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

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 324 by tim, Sun Feb 13 19:10:25 2005 UTC vs.
Revision 1610 by gezelter, Fri Aug 12 14:37:25 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	>	needParticlePot_ = simParams->getOutputParticlePotential();
64	>	createDumpFile_ = true;
65	>	#ifdef HAVE_LIBZ
66	>	if (needCompression_) {
67	>	filename_ += ".gz";
68	>	eorFilename_ += ".gz";
69	>	}
70	>	#endif
71	>
72		#ifdef IS_MPI
73
74		if (worldRank == 0) {
75		#endif // is_mpi
76	+
77	+	dumpFile_ = createOStream(filename_);
78
79	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
79	>	if (!dumpFile_) {
80	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
81	>	filename_.c_str());
82	>	painCave.isFatal = 1;
83	>	simError();
84	>	}
85
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	–
86		#ifdef IS_MPI
87
88		}
89
72	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73	–	MPIcheckPoint();
74	–
90		#endif // is_mpi
91
92	<	}
92	>	}
93
79	–	DumpWriter::~DumpWriter() {
94
95	+	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
96	+	: info_(info), filename_(filename){
97	+
98	+	Globals* simParams = info->getSimParams();
99	+	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
100	+
101	+	needCompression_ = simParams->getCompressDumpFile();
102	+	needForceVector_ = simParams->getOutputForceVector();
103	+	needParticlePot_ = simParams->getOutputParticlePotential();
104	+	createDumpFile_ = true;
105	+	#ifdef HAVE_LIBZ
106	+	if (needCompression_) {
107	+	filename_ += ".gz";
108	+	eorFilename_ += ".gz";
109	+	}
110	+	#endif
111	+
112		#ifdef IS_MPI
113
114		if (worldRank == 0) {
115		#endif // is_mpi
116
117	<	dumpFile_.close();
117	>
118	>	dumpFile_ = createOStream(filename_);
119
120	+	if (!dumpFile_) {
121	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
122	+	filename_.c_str());
123	+	painCave.isFatal = 1;
124	+	simError();
125	+	}
126	+
127		#ifdef IS_MPI
128
129		}
130
131		#endif // is_mpi
132
133	<	}
133	>	}
134	>
135	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
136	>	: info_(info), filename_(filename){
137	>
138	>	Globals* simParams = info->getSimParams();
139	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
140	>
141	>	needCompression_ = simParams->getCompressDumpFile();
142	>	needForceVector_ = simParams->getOutputForceVector();
143	>	needParticlePot_ = simParams->getOutputParticlePotential();
144	>
145	>	#ifdef HAVE_LIBZ
146	>	if (needCompression_) {
147	>	filename_ += ".gz";
148	>	eorFilename_ += ".gz";
149	>	}
150	>	#endif
151	>
152	>	#ifdef IS_MPI
153	>
154	>	if (worldRank == 0) {
155	>	#endif // is_mpi
156	>
157	>	createDumpFile_ = writeDumpFile;
158	>	if (createDumpFile_) {
159	>	dumpFile_ = createOStream(filename_);
160	>
161	>	if (!dumpFile_) {
162	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
163	>	filename_.c_str());
164	>	painCave.isFatal = 1;
165	>	simError();
166	>	}
167	>	}
168	>	#ifdef IS_MPI
169	>
170	>	}
171
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;
172
173	<	currentTime = s->getTime();
105	<	hmat = s->getHmat();
106	<	chi = s->getChi();
107	<	integralOfChiDt = s->getIntegralOfChiDt();
108	<	eta = s->getEta();
173	>	#endif // is_mpi
174
175	<	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";
175	>	}
176
177	<	//write out additional parameters, such as chi and eta
177	>	DumpWriter::~DumpWriter() {
178
179	<	os << chi << "\t" << integralOfChiDt << "\t;";
179	>	#ifdef IS_MPI
180
181	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
182	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
183	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
184	<
185	<	os << std::endl;
186	<	}
181	>	if (worldRank == 0) {
182	>	#endif // is_mpi
183	>	if (createDumpFile_){
184	>	writeClosing(*dumpFile_);
185	>	delete dumpFile_;
186	>	}
187	>	#ifdef IS_MPI
188
189	<	void DumpWriter::writeFrame(std::ostream& os) {
127	<	const int BUFFERSIZE = 2000;
128	<	const int MINIBUFFERSIZE = 100;
189	>	}
190
191	<	char tempBuffer[BUFFERSIZE];
131	<	char writeLine[BUFFERSIZE];
191	>	#endif // is_mpi
192
193	<	Quat4d q;
134	<	Vector3d ji;
135	<	Vector3d pos;
136	<	Vector3d vel;
193	>	}
194
195	<	Molecule* mol;
139	<	StuntDouble* integrableObject;
140	<	SimInfo::MoleculeIterator mi;
141	<	Molecule::IntegrableObjectIterator ii;
142	<
143	<	int nTotObjects;
144	<	nTotObjects = info_->getNGlobalIntegrableObjects();
195	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
196
197	<	#ifndef IS_MPI
197	>	char buffer[1024];
198
199	+	os << "    <FrameData>\n";
200
201	<	os << nTotObjects << "\n";
150	<
151	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
201	>	RealType currentTime = s->getTime();
202
203	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
203	>	if (isinf(currentTime) || isnan(currentTime)) {
204	>	sprintf( painCave.errMsg,
205	>	"DumpWriter detected a numerical error writing the time");
206	>	painCave.isFatal = 1;
207	>	simError();
208	>	}
209	>
210	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
211	>	os << buffer;
212
213	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
214	<	integrableObject = mol->nextIntegrableObject(ii)) {
157	<
213	>	Mat3x3d hmat;
214	>	hmat = s->getHmat();
215
216	<	pos = integrableObject->getPos();
217	<	vel = integrableObject->getVel();
218	<
219	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
220	<	integrableObject->getType().c_str(),
221	<	pos[0], pos[1], pos[2],
222	<	vel[0], vel[1], vel[2]);
223	<
224	<	strcpy(writeLine, tempBuffer);
225	<
226	<	if (integrableObject->isDirectional()) {
227	<	q = integrableObject->getQ();
228	<	ji = integrableObject->getJ();
229	<
230	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
231	<	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;
216	>	for (unsigned int i = 0; i < 3; i++) {
217	>	for (unsigned int j = 0; j < 3; j++) {
218	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
219	>	sprintf( painCave.errMsg,
220	>	"DumpWriter detected a numerical error writing the box");
221	>	painCave.isFatal = 1;
222	>	simError();
223	>	}
224	>	}
225	>	}
226	>
227	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
228	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
229	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
230	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
231	>	os << buffer;
232
233	<	}
233	>	RealType chi = s->getChi();
234	>	RealType integralOfChiDt = s->getIntegralOfChiDt();
235	>	if (isinf(chi) || isnan(chi) ||
236	>	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
237	>	sprintf( painCave.errMsg,
238	>	"DumpWriter detected a numerical error writing the thermostat");
239	>	painCave.isFatal = 1;
240	>	simError();
241		}
242	+	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
243	+	os << buffer;
244
245	<	os.flush();
246	<	#else // is_mpi
188	<	/*********************************************************************
189	<	* Documentation?  You want DOCUMENTATION?
190	<	*
191	<	* Why all the potatoes below?
192	<	*
193	<	* To make a long story short, the original version of DumpWriter
194	<	* worked in the most inefficient way possible.  Node 0 would
195	<	* poke each of the node for an individual atom's formatted data
196	<	* as node 0 worked its way down the global index. This was particularly
197	<	* inefficient since the method blocked all processors at every atom
198	<	* (and did it twice!).
199	<	*
200	<	* An intermediate version of DumpWriter could be described from Node
201	<	* zero's perspective as follows:
202	<	*
203	<	*  1) Have 100 of your friends stand in a circle.
204	<	*  2) When you say go, have all of them start tossing potatoes at
205	<	*     you (one at a time).
206	<	*  3) Catch the potatoes.
207	<	*
208	<	* It was an improvement, but MPI has buffers and caches that could
209	<	* best be described in this analogy as "potato nets", so there's no
210	<	* need to block the processors atom-by-atom.
211	<	*
212	<	* This new and improved DumpWriter works in an even more efficient
213	<	* way:
214	<	*
215	<	*  1) Have 100 of your friend stand in a circle.
216	<	*  2) When you say go, have them start tossing 5-pound bags of
217	<	*     potatoes at you.
218	<	*  3) Once you've caught a friend's bag of potatoes,
219	<	*     toss them a spud to let them know they can toss another bag.
220	<	*
221	<	* How's THAT for documentation?
222	<	*
223	<	*********************************************************************/
224	<	const int masterNode = 0;
245	>	Mat3x3d eta;
246	>	eta = s->getEta();
247
248	<	int * potatoes;
249	<	int myPotato;
250	<	int nProc;
251	<	int which_node;
252	<	double atomData[13];
253	<	int isDirectional;
254	<	const char * atomTypeString;
255	<	char MPIatomTypeString[MINIBUFFERSIZE];
256	<	int msgLen; // the length of message actually recieved at master nodes
257	<	int haveError;
248	>	for (unsigned int i = 0; i < 3; i++) {
249	>	for (unsigned int j = 0; j < 3; j++) {
250	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
251	>	sprintf( painCave.errMsg,
252	>	"DumpWriter detected a numerical error writing the barostat");
253	>	painCave.isFatal = 1;
254	>	simError();
255	>	}
256	>	}
257	>	}
258	>
259	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
260	>	eta(0, 0), eta(1, 0), eta(2, 0),
261	>	eta(0, 1), eta(1, 1), eta(2, 1),
262	>	eta(0, 2), eta(1, 2), eta(2, 2));
263	>	os << buffer;
264	>
265	>	os << "    </FrameData>\n";
266	>	}
267	>
268	>	void DumpWriter::writeFrame(std::ostream& os) {
269	>
270	>	#ifdef IS_MPI
271		MPI_Status istatus;
272	<	int nCurObj;
272	>	#endif
273	>
274	>	Molecule* mol;
275	>	StuntDouble* integrableObject;
276	>	SimInfo::MoleculeIterator mi;
277	>	Molecule::IntegrableObjectIterator ii;
278	>
279	>	#ifndef IS_MPI
280	>	os << "  <Snapshot>\n";
281	>
282	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
283	>
284	>	os << "    <StuntDoubles>\n";
285	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
286	>
287	>
288	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
289	>	integrableObject = mol->nextIntegrableObject(ii)) {
290	>	os << prepareDumpLine(integrableObject);
291	>
292	>	}
293	>	}
294	>	os << "    </StuntDoubles>\n";
295
296	<	// code to find maximum tag value
240	<	int * tagub;
241	<	int flag;
242	<	int MAXTAG;
243	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
296	>	os << "  </Snapshot>\n";
297
298	<	if (flag) {
299	<	MAXTAG = *tagub;
298	>	os.flush();
299	>	#else
300	>	//every node prepares the dump lines for integrable objects belong to itself
301	>	std::string buffer;
302	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
303	>
304	>
305	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
306	>	integrableObject = mol->nextIntegrableObject(ii)) {
307	>	buffer += prepareDumpLine(integrableObject);
308	>	}
309	>	}
310	>
311	>	const int masterNode = 0;
312	>	int nProc;
313	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
314	>	if (worldRank == masterNode) {
315	>	os << "  <Snapshot>\n";
316	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
317	>	os << "    <StuntDoubles>\n";
318	>
319	>	os << buffer;
320	>
321	>
322	>	for (int i = 1; i < nProc; ++i) {
323	>
324	>	// receive the length of the string buffer that was
325	>	// prepared by processor i
326	>
327	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
328	>	int recvLength;
329	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
330	>	char* recvBuffer = new char[recvLength];
331	>	if (recvBuffer == NULL) {
332	>	} else {
333	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
334	>	os << recvBuffer;
335	>	delete [] recvBuffer;
336	>	}
337	>	}
338	>	os << "    </StuntDoubles>\n";
339	>
340	>	os << "  </Snapshot>\n";
341	>	os.flush();
342		} else {
343	<	MAXTAG = 32767;
343	>	int sendBufferLength = buffer.size() + 1;
344	>	int myturn = 0;
345	>	for (int i = 1; i < nProc; ++i){
346	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
347	>	if (myturn == worldRank){
348	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
349	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
350	>	}
351	>	}
352		}
353
354	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
354	>	#endif // is_mpi
355
356	<	// Node 0 needs a list of the magic potatoes for each processor;
356	>	}
357
358	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
359	<	potatoes = new int[nProc];
358	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
359	>
360	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
361	>	std::string type("pv");
362	>	std::string line;
363	>	char tempBuffer[4096];
364	>
365	>	Vector3d pos;
366	>	Vector3d vel;
367	>	pos = integrableObject->getPos();
368	>
369	>	if (isinf(pos[0]) || isnan(pos[0]) ||
370	>	isinf(pos[1]) || isnan(pos[1]) ||
371	>	isinf(pos[2]) || isnan(pos[2]) ) {
372	>	sprintf( painCave.errMsg,
373	>	"DumpWriter detected a numerical error writing the position"
374	>	" for object %d", index);
375	>	painCave.isFatal = 1;
376	>	simError();
377	>	}
378	>
379	>	vel = integrableObject->getVel();
380	>
381	>	if (isinf(vel[0]) || isnan(vel[0]) ||
382	>	isinf(vel[1]) || isnan(vel[1]) ||
383	>	isinf(vel[2]) || isnan(vel[2]) ) {
384	>	sprintf( painCave.errMsg,
385	>	"DumpWriter detected a numerical error writing the velocity"
386	>	" for object %d", index);
387	>	painCave.isFatal = 1;
388	>	simError();
389	>	}
390	>
391	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
392	>	pos[0], pos[1], pos[2],
393	>	vel[0], vel[1], vel[2]);
394	>	line += tempBuffer;
395	>
396	>	if (integrableObject->isDirectional()) {
397	>	type += "qj";
398	>	Quat4d q;
399	>	Vector3d ji;
400	>	q = integrableObject->getQ();
401	>
402	>	if (isinf(q[0]) || isnan(q[0]) ||
403	>	isinf(q[1]) || isnan(q[1]) ||
404	>	isinf(q[2]) || isnan(q[2]) ||
405	>	isinf(q[3]) || isnan(q[3]) ) {
406	>	sprintf( painCave.errMsg,
407	>	"DumpWriter detected a numerical error writing the quaternion"
408	>	" for object %d", index);
409	>	painCave.isFatal = 1;
410	>	simError();
411	>	}
412
413	<	//write out the comment lines
259	<	for(int i = 0; i < nProc; i++) {
260	<	potatoes[i] = 0;
261	<	}
413	>	ji = integrableObject->getJ();
414
415	+	if (isinf(ji[0]) || isnan(ji[0]) ||
416	+	isinf(ji[1]) || isnan(ji[1]) ||
417	+	isinf(ji[2]) || isnan(ji[2]) ) {
418	+	sprintf( painCave.errMsg,
419	+	"DumpWriter detected a numerical error writing the angular"
420	+	" momentum for object %d", index);
421	+	painCave.isFatal = 1;
422	+	simError();
423	+	}
424
425	<	os << nTotObjects << "\n";
426	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
425	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
426	>	q[0], q[1], q[2], q[3],
427	>	ji[0], ji[1], ji[2]);
428	>	line += tempBuffer;
429	>	}
430
431	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
431	>	if (needForceVector_) {
432	>	type += "f";
433	>	Vector3d frc;
434
435	<	// Get the Node number which has this atom;
435	>	frc = integrableObject->getFrc();
436
437	<	which_node = info_->getMolToProc(i);
437	>	if (isinf(frc[0]) || isnan(frc[0]) ||
438	>	isinf(frc[1]) || isnan(frc[1]) ||
439	>	isinf(frc[2]) || isnan(frc[2]) ) {
440	>	sprintf( painCave.errMsg,
441	>	"DumpWriter detected a numerical error writing the force"
442	>	" for object %d", index);
443	>	painCave.isFatal = 1;
444	>	simError();
445	>	}
446	>	sprintf(tempBuffer, " %13e %13e %13e",
447	>	frc[0], frc[1], frc[2]);
448	>	line += tempBuffer;
449	>
450	>	if (integrableObject->isDirectional()) {
451	>	type += "t";
452	>	Vector3d trq;
453	>
454	>	trq = integrableObject->getTrq();
455	>
456	>	if (isinf(trq[0]) || isnan(trq[0]) ||
457	>	isinf(trq[1]) || isnan(trq[1]) ||
458	>	isinf(trq[2]) || isnan(trq[2]) ) {
459	>	sprintf( painCave.errMsg,
460	>	"DumpWriter detected a numerical error writing the torque"
461	>	" for object %d", index);
462	>	painCave.isFatal = 1;
463	>	simError();
464	>	}
465	>
466	>	sprintf(tempBuffer, " %13e %13e %13e",
467	>	trq[0], trq[1], trq[2]);
468	>	line += tempBuffer;
469	>	}
470	>	}
471	>	if (needParticlePot_) {
472	>	type += "u";
473	>	RealType particlePot;
474
475	<	if (which_node != masterNode) { //current molecule is in slave node
274	<	if (potatoes[which_node] + 1 >= MAXTAG) {
275	<	// The potato was going to exceed the maximum value,
276	<	// so wrap this processor potato back to 0:
475	>	particlePot = integrableObject->getParticlePot();
476
477	<	potatoes[which_node] = 0;
478	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
479	<	MPI_COMM_WORLD);
480	<	}
477	>	if (isinf(particlePot) || isnan(particlePot)) {
478	>	sprintf( painCave.errMsg,
479	>	"DumpWriter detected a numerical error writing the particle "
480	>	" potential for object %d", index);
481	>	painCave.isFatal = 1;
482	>	simError();
483	>	}
484	>	sprintf(tempBuffer, " %13e", particlePot);
485	>	line += tempBuffer;
486	>	}
487	>
488	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
489	>	return std::string(tempBuffer);
490	>	}
491
492	<	myPotato = potatoes[which_node];
492	>	void DumpWriter::writeDump() {
493	>	writeFrame(*dumpFile_);
494	>	}
495
496	<	//recieve the number of integrableObject in current molecule
497	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
498	<	MPI_COMM_WORLD, &istatus);
499	<	myPotato++;
496	>	void DumpWriter::writeEor() {
497	>	std::ostream* eorStream;
498	>
499	>	#ifdef IS_MPI
500	>	if (worldRank == 0) {
501	>	#endif // is_mpi
502
503	<	for(int l = 0; l < nCurObj; l++) {
291	<	if (potatoes[which_node] + 2 >= MAXTAG) {
292	<	// The potato was going to exceed the maximum value,
293	<	// so wrap this processor potato back to 0:
503	>	eorStream = createOStream(eorFilename_);
504
505	<	potatoes[which_node] = 0;
506	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
507	<	0, MPI_COMM_WORLD);
298	<	}
505	>	#ifdef IS_MPI
506	>	}
507	>	#endif // is_mpi
508
509	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
301	<	which_node, myPotato, MPI_COMM_WORLD,
302	<	&istatus);
509	>	writeFrame(*eorStream);
510
511	<	atomTypeString = MPIatomTypeString;
511	>	#ifdef IS_MPI
512	>	if (worldRank == 0) {
513	>	#endif // is_mpi
514	>	writeClosing(*eorStream);
515	>	delete eorStream;
516	>	#ifdef IS_MPI
517	>	}
518	>	#endif // is_mpi
519
520	<	myPotato++;
520	>	}
521
308	–	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
309	–	MPI_COMM_WORLD, &istatus);
310	–	myPotato++;
522
523	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
523	>	void DumpWriter::writeDumpAndEor() {
524	>	std::vector<std::streambuf*> buffers;
525	>	std::ostream* eorStream;
526	>	#ifdef IS_MPI
527	>	if (worldRank == 0) {
528	>	#endif // is_mpi
529
530	<	if (msgLen == 13)
315	<	isDirectional = 1;
316	<	else
317	<	isDirectional = 0;
530	>	buffers.push_back(dumpFile_->rdbuf());
531
532	<	// If we've survived to here, format the line:
532	>	eorStream = createOStream(eorFilename_);
533
534	<	if (!isDirectional) {
322	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
323	<	atomTypeString, atomData[0],
324	<	atomData[1], atomData[2],
325	<	atomData[3], atomData[4],
326	<	atomData[5]);
327	<
328	<	strcat(writeLine,
329	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
330	<	} else {
331	<	sprintf(writeLine,
332	<	"%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",
333	<	atomTypeString,
334	<	atomData[0],
335	<	atomData[1],
336	<	atomData[2],
337	<	atomData[3],
338	<	atomData[4],
339	<	atomData[5],
340	<	atomData[6],
341	<	atomData[7],
342	<	atomData[8],
343	<	atomData[9],
344	<	atomData[10],
345	<	atomData[11],
346	<	atomData[12]);
347	<	}
348	<
349	<	os << writeLine;
350	<
351	<	} // end for(int l =0)
352	<
353	<	potatoes[which_node] = myPotato;
354	<	} else { //master node has current molecule
355	<
356	<	mol = info_->getMoleculeByGlobalIndex(i);
357	<
358	<	if (mol == NULL) {
359	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
360	<	painCave.isFatal = 1;
361	<	simError();
362	<	}
363	<
364	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
365	<	integrableObject = mol->nextIntegrableObject(ii)) {
366	<
367	<	atomTypeString = integrableObject->getType().c_str();
368	<
369	<	pos = integrableObject->getPos();
370	<	vel = integrableObject->getVel();
371	<
372	<	atomData[0] = pos[0];
373	<	atomData[1] = pos[1];
374	<	atomData[2] = pos[2];
375	<
376	<	atomData[3] = vel[0];
377	<	atomData[4] = vel[1];
378	<	atomData[5] = vel[2];
379	<
380	<	isDirectional = 0;
381	<
382	<	if (integrableObject->isDirectional()) {
383	<	isDirectional = 1;
384	<
385	<	q = integrableObject->getQ();
386	<	ji = integrableObject->getJ();
387	<
388	<	for(int j = 0; j < 6; j++) {
389	<	atomData[j] = atomData[j];
390	<	}
391	<
392	<	atomData[6] = q[0];
393	<	atomData[7] = q[1];
394	<	atomData[8] = q[2];
395	<	atomData[9] = q[3];
396	<
397	<	atomData[10] = ji[0];
398	<	atomData[11] = ji[1];
399	<	atomData[12] = ji[2];
400	<	}
401	<
402	<	// If we've survived to here, format the line:
403	<
404	<	if (!isDirectional) {
405	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
406	<	atomTypeString, atomData[0],
407	<	atomData[1], atomData[2],
408	<	atomData[3], atomData[4],
409	<	atomData[5]);
410	<
411	<	strcat(writeLine,
412	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
413	<	} else {
414	<	sprintf(writeLine,
415	<	"%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",
416	<	atomTypeString,
417	<	atomData[0],
418	<	atomData[1],
419	<	atomData[2],
420	<	atomData[3],
421	<	atomData[4],
422	<	atomData[5],
423	<	atomData[6],
424	<	atomData[7],
425	<	atomData[8],
426	<	atomData[9],
427	<	atomData[10],
428	<	atomData[11],
429	<	atomData[12]);
430	<	}
431	<
432	<
433	<	os << writeLine;
434	<
435	<	} //end for(iter = integrableObject.begin())
436	<	}
437	<	} //end for(i = 0; i < mpiSim->getNmol())
438	<
439	<	os.flush();
534	>	buffers.push_back(eorStream->rdbuf());
535
536	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
537	<	MPIcheckPoint();
536	>	#ifdef IS_MPI
537	>	}
538	>	#endif // is_mpi
539
540	<	delete [] potatoes;
541	<	} else {
540	>	TeeBuf tbuf(buffers.begin(), buffers.end());
541	>	std::ostream os(&tbuf);
542
543	<	// worldRank != 0, so I'm a remote node.
543	>	writeFrame(os);
544
545	<	// Set my magic potato to 0:
545	>	#ifdef IS_MPI
546	>	if (worldRank == 0) {
547	>	#endif // is_mpi
548	>	writeClosing(*eorStream);
549	>	delete eorStream;
550	>	#ifdef IS_MPI
551	>	}
552	>	#endif // is_mpi
553	>
554	>	}
555
556	<	myPotato = 0;
556	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
557
558	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
559	<
560	<	// Am I the node which has this integrableObject?
561	<	int whichNode = info_->getMolToProc(i);
562	<	if (whichNode == worldRank) {
563	<	if (myPotato + 1 >= MAXTAG) {
459	<
460	<	// The potato was going to exceed the maximum value,
461	<	// so wrap this processor potato back to 0 (and block until
462	<	// node 0 says we can go:
463	<
464	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
465	<	&istatus);
466	<	}
467	<
468	<	mol = info_->getMoleculeByGlobalIndex(i);
469	<
470	<
471	<	nCurObj = mol->getNIntegrableObjects();
472	<
473	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
474	<	myPotato++;
475	<
476	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
477	<	integrableObject = mol->nextIntegrableObject(ii)) {
478	<
479	<	if (myPotato + 2 >= MAXTAG) {
480	<
481	<	// The potato was going to exceed the maximum value,
482	<	// so wrap this processor potato back to 0 (and block until
483	<	// node 0 says we can go:
484	<
485	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
486	<	&istatus);
487	<	}
488	<
489	<	atomTypeString = integrableObject->getType().c_str();
490	<
491	<	pos = integrableObject->getPos();
492	<	vel = integrableObject->getVel();
493	<
494	<	atomData[0] = pos[0];
495	<	atomData[1] = pos[1];
496	<	atomData[2] = pos[2];
497	<
498	<	atomData[3] = vel[0];
499	<	atomData[4] = vel[1];
500	<	atomData[5] = vel[2];
501	<
502	<	isDirectional = 0;
503	<
504	<	if (integrableObject->isDirectional()) {
505	<	isDirectional = 1;
506	<
507	<	q = integrableObject->getQ();
508	<	ji = integrableObject->getJ();
509	<
510	<	atomData[6] = q[0];
511	<	atomData[7] = q[1];
512	<	atomData[8] = q[2];
513	<	atomData[9] = q[3];
514	<
515	<	atomData[10] = ji[0];
516	<	atomData[11] = ji[1];
517	<	atomData[12] = ji[2];
518	<	}
519	<
520	<	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
521	<
522	<	// null terminate the  std::string before sending (just in case):
523	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
524	<
525	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
526	<	myPotato, MPI_COMM_WORLD);
527	<
528	<	myPotato++;
529	<
530	<	if (isDirectional) {
531	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
532	<	MPI_COMM_WORLD);
533	<	} else {
534	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
535	<	MPI_COMM_WORLD);
536	<	}
537	<
538	<	myPotato++;
539	<	}
540	<
541	<	}
542	<
543	<	}
544	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
545	<	MPIcheckPoint();
558	>	std::ostream* newOStream;
559	>	#ifdef HAVE_LIBZ
560	>	if (needCompression_) {
561	>	newOStream = new ogzstream(filename.c_str());
562	>	} else {
563	>	newOStream = new std::ofstream(filename.c_str());
564		}
565	+	#else
566	+	newOStream = new std::ofstream(filename.c_str());
567	+	#endif
568	+	//write out MetaData first
569	+	(*newOStream) << "<OpenMD version=1>" << std::endl;
570	+	(*newOStream) << "  <MetaData>" << std::endl;
571	+	(*newOStream) << info_->getRawMetaData();
572	+	(*newOStream) << "  </MetaData>" << std::endl;
573	+	return newOStream;
574	+	}
575
576	<	#endif // is_mpi
576	>	void DumpWriter::writeClosing(std::ostream& os) {
577
578	<	}
578	>	os << "</OpenMD>\n";
579	>	os.flush();
580	>	}
581
582	<	}//end namespace oopse
582	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpWriter.cpp (property svn:keywords):
Revision 324 by tim, Sun Feb 13 19:10:25 2005 UTC vs.
Revision 1610 by gezelter, Fri Aug 12 14:37:25 2011 UTC

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