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

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 615 by tim, Tue Sep 20 21:22:38 2005 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 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 "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()){
68
69		Globals* simParams = info->getSimParams();
70	<	needCompression_ = simParams->getCompressDumpFile();
70	>	needCompression_   = simParams->getCompressDumpFile();
71	>	needForceVector_   = simParams->getOutputForceVector();
72	>	needParticlePot_   = simParams->getOutputParticlePotential();
73	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
74	>	needElectricField_ = simParams->getOutputElectricField();
75
76	+	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
77	+	doSiteData_ = true;
78	+	} else {
79	+	doSiteData_ = false;
80	+	}
81	+
82	+	createDumpFile_ = true;
83	+	#ifdef HAVE_LIBZ
84		if (needCompression_) {
85	<	filename_ += ".gz";
86	<	eorFilename_ += ".gz";
85	>	filename_ += ".gz";
86	>	eorFilename_ += ".gz";
87		}
88	+	#endif
89
90		#ifdef IS_MPI
91
92	<	if (worldRank == 0) {
92	>	if (worldRank == 0) {
93		#endif // is_mpi
94	+
95	+	dumpFile_ = createOStream(filename_);
96
97	+	if (!dumpFile_) {
98	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
99	+	filename_.c_str());
100	+	painCave.isFatal = 1;
101	+	simError();
102	+	}
103
72	–	dumpFile_ = createOStream(filename_);
73	–
74	–	if (!dumpFile_) {
75	–	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
76	–	filename_.c_str());
77	–	painCave.isFatal = 1;
78	–	simError();
79	–	}
80	–
104		#ifdef IS_MPI
105
106	<	}
106	>	}
107
85	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
86	–	MPIcheckPoint();
87	–
108		#endif // is_mpi
109
110	<	}
110	>	}
111
112
113		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
#	Line 96 | Line 116 | namespace oopse {
116		Globals* simParams = info->getSimParams();
117		eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
118
119	<	needCompression_ = simParams->getCompressDumpFile();
119	>	needCompression_   = simParams->getCompressDumpFile();
120	>	needForceVector_   = simParams->getOutputForceVector();
121	>	needParticlePot_   = simParams->getOutputParticlePotential();
122	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
123	>	needElectricField_ = simParams->getOutputElectricField();
124	>
125	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
126	>	doSiteData_ = true;
127	>	} else {
128	>	doSiteData_ = false;
129	>	}
130	>
131	>	createDumpFile_ = true;
132	>	#ifdef HAVE_LIBZ
133		if (needCompression_) {
134	<	filename_ += ".gz";
135	<	eorFilename_ += ".gz";
134	>	filename_ += ".gz";
135	>	eorFilename_ += ".gz";
136		}
137	+	#endif
138
139		#ifdef IS_MPI
140
141	<	if (worldRank == 0) {
141	>	if (worldRank == 0) {
142		#endif // is_mpi
143
144	+
145	+	dumpFile_ = createOStream(filename_);
146
147	<	dumpFile_ = createOStream(filename_);
147	>	if (!dumpFile_) {
148	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
149	>	filename_.c_str());
150	>	painCave.isFatal = 1;
151	>	simError();
152	>	}
153
113	–	if (!dumpFile_) {
114	–	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
115	–	filename_.c_str());
116	–	painCave.isFatal = 1;
117	–	simError();
118	–	}
119	–
154		#ifdef IS_MPI
155
156	<	}
156	>	}
157
124	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
125	–	MPIcheckPoint();
126	–
158		#endif // is_mpi
159
160	+	}
161	+
162	+	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
163	+	: info_(info), filename_(filename){
164	+
165	+	Globals* simParams = info->getSimParams();
166	+	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
167	+
168	+	needCompression_   = simParams->getCompressDumpFile();
169	+	needForceVector_   = simParams->getOutputForceVector();
170	+	needParticlePot_   = simParams->getOutputParticlePotential();
171	+	needFlucQ_         = simParams->getOutputFluctuatingCharges();
172	+	needElectricField_ = simParams->getOutputElectricField();
173	+
174	+	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
175	+	doSiteData_ = true;
176	+	} else {
177	+	doSiteData_ = false;
178		}
179
180	+	#ifdef HAVE_LIBZ
181	+	if (needCompression_) {
182	+	filename_ += ".gz";
183	+	eorFilename_ += ".gz";
184	+	}
185	+	#endif
186	+
187	+	#ifdef IS_MPI
188	+
189	+	if (worldRank == 0) {
190	+	#endif // is_mpi
191	+
192	+	createDumpFile_ = writeDumpFile;
193	+	if (createDumpFile_) {
194	+	dumpFile_ = createOStream(filename_);
195	+
196	+	if (!dumpFile_) {
197	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
198	+	filename_.c_str());
199	+	painCave.isFatal = 1;
200	+	simError();
201	+	}
202	+	}
203	+	#ifdef IS_MPI
204	+
205	+	}
206	+
207	+
208	+	#endif // is_mpi
209	+
210	+	}
211	+
212		DumpWriter::~DumpWriter() {
213
214		#ifdef IS_MPI
215
216		if (worldRank == 0) {
217		#endif // is_mpi
218	<
219	<	delete dumpFile_;
220	<
218	>	if (createDumpFile_){
219	>	writeClosing(*dumpFile_);
220	>	delete dumpFile_;
221	>	}
222		#ifdef IS_MPI
223
224		}
#	Line 145 | Line 227 | namespace oopse {
227
228		}
229
230	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
230	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
231
232	<	double currentTime;
233	<	Mat3x3d hmat;
234	<	double chi;
235	<	double integralOfChiDt;
236	<	Mat3x3d eta;
232	>	char buffer[1024];
233	>
234	>	os << "    <FrameData>\n";
235	>
236	>	RealType currentTime = s->getTime();
237	>
238	>	if (isinf(currentTime) || isnan(currentTime)) {
239	>	sprintf( painCave.errMsg,
240	>	"DumpWriter detected a numerical error writing the time");
241	>	painCave.isFatal = 1;
242	>	simError();
243	>	}
244
245	<	currentTime = s->getTime();
245	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
246	>	os << buffer;
247	>
248	>	Mat3x3d hmat;
249		hmat = s->getHmat();
250	<	chi = s->getChi();
251	<	integralOfChiDt = s->getIntegralOfChiDt();
252	<	eta = s->getEta();
250	>
251	>	for (unsigned int i = 0; i < 3; i++) {
252	>	for (unsigned int j = 0; j < 3; j++) {
253	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
254	>	sprintf( painCave.errMsg,
255	>	"DumpWriter detected a numerical error writing the box");
256	>	painCave.isFatal = 1;
257	>	simError();
258	>	}
259	>	}
260	>	}
261
262	<	os << currentTime << ";\t"
263	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
264	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
265	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
262	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
263	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
264	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
265	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
266	>	os << buffer;
267
268	<	//write out additional parameters, such as chi and eta
268	>	pair<RealType, RealType> thermostat = s->getThermostat();
269
270	<	os << chi << "\t" << integralOfChiDt << "\t;";
270	>	if (isinf(thermostat.first)  || isnan(thermostat.first) ||
271	>	isinf(thermostat.second) || isnan(thermostat.second)) {
272	>	sprintf( painCave.errMsg,
273	>	"DumpWriter detected a numerical error writing the thermostat");
274	>	painCave.isFatal = 1;
275	>	simError();
276	>	}
277	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
278	>	thermostat.second);
279	>	os << buffer;
280
281	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
282	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
283	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
284	<
285	<	os << "\n";
281	>	Mat3x3d eta;
282	>	eta = s->getBarostat();
283	>
284	>	for (unsigned int i = 0; i < 3; i++) {
285	>	for (unsigned int j = 0; j < 3; j++) {
286	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
287	>	sprintf( painCave.errMsg,
288	>	"DumpWriter detected a numerical error writing the barostat");
289	>	painCave.isFatal = 1;
290	>	simError();
291	>	}
292	>	}
293	>	}
294	>
295	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
296	>	eta(0, 0), eta(1, 0), eta(2, 0),
297	>	eta(0, 1), eta(1, 1), eta(2, 1),
298	>	eta(0, 2), eta(1, 2), eta(2, 2));
299	>	os << buffer;
300	>
301	>	os << "    </FrameData>\n";
302		}
303
304		void DumpWriter::writeFrame(std::ostream& os) {
179	–	const int BUFFERSIZE = 2000;
180	–	const int MINIBUFFERSIZE = 100;
305
306	<	char tempBuffer[BUFFERSIZE];
307	<	char writeLine[BUFFERSIZE];
306	>	#ifdef IS_MPI
307	>	MPI::Status istatus;
308	>	#endif
309
185	–	Quat4d q;
186	–	Vector3d ji;
187	–	Vector3d pos;
188	–	Vector3d vel;
189	–
310		Molecule* mol;
311	<	StuntDouble* integrableObject;
311	>	StuntDouble* sd;
312		SimInfo::MoleculeIterator mi;
313		Molecule::IntegrableObjectIterator ii;
314	<
195	<	int nTotObjects;
196	<	nTotObjects = info_->getNGlobalIntegrableObjects();
314	>	RigidBody::AtomIterator ai;
315
316		#ifndef IS_MPI
317	+	os << "  <Snapshot>\n";
318	+
319	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
320
321	+	os << "    <StuntDoubles>\n";
322	+	for (mol = info_->beginMolecule(mi); mol != NULL;
323	+	mol = info_->nextMolecule(mi)) {
324	+
325	+	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
326	+	sd = mol->nextIntegrableObject(ii)) {
327	+	os << prepareDumpLine(sd);
328	+
329	+	}
330	+	}
331	+	os << "    </StuntDoubles>\n";
332
333	<	os << nTotObjects << "\n";
334	<
335	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
333	>	if (doSiteData_) {
334	>	os << "    <SiteData>\n";
335	>	for (mol = info_->beginMolecule(mi); mol != NULL;
336	>	mol = info_->nextMolecule(mi)) {
337	>
338	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
339	>	sd = mol->nextIntegrableObject(ii)) {
340
341	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
341	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
342	>	// do one for the IO itself
343	>	os << prepareSiteLine(sd, ioIndex, 0);
344
345	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
346	<	integrableObject = mol->nextIntegrableObject(ii)) {
347	<
345	>	if (sd->isRigidBody()) {
346	>
347	>	RigidBody* rb = static_cast<RigidBody*>(sd);
348	>	int siteIndex = 0;
349	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
350	>	atom = rb->nextAtom(ai)) {
351	>	os << prepareSiteLine(atom, ioIndex, siteIndex);
352	>	siteIndex++;
353	>	}
354	>	}
355	>	}
356	>	}
357	>	os << "    </SiteData>\n";
358	>	}
359	>	os << "  </Snapshot>\n";
360
361	<	pos = integrableObject->getPos();
362	<	vel = integrableObject->getVel();
361	>	os.flush();
362	>	#else
363
364	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
365	<	integrableObject->getType().c_str(),
366	<	pos[0], pos[1], pos[2],
217	<	vel[0], vel[1], vel[2]);
364	>	const int masterNode = 0;
365	>	int worldRank = MPI::COMM_WORLD.Get_rank();
366	>	int nProc = MPI::COMM_WORLD.Get_size();
367
368	<	strcpy(writeLine, tempBuffer);
368	>	if (worldRank == masterNode) {
369	>	os << "  <Snapshot>\n";
370	>	writeFrameProperties(os,
371	>	info_->getSnapshotManager()->getCurrentSnapshot());
372	>	os << "    <StuntDoubles>\n";
373	>	}
374
375	<	if (integrableObject->isDirectional()) {
376	<	q = integrableObject->getQ();
377	<	ji = integrableObject->getJ();
375	>	//every node prepares the dump lines for integrable objects belong to itself
376	>	std::string buffer;
377	>	for (mol = info_->beginMolecule(mi); mol != NULL;
378	>	mol = info_->nextMolecule(mi)) {
379	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
380	>	sd = mol->nextIntegrableObject(ii)) {
381	>	buffer += prepareDumpLine(sd);
382	>	}
383	>	}
384	>
385	>	if (worldRank == masterNode) {
386	>	os << buffer;
387	>
388	>	for (int i = 1; i < nProc; ++i) {
389	>	// tell processor i to start sending us data:
390	>	MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
391
392	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
393	<	q[0], q[1], q[2], q[3],
394	<	ji[0], ji[1], ji[2]);
395	<	strcat(writeLine, tempBuffer);
396	<	} else {
230	<	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
231	<	}
392	>	// receive the length of the string buffer that was
393	>	// prepared by processor i:
394	>	int recvLength;
395	>	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
396	>	istatus);
397
398	<	os << writeLine;
398	>	// create a buffer to receive the data
399	>	char* recvBuffer = new char[recvLength];
400	>	if (recvBuffer == NULL) {
401	>	} else {
402	>	// receive the data:
403	>	MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
404	>	MPI::ANY_TAG, istatus);
405	>	// send it to the file:
406	>	os << recvBuffer;
407	>	// get rid of the receive buffer:
408	>	delete [] recvBuffer;
409	>	}
410	>	}
411	>	} else {
412	>	int sendBufferLength = buffer.size() + 1;
413	>	int myturn = 0;
414	>	for (int i = 1; i < nProc; ++i){
415	>	// wait for the master node to call our number:
416	>	MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
417	>	if (myturn == worldRank){
418	>	// send the length of our buffer:
419	>	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
420
421	+	// send our buffer:
422	+	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
423	+	MPI::CHAR, masterNode, 0);
424	+
425	+	}
426		}
427		}
237	–
238	–	os.flush();
239	–	#else // is_mpi
240	–	/*********************************************************************
241	–	* Documentation?  You want DOCUMENTATION?
242	–	*
243	–	* Why all the potatoes below?
244	–	*
245	–	* To make a long story short, the original version of DumpWriter
246	–	* worked in the most inefficient way possible.  Node 0 would
247	–	* poke each of the node for an individual atom's formatted data
248	–	* as node 0 worked its way down the global index. This was particularly
249	–	* inefficient since the method blocked all processors at every atom
250	–	* (and did it twice!).
251	–	*
252	–	* An intermediate version of DumpWriter could be described from Node
253	–	* zero's perspective as follows:
254	–	*
255	–	*  1) Have 100 of your friends stand in a circle.
256	–	*  2) When you say go, have all of them start tossing potatoes at
257	–	*     you (one at a time).
258	–	*  3) Catch the potatoes.
259	–	*
260	–	* It was an improvement, but MPI has buffers and caches that could
261	–	* best be described in this analogy as "potato nets", so there's no
262	–	* need to block the processors atom-by-atom.
263	–	*
264	–	* This new and improved DumpWriter works in an even more efficient
265	–	* way:
266	–	*
267	–	*  1) Have 100 of your friend stand in a circle.
268	–	*  2) When you say go, have them start tossing 5-pound bags of
269	–	*     potatoes at you.
270	–	*  3) Once you've caught a friend's bag of potatoes,
271	–	*     toss them a spud to let them know they can toss another bag.
272	–	*
273	–	* How's THAT for documentation?
274	–	*
275	–	*********************************************************************/
276	–	const int masterNode = 0;
277	–
278	–	int * potatoes;
279	–	int myPotato;
280	–	int nProc;
281	–	int which_node;
282	–	double atomData[13];
283	–	int isDirectional;
284	–	char MPIatomTypeString[MINIBUFFERSIZE];
285	–	int msgLen; // the length of message actually recieved at master nodes
286	–	int haveError;
287	–	MPI_Status istatus;
288	–	int nCurObj;
428
429	<	// code to find maximum tag value
430	<	int * tagub;
292	<	int flag;
293	<	int MAXTAG;
294	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
295	<
296	<	if (flag) {
297	<	MAXTAG = *tagub;
298	<	} else {
299	<	MAXTAG = 32767;
429	>	if (worldRank == masterNode) {
430	>	os << "    </StuntDoubles>\n";
431		}
432
433	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
433	>	if (doSiteData_) {
434	>	if (worldRank == masterNode) {
435	>	os << "    <SiteData>\n";
436	>	}
437	>	buffer.clear();
438	>	for (mol = info_->beginMolecule(mi); mol != NULL;
439	>	mol = info_->nextMolecule(mi)) {
440	>
441	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
442	>	sd = mol->nextIntegrableObject(ii)) {
443	>
444	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
445	>	// do one for the IO itself
446	>	buffer += prepareSiteLine(sd, ioIndex, 0);
447
448	<	// Node 0 needs a list of the magic potatoes for each processor;
448	>	if (sd->isRigidBody()) {
449	>
450	>	RigidBody* rb = static_cast<RigidBody*>(sd);
451	>	int siteIndex = 0;
452	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
453	>	atom = rb->nextAtom(ai)) {
454	>	buffer += prepareSiteLine(atom, ioIndex, siteIndex);
455	>	siteIndex++;
456	>	}
457	>	}
458	>	}
459	>	}
460
461	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
462	<	potatoes = new int[nProc];
463	<
464	<	//write out the comment lines
465	<	for(int i = 0; i < nProc; i++) {
466	<	potatoes[i] = 0;
461	>	if (worldRank == masterNode) {
462	>	os << buffer;
463	>
464	>	for (int i = 1; i < nProc; ++i) {
465	>
466	>	// tell processor i to start sending us data:
467	>	MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
468	>
469	>	// receive the length of the string buffer that was
470	>	// prepared by processor i:
471	>	int recvLength;
472	>	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
473	>	istatus);
474	>
475	>	// create a buffer to receive the data
476	>	char* recvBuffer = new char[recvLength];
477	>	if (recvBuffer == NULL) {
478	>	} else {
479	>	// receive the data:
480	>	MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
481	>	MPI::ANY_TAG, istatus);
482	>	// send it to the file:
483	>	os << recvBuffer;
484	>	// get rid of the receive buffer:
485	>	delete [] recvBuffer;
486	>	}
487	>	}
488	>	} else {
489	>	int sendBufferLength = buffer.size() + 1;
490	>	int myturn = 0;
491	>	for (int i = 1; i < nProc; ++i){
492	>	// wait for the master node to call our number:
493	>	MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
494	>	if (myturn == worldRank){
495	>	// send the length of our buffer:
496	>	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
497	>	// send our buffer:
498	>	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
499	>	MPI::CHAR, masterNode, 0);
500	>	}
501	>	}
502		}
503	+
504	+	if (worldRank == masterNode) {
505	+	os << "    </SiteData>\n";
506	+	}
507	+	}
508	+
509	+	if (worldRank == masterNode) {
510	+	os << "  </Snapshot>\n";
511	+	os.flush();
512	+	}
513	+
514	+	#endif // is_mpi
515	+
516	+	}
517
518	+	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
519	+
520	+	int index = sd->getGlobalIntegrableObjectIndex();
521	+	std::string type("pv");
522	+	std::string line;
523	+	char tempBuffer[4096];
524
525	<	os << nTotObjects << "\n";
526	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
525	>	Vector3d pos;
526	>	Vector3d vel;
527	>	pos = sd->getPos();
528
529	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
529	>	if (isinf(pos[0]) || isnan(pos[0]) ||
530	>	isinf(pos[1]) || isnan(pos[1]) ||
531	>	isinf(pos[2]) || isnan(pos[2]) ) {
532	>	sprintf( painCave.errMsg,
533	>	"DumpWriter detected a numerical error writing the position"
534	>	" for object %d", index);
535	>	painCave.isFatal = 1;
536	>	simError();
537	>	}
538
539	<	// Get the Node number which has this atom;
539	>	vel = sd->getVel();
540
541	<	which_node = info_->getMolToProc(i);
541	>	if (isinf(vel[0]) || isnan(vel[0]) ||
542	>	isinf(vel[1]) || isnan(vel[1]) ||
543	>	isinf(vel[2]) || isnan(vel[2]) ) {
544	>	sprintf( painCave.errMsg,
545	>	"DumpWriter detected a numerical error writing the velocity"
546	>	" for object %d", index);
547	>	painCave.isFatal = 1;
548	>	simError();
549	>	}
550
551	<	if (which_node != masterNode) { //current molecule is in slave node
552	<	if (potatoes[which_node] + 1 >= MAXTAG) {
553	<	// The potato was going to exceed the maximum value,
554	<	// so wrap this processor potato back to 0:
551	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
552	>	pos[0], pos[1], pos[2],
553	>	vel[0], vel[1], vel[2]);
554	>	line += tempBuffer;
555
556	<	potatoes[which_node] = 0;
557	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
558	<	MPI_COMM_WORLD);
559	<	}
556	>	if (sd->isDirectional()) {
557	>	type += "qj";
558	>	Quat4d q;
559	>	Vector3d ji;
560	>	q = sd->getQ();
561
562	<	myPotato = potatoes[which_node];
562	>	if (isinf(q[0]) || isnan(q[0]) ||
563	>	isinf(q[1]) || isnan(q[1]) ||
564	>	isinf(q[2]) || isnan(q[2]) ||
565	>	isinf(q[3]) || isnan(q[3]) ) {
566	>	sprintf( painCave.errMsg,
567	>	"DumpWriter detected a numerical error writing the quaternion"
568	>	" for object %d", index);
569	>	painCave.isFatal = 1;
570	>	simError();
571	>	}
572
573	<	//recieve the number of integrableObject in current molecule
337	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
338	<	MPI_COMM_WORLD, &istatus);
339	<	myPotato++;
573	>	ji = sd->getJ();
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(ji[0]) || isnan(ji[0]) ||
576	>	isinf(ji[1]) || isnan(ji[1]) ||
577	>	isinf(ji[2]) || isnan(ji[2]) ) {
578	>	sprintf( painCave.errMsg,
579	>	"DumpWriter detected a numerical error writing the angular"
580	>	" momentum for object %d", index);
581	>	painCave.isFatal = 1;
582	>	simError();
583	>	}
584
585	<	potatoes[which_node] = 0;
586	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
587	<	0, MPI_COMM_WORLD);
588	<	}
585	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
586	>	q[0], q[1], q[2], q[3],
587	>	ji[0], ji[1], ji[2]);
588	>	line += tempBuffer;
589	>	}
590
591	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
592	<	which_node, myPotato, MPI_COMM_WORLD,
593	<	&istatus);
591	>	if (needForceVector_) {
592	>	type += "f";
593	>	Vector3d frc = sd->getFrc();
594	>	if (isinf(frc[0]) || isnan(frc[0]) ||
595	>	isinf(frc[1]) || isnan(frc[1]) ||
596	>	isinf(frc[2]) || isnan(frc[2]) ) {
597	>	sprintf( painCave.errMsg,
598	>	"DumpWriter detected a numerical error writing the force"
599	>	" for object %d", index);
600	>	painCave.isFatal = 1;
601	>	simError();
602	>	}
603	>	sprintf(tempBuffer, " %13e %13e %13e",
604	>	frc[0], frc[1], frc[2]);
605	>	line += tempBuffer;
606	>
607	>	if (sd->isDirectional()) {
608	>	type += "t";
609	>	Vector3d trq = sd->getTrq();
610	>	if (isinf(trq[0]) || isnan(trq[0]) ||
611	>	isinf(trq[1]) || isnan(trq[1]) ||
612	>	isinf(trq[2]) || isnan(trq[2]) ) {
613	>	sprintf( painCave.errMsg,
614	>	"DumpWriter detected a numerical error writing the torque"
615	>	" for object %d", index);
616	>	painCave.isFatal = 1;
617	>	simError();
618	>	}
619	>	sprintf(tempBuffer, " %13e %13e %13e",
620	>	trq[0], trq[1], trq[2]);
621	>	line += tempBuffer;
622	>	}
623	>	}
624
625	<	myPotato++;
625	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
626	>	return std::string(tempBuffer);
627	>	}
628
629	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
630	<	MPI_COMM_WORLD, &istatus);
359	<	myPotato++;
629	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
630	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
631
632	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
632	>	std::string id;
633	>	std::string type;
634	>	std::string line;
635	>	char tempBuffer[4096];
636
637	<	if (msgLen == 13)
638	<	isDirectional = 1;
639	<	else
640	<	isDirectional = 0;
637	>	if (sd->isRigidBody()) {
638	>	sprintf(tempBuffer, "%10d           ", ioIndex);
639	>	id = std::string(tempBuffer);
640	>	} else {
641	>	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
642	>	id = std::string(tempBuffer);
643	>	}
644	>
645	>	if (needFlucQ_) {
646	>	if (storageLayout & DataStorage::dslFlucQPosition) {
647	>	type += "c";
648	>	RealType fqPos = sd->getFlucQPos();
649	>	if (isinf(fqPos) || isnan(fqPos) ) {
650	>	sprintf( painCave.errMsg,
651	>	"DumpWriter detected a numerical error writing the"
652	>	" fluctuating charge for object %s", id.c_str());
653	>	painCave.isFatal = 1;
654	>	simError();
655	>	}
656	>	sprintf(tempBuffer, " %13e ", fqPos);
657	>	line += tempBuffer;
658	>	}
659
660	<	// If we've survived to here, format the line:
661	<
662	<	if (!isDirectional) {
663	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
664	<	MPIatomTypeString, atomData[0],
665	<	atomData[1], atomData[2],
666	<	atomData[3], atomData[4],
667	<	atomData[5]);
668	<
669	<	strcat(writeLine,
670	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
671	<	} else {
672	<	sprintf(writeLine,
381	<	"%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",
382	<	MPIatomTypeString,
383	<	atomData[0],
384	<	atomData[1],
385	<	atomData[2],
386	<	atomData[3],
387	<	atomData[4],
388	<	atomData[5],
389	<	atomData[6],
390	<	atomData[7],
391	<	atomData[8],
392	<	atomData[9],
393	<	atomData[10],
394	<	atomData[11],
395	<	atomData[12]);
396	<	}
397	<
398	<	os << writeLine;
399	<
400	<	} // end for(int l =0)
401	<
402	<	potatoes[which_node] = myPotato;
403	<	} else { //master node has current molecule
404	<
405	<	mol = info_->getMoleculeByGlobalIndex(i);
406	<
407	<	if (mol == NULL) {
408	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
409	<	painCave.isFatal = 1;
410	<	simError();
411	<	}
412	<
413	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
414	<	integrableObject = mol->nextIntegrableObject(ii)) {
415	<
416	<	pos = integrableObject->getPos();
417	<	vel = integrableObject->getVel();
418	<
419	<	atomData[0] = pos[0];
420	<	atomData[1] = pos[1];
421	<	atomData[2] = pos[2];
422	<
423	<	atomData[3] = vel[0];
424	<	atomData[4] = vel[1];
425	<	atomData[5] = vel[2];
426	<
427	<	isDirectional = 0;
428	<
429	<	if (integrableObject->isDirectional()) {
430	<	isDirectional = 1;
431	<
432	<	q = integrableObject->getQ();
433	<	ji = integrableObject->getJ();
434	<
435	<	for(int j = 0; j < 6; j++) {
436	<	atomData[j] = atomData[j];
437	<	}
438	<
439	<	atomData[6] = q[0];
440	<	atomData[7] = q[1];
441	<	atomData[8] = q[2];
442	<	atomData[9] = q[3];
443	<
444	<	atomData[10] = ji[0];
445	<	atomData[11] = ji[1];
446	<	atomData[12] = ji[2];
447	<	}
448	<
449	<	// If we've survived to here, format the line:
660	>	if (storageLayout & DataStorage::dslFlucQVelocity) {
661	>	type += "w";
662	>	RealType fqVel = sd->getFlucQVel();
663	>	if (isinf(fqVel) || isnan(fqVel) ) {
664	>	sprintf( painCave.errMsg,
665	>	"DumpWriter detected a numerical error writing the"
666	>	" fluctuating charge velocity for object %s", id.c_str());
667	>	painCave.isFatal = 1;
668	>	simError();
669	>	}
670	>	sprintf(tempBuffer, " %13e ", fqVel);
671	>	line += tempBuffer;
672	>	}
673
674	<	if (!isDirectional) {
675	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
676	<	integrableObject->getType().c_str(), atomData[0],
677	<	atomData[1], atomData[2],
678	<	atomData[3], atomData[4],
679	<	atomData[5]);
680	<
681	<	strcat(writeLine,
682	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
683	<	} else {
684	<	sprintf(writeLine,
685	<	"%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",
686	<	integrableObject->getType().c_str(),
687	<	atomData[0],
465	<	atomData[1],
466	<	atomData[2],
467	<	atomData[3],
468	<	atomData[4],
469	<	atomData[5],
470	<	atomData[6],
471	<	atomData[7],
472	<	atomData[8],
473	<	atomData[9],
474	<	atomData[10],
475	<	atomData[11],
476	<	atomData[12]);
477	<	}
478	<
479	<
480	<	os << writeLine;
481	<
482	<	} //end for(iter = integrableObject.begin())
483	<	}
484	<	} //end for(i = 0; i < mpiSim->getNmol())
485	<
486	<	os.flush();
487	<
488	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
489	<	MPIcheckPoint();
490	<
491	<	delete [] potatoes;
492	<	} else {
493	<
494	<	// worldRank != 0, so I'm a remote node.
495	<
496	<	// Set my magic potato to 0:
497	<
498	<	myPotato = 0;
499	<
500	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
501	<
502	<	// Am I the node which has this integrableObject?
503	<	int whichNode = info_->getMolToProc(i);
504	<	if (whichNode == worldRank) {
505	<	if (myPotato + 1 >= MAXTAG) {
506	<
507	<	// The potato was going to exceed the maximum value,
508	<	// so wrap this processor potato back to 0 (and block until
509	<	// node 0 says we can go:
510	<
511	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
512	<	&istatus);
513	<	}
514	<
515	<	mol = info_->getMoleculeByGlobalIndex(i);
516	<
517	<
518	<	nCurObj = mol->getNIntegrableObjects();
519	<
520	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
521	<	myPotato++;
522	<
523	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
524	<	integrableObject = mol->nextIntegrableObject(ii)) {
525	<
526	<	if (myPotato + 2 >= MAXTAG) {
527	<
528	<	// The potato was going to exceed the maximum value,
529	<	// so wrap this processor potato back to 0 (and block until
530	<	// node 0 says we can go:
531	<
532	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
533	<	&istatus);
534	<	}
535	<
536	<	pos = integrableObject->getPos();
537	<	vel = integrableObject->getVel();
538	<
539	<	atomData[0] = pos[0];
540	<	atomData[1] = pos[1];
541	<	atomData[2] = pos[2];
542	<
543	<	atomData[3] = vel[0];
544	<	atomData[4] = vel[1];
545	<	atomData[5] = vel[2];
546	<
547	<	isDirectional = 0;
548	<
549	<	if (integrableObject->isDirectional()) {
550	<	isDirectional = 1;
551	<
552	<	q = integrableObject->getQ();
553	<	ji = integrableObject->getJ();
554	<
555	<	atomData[6] = q[0];
556	<	atomData[7] = q[1];
557	<	atomData[8] = q[2];
558	<	atomData[9] = q[3];
559	<
560	<	atomData[10] = ji[0];
561	<	atomData[11] = ji[1];
562	<	atomData[12] = ji[2];
563	<	}
564	<
565	<	strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
566	<
567	<	// null terminate the  std::string before sending (just in case):
568	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
569	<
570	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
571	<	myPotato, MPI_COMM_WORLD);
572	<
573	<	myPotato++;
574	<
575	<	if (isDirectional) {
576	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
577	<	MPI_COMM_WORLD);
578	<	} else {
579	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
580	<	MPI_COMM_WORLD);
581	<	}
582	<
583	<	myPotato++;
584	<	}
585	<
586	<	}
587	<
674	>	if (needForceVector_) {
675	>	if (storageLayout & DataStorage::dslFlucQForce) {
676	>	type += "g";
677	>	RealType fqFrc = sd->getFlucQFrc();
678	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
679	>	sprintf( painCave.errMsg,
680	>	"DumpWriter detected a numerical error writing the"
681	>	" fluctuating charge force for object %s", id.c_str());
682	>	painCave.isFatal = 1;
683	>	simError();
684	>	}
685	>	sprintf(tempBuffer, " %13e ", fqFrc);
686	>	line += tempBuffer;
687	>	}
688		}
589	–	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
590	–	MPIcheckPoint();
689		}
690	+
691	+	if (needElectricField_) {
692	+	if (storageLayout & DataStorage::dslElectricField) {
693	+	type += "e";
694	+	Vector3d eField= sd->getElectricField();
695	+	if (isinf(eField[0]) || isnan(eField[0]) ||
696	+	isinf(eField[1]) || isnan(eField[1]) ||
697	+	isinf(eField[2]) || isnan(eField[2]) ) {
698	+	sprintf( painCave.errMsg,
699	+	"DumpWriter detected a numerical error writing the electric"
700	+	" field for object %s", id.c_str());
701	+	painCave.isFatal = 1;
702	+	simError();
703	+	}
704	+	sprintf(tempBuffer, " %13e %13e %13e",
705	+	eField[0], eField[1], eField[2]);
706	+	line += tempBuffer;
707	+	}
708	+	}
709
593	–	#endif // is_mpi
710
711	+	if (needParticlePot_) {
712	+	if (storageLayout & DataStorage::dslParticlePot) {
713	+	type += "u";
714	+	RealType particlePot = sd->getParticlePot();
715	+	if (isinf(particlePot) || isnan(particlePot)) {
716	+	sprintf( painCave.errMsg,
717	+	"DumpWriter detected a numerical error writing the particle "
718	+	" potential for object %s", id.c_str());
719	+	painCave.isFatal = 1;
720	+	simError();
721	+	}
722	+	sprintf(tempBuffer, " %13e", particlePot);
723	+	line += tempBuffer;
724	+	}
725	+	}
726	+
727	+	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
728	+	return std::string(tempBuffer);
729		}
730
731		void DumpWriter::writeDump() {
#	Line 604 | Line 738 | namespace oopse {
738		#ifdef IS_MPI
739		if (worldRank == 0) {
740		#endif // is_mpi
741	<
741	>
742		eorStream = createOStream(eorFilename_);
743
744		#ifdef IS_MPI
745		}
746	<	#endif // is_mpi
747	<
746	>	#endif
747	>
748		writeFrame(*eorStream);
749	<
749	>
750		#ifdef IS_MPI
751		if (worldRank == 0) {
752	<	#endif // is_mpi
753	<	delete eorStream;
754	<
752	>	#endif
753	>
754	>	writeClosing(*eorStream);
755	>	delete eorStream;
756	>
757		#ifdef IS_MPI
758		}
759		#endif // is_mpi
#	Line 650 | Line 786 | namespace oopse {
786		#ifdef IS_MPI
787		if (worldRank == 0) {
788		#endif // is_mpi
789	<	delete eorStream;
790	<
789	>	writeClosing(*eorStream);
790	>	delete eorStream;
791		#ifdef IS_MPI
792		}
793		#endif // is_mpi
794
795		}
796
797	<	std::ostream* DumpWriter::createOStream(const std::string& filename) {
797	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
798	>
799		std::ostream* newOStream;
800	+	#ifdef HAVE_ZLIB
801		if (needCompression_) {
802	<	newOStream = new ogzstream(filename.c_str());
802	>	newOStream = new ogzstream(filename.c_str());
803		} else {
804	<	newOStream = new std::ofstream(filename.c_str());
804	>	newOStream = new std::ofstream(filename.c_str());
805		}
806	+	#else
807	+	newOStream = new std::ofstream(filename.c_str());
808	+	#endif
809	+	//write out MetaData first
810	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
811	+	(*newOStream) << "  <MetaData>" << std::endl;
812	+	(*newOStream) << info_->getRawMetaData();
813	+	(*newOStream) << "  </MetaData>" << std::endl;
814		return newOStream;
815	<	}
815	>	}
816
817	<	}//end namespace oopse
817	>	void DumpWriter::writeClosing(std::ostream& os) {
818	>
819	>	os << "</OpenMD>\n";
820	>	os.flush();
821	>	}
822	>
823	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpWriter.cpp (property svn:keywords):
Revision 615 by tim, Tue Sep 20 21:22:38 2005 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC

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