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

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trunk/src/io/DumpWriter.cpp (file contents), Revision 251 by tim, Wed Jan 12 23:24:55 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1878 by gezelter, Thu Jun 13 14:26:09 2013 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, 234107 (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]);
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	<	strcpy(writeLine, tempBuffer);
266	>	pair<RealType, RealType> thermostat = s->getThermostat();
267
268	<	if (integrableObject->isDirectional()) {
269	<	q = integrableObject->getQ();
270	<	ji = integrableObject->getJ();
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	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
280	<	q[0], q[1], q[2], q[3],
175	<	ji[0], ji[1], ji[2]);
176	<	strcat(writeLine, tempBuffer);
177	<	} else {
178	<	strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
179	<	}
279	>	Mat3x3d eta;
280	>	eta = s->getBarostat();
281
282	<	os << writeLine;
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	<	}
294	<	}
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	<	#else // is_mpi
300	<	/*********************************************************************
188	<	* Documentation?  You want DOCUMENTATION?
189	<	*
190	<	* Why all the potatoes below?
191	<	*
192	<	* To make a long story short, the original version of DumpWriter
193	<	* worked in the most inefficient way possible.  Node 0 would
194	<	* poke each of the node for an individual atom's formatted data
195	<	* as node 0 worked its way down the global index. This was particularly
196	<	* inefficient since the method blocked all processors at every atom
197	<	* (and did it twice!).
198	<	*
199	<	* An intermediate version of DumpWriter could be described from Node
200	<	* zero's perspective as follows:
201	<	*
202	<	*  1) Have 100 of your friends stand in a circle.
203	<	*  2) When you say go, have all of them start tossing potatoes at
204	<	*     you (one at a time).
205	<	*  3) Catch the potatoes.
206	<	*
207	<	* It was an improvement, but MPI has buffers and caches that could
208	<	* best be described in this analogy as "potato nets", so there's no
209	<	* need to block the processors atom-by-atom.
210	<	*
211	<	* This new and improved DumpWriter works in an even more efficient
212	<	* way:
213	<	*
214	<	*  1) Have 100 of your friend stand in a circle.
215	<	*  2) When you say go, have them start tossing 5-pound bags of
216	<	*     potatoes at you.
217	<	*  3) Once you've caught a friend's bag of potatoes,
218	<	*     toss them a spud to let them know they can toss another bag.
219	<	*
220	<	* How's THAT for documentation?
221	<	*
222	<	*********************************************************************/
223	<	const int masterNode = 0;
299	>	os << "    </FrameData>\n";
300	>	}
301
302	<	int * potatoes;
226	<	int myPotato;
227	<	int nProc;
228	<	int which_node;
229	<	double atomData[13];
230	<	int isDirectional;
231	<	const char * atomTypeString;
232	<	char MPIatomTypeString[MINIBUFFERSIZE];
233	<	int msgLen; // the length of message actually recieved at master nodes
234	<	int haveError;
235	<	MPI_Status istatus;
236	<	int nCurObj;
237	<
238	<	// code to find maximum tag value
239	<	int * tagub;
240	<	int flag;
241	<	int MAXTAG;
242	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
302	>	void DumpWriter::writeFrame(std::ostream& os) {
303
304	<	if (flag) {
305	<	MAXTAG = *tagub;
306	<	} else {
247	<	MAXTAG = 32767;
248	<	}
304	>	#ifdef IS_MPI
305	>	MPI::Status istatus;
306	>	#endif
307
308	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
308	>	Molecule* mol;
309	>	StuntDouble* sd;
310	>	SimInfo::MoleculeIterator mi;
311	>	Molecule::IntegrableObjectIterator ii;
312	>	RigidBody::AtomIterator ai;
313
314	<	// Node 0 needs a list of the magic potatoes for each processor;
314	>	#ifndef IS_MPI
315	>	os << "  <Snapshot>\n";
316	>
317	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
318
319	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
320	<	potatoes = new int[nProc];
319	>	os << "    <StuntDoubles>\n";
320	>	for (mol = info_->beginMolecule(mi); mol != NULL;
321	>	mol = info_->nextMolecule(mi)) {
322	>
323	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
324	>	sd = mol->nextIntegrableObject(ii)) {
325	>	os << prepareDumpLine(sd);
326	>
327	>	}
328	>	}
329	>	os << "    </StuntDoubles>\n";
330
331	<	//write out the comment lines
332	<	for(int i = 0; i < nProc; i++) {
333	<	potatoes[i] = 0;
334	<	}
331	>	if (doSiteData_) {
332	>	os << "    <SiteData>\n";
333	>	for (mol = info_->beginMolecule(mi); mol != NULL;
334	>	mol = info_->nextMolecule(mi)) {
335	>
336	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
337	>	sd = mol->nextIntegrableObject(ii)) {
338
339	+	int ioIndex = sd->getGlobalIntegrableObjectIndex();
340	+	// do one for the IO itself
341	+	os << prepareSiteLine(sd, ioIndex, 0);
342
343	<	os << nTotObjects << "\n";
344	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
343	>	if (sd->isRigidBody()) {
344	>
345	>	RigidBody* rb = static_cast<RigidBody*>(sd);
346	>	int siteIndex = 0;
347	>	for (Atom* 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	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
359	>	os.flush();
360	>	#else
361
362	<	// Get the Node number which has this atom;
362	>	const int masterNode = 0;
363	>	int worldRank = MPI::COMM_WORLD.Get_rank();
364	>	int nProc = MPI::COMM_WORLD.Get_size();
365
366	<	which_node = info_->getMolToProc(i);
366	>	if (worldRank == masterNode) {
367	>	os << "  <Snapshot>\n";
368	>	writeFrameProperties(os,
369	>	info_->getSnapshotManager()->getCurrentSnapshot());
370	>	os << "    <StuntDoubles>\n";
371	>	}
372
373	<	if (which_node != masterNode) { //current molecule is in slave node
374	<	if (potatoes[which_node] + 1 >= MAXTAG) {
375	<	// The potato was going to exceed the maximum value,
376	<	// so wrap this processor potato back to 0:
373	>	//every node prepares the dump lines for integrable objects belong to itself
374	>	std::string buffer;
375	>	for (mol = info_->beginMolecule(mi); mol != NULL;
376	>	mol = info_->nextMolecule(mi)) {
377	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
378	>	sd = mol->nextIntegrableObject(ii)) {
379	>	buffer += prepareDumpLine(sd);
380	>	}
381	>	}
382	>
383	>	if (worldRank == masterNode) {
384	>	os << buffer;
385	>
386	>	for (int i = 1; i < nProc; ++i) {
387	>	// tell processor i to start sending us data:
388	>	MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
389
390	<	potatoes[which_node] = 0;
391	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
392	<	MPI_COMM_WORLD);
393	<	}
390	>	// receive the length of the string buffer that was
391	>	// prepared by processor i:
392	>	int recvLength;
393	>	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
394	>	istatus);
395
396	<	myPotato = potatoes[which_node];
396	>	// create a buffer to receive the data
397	>	char* recvBuffer = new char[recvLength];
398	>	if (recvBuffer == NULL) {
399	>	} else {
400	>	// receive the data:
401	>	MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
402	>	MPI::ANY_TAG, istatus);
403	>	// send it to the file:
404	>	os << recvBuffer;
405	>	// get rid of the receive buffer:
406	>	delete [] recvBuffer;
407	>	}
408	>	}
409	>	} else {
410	>	int sendBufferLength = buffer.size() + 1;
411	>	int myturn = 0;
412	>	for (int i = 1; i < nProc; ++i){
413	>	// wait for the master node to call our number:
414	>	MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
415	>	if (myturn == worldRank){
416	>	// send the length of our buffer:
417	>	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
418
419	<	//recieve the number of integrableObject in current molecule
420	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
421	<	MPI_COMM_WORLD, &istatus);
287	<	myPotato++;
419	>	// send our buffer:
420	>	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
421	>	MPI::CHAR, masterNode, 0);
422
423	<	for(int l = 0; l < nCurObj; l++) {
424	<	if (potatoes[which_node] + 2 >= MAXTAG) {
425	<	// The potato was going to exceed the maximum value,
426	<	// so wrap this processor potato back to 0:
423	>	}
424	>	}
425	>	}
426	>
427	>	if (worldRank == masterNode) {
428	>	os << "    </StuntDoubles>\n";
429	>	}
430
431	<	potatoes[which_node] = 0;
432	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
433	<	0, MPI_COMM_WORLD);
434	<	}
431	>	if (doSiteData_) {
432	>	if (worldRank == masterNode) {
433	>	os << "    <SiteData>\n";
434	>	}
435	>	buffer.clear();
436	>	for (mol = info_->beginMolecule(mi); mol != NULL;
437	>	mol = info_->nextMolecule(mi)) {
438	>
439	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
440	>	sd = mol->nextIntegrableObject(ii)) {
441	>
442	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
443	>	// do one for the IO itself
444	>	buffer += prepareSiteLine(sd, ioIndex, 0);
445
446	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
447	<	which_node, myPotato, MPI_COMM_WORLD,
448	<	&istatus);
446	>	if (sd->isRigidBody()) {
447	>
448	>	RigidBody* rb = static_cast<RigidBody*>(sd);
449	>	int siteIndex = 0;
450	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
451	>	atom = rb->nextAtom(ai)) {
452	>	buffer += prepareSiteLine(atom, ioIndex, siteIndex);
453	>	siteIndex++;
454	>	}
455	>	}
456	>	}
457	>	}
458
459	<	atomTypeString = MPIatomTypeString;
460	<
461	<	myPotato++;
462	<
463	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
464	<	MPI_COMM_WORLD, &istatus);
465	<	myPotato++;
466	<
467	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
468	<
469	<	if (msgLen == 13)
470	<	isDirectional = 1;
471	<	else
472	<	isDirectional = 0;
473	<
474	<	// If we've survived to here, format the line:
475	<
476	<	if (!isDirectional) {
477	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
478	<	atomTypeString, atomData[0],
479	<	atomData[1], atomData[2],
480	<	atomData[3], atomData[4],
481	<	atomData[5]);
459	>	if (worldRank == masterNode) {
460	>	os << buffer;
461	>
462	>	for (int i = 1; i < nProc; ++i) {
463	>
464	>	// tell processor i to start sending us data:
465	>	MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
466	>
467	>	// receive the length of the string buffer that was
468	>	// prepared by processor i:
469	>	int recvLength;
470	>	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
471	>	istatus);
472	>
473	>	// create a buffer to receive the data
474	>	char* recvBuffer = new char[recvLength];
475	>	if (recvBuffer == NULL) {
476	>	} else {
477	>	// receive the data:
478	>	MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
479	>	MPI::ANY_TAG, istatus);
480	>	// send it to the file:
481	>	os << recvBuffer;
482	>	// get rid of the receive buffer:
483	>	delete [] recvBuffer;
484	>	}
485	>	}
486	>	} else {
487	>	int sendBufferLength = buffer.size() + 1;
488	>	int myturn = 0;
489	>	for (int i = 1; i < nProc; ++i){
490	>	// wait for the master node to call our number:
491	>	MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
492	>	if (myturn == worldRank){
493	>	// send the length of our buffer:
494	>	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
495	>	// send our buffer:
496	>	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
497	>	MPI::CHAR, masterNode, 0);
498	>	}
499	>	}
500	>	}
501	>
502	>	if (worldRank == masterNode) {
503	>	os << "    </SiteData>\n";
504	>	}
505	>	}
506	>
507	>	if (worldRank == masterNode) {
508	>	os << "  </Snapshot>\n";
509	>	os.flush();
510	>	}
511	>
512	>	#endif // is_mpi
513	>
514	>	}
515
516	<	strcat(writeLine,
517	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
518	<	} else {
519	<	sprintf(writeLine,
520	<	"%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",
521	<	atomTypeString,
333	<	atomData[0],
334	<	atomData[1],
335	<	atomData[2],
336	<	atomData[3],
337	<	atomData[4],
338	<	atomData[5],
339	<	atomData[6],
340	<	atomData[7],
341	<	atomData[8],
342	<	atomData[9],
343	<	atomData[10],
344	<	atomData[11],
345	<	atomData[12]);
346	<	}
516	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
517	>
518	>	int index = sd->getGlobalIntegrableObjectIndex();
519	>	std::string type("pv");
520	>	std::string line;
521	>	char tempBuffer[4096];
522
523	<	os << writeLine;
523	>	Vector3d pos;
524	>	Vector3d vel;
525	>	pos = sd->getPos();
526
527	<	} // end for(int l =0)
527	>	if (isinf(pos[0]) || isnan(pos[0]) ||
528	>	isinf(pos[1]) || isnan(pos[1]) ||
529	>	isinf(pos[2]) || isnan(pos[2]) ) {
530	>	sprintf( painCave.errMsg,
531	>	"DumpWriter detected a numerical error writing the position"
532	>	" for object %d", index);
533	>	painCave.isFatal = 1;
534	>	simError();
535	>	}
536
537	<	potatoes[which_node] = myPotato;
353	<	} else { //master node has current molecule
537	>	vel = sd->getVel();
538
539	<	mol = info_->getMoleculeByGlobalIndex(i);
539	>	if (isinf(vel[0]) || isnan(vel[0]) ||
540	>	isinf(vel[1]) || isnan(vel[1]) ||
541	>	isinf(vel[2]) || isnan(vel[2]) ) {
542	>	sprintf( painCave.errMsg,
543	>	"DumpWriter detected a numerical error writing the velocity"
544	>	" for object %d", index);
545	>	painCave.isFatal = 1;
546	>	simError();
547	>	}
548
549	<	if (mol == NULL) {
550	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
551	<	painCave.isFatal = 1;
552	<	simError();
361	<	}
362	<
363	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
364	<	integrableObject = mol->nextIntegrableObject(ii)) {
365	<
366	<	atomTypeString = integrableObject->getType().c_str();
549	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
550	>	pos[0], pos[1], pos[2],
551	>	vel[0], vel[1], vel[2]);
552	>	line += tempBuffer;
553
554	<	pos = integrableObject->getPos();
555	<	vel = integrableObject->getVel();
554	>	if (sd->isDirectional()) {
555	>	type += "qj";
556	>	Quat4d q;
557	>	Vector3d ji;
558	>	q = sd->getQ();
559
560	<	atomData[0] = pos[0];
561	<	atomData[1] = pos[1];
562	<	atomData[2] = pos[2];
560	>	if (isinf(q[0]) || isnan(q[0]) ||
561	>	isinf(q[1]) || isnan(q[1]) ||
562	>	isinf(q[2]) || isnan(q[2]) ||
563	>	isinf(q[3]) || isnan(q[3]) ) {
564	>	sprintf( painCave.errMsg,
565	>	"DumpWriter detected a numerical error writing the quaternion"
566	>	" for object %d", index);
567	>	painCave.isFatal = 1;
568	>	simError();
569	>	}
570
571	<	atomData[3] = vel[0];
376	<	atomData[4] = vel[1];
377	<	atomData[5] = vel[2];
571	>	ji = sd->getJ();
572
573	<	isDirectional = 0;
573	>	if (isinf(ji[0]) || isnan(ji[0]) ||
574	>	isinf(ji[1]) || isnan(ji[1]) ||
575	>	isinf(ji[2]) || isnan(ji[2]) ) {
576	>	sprintf( painCave.errMsg,
577	>	"DumpWriter detected a numerical error writing the angular"
578	>	" momentum for object %d", index);
579	>	painCave.isFatal = 1;
580	>	simError();
581	>	}
582
583	<	if (integrableObject->isDirectional()) {
584	<	isDirectional = 1;
583	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
584	>	q[0], q[1], q[2], q[3],
585	>	ji[0], ji[1], ji[2]);
586	>	line += tempBuffer;
587	>	}
588
589	<	q = integrableObject->getQ();
590	<	ji = integrableObject->getJ();
589	>	if (needForceVector_) {
590	>	type += "f";
591	>	Vector3d frc = sd->getFrc();
592	>	if (isinf(frc[0]) || isnan(frc[0]) ||
593	>	isinf(frc[1]) || isnan(frc[1]) ||
594	>	isinf(frc[2]) || isnan(frc[2]) ) {
595	>	sprintf( painCave.errMsg,
596	>	"DumpWriter detected a numerical error writing the force"
597	>	" for object %d", index);
598	>	painCave.isFatal = 1;
599	>	simError();
600	>	}
601	>	sprintf(tempBuffer, " %13e %13e %13e",
602	>	frc[0], frc[1], frc[2]);
603	>	line += tempBuffer;
604	>
605	>	if (sd->isDirectional()) {
606	>	type += "t";
607	>	Vector3d trq = sd->getTrq();
608	>	if (isinf(trq[0]) || isnan(trq[0]) ||
609	>	isinf(trq[1]) || isnan(trq[1]) ||
610	>	isinf(trq[2]) || isnan(trq[2]) ) {
611	>	sprintf( painCave.errMsg,
612	>	"DumpWriter detected a numerical error writing the torque"
613	>	" for object %d", index);
614	>	painCave.isFatal = 1;
615	>	simError();
616	>	}
617	>	sprintf(tempBuffer, " %13e %13e %13e",
618	>	trq[0], trq[1], trq[2]);
619	>	line += tempBuffer;
620	>	}
621	>	}
622
623	<	for(int j = 0; j < 6; j++) {
624	<	atomData[j] = atomData[j];
625	<	}
623	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
624	>	return std::string(tempBuffer);
625	>	}
626
627	<	atomData[6] = q[0];
628	<	atomData[7] = q[1];
393	<	atomData[8] = q[2];
394	<	atomData[9] = q[3];
627	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
628	>
629
630	<	atomData[10] = ji[0];
631	<	atomData[11] = ji[1];
632	<	atomData[12] = ji[2];
633	<	}
630	>	std::string id;
631	>	std::string type;
632	>	std::string line;
633	>	char tempBuffer[4096];
634
635	<	// If we've survived to here, format the line:
636	<
637	<	if (!isDirectional) {
638	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
639	<	atomTypeString, atomData[0],
640	<	atomData[1], atomData[2],
641	<	atomData[3], atomData[4],
642	<	atomData[5]);
643	<
644	<	strcat(writeLine,
645	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
646	<	} else {
647	<	sprintf(writeLine,
648	<	"%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",
649	<	atomTypeString,
650	<	atomData[0],
651	<	atomData[1],
652	<	atomData[2],
653	<	atomData[3],
654	<	atomData[4],
655	<	atomData[5],
656	<	atomData[6],
657	<	atomData[7],
658	<	atomData[8],
659	<	atomData[9],
660	<	atomData[10],
661	<	atomData[11],
662	<	atomData[12]);
663	<	}
664	<
665	<
432	<	os << writeLine;
433	<
434	<	} //end for(iter = integrableObject.begin())
435	<	}
436	<	} //end for(i = 0; i < mpiSim->getNmol())
437	<
438	<	os.flush();
439	<
440	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
441	<	MPIcheckPoint();
635	>	if (sd->isRigidBody()) {
636	>	sprintf(tempBuffer, "%10d           ", ioIndex);
637	>	id = std::string(tempBuffer);
638	>	} else {
639	>	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
640	>	id = std::string(tempBuffer);
641	>	}
642	>
643	>	if (needFlucQ_) {
644	>	type += "cw";
645	>	RealType fqPos = sd->getFlucQPos();
646	>	if (isinf(fqPos) || isnan(fqPos) ) {
647	>	sprintf( painCave.errMsg,
648	>	"DumpWriter detected a numerical error writing the"
649	>	" fluctuating charge for object %s", id.c_str());
650	>	painCave.isFatal = 1;
651	>	simError();
652	>	}
653	>	sprintf(tempBuffer, " %13e ", fqPos);
654	>	line += tempBuffer;
655	>
656	>	RealType fqVel = sd->getFlucQVel();
657	>	if (isinf(fqVel) || isnan(fqVel) ) {
658	>	sprintf( painCave.errMsg,
659	>	"DumpWriter detected a numerical error writing the"
660	>	" fluctuating charge velocity for object %s", id.c_str());
661	>	painCave.isFatal = 1;
662	>	simError();
663	>	}
664	>	sprintf(tempBuffer, " %13e ", fqVel);
665	>	line += tempBuffer;
666
667	<	delete [] potatoes;
668	<	} else {
667	>	if (needForceVector_) {
668	>	type += "g";
669	>	RealType fqFrc = sd->getFlucQFrc();
670	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
671	>	sprintf( painCave.errMsg,
672	>	"DumpWriter detected a numerical error writing the"
673	>	" fluctuating charge force for object %s", id.c_str());
674	>	painCave.isFatal = 1;
675	>	simError();
676	>	}
677	>	sprintf(tempBuffer, " %13e ", fqFrc);
678	>	line += tempBuffer;
679	>	}
680	>	}
681
682	<	// worldRank != 0, so I'm a remote node.
682	>	if (needElectricField_) {
683	>	type += "e";
684	>	Vector3d eField= sd->getElectricField();
685	>	if (isinf(eField[0]) || isnan(eField[0]) ||
686	>	isinf(eField[1]) || isnan(eField[1]) ||
687	>	isinf(eField[2]) || isnan(eField[2]) ) {
688	>	sprintf( painCave.errMsg,
689	>	"DumpWriter detected a numerical error writing the electric"
690	>	" field for object %s", id.c_str());
691	>	painCave.isFatal = 1;
692	>	simError();
693	>	}
694	>	sprintf(tempBuffer, " %13e %13e %13e",
695	>	eField[0], eField[1], eField[2]);
696	>	line += tempBuffer;
697	>	}
698
448	–	// Set my magic potato to 0:
699
700	<	myPotato = 0;
700	>	if (needParticlePot_) {
701	>	type += "u";
702	>	RealType particlePot = sd->getParticlePot();
703	>	if (isinf(particlePot) || isnan(particlePot)) {
704	>	sprintf( painCave.errMsg,
705	>	"DumpWriter detected a numerical error writing the particle "
706	>	" potential for object %s", id.c_str());
707	>	painCave.isFatal = 1;
708	>	simError();
709	>	}
710	>	sprintf(tempBuffer, " %13e", particlePot);
711	>	line += tempBuffer;
712	>	}
713	>
714
715	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
715	>	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
716	>	return std::string(tempBuffer);
717	>	}
718
719	<	// Am I the node which has this integrableObject?
720	<	int whichNode = info_->getMolToProc(i);
721	<	if (whichNode == worldRank) {
457	<	if (myPotato + 1 >= MAXTAG) {
719	>	void DumpWriter::writeDump() {
720	>	writeFrame(*dumpFile_);
721	>	}
722
723	<	// The potato was going to exceed the maximum value,
724	<	// so wrap this processor potato back to 0 (and block until
725	<	// node 0 says we can go:
723	>	void DumpWriter::writeEor() {
724	>	std::ostream* eorStream;
725	>
726	>	#ifdef IS_MPI
727	>	if (worldRank == 0) {
728	>	#endif // is_mpi
729	>
730	>	eorStream = createOStream(eorFilename_);
731
732	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
733	<	&istatus);
734	<	}
732	>	#ifdef IS_MPI
733	>	}
734	>	#endif
735	>
736	>	writeFrame(*eorStream);
737	>
738	>	#ifdef IS_MPI
739	>	if (worldRank == 0) {
740	>	#endif
741	>
742	>	writeClosing(*eorStream);
743	>	delete eorStream;
744	>
745	>	#ifdef IS_MPI
746	>	}
747	>	#endif // is_mpi
748
749	<	mol = info_->getMoleculeByGlobalIndex(i);
749	>	}
750
469	–
470	–	nCurObj = mol->getNIntegrableObjects();
751
752	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
753	<	myPotato++;
752	>	void DumpWriter::writeDumpAndEor() {
753	>	std::vector<std::streambuf*> buffers;
754	>	std::ostream* eorStream;
755	>	#ifdef IS_MPI
756	>	if (worldRank == 0) {
757	>	#endif // is_mpi
758
759	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
476	<	integrableObject = mol->nextIntegrableObject(ii)) {
759	>	buffers.push_back(dumpFile_->rdbuf());
760
761	<	if (myPotato + 2 >= MAXTAG) {
761	>	eorStream = createOStream(eorFilename_);
762
763	<	// The potato was going to exceed the maximum value,
764	<	// so wrap this processor potato back to 0 (and block until
765	<	// node 0 says we can go:
763	>	buffers.push_back(eorStream->rdbuf());
764	>
765	>	#ifdef IS_MPI
766	>	}
767	>	#endif // is_mpi
768
769	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
770	<	&istatus);
486	<	}
769	>	TeeBuf tbuf(buffers.begin(), buffers.end());
770	>	std::ostream os(&tbuf);
771
772	<	atomTypeString = integrableObject->getType().c_str();
772	>	writeFrame(os);
773
774	<	pos = integrableObject->getPos();
775	<	vel = integrableObject->getVel();
774	>	#ifdef IS_MPI
775	>	if (worldRank == 0) {
776	>	#endif // is_mpi
777	>	writeClosing(*eorStream);
778	>	delete eorStream;
779	>	#ifdef IS_MPI
780	>	}
781	>	#endif // is_mpi
782	>
783	>	}
784
785	<	atomData[0] = pos[0];
494	<	atomData[1] = pos[1];
495	<	atomData[2] = pos[2];
785	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
786
787	<	atomData[3] = vel[0];
788	<	atomData[4] = vel[1];
789	<	atomData[5] = vel[2];
790	<
791	<	isDirectional = 0;
792	<
503	<	if (integrableObject->isDirectional()) {
504	<	isDirectional = 1;
505	<
506	<	q = integrableObject->getQ();
507	<	ji = integrableObject->getJ();
508	<
509	<	atomData[6] = q[0];
510	<	atomData[7] = q[1];
511	<	atomData[8] = q[2];
512	<	atomData[9] = q[3];
513	<
514	<	atomData[10] = ji[0];
515	<	atomData[11] = ji[1];
516	<	atomData[12] = ji[2];
517	<	}
518	<
519	<	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
520	<
521	<	// null terminate the  std::string before sending (just in case):
522	<	MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
523	<
524	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
525	<	myPotato, MPI_COMM_WORLD);
526	<
527	<	myPotato++;
528	<
529	<	if (isDirectional) {
530	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
531	<	MPI_COMM_WORLD);
532	<	} else {
533	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
534	<	MPI_COMM_WORLD);
535	<	}
536	<
537	<	myPotato++;
538	<	}
539	<
540	<	}
541	<
542	<	}
543	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
544	<	MPIcheckPoint();
787	>	std::ostream* newOStream;
788	>	#ifdef HAVE_ZLIB
789	>	if (needCompression_) {
790	>	newOStream = new ogzstream(filename.c_str());
791	>	} else {
792	>	newOStream = new std::ofstream(filename.c_str());
793		}
794	+	#else
795	+	newOStream = new std::ofstream(filename.c_str());
796	+	#endif
797	+	//write out MetaData first
798	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
799	+	(*newOStream) << "  <MetaData>" << std::endl;
800	+	(*newOStream) << info_->getRawMetaData();
801	+	(*newOStream) << "  </MetaData>" << std::endl;
802	+	return newOStream;
803	+	}
804
805	<	#endif // is_mpi
805	>	void DumpWriter::writeClosing(std::ostream& os) {
806
807	<	}
807	>	os << "</OpenMD>\n";
808	>	os.flush();
809	>	}
810
811	<	}//end namespace oopse
811	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 251 by tim, Wed Jan 12 23:24:55 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1878 by gezelter, Thu Jun 13 14:26:09 2013 UTC

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