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

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trunk/src/io/DumpWriter.cpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
1	>	/*
2	>	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include "io/DumpWriter.hpp"
44		#include "primitives/Molecule.hpp"
45		#include "utils/simError.h"
46	+	#include "io/basic_teebuf.hpp"
47	+	#include "io/gzstream.hpp"
48	+	#include "io/Globals.hpp"
49
50	+
51		#ifdef IS_MPI
52		#include <mpi.h>
53	<	#endif //is_mpi
53	>	#endif
54
55	<	namespace oopse {
55	>	using namespace std;
56	>	namespace OpenMD {
57
58	<	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
59	<	: info_(info), filename_(filename){
58	>	DumpWriter::DumpWriter(SimInfo* info)
59	>	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
60	>
61	>	Globals* simParams = info->getSimParams();
62	>	needCompression_   = simParams->getCompressDumpFile();
63	>	needForceVector_   = simParams->getOutputForceVector();
64	>	needParticlePot_   = simParams->getOutputParticlePotential();
65	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
66	>	needElectricField_ = simParams->getOutputElectricField();
67	>
68	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
69	>	doSiteData_ = true;
70	>	} else {
71	>	doSiteData_ = false;
72	>	}
73	>
74	>	createDumpFile_ = true;
75	>	#ifdef HAVE_LIBZ
76	>	if (needCompression_) {
77	>	filename_ += ".gz";
78	>	eorFilename_ += ".gz";
79	>	}
80	>	#endif
81	>
82		#ifdef IS_MPI
83
84		if (worldRank == 0) {
85		#endif // is_mpi
86	+
87	+	dumpFile_ = createOStream(filename_);
88
89	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
89	>	if (!dumpFile_) {
90	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
91	>	filename_.c_str());
92	>	painCave.isFatal = 1;
93	>	simError();
94	>	}
95
61	–	if (!dumpFile_) {
62	–	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
63	–	filename_.c_str());
64	–	painCave.isFatal = 1;
65	–	simError();
66	–	}
67	–
96		#ifdef IS_MPI
97
98		}
99
72	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73	–	MPIcheckPoint();
74	–
100		#endif // is_mpi
101
102	<	}
102	>	}
103
79	–	DumpWriter::~DumpWriter() {
104
105	+	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
106	+	: info_(info), filename_(filename){
107	+
108	+	Globals* simParams = info->getSimParams();
109	+	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
110	+
111	+	needCompression_   = simParams->getCompressDumpFile();
112	+	needForceVector_   = simParams->getOutputForceVector();
113	+	needParticlePot_   = simParams->getOutputParticlePotential();
114	+	needFlucQ_         = simParams->getOutputFluctuatingCharges();
115	+	needElectricField_ = simParams->getOutputElectricField();
116	+
117	+	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
118	+	doSiteData_ = true;
119	+	} else {
120	+	doSiteData_ = false;
121	+	}
122	+
123	+	createDumpFile_ = true;
124	+	#ifdef HAVE_LIBZ
125	+	if (needCompression_) {
126	+	filename_ += ".gz";
127	+	eorFilename_ += ".gz";
128	+	}
129	+	#endif
130	+
131		#ifdef IS_MPI
132
133		if (worldRank == 0) {
134		#endif // is_mpi
135
136	<	dumpFile_.close();
136	>
137	>	dumpFile_ = createOStream(filename_);
138
139	+	if (!dumpFile_) {
140	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
141	+	filename_.c_str());
142	+	painCave.isFatal = 1;
143	+	simError();
144	+	}
145	+
146		#ifdef IS_MPI
147
148		}
149
150		#endif // is_mpi
151
152	<	}
152	>	}
153	>
154	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
155	>	: info_(info), filename_(filename){
156	>
157	>	Globals* simParams = info->getSimParams();
158	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
159	>
160	>	needCompression_   = simParams->getCompressDumpFile();
161	>	needForceVector_   = simParams->getOutputForceVector();
162	>	needParticlePot_   = simParams->getOutputParticlePotential();
163	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
164	>	needElectricField_ = simParams->getOutputElectricField();
165
166	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
166	>	if (needParticlePot_ || needFlucQ_ || needElectricField_) {
167	>	doSiteData_ = true;
168	>	} else {
169	>	doSiteData_ = false;
170	>	}
171
172	<	double currentTime;
173	<	Mat3x3d hmat;
174	<	double chi;
175	<	double integralOfChiDt;
176	<	Mat3x3d eta;
172	>	#ifdef HAVE_LIBZ
173	>	if (needCompression_) {
174	>	filename_ += ".gz";
175	>	eorFilename_ += ".gz";
176	>	}
177	>	#endif
178
179	<	currentTime = s->getTime();
105	<	hmat = s->getHmat();
106	<	chi = s->getChi();
107	<	integralOfChiDt = s->getIntegralOfChiDt();
108	<	eta = s->getEta();
179	>	#ifdef IS_MPI
180
181	<	os << currentTime << ";\t"
182	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
183	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
184	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
181	>	if (worldRank == 0) {
182	>	#endif // is_mpi
183	>
184	>	createDumpFile_ = writeDumpFile;
185	>	if (createDumpFile_) {
186	>	dumpFile_ = createOStream(filename_);
187	>
188	>	if (!dumpFile_) {
189	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
190	>	filename_.c_str());
191	>	painCave.isFatal = 1;
192	>	simError();
193	>	}
194	>	}
195	>	#ifdef IS_MPI
196	>
197	>	}
198
199	<	//write out additional parameters, such as chi and eta
199	>
200	>	#endif // is_mpi
201	>
202	>	}
203
204	<	os << chi << "\t" << integralOfChiDt << "\t;";
204	>	DumpWriter::~DumpWriter() {
205
206	<	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	<	}
206	>	#ifdef IS_MPI
207
208	<	void DumpWriter::writeFrame(std::ostream& os) {
209	<	const int BUFFERSIZE = 2000;
210	<	const int MINIBUFFERSIZE = 100;
208	>	if (worldRank == 0) {
209	>	#endif // is_mpi
210	>	if (createDumpFile_){
211	>	writeClosing(*dumpFile_);
212	>	delete dumpFile_;
213	>	}
214	>	#ifdef IS_MPI
215
216	<	char tempBuffer[BUFFERSIZE];
131	<	char writeLine[BUFFERSIZE];
216	>	}
217
218	<	Quat4d q;
134	<	Vector3d ji;
135	<	Vector3d pos;
136	<	Vector3d vel;
218	>	#endif // is_mpi
219
220	<	Molecule* mol;
139	<	StuntDouble* integrableObject;
140	<	SimInfo::MoleculeIterator mi;
141	<	Molecule::IntegrableObjectIterator ii;
142	<
143	<	int nTotObjects;
144	<	nTotObjects = info_->getNGlobalIntegrableObjects();
220	>	}
221
222	<	#ifndef IS_MPI
222	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
223
224	+	char buffer[1024];
225
226	<	os << nTotObjects << "\n";
150	<
151	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
226	>	os << "    <FrameData>\n";
227
228	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
228	>	RealType currentTime = s->getTime();
229
230	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
231	<	integrableObject = mol->nextIntegrableObject(ii)) {
232	<
230	>	if (isinf(currentTime) || isnan(currentTime)) {
231	>	sprintf( painCave.errMsg,
232	>	"DumpWriter detected a numerical error writing the time");
233	>	painCave.isFatal = 1;
234	>	simError();
235	>	}
236	>
237	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
238	>	os << buffer;
239
240	<	pos = integrableObject->getPos();
241	<	vel = integrableObject->getVel();
240	>	Mat3x3d hmat;
241	>	hmat = s->getHmat();
242
243	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
244	<	integrableObject->getType().c_str(),
245	<	pos[0], pos[1], pos[2],
246	<	vel[0], vel[1], vel[2]);
243	>	for (unsigned int i = 0; i < 3; i++) {
244	>	for (unsigned int j = 0; j < 3; j++) {
245	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
246	>	sprintf( painCave.errMsg,
247	>	"DumpWriter detected a numerical error writing the box");
248	>	painCave.isFatal = 1;
249	>	simError();
250	>	}
251	>	}
252	>	}
253	>
254	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
255	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
256	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
257	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
258	>	os << buffer;
259
260	<	strcpy(writeLine, tempBuffer);
260	>	pair<RealType, RealType> thermostat = s->getThermostat();
261
262	<	if (integrableObject->isDirectional()) {
263	<	q = integrableObject->getQ();
264	<	ji = integrableObject->getJ();
265	<
266	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
267	<	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	<	}
180	<
181	<	os << writeLine;
182	<
183	<	}
262	>	if (isinf(thermostat.first)  || isnan(thermostat.first) ||
263	>	isinf(thermostat.second) || isnan(thermostat.second)) {
264	>	sprintf( painCave.errMsg,
265	>	"DumpWriter detected a numerical error writing the thermostat");
266	>	painCave.isFatal = 1;
267	>	simError();
268		}
269	+	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
270	+	thermostat.second);
271	+	os << buffer;
272
273	<	#else // is_mpi
274	<	/*********************************************************************
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;
273	>	Mat3x3d eta;
274	>	eta = s->getBarostat();
275
276	<	int * potatoes;
277	<	int myPotato;
278	<	int nProc;
279	<	int which_node;
280	<	double atomData[13];
281	<	int isDirectional;
282	<	const char * atomTypeString;
283	<	char MPIatomTypeString[MINIBUFFERSIZE];
284	<	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);
243	<
244	<	if (flag) {
245	<	MAXTAG = *tagub;
246	<	} else {
247	<	MAXTAG = 32767;
276	>	for (unsigned int i = 0; i < 3; i++) {
277	>	for (unsigned int j = 0; j < 3; j++) {
278	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
279	>	sprintf( painCave.errMsg,
280	>	"DumpWriter detected a numerical error writing the barostat");
281	>	painCave.isFatal = 1;
282	>	simError();
283	>	}
284	>	}
285		}
286
287	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
287	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
288	>	eta(0, 0), eta(1, 0), eta(2, 0),
289	>	eta(0, 1), eta(1, 1), eta(2, 1),
290	>	eta(0, 2), eta(1, 2), eta(2, 2));
291	>	os << buffer;
292
293	<	// Node 0 needs a list of the magic potatoes for each processor;
293	>	os << "    </FrameData>\n";
294	>	}
295
296	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
255	<	potatoes = new int[nProc];
296	>	void DumpWriter::writeFrame(std::ostream& os) {
297
298	<	//write out the comment lines
299	<	for(int i = 0; i < nProc; i++) {
300	<	potatoes[i] = 0;
260	<	}
298	>	#ifdef IS_MPI
299	>	MPI_Status istatus;
300	>	#endif
301
302	+	Molecule* mol;
303	+	StuntDouble* integrableObject;
304	+	SimInfo::MoleculeIterator mi;
305	+	Molecule::IntegrableObjectIterator ii;
306	+	RigidBody::AtomIterator ai;
307	+	Atom* atom;
308
309	<	os << nTotObjects << "\n";
310	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
309	>	#ifndef IS_MPI
310	>	os << "  <Snapshot>\n";
311	>
312	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
313
314	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
314	>	os << "    <StuntDoubles>\n";
315	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
316
317	<	// Get the Node number which has this atom;
317	>
318	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
319	>	integrableObject = mol->nextIntegrableObject(ii)) {
320	>	os << prepareDumpLine(integrableObject);
321	>
322	>	}
323	>	}
324	>	os << "    </StuntDoubles>\n";
325
326	<	which_node = info_->getMolToProc(i);
326	>	if (doSiteData_) {
327	>	os << "    <SiteData>\n";
328	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
329	>
330	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
331	>	integrableObject = mol->nextIntegrableObject(ii)) {
332
333	<	if (which_node != masterNode) { //current molecule is in slave node
334	<	if (potatoes[which_node] + 1 >= MAXTAG) {
335	<	// The potato was going to exceed the maximum value,
275	<	// so wrap this processor potato back to 0:
333	>	int ioIndex = integrableObject->getGlobalIntegrableObjectIndex();
334	>	// do one for the IO itself
335	>	os << prepareSiteLine(integrableObject, ioIndex, 0);
336
337	<	potatoes[which_node] = 0;
338	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
339	<	MPI_COMM_WORLD);
340	<	}
337	>	if (integrableObject->isRigidBody()) {
338	>
339	>	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
340	>	int siteIndex = 0;
341	>	for (atom = rb->beginAtom(ai); atom != NULL;
342	>	atom = rb->nextAtom(ai)) {
343	>	os << prepareSiteLine(atom, ioIndex, siteIndex);
344	>	siteIndex++;
345	>	}
346	>	}
347	>	}
348	>	}
349	>	os << "    </SiteData>\n";
350	>	}
351	>	os << "  </Snapshot>\n";
352
353	<	myPotato = potatoes[which_node];
353	>	os.flush();
354	>	#else
355	>	//every node prepares the dump lines for integrable objects belong to itself
356	>	std::string buffer;
357	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
358
284	–	//recieve the number of integrableObject in current molecule
285	–	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
286	–	MPI_COMM_WORLD, &istatus);
287	–	myPotato++;
359
360	<	for(int l = 0; l < nCurObj; l++) {
361	<	if (potatoes[which_node] + 2 >= MAXTAG) {
362	<	// The potato was going to exceed the maximum value,
363	<	// so wrap this processor potato back to 0:
360	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
361	>	integrableObject = mol->nextIntegrableObject(ii)) {
362	>	buffer += prepareDumpLine(integrableObject);
363	>	}
364	>	}
365	>
366	>	const int masterNode = 0;
367	>	int nProc;
368	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
369	>	if (worldRank == masterNode) {
370	>	os << "  <Snapshot>\n";
371	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
372	>	os << "    <StuntDoubles>\n";
373	>
374	>	os << buffer;
375
376	<	potatoes[which_node] = 0;
295	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
296	<	0, MPI_COMM_WORLD);
297	<	}
376	>	for (int i = 1; i < nProc; ++i) {
377
378	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
379	<	which_node, myPotato, MPI_COMM_WORLD,
301	<	&istatus);
378	>	// receive the length of the string buffer that was
379	>	// prepared by processor i
380
381	<	atomTypeString = MPIatomTypeString;
381	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
382	>	int recvLength;
383	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
384	>	char* recvBuffer = new char[recvLength];
385	>	if (recvBuffer == NULL) {
386	>	} else {
387	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
388	>	os << recvBuffer;
389	>	delete [] recvBuffer;
390	>	}
391	>	}
392	>	os << "    </StuntDoubles>\n";
393	>
394	>	os << "  </Snapshot>\n";
395	>	os.flush();
396	>	} else {
397	>	int sendBufferLength = buffer.size() + 1;
398	>	int myturn = 0;
399	>	for (int i = 1; i < nProc; ++i){
400	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
401	>	if (myturn == worldRank){
402	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
403	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
404	>	}
405	>	}
406	>	}
407
408	<	myPotato++;
408	>	#endif // is_mpi
409
410	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
308	<	MPI_COMM_WORLD, &istatus);
309	<	myPotato++;
410	>	}
411
412	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
412	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
413	>
414	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
415	>	std::string type("pv");
416	>	std::string line;
417	>	char tempBuffer[4096];
418
419	<	if (msgLen == 13)
420	<	isDirectional = 1;
421	<	else
316	<	isDirectional = 0;
419	>	Vector3d pos;
420	>	Vector3d vel;
421	>	pos = integrableObject->getPos();
422
423	<	// If we've survived to here, format the line:
423	>	if (isinf(pos[0]) || isnan(pos[0]) ||
424	>	isinf(pos[1]) || isnan(pos[1]) ||
425	>	isinf(pos[2]) || isnan(pos[2]) ) {
426	>	sprintf( painCave.errMsg,
427	>	"DumpWriter detected a numerical error writing the position"
428	>	" for object %d", index);
429	>	painCave.isFatal = 1;
430	>	simError();
431	>	}
432
433	<	if (!isDirectional) {
321	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
322	<	atomTypeString, atomData[0],
323	<	atomData[1], atomData[2],
324	<	atomData[3], atomData[4],
325	<	atomData[5]);
433	>	vel = integrableObject->getVel();
434
435	<	strcat(writeLine,
436	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
437	<	} else {
438	<	sprintf(writeLine,
439	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
440	<	atomTypeString,
441	<	atomData[0],
442	<	atomData[1],
443	<	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	<	}
435	>	if (isinf(vel[0]) || isnan(vel[0]) ||
436	>	isinf(vel[1]) || isnan(vel[1]) ||
437	>	isinf(vel[2]) || isnan(vel[2]) ) {
438	>	sprintf( painCave.errMsg,
439	>	"DumpWriter detected a numerical error writing the velocity"
440	>	" for object %d", index);
441	>	painCave.isFatal = 1;
442	>	simError();
443	>	}
444
445	<	os << writeLine;
445	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
446	>	pos[0], pos[1], pos[2],
447	>	vel[0], vel[1], vel[2]);
448	>	line += tempBuffer;
449
450	<	} // end for(int l =0)
450	>	if (integrableObject->isDirectional()) {
451	>	type += "qj";
452	>	Quat4d q;
453	>	Vector3d ji;
454	>	q = integrableObject->getQ();
455
456	<	potatoes[which_node] = myPotato;
457	<	} else { //master node has current molecule
456	>	if (isinf(q[0]) || isnan(q[0]) ||
457	>	isinf(q[1]) || isnan(q[1]) ||
458	>	isinf(q[2]) || isnan(q[2]) ||
459	>	isinf(q[3]) || isnan(q[3]) ) {
460	>	sprintf( painCave.errMsg,
461	>	"DumpWriter detected a numerical error writing the quaternion"
462	>	" for object %d", index);
463	>	painCave.isFatal = 1;
464	>	simError();
465	>	}
466
467	<	mol = info_->getMoleculeByGlobalIndex(i);
467	>	ji = integrableObject->getJ();
468
469	<	if (mol == NULL) {
470	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
471	<	painCave.isFatal = 1;
472	<	simError();
473	<	}
474	<
475	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
476	<	integrableObject = mol->nextIntegrableObject(ii)) {
477	<
366	<	atomTypeString = integrableObject->getType().c_str();
469	>	if (isinf(ji[0]) || isnan(ji[0]) ||
470	>	isinf(ji[1]) || isnan(ji[1]) ||
471	>	isinf(ji[2]) || isnan(ji[2]) ) {
472	>	sprintf( painCave.errMsg,
473	>	"DumpWriter detected a numerical error writing the angular"
474	>	" momentum for object %d", index);
475	>	painCave.isFatal = 1;
476	>	simError();
477	>	}
478
479	<	pos = integrableObject->getPos();
480	<	vel = integrableObject->getVel();
479	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
480	>	q[0], q[1], q[2], q[3],
481	>	ji[0], ji[1], ji[2]);
482	>	line += tempBuffer;
483	>	}
484
485	<	atomData[0] = pos[0];
486	<	atomData[1] = pos[1];
487	<	atomData[2] = pos[2];
485	>	if (needForceVector_) {
486	>	type += "f";
487	>	Vector3d frc = integrableObject->getFrc();
488	>	if (isinf(frc[0]) || isnan(frc[0]) ||
489	>	isinf(frc[1]) || isnan(frc[1]) ||
490	>	isinf(frc[2]) || isnan(frc[2]) ) {
491	>	sprintf( painCave.errMsg,
492	>	"DumpWriter detected a numerical error writing the force"
493	>	" for object %d", index);
494	>	painCave.isFatal = 1;
495	>	simError();
496	>	}
497	>	sprintf(tempBuffer, " %13e %13e %13e",
498	>	frc[0], frc[1], frc[2]);
499	>	line += tempBuffer;
500	>
501	>	if (integrableObject->isDirectional()) {
502	>	type += "t";
503	>	Vector3d trq = integrableObject->getTrq();
504	>	if (isinf(trq[0]) || isnan(trq[0]) ||
505	>	isinf(trq[1]) || isnan(trq[1]) ||
506	>	isinf(trq[2]) || isnan(trq[2]) ) {
507	>	sprintf( painCave.errMsg,
508	>	"DumpWriter detected a numerical error writing the torque"
509	>	" for object %d", index);
510	>	painCave.isFatal = 1;
511	>	simError();
512	>	}
513	>	sprintf(tempBuffer, " %13e %13e %13e",
514	>	trq[0], trq[1], trq[2]);
515	>	line += tempBuffer;
516	>	}
517	>	}
518
519	<	atomData[3] = vel[0];
520	<	atomData[4] = vel[1];
521	<	atomData[5] = vel[2];
519	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
520	>	return std::string(tempBuffer);
521	>	}
522
523	<	isDirectional = 0;
523	>	std::string DumpWriter::prepareSiteLine(StuntDouble* integrableObject, int ioIndex, int siteIndex) {
524	>
525
526	<	if (integrableObject->isDirectional()) {
527	<	isDirectional = 1;
526	>	std::string id;
527	>	std::string type;
528	>	std::string line;
529	>	char tempBuffer[4096];
530
531	<	q = integrableObject->getQ();
532	<	ji = integrableObject->getJ();
531	>	if (integrableObject->isRigidBody()) {
532	>	sprintf(tempBuffer, "%10d           ", ioIndex);
533	>	id = std::string(tempBuffer);
534	>	} else {
535	>	sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
536	>	id = std::string(tempBuffer);
537	>	}
538	>
539	>	if (needFlucQ_) {
540	>	type += "cw";
541	>	RealType fqPos = integrableObject->getFlucQPos();
542	>	if (isinf(fqPos) || isnan(fqPos) ) {
543	>	sprintf( painCave.errMsg,
544	>	"DumpWriter detected a numerical error writing the"
545	>	" fluctuating charge for object %s", id.c_str());
546	>	painCave.isFatal = 1;
547	>	simError();
548	>	}
549	>	sprintf(tempBuffer, " %13e ", fqPos);
550	>	line += tempBuffer;
551	>
552	>	RealType fqVel = integrableObject->getFlucQVel();
553	>	if (isinf(fqVel) || isnan(fqVel) ) {
554	>	sprintf( painCave.errMsg,
555	>	"DumpWriter detected a numerical error writing the"
556	>	" fluctuating charge velocity for object %s", id.c_str());
557	>	painCave.isFatal = 1;
558	>	simError();
559	>	}
560	>	sprintf(tempBuffer, " %13e ", fqVel);
561	>	line += tempBuffer;
562
563	<	for(int j = 0; j < 6; j++) {
564	<	atomData[j] = atomData[j];
565	<	}
563	>	if (needForceVector_) {
564	>	type += "g";
565	>	RealType fqFrc = integrableObject->getFlucQFrc();
566	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
567	>	sprintf( painCave.errMsg,
568	>	"DumpWriter detected a numerical error writing the"
569	>	" fluctuating charge force for object %s", id.c_str());
570	>	painCave.isFatal = 1;
571	>	simError();
572	>	}
573	>	sprintf(tempBuffer, " %13e ", fqFrc);
574	>	line += tempBuffer;
575	>	}
576	>	}
577
578	<	atomData[6] = q[0];
579	<	atomData[7] = q[1];
580	<	atomData[8] = q[2];
581	<	atomData[9] = q[3];
578	>	if (needElectricField_) {
579	>	type += "e";
580	>	Vector3d eField= integrableObject->getElectricField();
581	>	if (isinf(eField[0]) || isnan(eField[0]) ||
582	>	isinf(eField[1]) || isnan(eField[1]) ||
583	>	isinf(eField[2]) || isnan(eField[2]) ) {
584	>	sprintf( painCave.errMsg,
585	>	"DumpWriter detected a numerical error writing the electric"
586	>	" field for object %s", id.c_str());
587	>	painCave.isFatal = 1;
588	>	simError();
589	>	}
590	>	sprintf(tempBuffer, " %13e %13e %13e",
591	>	eField[0], eField[1], eField[2]);
592	>	line += tempBuffer;
593	>	}
594
396	–	atomData[10] = ji[0];
397	–	atomData[11] = ji[1];
398	–	atomData[12] = ji[2];
399	–	}
595
596	<	// If we've survived to here, format the line:
597	<
598	<	if (!isDirectional) {
599	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
600	<	atomTypeString, atomData[0],
601	<	atomData[1], atomData[2],
602	<	atomData[3], atomData[4],
603	<	atomData[5]);
596	>	if (needParticlePot_) {
597	>	type += "u";
598	>	RealType particlePot = integrableObject->getParticlePot();
599	>	if (isinf(particlePot) || isnan(particlePot)) {
600	>	sprintf( painCave.errMsg,
601	>	"DumpWriter detected a numerical error writing the particle "
602	>	" potential for object %s", id.c_str());
603	>	painCave.isFatal = 1;
604	>	simError();
605	>	}
606	>	sprintf(tempBuffer, " %13e", particlePot);
607	>	line += tempBuffer;
608	>	}
609	>
610
611	<	strcat(writeLine,
612	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
613	<	} else {
413	<	sprintf(writeLine,
414	<	"%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",
415	<	atomTypeString,
416	<	atomData[0],
417	<	atomData[1],
418	<	atomData[2],
419	<	atomData[3],
420	<	atomData[4],
421	<	atomData[5],
422	<	atomData[6],
423	<	atomData[7],
424	<	atomData[8],
425	<	atomData[9],
426	<	atomData[10],
427	<	atomData[11],
428	<	atomData[12]);
429	<	}
611	>	sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
612	>	return std::string(tempBuffer);
613	>	}
614
615	+	void DumpWriter::writeDump() {
616	+	writeFrame(*dumpFile_);
617	+	}
618
619	<	os << writeLine;
619	>	void DumpWriter::writeEor() {
620	>	std::ostream* eorStream;
621	>
622	>	#ifdef IS_MPI
623	>	if (worldRank == 0) {
624	>	#endif // is_mpi
625
626	<	} //end for(iter = integrableObject.begin())
435	<	}
436	<	} //end for(i = 0; i < mpiSim->getNmol())
626	>	eorStream = createOStream(eorFilename_);
627
628	<	os.flush();
629	<	std::cout << "master" << std::endl;
630	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
628	>	#ifdef IS_MPI
629	>	}
630	>	#endif // is_mpi
631
632	<	MPIcheckPoint();
632	>	writeFrame(*eorStream);
633
634	<	delete [] potatoes;
635	<	} else {
634	>	#ifdef IS_MPI
635	>	if (worldRank == 0) {
636	>	#endif // is_mpi
637	>	writeClosing(*eorStream);
638	>	delete eorStream;
639	>	#ifdef IS_MPI
640	>	}
641	>	#endif // is_mpi
642
643	<	// worldRank != 0, so I'm a remote node.
643	>	}
644
449	–	// Set my magic potato to 0:
645
646	<	myPotato = 0;
646	>	void DumpWriter::writeDumpAndEor() {
647	>	std::vector<std::streambuf*> buffers;
648	>	std::ostream* eorStream;
649	>	#ifdef IS_MPI
650	>	if (worldRank == 0) {
651	>	#endif // is_mpi
652
653	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
653	>	buffers.push_back(dumpFile_->rdbuf());
654
655	<	// Am I the node which has this integrableObject?
456	<	int whichNode = info_->getMolToProc(i);
457	<	if (whichNode == worldRank) {
458	<	if (myPotato + 1 >= MAXTAG) {
655	>	eorStream = createOStream(eorFilename_);
656
657	<	// The potato was going to exceed the maximum value,
658	<	// so wrap this processor potato back to 0 (and block until
659	<	// node 0 says we can go:
657	>	buffers.push_back(eorStream->rdbuf());
658	>
659	>	#ifdef IS_MPI
660	>	}
661	>	#endif // is_mpi
662
663	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
664	<	&istatus);
466	<	}
663	>	TeeBuf tbuf(buffers.begin(), buffers.end());
664	>	std::ostream os(&tbuf);
665
666	<	mol = info_->getMoleculeByGlobalIndex(i);
666	>	writeFrame(os);
667
668	<
669	<	nCurObj = mol->getNIntegrableObjects();
668	>	#ifdef IS_MPI
669	>	if (worldRank == 0) {
670	>	#endif // is_mpi
671	>	writeClosing(*eorStream);
672	>	delete eorStream;
673	>	#ifdef IS_MPI
674	>	}
675	>	#endif // is_mpi
676	>
677	>	}
678
679	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
474	<	myPotato++;
679	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
680
681	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
682	<	integrableObject = mol->nextIntegrableObject(ii)) {
683	<
684	<	if (myPotato + 2 >= MAXTAG) {
685	<
686	<	// 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	<	std::cout << "slave" << std::endl;
545	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
546	<	MPIcheckPoint();
681	>	std::ostream* newOStream;
682	>	#ifdef HAVE_LIBZ
683	>	if (needCompression_) {
684	>	newOStream = new ogzstream(filename.c_str());
685	>	} else {
686	>	newOStream = new std::ofstream(filename.c_str());
687		}
688	+	#else
689	+	newOStream = new std::ofstream(filename.c_str());
690	+	#endif
691	+	//write out MetaData first
692	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
693	+	(*newOStream) << "  <MetaData>" << std::endl;
694	+	(*newOStream) << info_->getRawMetaData();
695	+	(*newOStream) << "  </MetaData>" << std::endl;
696	+	return newOStream;
697	+	}
698
699	<	#endif // is_mpi
699	>	void DumpWriter::writeClosing(std::ostream& os) {
700
701	<	}
701	>	os << "</OpenMD>\n";
702	>	os.flush();
703	>	}
704
705	<	}//end namespace oopse
705	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

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