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

Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 996 by chrisfen, Wed Jun 28 14:35:14 2006 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 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
19	<	*    notice, this list of conditions and the following disclaimer.
20	<	*
21	<	* 3. Redistributions in binary form must reproduce the above copyright
22	<	*    notice, this list of conditions and the following disclaimer in the
23	<	*    documentation and/or other materials provided with the
24	<	*    distribution.
25	<	*
26	<	* This software is provided "AS IS," without a warranty of any
27	<	* kind. All express or implied conditions, representations and
28	<	* warranties, including any implied warranty of merchantability,
29	<	* fitness for a particular purpose or non-infringement, are hereby
30	<	* excluded.  The University of Notre Dame and its licensors shall not
31	<	* be liable for any damages suffered by licensee as a result of
32	<	* using, modifying or distributing the software or its
33	<	* derivatives. In no event will the University of Notre Dame or its
34	<	* licensors be liable for any lost revenue, profit or data, or for
35	<	* direct, indirect, special, consequential, incidental or punitive
36	<	* damages, however caused and regardless of the theory of liability,
37	<	* arising out of the use of or inability to use software, even if the
38	<	* University of Notre Dame has been advised of the possibility of
39	<	* such damages.
40	<	*/
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. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
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.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
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]  Vardeman & Gezelter, in progress (2009).
40	>	*/
41
42		#define _LARGEFILE_SOURCE64
43		#define _FILE_OFFSET_BITS 64
#	Line 67 | Line 67
67		#endif // is_mpi
68
69
70	<	namespace oopse {
70	>	namespace OpenMD {
71
72		DumpReader::DumpReader(SimInfo* info, const std::string& filename)
73	<	: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
73	>	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
74
75		#ifdef IS_MPI
76
#	Line 92 | Line 92 | namespace oopse {
92		}
93
94		strcpy(checkPointMsg, "Dump file opened for reading successfully.");
95	<	MPIcheckPoint();
95	>	errorCheckPoint();
96
97		#endif
98
#	Line 113 | Line 113 | namespace oopse {
113		}
114
115		strcpy(checkPointMsg, "Dump file closed successfully.");
116	<	MPIcheckPoint();
116	>	errorCheckPoint();
117
118		#endif
119
#	Line 129 | Line 129 | namespace oopse {
129		}
130
131		void DumpReader::scanFile(void) {
132	<	int i, j;
133	<	int lineNum = 0;
134	<	char readBuffer[maxBufferSize];
132	>	int lineNo = 0;
133	>	std::streampos prevPos;
134		std::streampos  currPos;
135	<
135	>
136		#ifdef IS_MPI
137	<
137	>
138		if (worldRank == 0) {
139		#endif // is_mpi
140	<
141	<	inFile_->seekg (0, std::ios::beg);
142	<
143	<
144	<	currPos = inFile_->tellg();
145	<	inFile_->getline(readBuffer, sizeof(readBuffer));
146	<	lineNum++;
147	<
148	<	if (inFile_->eof()) {
149	<	sprintf(painCave.errMsg,
150	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
151	<	filename_.c_str(),
153	<	lineNum);
154	<	painCave.isFatal = 1;
155	<	simError();
156	<	}
157	<
158	<	while (!inFile_->eof()) {
159	<	framePos_.push_back(currPos);
160	<
161	<	i = atoi(readBuffer);
162	<
163	<	inFile_->getline(readBuffer, sizeof(readBuffer));
164	<	lineNum++;
165	<
166	<	if (inFile_->eof()) {
167	<	sprintf(painCave.errMsg,
168	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
169	<	filename_.c_str(),
170	<	lineNum);
171	<	painCave.isFatal = 1;
172	<	simError();
173	<	}
174	<
175	<	for(j = 0; j < i; j++) {
176	<	inFile_->getline(readBuffer, sizeof(readBuffer));
177	<	lineNum++;
178	<
179	<	if (inFile_->eof()) {
140	>
141	>	currPos = inFile_->tellg();
142	>	prevPos = currPos;
143	>	bool foundOpenSnapshotTag = false;
144	>	bool foundClosedSnapshotTag = false;
145	>	while(inFile_->getline(buffer, bufferSize)) {
146	>	++lineNo;
147	>
148	>	std::string line = buffer;
149	>	currPos = inFile_->tellg();
150	>	if (line.find("<Snapshot>")!= std::string::npos) {
151	>	if (foundOpenSnapshotTag) {
152		sprintf(painCave.errMsg,
153	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d,"
154	<	" with atom %d\n", filename_.c_str(),
183	<	lineNum,
184	<	j);
185	<
153	>	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
154	>	filename_.c_str());
155		painCave.isFatal = 1;
156	+	simError();
157	+	}
158	+	foundOpenSnapshotTag = true;
159	+	foundClosedSnapshotTag = false;
160	+	framePos_.push_back(prevPos);
161	+
162	+	} else if (line.find("</Snapshot>") != std::string::npos){
163	+	if (!foundOpenSnapshotTag) {
164	+	sprintf(painCave.errMsg,
165	+	"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
166	+	filename_.c_str());
167	+	painCave.isFatal = 1;
168		simError();
169	<	}
170	<	}
171	<
172	<	currPos = inFile_->tellg();
173	<	inFile_->getline(readBuffer, sizeof(readBuffer));
174	<	lineNum++;
175	<	}
176	<
177	<	inFile_->seekg (0, std::ios::beg);
178	<
169	>	}
170	>
171	>	if (foundClosedSnapshotTag) {
172	>	sprintf(painCave.errMsg,
173	>	"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
174	>	filename_.c_str());
175	>	painCave.isFatal = 1;
176	>	simError();
177	>	}
178	>	foundClosedSnapshotTag = true;
179	>	foundOpenSnapshotTag = false;
180	>	}
181	>	prevPos = currPos;
182	>	}
183	>
184	>	// only found <Snapshot> for the last frame means the file is corrupted, we should discard
185	>	// it and give a warning message
186	>	if (foundOpenSnapshotTag) {
187	>	sprintf(painCave.errMsg,
188	>	"DumpReader: last frame in %s is invalid\n", filename_.c_str());
189	>	painCave.isFatal = 0;
190	>	simError();
191	>	framePos_.pop_back();
192	>	}
193	>
194		nframes_ = framePos_.size();
195	+
196	+	if (nframes_ == 0) {
197	+	sprintf(painCave.errMsg,
198	+	"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
199	+	painCave.isFatal = 1;
200	+	simError();
201	+	}
202		#ifdef IS_MPI
203		}
204
205		MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
206	<
204	<	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
205	<	MPIcheckPoint();
206	<
206	>
207		#endif // is_mpi
208	<
208	>
209		isScanned_ = true;
210		}
211
#	Line 240 | Line 240 | namespace oopse {
240		}
241
242		readSet(whichFrame);
243	+
244	+	if (needCOMprops_) {
245	+	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
246	+	Vector3d com;
247	+	Vector3d comvel;
248	+	Vector3d comw;
249	+	if (needPos_ && needVel_){
250	+	info_->getComAll(com, comvel);
251	+	comw = info_->getAngularMomentum();
252	+	}else{
253	+	com = info_->getCom();
254	+	comvel = 0.0;
255	+	comw   = 0.0;
256	+	}
257	+	s->setCOMprops(com, comvel, comw);
258	+	}
259	+
260		}
261
262	<	void DumpReader::readSet(int whichFrame) {
263	<	int i;
264	<	int nTotObjs;                  // the number of atoms
248	<	char read_buffer[maxBufferSize];  //the line buffer for reading
249	<	char * eof_test;               // ptr to see when we reach the end of the file
250	<
251	<	Molecule* mol;
252	<	StuntDouble* integrableObject;
253	<	SimInfo::MoleculeIterator mi;
254	<	Molecule::IntegrableObjectIterator ii;
255	<
262	>	void DumpReader::readSet(int whichFrame) {
263	>	std::string line;
264	>
265		#ifndef IS_MPI
266		inFile_->clear();
267		inFile_->seekg(framePos_[whichFrame]);
268	<
269	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
268	>
269	>	std::istream& inputStream = *inFile_;
270	>
271	>	#else
272	>	int masterNode = 0;
273	>	std::stringstream sstream;
274	>	if (worldRank == masterNode) {
275	>	std::string sendBuffer;
276	>
277	>	inFile_->clear();
278	>	inFile_->seekg(framePos_[whichFrame]);
279	>
280	>	while (inFile_->getline(buffer, bufferSize)) {
281	>
282	>	line = buffer;
283	>	sendBuffer += line;
284	>	sendBuffer += '\n';
285	>	if (line.find("</Snapshot>") != std::string::npos) {
286	>	break;
287	>	}
288	>	}
289	>
290	>	int sendBufferSize = sendBuffer.size();
291	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
292	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
293	>
294	>	sstream.str(sendBuffer);
295	>	} else {
296	>	int sendBufferSize;
297	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
298	>	char * recvBuffer = new char[sendBufferSize+1];
299	>	assert(recvBuffer);
300	>	recvBuffer[sendBufferSize] = '\0';
301	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
302	>	sstream.str(recvBuffer);
303	>	delete [] recvBuffer;
304	>	}
305	>
306	>	std::istream& inputStream = sstream;
307	>	#endif
308	>
309	>	inputStream.getline(buffer, bufferSize);
310	>
311	>	line = buffer;
312	>	if (line.find("<Snapshot>") == std::string::npos) {
313		sprintf(painCave.errMsg,
314	<	"DumpReader error: error reading 1st line of \"%s\"\n",
263	<	filename_.c_str());
314	>	"DumpReader Error: can not find <Snapshot>\n");
315		painCave.isFatal = 1;
316		simError();
317		}
318	<
319	<	nTotObjs = atoi(read_buffer);
320	<
321	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
318	>
319	>	//read frameData
320	>	readFrameProperties(inputStream);
321	>
322	>	//read StuntDoubles
323	>	readStuntDoubles(inputStream);
324	>
325	>	inputStream.getline(buffer, bufferSize);
326	>	line = buffer;
327	>	if (line.find("</Snapshot>") == std::string::npos) {
328		sprintf(painCave.errMsg,
329	<	"DumpReader error. %s nIntegrable, %d, "
273	<	"does not match the meta-data file's nIntegrable, %d.\n",
274	<	filename_.c_str(),
275	<	nTotObjs,
276	<	info_->getNGlobalIntegrableObjects());
277	<
329	>	"DumpReader Error: can not find </Snapshot>\n");
330		painCave.isFatal = 1;
331		simError();
332	<	}
333	<
282	<	//read the box mat from the comment line
283	<
284	<
285	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
286	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
287	<	filename_.c_str());
288	<	painCave.isFatal = 1;
289	<	simError();
290	<	}
291	<
292	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
293	<
294	<	//parse dump lines
295	<
296	<	i = 0;
297	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
298	<
299	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
300	<	integrableObject = mol->nextIntegrableObject(ii)) {
301	<
302	<
303	<
304	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
305	<	sprintf(painCave.errMsg,
306	<	"DumpReader Error: error in reading file %s\n"
307	<	"natoms  = %d; index = %d\n"
308	<	"error reading the line from the file.\n",
309	<	filename_.c_str(),
310	<	nTotObjs,
311	<	i);
312	<
313	<	painCave.isFatal = 1;
314	<	simError();
315	<	}
316	<
317	<	parseDumpLine(read_buffer, integrableObject);
318	<	i++;
319	<	}
320	<	}
321	<
322	<	// MPI Section of code..........
323	<
324	<	#else //IS_MPI
325	<
326	<	// first thing first, suspend fatalities.
327	<	int masterNode = 0;
328	<	int nCurObj;
329	<	painCave.isEventLoop = 1;
330	<
331	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
332	<	int haveError;
333	<
334	<	MPI_Status istatus;
335	<	int nitems;
336	<
337	<	nTotObjs = info_->getNGlobalIntegrableObjects();
338	<	haveError = 0;
339	<
340	<	if (worldRank == masterNode) {
341	<	inFile_->clear();
342	<	inFile_->seekg(framePos_[whichFrame]);
343	<
344	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
345	<	sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ",
346	<	filename_.c_str());
347	<	painCave.isFatal = 1;
348	<	simError();
349	<	}
350	<
351	<	nitems = atoi(read_buffer);
352	<
353	<	// Check to see that the number of integrable objects in the
354	<	// intial configuration file is the same as derived from the
355	<	// meta-data file.
356	<
357	<	if (nTotObjs != nitems) {
358	<	sprintf(painCave.errMsg,
359	<	"DumpReader Error. %s nIntegrable, %d, "
360	<	"does not match the meta-data file's nIntegrable, %d.\n",
361	<	filename_.c_str(),
362	<	nTotObjs,
363	<	info_->getNGlobalIntegrableObjects());
364	<
365	<	painCave.isFatal = 1;
366	<	simError();
367	<	}
368	<
369	<	//read the boxMat from the comment line
370	<
371	<
372	<
373	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
374	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
375	<	filename_.c_str());
376	<	painCave.isFatal = 1;
377	<	simError();
378	<	}
379	<
380	<	//Every single processor will parse the comment line by itself
381	<	//By using this way, we might lose some efficiency, but if we want to add
382	<	//more parameters into comment line, we only need to modify function
383	<	//parseCommentLine
384	<
385	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
386	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
387	<
388	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
389	<	int which_node = info_->getMolToProc(i);
390	<
391	<	if (which_node == masterNode) {
392	<	//molecules belong to master node
393	<
394	<	mol = info_->getMoleculeByGlobalIndex(i);
395	<
396	<	if (mol == NULL) {
397	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
398	<	painCave.isFatal = 1;
399	<	simError();
400	<	}
401	<
402	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
403	<	integrableObject = mol->nextIntegrableObject(ii)){
404	<
405	<
406	<
407	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
408	<	sprintf(painCave.errMsg,
409	<	"DumpReader Error: error in reading file %s\n"
410	<	"natoms  = %d; index = %d\n"
411	<	"error reading the line from the file.\n",
412	<	filename_.c_str(),
413	<	nTotObjs,
414	<	i);
415	<
416	<	painCave.isFatal = 1;
417	<	simError();
418	<	}
419	<
420	<	parseDumpLine(read_buffer, integrableObject);
421	<	}
422	<	} else {
423	<	//molecule belongs to slave nodes
424	<
425	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
426	<	MPI_COMM_WORLD, &istatus);
427	<
428	<	for(int j = 0; j < nCurObj; j++) {
429	<
430	<
431	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
432	<	sprintf(painCave.errMsg,
433	<	"DumpReader Error: error in reading file %s\n"
434	<	"natoms  = %d; index = %d\n"
435	<	"error reading the line from the file.\n",
436	<	filename_.c_str(),
437	<	nTotObjs,
438	<	i);
439	<
440	<	painCave.isFatal = 1;
441	<	simError();
442	<	}
443	<
444	<	MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
445	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
446	<	}
447	<	}
448	<	}
449	<	} else {
450	<	//actions taken at slave nodes
451	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
452	<
453	<	/**@todo*/
454	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
455	<
456	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
457	<	int which_node = info_->getMolToProc(i);
458	<
459	<	if (which_node == worldRank) {
460	<	//molecule with global index i belongs to this processor
461	<
462	<	mol = info_->getMoleculeByGlobalIndex(i);
463	<	if (mol == NULL) {
464	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
465	<	painCave.isFatal = 1;
466	<	simError();
467	<	}
468	<
469	<	nCurObj = mol->getNIntegrableObjects();
470	<
471	<	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
472	<	MPI_COMM_WORLD);
473	<
474	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
475	<	integrableObject = mol->nextIntegrableObject(ii)){
476	<
477	<	MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
478	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
479	<
480	<	parseDumpLine(read_buffer, integrableObject);
481	<	}
482	<
483	<	}
484	<
485	<	}
486	<
487	<	}
488	<
489	<	#endif
490	<
332	>	}
333	>
334		}
335
336	<	void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
337	<
338	<	Vector3d pos;  // position place holders
496	<	Vector3d vel;  // velocity placeholders
497	<	Quat4d q;    // the quaternions
498	<	Vector3d ji;   // angular velocity placeholders;
336	>	void DumpReader::parseDumpLine(const std::string& line) {
337	>
338	>
339		StringTokenizer tokenizer(line);
340		int nTokens;
341
342		nTokens = tokenizer.countTokens();
343
344	<	if (nTokens < 14) {
344	>	if (nTokens < 2) {
345		sprintf(painCave.errMsg,
346	<	"DumpReader Error: Not enough Tokens.\n%s\n", line);
346	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
347		painCave.isFatal = 1;
348		simError();
349		}
350	+
351	+	int index = tokenizer.nextTokenAsInt();
352	+
353	+	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
354	+
355	+	if (integrableObject == NULL) {
356	+	return;
357	+	}
358	+	std::string type = tokenizer.nextToken();
359	+	int size = type.size();
360	+
361	+	for(int i = 0; i < size; ++i) {
362	+	switch(type[i]) {
363	+
364	+	case 'p': {
365	+	Vector3d pos;
366	+	pos[0] = tokenizer.nextTokenAsDouble();
367	+	pos[1] = tokenizer.nextTokenAsDouble();
368	+	pos[2] = tokenizer.nextTokenAsDouble();
369	+	if (needPos_) {
370	+	integrableObject->setPos(pos);
371	+	}
372	+	break;
373	+	}
374	+	case 'v' : {
375	+	Vector3d vel;
376	+	vel[0] = tokenizer.nextTokenAsDouble();
377	+	vel[1] = tokenizer.nextTokenAsDouble();
378	+	vel[2] = tokenizer.nextTokenAsDouble();
379	+	if (needVel_) {
380	+	integrableObject->setVel(vel);
381	+	}
382	+	break;
383	+	}
384	+
385	+	case 'q' : {
386	+	Quat4d q;
387	+	if (integrableObject->isDirectional()) {
388	+
389	+	q[0] = tokenizer.nextTokenAsDouble();
390	+	q[1] = tokenizer.nextTokenAsDouble();
391	+	q[2] = tokenizer.nextTokenAsDouble();
392	+	q[3] = tokenizer.nextTokenAsDouble();
393	+
394	+	RealType qlen = q.length();
395	+	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
396	+
397	+	sprintf(painCave.errMsg,
398	+	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
399	+	painCave.isFatal = 1;
400	+	simError();
401	+
402	+	}
403	+
404	+	q.normalize();
405	+	if (needQuaternion_) {
406	+	integrableObject->setQ(q);
407	+	}
408	+	}
409	+	break;
410	+	}
411	+	case 'j' : {
412	+	Vector3d ji;
413	+	if (integrableObject->isDirectional()) {
414	+	ji[0] = tokenizer.nextTokenAsDouble();
415	+	ji[1] = tokenizer.nextTokenAsDouble();
416	+	ji[2] = tokenizer.nextTokenAsDouble();
417	+	if (needAngMom_) {
418	+	integrableObject->setJ(ji);
419	+	}
420	+	}
421	+	break;
422	+	}
423	+	case 'f': {
424	+
425	+	Vector3d force;
426	+	force[0] = tokenizer.nextTokenAsDouble();
427	+	force[1] = tokenizer.nextTokenAsDouble();
428	+	force[2] = tokenizer.nextTokenAsDouble();
429	+	integrableObject->setFrc(force);
430	+	break;
431	+	}
432	+	case 't' : {
433	+
434	+	Vector3d torque;
435	+	torque[0] = tokenizer.nextTokenAsDouble();
436	+	torque[1] = tokenizer.nextTokenAsDouble();
437	+	torque[2] = tokenizer.nextTokenAsDouble();
438	+	integrableObject->setTrq(torque);
439	+	break;
440	+	}
441	+	default: {
442	+	sprintf(painCave.errMsg,
443	+	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
444	+	painCave.isFatal = 1;
445	+	simError();
446	+	break;
447	+	}
448	+
449	+	}
450	+	}
451
452	<	std::string name = tokenizer.nextToken();
453	<
454	<	if (name != integrableObject->getType()) {
455	<
452	>	}
453	>
454	>
455	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
456	>
457	>	inputStream.getline(buffer, bufferSize);
458	>	std::string line(buffer);
459	>
460	>	if (line.find("<StuntDoubles>") == std::string::npos) {
461		sprintf(painCave.errMsg,
462	<	"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
517	<	name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
462	>	"DumpReader Error: Missing <StuntDoubles>\n");
463		painCave.isFatal = 1;
464	<	simError();
465	<	}
466	<
467	<	pos[0] = tokenizer.nextTokenAsDouble();
468	<	pos[1] = tokenizer.nextTokenAsDouble();
469	<	pos[2] = tokenizer.nextTokenAsDouble();
470	<	if (needPos_) {
471	<	integrableObject->setPos(pos);
472	<	}
473	<
474	<	vel[0] = tokenizer.nextTokenAsDouble();
475	<	vel[1] = tokenizer.nextTokenAsDouble();
476	<	vel[2] = tokenizer.nextTokenAsDouble();
477	<	if (needVel_) {
478	<	integrableObject->setVel(vel);
479	<	}
480	<
481	<	if (integrableObject->isDirectional()) {
482	<
483	<	q[0] = tokenizer.nextTokenAsDouble();
484	<	q[1] = tokenizer.nextTokenAsDouble();
485	<	q[2] = tokenizer.nextTokenAsDouble();
486	<	q[3] = tokenizer.nextTokenAsDouble();
487	<
488	<	RealType qlen = q.length();
489	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
490	<
464	>	simError();
465	>	}
466	>
467	>	while(inputStream.getline(buffer, bufferSize)) {
468	>	line = buffer;
469	>
470	>	if(line.find("</StuntDoubles>") != std::string::npos) {
471	>	break;
472	>	}
473	>
474	>	parseDumpLine(line);
475	>	}
476	>
477	>	}
478	>
479	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
480	>
481	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
482	>	inputStream.getline(buffer, bufferSize);
483	>	std::string line(buffer);
484	>
485	>	if (line.find("<FrameData>") == std::string::npos) {
486	>	sprintf(painCave.errMsg,
487	>	"DumpReader Error: Missing <FrameData>\n");
488	>	painCave.isFatal = 1;
489	>	simError();
490	>	}
491	>
492	>	while(inputStream.getline(buffer, bufferSize)) {
493	>	line = buffer;
494	>
495	>	if(line.find("</FrameData>") != std::string::npos) {
496	>	break;
497	>	}
498	>
499	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
500	>	if (!tokenizer.hasMoreTokens()) {
501		sprintf(painCave.errMsg,
502	<	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
502	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
503		painCave.isFatal = 1;
504	<	simError();
505	<
506	<	}
507	<
508	<	q.normalize();
509	<	if (needQuaternion_) {
510	<	integrableObject->setQ(q);
511	<	}
512	<
513	<	ji[0] = tokenizer.nextTokenAsDouble();
514	<	ji[1] = tokenizer.nextTokenAsDouble();
515	<	ji[2] = tokenizer.nextTokenAsDouble();
516	<	if (needAngMom_) {
517	<	integrableObject->setJ(ji);
518	<	}
519	<	}
520	<
521	<	}
504	>	simError();
505	>	}
506	>
507	>	std::string propertyName = tokenizer.nextToken();
508	>	if (propertyName == "Time") {
509	>	RealType currTime = tokenizer.nextTokenAsDouble();
510	>	s->setTime(currTime);
511	>	} else if (propertyName == "Hmat"){
512	>	Mat3x3d hmat;
513	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
514	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
515	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
516	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
517	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
518	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
519	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
520	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
521	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
522	>	s->setHmat(hmat);
523	>	} else if (propertyName == "Thermostat") {
524	>	RealType chi = tokenizer.nextTokenAsDouble();
525	>	RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
526	>	s->setChi(chi);
527	>	s->setIntegralOfChiDt(integralOfChiDt);
528	>	} else if (propertyName == "Barostat") {
529	>	Mat3x3d eta;
530	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
531	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
532	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
533	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
534	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
535	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
536	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
537	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
538	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
539	>	s->setEta(eta);
540	>	} else {
541	>	sprintf(painCave.errMsg,
542	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
543	>	painCave.isFatal = 0;
544	>	simError();
545	>	}
546	>
547	>	}
548	>
549	>	}
550	>
551
552	<
569	<	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
570	<	RealType currTime;
571	<	Mat3x3d hmat;
572	<	RealType chi;
573	<	RealType integralOfChiDt;
574	<	Mat3x3d eta;
575	<
576	<	StringTokenizer tokenizer(line);
577	<	int nTokens;
578	<
579	<	nTokens = tokenizer.countTokens();
580	<
581	<	//comment line should at least contain 10 tokens: current time(1 token) and  h-matrix(9 tokens)
582	<	if (nTokens < 10) {
583	<	sprintf(painCave.errMsg,
584	<	"DumpReader Error: Not enough tokens in comment line: %s", line);
585	<	painCave.isFatal = 1;
586	<	simError();
587	<	}
588	<
589	<	//read current time
590	<	currTime = tokenizer.nextTokenAsDouble();
591	<	s->setTime(currTime);
592	<
593	<	//read h-matrix
594	<	hmat(0, 0) = tokenizer.nextTokenAsDouble();
595	<	hmat(0, 1) = tokenizer.nextTokenAsDouble();
596	<	hmat(0, 2) = tokenizer.nextTokenAsDouble();
597	<	hmat(1, 0) = tokenizer.nextTokenAsDouble();
598	<	hmat(1, 1) = tokenizer.nextTokenAsDouble();
599	<	hmat(1, 2) = tokenizer.nextTokenAsDouble();
600	<	hmat(2, 0) = tokenizer.nextTokenAsDouble();
601	<	hmat(2, 1) = tokenizer.nextTokenAsDouble();
602	<	hmat(2, 2) = tokenizer.nextTokenAsDouble();
603	<	s->setHmat(hmat);
604	<
605	<	//read chi and integralOfChidt, they should apprear in pair
606	<	if (tokenizer.countTokens() >= 2) {
607	<	chi = tokenizer.nextTokenAsDouble();
608	<	integralOfChiDt = tokenizer.nextTokenAsDouble();
609	<
610	<	s->setChi(chi);
611	<	s->setIntegralOfChiDt(integralOfChiDt);
612	<	}
613	<
614	<	//read eta (eta is 3x3 matrix)
615	<	if (tokenizer.countTokens() >= 9) {
616	<	eta(0, 0) = tokenizer.nextTokenAsDouble();
617	<	eta(0, 1) = tokenizer.nextTokenAsDouble();
618	<	eta(0, 2) = tokenizer.nextTokenAsDouble();
619	<	eta(1, 0) = tokenizer.nextTokenAsDouble();
620	<	eta(1, 1) = tokenizer.nextTokenAsDouble();
621	<	eta(1, 2) = tokenizer.nextTokenAsDouble();
622	<	eta(2, 0) = tokenizer.nextTokenAsDouble();
623	<	eta(2, 1) = tokenizer.nextTokenAsDouble();
624	<	eta(2, 2) = tokenizer.nextTokenAsDouble();
625	<
626	<	s->setEta(eta);
627	<	}
628	<
629	<
630	<	}
631	<
632	<	}//end namespace oopse
552	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpReader.cpp (property svn:keywords):
Revision 996 by chrisfen, Wed Jun 28 14:35:14 2006 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

#	Line 0 | Line 1
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