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

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 251 by tim, Wed Jan 12 23:24:55 2005 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 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 "config.h"
44	+
45	+	#ifdef IS_MPI
46	+	#include <mpi.h>
47	+	#endif
48
49		#include "io/DumpWriter.hpp"
50		#include "primitives/Molecule.hpp"
51		#include "utils/simError.h"
52	+	#include "io/basic_teebuf.hpp"
53	+	#ifdef HAVE_ZLIB
54	+	#include "io/gzstream.hpp"
55	+	#endif
56	+	#include "io/Globals.hpp"
57
58	<	#ifdef IS_MPI
59	<	#include <mpi.h>
60	<	#endif //is_mpi
58	>	#ifdef _MSC_VER
59	>	#define isnan(x) _isnan((x))
60	>	#define isinf(x) (!_finite(x) && !_isnan(x))
61	>	#endif
62
63	<	namespace oopse {
63	>	using namespace std;
64	>	namespace OpenMD {
65
66	<	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
67	<	: info_(info), filename_(filename){
66	>	DumpWriter::DumpWriter(SimInfo* info)
67	>	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
68	>
69	>	Globals* simParams = info->getSimParams();
70	>	needCompression_   = simParams->getCompressDumpFile();
71	>	needForceVector_   = simParams->getOutputForceVector();
72	>	needParticlePot_   = simParams->getOutputParticlePotential();
73	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
74	>	needElectricField_ = simParams->getOutputElectricField();
75	>
76	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
77	>	doSiteData_ = true;
78	>	} else {
79	>	doSiteData_ = false;
80	>	}
81	>
82	>	createDumpFile_ = true;
83	>	#ifdef HAVE_LIBZ
84	>	if (needCompression_) {
85	>	filename_ += ".gz";
86	>	eorFilename_ += ".gz";
87	>	}
88	>	#endif
89	>
90		#ifdef IS_MPI
91
92		if (worldRank == 0) {
93		#endif // is_mpi
94	+
95	+	dumpFile_ = createOStream(filename_);
96
97	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
97	>	if (!dumpFile_) {
98	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
99	>	filename_.c_str());
100	>	painCave.isFatal = 1;
101	>	simError();
102	>	}
103
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	–
104		#ifdef IS_MPI
105
106		}
107
72	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73	–	MPIcheckPoint();
74	–
108		#endif // is_mpi
109
110	<	}
110	>	}
111
79	–	DumpWriter::~DumpWriter() {
112
113	+	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
114	+	: info_(info), filename_(filename){
115	+
116	+	Globals* simParams = info->getSimParams();
117	+	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
118	+
119	+	needCompression_   = simParams->getCompressDumpFile();
120	+	needForceVector_   = simParams->getOutputForceVector();
121	+	needParticlePot_   = simParams->getOutputParticlePotential();
122	+	needFlucQ_         = simParams->getOutputFluctuatingCharges();
123	+	needElectricField_ = simParams->getOutputElectricField();
124	+
125	+	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
126	+	doSiteData_ = true;
127	+	} else {
128	+	doSiteData_ = false;
129	+	}
130	+
131	+	createDumpFile_ = true;
132	+	#ifdef HAVE_LIBZ
133	+	if (needCompression_) {
134	+	filename_ += ".gz";
135	+	eorFilename_ += ".gz";
136	+	}
137	+	#endif
138	+
139		#ifdef IS_MPI
140
141		if (worldRank == 0) {
142		#endif // is_mpi
143
144	<	dumpFile_.close();
144	>
145	>	dumpFile_ = createOStream(filename_);
146
147	+	if (!dumpFile_) {
148	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
149	+	filename_.c_str());
150	+	painCave.isFatal = 1;
151	+	simError();
152	+	}
153	+
154		#ifdef IS_MPI
155
156		}
157
158		#endif // is_mpi
159
160	<	}
160	>	}
161	>
162	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
163	>	: info_(info), filename_(filename){
164	>
165	>	Globals* simParams = info->getSimParams();
166	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
167	>
168	>	needCompression_   = simParams->getCompressDumpFile();
169	>	needForceVector_   = simParams->getOutputForceVector();
170	>	needParticlePot_   = simParams->getOutputParticlePotential();
171	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
172	>	needElectricField_ = simParams->getOutputElectricField();
173
174	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
174	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
175	>	doSiteData_ = true;
176	>	} else {
177	>	doSiteData_ = false;
178	>	}
179
180	<	double currentTime;
181	<	Mat3x3d hmat;
182	<	double chi;
183	<	double integralOfChiDt;
184	<	Mat3x3d eta;
180	>	#ifdef HAVE_LIBZ
181	>	if (needCompression_) {
182	>	filename_ += ".gz";
183	>	eorFilename_ += ".gz";
184	>	}
185	>	#endif
186
187	<	currentTime = s->getTime();
105	<	hmat = s->getHmat();
106	<	chi = s->getChi();
107	<	integralOfChiDt = s->getIntegralOfChiDt();
108	<	eta = s->getEta();
187	>	#ifdef IS_MPI
188
189	<	os << currentTime << ";\t"
190	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
191	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
192	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
189	>	if (worldRank == 0) {
190	>	#endif // is_mpi
191	>
192	>	createDumpFile_ = writeDumpFile;
193	>	if (createDumpFile_) {
194	>	dumpFile_ = createOStream(filename_);
195	>
196	>	if (!dumpFile_) {
197	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
198	>	filename_.c_str());
199	>	painCave.isFatal = 1;
200	>	simError();
201	>	}
202	>	}
203	>	#ifdef IS_MPI
204	>
205	>	}
206
207	<	//write out additional parameters, such as chi and eta
207	>
208	>	#endif // is_mpi
209	>
210	>	}
211
212	<	os << chi << "\t" << integralOfChiDt << "\t;";
212	>	DumpWriter::~DumpWriter() {
213
214	<	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	<	}
214	>	#ifdef IS_MPI
215
216	<	void DumpWriter::writeFrame(std::ostream& os) {
217	<	const int BUFFERSIZE = 2000;
218	<	const int MINIBUFFERSIZE = 100;
216	>	if (worldRank == 0) {
217	>	#endif // is_mpi
218	>	if (createDumpFile_){
219	>	writeClosing(*dumpFile_);
220	>	delete dumpFile_;
221	>	}
222	>	#ifdef IS_MPI
223
224	<	char tempBuffer[BUFFERSIZE];
131	<	char writeLine[BUFFERSIZE];
224	>	}
225
226	<	Quat4d q;
134	<	Vector3d ji;
135	<	Vector3d pos;
136	<	Vector3d vel;
226	>	#endif // is_mpi
227
228	<	Molecule* mol;
139	<	StuntDouble* integrableObject;
140	<	SimInfo::MoleculeIterator mi;
141	<	Molecule::IntegrableObjectIterator ii;
142	<
143	<	int nTotObjects;
144	<	nTotObjects = info_->getNGlobalIntegrableObjects();
228	>	}
229
230	<	#ifndef IS_MPI
230	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
231
232	+	char buffer[1024];
233
234	<	os << nTotObjects << "\n";
150	<
151	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
234	>	os << "    <FrameData>\n";
235
236	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
236	>	RealType currentTime = s->getTime();
237
238	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
239	<	integrableObject = mol->nextIntegrableObject(ii)) {
240	<
238	>	if (isinf(currentTime) || isnan(currentTime)) {
239	>	sprintf( painCave.errMsg,
240	>	"DumpWriter detected a numerical error writing the time");
241	>	painCave.isFatal = 1;
242	>	simError();
243	>	}
244	>
245	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
246	>	os << buffer;
247
248	<	pos = integrableObject->getPos();
249	<	vel = integrableObject->getVel();
248	>	Mat3x3d hmat;
249	>	hmat = s->getHmat();
250
251	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
252	<	integrableObject->getType().c_str(),
253	<	pos[0], pos[1], pos[2],
254	<	vel[0], vel[1], vel[2]);
251	>	for (unsigned int i = 0; i < 3; i++) {
252	>	for (unsigned int j = 0; j < 3; j++) {
253	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
254	>	sprintf( painCave.errMsg,
255	>	"DumpWriter detected a numerical error writing the box");
256	>	painCave.isFatal = 1;
257	>	simError();
258	>	}
259	>	}
260	>	}
261	>
262	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
263	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
264	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
265	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
266	>	os << buffer;
267
268	<	strcpy(writeLine, tempBuffer);
268	>	pair<RealType, RealType> thermostat = s->getThermostat();
269
270	<	if (integrableObject->isDirectional()) {
271	<	q = integrableObject->getQ();
272	<	ji = integrableObject->getJ();
270	>	if (isinf(thermostat.first)  || isnan(thermostat.first) ||
271	>	isinf(thermostat.second) || isnan(thermostat.second)) {
272	>	sprintf( painCave.errMsg,
273	>	"DumpWriter detected a numerical error writing the thermostat");
274	>	painCave.isFatal = 1;
275	>	simError();
276	>	}
277	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
278	>	thermostat.second);
279	>	os << buffer;
280
281	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
282	<	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	<	}
281	>	Mat3x3d eta;
282	>	eta = s->getBarostat();
283
284	<	os << writeLine;
285	<
286	<	}
284	>	for (unsigned int i = 0; i < 3; i++) {
285	>	for (unsigned int j = 0; j < 3; j++) {
286	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
287	>	sprintf( painCave.errMsg,
288	>	"DumpWriter detected a numerical error writing the barostat");
289	>	painCave.isFatal = 1;
290	>	simError();
291	>	}
292	>	}
293		}
294
295	<	#else // is_mpi
296	<	/*********************************************************************
297	<	* Documentation?  You want DOCUMENTATION?
298	<	*
299	<	* 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;
295	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
296	>	eta(0, 0), eta(1, 0), eta(2, 0),
297	>	eta(0, 1), eta(1, 1), eta(2, 1),
298	>	eta(0, 2), eta(1, 2), eta(2, 2));
299	>	os << buffer;
300
301	<	int * potatoes;
302	<	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);
301	>	os << "    </FrameData>\n";
302	>	}
303
304	<	if (flag) {
245	<	MAXTAG = *tagub;
246	<	} else {
247	<	MAXTAG = 32767;
248	<	}
304	>	void DumpWriter::writeFrame(std::ostream& os) {
305
306	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
306	>	#ifdef IS_MPI
307	>	MPI_Status* istatus;
308	>	#endif
309
310	<	// Node 0 needs a list of the magic potatoes for each processor;
310	>	Molecule* mol;
311	>	StuntDouble* sd;
312	>	SimInfo::MoleculeIterator mi;
313	>	Molecule::IntegrableObjectIterator ii;
314	>	RigidBody::AtomIterator ai;
315
316	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
317	<	potatoes = new int[nProc];
316	>	#ifndef IS_MPI
317	>	os << "  <Snapshot>\n";
318	>
319	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
320
321	<	//write out the comment lines
322	<	for(int i = 0; i < nProc; i++) {
323	<	potatoes[i] = 0;
324	<	}
321	>	os << "    <StuntDoubles>\n";
322	>	for (mol = info_->beginMolecule(mi); mol != NULL;
323	>	mol = info_->nextMolecule(mi)) {
324	>
325	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
326	>	sd = mol->nextIntegrableObject(ii)) {
327	>	os << prepareDumpLine(sd);
328	>
329	>	}
330	>	}
331	>	os << "    </StuntDoubles>\n";
332
333	+	if (doSiteData_) {
334	+	os << "    <SiteData>\n";
335	+	for (mol = info_->beginMolecule(mi); mol != NULL;
336	+	mol = info_->nextMolecule(mi)) {
337	+
338	+	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
339	+	sd = mol->nextIntegrableObject(ii)) {
340
341	<	os << nTotObjects << "\n";
342	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
341	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
342	>	// do one for the IO itself
343	>	os << prepareSiteLine(sd, ioIndex, 0);
344
345	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
345	>	if (sd->isRigidBody()) {
346	>
347	>	RigidBody* rb = static_cast<RigidBody*>(sd);
348	>	int siteIndex = 0;
349	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
350	>	atom = rb->nextAtom(ai)) {
351	>	os << prepareSiteLine(atom, ioIndex, siteIndex);
352	>	siteIndex++;
353	>	}
354	>	}
355	>	}
356	>	}
357	>	os << "    </SiteData>\n";
358	>	}
359	>	os << "  </Snapshot>\n";
360
361	<	// Get the Node number which has this atom;
361	>	os.flush();
362	>	#else
363
364	<	which_node = info_->getMolToProc(i);
364	>	const int masterNode = 0;
365	>	int worldRank;
366	>	int nProc;
367
368	<	if (which_node != masterNode) { //current molecule is in slave node
369	<	if (potatoes[which_node] + 1 >= MAXTAG) {
274	<	// The potato was going to exceed the maximum value,
275	<	// so wrap this processor potato back to 0:
368	>	MPI_Comm_size( MPI_COMM_WORLD, &nProc);
369	>	MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
370
277	–	potatoes[which_node] = 0;
278	–	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
279	–	MPI_COMM_WORLD);
280	–	}
371
372	<	myPotato = potatoes[which_node];
372	>	if (worldRank == masterNode) {
373	>	os << "  <Snapshot>\n";
374	>	writeFrameProperties(os,
375	>	info_->getSnapshotManager()->getCurrentSnapshot());
376	>	os << "    <StuntDoubles>\n";
377	>	}
378
379	<	//recieve the number of integrableObject in current molecule
380	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
381	<	MPI_COMM_WORLD, &istatus);
382	<	myPotato++;
379	>	//every node prepares the dump lines for integrable objects belong to itself
380	>	std::string buffer;
381	>	for (mol = info_->beginMolecule(mi); mol != NULL;
382	>	mol = info_->nextMolecule(mi)) {
383	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
384	>	sd = mol->nextIntegrableObject(ii)) {
385	>	buffer += prepareDumpLine(sd);
386	>	}
387	>	}
388	>
389	>	if (worldRank == masterNode) {
390	>	os << buffer;
391	>
392	>	for (int i = 1; i < nProc; ++i) {
393	>	// tell processor i to start sending us data:
394	>	MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
395
396	<	for(int l = 0; l < nCurObj; l++) {
397	<	if (potatoes[which_node] + 2 >= MAXTAG) {
398	<	// The potato was going to exceed the maximum value,
399	<	// so wrap this processor potato back to 0:
396	>	// receive the length of the string buffer that was
397	>	// prepared by processor i:
398	>	int recvLength;
399	>	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
400	>	istatus);
401
402	<	potatoes[which_node] = 0;
403	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
404	<	0, MPI_COMM_WORLD);
405	<	}
402	>	// create a buffer to receive the data
403	>	char* recvBuffer = new char[recvLength];
404	>	if (recvBuffer == NULL) {
405	>	} else {
406	>	// receive the data:
407	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
408	>	MPI_ANY_TAG, MPI_COMM_WORLD, istatus);
409	>	// send it to the file:
410	>	os << recvBuffer;
411	>	// get rid of the receive buffer:
412	>	delete [] recvBuffer;
413	>	}
414	>	}
415	>	} else {
416	>	int sendBufferLength = buffer.size() + 1;
417	>	int myturn = 0;
418	>	for (int i = 1; i < nProc; ++i){
419	>	// wait for the master node to call our number:
420	>	MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
421	>	if (myturn == worldRank){
422	>	// send the length of our buffer:
423	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
424
425	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
426	<	which_node, myPotato, MPI_COMM_WORLD,
427	<	&istatus);
425	>	// send our buffer:
426	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
427	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
428
429	<	atomTypeString = MPIatomTypeString;
429	>	}
430	>	}
431	>	}
432	>
433	>	if (worldRank == masterNode) {
434	>	os << "    </StuntDoubles>\n";
435	>	}
436
437	<	myPotato++;
437	>	if (doSiteData_) {
438	>	if (worldRank == masterNode) {
439	>	os << "    <SiteData>\n";
440	>	}
441	>	buffer.clear();
442	>	for (mol = info_->beginMolecule(mi); mol != NULL;
443	>	mol = info_->nextMolecule(mi)) {
444	>
445	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
446	>	sd = mol->nextIntegrableObject(ii)) {
447	>
448	>	int ioIndex = sd->getGlobalIntegrableObjectIndex();
449	>	// do one for the IO itself
450	>	buffer += prepareSiteLine(sd, ioIndex, 0);
451
452	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
453	<	MPI_COMM_WORLD, &istatus);
454	<	myPotato++;
452	>	if (sd->isRigidBody()) {
453	>
454	>	RigidBody* rb = static_cast<RigidBody*>(sd);
455	>	int siteIndex = 0;
456	>	for (Atom* atom = rb->beginAtom(ai); atom != NULL;
457	>	atom = rb->nextAtom(ai)) {
458	>	buffer += prepareSiteLine(atom, ioIndex, siteIndex);
459	>	siteIndex++;
460	>	}
461	>	}
462	>	}
463	>	}
464
465	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
466	<
467	<	if (msgLen == 13)
468	<	isDirectional = 1;
469	<	else
470	<	isDirectional = 0;
471	<
472	<	// If we've survived to here, format the line:
473	<
474	<	if (!isDirectional) {
475	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
476	<	atomTypeString, atomData[0],
477	<	atomData[1], atomData[2],
478	<	atomData[3], atomData[4],
479	<	atomData[5]);
465	>	if (worldRank == masterNode) {
466	>	os << buffer;
467	>
468	>	for (int i = 1; i < nProc; ++i) {
469	>
470	>	// tell processor i to start sending us data:
471	>	MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
472	>
473	>	// receive the length of the string buffer that was
474	>	// prepared by processor i:
475	>	int recvLength;
476	>	MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
477	>	istatus);
478	>
479	>	// create a buffer to receive the data
480	>	char* recvBuffer = new char[recvLength];
481	>	if (recvBuffer == NULL) {
482	>	} else {
483	>	// receive the data:
484	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
485	>	MPI_ANY_TAG, MPI_COMM_WORLD, istatus);
486	>	// send it to the file:
487	>	os << recvBuffer;
488	>	// get rid of the receive buffer:
489	>	delete [] recvBuffer;
490	>	}
491	>	}
492	>	} else {
493	>	int sendBufferLength = buffer.size() + 1;
494	>	int myturn = 0;
495	>	for (int i = 1; i < nProc; ++i){
496	>	// wait for the master node to call our number:
497	>	MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
498	>	if (myturn == worldRank){
499	>	// send the length of our buffer:
500	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
501	>	// send our buffer:
502	>	MPI_Send((void *)buffer.c_str(), sendBufferLength,
503	>	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
504	>	}
505	>	}
506	>	}
507	>
508	>	if (worldRank == masterNode) {
509	>	os << "    </SiteData>\n";
510	>	}
511	>	}
512	>
513	>	if (worldRank == masterNode) {
514	>	os << "  </Snapshot>\n";
515	>	os.flush();
516	>	}
517	>
518	>	#endif // is_mpi
519	>
520	>	}
521
522	<	strcat(writeLine,
523	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
524	<	} else {
525	<	sprintf(writeLine,
526	<	"%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",
527	<	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	<	}
522	>	std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
523	>
524	>	int index = sd->getGlobalIntegrableObjectIndex();
525	>	std::string type("pv");
526	>	std::string line;
527	>	char tempBuffer[4096];
528
529	<	os << writeLine;
529	>	Vector3d pos;
530	>	Vector3d vel;
531	>	pos = sd->getPos();
532
533	<	} // end for(int l =0)
533	>	if (isinf(pos[0]) || isnan(pos[0]) ||
534	>	isinf(pos[1]) || isnan(pos[1]) ||
535	>	isinf(pos[2]) || isnan(pos[2]) ) {
536	>	sprintf( painCave.errMsg,
537	>	"DumpWriter detected a numerical error writing the position"
538	>	" for object %d", index);
539	>	painCave.isFatal = 1;
540	>	simError();
541	>	}
542
543	<	potatoes[which_node] = myPotato;
353	<	} else { //master node has current molecule
543	>	vel = sd->getVel();
544
545	<	mol = info_->getMoleculeByGlobalIndex(i);
545	>	if (isinf(vel[0]) || isnan(vel[0]) ||
546	>	isinf(vel[1]) || isnan(vel[1]) ||
547	>	isinf(vel[2]) || isnan(vel[2]) ) {
548	>	sprintf( painCave.errMsg,
549	>	"DumpWriter detected a numerical error writing the velocity"
550	>	" for object %d", index);
551	>	painCave.isFatal = 1;
552	>	simError();
553	>	}
554
555	<	if (mol == NULL) {
556	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
557	<	painCave.isFatal = 1;
558	<	simError();
361	<	}
362	<
363	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
364	<	integrableObject = mol->nextIntegrableObject(ii)) {
365	<
366	<	atomTypeString = integrableObject->getType().c_str();
555	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
556	>	pos[0], pos[1], pos[2],
557	>	vel[0], vel[1], vel[2]);
558	>	line += tempBuffer;
559
560	<	pos = integrableObject->getPos();
561	<	vel = integrableObject->getVel();
560	>	if (sd->isDirectional()) {
561	>	type += "qj";
562	>	Quat4d q;
563	>	Vector3d ji;
564	>	q = sd->getQ();
565
566	<	atomData[0] = pos[0];
567	<	atomData[1] = pos[1];
568	<	atomData[2] = pos[2];
566	>	if (isinf(q[0]) || isnan(q[0]) ||
567	>	isinf(q[1]) || isnan(q[1]) ||
568	>	isinf(q[2]) || isnan(q[2]) ||
569	>	isinf(q[3]) || isnan(q[3]) ) {
570	>	sprintf( painCave.errMsg,
571	>	"DumpWriter detected a numerical error writing the quaternion"
572	>	" for object %d", index);
573	>	painCave.isFatal = 1;
574	>	simError();
575	>	}
576
577	<	atomData[3] = vel[0];
376	<	atomData[4] = vel[1];
377	<	atomData[5] = vel[2];
577	>	ji = sd->getJ();
578
579	<	isDirectional = 0;
579	>	if (isinf(ji[0]) || isnan(ji[0]) ||
580	>	isinf(ji[1]) || isnan(ji[1]) ||
581	>	isinf(ji[2]) || isnan(ji[2]) ) {
582	>	sprintf( painCave.errMsg,
583	>	"DumpWriter detected a numerical error writing the angular"
584	>	" momentum for object %d", index);
585	>	painCave.isFatal = 1;
586	>	simError();
587	>	}
588
589	<	if (integrableObject->isDirectional()) {
590	<	isDirectional = 1;
589	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
590	>	q[0], q[1], q[2], q[3],
591	>	ji[0], ji[1], ji[2]);
592	>	line += tempBuffer;
593	>	}
594
595	<	q = integrableObject->getQ();
596	<	ji = integrableObject->getJ();
595	>	if (needForceVector_) {
596	>	type += "f";
597	>	Vector3d frc = sd->getFrc();
598	>	if (isinf(frc[0]) || isnan(frc[0]) ||
599	>	isinf(frc[1]) || isnan(frc[1]) ||
600	>	isinf(frc[2]) || isnan(frc[2]) ) {
601	>	sprintf( painCave.errMsg,
602	>	"DumpWriter detected a numerical error writing the force"
603	>	" for object %d", index);
604	>	painCave.isFatal = 1;
605	>	simError();
606	>	}
607	>	sprintf(tempBuffer, " %13e %13e %13e",
608	>	frc[0], frc[1], frc[2]);
609	>	line += tempBuffer;
610	>
611	>	if (sd->isDirectional()) {
612	>	type += "t";
613	>	Vector3d trq = sd->getTrq();
614	>	if (isinf(trq[0]) || isnan(trq[0]) ||
615	>	isinf(trq[1]) || isnan(trq[1]) ||
616	>	isinf(trq[2]) || isnan(trq[2]) ) {
617	>	sprintf( painCave.errMsg,
618	>	"DumpWriter detected a numerical error writing the torque"
619	>	" for object %d", index);
620	>	painCave.isFatal = 1;
621	>	simError();
622	>	}
623	>	sprintf(tempBuffer, " %13e %13e %13e",
624	>	trq[0], trq[1], trq[2]);
625	>	line += tempBuffer;
626	>	}
627	>	}
628
629	<	for(int j = 0; j < 6; j++) {
630	<	atomData[j] = atomData[j];
631	<	}
629	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
630	>	return std::string(tempBuffer);
631	>	}
632
633	<	atomData[6] = q[0];
634	<	atomData[7] = q[1];
393	<	atomData[8] = q[2];
394	<	atomData[9] = q[3];
633	>	std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
634	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
635
636	<	atomData[10] = ji[0];
637	<	atomData[11] = ji[1];
638	<	atomData[12] = ji[2];
639	<	}
636	>	std::string id;
637	>	std::string type;
638	>	std::string line;
639	>	char tempBuffer[4096];
640
641	<	// If we've survived to here, format the line:
642	<
643	<	if (!isDirectional) {
644	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
645	<	atomTypeString, atomData[0],
646	<	atomData[1], atomData[2],
647	<	atomData[3], atomData[4],
648	<	atomData[5]);
649	<
650	<	strcat(writeLine,
651	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
652	<	} else {
653	<	sprintf(writeLine,
654	<	"%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",
655	<	atomTypeString,
656	<	atomData[0],
657	<	atomData[1],
658	<	atomData[2],
659	<	atomData[3],
660	<	atomData[4],
661	<	atomData[5],
662	<	atomData[6],
423	<	atomData[7],
424	<	atomData[8],
425	<	atomData[9],
426	<	atomData[10],
427	<	atomData[11],
428	<	atomData[12]);
429	<	}
430	<
431	<
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();
641	>	if (sd->isRigidBody()) {
642	>	sprintf(tempBuffer, "%10d           ", ioIndex);
643	>	id = std::string(tempBuffer);
644	>	} else {
645	>	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
646	>	id = std::string(tempBuffer);
647	>	}
648	>
649	>	if (needFlucQ_) {
650	>	if (storageLayout & DataStorage::dslFlucQPosition) {
651	>	type += "c";
652	>	RealType fqPos = sd->getFlucQPos();
653	>	if (isinf(fqPos) || isnan(fqPos) ) {
654	>	sprintf( painCave.errMsg,
655	>	"DumpWriter detected a numerical error writing the"
656	>	" fluctuating charge for object %s", id.c_str());
657	>	painCave.isFatal = 1;
658	>	simError();
659	>	}
660	>	sprintf(tempBuffer, " %13e ", fqPos);
661	>	line += tempBuffer;
662	>	}
663
664	<	delete [] potatoes;
665	<	} else {
664	>	if (storageLayout & DataStorage::dslFlucQVelocity) {
665	>	type += "w";
666	>	RealType fqVel = sd->getFlucQVel();
667	>	if (isinf(fqVel) || isnan(fqVel) ) {
668	>	sprintf( painCave.errMsg,
669	>	"DumpWriter detected a numerical error writing the"
670	>	" fluctuating charge velocity for object %s", id.c_str());
671	>	painCave.isFatal = 1;
672	>	simError();
673	>	}
674	>	sprintf(tempBuffer, " %13e ", fqVel);
675	>	line += tempBuffer;
676	>	}
677
678	<	// worldRank != 0, so I'm a remote node.
678	>	if (needForceVector_) {
679	>	if (storageLayout & DataStorage::dslFlucQForce) {
680	>	type += "g";
681	>	RealType fqFrc = sd->getFlucQFrc();
682	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
683	>	sprintf( painCave.errMsg,
684	>	"DumpWriter detected a numerical error writing the"
685	>	" fluctuating charge force for object %s", id.c_str());
686	>	painCave.isFatal = 1;
687	>	simError();
688	>	}
689	>	sprintf(tempBuffer, " %13e ", fqFrc);
690	>	line += tempBuffer;
691	>	}
692	>	}
693	>	}
694	>
695	>	if (needElectricField_) {
696	>	if (storageLayout & DataStorage::dslElectricField) {
697	>	type += "e";
698	>	Vector3d eField= sd->getElectricField();
699	>	if (isinf(eField[0]) || isnan(eField[0]) ||
700	>	isinf(eField[1]) || isnan(eField[1]) ||
701	>	isinf(eField[2]) || isnan(eField[2]) ) {
702	>	sprintf( painCave.errMsg,
703	>	"DumpWriter detected a numerical error writing the electric"
704	>	" field for object %s", id.c_str());
705	>	painCave.isFatal = 1;
706	>	simError();
707	>	}
708	>	sprintf(tempBuffer, " %13e %13e %13e",
709	>	eField[0], eField[1], eField[2]);
710	>	line += tempBuffer;
711	>	}
712	>	}
713
448	–	// Set my magic potato to 0:
714
715	<	myPotato = 0;
715	>	if (needParticlePot_) {
716	>	if (storageLayout & DataStorage::dslParticlePot) {
717	>	type += "u";
718	>	RealType particlePot = sd->getParticlePot();
719	>	if (isinf(particlePot) || isnan(particlePot)) {
720	>	sprintf( painCave.errMsg,
721	>	"DumpWriter detected a numerical error writing the particle "
722	>	" potential for object %s", id.c_str());
723	>	painCave.isFatal = 1;
724	>	simError();
725	>	}
726	>	sprintf(tempBuffer, " %13e", particlePot);
727	>	line += tempBuffer;
728	>	}
729	>	}
730	>
731	>	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
732	>	return std::string(tempBuffer);
733	>	}
734
735	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
735	>	void DumpWriter::writeDump() {
736	>	writeFrame(*dumpFile_);
737	>	}
738
739	<	// Am I the node which has this integrableObject?
740	<	int whichNode = info_->getMolToProc(i);
741	<	if (whichNode == worldRank) {
742	<	if (myPotato + 1 >= MAXTAG) {
739	>	void DumpWriter::writeEor() {
740	>	std::ostream* eorStream;
741	>
742	>	#ifdef IS_MPI
743	>	if (worldRank == 0) {
744	>	#endif // is_mpi
745	>
746	>	eorStream = createOStream(eorFilename_);
747
748	<	// The potato was going to exceed the maximum value,
749	<	// so wrap this processor potato back to 0 (and block until
750	<	// node 0 says we can go:
748	>	#ifdef IS_MPI
749	>	}
750	>	#endif
751	>
752	>	writeFrame(*eorStream);
753	>
754	>	#ifdef IS_MPI
755	>	if (worldRank == 0) {
756	>	#endif
757	>
758	>	writeClosing(*eorStream);
759	>	delete eorStream;
760	>
761	>	#ifdef IS_MPI
762	>	}
763	>	#endif // is_mpi
764
765	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
464	<	&istatus);
465	<	}
765	>	}
766
467	–	mol = info_->getMoleculeByGlobalIndex(i);
767
768	<
769	<	nCurObj = mol->getNIntegrableObjects();
768	>	void DumpWriter::writeDumpAndEor() {
769	>	std::vector<std::streambuf*> buffers;
770	>	std::ostream* eorStream;
771	>	#ifdef IS_MPI
772	>	if (worldRank == 0) {
773	>	#endif // is_mpi
774	>	buffers.push_back(dumpFile_->rdbuf());
775	>	eorStream = createOStream(eorFilename_);
776	>	buffers.push_back(eorStream->rdbuf());
777	>	#ifdef IS_MPI
778	>	}
779	>	#endif // is_mpi
780
781	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
782	<	myPotato++;
781	>	TeeBuf tbuf(buffers.begin(), buffers.end());
782	>	std::ostream os(&tbuf);
783	>	writeFrame(os);
784
785	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
786	<	integrableObject = mol->nextIntegrableObject(ii)) {
785	>	#ifdef IS_MPI
786	>	if (worldRank == 0) {
787	>	#endif // is_mpi
788	>	writeClosing(*eorStream);
789	>	delete eorStream;
790	>	#ifdef IS_MPI
791	>	}
792	>	#endif // is_mpi
793	>	}
794
795	<	if (myPotato + 2 >= MAXTAG) {
795	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
796
797	<	// The potato was going to exceed the maximum value,
798	<	// so wrap this processor potato back to 0 (and block until
799	<	// node 0 says we can go:
800	<
801	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
802	<	&istatus);
486	<	}
487	<
488	<	atomTypeString = integrableObject->getType().c_str();
489	<
490	<	pos = integrableObject->getPos();
491	<	vel = integrableObject->getVel();
492	<
493	<	atomData[0] = pos[0];
494	<	atomData[1] = pos[1];
495	<	atomData[2] = pos[2];
496	<
497	<	atomData[3] = vel[0];
498	<	atomData[4] = vel[1];
499	<	atomData[5] = vel[2];
500	<
501	<	isDirectional = 0;
502	<
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();
797	>	std::ostream* newOStream;
798	>	#ifdef HAVE_ZLIB
799	>	if (needCompression_) {
800	>	newOStream = new ogzstream(filename.c_str());
801	>	} else {
802	>	newOStream = new std::ofstream(filename.c_str());
803		}
804	+	#else
805	+	newOStream = new std::ofstream(filename.c_str());
806	+	#endif
807	+	//write out MetaData first
808	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
809	+	(*newOStream) << "  <MetaData>" << std::endl;
810	+	(*newOStream) << info_->getRawMetaData();
811	+	(*newOStream) << "  </MetaData>" << std::endl;
812	+	return newOStream;
813	+	}
814
815	<	#endif // is_mpi
815	>	void DumpWriter::writeClosing(std::ostream& os) {
816
817	<	}
817	>	os << "</OpenMD>\n";
818	>	os.flush();
819	>	}
820
821	<	}//end namespace oopse
821	>	}//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.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

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