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

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trunk/src/io/DumpWriter.cpp (file contents), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 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, 24107 (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	+	#include "io/gzstream.hpp"
48	+	#include "io/Globals.hpp"
49	+
50	+
51		#ifdef IS_MPI
52		#include <mpi.h>
53	<	#endif //is_mpi
53	>	#endif
54
55	<	namespace oopse {
55	>	using namespace std;
56	>	namespace OpenMD {
57
58		DumpWriter::DumpWriter(SimInfo* info)
59		: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
54	–	#ifdef IS_MPI
60
61	<	if (worldRank == 0) {
62	<	#endif // is_mpi
61	>	Globals* simParams = info->getSimParams();
62	>	needCompression_   = simParams->getCompressDumpFile();
63	>	needForceVector_   = simParams->getOutputForceVector();
64	>	needParticlePot_   = simParams->getOutputParticlePotential();
65	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
66	>	needElectricField_ = simParams->getOutputElectricField();
67
68	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
68	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
69	>	doSiteData_ = true;
70	>	} else {
71	>	doSiteData_ = false;
72	>	}
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	<
74	>	createDumpFile_ = true;
75	>	#ifdef HAVE_LIBZ
76	>	if (needCompression_) {
77	>	filename_ += ".gz";
78	>	eorFilename_ += ".gz";
79	>	}
80	>	#endif
81	>
82		#ifdef IS_MPI
83
84	+	if (worldRank == 0) {
85	+	#endif // is_mpi
86	+
87	+	dumpFile_ = createOStream(filename_);
88	+
89	+	if (!dumpFile_) {
90	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
91	+	filename_.c_str());
92	+	painCave.isFatal = 1;
93	+	simError();
94		}
95
96	<	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73	<	MPIcheckPoint();
96	>	#ifdef IS_MPI
97
98	+	}
99	+
100		#endif // is_mpi
101
102	<	}
102	>	}
103
104
105		DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
106		: info_(info), filename_(filename){
82	–	#ifdef IS_MPI
107
108	<	if (worldRank == 0) {
109	<	#endif // is_mpi
108	>	Globals* simParams = info->getSimParams();
109	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
110
111	<	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
112	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
111	>	needCompression_   = simParams->getCompressDumpFile();
112	>	needForceVector_   = simParams->getOutputForceVector();
113	>	needParticlePot_   = simParams->getOutputParticlePotential();
114	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
115	>	needElectricField_ = simParams->getOutputElectricField();
116
117	<	if (!dumpFile_) {
118	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
119	<	filename_.c_str());
120	<	painCave.isFatal = 1;
121	<	simError();
95	<	}
117	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
118	>	doSiteData_ = true;
119	>	} else {
120	>	doSiteData_ = false;
121	>	}
122
123	+	createDumpFile_ = true;
124	+	#ifdef HAVE_LIBZ
125	+	if (needCompression_) {
126	+	filename_ += ".gz";
127	+	eorFilename_ += ".gz";
128	+	}
129	+	#endif
130	+
131		#ifdef IS_MPI
132
133	+	if (worldRank == 0) {
134	+	#endif // is_mpi
135	+
136	+
137	+	dumpFile_ = createOStream(filename_);
138	+
139	+	if (!dumpFile_) {
140	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
141	+	filename_.c_str());
142	+	painCave.isFatal = 1;
143	+	simError();
144		}
145
146	<	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
102	<	MPIcheckPoint();
146	>	#ifdef IS_MPI
147
148	+	}
149	+
150		#endif // is_mpi
151
152	+	}
153	+
154	+	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
155	+	: info_(info), filename_(filename){
156	+
157	+	Globals* simParams = info->getSimParams();
158	+	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
159	+
160	+	needCompression_   = simParams->getCompressDumpFile();
161	+	needForceVector_   = simParams->getOutputForceVector();
162	+	needParticlePot_   = simParams->getOutputParticlePotential();
163	+	needFlucQ_         = simParams->getOutputFluctuatingCharges();
164	+	needElectricField_ = simParams->getOutputElectricField();
165	+
166	+	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
167	+	doSiteData_ = true;
168	+	} else {
169	+	doSiteData_ = false;
170		}
171
172	+	#ifdef HAVE_LIBZ
173	+	if (needCompression_) {
174	+	filename_ += ".gz";
175	+	eorFilename_ += ".gz";
176	+	}
177	+	#endif
178	+
179	+	#ifdef IS_MPI
180	+
181	+	if (worldRank == 0) {
182	+	#endif // is_mpi
183	+
184	+	createDumpFile_ = writeDumpFile;
185	+	if (createDumpFile_) {
186	+	dumpFile_ = createOStream(filename_);
187	+
188	+	if (!dumpFile_) {
189	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
190	+	filename_.c_str());
191	+	painCave.isFatal = 1;
192	+	simError();
193	+	}
194	+	}
195	+	#ifdef IS_MPI
196	+
197	+	}
198	+
199	+
200	+	#endif // is_mpi
201	+
202	+	}
203	+
204		DumpWriter::~DumpWriter() {
205
206		#ifdef IS_MPI
207
208		if (worldRank == 0) {
209		#endif // is_mpi
210	<
211	<	dumpFile_.close();
212	<
210	>	if (createDumpFile_){
211	>	writeClosing(*dumpFile_);
212	>	delete dumpFile_;
213	>	}
214		#ifdef IS_MPI
215
216		}
#	Line 122 | Line 219 | namespace oopse {
219
220		}
221
222	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
222	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
223
224	<	double currentTime;
225	<	Mat3x3d hmat;
226	<	double chi;
227	<	double integralOfChiDt;
228	<	Mat3x3d eta;
224	>	char buffer[1024];
225	>
226	>	os << "    <FrameData>\n";
227	>
228	>	RealType currentTime = s->getTime();
229	>
230	>	if (isinf(currentTime) || isnan(currentTime)) {
231	>	sprintf( painCave.errMsg,
232	>	"DumpWriter detected a numerical error writing the time");
233	>	painCave.isFatal = 1;
234	>	simError();
235	>	}
236
237	<	currentTime = s->getTime();
237	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
238	>	os << buffer;
239	>
240	>	Mat3x3d hmat;
241		hmat = s->getHmat();
242	<	chi = s->getChi();
243	<	integralOfChiDt = s->getIntegralOfChiDt();
244	<	eta = s->getEta();
242	>
243	>	for (unsigned int i = 0; i < 3; i++) {
244	>	for (unsigned int j = 0; j < 3; j++) {
245	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
246	>	sprintf( painCave.errMsg,
247	>	"DumpWriter detected a numerical error writing the box");
248	>	painCave.isFatal = 1;
249	>	simError();
250	>	}
251	>	}
252	>	}
253
254	<	os << currentTime << ";\t"
255	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
256	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
257	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
254	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
255	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
256	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
257	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
258	>	os << buffer;
259
260	<	//write out additional parameters, such as chi and eta
260	>	pair<RealType, RealType> thermostat = s->getThermostat();
261
262	<	os << chi << "\t" << integralOfChiDt << "\t;";
262	>	if (isinf(thermostat.first)  || isnan(thermostat.first) ||
263	>	isinf(thermostat.second) || isnan(thermostat.second)) {
264	>	sprintf( painCave.errMsg,
265	>	"DumpWriter detected a numerical error writing the thermostat");
266	>	painCave.isFatal = 1;
267	>	simError();
268	>	}
269	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
270	>	thermostat.second);
271	>	os << buffer;
272
273	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
274	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
275	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
276	<
277	<	os << "\n";
273	>	Mat3x3d eta;
274	>	eta = s->getBarostat();
275	>
276	>	for (unsigned int i = 0; i < 3; i++) {
277	>	for (unsigned int j = 0; j < 3; j++) {
278	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
279	>	sprintf( painCave.errMsg,
280	>	"DumpWriter detected a numerical error writing the barostat");
281	>	painCave.isFatal = 1;
282	>	simError();
283	>	}
284	>	}
285	>	}
286	>
287	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
288	>	eta(0, 0), eta(1, 0), eta(2, 0),
289	>	eta(0, 1), eta(1, 1), eta(2, 1),
290	>	eta(0, 2), eta(1, 2), eta(2, 2));
291	>	os << buffer;
292	>
293	>	os << "    </FrameData>\n";
294		}
295
296		void DumpWriter::writeFrame(std::ostream& os) {
156	–	const int BUFFERSIZE = 2000;
157	–	const int MINIBUFFERSIZE = 100;
297
298	<	char tempBuffer[BUFFERSIZE];
299	<	char writeLine[BUFFERSIZE];
298	>	#ifdef IS_MPI
299	>	MPI_Status istatus;
300	>	#endif
301
162	–	Quat4d q;
163	–	Vector3d ji;
164	–	Vector3d pos;
165	–	Vector3d vel;
166	–
302		Molecule* mol;
303		StuntDouble* integrableObject;
304		SimInfo::MoleculeIterator mi;
305		Molecule::IntegrableObjectIterator ii;
306	<
307	<	int nTotObjects;
173	<	nTotObjects = info_->getNGlobalIntegrableObjects();
306	>	RigidBody::AtomIterator ai;
307	>	Atom* atom;
308
309		#ifndef IS_MPI
310	+	os << "  <Snapshot>\n";
311	+
312	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
313
314	<
178	<	os << nTotObjects << "\n";
179	<
180	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
181	<
314	>	os << "    <StuntDoubles>\n";
315		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
316
317	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
318	<	integrableObject = mol->nextIntegrableObject(ii)) {
319	<
317	>
318	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
319	>	integrableObject = mol->nextIntegrableObject(ii)) {
320	>	os << prepareDumpLine(integrableObject);
321	>
322	>	}
323	>	}
324	>	os << "    </StuntDoubles>\n";
325
326	<	pos = integrableObject->getPos();
327	<	vel = integrableObject->getVel();
326	>	if (doSiteData_) {
327	>	os << "    <SiteData>\n";
328	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
329	>
330	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
331	>	integrableObject = mol->nextIntegrableObject(ii)) {
332
333	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
334	<	integrableObject->getType().c_str(),
335	<	pos[0], pos[1], pos[2],
194	<	vel[0], vel[1], vel[2]);
333	>	int ioIndex = integrableObject->getGlobalIntegrableObjectIndex();
334	>	// do one for the IO itself
335	>	os << prepareSiteLine(integrableObject, ioIndex, 0);
336
337	<	strcpy(writeLine, tempBuffer);
337	>	if (integrableObject->isRigidBody()) {
338	>
339	>	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
340	>	int siteIndex = 0;
341	>	for (atom = rb->beginAtom(ai); atom != NULL;
342	>	atom = rb->nextAtom(ai)) {
343	>	os << prepareSiteLine(atom, ioIndex, siteIndex);
344	>	siteIndex++;
345	>	}
346	>	}
347	>	}
348	>	}
349	>	os << "    </SiteData>\n";
350	>	}
351	>	os << "  </Snapshot>\n";
352
353	<	if (integrableObject->isDirectional()) {
354	<	q = integrableObject->getQ();
355	<	ji = integrableObject->getJ();
353	>	os.flush();
354	>	#else
355	>	//every node prepares the dump lines for integrable objects belong to itself
356	>	std::string buffer;
357	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
358
202	–	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
203	–	q[0], q[1], q[2], q[3],
204	–	ji[0], ji[1], ji[2]);
205	–	strcat(writeLine, tempBuffer);
206	–	} else {
207	–	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
208	–	}
359
360	<	os << writeLine;
361	<
360	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
361	>	integrableObject = mol->nextIntegrableObject(ii)) {
362	>	buffer += prepareDumpLine(integrableObject);
363		}
364		}
365	<
215	<	os.flush();
216	<	#else // is_mpi
217	<	/*********************************************************************
218	<	* Documentation?  You want DOCUMENTATION?
219	<	*
220	<	* Why all the potatoes below?
221	<	*
222	<	* To make a long story short, the original version of DumpWriter
223	<	* worked in the most inefficient way possible.  Node 0 would
224	<	* poke each of the node for an individual atom's formatted data
225	<	* as node 0 worked its way down the global index. This was particularly
226	<	* inefficient since the method blocked all processors at every atom
227	<	* (and did it twice!).
228	<	*
229	<	* An intermediate version of DumpWriter could be described from Node
230	<	* zero's perspective as follows:
231	<	*
232	<	*  1) Have 100 of your friends stand in a circle.
233	<	*  2) When you say go, have all of them start tossing potatoes at
234	<	*     you (one at a time).
235	<	*  3) Catch the potatoes.
236	<	*
237	<	* It was an improvement, but MPI has buffers and caches that could
238	<	* best be described in this analogy as "potato nets", so there's no
239	<	* need to block the processors atom-by-atom.
240	<	*
241	<	* This new and improved DumpWriter works in an even more efficient
242	<	* way:
243	<	*
244	<	*  1) Have 100 of your friend stand in a circle.
245	<	*  2) When you say go, have them start tossing 5-pound bags of
246	<	*     potatoes at you.
247	<	*  3) Once you've caught a friend's bag of potatoes,
248	<	*     toss them a spud to let them know they can toss another bag.
249	<	*
250	<	* How's THAT for documentation?
251	<	*
252	<	*********************************************************************/
365	>
366		const int masterNode = 0;
254	–
255	–	int * potatoes;
256	–	int myPotato;
367		int nProc;
368	<	int which_node;
369	<	double atomData[13];
370	<	int isDirectional;
371	<	char MPIatomTypeString[MINIBUFFERSIZE];
372	<	int msgLen; // the length of message actually recieved at master nodes
373	<	int haveError;
374	<	MPI_Status istatus;
265	<	int nCurObj;
266	<
267	<	// code to find maximum tag value
268	<	int * tagub;
269	<	int flag;
270	<	int MAXTAG;
271	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
368	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
369	>	if (worldRank == masterNode) {
370	>	os << "  <Snapshot>\n";
371	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
372	>	os << "    <StuntDoubles>\n";
373	>
374	>	os << buffer;
375
376	<	if (flag) {
274	<	MAXTAG = *tagub;
275	<	} else {
276	<	MAXTAG = 32767;
277	<	}
376	>	for (int i = 1; i < nProc; ++i) {
377
378	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
378	>	// receive the length of the string buffer that was
379	>	// prepared by processor i
380
381	<	// Node 0 needs a list of the magic potatoes for each processor;
382	<
383	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
384	<	potatoes = new int[nProc];
385	<
386	<	//write out the comment lines
387	<	for(int i = 0; i < nProc; i++) {
388	<	potatoes[i] = 0;
381	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
382	>	int recvLength;
383	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
384	>	char* recvBuffer = new char[recvLength];
385	>	if (recvBuffer == NULL) {
386	>	} else {
387	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
388	>	os << recvBuffer;
389	>	delete [] recvBuffer;
390	>	}
391	>	}
392	>	os << "    </StuntDoubles>\n";
393	>
394	>	os << "  </Snapshot>\n";
395	>	os.flush();
396	>	} else {
397	>	int sendBufferLength = buffer.size() + 1;
398	>	int myturn = 0;
399	>	for (int i = 1; i < nProc; ++i){
400	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
401	>	if (myturn == worldRank){
402	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
403	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
404	>	}
405		}
406	+	}
407
408	+	#endif // is_mpi
409
410	<	os << nTotObjects << "\n";
293	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
410	>	}
411
412	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
412	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
413	>
414	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
415	>	std::string type("pv");
416	>	std::string line;
417	>	char tempBuffer[4096];
418
419	<	// Get the Node number which has this atom;
419	>	Vector3d pos;
420	>	Vector3d vel;
421	>	pos = integrableObject->getPos();
422
423	<	which_node = info_->getMolToProc(i);
423	>	if (isinf(pos[0]) || isnan(pos[0]) ||
424	>	isinf(pos[1]) || isnan(pos[1]) ||
425	>	isinf(pos[2]) || isnan(pos[2]) ) {
426	>	sprintf( painCave.errMsg,
427	>	"DumpWriter detected a numerical error writing the position"
428	>	" for object %d", index);
429	>	painCave.isFatal = 1;
430	>	simError();
431	>	}
432
433	<	if (which_node != masterNode) { //current molecule is in slave node
302	<	if (potatoes[which_node] + 1 >= MAXTAG) {
303	<	// The potato was going to exceed the maximum value,
304	<	// so wrap this processor potato back to 0:
433	>	vel = integrableObject->getVel();
434
435	<	potatoes[which_node] = 0;
436	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
437	<	MPI_COMM_WORLD);
438	<	}
435	>	if (isinf(vel[0]) || isnan(vel[0]) ||
436	>	isinf(vel[1]) || isnan(vel[1]) ||
437	>	isinf(vel[2]) || isnan(vel[2]) ) {
438	>	sprintf( painCave.errMsg,
439	>	"DumpWriter detected a numerical error writing the velocity"
440	>	" for object %d", index);
441	>	painCave.isFatal = 1;
442	>	simError();
443	>	}
444
445	<	myPotato = potatoes[which_node];
445	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
446	>	pos[0], pos[1], pos[2],
447	>	vel[0], vel[1], vel[2]);
448	>	line += tempBuffer;
449
450	<	//recieve the number of integrableObject in current molecule
451	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
452	<	MPI_COMM_WORLD, &istatus);
453	<	myPotato++;
450	>	if (integrableObject->isDirectional()) {
451	>	type += "qj";
452	>	Quat4d q;
453	>	Vector3d ji;
454	>	q = integrableObject->getQ();
455
456	<	for(int l = 0; l < nCurObj; l++) {
457	<	if (potatoes[which_node] + 2 >= MAXTAG) {
458	<	// The potato was going to exceed the maximum value,
459	<	// so wrap this processor potato back to 0:
456	>	if (isinf(q[0]) || isnan(q[0]) ||
457	>	isinf(q[1]) || isnan(q[1]) ||
458	>	isinf(q[2]) || isnan(q[2]) ||
459	>	isinf(q[3]) || isnan(q[3]) ) {
460	>	sprintf( painCave.errMsg,
461	>	"DumpWriter detected a numerical error writing the quaternion"
462	>	" for object %d", index);
463	>	painCave.isFatal = 1;
464	>	simError();
465	>	}
466
467	<	potatoes[which_node] = 0;
324	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
325	<	0, MPI_COMM_WORLD);
326	<	}
467	>	ji = integrableObject->getJ();
468
469	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
470	<	which_node, myPotato, MPI_COMM_WORLD,
471	<	&istatus);
469	>	if (isinf(ji[0]) || isnan(ji[0]) ||
470	>	isinf(ji[1]) || isnan(ji[1]) ||
471	>	isinf(ji[2]) || isnan(ji[2]) ) {
472	>	sprintf( painCave.errMsg,
473	>	"DumpWriter detected a numerical error writing the angular"
474	>	" momentum for object %d", index);
475	>	painCave.isFatal = 1;
476	>	simError();
477	>	}
478
479	<	myPotato++;
479	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
480	>	q[0], q[1], q[2], q[3],
481	>	ji[0], ji[1], ji[2]);
482	>	line += tempBuffer;
483	>	}
484
485	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
486	<	MPI_COMM_WORLD, &istatus);
487	<	myPotato++;
485	>	if (needForceVector_) {
486	>	type += "f";
487	>	Vector3d frc = integrableObject->getFrc();
488	>	if (isinf(frc[0]) || isnan(frc[0]) ||
489	>	isinf(frc[1]) || isnan(frc[1]) ||
490	>	isinf(frc[2]) || isnan(frc[2]) ) {
491	>	sprintf( painCave.errMsg,
492	>	"DumpWriter detected a numerical error writing the force"
493	>	" for object %d", index);
494	>	painCave.isFatal = 1;
495	>	simError();
496	>	}
497	>	sprintf(tempBuffer, " %13e %13e %13e",
498	>	frc[0], frc[1], frc[2]);
499	>	line += tempBuffer;
500	>
501	>	if (integrableObject->isDirectional()) {
502	>	type += "t";
503	>	Vector3d trq = integrableObject->getTrq();
504	>	if (isinf(trq[0]) || isnan(trq[0]) ||
505	>	isinf(trq[1]) || isnan(trq[1]) ||
506	>	isinf(trq[2]) || isnan(trq[2]) ) {
507	>	sprintf( painCave.errMsg,
508	>	"DumpWriter detected a numerical error writing the torque"
509	>	" for object %d", index);
510	>	painCave.isFatal = 1;
511	>	simError();
512	>	}
513	>	sprintf(tempBuffer, " %13e %13e %13e",
514	>	trq[0], trq[1], trq[2]);
515	>	line += tempBuffer;
516	>	}
517	>	}
518
519	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
519	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
520	>	return std::string(tempBuffer);
521	>	}
522
523	<	if (msgLen == 13)
524	<	isDirectional = 1;
342	<	else
343	<	isDirectional = 0;
523	>	std::string DumpWriter::prepareSiteLine(StuntDouble* integrableObject, int ioIndex, int siteIndex) {
524	>
525
526	<	// If we've survived to here, format the line:
526	>	std::string id;
527	>	std::string type;
528	>	std::string line;
529	>	char tempBuffer[4096];
530
531	<	if (!isDirectional) {
532	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
533	<	MPIatomTypeString, atomData[0],
534	<	atomData[1], atomData[2],
535	<	atomData[3], atomData[4],
536	<	atomData[5]);
531	>	if (integrableObject->isRigidBody()) {
532	>	sprintf(tempBuffer, "%10d           ", ioIndex);
533	>	id = std::string(tempBuffer);
534	>	} else {
535	>	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
536	>	id = std::string(tempBuffer);
537	>	}
538	>
539	>	if (needFlucQ_) {
540	>	type += "cw";
541	>	RealType fqPos = integrableObject->getFlucQPos();
542	>	if (isinf(fqPos) || isnan(fqPos) ) {
543	>	sprintf( painCave.errMsg,
544	>	"DumpWriter detected a numerical error writing the"
545	>	" fluctuating charge for object %s", id.c_str());
546	>	painCave.isFatal = 1;
547	>	simError();
548	>	}
549	>	sprintf(tempBuffer, " %13e ", fqPos);
550	>	line += tempBuffer;
551	>
552	>	RealType fqVel = integrableObject->getFlucQVel();
553	>	if (isinf(fqVel) || isnan(fqVel) ) {
554	>	sprintf( painCave.errMsg,
555	>	"DumpWriter detected a numerical error writing the"
556	>	" fluctuating charge velocity for object %s", id.c_str());
557	>	painCave.isFatal = 1;
558	>	simError();
559	>	}
560	>	sprintf(tempBuffer, " %13e ", fqVel);
561	>	line += tempBuffer;
562
563	<	strcat(writeLine,
564	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
565	<	} else {
566	<	sprintf(writeLine,
567	<	"%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",
568	<	MPIatomTypeString,
569	<	atomData[0],
570	<	atomData[1],
571	<	atomData[2],
572	<	atomData[3],
573	<	atomData[4],
574	<	atomData[5],
575	<	atomData[6],
576	<	atomData[7],
368	<	atomData[8],
369	<	atomData[9],
370	<	atomData[10],
371	<	atomData[11],
372	<	atomData[12]);
373	<	}
563	>	if (needForceVector_) {
564	>	type += "g";
565	>	RealType fqFrc = integrableObject->getFlucQFrc();
566	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
567	>	sprintf( painCave.errMsg,
568	>	"DumpWriter detected a numerical error writing the"
569	>	" fluctuating charge force for object %s", id.c_str());
570	>	painCave.isFatal = 1;
571	>	simError();
572	>	}
573	>	sprintf(tempBuffer, " %13e ", fqFrc);
574	>	line += tempBuffer;
575	>	}
576	>	}
577
578	<	os << writeLine;
578	>	if (needElectricField_) {
579	>	type += "e";
580	>	Vector3d eField= integrableObject->getElectricField();
581	>	if (isinf(eField[0]) || isnan(eField[0]) ||
582	>	isinf(eField[1]) || isnan(eField[1]) ||
583	>	isinf(eField[2]) || isnan(eField[2]) ) {
584	>	sprintf( painCave.errMsg,
585	>	"DumpWriter detected a numerical error writing the electric"
586	>	" field for object %s", id.c_str());
587	>	painCave.isFatal = 1;
588	>	simError();
589	>	}
590	>	sprintf(tempBuffer, " %13e %13e %13e",
591	>	eField[0], eField[1], eField[2]);
592	>	line += tempBuffer;
593	>	}
594
377	–	} // end for(int l =0)
595
596	<	potatoes[which_node] = myPotato;
597	<	} else { //master node has current molecule
598	<
599	<	mol = info_->getMoleculeByGlobalIndex(i);
600	<
601	<	if (mol == NULL) {
602	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
603	<	painCave.isFatal = 1;
604	<	simError();
388	<	}
389	<
390	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
391	<	integrableObject = mol->nextIntegrableObject(ii)) {
392	<
393	<	pos = integrableObject->getPos();
394	<	vel = integrableObject->getVel();
395	<
396	<	atomData[0] = pos[0];
397	<	atomData[1] = pos[1];
398	<	atomData[2] = pos[2];
399	<
400	<	atomData[3] = vel[0];
401	<	atomData[4] = vel[1];
402	<	atomData[5] = vel[2];
403	<
404	<	isDirectional = 0;
405	<
406	<	if (integrableObject->isDirectional()) {
407	<	isDirectional = 1;
408	<
409	<	q = integrableObject->getQ();
410	<	ji = integrableObject->getJ();
411	<
412	<	for(int j = 0; j < 6; j++) {
413	<	atomData[j] = atomData[j];
414	<	}
415	<
416	<	atomData[6] = q[0];
417	<	atomData[7] = q[1];
418	<	atomData[8] = q[2];
419	<	atomData[9] = q[3];
420	<
421	<	atomData[10] = ji[0];
422	<	atomData[11] = ji[1];
423	<	atomData[12] = ji[2];
424	<	}
425	<
426	<	// If we've survived to here, format the line:
427	<
428	<	if (!isDirectional) {
429	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
430	<	integrableObject->getType().c_str(), atomData[0],
431	<	atomData[1], atomData[2],
432	<	atomData[3], atomData[4],
433	<	atomData[5]);
434	<
435	<	strcat(writeLine,
436	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
437	<	} else {
438	<	sprintf(writeLine,
439	<	"%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",
440	<	integrableObject->getType().c_str(),
441	<	atomData[0],
442	<	atomData[1],
443	<	atomData[2],
444	<	atomData[3],
445	<	atomData[4],
446	<	atomData[5],
447	<	atomData[6],
448	<	atomData[7],
449	<	atomData[8],
450	<	atomData[9],
451	<	atomData[10],
452	<	atomData[11],
453	<	atomData[12]);
454	<	}
455	<
456	<
457	<	os << writeLine;
458	<
459	<	} //end for(iter = integrableObject.begin())
460	<	}
461	<	} //end for(i = 0; i < mpiSim->getNmol())
462	<
463	<	os.flush();
464	<
465	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
466	<	MPIcheckPoint();
467	<
468	<	delete [] potatoes;
469	<	} else {
470	<
471	<	// worldRank != 0, so I'm a remote node.
472	<
473	<	// Set my magic potato to 0:
474	<
475	<	myPotato = 0;
476	<
477	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
478	<
479	<	// Am I the node which has this integrableObject?
480	<	int whichNode = info_->getMolToProc(i);
481	<	if (whichNode == worldRank) {
482	<	if (myPotato + 1 >= MAXTAG) {
483	<
484	<	// The potato was going to exceed the maximum value,
485	<	// so wrap this processor potato back to 0 (and block until
486	<	// node 0 says we can go:
487	<
488	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
489	<	&istatus);
490	<	}
491	<
492	<	mol = info_->getMoleculeByGlobalIndex(i);
493	<
494	<
495	<	nCurObj = mol->getNIntegrableObjects();
496	<
497	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
498	<	myPotato++;
499	<
500	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
501	<	integrableObject = mol->nextIntegrableObject(ii)) {
502	<
503	<	if (myPotato + 2 >= MAXTAG) {
504	<
505	<	// The potato was going to exceed the maximum value,
506	<	// so wrap this processor potato back to 0 (and block until
507	<	// node 0 says we can go:
508	<
509	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
510	<	&istatus);
511	<	}
512	<
513	<	pos = integrableObject->getPos();
514	<	vel = integrableObject->getVel();
515	<
516	<	atomData[0] = pos[0];
517	<	atomData[1] = pos[1];
518	<	atomData[2] = pos[2];
519	<
520	<	atomData[3] = vel[0];
521	<	atomData[4] = vel[1];
522	<	atomData[5] = vel[2];
523	<
524	<	isDirectional = 0;
525	<
526	<	if (integrableObject->isDirectional()) {
527	<	isDirectional = 1;
528	<
529	<	q = integrableObject->getQ();
530	<	ji = integrableObject->getJ();
531	<
532	<	atomData[6] = q[0];
533	<	atomData[7] = q[1];
534	<	atomData[8] = q[2];
535	<	atomData[9] = q[3];
536	<
537	<	atomData[10] = ji[0];
538	<	atomData[11] = ji[1];
539	<	atomData[12] = ji[2];
540	<	}
541	<
542	<	strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
543	<
544	<	// null terminate the  std::string before sending (just in case):
545	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
546	<
547	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
548	<	myPotato, MPI_COMM_WORLD);
549	<
550	<	myPotato++;
551	<
552	<	if (isDirectional) {
553	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
554	<	MPI_COMM_WORLD);
555	<	} else {
556	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
557	<	MPI_COMM_WORLD);
558	<	}
559	<
560	<	myPotato++;
561	<	}
562	<
563	<	}
564	<
596	>	if (needParticlePot_) {
597	>	type += "u";
598	>	RealType particlePot = integrableObject->getParticlePot();
599	>	if (isinf(particlePot) || isnan(particlePot)) {
600	>	sprintf( painCave.errMsg,
601	>	"DumpWriter detected a numerical error writing the particle "
602	>	" potential for object %s", id.c_str());
603	>	painCave.isFatal = 1;
604	>	simError();
605		}
606	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
607	<	MPIcheckPoint();
606	>	sprintf(tempBuffer, " %13e", particlePot);
607	>	line += tempBuffer;
608		}
609	+
610
611	<	#endif // is_mpi
612	<
611	>	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
612	>	return std::string(tempBuffer);
613		}
614
615		void DumpWriter::writeDump() {
616	<	writeFrame(dumpFile_);
576	<
616	>	writeFrame(*dumpFile_);
617		}
618
619		void DumpWriter::writeEor() {
620	<	std::ofstream eorStream;
620	>	std::ostream* eorStream;
621
622		#ifdef IS_MPI
623		if (worldRank == 0) {
624		#endif // is_mpi
625
626	<	eorStream.open(eorFilename_.c_str());
587	<	if (!eorStream.is_open()) {
588	<	sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n",
589	<	eorFilename_.c_str());
590	<	painCave.isFatal = 1;
591	<	simError();
592	<	}
626	>	eorStream = createOStream(eorFilename_);
627
628		#ifdef IS_MPI
629		}
630		#endif // is_mpi
631
632	<	writeFrame(eorStream);
632	>	writeFrame(*eorStream);
633	>
634	>	#ifdef IS_MPI
635	>	if (worldRank == 0) {
636	>	#endif // is_mpi
637	>	writeClosing(*eorStream);
638	>	delete eorStream;
639	>	#ifdef IS_MPI
640	>	}
641	>	#endif // is_mpi
642	>
643		}
644
645
646		void DumpWriter::writeDumpAndEor() {
603	–	std::ofstream eorStream;
647		std::vector<std::streambuf*> buffers;
648	+	std::ostream* eorStream;
649		#ifdef IS_MPI
650		if (worldRank == 0) {
651		#endif // is_mpi
652
653	<	buffers.push_back(dumpFile_.rdbuf());
653	>	buffers.push_back(dumpFile_->rdbuf());
654
655	<	eorStream.open(eorFilename_.c_str());
612	<	if (!eorStream.is_open()) {
613	<	sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n",
614	<	eorFilename_.c_str());
615	<	painCave.isFatal = 1;
616	<	simError();
617	<	}
655	>	eorStream = createOStream(eorFilename_);
656
657	<	buffers.push_back(eorStream.rdbuf());
657	>	buffers.push_back(eorStream->rdbuf());
658
659		#ifdef IS_MPI
660		}
#	Line 626 | Line 664 | namespace oopse {
664		std::ostream os(&tbuf);
665
666		writeFrame(os);
667	+
668	+	#ifdef IS_MPI
669	+	if (worldRank == 0) {
670	+	#endif // is_mpi
671	+	writeClosing(*eorStream);
672	+	delete eorStream;
673	+	#ifdef IS_MPI
674	+	}
675	+	#endif // is_mpi
676
677		}
678
679	+	std::ostream* DumpWriter::createOStream(const std::string& filename) {
680
681	+	std::ostream* newOStream;
682	+	#ifdef HAVE_LIBZ
683	+	if (needCompression_) {
684	+	newOStream = new ogzstream(filename.c_str());
685	+	} else {
686	+	newOStream = new std::ofstream(filename.c_str());
687	+	}
688	+	#else
689	+	newOStream = new std::ofstream(filename.c_str());
690	+	#endif
691	+	//write out MetaData first
692	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
693	+	(*newOStream) << "  <MetaData>" << std::endl;
694	+	(*newOStream) << info_->getRawMetaData();
695	+	(*newOStream) << "  </MetaData>" << std::endl;
696	+	return newOStream;
697	+	}
698
699	<	}//end namespace oopse
699	>	void DumpWriter::writeClosing(std::ostream& os) {
700	>
701	>	os << "</OpenMD>\n";
702	>	os.flush();
703	>	}
704	>
705	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

#	Line 0 | Line 1
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