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root/OpenMD/branches/development/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.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1746 by gezelter, Wed Jun 6 02:18:54 2012 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
1	>	/*
2	>	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include "io/DumpWriter.hpp"
44		#include "primitives/Molecule.hpp"
45		#include "utils/simError.h"
46	+	#include "io/basic_teebuf.hpp"
47	+	#include "io/gzstream.hpp"
48	+	#include "io/Globals.hpp"
49
50	+
51		#ifdef IS_MPI
52		#include <mpi.h>
53		#endif //is_mpi
54
55	<	namespace oopse {
55	>	using namespace std;
56	>	namespace OpenMD {
57
58	<	DumpWriter::DumpWriter(SimInfo* info, 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	>	createDumpFile_ = true;
69	>	#ifdef HAVE_LIBZ
70	>	if (needCompression_) {
71	>	filename_ += ".gz";
72	>	eorFilename_ += ".gz";
73	>	}
74	>	#endif
75	>
76		#ifdef IS_MPI
77
78		if (worldRank == 0) {
79		#endif // is_mpi
80	+
81	+	dumpFile_ = createOStream(filename_);
82
83	<	dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
83	>	if (!dumpFile_) {
84	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
85	>	filename_.c_str());
86	>	painCave.isFatal = 1;
87	>	simError();
88	>	}
89
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	–
90		#ifdef IS_MPI
91
92		}
93
72	–	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73	–	MPIcheckPoint();
74	–
94		#endif // is_mpi
95
96	<	}
96	>	}
97
79	–	DumpWriter::~DumpWriter() {
98
99	+	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
100	+	: info_(info), filename_(filename){
101	+
102	+	Globals* simParams = info->getSimParams();
103	+	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
104	+
105	+	needCompression_   = simParams->getCompressDumpFile();
106	+	needForceVector_   = simParams->getOutputForceVector();
107	+	needParticlePot_   = simParams->getOutputParticlePotential();
108	+	needFlucQ_         = simParams->getOutputFluctuatingCharges();
109	+	needElectricField_ = simParams->getOutputElectricField();
110	+
111	+	createDumpFile_ = true;
112	+	#ifdef HAVE_LIBZ
113	+	if (needCompression_) {
114	+	filename_ += ".gz";
115	+	eorFilename_ += ".gz";
116	+	}
117	+	#endif
118	+
119		#ifdef IS_MPI
120
121		if (worldRank == 0) {
122		#endif // is_mpi
123
124	<	dumpFile_.close();
124	>
125	>	dumpFile_ = createOStream(filename_);
126
127	+	if (!dumpFile_) {
128	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
129	+	filename_.c_str());
130	+	painCave.isFatal = 1;
131	+	simError();
132	+	}
133	+
134		#ifdef IS_MPI
135
136		}
137
138		#endif // is_mpi
139
140	<	}
140	>	}
141	>
142	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
143	>	: info_(info), filename_(filename){
144	>
145	>	Globals* simParams = info->getSimParams();
146	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
147	>
148	>	needCompression_   = simParams->getCompressDumpFile();
149	>	needForceVector_   = simParams->getOutputForceVector();
150	>	needParticlePot_   = simParams->getOutputParticlePotential();
151	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
152	>	needElectricField_ = simParams->getOutputElectricField();
153
154	<	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
154	>	#ifdef HAVE_LIBZ
155	>	if (needCompression_) {
156	>	filename_ += ".gz";
157	>	eorFilename_ += ".gz";
158	>	}
159	>	#endif
160	>
161	>	#ifdef IS_MPI
162	>
163	>	if (worldRank == 0) {
164	>	#endif // is_mpi
165	>
166	>	createDumpFile_ = writeDumpFile;
167	>	if (createDumpFile_) {
168	>	dumpFile_ = createOStream(filename_);
169	>
170	>	if (!dumpFile_) {
171	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
172	>	filename_.c_str());
173	>	painCave.isFatal = 1;
174	>	simError();
175	>	}
176	>	}
177	>	#ifdef IS_MPI
178	>
179	>	}
180
98	–	double currentTime;
99	–	Mat3x3d hmat;
100	–	double chi;
101	–	double integralOfChiDt;
102	–	Mat3x3d eta;
181
182	<	currentTime = s->getTime();
105	<	hmat = s->getHmat();
106	<	chi = s->getChi();
107	<	integralOfChiDt = s->getIntegralOfChiDt();
108	<	eta = s->getEta();
182	>	#endif // is_mpi
183
184	<	os << currentTime << ";\t"
111	<	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
112	<	<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
113	<	<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
184	>	}
185
186	<	//write out additional parameters, such as chi and eta
186	>	DumpWriter::~DumpWriter() {
187
188	<	os << chi << "\t" << integralOfChiDt << "\t;";
188	>	#ifdef IS_MPI
189
190	<	os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
191	<	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
192	<	<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
193	<
194	<	os << std::endl;
195	<	}
190	>	if (worldRank == 0) {
191	>	#endif // is_mpi
192	>	if (createDumpFile_){
193	>	writeClosing(*dumpFile_);
194	>	delete dumpFile_;
195	>	}
196	>	#ifdef IS_MPI
197
198	<	void DumpWriter::writeFrame(std::ostream& os) {
127	<	const int BUFFERSIZE = 2000;
128	<	const int MINIBUFFERSIZE = 100;
198	>	}
199
200	<	char tempBuffer[BUFFERSIZE];
131	<	char writeLine[BUFFERSIZE];
200	>	#endif // is_mpi
201
202	<	Quat4d q;
134	<	Vector3d ji;
135	<	Vector3d pos;
136	<	Vector3d vel;
202	>	}
203
204	<	Molecule* mol;
139	<	StuntDouble* integrableObject;
140	<	SimInfo::MoleculeIterator mi;
141	<	Molecule::IntegrableObjectIterator ii;
142	<
143	<	int nTotObjects;
144	<	nTotObjects = info_->getNGlobalIntegrableObjects();
204	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
205
206	<	#ifndef IS_MPI
206	>	char buffer[1024];
207
208	+	os << "    <FrameData>\n";
209
210	<	os << nTotObjects << "\n";
150	<
151	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
210	>	RealType currentTime = s->getTime();
211
212	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
212	>	if (isinf(currentTime) || isnan(currentTime)) {
213	>	sprintf( painCave.errMsg,
214	>	"DumpWriter detected a numerical error writing the time");
215	>	painCave.isFatal = 1;
216	>	simError();
217	>	}
218	>
219	>	sprintf(buffer, "        Time: %.10g\n", currentTime);
220	>	os << buffer;
221
222	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
223	<	integrableObject = mol->nextIntegrableObject(ii)) {
157	<
222	>	Mat3x3d hmat;
223	>	hmat = s->getHmat();
224
225	<	pos = integrableObject->getPos();
226	<	vel = integrableObject->getVel();
225	>	for (unsigned int i = 0; i < 3; i++) {
226	>	for (unsigned int j = 0; j < 3; j++) {
227	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
228	>	sprintf( painCave.errMsg,
229	>	"DumpWriter detected a numerical error writing the box");
230	>	painCave.isFatal = 1;
231	>	simError();
232	>	}
233	>	}
234	>	}
235	>
236	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
237	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
238	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
239	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
240	>	os << buffer;
241
242	<	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
243	<	integrableObject->getType().c_str(),
244	<	pos[0], pos[1], pos[2],
245	<	vel[0], vel[1], vel[2]);
246	<
247	<	strcpy(writeLine, tempBuffer);
248	<
249	<	if (integrableObject->isDirectional()) {
170	<	q = integrableObject->getQ();
171	<	ji = integrableObject->getJ();
172	<
173	<	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
174	<	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	<	}
242	>	RealType chi = s->getChi();
243	>	RealType integralOfChiDt = s->getIntegralOfChiDt();
244	>	if (isinf(chi) || isnan(chi) ||
245	>	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
246	>	sprintf( painCave.errMsg,
247	>	"DumpWriter detected a numerical error writing the thermostat");
248	>	painCave.isFatal = 1;
249	>	simError();
250		}
251	+	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
252	+	os << buffer;
253
254	<	#else // is_mpi
255	<	/*********************************************************************
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;
254	>	Mat3x3d eta;
255	>	eta = s->getEta();
256
257	<	int * potatoes;
258	<	int myPotato;
259	<	int nProc;
260	<	int which_node;
261	<	double atomData[13];
262	<	int isDirectional;
263	<	const char * atomTypeString;
264	<	char MPIatomTypeString[MINIBUFFERSIZE];
265	<	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;
257	>	for (unsigned int i = 0; i < 3; i++) {
258	>	for (unsigned int j = 0; j < 3; j++) {
259	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
260	>	sprintf( painCave.errMsg,
261	>	"DumpWriter detected a numerical error writing the barostat");
262	>	painCave.isFatal = 1;
263	>	simError();
264	>	}
265	>	}
266		}
267
268	<	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
268	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
269	>	eta(0, 0), eta(1, 0), eta(2, 0),
270	>	eta(0, 1), eta(1, 1), eta(2, 1),
271	>	eta(0, 2), eta(1, 2), eta(2, 2));
272	>	os << buffer;
273
274	<	// Node 0 needs a list of the magic potatoes for each processor;
274	>	os << "    </FrameData>\n";
275	>	}
276
277	<	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
255	<	potatoes = new int[nProc];
277	>	void DumpWriter::writeFrame(std::ostream& os) {
278
279	<	//write out the comment lines
280	<	for(int i = 0; i < nProc; i++) {
281	<	potatoes[i] = 0;
260	<	}
279	>	#ifdef IS_MPI
280	>	MPI_Status istatus;
281	>	#endif
282
283	+	Molecule* mol;
284	+	StuntDouble* integrableObject;
285	+	SimInfo::MoleculeIterator mi;
286	+	Molecule::IntegrableObjectIterator ii;
287
288	<	os << nTotObjects << "\n";
289	<	writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
288	>	#ifndef IS_MPI
289	>	os << "  <Snapshot>\n";
290	>
291	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
292
293	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
293	>	os << "    <StuntDoubles>\n";
294	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
295
296	<	// Get the Node number which has this atom;
296	>
297	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
298	>	integrableObject = mol->nextIntegrableObject(ii)) {
299	>	os << prepareDumpLine(integrableObject);
300	>
301	>	}
302	>	}
303	>	os << "    </StuntDoubles>\n";
304	>
305	>	os << "  </Snapshot>\n";
306
307	<	which_node = info_->getMolToProc(i);
307	>	os.flush();
308	>	#else
309	>	//every node prepares the dump lines for integrable objects belong to itself
310	>	std::string buffer;
311	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
312
272	–	if (which_node != masterNode) { //current molecule is in slave node
273	–	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:
313
314	<	potatoes[which_node] = 0;
315	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
316	<	MPI_COMM_WORLD);
317	<	}
314	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
315	>	integrableObject = mol->nextIntegrableObject(ii)) {
316	>	buffer += prepareDumpLine(integrableObject);
317	>	}
318	>	}
319	>
320	>	const int masterNode = 0;
321	>	int nProc;
322	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
323	>	if (worldRank == masterNode) {
324	>	os << "  <Snapshot>\n";
325	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
326	>	os << "    <StuntDoubles>\n";
327	>
328	>	os << buffer;
329
330	<	myPotato = potatoes[which_node];
330	>	for (int i = 1; i < nProc; ++i) {
331
332	<	//recieve the number of integrableObject in current molecule
333	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
286	<	MPI_COMM_WORLD, &istatus);
287	<	myPotato++;
332	>	// receive the length of the string buffer that was
333	>	// prepared by processor i
334
335	<	for(int l = 0; l < nCurObj; l++) {
336	<	if (potatoes[which_node] + 2 >= MAXTAG) {
337	<	// The potato was going to exceed the maximum value,
338	<	// so wrap this processor potato back to 0:
335	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
336	>	int recvLength;
337	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
338	>	char* recvBuffer = new char[recvLength];
339	>	if (recvBuffer == NULL) {
340	>	} else {
341	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
342	>	os << recvBuffer;
343	>	delete [] recvBuffer;
344	>	}
345	>	}
346	>	os << "    </StuntDoubles>\n";
347	>
348	>	os << "  </Snapshot>\n";
349	>	os.flush();
350	>	} else {
351	>	int sendBufferLength = buffer.size() + 1;
352	>	int myturn = 0;
353	>	for (int i = 1; i < nProc; ++i){
354	>	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
355	>	if (myturn == worldRank){
356	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
357	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
358	>	}
359	>	}
360	>	}
361
362	<	potatoes[which_node] = 0;
295	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
296	<	0, MPI_COMM_WORLD);
297	<	}
362	>	#endif // is_mpi
363
364	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
300	<	which_node, myPotato, MPI_COMM_WORLD,
301	<	&istatus);
364	>	}
365
366	<	atomTypeString = MPIatomTypeString;
366	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
367	>
368	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
369	>	std::string type("pv");
370	>	std::string line;
371	>	char tempBuffer[4096];
372
373	<	myPotato++;
373	>	Vector3d pos;
374	>	Vector3d vel;
375	>	pos = integrableObject->getPos();
376
377	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
378	<	MPI_COMM_WORLD, &istatus);
379	<	myPotato++;
380	<
381	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
382	<
383	<	if (msgLen == 13)
384	<	isDirectional = 1;
385	<	else
316	<	isDirectional = 0;
317	<
318	<	// If we've survived to here, format the line:
377	>	if (isinf(pos[0]) || isnan(pos[0]) ||
378	>	isinf(pos[1]) || isnan(pos[1]) ||
379	>	isinf(pos[2]) || isnan(pos[2]) ) {
380	>	sprintf( painCave.errMsg,
381	>	"DumpWriter detected a numerical error writing the position"
382	>	" for object %d", index);
383	>	painCave.isFatal = 1;
384	>	simError();
385	>	}
386
387	<	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]);
387	>	vel = integrableObject->getVel();
388
389	<	strcat(writeLine,
390	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
391	<	} else {
392	<	sprintf(writeLine,
393	<	"%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",
394	<	atomTypeString,
395	<	atomData[0],
396	<	atomData[1],
397	<	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	<	}
389	>	if (isinf(vel[0]) || isnan(vel[0]) ||
390	>	isinf(vel[1]) || isnan(vel[1]) ||
391	>	isinf(vel[2]) || isnan(vel[2]) ) {
392	>	sprintf( painCave.errMsg,
393	>	"DumpWriter detected a numerical error writing the velocity"
394	>	" for object %d", index);
395	>	painCave.isFatal = 1;
396	>	simError();
397	>	}
398
399	<	os << writeLine;
399	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
400	>	pos[0], pos[1], pos[2],
401	>	vel[0], vel[1], vel[2]);
402	>	line += tempBuffer;
403
404	<	} // end for(int l =0)
404	>	if (integrableObject->isDirectional()) {
405	>	type += "qj";
406	>	Quat4d q;
407	>	Vector3d ji;
408	>	q = integrableObject->getQ();
409
410	<	potatoes[which_node] = myPotato;
411	<	} else { //master node has current molecule
410	>	if (isinf(q[0]) || isnan(q[0]) ||
411	>	isinf(q[1]) || isnan(q[1]) ||
412	>	isinf(q[2]) || isnan(q[2]) ||
413	>	isinf(q[3]) || isnan(q[3]) ) {
414	>	sprintf( painCave.errMsg,
415	>	"DumpWriter detected a numerical error writing the quaternion"
416	>	" for object %d", index);
417	>	painCave.isFatal = 1;
418	>	simError();
419	>	}
420
421	<	mol = info_->getMoleculeByGlobalIndex(i);
421	>	ji = integrableObject->getJ();
422
423	<	if (mol == NULL) {
424	<	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
425	<	painCave.isFatal = 1;
426	<	simError();
427	<	}
428	<
429	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
430	<	integrableObject = mol->nextIntegrableObject(ii)) {
431	<
366	<	atomTypeString = integrableObject->getType().c_str();
423	>	if (isinf(ji[0]) || isnan(ji[0]) ||
424	>	isinf(ji[1]) || isnan(ji[1]) ||
425	>	isinf(ji[2]) || isnan(ji[2]) ) {
426	>	sprintf( painCave.errMsg,
427	>	"DumpWriter detected a numerical error writing the angular"
428	>	" momentum for object %d", index);
429	>	painCave.isFatal = 1;
430	>	simError();
431	>	}
432
433	<	pos = integrableObject->getPos();
434	<	vel = integrableObject->getVel();
433	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
434	>	q[0], q[1], q[2], q[3],
435	>	ji[0], ji[1], ji[2]);
436	>	line += tempBuffer;
437	>	}
438
439	<	atomData[0] = pos[0];
440	<	atomData[1] = pos[1];
441	<	atomData[2] = pos[2];
439	>	if (needForceVector_) {
440	>	type += "f";
441	>	Vector3d frc = integrableObject->getFrc();
442	>	if (isinf(frc[0]) || isnan(frc[0]) ||
443	>	isinf(frc[1]) || isnan(frc[1]) ||
444	>	isinf(frc[2]) || isnan(frc[2]) ) {
445	>	sprintf( painCave.errMsg,
446	>	"DumpWriter detected a numerical error writing the force"
447	>	" for object %d", index);
448	>	painCave.isFatal = 1;
449	>	simError();
450	>	}
451	>	sprintf(tempBuffer, " %13e %13e %13e",
452	>	frc[0], frc[1], frc[2]);
453	>	line += tempBuffer;
454	>
455	>	if (integrableObject->isDirectional()) {
456	>	type += "t";
457	>	Vector3d trq = integrableObject->getTrq();
458	>	if (isinf(trq[0]) || isnan(trq[0]) ||
459	>	isinf(trq[1]) || isnan(trq[1]) ||
460	>	isinf(trq[2]) || isnan(trq[2]) ) {
461	>	sprintf( painCave.errMsg,
462	>	"DumpWriter detected a numerical error writing the torque"
463	>	" for object %d", index);
464	>	painCave.isFatal = 1;
465	>	simError();
466	>	}
467	>	sprintf(tempBuffer, " %13e %13e %13e",
468	>	trq[0], trq[1], trq[2]);
469	>	line += tempBuffer;
470	>	}
471	>	}
472
473	<	atomData[3] = vel[0];
474	<	atomData[4] = vel[1];
475	<	atomData[5] = vel[2];
473	>	if (needParticlePot_) {
474	>	type += "u";
475	>	RealType particlePot = integrableObject->getParticlePot();
476	>	if (isinf(particlePot) || isnan(particlePot)) {
477	>	sprintf( painCave.errMsg,
478	>	"DumpWriter detected a numerical error writing the particle "
479	>	" potential for object %d", index);
480	>	painCave.isFatal = 1;
481	>	simError();
482	>	}
483	>	sprintf(tempBuffer, " %13e", particlePot);
484	>	line += tempBuffer;
485	>	}
486	>
487	>	if (needFlucQ_) {
488	>	type += "cw";
489	>	RealType fqPos = integrableObject->getFlucQPos();
490	>	if (isinf(fqPos) || isnan(fqPos) ) {
491	>	sprintf( painCave.errMsg,
492	>	"DumpWriter detected a numerical error writing the"
493	>	" fluctuating charge for object %d", index);
494	>	painCave.isFatal = 1;
495	>	simError();
496	>	}
497	>	sprintf(tempBuffer, " %13e ", fqPos);
498	>	line += tempBuffer;
499	>
500	>	RealType fqVel = integrableObject->getFlucQVel();
501	>	if (isinf(fqVel) || isnan(fqVel) ) {
502	>	sprintf( painCave.errMsg,
503	>	"DumpWriter detected a numerical error writing the"
504	>	" fluctuating charge velocity for object %d", index);
505	>	painCave.isFatal = 1;
506	>	simError();
507	>	}
508	>	sprintf(tempBuffer, " %13e ", fqVel);
509	>	line += tempBuffer;
510
511	<	isDirectional = 0;
511	>	if (needForceVector_) {
512	>	type += "g";
513	>	RealType fqFrc = integrableObject->getFlucQFrc();
514	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
515	>	sprintf( painCave.errMsg,
516	>	"DumpWriter detected a numerical error writing the"
517	>	" fluctuating charge force for object %d", index);
518	>	painCave.isFatal = 1;
519	>	simError();
520	>	}
521	>	sprintf(tempBuffer, " %13e ", fqFrc);
522	>	line += tempBuffer;
523	>	}
524	>	}
525
526	<	if (integrableObject->isDirectional()) {
527	<	isDirectional = 1;
526	>	if (needElectricField_) {
527	>	type += "e";
528	>	Vector3d eField= integrableObject->getElectricField();
529	>	if (isinf(eField[0]) || isnan(eField[0]) ||
530	>	isinf(eField[1]) || isnan(eField[1]) ||
531	>	isinf(eField[2]) || isnan(eField[2]) ) {
532	>	sprintf( painCave.errMsg,
533	>	"DumpWriter detected a numerical error writing the electric"
534	>	" field for object %d", index);
535	>	painCave.isFatal = 1;
536	>	simError();
537	>	}
538	>	sprintf(tempBuffer, " %13e %13e %13e",
539	>	eField[0], eField[1], eField[2]);
540	>	line += tempBuffer;
541	>	}
542
543	<	q = integrableObject->getQ();
544	<	ji = integrableObject->getJ();
543	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
544	>	return std::string(tempBuffer);
545	>	}
546
547	<	for(int j = 0; j < 6; j++) {
548	<	atomData[j] = atomData[j];
549	<	}
547	>	void DumpWriter::writeDump() {
548	>	writeFrame(*dumpFile_);
549	>	}
550
551	<	atomData[6] = q[0];
552	<	atomData[7] = q[1];
553	<	atomData[8] = q[2];
554	<	atomData[9] = q[3];
551	>	void DumpWriter::writeEor() {
552	>	std::ostream* eorStream;
553	>
554	>	#ifdef IS_MPI
555	>	if (worldRank == 0) {
556	>	#endif // is_mpi
557
558	<	atomData[10] = ji[0];
397	<	atomData[11] = ji[1];
398	<	atomData[12] = ji[2];
399	<	}
558	>	eorStream = createOStream(eorFilename_);
559
560	<	// If we've survived to here, format the line:
560	>	#ifdef IS_MPI
561	>	}
562	>	#endif // is_mpi
563
564	<	if (!isDirectional) {
404	<	sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
405	<	atomTypeString, atomData[0],
406	<	atomData[1], atomData[2],
407	<	atomData[3], atomData[4],
408	<	atomData[5]);
564	>	writeFrame(*eorStream);
565
566	<	strcat(writeLine,
567	<	"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
568	<	} else {
569	<	sprintf(writeLine,
570	<	"%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",
571	<	atomTypeString,
572	<	atomData[0],
573	<	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	<	}
566	>	#ifdef IS_MPI
567	>	if (worldRank == 0) {
568	>	#endif // is_mpi
569	>	writeClosing(*eorStream);
570	>	delete eorStream;
571	>	#ifdef IS_MPI
572	>	}
573	>	#endif // is_mpi
574
575	+	}
576
432	–	os << writeLine;
577
578	<	} //end for(iter = integrableObject.begin())
579	<	}
580	<	} //end for(i = 0; i < mpiSim->getNmol())
578	>	void DumpWriter::writeDumpAndEor() {
579	>	std::vector<std::streambuf*> buffers;
580	>	std::ostream* eorStream;
581	>	#ifdef IS_MPI
582	>	if (worldRank == 0) {
583	>	#endif // is_mpi
584
585	<	os.flush();
439	<
440	<	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
441	<	MPIcheckPoint();
585	>	buffers.push_back(dumpFile_->rdbuf());
586
587	<	delete [] potatoes;
444	<	} else {
587	>	eorStream = createOStream(eorFilename_);
588
589	<	// worldRank != 0, so I'm a remote node.
589	>	buffers.push_back(eorStream->rdbuf());
590	>
591	>	#ifdef IS_MPI
592	>	}
593	>	#endif // is_mpi
594
595	<	// Set my magic potato to 0:
595	>	TeeBuf tbuf(buffers.begin(), buffers.end());
596	>	std::ostream os(&tbuf);
597
598	<	myPotato = 0;
598	>	writeFrame(os);
599
600	<	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
600	>	#ifdef IS_MPI
601	>	if (worldRank == 0) {
602	>	#endif // is_mpi
603	>	writeClosing(*eorStream);
604	>	delete eorStream;
605	>	#ifdef IS_MPI
606	>	}
607	>	#endif // is_mpi
608	>
609	>	}
610
611	<	// Am I the node which has this integrableObject?
455	<	int whichNode = info_->getMolToProc(i);
456	<	if (whichNode == worldRank) {
457	<	if (myPotato + 1 >= MAXTAG) {
611	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
612
613	<	// The potato was going to exceed the maximum value,
614	<	// so wrap this processor potato back to 0 (and block until
615	<	// node 0 says we can go:
616	<
617	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
618	<	&istatus);
465	<	}
466	<
467	<	mol = info_->getMoleculeByGlobalIndex(i);
468	<
469	<
470	<	nCurObj = mol->getNIntegrableObjects();
471	<
472	<	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
473	<	myPotato++;
474	<
475	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
476	<	integrableObject = mol->nextIntegrableObject(ii)) {
477	<
478	<	if (myPotato + 2 >= MAXTAG) {
479	<
480	<	// The potato was going to exceed the maximum value,
481	<	// so wrap this processor potato back to 0 (and block until
482	<	// node 0 says we can go:
483	<
484	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
485	<	&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();
613	>	std::ostream* newOStream;
614	>	#ifdef HAVE_LIBZ
615	>	if (needCompression_) {
616	>	newOStream = new ogzstream(filename.c_str());
617	>	} else {
618	>	newOStream = new std::ofstream(filename.c_str());
619		}
620	+	#else
621	+	newOStream = new std::ofstream(filename.c_str());
622	+	#endif
623	+	//write out MetaData first
624	+	(*newOStream) << "<OpenMD version=2>" << std::endl;
625	+	(*newOStream) << "  <MetaData>" << std::endl;
626	+	(*newOStream) << info_->getRawMetaData();
627	+	(*newOStream) << "  </MetaData>" << std::endl;
628	+	return newOStream;
629	+	}
630
631	<	#endif // is_mpi
631	>	void DumpWriter::writeClosing(std::ostream& os) {
632
633	<	}
633	>	os << "</OpenMD>\n";
634	>	os.flush();
635	>	}
636
637	<	}//end namespace oopse
637	>	}//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 1746 by gezelter, Wed Jun 6 02:18:54 2012 UTC

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