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

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trunk/src/io/DumpWriter.cpp (file contents), Revision 395 by tim, Thu Mar 3 14:40:20 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1769 by gezelter, Mon Jul 9 14:15:52 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	+	#ifdef HAVE_ZLIB
48	+	#include "io/gzstream.hpp"
49	+	#endif
50	+	#include "io/Globals.hpp"
51	+
52	+	#ifdef _MSC_VER
53	+	#define isnan(x) _isnan((x))
54	+	#define isinf(x) (!_finite(x) && !_isnan(x))
55	+	#endif
56	+
57		#ifdef IS_MPI
58		#include <mpi.h>
59	<	#endif //is_mpi
59	>	#endif
60
61	<	namespace oopse {
61	>	using namespace std;
62	>	namespace OpenMD {
63
64	<	DumpWriter::DumpWriter(SimInfo* info)
65	<	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
64	>	DumpWriter::DumpWriter(SimInfo* info)
65	>	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
66	>
67	>	Globals* simParams = info->getSimParams();
68	>	needCompression_   = simParams->getCompressDumpFile();
69	>	needForceVector_   = simParams->getOutputForceVector();
70	>	needParticlePot_   = simParams->getOutputParticlePotential();
71	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
72	>	needElectricField_ = simParams->getOutputElectricField();
73	>
74	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
75	>	doSiteData_ = true;
76	>	} else {
77	>	doSiteData_ = false;
78	>	}
79	>
80	>	createDumpFile_ = true;
81	>	#ifdef HAVE_LIBZ
82	>	if (needCompression_) {
83	>	filename_ += ".gz";
84	>	eorFilename_ += ".gz";
85	>	}
86	>	#endif
87	>
88		#ifdef IS_MPI
89
90		if (worldRank == 0) {
91		#endif // is_mpi
92	+
93	+	dumpFile_ = createOStream(filename_);
94
95	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
95	>	if (!dumpFile_) {
96	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
97	>	filename_.c_str());
98	>	painCave.isFatal = 1;
99	>	simError();
100	>	}
101
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	–
102		#ifdef IS_MPI
103
104		}
105
72	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73	–	MPIcheckPoint();
74	–
106		#endif // is_mpi
107
108	<	}
108	>	}
109
110
111	<	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
112	<	: info_(info), filename_(filename){
111	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
112	>	: info_(info), filename_(filename){
113	>
114	>	Globals* simParams = info->getSimParams();
115	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
116	>
117	>	needCompression_   = simParams->getCompressDumpFile();
118	>	needForceVector_   = simParams->getOutputForceVector();
119	>	needParticlePot_   = simParams->getOutputParticlePotential();
120	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
121	>	needElectricField_ = simParams->getOutputElectricField();
122	>
123	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
124	>	doSiteData_ = true;
125	>	} else {
126	>	doSiteData_ = false;
127	>	}
128	>
129	>	createDumpFile_ = true;
130	>	#ifdef HAVE_LIBZ
131	>	if (needCompression_) {
132	>	filename_ += ".gz";
133	>	eorFilename_ += ".gz";
134	>	}
135	>	#endif
136	>
137		#ifdef IS_MPI
138
139		if (worldRank == 0) {
140		#endif // is_mpi
141
142	<	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
143	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
142	>
143	>	dumpFile_ = createOStream(filename_);
144
145	<	if (!dumpFile_) {
146	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
147	<	filename_.c_str());
148	<	painCave.isFatal = 1;
149	<	simError();
150	<	}
145	>	if (!dumpFile_) {
146	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
147	>	filename_.c_str());
148	>	painCave.isFatal = 1;
149	>	simError();
150	>	}
151
152		#ifdef IS_MPI
153
154		}
155
101	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
102	–	MPIcheckPoint();
103	–
156		#endif // is_mpi
157
158	<	}
158	>	}
159	>
160	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
161	>	: info_(info), filename_(filename){
162	>
163	>	Globals* simParams = info->getSimParams();
164	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
165	>
166	>	needCompression_   = simParams->getCompressDumpFile();
167	>	needForceVector_   = simParams->getOutputForceVector();
168	>	needParticlePot_   = simParams->getOutputParticlePotential();
169	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
170	>	needElectricField_ = simParams->getOutputElectricField();
171
172	<	DumpWriter::~DumpWriter() {
172	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
173	>	doSiteData_ = true;
174	>	} else {
175	>	doSiteData_ = false;
176	>	}
177
178	+	#ifdef HAVE_LIBZ
179	+	if (needCompression_) {
180	+	filename_ += ".gz";
181	+	eorFilename_ += ".gz";
182	+	}
183	+	#endif
184	+
185		#ifdef IS_MPI
186	<
186	>
187		if (worldRank == 0) {
188		#endif // is_mpi
189	+
190	+	createDumpFile_ = writeDumpFile;
191	+	if (createDumpFile_) {
192	+	dumpFile_ = createOStream(filename_);
193	+
194	+	if (!dumpFile_) {
195	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
196	+	filename_.c_str());
197	+	painCave.isFatal = 1;
198	+	simError();
199	+	}
200	+	}
201	+	#ifdef IS_MPI
202	+
203	+	}
204
205	<	dumpFile_.close();
205	>
206	>	#endif // is_mpi
207	>
208	>	}
209
210	+	DumpWriter::~DumpWriter() {
211	+
212		#ifdef IS_MPI
213
214	+	if (worldRank == 0) {
215	+	#endif // is_mpi
216	+	if (createDumpFile_){
217	+	writeClosing(*dumpFile_);
218	+	delete dumpFile_;
219	+	}
220	+	#ifdef IS_MPI
221	+
222		}
223
224		#endif // is_mpi
225
226	<	}
226	>	}
227
228	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
228	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
229
230	<	double currentTime;
231	<	Mat3x3d hmat;
232	<	double chi;
233	<	double integralOfChiDt;
234	<	Mat3x3d eta;
230	>	char buffer[1024];
231	>
232	>	os << "    <FrameData>\n";
233	>
234	>	RealType currentTime = s->getTime();
235	>
236	>	if (isinf(currentTime) || isnan(currentTime)) {
237	>	sprintf( painCave.errMsg,
238	>	"DumpWriter detected a numerical error writing the time");
239	>	painCave.isFatal = 1;
240	>	simError();
241	>	}
242
243	<	currentTime = s->getTime();
243	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
244	>	os << buffer;
245	>
246	>	Mat3x3d hmat;
247		hmat = s->getHmat();
248	<	chi = s->getChi();
249	<	integralOfChiDt = s->getIntegralOfChiDt();
250	<	eta = s->getEta();
248	>
249	>	for (unsigned int i = 0; i < 3; i++) {
250	>	for (unsigned int j = 0; j < 3; j++) {
251	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
252	>	sprintf( painCave.errMsg,
253	>	"DumpWriter detected a numerical error writing the box");
254	>	painCave.isFatal = 1;
255	>	simError();
256	>	}
257	>	}
258	>	}
259
260	<	os << currentTime << ";\t"
261	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
262	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
263	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
260	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
261	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
262	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
263	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
264	>	os << buffer;
265
266	<	//write out additional parameters, such as chi and eta
266	>	pair<RealType, RealType> thermostat = s->getThermostat();
267
268	<	os << chi << "\t" << integralOfChiDt << "\t;";
268	>	if (isinf(thermostat.first)  || isnan(thermostat.first) ||
269	>	isinf(thermostat.second) || isnan(thermostat.second)) {
270	>	sprintf( painCave.errMsg,
271	>	"DumpWriter detected a numerical error writing the thermostat");
272	>	painCave.isFatal = 1;
273	>	simError();
274	>	}
275	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
276	>	thermostat.second);
277	>	os << buffer;
278
279	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
280	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
150	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
151	<
152	<	os << "\n";
153	<	}
279	>	Mat3x3d eta;
280	>	eta = s->getBarostat();
281
282	<	void DumpWriter::writeFrame(std::ostream& os) {
283	<	const int BUFFERSIZE = 2000;
284	<	const int MINIBUFFERSIZE = 100;
285	<
286	<	char tempBuffer[BUFFERSIZE];
287	<	char writeLine[BUFFERSIZE];
282	>	for (unsigned int i = 0; i < 3; i++) {
283	>	for (unsigned int j = 0; j < 3; j++) {
284	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
285	>	sprintf( painCave.errMsg,
286	>	"DumpWriter detected a numerical error writing the barostat");
287	>	painCave.isFatal = 1;
288	>	simError();
289	>	}
290	>	}
291	>	}
292
293	<	Quat4d q;
294	<	Vector3d ji;
295	<	Vector3d pos;
296	<	Vector3d vel;
293	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
294	>	eta(0, 0), eta(1, 0), eta(2, 0),
295	>	eta(0, 1), eta(1, 1), eta(2, 1),
296	>	eta(0, 2), eta(1, 2), eta(2, 2));
297	>	os << buffer;
298
299	+	os << "    </FrameData>\n";
300	+	}
301	+
302	+	void DumpWriter::writeFrame(std::ostream& os) {
303	+
304	+	#ifdef IS_MPI
305	+	MPI_Status istatus;
306	+	#endif
307	+
308		Molecule* mol;
309	<	StuntDouble* integrableObject;
309	>	StuntDouble* sd;
310		SimInfo::MoleculeIterator mi;
311		Molecule::IntegrableObjectIterator ii;
312	<
313	<	int nTotObjects;
173	<	nTotObjects = info_->getNGlobalIntegrableObjects();
312	>	RigidBody::AtomIterator ai;
313	>	Atom* atom;
314
315		#ifndef IS_MPI
316	+	os << "  <Snapshot>\n";
317	+
318	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
319
320	<
178	<	os << nTotObjects << "\n";
179	<
180	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
181	<
320	>	os << "    <StuntDoubles>\n";
321		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
322
323	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
324	<	integrableObject = mol->nextIntegrableObject(ii)) {
325	<
323	>
324	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
325	>	sd = mol->nextIntegrableObject(ii)) {
326	>	os << prepareDumpLine(sd);
327	>
328	>	}
329	>	}
330	>	os << "    </StuntDoubles>\n";
331
332	<	pos = integrableObject->getPos();
333	<	vel = integrableObject->getVel();
332	>	if (doSiteData_) {
333	>	os << "    <SiteData>\n";
334	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
335	>
336	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
337	>	sd = mol->nextIntegrableObject(ii)) {
338
339	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
340	<	integrableObject->getType().c_str(),
341	<	pos[0], pos[1], pos[2],
194	<	vel[0], vel[1], vel[2]);
339	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
340	>	// do one for the IO itself
341	>	os << prepareSiteLine(sd, ioIndex, 0);
342
343	<	strcpy(writeLine, tempBuffer);
344	<
345	<	if (integrableObject->isDirectional()) {
346	<	q = integrableObject->getQ();
347	<	ji = integrableObject->getJ();
348	<
349	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
350	<	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");
343	>	if (sd->isRigidBody()) {
344	>
345	>	RigidBody* rb = static_cast<RigidBody*>(sd);
346	>	int siteIndex = 0;
347	>	for (atom = rb->beginAtom(ai); atom != NULL;
348	>	atom = rb->nextAtom(ai)) {
349	>	os << prepareSiteLine(atom, ioIndex, siteIndex);
350	>	siteIndex++;
351		}
352	<
210	<	os << writeLine;
211	<
352	>	}
353		}
354	+	}
355	+	os << "    </SiteData>\n";
356		}
357	+	os << "  </Snapshot>\n";
358
359		os.flush();
360	<	#else // is_mpi
361	<	/*********************************************************************
362	<	* Documentation?  You want DOCUMENTATION?
363	<	*
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	<	*********************************************************************/
253	<	const int masterNode = 0;
360	>	#else
361	>	//every node prepares the dump lines for integrable objects belong to itself
362	>	std::string buffer;
363	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
364
255	–	int * potatoes;
256	–	int myPotato;
257	–	int nProc;
258	–	int which_node;
259	–	double atomData[13];
260	–	int isDirectional;
261	–	char MPIatomTypeString[MINIBUFFERSIZE];
262	–	int msgLen; // the length of message actually recieved at master nodes
263	–	int haveError;
264	–	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);
365
366	<	if (flag) {
367	<	MAXTAG = *tagub;
368	<	} else {
369	<	MAXTAG = 32767;
366	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
367	>	sd = mol->nextIntegrableObject(ii)) {
368	>	buffer += prepareDumpLine(sd);
369	>	}
370		}
371	+
372	+	const int masterNode = 0;
373	+	int nProc;
374	+	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
375	+	if (worldRank == masterNode) {
376	+	os << "  <Snapshot>\n";
377	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
378	+	os << "    <StuntDoubles>\n";
379	+
380	+	os << buffer;
381
382	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
382	>	for (int i = 1; i < nProc; ++i) {
383
384	<	// Node 0 needs a list of the magic potatoes for each processor;
384	>	// receive the length of the string buffer that was
385	>	// prepared by processor i
386
387	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
388	<	potatoes = new int[nProc];
389	<
390	<	//write out the comment lines
391	<	for(int i = 0; i < nProc; i++) {
392	<	potatoes[i] = 0;
387	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
388	>	int recvLength;
389	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
390	>	char* recvBuffer = new char[recvLength];
391	>	if (recvBuffer == NULL) {
392	>	} else {
393	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
394	>	os << recvBuffer;
395	>	delete [] recvBuffer;
396		}
397	+	}
398	+	os << "    </StuntDoubles>\n";
399	+
400	+	os << "  </Snapshot>\n";
401	+	os.flush();
402	+	} else {
403	+	int sendBufferLength = buffer.size() + 1;
404	+	int myturn = 0;
405	+	for (int i = 1; i < nProc; ++i){
406	+	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
407	+	if (myturn == worldRank){
408	+	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
409	+	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
410	+	}
411	+	}
412	+	}
413
414	+	#endif // is_mpi
415
416	<	os << nTotObjects << "\n";
293	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
416	>	}
417
418	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
418	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
419	>
420	>	int index = sd->getGlobalIntegrableObjectIndex();
421	>	std::string type("pv");
422	>	std::string line;
423	>	char tempBuffer[4096];
424
425	<	// Get the Node number which has this atom;
425	>	Vector3d pos;
426	>	Vector3d vel;
427	>	pos = sd->getPos();
428
429	<	which_node = info_->getMolToProc(i);
429	>	if (isinf(pos[0]) || isnan(pos[0]) ||
430	>	isinf(pos[1]) || isnan(pos[1]) ||
431	>	isinf(pos[2]) || isnan(pos[2]) ) {
432	>	sprintf( painCave.errMsg,
433	>	"DumpWriter detected a numerical error writing the position"
434	>	" for object %d", index);
435	>	painCave.isFatal = 1;
436	>	simError();
437	>	}
438
439	<	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:
439	>	vel = sd->getVel();
440
441	<	potatoes[which_node] = 0;
442	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
443	<	MPI_COMM_WORLD);
444	<	}
441	>	if (isinf(vel[0]) || isnan(vel[0]) ||
442	>	isinf(vel[1]) || isnan(vel[1]) ||
443	>	isinf(vel[2]) || isnan(vel[2]) ) {
444	>	sprintf( painCave.errMsg,
445	>	"DumpWriter detected a numerical error writing the velocity"
446	>	" for object %d", index);
447	>	painCave.isFatal = 1;
448	>	simError();
449	>	}
450
451	<	myPotato = potatoes[which_node];
451	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
452	>	pos[0], pos[1], pos[2],
453	>	vel[0], vel[1], vel[2]);
454	>	line += tempBuffer;
455
456	<	//recieve the number of integrableObject in current molecule
457	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
458	<	MPI_COMM_WORLD, &istatus);
459	<	myPotato++;
456	>	if (sd->isDirectional()) {
457	>	type += "qj";
458	>	Quat4d q;
459	>	Vector3d ji;
460	>	q = sd->getQ();
461
462	<	for(int l = 0; l < nCurObj; l++) {
463	<	if (potatoes[which_node] + 2 >= MAXTAG) {
464	<	// The potato was going to exceed the maximum value,
465	<	// so wrap this processor potato back to 0:
462	>	if (isinf(q[0]) || isnan(q[0]) ||
463	>	isinf(q[1]) || isnan(q[1]) ||
464	>	isinf(q[2]) || isnan(q[2]) ||
465	>	isinf(q[3]) || isnan(q[3]) ) {
466	>	sprintf( painCave.errMsg,
467	>	"DumpWriter detected a numerical error writing the quaternion"
468	>	" for object %d", index);
469	>	painCave.isFatal = 1;
470	>	simError();
471	>	}
472
473	<	potatoes[which_node] = 0;
324	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
325	<	0, MPI_COMM_WORLD);
326	<	}
473	>	ji = sd->getJ();
474
475	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
476	<	which_node, myPotato, MPI_COMM_WORLD,
477	<	&istatus);
475	>	if (isinf(ji[0]) || isnan(ji[0]) ||
476	>	isinf(ji[1]) || isnan(ji[1]) ||
477	>	isinf(ji[2]) || isnan(ji[2]) ) {
478	>	sprintf( painCave.errMsg,
479	>	"DumpWriter detected a numerical error writing the angular"
480	>	" momentum for object %d", index);
481	>	painCave.isFatal = 1;
482	>	simError();
483	>	}
484
485	<	myPotato++;
485	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
486	>	q[0], q[1], q[2], q[3],
487	>	ji[0], ji[1], ji[2]);
488	>	line += tempBuffer;
489	>	}
490
491	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
492	<	MPI_COMM_WORLD, &istatus);
493	<	myPotato++;
491	>	if (needForceVector_) {
492	>	type += "f";
493	>	Vector3d frc = sd->getFrc();
494	>	if (isinf(frc[0]) || isnan(frc[0]) ||
495	>	isinf(frc[1]) || isnan(frc[1]) ||
496	>	isinf(frc[2]) || isnan(frc[2]) ) {
497	>	sprintf( painCave.errMsg,
498	>	"DumpWriter detected a numerical error writing the force"
499	>	" for object %d", index);
500	>	painCave.isFatal = 1;
501	>	simError();
502	>	}
503	>	sprintf(tempBuffer, " %13e %13e %13e",
504	>	frc[0], frc[1], frc[2]);
505	>	line += tempBuffer;
506	>
507	>	if (sd->isDirectional()) {
508	>	type += "t";
509	>	Vector3d trq = sd->getTrq();
510	>	if (isinf(trq[0]) || isnan(trq[0]) ||
511	>	isinf(trq[1]) || isnan(trq[1]) ||
512	>	isinf(trq[2]) || isnan(trq[2]) ) {
513	>	sprintf( painCave.errMsg,
514	>	"DumpWriter detected a numerical error writing the torque"
515	>	" for object %d", index);
516	>	painCave.isFatal = 1;
517	>	simError();
518	>	}
519	>	sprintf(tempBuffer, " %13e %13e %13e",
520	>	trq[0], trq[1], trq[2]);
521	>	line += tempBuffer;
522	>	}
523	>	}
524
525	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
525	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
526	>	return std::string(tempBuffer);
527	>	}
528
529	<	if (msgLen == 13)
530	<	isDirectional = 1;
342	<	else
343	<	isDirectional = 0;
529	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
530	>
531
532	<	// If we've survived to here, format the line:
532	>	std::string id;
533	>	std::string type;
534	>	std::string line;
535	>	char tempBuffer[4096];
536
537	<	if (!isDirectional) {
538	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
539	<	MPIatomTypeString, atomData[0],
540	<	atomData[1], atomData[2],
541	<	atomData[3], atomData[4],
542	<	atomData[5]);
537	>	if (sd->isRigidBody()) {
538	>	sprintf(tempBuffer, "%10d           ", ioIndex);
539	>	id = std::string(tempBuffer);
540	>	} else {
541	>	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
542	>	id = std::string(tempBuffer);
543	>	}
544	>
545	>	if (needFlucQ_) {
546	>	type += "cw";
547	>	RealType fqPos = sd->getFlucQPos();
548	>	if (isinf(fqPos) || isnan(fqPos) ) {
549	>	sprintf( painCave.errMsg,
550	>	"DumpWriter detected a numerical error writing the"
551	>	" fluctuating charge for object %s", id.c_str());
552	>	painCave.isFatal = 1;
553	>	simError();
554	>	}
555	>	sprintf(tempBuffer, " %13e ", fqPos);
556	>	line += tempBuffer;
557	>
558	>	RealType fqVel = sd->getFlucQVel();
559	>	if (isinf(fqVel) || isnan(fqVel) ) {
560	>	sprintf( painCave.errMsg,
561	>	"DumpWriter detected a numerical error writing the"
562	>	" fluctuating charge velocity for object %s", id.c_str());
563	>	painCave.isFatal = 1;
564	>	simError();
565	>	}
566	>	sprintf(tempBuffer, " %13e ", fqVel);
567	>	line += tempBuffer;
568
569	<	strcat(writeLine,
570	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
571	<	} else {
572	<	sprintf(writeLine,
573	<	"%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",
574	<	MPIatomTypeString,
575	<	atomData[0],
576	<	atomData[1],
577	<	atomData[2],
578	<	atomData[3],
579	<	atomData[4],
580	<	atomData[5],
581	<	atomData[6],
582	<	atomData[7],
368	<	atomData[8],
369	<	atomData[9],
370	<	atomData[10],
371	<	atomData[11],
372	<	atomData[12]);
373	<	}
569	>	if (needForceVector_) {
570	>	type += "g";
571	>	RealType fqFrc = sd->getFlucQFrc();
572	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
573	>	sprintf( painCave.errMsg,
574	>	"DumpWriter detected a numerical error writing the"
575	>	" fluctuating charge force for object %s", id.c_str());
576	>	painCave.isFatal = 1;
577	>	simError();
578	>	}
579	>	sprintf(tempBuffer, " %13e ", fqFrc);
580	>	line += tempBuffer;
581	>	}
582	>	}
583
584	<	os << writeLine;
584	>	if (needElectricField_) {
585	>	type += "e";
586	>	Vector3d eField= sd->getElectricField();
587	>	if (isinf(eField[0]) || isnan(eField[0]) ||
588	>	isinf(eField[1]) || isnan(eField[1]) ||
589	>	isinf(eField[2]) || isnan(eField[2]) ) {
590	>	sprintf( painCave.errMsg,
591	>	"DumpWriter detected a numerical error writing the electric"
592	>	" field for object %s", id.c_str());
593	>	painCave.isFatal = 1;
594	>	simError();
595	>	}
596	>	sprintf(tempBuffer, " %13e %13e %13e",
597	>	eField[0], eField[1], eField[2]);
598	>	line += tempBuffer;
599	>	}
600
377	–	} // end for(int l =0)
601
602	<	potatoes[which_node] = myPotato;
603	<	} else { //master node has current molecule
602	>	if (needParticlePot_) {
603	>	type += "u";
604	>	RealType particlePot = sd->getParticlePot();
605	>	if (isinf(particlePot) || isnan(particlePot)) {
606	>	sprintf( painCave.errMsg,
607	>	"DumpWriter detected a numerical error writing the particle "
608	>	" potential for object %s", id.c_str());
609	>	painCave.isFatal = 1;
610	>	simError();
611	>	}
612	>	sprintf(tempBuffer, " %13e", particlePot);
613	>	line += tempBuffer;
614	>	}
615	>
616
617	<	mol = info_->getMoleculeByGlobalIndex(i);
617	>	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
618	>	return std::string(tempBuffer);
619	>	}
620
621	<	if (mol == NULL) {
622	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
623	<	painCave.isFatal = 1;
387	<	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	<	}
621	>	void DumpWriter::writeDump() {
622	>	writeFrame(*dumpFile_);
623	>	}
624
625	<	// If we've survived to here, format the line:
625	>	void DumpWriter::writeEor() {
626	>	std::ostream* eorStream;
627	>
628	>	#ifdef IS_MPI
629	>	if (worldRank == 0) {
630	>	#endif // is_mpi
631
632	<	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]);
632	>	eorStream = createOStream(eorFilename_);
633
634	<	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	<
565	<	}
566	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
567	<	MPIcheckPoint();
634	>	#ifdef IS_MPI
635		}
636	+	#endif // is_mpi
637
638	<	#endif // is_mpi
638	>	writeFrame(*eorStream);
639
572	–	}
573	–
574	–	void DumpWriter::writeDump() {
575	–	writeFrame(dumpFile_);
576	–
577	–	}
578	–
579	–	void DumpWriter::writeEor() {
580	–	std::ofstream eorStream;
581	–
640		#ifdef IS_MPI
641		if (worldRank == 0) {
642		#endif // is_mpi
643	<
644	<	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	<	}
593	<
643	>	writeClosing(*eorStream);
644	>	delete eorStream;
645		#ifdef IS_MPI
646		}
647	<	#endif // is_mpi
647	>	#endif // is_mpi
648
649	<	writeFrame(eorStream);
599	<	}
649	>	}
650
651
652	<	void DumpWriter::writeDumpAndEor() {
603	<	std::ofstream eorStream;
652	>	void DumpWriter::writeDumpAndEor() {
653		std::vector<std::streambuf*> buffers;
654	+	std::ostream* eorStream;
655		#ifdef IS_MPI
656		if (worldRank == 0) {
657		#endif // is_mpi
658
659	<	buffers.push_back(dumpFile_.rdbuf());
659	>	buffers.push_back(dumpFile_->rdbuf());
660
661	<	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	<	}
661	>	eorStream = createOStream(eorFilename_);
662
663	<	buffers.push_back(eorStream.rdbuf());
663	>	buffers.push_back(eorStream->rdbuf());
664
665		#ifdef IS_MPI
666		}
#	Line 626 | Line 670 | void DumpWriter::writeDumpAndEor() {
670		std::ostream os(&tbuf);
671
672		writeFrame(os);
673	+
674	+	#ifdef IS_MPI
675	+	if (worldRank == 0) {
676	+	#endif // is_mpi
677	+	writeClosing(*eorStream);
678	+	delete eorStream;
679	+	#ifdef IS_MPI
680	+	}
681	+	#endif // is_mpi
682
683	<	}
683	>	}
684
685	+	std::ostream* DumpWriter::createOStream(const std::string& filename) {
686
687	+	std::ostream* newOStream;
688	+	#ifdef HAVE_ZLIB
689	+	if (needCompression_) {
690	+	newOStream = new ogzstream(filename.c_str());
691	+	} else {
692	+	newOStream = new std::ofstream(filename.c_str());
693	+	}
694	+	#else
695	+	newOStream = new std::ofstream(filename.c_str());
696	+	#endif
697	+	//write out MetaData first
698	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
699	+	(*newOStream) << "  <MetaData>" << std::endl;
700	+	(*newOStream) << info_->getRawMetaData();
701	+	(*newOStream) << "  </MetaData>" << std::endl;
702	+	return newOStream;
703	+	}
704
705	<	}//end namespace oopse
705	>	void DumpWriter::writeClosing(std::ostream& os) {
706	>
707	>	os << "</OpenMD>\n";
708	>	os.flush();
709	>	}
710	>
711	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 395 by tim, Thu Mar 3 14:40:20 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

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