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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 1782 by gezelter, Wed Aug 22 02:28:28 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, const std::string& filename)
65	<	: info_(info), filename_(filename){
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
79	–	DumpWriter::~DumpWriter() {
110
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	<	dumpFile_.close();
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	+	}
151	+
152		#ifdef IS_MPI
153
154		}
155
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	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
172	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
173	>	doSiteData_ = true;
174	>	} else {
175	>	doSiteData_ = false;
176	>	}
177
178	<	double currentTime;
179	<	Mat3x3d hmat;
180	<	double chi;
181	<	double integralOfChiDt;
182	<	Mat3x3d eta;
178	>	#ifdef HAVE_LIBZ
179	>	if (needCompression_) {
180	>	filename_ += ".gz";
181	>	eorFilename_ += ".gz";
182	>	}
183	>	#endif
184
185	<	currentTime = s->getTime();
105	<	hmat = s->getHmat();
106	<	chi = s->getChi();
107	<	integralOfChiDt = s->getIntegralOfChiDt();
108	<	eta = s->getEta();
185	>	#ifdef IS_MPI
186
187	<	os << currentTime << ";\t"
188	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
189	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
190	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
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	<	//write out additional parameters, such as chi and eta
205	>
206	>	#endif // is_mpi
207	>
208	>	}
209
210	<	os << chi << "\t" << integralOfChiDt << "\t;";
210	>	DumpWriter::~DumpWriter() {
211
212	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
120	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
121	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
122	<
123	<	os << std::endl;
124	<	}
212	>	#ifdef IS_MPI
213
214	<	void DumpWriter::writeFrame(std::ostream& os) {
215	<	const int BUFFERSIZE = 2000;
216	<	const int MINIBUFFERSIZE = 100;
214	>	if (worldRank == 0) {
215	>	#endif // is_mpi
216	>	if (createDumpFile_){
217	>	writeClosing(*dumpFile_);
218	>	delete dumpFile_;
219	>	}
220	>	#ifdef IS_MPI
221
222	<	char tempBuffer[BUFFERSIZE];
131	<	char writeLine[BUFFERSIZE];
222	>	}
223
224	<	Quat4d q;
134	<	Vector3d ji;
135	<	Vector3d pos;
136	<	Vector3d vel;
224	>	#endif // is_mpi
225
226	<	Molecule* mol;
139	<	StuntDouble* integrableObject;
140	<	SimInfo::MoleculeIterator mi;
141	<	Molecule::IntegrableObjectIterator ii;
142	<
143	<	int nTotObjects;
144	<	nTotObjects = info_->getNGlobalIntegrableObjects();
226	>	}
227
228	<	#ifndef IS_MPI
228	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
229
230	+	char buffer[1024];
231
232	<	os << nTotObjects << "\n";
150	<
151	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
232	>	os << "    <FrameData>\n";
233
234	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
234	>	RealType currentTime = s->getTime();
235
236	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
237	<	integrableObject = mol->nextIntegrableObject(ii)) {
238	<
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	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
244	>	os << buffer;
245
246	<	pos = integrableObject->getPos();
247	<	vel = integrableObject->getVel();
246	>	Mat3x3d hmat;
247	>	hmat = s->getHmat();
248
249	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
250	<	integrableObject->getType().c_str(),
251	<	pos[0], pos[1], pos[2],
252	<	vel[0], vel[1], vel[2]);
253	<
254	<	strcpy(writeLine, tempBuffer);
255	<
256	<	if (integrableObject->isDirectional()) {
257	<	q = integrableObject->getQ();
258	<	ji = integrableObject->getJ();
259	<
260	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
261	<	q[0], q[1], q[2], q[3],
262	<	ji[0], ji[1], ji[2]);
263	<	strcat(writeLine, tempBuffer);
264	<	} else {
178	<	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
179	<	}
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	>	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	<	os << writeLine;
266	>	pair<RealType, RealType> thermostat = s->getThermostat();
267
268	<	}
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.flush();
280	<	#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;
279	>	Mat3x3d eta;
280	>	eta = s->getBarostat();
281
282	<	int * potatoes;
283	<	int myPotato;
284	<	int nProc;
285	<	int which_node;
286	<	double atomData[13];
287	<	int isDirectional;
288	<	const char * atomTypeString;
289	<	char MPIatomTypeString[MINIBUFFERSIZE];
290	<	int msgLen; // the length of message actually recieved at master nodes
235	<	int haveError;
236	<	MPI_Status istatus;
237	<	int nCurObj;
238	<
239	<	// 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);
244	<
245	<	if (flag) {
246	<	MAXTAG = *tagub;
247	<	} else {
248	<	MAXTAG = 32767;
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	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
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	<	// Node 0 needs a list of the magic potatoes for each processor;
299	>	os << "    </FrameData>\n";
300	>	}
301
302	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
256	<	potatoes = new int[nProc];
302	>	void DumpWriter::writeFrame(std::ostream& os) {
303
304	<	//write out the comment lines
305	<	for(int i = 0; i < nProc; i++) {
306	<	potatoes[i] = 0;
261	<	}
304	>	#ifdef IS_MPI
305	>	MPI_Status istatus;
306	>	#endif
307
308	+	Molecule* mol;
309	+	StuntDouble* sd;
310	+	SimInfo::MoleculeIterator mi;
311	+	Molecule::IntegrableObjectIterator ii;
312	+	RigidBody::AtomIterator ai;
313	+	Atom* atom;
314
315	<	os << nTotObjects << "\n";
316	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
315	>	#ifndef IS_MPI
316	>	os << "  <Snapshot>\n";
317	>
318	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
319
320	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
320	>	os << "    <StuntDoubles>\n";
321	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
322
323	<	// Get the Node number which has this atom;
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	<	which_node = info_->getMolToProc(i);
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	<	if (which_node != masterNode) { //current molecule is in slave node
340	<	if (potatoes[which_node] + 1 >= MAXTAG) {
341	<	// The potato was going to exceed the maximum value,
276	<	// so wrap this processor potato back to 0:
339	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
340	>	// do one for the IO itself
341	>	os << prepareSiteLine(sd, ioIndex, 0);
342
343	<	potatoes[which_node] = 0;
344	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
345	<	MPI_COMM_WORLD);
346	<	}
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	>	}
353	>	}
354	>	}
355	>	os << "    </SiteData>\n";
356	>	}
357	>	os << "  </Snapshot>\n";
358
359	<	myPotato = potatoes[which_node];
359	>	os.flush();
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
285	–	//recieve the number of integrableObject in current molecule
286	–	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
287	–	MPI_COMM_WORLD, &istatus);
288	–	myPotato++;
365
366	<	for(int l = 0; l < nCurObj; l++) {
367	<	if (potatoes[which_node] + 2 >= MAXTAG) {
368	<	// The potato was going to exceed the maximum value,
369	<	// so wrap this processor potato back to 0:
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	<	potatoes[which_node] = 0;
296	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
297	<	0, MPI_COMM_WORLD);
298	<	}
382	>	for (int i = 1; i < nProc; ++i) {
383
384	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
385	<	which_node, myPotato, MPI_COMM_WORLD,
302	<	&istatus);
384	>	// receive the length of the string buffer that was
385	>	// prepared by processor i
386
387	<	atomTypeString = MPIatomTypeString;
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	<	myPotato++;
414	>	#endif // is_mpi
415
416	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
417	<	MPI_COMM_WORLD, &istatus);
418	<	myPotato++;
416	>	}
417	>
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	>	Vector3d pos;
426	>	Vector3d vel;
427	>	pos = sd->getPos();
428	>
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	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
439	>	vel = sd->getVel();
440
441	<	if (msgLen == 13)
442	<	isDirectional = 1;
443	<	else
444	<	isDirectional = 0;
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	<	// If we've survived to here, format the line:
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	<	if (!isDirectional) {
457	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
458	<	atomTypeString, atomData[0],
459	<	atomData[1], atomData[2],
460	<	atomData[3], atomData[4],
326	<	atomData[5]);
456	>	if (sd->isDirectional()) {
457	>	type += "qj";
458	>	Quat4d q;
459	>	Vector3d ji;
460	>	q = sd->getQ();
461
462	<	strcat(writeLine,
463	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
464	<	} else {
465	<	sprintf(writeLine,
466	<	"%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",
467	<	atomTypeString,
468	<	atomData[0],
469	<	atomData[1],
470	<	atomData[2],
471	<	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	<	}
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	<	os << writeLine;
473	>	ji = sd->getJ();
474
475	<	} // end for(int l =0)
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	<	potatoes[which_node] = myPotato;
486	<	} else { //master node has current molecule
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	<	mol = info_->getMoleculeByGlobalIndex(i);
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	<	if (mol == NULL) {
526	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
527	<	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();
525	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
526	>	return std::string(tempBuffer);
527	>	}
528
529	<	pos = integrableObject->getPos();
530	<	vel = integrableObject->getVel();
529	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
530	>
531
532	<	atomData[0] = pos[0];
533	<	atomData[1] = pos[1];
534	<	atomData[2] = pos[2];
532	>	std::string id;
533	>	std::string type;
534	>	std::string line;
535	>	char tempBuffer[4096];
536
537	<	atomData[3] = vel[0];
538	<	atomData[4] = vel[1];
539	<	atomData[5] = vel[2];
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	<	isDirectional = 0;
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	<	if (integrableObject->isDirectional()) {
585	<	isDirectional = 1;
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
385	–	q = integrableObject->getQ();
386	–	ji = integrableObject->getJ();
601
602	<	for(int j = 0; j < 6; j++) {
603	<	atomData[j] = atomData[j];
604	<	}
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	<	atomData[6] = q[0];
618	<	atomData[7] = q[1];
619	<	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:
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 (!isDirectional) {
622	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
623	<	atomTypeString, atomData[0],
407	<	atomData[1], atomData[2],
408	<	atomData[3], atomData[4],
409	<	atomData[5]);
621	>	void DumpWriter::writeDump() {
622	>	writeFrame(*dumpFile_);
623	>	}
624
625	<	strcat(writeLine,
626	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
627	<	} else {
628	<	sprintf(writeLine,
629	<	"%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",
630	<	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	<	}
625	>	void DumpWriter::writeEor() {
626	>	std::ostream* eorStream;
627	>
628	>	#ifdef IS_MPI
629	>	if (worldRank == 0) {
630	>	#endif // is_mpi
631
632	+	eorStream = createOStream(eorFilename_);
633
634	<	os << writeLine;
634	>	#ifdef IS_MPI
635	>	}
636	>	#endif // is_mpi
637
638	<	} //end for(iter = integrableObject.begin())
436	<	}
437	<	} //end for(i = 0; i < mpiSim->getNmol())
638	>	writeFrame(*eorStream);
639
640	<	os.flush();
641	<
642	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
643	<	MPIcheckPoint();
640	>	#ifdef IS_MPI
641	>	if (worldRank == 0) {
642	>	#endif // is_mpi
643	>	writeClosing(*eorStream);
644	>	delete eorStream;
645	>	#ifdef IS_MPI
646	>	}
647	>	#endif // is_mpi
648
649	<	delete [] potatoes;
445	<	} else {
649	>	}
650
447	–	// worldRank != 0, so I'm a remote node.
651
652	<	// Set my magic potato to 0:
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	<	myPotato = 0;
659	>	buffers.push_back(dumpFile_->rdbuf());
660
661	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
661	>	eorStream = createOStream(eorFilename_);
662
663	<	// Am I the node which has this integrableObject?
664	<	int whichNode = info_->getMolToProc(i);
665	<	if (whichNode == worldRank) {
666	<	if (myPotato + 1 >= MAXTAG) {
663	>	buffers.push_back(eorStream->rdbuf());
664	>
665	>	#ifdef IS_MPI
666	>	}
667	>	#endif // is_mpi
668
669	<	// The potato was going to exceed the maximum value,
670	<	// so wrap this processor potato back to 0 (and block until
462	<	// node 0 says we can go:
669	>	TeeBuf tbuf(buffers.begin(), buffers.end());
670	>	std::ostream os(&tbuf);
671
672	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
465	<	&istatus);
466	<	}
672	>	writeFrame(os);
673
674	<	mol = info_->getMoleculeByGlobalIndex(i);
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	>	}
684
685	<
471	<	nCurObj = mol->getNIntegrableObjects();
685	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
686
687	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
688	<	myPotato++;
689	<
690	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
691	<	integrableObject = mol->nextIntegrableObject(ii)) {
692	<
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();
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	<	#endif // is_mpi
705	>	void DumpWriter::writeClosing(std::ostream& os) {
706
707	<	}
707	>	os << "</OpenMD>\n";
708	>	os.flush();
709	>	}
710
711	<	}//end namespace oopse
711	>	}//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 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

#	Line 0 | Line 1
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