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

Comparing:
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 1752 by gezelter, Sun Jun 10 14:05:02 2012 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
1	>	/*
2	>	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include "io/DumpWriter.hpp"
44		#include "primitives/Molecule.hpp"
45		#include "utils/simError.h"
46		#include "io/basic_teebuf.hpp"
47	+	#include "io/gzstream.hpp"
48	+	#include "io/Globals.hpp"
49	+
50	+
51		#ifdef IS_MPI
52		#include <mpi.h>
53		#endif //is_mpi
54
55	<	namespace oopse {
55	>	using namespace std;
56	>	namespace OpenMD {
57
58	<	DumpWriter::DumpWriter(SimInfo* info)
59	<	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
58	>	DumpWriter::DumpWriter(SimInfo* info)
59	>	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
60	>
61	>	Globals* simParams = info->getSimParams();
62	>	needCompression_   = simParams->getCompressDumpFile();
63	>	needForceVector_   = simParams->getOutputForceVector();
64	>	needParticlePot_   = simParams->getOutputParticlePotential();
65	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
66	>	needElectricField_ = simParams->getOutputElectricField();
67	>
68	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
69	>	doSiteData_ = true;
70	>	} else {
71	>	doSiteData_ = false;
72	>	}
73	>
74	>	createDumpFile_ = true;
75	>	#ifdef HAVE_LIBZ
76	>	if (needCompression_) {
77	>	filename_ += ".gz";
78	>	eorFilename_ += ".gz";
79	>	}
80	>	#endif
81	>
82		#ifdef IS_MPI
83
84		if (worldRank == 0) {
85		#endif // is_mpi
86	+
87	+	dumpFile_ = createOStream(filename_);
88
89	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
89	>	if (!dumpFile_) {
90	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
91	>	filename_.c_str());
92	>	painCave.isFatal = 1;
93	>	simError();
94	>	}
95
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	–
96		#ifdef IS_MPI
97
98		}
99
72	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73	–	MPIcheckPoint();
74	–
100		#endif // is_mpi
101
102	<	}
102	>	}
103
104
105	<	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
106	<	: info_(info), filename_(filename){
105	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
106	>	: info_(info), filename_(filename){
107	>
108	>	Globals* simParams = info->getSimParams();
109	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
110	>
111	>	needCompression_   = simParams->getCompressDumpFile();
112	>	needForceVector_   = simParams->getOutputForceVector();
113	>	needParticlePot_   = simParams->getOutputParticlePotential();
114	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
115	>	needElectricField_ = simParams->getOutputElectricField();
116	>
117	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
118	>	doSiteData_ = true;
119	>	} else {
120	>	doSiteData_ = false;
121	>	}
122	>
123	>	createDumpFile_ = true;
124	>	#ifdef HAVE_LIBZ
125	>	if (needCompression_) {
126	>	filename_ += ".gz";
127	>	eorFilename_ += ".gz";
128	>	}
129	>	#endif
130	>
131		#ifdef IS_MPI
132
133		if (worldRank == 0) {
134		#endif // is_mpi
135
136	<	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
137	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
136	>
137	>	dumpFile_ = createOStream(filename_);
138
139	<	if (!dumpFile_) {
140	<	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
141	<	filename_.c_str());
142	<	painCave.isFatal = 1;
143	<	simError();
144	<	}
139	>	if (!dumpFile_) {
140	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
141	>	filename_.c_str());
142	>	painCave.isFatal = 1;
143	>	simError();
144	>	}
145
146		#ifdef IS_MPI
147
148		}
149
101	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
102	–	MPIcheckPoint();
103	–
150		#endif // is_mpi
151
152	<	}
152	>	}
153	>
154	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
155	>	: info_(info), filename_(filename){
156	>
157	>	Globals* simParams = info->getSimParams();
158	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
159	>
160	>	needCompression_   = simParams->getCompressDumpFile();
161	>	needForceVector_   = simParams->getOutputForceVector();
162	>	needParticlePot_   = simParams->getOutputParticlePotential();
163	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
164	>	needElectricField_ = simParams->getOutputElectricField();
165
166	<	DumpWriter::~DumpWriter() {
166	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
167	>	doSiteData_ = true;
168	>	} else {
169	>	doSiteData_ = false;
170	>	}
171
172	+	#ifdef HAVE_LIBZ
173	+	if (needCompression_) {
174	+	filename_ += ".gz";
175	+	eorFilename_ += ".gz";
176	+	}
177	+	#endif
178	+
179		#ifdef IS_MPI
180	<
180	>
181		if (worldRank == 0) {
182		#endif // is_mpi
183	+
184	+	createDumpFile_ = writeDumpFile;
185	+	if (createDumpFile_) {
186	+	dumpFile_ = createOStream(filename_);
187	+
188	+	if (!dumpFile_) {
189	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
190	+	filename_.c_str());
191	+	painCave.isFatal = 1;
192	+	simError();
193	+	}
194	+	}
195	+	#ifdef IS_MPI
196	+
197	+	}
198
199	<	dumpFile_.close();
199	>
200	>	#endif // is_mpi
201	>
202	>	}
203
204	+	DumpWriter::~DumpWriter() {
205	+
206		#ifdef IS_MPI
207
208	+	if (worldRank == 0) {
209	+	#endif // is_mpi
210	+	if (createDumpFile_){
211	+	writeClosing(*dumpFile_);
212	+	delete dumpFile_;
213	+	}
214	+	#ifdef IS_MPI
215	+
216		}
217
218		#endif // is_mpi
219
220	<	}
220	>	}
221
222	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
222	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
223
224	<	double currentTime;
225	<	Mat3x3d hmat;
226	<	double chi;
227	<	double integralOfChiDt;
228	<	Mat3x3d eta;
224	>	char buffer[1024];
225	>
226	>	os << "    <FrameData>\n";
227	>
228	>	RealType currentTime = s->getTime();
229	>
230	>	if (isinf(currentTime) || isnan(currentTime)) {
231	>	sprintf( painCave.errMsg,
232	>	"DumpWriter detected a numerical error writing the time");
233	>	painCave.isFatal = 1;
234	>	simError();
235	>	}
236
237	<	currentTime = s->getTime();
237	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
238	>	os << buffer;
239	>
240	>	Mat3x3d hmat;
241		hmat = s->getHmat();
242	<	chi = s->getChi();
243	<	integralOfChiDt = s->getIntegralOfChiDt();
244	<	eta = s->getEta();
242	>
243	>	for (unsigned int i = 0; i < 3; i++) {
244	>	for (unsigned int j = 0; j < 3; j++) {
245	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
246	>	sprintf( painCave.errMsg,
247	>	"DumpWriter detected a numerical error writing the box");
248	>	painCave.isFatal = 1;
249	>	simError();
250	>	}
251	>	}
252	>	}
253
254	<	os << currentTime << ";\t"
255	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
256	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
257	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
254	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
255	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
256	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
257	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
258	>	os << buffer;
259
260	<	//write out additional parameters, such as chi and eta
260	>	RealType chi = s->getChi();
261	>	RealType integralOfChiDt = s->getIntegralOfChiDt();
262	>	if (isinf(chi) || isnan(chi) ||
263	>	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
264	>	sprintf( painCave.errMsg,
265	>	"DumpWriter detected a numerical error writing the thermostat");
266	>	painCave.isFatal = 1;
267	>	simError();
268	>	}
269	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
270	>	os << buffer;
271
272	<	os << chi << "\t" << integralOfChiDt << "\t;";
272	>	Mat3x3d eta;
273	>	eta = s->getEta();
274
275	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
276	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
277	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
278	<
279	<	os << "\n";
280	<	}
275	>	for (unsigned int i = 0; i < 3; i++) {
276	>	for (unsigned int j = 0; j < 3; j++) {
277	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
278	>	sprintf( painCave.errMsg,
279	>	"DumpWriter detected a numerical error writing the barostat");
280	>	painCave.isFatal = 1;
281	>	simError();
282	>	}
283	>	}
284	>	}
285
286	<	void DumpWriter::writeFrame(std::ostream& os) {
287	<	const int BUFFERSIZE = 2000;
288	<	const int MINIBUFFERSIZE = 100;
289	<
290	<	char tempBuffer[BUFFERSIZE];
160	<	char writeLine[BUFFERSIZE];
286	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
287	>	eta(0, 0), eta(1, 0), eta(2, 0),
288	>	eta(0, 1), eta(1, 1), eta(2, 1),
289	>	eta(0, 2), eta(1, 2), eta(2, 2));
290	>	os << buffer;
291
292	<	Quat4d q;
293	<	Vector3d ji;
164	<	Vector3d pos;
165	<	Vector3d vel;
292	>	os << "    </FrameData>\n";
293	>	}
294
295	+	void DumpWriter::writeFrame(std::ostream& os) {
296	+
297	+	#ifdef IS_MPI
298	+	MPI_Status istatus;
299	+	#endif
300	+
301		Molecule* mol;
302		StuntDouble* integrableObject;
303		SimInfo::MoleculeIterator mi;
304		Molecule::IntegrableObjectIterator ii;
305	<
306	<	int nTotObjects;
173	<	nTotObjects = info_->getNGlobalIntegrableObjects();
305	>	RigidBody::AtomIterator ai;
306	>	Atom* atom;
307
308		#ifndef IS_MPI
309	+	os << "  <Snapshot>\n";
310	+
311	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
312
313	<
178	<	os << nTotObjects << "\n";
179	<
180	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
181	<
313	>	os << "    <StuntDoubles>\n";
314		for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
315
316	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
317	<	integrableObject = mol->nextIntegrableObject(ii)) {
318	<
316	>
317	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
318	>	integrableObject = mol->nextIntegrableObject(ii)) {
319	>	os << prepareDumpLine(integrableObject);
320	>
321	>	}
322	>	}
323	>	os << "    </StuntDoubles>\n";
324
325	<	pos = integrableObject->getPos();
326	<	vel = integrableObject->getVel();
325	>	if (doSiteData_) {
326	>	os << "    <SiteData>\n";
327	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
328	>
329	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
330	>	integrableObject = mol->nextIntegrableObject(ii)) {
331
332	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
333	<	integrableObject->getType().c_str(),
334	<	pos[0], pos[1], pos[2],
194	<	vel[0], vel[1], vel[2]);
332	>	int ioIndex = integrableObject->getGlobalIntegrableObjectIndex();
333	>	// do one for the IO itself
334	>	os << prepareSiteLine(integrableObject, ioIndex, 0);
335
336	<	strcpy(writeLine, tempBuffer);
337	<
338	<	if (integrableObject->isDirectional()) {
339	<	q = integrableObject->getQ();
340	<	ji = integrableObject->getJ();
341	<
342	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
343	<	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");
336	>	if (integrableObject->isRigidBody()) {
337	>
338	>	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
339	>	int siteIndex = 0;
340	>	for (atom = rb->beginAtom(ai); atom != NULL;
341	>	atom = rb->nextAtom(ai)) {
342	>	os << prepareSiteLine(atom, ioIndex, siteIndex);
343	>	siteIndex++;
344		}
345	<
210	<	os << writeLine;
211	<
345	>	}
346		}
347	+	}
348	+	os << "    </SiteData>\n";
349		}
350	+	os << "  </Snapshot>\n";
351
352		os.flush();
353	<	#else // is_mpi
354	<	/*********************************************************************
355	<	* Documentation?  You want DOCUMENTATION?
356	<	*
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;
353	>	#else
354	>	//every node prepares the dump lines for integrable objects belong to itself
355	>	std::string buffer;
356	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
357
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);
358
359	<	if (flag) {
360	<	MAXTAG = *tagub;
361	<	} else {
362	<	MAXTAG = 32767;
359	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
360	>	integrableObject = mol->nextIntegrableObject(ii)) {
361	>	buffer += prepareDumpLine(integrableObject);
362	>	}
363		}
364	+
365	+	const int masterNode = 0;
366	+	int nProc;
367	+	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
368	+	if (worldRank == masterNode) {
369	+	os << "  <Snapshot>\n";
370	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
371	+	os << "    <StuntDoubles>\n";
372	+
373	+	os << buffer;
374
375	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
375	>	for (int i = 1; i < nProc; ++i) {
376
377	<	// Node 0 needs a list of the magic potatoes for each processor;
377	>	// receive the length of the string buffer that was
378	>	// prepared by processor i
379
380	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
381	<	potatoes = new int[nProc];
382	<
383	<	//write out the comment lines
384	<	for(int i = 0; i < nProc; i++) {
385	<	potatoes[i] = 0;
380	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
381	>	int recvLength;
382	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
383	>	char* recvBuffer = new char[recvLength];
384	>	if (recvBuffer == NULL) {
385	>	} else {
386	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
387	>	os << recvBuffer;
388	>	delete [] recvBuffer;
389		}
390	+	}
391	+	os << "    </StuntDoubles>\n";
392	+
393	+	os << "  </Snapshot>\n";
394	+	os.flush();
395	+	} else {
396	+	int sendBufferLength = buffer.size() + 1;
397	+	int myturn = 0;
398	+	for (int i = 1; i < nProc; ++i){
399	+	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
400	+	if (myturn == worldRank){
401	+	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
402	+	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
403	+	}
404	+	}
405	+	}
406
407	+	#endif // is_mpi
408
409	<	os << nTotObjects << "\n";
293	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
409	>	}
410
411	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
411	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
412	>
413	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
414	>	std::string type("pv");
415	>	std::string line;
416	>	char tempBuffer[4096];
417
418	<	// Get the Node number which has this atom;
418	>	Vector3d pos;
419	>	Vector3d vel;
420	>	pos = integrableObject->getPos();
421
422	<	which_node = info_->getMolToProc(i);
422	>	if (isinf(pos[0]) || isnan(pos[0]) ||
423	>	isinf(pos[1]) || isnan(pos[1]) ||
424	>	isinf(pos[2]) || isnan(pos[2]) ) {
425	>	sprintf( painCave.errMsg,
426	>	"DumpWriter detected a numerical error writing the position"
427	>	" for object %d", index);
428	>	painCave.isFatal = 1;
429	>	simError();
430	>	}
431
432	<	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:
432	>	vel = integrableObject->getVel();
433
434	<	potatoes[which_node] = 0;
435	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
436	<	MPI_COMM_WORLD);
437	<	}
434	>	if (isinf(vel[0]) || isnan(vel[0]) ||
435	>	isinf(vel[1]) || isnan(vel[1]) ||
436	>	isinf(vel[2]) || isnan(vel[2]) ) {
437	>	sprintf( painCave.errMsg,
438	>	"DumpWriter detected a numerical error writing the velocity"
439	>	" for object %d", index);
440	>	painCave.isFatal = 1;
441	>	simError();
442	>	}
443
444	<	myPotato = potatoes[which_node];
444	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
445	>	pos[0], pos[1], pos[2],
446	>	vel[0], vel[1], vel[2]);
447	>	line += tempBuffer;
448
449	<	//recieve the number of integrableObject in current molecule
450	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
451	<	MPI_COMM_WORLD, &istatus);
452	<	myPotato++;
449	>	if (integrableObject->isDirectional()) {
450	>	type += "qj";
451	>	Quat4d q;
452	>	Vector3d ji;
453	>	q = integrableObject->getQ();
454
455	<	for(int l = 0; l < nCurObj; l++) {
456	<	if (potatoes[which_node] + 2 >= MAXTAG) {
457	<	// The potato was going to exceed the maximum value,
458	<	// so wrap this processor potato back to 0:
455	>	if (isinf(q[0]) || isnan(q[0]) ||
456	>	isinf(q[1]) || isnan(q[1]) ||
457	>	isinf(q[2]) || isnan(q[2]) ||
458	>	isinf(q[3]) || isnan(q[3]) ) {
459	>	sprintf( painCave.errMsg,
460	>	"DumpWriter detected a numerical error writing the quaternion"
461	>	" for object %d", index);
462	>	painCave.isFatal = 1;
463	>	simError();
464	>	}
465
466	<	potatoes[which_node] = 0;
324	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
325	<	0, MPI_COMM_WORLD);
326	<	}
466	>	ji = integrableObject->getJ();
467
468	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
469	<	which_node, myPotato, MPI_COMM_WORLD,
470	<	&istatus);
468	>	if (isinf(ji[0]) || isnan(ji[0]) ||
469	>	isinf(ji[1]) || isnan(ji[1]) ||
470	>	isinf(ji[2]) || isnan(ji[2]) ) {
471	>	sprintf( painCave.errMsg,
472	>	"DumpWriter detected a numerical error writing the angular"
473	>	" momentum for object %d", index);
474	>	painCave.isFatal = 1;
475	>	simError();
476	>	}
477
478	<	myPotato++;
478	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
479	>	q[0], q[1], q[2], q[3],
480	>	ji[0], ji[1], ji[2]);
481	>	line += tempBuffer;
482	>	}
483
484	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
485	<	MPI_COMM_WORLD, &istatus);
486	<	myPotato++;
484	>	if (needForceVector_) {
485	>	type += "f";
486	>	Vector3d frc = integrableObject->getFrc();
487	>	if (isinf(frc[0]) || isnan(frc[0]) ||
488	>	isinf(frc[1]) || isnan(frc[1]) ||
489	>	isinf(frc[2]) || isnan(frc[2]) ) {
490	>	sprintf( painCave.errMsg,
491	>	"DumpWriter detected a numerical error writing the force"
492	>	" for object %d", index);
493	>	painCave.isFatal = 1;
494	>	simError();
495	>	}
496	>	sprintf(tempBuffer, " %13e %13e %13e",
497	>	frc[0], frc[1], frc[2]);
498	>	line += tempBuffer;
499	>
500	>	if (integrableObject->isDirectional()) {
501	>	type += "t";
502	>	Vector3d trq = integrableObject->getTrq();
503	>	if (isinf(trq[0]) || isnan(trq[0]) ||
504	>	isinf(trq[1]) || isnan(trq[1]) ||
505	>	isinf(trq[2]) || isnan(trq[2]) ) {
506	>	sprintf( painCave.errMsg,
507	>	"DumpWriter detected a numerical error writing the torque"
508	>	" for object %d", index);
509	>	painCave.isFatal = 1;
510	>	simError();
511	>	}
512	>	sprintf(tempBuffer, " %13e %13e %13e",
513	>	trq[0], trq[1], trq[2]);
514	>	line += tempBuffer;
515	>	}
516	>	}
517
518	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
518	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
519	>	return std::string(tempBuffer);
520	>	}
521
522	<	if (msgLen == 13)
523	<	isDirectional = 1;
342	<	else
343	<	isDirectional = 0;
522	>	std::string DumpWriter::prepareSiteLine(StuntDouble* integrableObject, int ioIndex, int siteIndex) {
523	>
524
525	<	// If we've survived to here, format the line:
525	>	std::string id;
526	>	std::string type;
527	>	std::string line;
528	>	char tempBuffer[4096];
529
530	<	if (!isDirectional) {
531	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
532	<	MPIatomTypeString, atomData[0],
533	<	atomData[1], atomData[2],
534	<	atomData[3], atomData[4],
535	<	atomData[5]);
530	>	if (integrableObject->isRigidBody()) {
531	>	sprintf(tempBuffer, "%10d           ", ioIndex);
532	>	id = std::string(tempBuffer);
533	>	} else {
534	>	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
535	>	id = std::string(tempBuffer);
536	>	}
537	>
538	>	if (needFlucQ_) {
539	>	type += "cw";
540	>	RealType fqPos = integrableObject->getFlucQPos();
541	>	if (isinf(fqPos) || isnan(fqPos) ) {
542	>	sprintf( painCave.errMsg,
543	>	"DumpWriter detected a numerical error writing the"
544	>	" fluctuating charge for object %s", id.c_str());
545	>	painCave.isFatal = 1;
546	>	simError();
547	>	}
548	>	sprintf(tempBuffer, " %13e ", fqPos);
549	>	line += tempBuffer;
550	>
551	>	RealType fqVel = integrableObject->getFlucQVel();
552	>	if (isinf(fqVel) || isnan(fqVel) ) {
553	>	sprintf( painCave.errMsg,
554	>	"DumpWriter detected a numerical error writing the"
555	>	" fluctuating charge velocity for object %s", id.c_str());
556	>	painCave.isFatal = 1;
557	>	simError();
558	>	}
559	>	sprintf(tempBuffer, " %13e ", fqVel);
560	>	line += tempBuffer;
561
562	<	strcat(writeLine,
563	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
564	<	} else {
565	<	sprintf(writeLine,
566	<	"%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",
567	<	MPIatomTypeString,
568	<	atomData[0],
569	<	atomData[1],
570	<	atomData[2],
571	<	atomData[3],
572	<	atomData[4],
573	<	atomData[5],
574	<	atomData[6],
575	<	atomData[7],
368	<	atomData[8],
369	<	atomData[9],
370	<	atomData[10],
371	<	atomData[11],
372	<	atomData[12]);
373	<	}
562	>	if (needForceVector_) {
563	>	type += "g";
564	>	RealType fqFrc = integrableObject->getFlucQFrc();
565	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
566	>	sprintf( painCave.errMsg,
567	>	"DumpWriter detected a numerical error writing the"
568	>	" fluctuating charge force for object %s", id.c_str());
569	>	painCave.isFatal = 1;
570	>	simError();
571	>	}
572	>	sprintf(tempBuffer, " %13e ", fqFrc);
573	>	line += tempBuffer;
574	>	}
575	>	}
576
577	<	os << writeLine;
577	>	if (needElectricField_) {
578	>	type += "e";
579	>	Vector3d eField= integrableObject->getElectricField();
580	>	if (isinf(eField[0]) || isnan(eField[0]) ||
581	>	isinf(eField[1]) || isnan(eField[1]) ||
582	>	isinf(eField[2]) || isnan(eField[2]) ) {
583	>	sprintf( painCave.errMsg,
584	>	"DumpWriter detected a numerical error writing the electric"
585	>	" field for object %s", id.c_str());
586	>	painCave.isFatal = 1;
587	>	simError();
588	>	}
589	>	sprintf(tempBuffer, " %13e %13e %13e",
590	>	eField[0], eField[1], eField[2]);
591	>	line += tempBuffer;
592	>	}
593
377	–	} // end for(int l =0)
594
595	<	potatoes[which_node] = myPotato;
596	<	} else { //master node has current molecule
595	>	if (needParticlePot_) {
596	>	type += "u";
597	>	RealType particlePot = integrableObject->getParticlePot();
598	>	if (isinf(particlePot) || isnan(particlePot)) {
599	>	sprintf( painCave.errMsg,
600	>	"DumpWriter detected a numerical error writing the particle "
601	>	" potential for object %s", id.c_str());
602	>	painCave.isFatal = 1;
603	>	simError();
604	>	}
605	>	sprintf(tempBuffer, " %13e", particlePot);
606	>	line += tempBuffer;
607	>	}
608	>
609
610	<	mol = info_->getMoleculeByGlobalIndex(i);
610	>	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
611	>	return std::string(tempBuffer);
612	>	}
613
614	<	if (mol == NULL) {
615	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
616	<	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	<	}
425	<
426	<	// If we've survived to here, format the line:
614	>	void DumpWriter::writeDump() {
615	>	writeFrame(*dumpFile_);
616	>	}
617
618	<	if (!isDirectional) {
619	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
620	<	integrableObject->getType().c_str(), atomData[0],
621	<	atomData[1], atomData[2],
622	<	atomData[3], atomData[4],
623	<	atomData[5]);
618	>	void DumpWriter::writeEor() {
619	>	std::ostream* eorStream;
620	>
621	>	#ifdef IS_MPI
622	>	if (worldRank == 0) {
623	>	#endif // is_mpi
624
625	<	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	<	}
625	>	eorStream = createOStream(eorFilename_);
626
627	<
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();
627	>	#ifdef IS_MPI
628		}
629	+	#endif // is_mpi
630
631	<	#endif // is_mpi
631	>	writeFrame(*eorStream);
632
572	–	}
573	–
574	–	void DumpWriter::writeDump() {
575	–	writeFrame(dumpFile_);
576	–
577	–	}
578	–
579	–	void DumpWriter::writeEor() {
580	–	std::ofstream eorStream;
581	–
633		#ifdef IS_MPI
634		if (worldRank == 0) {
635		#endif // is_mpi
636	<
637	<	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	<
636	>	writeClosing(*eorStream);
637	>	delete eorStream;
638		#ifdef IS_MPI
639		}
640	<	#endif // is_mpi
640	>	#endif // is_mpi
641
642	<	writeFrame(eorStream);
599	<	}
642	>	}
643
644
645	<	void DumpWriter::writeDumpAndEor() {
603	<	std::ofstream eorStream;
645	>	void DumpWriter::writeDumpAndEor() {
646		std::vector<std::streambuf*> buffers;
647	+	std::ostream* eorStream;
648		#ifdef IS_MPI
649		if (worldRank == 0) {
650		#endif // is_mpi
651
652	<	buffers.push_back(dumpFile_.rdbuf());
652	>	buffers.push_back(dumpFile_->rdbuf());
653
654	<	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	<	}
654	>	eorStream = createOStream(eorFilename_);
655
656	<	buffers.push_back(eorStream.rdbuf());
656	>	buffers.push_back(eorStream->rdbuf());
657
658		#ifdef IS_MPI
659		}
#	Line 626 | Line 663 | void DumpWriter::writeDumpAndEor() {
663		std::ostream os(&tbuf);
664
665		writeFrame(os);
666	+
667	+	#ifdef IS_MPI
668	+	if (worldRank == 0) {
669	+	#endif // is_mpi
670	+	writeClosing(*eorStream);
671	+	delete eorStream;
672	+	#ifdef IS_MPI
673	+	}
674	+	#endif // is_mpi
675
676	<	}
676	>	}
677
678	+	std::ostream* DumpWriter::createOStream(const std::string& filename) {
679
680	+	std::ostream* newOStream;
681	+	#ifdef HAVE_LIBZ
682	+	if (needCompression_) {
683	+	newOStream = new ogzstream(filename.c_str());
684	+	} else {
685	+	newOStream = new std::ofstream(filename.c_str());
686	+	}
687	+	#else
688	+	newOStream = new std::ofstream(filename.c_str());
689	+	#endif
690	+	//write out MetaData first
691	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
692	+	(*newOStream) << "  <MetaData>" << std::endl;
693	+	(*newOStream) << info_->getRawMetaData();
694	+	(*newOStream) << "  </MetaData>" << std::endl;
695	+	return newOStream;
696	+	}
697
698	<	}//end namespace oopse
698	>	void DumpWriter::writeClosing(std::ostream& os) {
699	>
700	>	os << "</OpenMD>\n";
701	>	os.flush();
702	>	}
703	>
704	>	}//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 1752 by gezelter, Sun Jun 10 14:05:02 2012 UTC

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