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

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trunk/src/io/DumpWriter.cpp (file contents), Revision 251 by tim, Wed Jan 12 23:24:55 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1712 by gezelter, Sat May 19 13:30:21 2012 UTC

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

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 251 by tim, Wed Jan 12 23:24:55 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1712 by gezelter, Sat May 19 13:30:21 2012 UTC

#	Line 0 | Line 1
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