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

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 251 by tim, Wed Jan 12 23:24:55 2005 UTC vs.
Revision 1564 by chuckv, Wed May 18 19:28:52 2011 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include "io/DumpWriter.hpp"
43		#include "primitives/Molecule.hpp"
44		#include "utils/simError.h"
45	+	#include "io/basic_teebuf.hpp"
46	+	#include "io/gzstream.hpp"
47	+	#include "io/Globals.hpp"
48
49	+
50		#ifdef IS_MPI
51		#include <mpi.h>
52		#endif //is_mpi
53
54	<	namespace oopse {
54	>	using namespace std;
55	>	namespace OpenMD {
56
57	<	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
58	<	: info_(info), filename_(filename){
57	>	DumpWriter::DumpWriter(SimInfo* info)
58	>	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
59	>
60	>	Globals* simParams = info->getSimParams();
61	>	needCompression_ = simParams->getCompressDumpFile();
62	>	needForceVector_ = simParams->getOutputForceVector();
63	>	createDumpFile_ = true;
64	>	#ifdef HAVE_LIBZ
65	>	if (needCompression_) {
66	>	filename_ += ".gz";
67	>	eorFilename_ += ".gz";
68	>	}
69	>	#endif
70	>
71		#ifdef IS_MPI
72
73		if (worldRank == 0) {
74		#endif // is_mpi
75	+
76	+	dumpFile_ = createOStream(filename_);
77
78	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
78	>	if (!dumpFile_) {
79	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
80	>	filename_.c_str());
81	>	painCave.isFatal = 1;
82	>	simError();
83	>	}
84
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	–
85		#ifdef IS_MPI
86
87		}
88
72	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73	–	MPIcheckPoint();
74	–
89		#endif // is_mpi
90
91	<	}
91	>	}
92
79	–	DumpWriter::~DumpWriter() {
93
94	+	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
95	+	: info_(info), filename_(filename){
96	+
97	+	Globals* simParams = info->getSimParams();
98	+	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
99	+
100	+	needCompression_ = simParams->getCompressDumpFile();
101	+	needForceVector_ = simParams->getOutputForceVector();
102	+	createDumpFile_ = true;
103	+	#ifdef HAVE_LIBZ
104	+	if (needCompression_) {
105	+	filename_ += ".gz";
106	+	eorFilename_ += ".gz";
107	+	}
108	+	#endif
109	+
110		#ifdef IS_MPI
111
112		if (worldRank == 0) {
113		#endif // is_mpi
114
115	<	dumpFile_.close();
115	>
116	>	dumpFile_ = createOStream(filename_);
117
118	+	if (!dumpFile_) {
119	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
120	+	filename_.c_str());
121	+	painCave.isFatal = 1;
122	+	simError();
123	+	}
124	+
125		#ifdef IS_MPI
126
127		}
128
129		#endif // is_mpi
130
131	<	}
131	>	}
132	>
133	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
134	>	: info_(info), filename_(filename){
135	>
136	>	Globals* simParams = info->getSimParams();
137	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
138	>
139	>	needCompression_ = simParams->getCompressDumpFile();
140	>	needForceVector_ = simParams->getOutputForceVector();
141	>
142	>	#ifdef HAVE_LIBZ
143	>	if (needCompression_) {
144	>	filename_ += ".gz";
145	>	eorFilename_ += ".gz";
146	>	}
147	>	#endif
148	>
149	>	#ifdef IS_MPI
150	>
151	>	if (worldRank == 0) {
152	>	#endif // is_mpi
153	>
154	>	createDumpFile_ = writeDumpFile;
155	>	if (createDumpFile_) {
156	>	dumpFile_ = createOStream(filename_);
157	>
158	>	if (!dumpFile_) {
159	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
160	>	filename_.c_str());
161	>	painCave.isFatal = 1;
162	>	simError();
163	>	}
164	>	}
165	>	#ifdef IS_MPI
166	>
167	>	}
168
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;
169
170	<	currentTime = s->getTime();
105	<	hmat = s->getHmat();
106	<	chi = s->getChi();
107	<	integralOfChiDt = s->getIntegralOfChiDt();
108	<	eta = s->getEta();
170	>	#endif // is_mpi
171
172	<	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";
172	>	}
173
174	<	//write out additional parameters, such as chi and eta
174	>	DumpWriter::~DumpWriter() {
175
176	<	os << chi << "\t" << integralOfChiDt << "\t;";
176	>	#ifdef IS_MPI
177
178	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
179	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
180	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
181	<
182	<	os << std::endl;
183	<	}
178	>	if (worldRank == 0) {
179	>	#endif // is_mpi
180	>	if (createDumpFile_){
181	>	writeClosing(*dumpFile_);
182	>	delete dumpFile_;
183	>	}
184	>	#ifdef IS_MPI
185
186	<	void DumpWriter::writeFrame(std::ostream& os) {
127	<	const int BUFFERSIZE = 2000;
128	<	const int MINIBUFFERSIZE = 100;
186	>	}
187
188	<	char tempBuffer[BUFFERSIZE];
131	<	char writeLine[BUFFERSIZE];
188	>	#endif // is_mpi
189
190	<	Quat4d q;
134	<	Vector3d ji;
135	<	Vector3d pos;
136	<	Vector3d vel;
190	>	}
191
192	<	Molecule* mol;
139	<	StuntDouble* integrableObject;
140	<	SimInfo::MoleculeIterator mi;
141	<	Molecule::IntegrableObjectIterator ii;
142	<
143	<	int nTotObjects;
144	<	nTotObjects = info_->getNGlobalIntegrableObjects();
192	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
193
194	<	#ifndef IS_MPI
194	>	char buffer[1024];
195
196	+	os << "    <FrameData>\n";
197
198	<	os << nTotObjects << "\n";
150	<
151	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
198	>	RealType currentTime = s->getTime();
199
200	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
200	>	if (isinf(currentTime) || isnan(currentTime)) {
201	>	sprintf( painCave.errMsg,
202	>	"DumpWriter detected a numerical error writing the time");
203	>	painCave.isFatal = 1;
204	>	simError();
205	>	}
206	>
207	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
208	>	os << buffer;
209
210	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
211	<	integrableObject = mol->nextIntegrableObject(ii)) {
157	<
210	>	Mat3x3d hmat;
211	>	hmat = s->getHmat();
212
213	<	pos = integrableObject->getPos();
214	<	vel = integrableObject->getVel();
215	<
216	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
217	<	integrableObject->getType().c_str(),
218	<	pos[0], pos[1], pos[2],
219	<	vel[0], vel[1], vel[2]);
220	<
221	<	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	<	}
213	>	for (unsigned int i = 0; i < 3; i++) {
214	>	for (unsigned int j = 0; j < 3; j++) {
215	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
216	>	sprintf( painCave.errMsg,
217	>	"DumpWriter detected a numerical error writing the box");
218	>	painCave.isFatal = 1;
219	>	simError();
220	>	}
221	>	}
222		}
223	+
224	+	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
225	+	hmat(0, 0), hmat(1, 0), hmat(2, 0),
226	+	hmat(0, 1), hmat(1, 1), hmat(2, 1),
227	+	hmat(0, 2), hmat(1, 2), hmat(2, 2));
228	+	os << buffer;
229
230	<	#else // is_mpi
231	<	/*********************************************************************
232	<	* Documentation?  You want DOCUMENTATION?
233	<	*
234	<	* Why all the potatoes below?
235	<	*
236	<	* To make a long story short, the original version of DumpWriter
237	<	* worked in the most inefficient way possible.  Node 0 would
238	<	* poke each of the node for an individual atom's formatted data
239	<	* as node 0 worked its way down the global index. This was particularly
240	<	* 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;
230	>	RealType chi = s->getChi();
231	>	RealType integralOfChiDt = s->getIntegralOfChiDt();
232	>	if (isinf(chi) || isnan(chi) ||
233	>	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
234	>	sprintf( painCave.errMsg,
235	>	"DumpWriter detected a numerical error writing the thermostat");
236	>	painCave.isFatal = 1;
237	>	simError();
238	>	}
239	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
240	>	os << buffer;
241
242	<	int * potatoes;
243	<	int myPotato;
244	<	int nProc;
245	<	int which_node;
246	<	double atomData[13];
247	<	int isDirectional;
248	<	const char * atomTypeString;
249	<	char MPIatomTypeString[MINIBUFFERSIZE];
250	<	int msgLen; // the length of message actually recieved at master nodes
251	<	int haveError;
242	>	Mat3x3d eta;
243	>	eta = s->getEta();
244	>
245	>	for (unsigned int i = 0; i < 3; i++) {
246	>	for (unsigned int j = 0; j < 3; j++) {
247	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
248	>	sprintf( painCave.errMsg,
249	>	"DumpWriter detected a numerical error writing the barostat");
250	>	painCave.isFatal = 1;
251	>	simError();
252	>	}
253	>	}
254	>	}
255	>
256	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
257	>	eta(0, 0), eta(1, 0), eta(2, 0),
258	>	eta(0, 1), eta(1, 1), eta(2, 1),
259	>	eta(0, 2), eta(1, 2), eta(2, 2));
260	>	os << buffer;
261	>
262	>	os << "    </FrameData>\n";
263	>	}
264	>
265	>	void DumpWriter::writeFrame(std::ostream& os) {
266	>
267	>	#ifdef IS_MPI
268		MPI_Status istatus;
269	<	int nCurObj;
269	>	#endif
270	>
271	>	Molecule* mol;
272	>	StuntDouble* integrableObject;
273	>	SimInfo::MoleculeIterator mi;
274	>	Molecule::IntegrableObjectIterator ii;
275	>
276	>	#ifndef IS_MPI
277	>	os << "  <Snapshot>\n";
278	>
279	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
280	>
281	>	os << "    <StuntDoubles>\n";
282	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
283	>
284	>
285	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
286	>	integrableObject = mol->nextIntegrableObject(ii)) {
287	>	os << prepareDumpLine(integrableObject);
288	>
289	>	}
290	>	}
291	>	os << "    </StuntDoubles>\n";
292
293	<	// 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);
293	>	os << "  </Snapshot>\n";
294
295	<	if (flag) {
296	<	MAXTAG = *tagub;
295	>	os.flush();
296	>	#else
297	>	//every node prepares the dump lines for integrable objects belong to itself
298	>	std::string buffer;
299	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
300	>
301	>
302	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
303	>	integrableObject = mol->nextIntegrableObject(ii)) {
304	>	buffer += prepareDumpLine(integrableObject);
305	>	}
306	>	}
307	>
308	>	const int masterNode = 0;
309	>	int nProc;
310	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
311	>	if (worldRank == masterNode) {
312	>	os << "  <Snapshot>\n";
313	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
314	>	os << "    <StuntDoubles>\n";
315	>
316	>	os << buffer;
317	>
318	>
319	>	for (int i = 1; i < nProc; ++i) {
320	>
321	>	// receive the length of the string buffer that was
322	>	// prepared by processor i
323	>
324	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
325	>	int recvLength;
326	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
327	>	char* recvBuffer = new char[recvLength];
328	>	if (recvBuffer == NULL) {
329	>	} else {
330	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
331	>	os << recvBuffer;
332	>	delete [] recvBuffer;
333	>	}
334	>	}
335	>	os << "    </StuntDoubles>\n";
336	>
337	>	os << "  </Snapshot>\n";
338	>	os.flush();
339		} else {
340	<	MAXTAG = 32767;
340	>	int sendBufferLength = buffer.size() + 1;
341	>	int myturn = 0;
342	>	for (int i = 1; i < nProc; ++i){
343	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
344	>	if (myturn == worldRank){
345	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
346	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
347	>	}
348	>	}
349		}
350
351	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
351	>	#endif // is_mpi
352
353	<	// Node 0 needs a list of the magic potatoes for each processor;
353	>	}
354
355	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
356	<	potatoes = new int[nProc];
355	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
356	>
357	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
358	>	std::string type("pv");
359	>	std::string line;
360	>	char tempBuffer[4096];
361	>
362	>	Vector3d pos;
363	>	Vector3d vel;
364	>	pos = integrableObject->getPos();
365	>
366	>	if (isinf(pos[0]) || isnan(pos[0]) ||
367	>	isinf(pos[1]) || isnan(pos[1]) ||
368	>	isinf(pos[2]) || isnan(pos[2]) ) {
369	>	sprintf( painCave.errMsg,
370	>	"DumpWriter detected a numerical error writing the position"
371	>	" for object %d", index);
372	>	painCave.isFatal = 1;
373	>	simError();
374	>	}
375	>
376	>	vel = integrableObject->getVel();
377	>
378	>	if (isinf(vel[0]) || isnan(vel[0]) ||
379	>	isinf(vel[1]) || isnan(vel[1]) ||
380	>	isinf(vel[2]) || isnan(vel[2]) ) {
381	>	sprintf( painCave.errMsg,
382	>	"DumpWriter detected a numerical error writing the velocity"
383	>	" for object %d", index);
384	>	painCave.isFatal = 1;
385	>	simError();
386	>	}
387	>
388	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
389	>	pos[0], pos[1], pos[2],
390	>	vel[0], vel[1], vel[2]);
391	>	line += tempBuffer;
392	>
393	>	if (integrableObject->isDirectional()) {
394	>	type += "qj";
395	>	Quat4d q;
396	>	Vector3d ji;
397	>	q = integrableObject->getQ();
398	>
399	>	if (isinf(q[0]) || isnan(q[0]) ||
400	>	isinf(q[1]) || isnan(q[1]) ||
401	>	isinf(q[2]) || isnan(q[2]) ||
402	>	isinf(q[3]) || isnan(q[3]) ) {
403	>	sprintf( painCave.errMsg,
404	>	"DumpWriter detected a numerical error writing the quaternion"
405	>	" for object %d", index);
406	>	painCave.isFatal = 1;
407	>	simError();
408	>	}
409
410	<	//write out the comment lines
258	<	for(int i = 0; i < nProc; i++) {
259	<	potatoes[i] = 0;
260	<	}
410	>	ji = integrableObject->getJ();
411
412	+	if (isinf(ji[0]) || isnan(ji[0]) ||
413	+	isinf(ji[1]) || isnan(ji[1]) ||
414	+	isinf(ji[2]) || isnan(ji[2]) ) {
415	+	sprintf( painCave.errMsg,
416	+	"DumpWriter detected a numerical error writing the angular"
417	+	" momentum for object %d", index);
418	+	painCave.isFatal = 1;
419	+	simError();
420	+	}
421
422	<	os << nTotObjects << "\n";
423	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
422	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
423	>	q[0], q[1], q[2], q[3],
424	>	ji[0], ji[1], ji[2]);
425	>	line += tempBuffer;
426	>	}
427
428	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
428	>	if (needForceVector_) {
429	>	type += "f";
430	>	Vector3d frc;
431
432	<	// Get the Node number which has this atom;
432	>	frc = integrableObject->getFrc();
433
434	<	which_node = info_->getMolToProc(i);
434	>	if (isinf(frc[0]) || isnan(frc[0]) ||
435	>	isinf(frc[1]) || isnan(frc[1]) ||
436	>	isinf(frc[2]) || isnan(frc[2]) ) {
437	>	sprintf( painCave.errMsg,
438	>	"DumpWriter detected a numerical error writing the force"
439	>	" for object %d", index);
440	>	painCave.isFatal = 1;
441	>	simError();
442	>	}
443	>	sprintf(tempBuffer, " %13e %13e %13e",
444	>	frc[0], frc[1], frc[2]);
445	>	line += tempBuffer;
446	>
447	>	if (integrableObject->isDirectional()) {
448	>	type += "t";
449	>	Vector3d trq;
450	>
451	>	trq = integrableObject->getTrq();
452	>
453	>	if (isinf(trq[0]) || isnan(trq[0]) ||
454	>	isinf(trq[1]) || isnan(trq[1]) ||
455	>	isinf(trq[2]) || isnan(trq[2]) ) {
456	>	sprintf( painCave.errMsg,
457	>	"DumpWriter detected a numerical error writing the torque"
458	>	" for object %d", index);
459	>	painCave.isFatal = 1;
460	>	simError();
461	>	}
462	>
463	>	sprintf(tempBuffer, " %13e %13e %13e",
464	>	trq[0], trq[1], trq[2]);
465	>	line += tempBuffer;
466	>	}
467	>	}
468	>
469	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
470	>	return std::string(tempBuffer);
471	>	}
472
473	<	if (which_node != masterNode) { //current molecule is in slave node
474	<	if (potatoes[which_node] + 1 >= MAXTAG) {
475	<	// The potato was going to exceed the maximum value,
275	<	// so wrap this processor potato back to 0:
473	>	void DumpWriter::writeDump() {
474	>	writeFrame(*dumpFile_);
475	>	}
476
477	<	potatoes[which_node] = 0;
478	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
479	<	MPI_COMM_WORLD);
480	<	}
477	>	void DumpWriter::writeEor() {
478	>	std::ostream* eorStream;
479	>
480	>	#ifdef IS_MPI
481	>	if (worldRank == 0) {
482	>	#endif // is_mpi
483
484	<	myPotato = potatoes[which_node];
484	>	eorStream = createOStream(eorFilename_);
485
486	<	//recieve the number of integrableObject in current molecule
487	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
488	<	MPI_COMM_WORLD, &istatus);
287	<	myPotato++;
486	>	#ifdef IS_MPI
487	>	}
488	>	#endif // is_mpi
489
490	<	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:
490	>	writeFrame(*eorStream);
491
492	<	potatoes[which_node] = 0;
493	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
494	<	0, MPI_COMM_WORLD);
495	<	}
492	>	#ifdef IS_MPI
493	>	if (worldRank == 0) {
494	>	#endif // is_mpi
495	>	writeClosing(*eorStream);
496	>	delete eorStream;
497	>	#ifdef IS_MPI
498	>	}
499	>	#endif // is_mpi
500
501	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
300	<	which_node, myPotato, MPI_COMM_WORLD,
301	<	&istatus);
501	>	}
502
303	–	atomTypeString = MPIatomTypeString;
503
504	<	myPotato++;
504	>	void DumpWriter::writeDumpAndEor() {
505	>	std::vector<std::streambuf*> buffers;
506	>	std::ostream* eorStream;
507	>	#ifdef IS_MPI
508	>	if (worldRank == 0) {
509	>	#endif // is_mpi
510
511	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
308	<	MPI_COMM_WORLD, &istatus);
309	<	myPotato++;
511	>	buffers.push_back(dumpFile_->rdbuf());
512
513	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
513	>	eorStream = createOStream(eorFilename_);
514
515	<	if (msgLen == 13)
314	<	isDirectional = 1;
315	<	else
316	<	isDirectional = 0;
317	<
318	<	// If we've survived to here, format the line:
319	<
320	<	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();
515	>	buffers.push_back(eorStream->rdbuf());
516
517	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
518	<	MPIcheckPoint();
517	>	#ifdef IS_MPI
518	>	}
519	>	#endif // is_mpi
520
521	<	delete [] potatoes;
522	<	} else {
521	>	TeeBuf tbuf(buffers.begin(), buffers.end());
522	>	std::ostream os(&tbuf);
523
524	<	// worldRank != 0, so I'm a remote node.
524	>	writeFrame(os);
525
526	<	// Set my magic potato to 0:
526	>	#ifdef IS_MPI
527	>	if (worldRank == 0) {
528	>	#endif // is_mpi
529	>	writeClosing(*eorStream);
530	>	delete eorStream;
531	>	#ifdef IS_MPI
532	>	}
533	>	#endif // is_mpi
534	>
535	>	}
536
537	<	myPotato = 0;
537	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
538
539	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
540	<
541	<	// Am I the node which has this integrableObject?
542	<	int whichNode = info_->getMolToProc(i);
543	<	if (whichNode == worldRank) {
544	<	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();
539	>	std::ostream* newOStream;
540	>	#ifdef HAVE_LIBZ
541	>	if (needCompression_) {
542	>	newOStream = new ogzstream(filename.c_str());
543	>	} else {
544	>	newOStream = new std::ofstream(filename.c_str());
545		}
546	+	#else
547	+	newOStream = new std::ofstream(filename.c_str());
548	+	#endif
549	+	//write out MetaData first
550	+	(*newOStream) << "<OpenMD version=1>" << std::endl;
551	+	(*newOStream) << "  <MetaData>" << std::endl;
552	+	(*newOStream) << info_->getRawMetaData();
553	+	(*newOStream) << "  </MetaData>" << std::endl;
554	+	return newOStream;
555	+	}
556
557	<	#endif // is_mpi
557	>	void DumpWriter::writeClosing(std::ostream& os) {
558
559	<	}
559	>	os << "</OpenMD>\n";
560	>	os.flush();
561	>	}
562
563	<	}//end namespace oopse
563	>	}//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.
Revision 1564 by chuckv, Wed May 18 19:28:52 2011 UTC

#	Line 0 | Line 1
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