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

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trunk/src/io/DumpReader.cpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	>	*/
42
43		#define _LARGEFILE_SOURCE64
44		#define _FILE_OFFSET_BITS 64
#	Line 67 | Line 68
68		#endif // is_mpi
69
70
71	<	namespace oopse {
71	>	namespace OpenMD {
72
73		DumpReader::DumpReader(SimInfo* info, const std::string& filename)
74	<	: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
75	<
74	>	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
75	>
76		#ifdef IS_MPI
77	<
78	<	if (worldRank == 0) {
77	>
78	>	if (worldRank == 0) {
79		#endif
80	<
80	>
81		inFile_ = new std::ifstream(filename_.c_str());
82	<
83	<	if (inFile_->fail()) {
84	<	sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
85	<	painCave.isFatal = 1;
86	<	simError();
87	<	}
88	<
88	<	#ifdef IS_MPI
89	<
82	>
83	>	if (inFile_->fail()) {
84	>	sprintf(painCave.errMsg,
85	>	"DumpReader: Cannot open file: %s\n",
86	>	filename_.c_str());
87	>	painCave.isFatal = 1;
88	>	simError();
89		}
90	<
91	<	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
92	<	MPIcheckPoint();
94	<
95	<	#endif
96	<
97	<	return;
90	>
91	>	#ifdef IS_MPI
92	>
93		}
94	<
94	>
95	>	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
96	>	errorCheckPoint();
97	>
98	>	#endif
99	>
100	>	return;
101	>	}
102	>
103		DumpReader::~DumpReader() {
104	<
104	>
105		#ifdef IS_MPI
106	<
106	>
107		if (worldRank == 0) {
108		#endif
109	<
109	>
110		delete inFile_;
111	<
111	>
112		#ifdef IS_MPI
113	<
113	>
114		}
115	<
115	>
116		strcpy(checkPointMsg, "Dump file closed successfully.");
117	<	MPIcheckPoint();
118	<
117	>	errorCheckPoint();
118	>
119		#endif
120	<
120	>
121		return;
122		}
123	<
123	>
124		int DumpReader::getNFrames(void) {
125
126		if (!isScanned_)
#	Line 127 | Line 130 | namespace oopse {
130		}
131
132		void DumpReader::scanFile(void) {
133	<	int i, j;
134	<	int lineNum = 0;
132	<	char readBuffer[maxBufferSize];
133	>	int lineNo = 0;
134	>	std::streampos prevPos;
135		std::streampos  currPos;
136	<
136	>
137		#ifdef IS_MPI
138	<
138	>
139		if (worldRank == 0) {
140		#endif // is_mpi
141	<
142	<	inFile_->seekg (0, std::ios::beg);
143	<
144	<
145	<	currPos = inFile_->tellg();
146	<	inFile_->getline(readBuffer, sizeof(readBuffer));
147	<	lineNum++;
148	<
149	<	if (inFile_->eof()) {
150	<	sprintf(painCave.errMsg,
151	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
152	<	filename_.c_str(),
151	<	lineNum);
152	<	painCave.isFatal = 1;
153	<	simError();
154	<	}
155	<
156	<	while (!inFile_->eof()) {
157	<	framePos_.push_back(currPos);
158	<
159	<	i = atoi(readBuffer);
160	<
161	<	inFile_->getline(readBuffer, sizeof(readBuffer));
162	<	lineNum++;
163	<
164	<	if (inFile_->eof()) {
165	<	sprintf(painCave.errMsg,
166	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
167	<	filename_.c_str(),
168	<	lineNum);
169	<	painCave.isFatal = 1;
170	<	simError();
171	<	}
172	<
173	<	for(j = 0; j < i; j++) {
174	<	inFile_->getline(readBuffer, sizeof(readBuffer));
175	<	lineNum++;
176	<
177	<	if (inFile_->eof()) {
141	>
142	>	currPos = inFile_->tellg();
143	>	prevPos = currPos;
144	>	bool foundOpenSnapshotTag = false;
145	>	bool foundClosedSnapshotTag = false;
146	>	while(inFile_->getline(buffer, bufferSize)) {
147	>	++lineNo;
148	>
149	>	std::string line = buffer;
150	>	currPos = inFile_->tellg();
151	>	if (line.find("<Snapshot>")!= std::string::npos) {
152	>	if (foundOpenSnapshotTag) {
153		sprintf(painCave.errMsg,
154	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d,"
155	<	" with atom %d\n", filename_.c_str(),
181	<	lineNum,
182	<	j);
183	<
154	>	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
155	>	filename_.c_str());
156		painCave.isFatal = 1;
157	+	simError();
158	+	}
159	+	foundOpenSnapshotTag = true;
160	+	foundClosedSnapshotTag = false;
161	+	framePos_.push_back(prevPos);
162	+
163	+	} else if (line.find("</Snapshot>") != std::string::npos){
164	+	if (!foundOpenSnapshotTag) {
165	+	sprintf(painCave.errMsg,
166	+	"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
167	+	filename_.c_str());
168	+	painCave.isFatal = 1;
169		simError();
170	<	}
171	<	}
172	<
173	<	currPos = inFile_->tellg();
174	<	inFile_->getline(readBuffer, sizeof(readBuffer));
175	<	lineNum++;
176	<	}
177	<
178	<	inFile_->seekg (0, std::ios::beg);
179	<
170	>	}
171	>
172	>	if (foundClosedSnapshotTag) {
173	>	sprintf(painCave.errMsg,
174	>	"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
175	>	filename_.c_str());
176	>	painCave.isFatal = 1;
177	>	simError();
178	>	}
179	>	foundClosedSnapshotTag = true;
180	>	foundOpenSnapshotTag = false;
181	>	}
182	>	prevPos = currPos;
183	>	}
184	>
185	>	// only found <Snapshot> for the last frame means the file is corrupted, we should discard
186	>	// it and give a warning message
187	>	if (foundOpenSnapshotTag) {
188	>	sprintf(painCave.errMsg,
189	>	"DumpReader: last frame in %s is invalid\n", filename_.c_str());
190	>	painCave.isFatal = 0;
191	>	simError();
192	>	framePos_.pop_back();
193	>	}
194	>
195		nframes_ = framePos_.size();
196	+
197	+	if (nframes_ == 0) {
198	+	sprintf(painCave.errMsg,
199	+	"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
200	+	painCave.isFatal = 1;
201	+	simError();
202	+	}
203		#ifdef IS_MPI
204		}
205
206		MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
207	<
202	<	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
203	<	MPIcheckPoint();
204	<
207	>
208		#endif // is_mpi
209	<
209	>
210		isScanned_ = true;
211		}
212
#	Line 238 | Line 241 | namespace oopse {
241		}
242
243		readSet(whichFrame);
244	+
245	+	if (needCOMprops_) {
246	+	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
247	+	Vector3d com;
248	+	Vector3d comvel;
249	+	Vector3d comw;
250	+	if (needPos_ && needVel_){
251	+	info_->getComAll(com, comvel);
252	+	comw = info_->getAngularMomentum();
253	+	}else{
254	+	com = info_->getCom();
255	+	comvel = 0.0;
256	+	comw   = 0.0;
257	+	}
258	+	s->setCOMprops(com, comvel, comw);
259	+	}
260	+
261		}
262
263	<	void DumpReader::readSet(int whichFrame) {
264	<	int i;
265	<	int nTotObjs;                  // the number of atoms
246	<	char read_buffer[maxBufferSize];  //the line buffer for reading
247	<	char * eof_test;               // ptr to see when we reach the end of the file
248	<
249	<	Molecule* mol;
250	<	StuntDouble* integrableObject;
251	<	SimInfo::MoleculeIterator mi;
252	<	Molecule::IntegrableObjectIterator ii;
253	<
263	>	void DumpReader::readSet(int whichFrame) {
264	>	std::string line;
265	>
266		#ifndef IS_MPI
267		inFile_->clear();
268		inFile_->seekg(framePos_[whichFrame]);
269	<
270	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
269	>
270	>	std::istream& inputStream = *inFile_;
271	>
272	>	#else
273	>	int masterNode = 0;
274	>	std::stringstream sstream;
275	>	if (worldRank == masterNode) {
276	>	std::string sendBuffer;
277	>
278	>	inFile_->clear();
279	>	inFile_->seekg(framePos_[whichFrame]);
280	>
281	>	while (inFile_->getline(buffer, bufferSize)) {
282	>
283	>	line = buffer;
284	>	sendBuffer += line;
285	>	sendBuffer += '\n';
286	>	if (line.find("</Snapshot>") != std::string::npos) {
287	>	break;
288	>	}
289	>	}
290	>
291	>	int sendBufferSize = sendBuffer.size();
292	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
293	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
294	>
295	>	sstream.str(sendBuffer);
296	>	} else {
297	>	int sendBufferSize;
298	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
299	>	char * recvBuffer = new char[sendBufferSize+1];
300	>	assert(recvBuffer);
301	>	recvBuffer[sendBufferSize] = '\0';
302	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
303	>	sstream.str(recvBuffer);
304	>	delete [] recvBuffer;
305	>	}
306	>
307	>	std::istream& inputStream = sstream;
308	>	#endif
309	>
310	>	inputStream.getline(buffer, bufferSize);
311	>
312	>	line = buffer;
313	>	if (line.find("<Snapshot>") == std::string::npos) {
314		sprintf(painCave.errMsg,
315	<	"DumpReader error: error reading 1st line of \"%s\"\n",
261	<	filename_.c_str());
315	>	"DumpReader Error: can not find <Snapshot>\n");
316		painCave.isFatal = 1;
317		simError();
318		}
319	<
320	<	nTotObjs = atoi(read_buffer);
321	<
322	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
319	>
320	>	//read frameData
321	>	readFrameProperties(inputStream);
322	>
323	>	//read StuntDoubles
324	>	readStuntDoubles(inputStream);
325	>
326	>	inputStream.getline(buffer, bufferSize);
327	>	line = buffer;
328	>	if (line.find("</Snapshot>") == std::string::npos) {
329		sprintf(painCave.errMsg,
330	<	"DumpReader error. %s nIntegrable, %d, "
271	<	"does not match the meta-data file's nIntegrable, %d.\n",
272	<	filename_.c_str(),
273	<	nTotObjs,
274	<	info_->getNGlobalIntegrableObjects());
275	<
330	>	"DumpReader Error: can not find </Snapshot>\n");
331		painCave.isFatal = 1;
332		simError();
333	<	}
334	<
280	<	//read the box mat from the comment line
281	<
282	<
283	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
284	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
285	<	filename_.c_str());
286	<	painCave.isFatal = 1;
287	<	simError();
288	<	}
289	<
290	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
291	<
292	<	//parse dump lines
293	<
294	<	i = 0;
295	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
296	<
297	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
298	<	integrableObject = mol->nextIntegrableObject(ii)) {
299	<
300	<
301	<
302	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
303	<	sprintf(painCave.errMsg,
304	<	"DumpReader Error: error in reading file %s\n"
305	<	"natoms  = %d; index = %d\n"
306	<	"error reading the line from the file.\n",
307	<	filename_.c_str(),
308	<	nTotObjs,
309	<	i);
310	<
311	<	painCave.isFatal = 1;
312	<	simError();
313	<	}
314	<
315	<	parseDumpLine(read_buffer, integrableObject);
316	<	i++;
317	<	}
318	<	}
319	<
320	<	// MPI Section of code..........
321	<
322	<	#else //IS_MPI
323	<
324	<	// first thing first, suspend fatalities.
325	<	int masterNode = 0;
326	<	int nCurObj;
327	<	painCave.isEventLoop = 1;
328	<
329	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
330	<	int haveError;
331	<
332	<	MPI_Status istatus;
333	<	int nitems;
334	<
335	<	nTotObjs = info_->getNGlobalIntegrableObjects();
336	<	haveError = 0;
337	<
338	<	if (worldRank == masterNode) {
339	<	inFile_->clear();
340	<	inFile_->seekg(framePos_[whichFrame]);
341	<
342	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
343	<	sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ",
344	<	filename_.c_str());
345	<	painCave.isFatal = 1;
346	<	simError();
347	<	}
348	<
349	<	nitems = atoi(read_buffer);
350	<
351	<	// Check to see that the number of integrable objects in the
352	<	// intial configuration file is the same as derived from the
353	<	// meta-data file.
354	<
355	<	if (nTotObjs != nitems) {
356	<	sprintf(painCave.errMsg,
357	<	"DumpReader Error. %s nIntegrable, %d, "
358	<	"does not match the meta-data file's nIntegrable, %d.\n",
359	<	filename_.c_str(),
360	<	nTotObjs,
361	<	info_->getNGlobalIntegrableObjects());
362	<
363	<	painCave.isFatal = 1;
364	<	simError();
365	<	}
366	<
367	<	//read the boxMat from the comment line
368	<
369	<
370	<
371	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
372	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
373	<	filename_.c_str());
374	<	painCave.isFatal = 1;
375	<	simError();
376	<	}
377	<
378	<	//Every single processor will parse the comment line by itself
379	<	//By using this way, we might lose some efficiency, but if we want to add
380	<	//more parameters into comment line, we only need to modify function
381	<	//parseCommentLine
382	<
383	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
384	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
385	<
386	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
387	<	int which_node = info_->getMolToProc(i);
388	<
389	<	if (which_node == masterNode) {
390	<	//molecules belong to master node
391	<
392	<	mol = info_->getMoleculeByGlobalIndex(i);
393	<
394	<	if (mol == NULL) {
395	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
396	<	painCave.isFatal = 1;
397	<	simError();
398	<	}
399	<
400	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
401	<	integrableObject = mol->nextIntegrableObject(ii)){
402	<
403	<
404	<
405	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
406	<	sprintf(painCave.errMsg,
407	<	"DumpReader Error: error in reading file %s\n"
408	<	"natoms  = %d; index = %d\n"
409	<	"error reading the line from the file.\n",
410	<	filename_.c_str(),
411	<	nTotObjs,
412	<	i);
413	<
414	<	painCave.isFatal = 1;
415	<	simError();
416	<	}
417	<
418	<	parseDumpLine(read_buffer, integrableObject);
419	<	}
420	<	} else {
421	<	//molecule belongs to slave nodes
422	<
423	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
424	<	MPI_COMM_WORLD, &istatus);
425	<
426	<	for(int j = 0; j < nCurObj; j++) {
427	<
428	<
429	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
430	<	sprintf(painCave.errMsg,
431	<	"DumpReader Error: error in reading file %s\n"
432	<	"natoms  = %d; index = %d\n"
433	<	"error reading the line from the file.\n",
434	<	filename_.c_str(),
435	<	nTotObjs,
436	<	i);
437	<
438	<	painCave.isFatal = 1;
439	<	simError();
440	<	}
441	<
442	<	MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
443	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
444	<	}
445	<	}
446	<	}
447	<	} else {
448	<	//actions taken at slave nodes
449	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
450	<
451	<	/**@todo*/
452	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
453	<
454	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
455	<	int which_node = info_->getMolToProc(i);
456	<
457	<	if (which_node == worldRank) {
458	<	//molecule with global index i belongs to this processor
459	<
460	<	mol = info_->getMoleculeByGlobalIndex(i);
461	<	if (mol == NULL) {
462	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
463	<	painCave.isFatal = 1;
464	<	simError();
465	<	}
466	<
467	<	nCurObj = mol->getNIntegrableObjects();
468	<
469	<	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
470	<	MPI_COMM_WORLD);
471	<
472	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
473	<	integrableObject = mol->nextIntegrableObject(ii)){
474	<
475	<	MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
476	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
477	<
478	<	parseDumpLine(read_buffer, integrableObject);
479	<	}
480	<
481	<	}
482	<
483	<	}
484	<
485	<	}
486	<
487	<	#endif
488	<
333	>	}
334	>
335		}
336
337	<	void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
338	<
339	<	Vector3d pos;  // position place holders
494	<	Vector3d vel;  // velocity placeholders
495	<	Quat4d q;    // the quaternions
496	<	Vector3d ji;   // angular velocity placeholders;
337	>	void DumpReader::parseDumpLine(const std::string& line) {
338	>
339	>
340		StringTokenizer tokenizer(line);
341		int nTokens;
342
343		nTokens = tokenizer.countTokens();
344
345	<	if (nTokens < 14) {
345	>	if (nTokens < 2) {
346		sprintf(painCave.errMsg,
347	<	"DumpReader Error: Not enough Tokens.\n%s\n", line);
347	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
348		painCave.isFatal = 1;
349		simError();
350		}
351	<
352	<	std::string name = tokenizer.nextToken();
353	<
354	<	if (name != integrableObject->getType()) {
355	<
356	<	sprintf(painCave.errMsg,
357	<	"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
358	<	name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
359	<	painCave.isFatal = 1;
360	<	simError();
361	<	}
362	<
363	<	pos[0] = tokenizer.nextTokenAsDouble();
364	<	pos[1] = tokenizer.nextTokenAsDouble();
365	<	pos[2] = tokenizer.nextTokenAsDouble();
366	<	if (needPos_) {
524	<	integrableObject->setPos(pos);
525	<	}
526	<
527	<	vel[0] = tokenizer.nextTokenAsDouble();
528	<	vel[1] = tokenizer.nextTokenAsDouble();
529	<	vel[2] = tokenizer.nextTokenAsDouble();
530	<	if (needVel_) {
531	<	integrableObject->setVel(vel);
532	<	}
533	<
534	<	if (integrableObject->isDirectional()) {
535	<
536	<	q[0] = tokenizer.nextTokenAsDouble();
537	<	q[1] = tokenizer.nextTokenAsDouble();
538	<	q[2] = tokenizer.nextTokenAsDouble();
539	<	q[3] = tokenizer.nextTokenAsDouble();
540	<
541	<	RealType qlen = q.length();
542	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
543	<
351	>
352	>	int index = tokenizer.nextTokenAsInt();
353	>
354	>	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
355	>
356	>	if (integrableObject == NULL) {
357	>	return;
358	>	}
359	>	std::string type = tokenizer.nextToken();
360	>	int size = type.size();
361	>
362	>	size_t found;
363	>
364	>	if (needPos_) {
365	>	found = type.find("p");
366	>	if (found == std::string::npos) {
367		sprintf(painCave.errMsg,
368	<	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0\n");
368	>	"DumpReader Error: StuntDouble %d has no Position\n"
369	>	"\tField (\"p\") specified.\n%s\n", index,
370	>	line.c_str());
371		painCave.isFatal = 1;
372		simError();
373	<
374	<	}
375	<
376	<	q.normalize();
377	<	if (needQuaternion_) {
378	<	integrableObject->setQ(q);
379	<	}
380	<
381	<	ji[0] = tokenizer.nextTokenAsDouble();
382	<	ji[1] = tokenizer.nextTokenAsDouble();
383	<	ji[2] = tokenizer.nextTokenAsDouble();
384	<	if (needAngMom_) {
385	<	integrableObject->setJ(ji);
386	<	}
387	<	}
373	>	}
374	>	}
375	>
376	>	if (integrableObject->isDirectional()) {
377	>	if (needQuaternion_) {
378	>	found = type.find("q");
379	>	if (found == std::string::npos) {
380	>	sprintf(painCave.errMsg,
381	>	"DumpReader Error: Directional StuntDouble %d has no\n"
382	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
383	>	line.c_str());
384	>	painCave.isFatal = 1;
385	>	simError();
386	>	}
387	>	}
388	>	}
389	>
390	>	for(int i = 0; i < size; ++i) {
391	>	switch(type[i]) {
392	>
393	>	case 'p': {
394	>	Vector3d pos;
395	>	pos[0] = tokenizer.nextTokenAsDouble();
396	>	pos[1] = tokenizer.nextTokenAsDouble();
397	>	pos[2] = tokenizer.nextTokenAsDouble();
398	>	if (needPos_) {
399	>	integrableObject->setPos(pos);
400	>	}
401	>	break;
402	>	}
403	>	case 'v' : {
404	>	Vector3d vel;
405	>	vel[0] = tokenizer.nextTokenAsDouble();
406	>	vel[1] = tokenizer.nextTokenAsDouble();
407	>	vel[2] = tokenizer.nextTokenAsDouble();
408	>	if (needVel_) {
409	>	integrableObject->setVel(vel);
410	>	}
411	>	break;
412	>	}
413	>
414	>	case 'q' : {
415	>	Quat4d q;
416	>	if (integrableObject->isDirectional()) {
417	>
418	>	q[0] = tokenizer.nextTokenAsDouble();
419	>	q[1] = tokenizer.nextTokenAsDouble();
420	>	q[2] = tokenizer.nextTokenAsDouble();
421	>	q[3] = tokenizer.nextTokenAsDouble();
422	>
423	>	RealType qlen = q.length();
424	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
425	>
426	>	sprintf(painCave.errMsg,
427	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
428	>	painCave.isFatal = 1;
429	>	simError();
430	>
431	>	}
432	>
433	>	q.normalize();
434	>	if (needQuaternion_) {
435	>	integrableObject->setQ(q);
436	>	}
437	>	}
438	>	break;
439	>	}
440	>	case 'j' : {
441	>	Vector3d ji;
442	>	if (integrableObject->isDirectional()) {
443	>	ji[0] = tokenizer.nextTokenAsDouble();
444	>	ji[1] = tokenizer.nextTokenAsDouble();
445	>	ji[2] = tokenizer.nextTokenAsDouble();
446	>	if (needAngMom_) {
447	>	integrableObject->setJ(ji);
448	>	}
449	>	}
450	>	break;
451	>	}
452	>	case 'f': {
453	>
454	>	Vector3d force;
455	>	force[0] = tokenizer.nextTokenAsDouble();
456	>	force[1] = tokenizer.nextTokenAsDouble();
457	>	force[2] = tokenizer.nextTokenAsDouble();
458	>	integrableObject->setFrc(force);
459	>	break;
460	>	}
461	>	case 't' : {
462	>
463	>	Vector3d torque;
464	>	torque[0] = tokenizer.nextTokenAsDouble();
465	>	torque[1] = tokenizer.nextTokenAsDouble();
466	>	torque[2] = tokenizer.nextTokenAsDouble();
467	>	integrableObject->setTrq(torque);
468	>	break;
469	>	}
470	>	case 'u' : {
471	>
472	>	RealType particlePot;
473	>	particlePot = tokenizer.nextTokenAsDouble();
474	>	integrableObject->setParticlePot(particlePot);
475	>	break;
476	>	}
477	>	default: {
478	>	sprintf(painCave.errMsg,
479	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
480	>	painCave.isFatal = 1;
481	>	simError();
482	>	break;
483	>	}
484	>
485	>	}
486	>	}
487
488		}
489
490	<
491	<	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
492	<	RealType currTime;
493	<	Mat3x3d hmat;
494	<	RealType chi;
495	<	RealType integralOfChiDt;
496	<	Mat3x3d eta;
573	<
574	<	StringTokenizer tokenizer(line);
575	<	int nTokens;
576	<
577	<	nTokens = tokenizer.countTokens();
578	<
579	<	//comment line should at least contain 10 tokens: current time(1 token) and  h-matrix(9 tokens)
580	<	if (nTokens < 10) {
490	>
491	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
492	>
493	>	inputStream.getline(buffer, bufferSize);
494	>	std::string line(buffer);
495	>
496	>	if (line.find("<StuntDoubles>") == std::string::npos) {
497		sprintf(painCave.errMsg,
498	<	"DumpReader Error: Not enough tokens in comment line: %s", line);
498	>	"DumpReader Error: Missing <StuntDoubles>\n");
499		painCave.isFatal = 1;
500	<	simError();
501	<	}
502	<
503	<	//read current time
504	<	currTime = tokenizer.nextTokenAsDouble();
505	<	s->setTime(currTime);
506	<
507	<	//read h-matrix
508	<	hmat(0, 0) = tokenizer.nextTokenAsDouble();
509	<	hmat(0, 1) = tokenizer.nextTokenAsDouble();
510	<	hmat(0, 2) = tokenizer.nextTokenAsDouble();
511	<	hmat(1, 0) = tokenizer.nextTokenAsDouble();
512	<	hmat(1, 1) = tokenizer.nextTokenAsDouble();
513	<	hmat(1, 2) = tokenizer.nextTokenAsDouble();
514	<	hmat(2, 0) = tokenizer.nextTokenAsDouble();
515	<	hmat(2, 1) = tokenizer.nextTokenAsDouble();
516	<	hmat(2, 2) = tokenizer.nextTokenAsDouble();
517	<	s->setHmat(hmat);
518	<
519	<	//read chi and integralOfChidt, they should apprear in pair
520	<	if (tokenizer.countTokens() >= 2) {
521	<	chi = tokenizer.nextTokenAsDouble();
522	<	integralOfChiDt = tokenizer.nextTokenAsDouble();
523	<
524	<	s->setChi(chi);
525	<	s->setIntegralOfChiDt(integralOfChiDt);
526	<	}
527	<
528	<	//read eta (eta is 3x3 matrix)
529	<	if (tokenizer.countTokens() >= 9) {
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	<
540	<	s->setEta(eta);
541	<	}
542	<
543	<
544	<	}
500	>	simError();
501	>	}
502	>
503	>	while(inputStream.getline(buffer, bufferSize)) {
504	>	line = buffer;
505	>
506	>	if(line.find("</StuntDoubles>") != std::string::npos) {
507	>	break;
508	>	}
509	>
510	>	parseDumpLine(line);
511	>	}
512	>
513	>	}
514	>
515	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
516	>
517	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
518	>	inputStream.getline(buffer, bufferSize);
519	>	std::string line(buffer);
520	>
521	>	if (line.find("<FrameData>") == std::string::npos) {
522	>	sprintf(painCave.errMsg,
523	>	"DumpReader Error: Missing <FrameData>\n");
524	>	painCave.isFatal = 1;
525	>	simError();
526	>	}
527	>
528	>	while(inputStream.getline(buffer, bufferSize)) {
529	>	line = buffer;
530	>
531	>	if(line.find("</FrameData>") != std::string::npos) {
532	>	break;
533	>	}
534	>
535	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
536	>	if (!tokenizer.hasMoreTokens()) {
537	>	sprintf(painCave.errMsg,
538	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
539	>	painCave.isFatal = 1;
540	>	simError();
541	>	}
542	>
543	>	std::string propertyName = tokenizer.nextToken();
544	>	if (propertyName == "Time") {
545	>	RealType currTime = tokenizer.nextTokenAsDouble();
546	>	s->setTime(currTime);
547	>	} else if (propertyName == "Hmat"){
548	>	Mat3x3d hmat;
549	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
550	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
551	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
552	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
553	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
554	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
555	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
556	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
557	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
558	>	s->setHmat(hmat);
559	>	} else if (propertyName == "Thermostat") {
560	>	RealType chi = tokenizer.nextTokenAsDouble();
561	>	RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
562	>	s->setChi(chi);
563	>	s->setIntegralOfChiDt(integralOfChiDt);
564	>	} else if (propertyName == "Barostat") {
565	>	Mat3x3d eta;
566	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
567	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
568	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
569	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
570	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
571	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
572	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
573	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
574	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
575	>	s->setEta(eta);
576	>	} else {
577	>	sprintf(painCave.errMsg,
578	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
579	>	painCave.isFatal = 0;
580	>	simError();
581	>	}
582	>
583	>	}
584	>
585	>	}
586	>
587
588	<	}//end namespace oopse
588	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpReader.cpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/io/DumpReader.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 0 | Line 1
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