	>	}
641	>
642	>	if (needFlucQ_) {
643	>	type += "cw";
644	>	RealType fqPos = sd->getFlucQPos();
645	>	if (isinf(fqPos) || isnan(fqPos) ) {
646	>	sprintf( painCave.errMsg,
647	>	"DumpWriter detected a numerical error writing the"
648	>	" fluctuating charge for object %s", id.c_str());
649	>	painCave.isFatal = 1;
650	>	simError();
651	>	}
652	>	sprintf(tempBuffer, " %13e ", fqPos);
653	>	line += tempBuffer;
654	>
655	>	RealType fqVel = sd->getFlucQVel();
656	>	if (isinf(fqVel) || isnan(fqVel) ) {
657	>	sprintf( painCave.errMsg,
658	>	"DumpWriter detected a numerical error writing the"
659	>	" fluctuating charge velocity for object %s", id.c_str());
660	>	painCave.isFatal = 1;
661	>	simError();
662	>	}
663	>	sprintf(tempBuffer, " %13e ", fqVel);
664	>	line += tempBuffer;
665
666	<	// If we've survived to here, format the line:
666	>	if (needForceVector_) {
667	>	type += "g";
668	>	RealType fqFrc = sd->getFlucQFrc();
669	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
670	>	sprintf( painCave.errMsg,
671	>	"DumpWriter detected a numerical error writing the"
672	>	" fluctuating charge force for object %s", id.c_str());
673	>	painCave.isFatal = 1;
674	>	simError();
675	>	}
676	>	sprintf(tempBuffer, " %13e ", fqFrc);
677	>	line += tempBuffer;
678	>	}
679	>	}
680
681	<	if (!isDirectional) {
682	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
683	<	MPIatomTypeString, atomData[0],
684	<	atomData[1], atomData[2],
685	<	atomData[3], atomData[4],
686	<	atomData[5]);
681	>	if (needElectricField_) {
682	>	type += "e";
683	>	Vector3d eField= sd->getElectricField();
684	>	if (isinf(eField[0]) || isnan(eField[0]) ||
685	>	isinf(eField[1]) || isnan(eField[1]) ||
686	>	isinf(eField[2]) || isnan(eField[2]) ) {
687	>	sprintf( painCave.errMsg,
688	>	"DumpWriter detected a numerical error writing the electric"
689	>	" field for object %s", id.c_str());
690	>	painCave.isFatal = 1;
691	>	simError();
692	>	}
693	>	sprintf(tempBuffer, " %13e %13e %13e",
694	>	eField[0], eField[1], eField[2]);
695	>	line += tempBuffer;
696	>	}
697
382	–	strcat(writeLine,
383	–	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
384	–	} else {
385	–	sprintf(writeLine,
386	–	"%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\n",
387	–	MPIatomTypeString,
388	–	atomData[0],
389	–	atomData[1],
390	–	atomData[2],
391	–	atomData[3],
392	–	atomData[4],
393	–	atomData[5],
394	–	atomData[6],
395	–	atomData[7],
396	–	atomData[8],
397	–	atomData[9],
398	–	atomData[10],
399	–	atomData[11],
400	–	atomData[12]);
401	–	}
698
699	<	os << writeLine;
700	<
701	<	} // end for(int l =0)
702	<
703	<	potatoes[which_node] = myPotato;
704	<	} else { //master node has current molecule
705	<
706	<	mol = info_->getMoleculeByGlobalIndex(i);
707	<
412	<	if (mol == NULL) {
413	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
414	<	painCave.isFatal = 1;
415	<	simError();
416	<	}
417	<
418	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
419	<	integrableObject = mol->nextIntegrableObject(ii)) {
420	<
421	<	pos = integrableObject->getPos();
422	<	vel = integrableObject->getVel();
423	<
424	<	atomData[0] = pos[0];
425	<	atomData[1] = pos[1];
426	<	atomData[2] = pos[2];
427	<
428	<	atomData[3] = vel[0];
429	<	atomData[4] = vel[1];
430	<	atomData[5] = vel[2];
431	<
432	<	isDirectional = 0;
433	<
434	<	if (integrableObject->isDirectional()) {
435	<	isDirectional = 1;
436	<
437	<	q = integrableObject->getQ();
438	<	ji = integrableObject->getJ();
439	<
440	<	for(int j = 0; j < 6; j++) {
441	<	atomData[j] = atomData[j];
442	<	}
443	<
444	<	atomData[6] = q[0];
445	<	atomData[7] = q[1];
446	<	atomData[8] = q[2];
447	<	atomData[9] = q[3];
448	<
449	<	atomData[10] = ji[0];
450	<	atomData[11] = ji[1];
451	<	atomData[12] = ji[2];
452	<	}
453	<
454	<	// If we've survived to here, format the line:
455	<
456	<	if (!isDirectional) {
457	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
458	<	integrableObject->getType().c_str(), atomData[0],
459	<	atomData[1], atomData[2],
460	<	atomData[3], atomData[4],
461	<	atomData[5]);
462	<
463	<	strcat(writeLine,
464	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
465	<	} else {
466	<	sprintf(writeLine,
467	<	"%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\n",
468	<	integrableObject->getType().c_str(),
469	<	atomData[0],
470	<	atomData[1],
471	<	atomData[2],
472	<	atomData[3],
473	<	atomData[4],
474	<	atomData[5],
475	<	atomData[6],
476	<	atomData[7],
477	<	atomData[8],
478	<	atomData[9],
479	<	atomData[10],
480	<	atomData[11],
481	<	atomData[12]);
482	<	}
483	<
484	<
485	<	os << writeLine;
486	<
487	<	} //end for(iter = integrableObject.begin())
488	<	}
489	<	} //end for(i = 0; i < mpiSim->getNmol())
490	<
491	<	os.flush();
492	<
493	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
494	<	MPIcheckPoint();
495	<
496	<	delete [] potatoes;
497	<	} else {
498	<
499	<	// worldRank != 0, so I'm a remote node.
500	<
501	<	// Set my magic potato to 0:
502	<
503	<	myPotato = 0;
504	<
505	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
506	<
507	<	// Am I the node which has this integrableObject?
508	<	int whichNode = info_->getMolToProc(i);
509	<	if (whichNode == worldRank) {
510	<	if (myPotato + 1 >= MAXTAG) {
511	<
512	<	// The potato was going to exceed the maximum value,
513	<	// so wrap this processor potato back to 0 (and block until
514	<	// node 0 says we can go:
515	<
516	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
517	<	&istatus);
518	<	}
519	<
520	<	mol = info_->getMoleculeByGlobalIndex(i);
521	<
522	<
523	<	nCurObj = mol->getNIntegrableObjects();
524	<
525	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
526	<	myPotato++;
527	<
528	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
529	<	integrableObject = mol->nextIntegrableObject(ii)) {
530	<
531	<	if (myPotato + 2 >= MAXTAG) {
532	<
533	<	// The potato was going to exceed the maximum value,
534	<	// so wrap this processor potato back to 0 (and block until
535	<	// node 0 says we can go:
536	<
537	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
538	<	&istatus);
539	<	}
540	<
541	<	pos = integrableObject->getPos();
542	<	vel = integrableObject->getVel();
543	<
544	<	atomData[0] = pos[0];
545	<	atomData[1] = pos[1];
546	<	atomData[2] = pos[2];
547	<
548	<	atomData[3] = vel[0];
549	<	atomData[4] = vel[1];
550	<	atomData[5] = vel[2];
551	<
552	<	isDirectional = 0;
553	<
554	<	if (integrableObject->isDirectional()) {
555	<	isDirectional = 1;
556	<
557	<	q = integrableObject->getQ();
558	<	ji = integrableObject->getJ();
559	<
560	<	atomData[6] = q[0];
561	<	atomData[7] = q[1];
562	<	atomData[8] = q[2];
563	<	atomData[9] = q[3];
564	<
565	<	atomData[10] = ji[0];
566	<	atomData[11] = ji[1];
567	<	atomData[12] = ji[2];
568	<	}
569	<
570	<	strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
571	<
572	<	// null terminate the  std::string before sending (just in case):
573	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
574	<
575	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
576	<	myPotato, MPI_COMM_WORLD);
577	<
578	<	myPotato++;
579	<
580	<	if (isDirectional) {
581	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
582	<	MPI_COMM_WORLD);
583	<	} else {
584	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
585	<	MPI_COMM_WORLD);
586	<	}
587	<
588	<	myPotato++;
589	<	}
590	<
591	<	}
592	<
699	>	if (needParticlePot_) {
700	>	type += "u";
701	>	RealType particlePot = sd->getParticlePot();
702	>	if (isinf(particlePot) || isnan(particlePot)) {
703	>	sprintf( painCave.errMsg,
704	>	"DumpWriter detected a numerical error writing the particle "
705	>	" potential for object %s", id.c_str());
706	>	painCave.isFatal = 1;
707	>	simError();
708		}
709	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
710	<	MPIcheckPoint();
709	>	sprintf(tempBuffer, " %13e", particlePot);
710	>	line += tempBuffer;
711		}
712	+
713
714	<	#endif // is_mpi
715	<
714	>	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
715	>	return std::string(tempBuffer);
716		}
717
718		void DumpWriter::writeDump() {
#	Line 609 | Line 725 | namespace oopse {
725		#ifdef IS_MPI
726		if (worldRank == 0) {
727		#endif // is_mpi
728	<
728	>
729		eorStream = createOStream(eorFilename_);
730	<
730	>	writeFrame(*eorStream);
731	>
732		#ifdef IS_MPI
733		}
617	–	#endif // is_mpi
618	–
619	–	writeFrame(*eorStream);
620	–
621	–	#ifdef IS_MPI
734		if (worldRank == 0) {
735		#endif // is_mpi
624	–	delete eorStream;
736
737	+	writeClosing(*eorStream);
738	+	delete eorStream;
739	+
740		#ifdef IS_MPI
741		}
742		#endif // is_mpi
#	Line 655 | Line 769 | namespace oopse {
769		#ifdef IS_MPI
770		if (worldRank == 0) {
771		#endif // is_mpi
772	<	delete eorStream;
773	<
772	>	writeClosing(*eorStream);
773	>	delete eorStream;
774		#ifdef IS_MPI
775		}
776		#endif // is_mpi
777
778		}
779
780	<	std::ostream* DumpWriter::createOStream(const std::string& filename) {
780	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
781
782		std::ostream* newOStream;
783	<	#ifdef HAVE_LIBZ
783	>	#ifdef HAVE_ZLIB
784		if (needCompression_) {
785	<	newOStream = new ogzstream(filename.c_str());
785	>	newOStream = new ogzstream(filename.c_str());
786		} else {
787	<	newOStream = new std::ofstream(filename.c_str());
787	>	newOStream = new std::ofstream(filename.c_str());
788		}
789		#else
790		newOStream = new std::ofstream(filename.c_str());
791		#endif
792	+	//write out MetaData first
793	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
794	+	(*newOStream) << "  <MetaData>" << std::endl;
795	+	(*newOStream) << info_->getRawMetaData();
796	+	(*newOStream) << "  </MetaData>" << std::endl;
797		return newOStream;
798	<	}
798	>	}
799
800	<	}//end namespace oopse
800	>	void DumpWriter::writeClosing(std::ostream& os) {
801	>
802	>	os << "</OpenMD>\n";
803	>	os.flush();
804	>	}
805	>
806	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 619 by tim, Wed Sep 21 20:59:31 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

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