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

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trunk/src/io/DumpReader.cpp (file contents), Revision 721 by chrisfen, Tue Nov 8 13:32:27 2005 UTC vs.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 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 57 | Line 58
58		#include "utils/simError.h"
59		#include "utils/MemoryUtils.hpp"
60		#include "utils/StringTokenizer.hpp"
61	+	#include "brains/Thermo.hpp"
62
63		#ifdef IS_MPI
62	–
64		#include <mpi.h>
65	<	#define TAKE_THIS_TAG_CHAR 0
65	<	#define TAKE_THIS_TAG_INT 1
65	>	#endif
66
67	–	#endif // is_mpi
67
68	<
70	<	namespace oopse {
68	>	namespace OpenMD {
69
70		DumpReader::DumpReader(SimInfo* info, const std::string& filename)
71	<	: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
72	<
71	>	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
72	>
73		#ifdef IS_MPI
74	<
75	<	if (worldRank == 0) {
74	>
75	>	if (worldRank == 0) {
76		#endif
77	<
78	<	inFile_ = new std::ifstream(filename_.c_str());
79	<
80	<	if (inFile_->fail()) {
81	<	sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
82	<	painCave.isFatal = 1;
83	<	simError();
84	<	}
85	<
86	<	#ifdef IS_MPI
89	<
77	>
78	>	inFile_ = new std::ifstream(filename_.c_str(),
79	>	ifstream::in | ifstream::binary);
80	>
81	>	if (inFile_->fail()) {
82	>	sprintf(painCave.errMsg,
83	>	"DumpReader: Cannot open file: %s\n",
84	>	filename_.c_str());
85	>	painCave.isFatal = 1;
86	>	simError();
87		}
88	<
89	<	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
90	<	MPIcheckPoint();
94	<
95	<	#endif
96	<
97	<	return;
88	>
89	>	#ifdef IS_MPI
90	>
91		}
92	<
92	>
93	>	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
94	>	errorCheckPoint();
95	>
96	>	#endif
97	>
98	>	return;
99	>	}
100	>
101		DumpReader::~DumpReader() {
102	<
102	>
103		#ifdef IS_MPI
104	<
104	>
105		if (worldRank == 0) {
106		#endif
107	<
107	>
108		delete inFile_;
109	<
109	>
110		#ifdef IS_MPI
111	<
111	>
112		}
113	<
113	>
114		strcpy(checkPointMsg, "Dump file closed successfully.");
115	<	MPIcheckPoint();
116	<
115	>	errorCheckPoint();
116	>
117		#endif
118	<
118	>
119		return;
120		}
121	<
121	>
122		int DumpReader::getNFrames(void) {
123
124		if (!isScanned_)
#	Line 127 | Line 128 | namespace oopse {
128		}
129
130		void DumpReader::scanFile(void) {
131	<	int i, j;
132	<	int lineNum = 0;
132	<	char readBuffer[maxBufferSize];
131	>	int lineNo = 0;
132	>	std::streampos prevPos;
133		std::streampos  currPos;
134	<
134	>
135		#ifdef IS_MPI
136	<
136	>
137		if (worldRank == 0) {
138		#endif // is_mpi
139	<
140	<	inFile_->seekg (0, std::ios::beg);
141	<
142	<
143	<	currPos = inFile_->tellg();
144	<	inFile_->getline(readBuffer, sizeof(readBuffer));
145	<	lineNum++;
146	<
147	<	if (inFile_->eof()) {
148	<	sprintf(painCave.errMsg,
149	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
150	<	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()) {
139	>
140	>	currPos = inFile_->tellg();
141	>	prevPos = currPos;
142	>	bool foundOpenSnapshotTag = false;
143	>	bool foundClosedSnapshotTag = false;
144	>
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(),
181	<	lineNum,
182	<	j);
183	<
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		}
199	–
200	–	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
201	–
202	–	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
203	–	MPIcheckPoint();
204
205	+	MPI::COMM_WORLD.Bcast(&nframes_, 1, MPI::INT, 0);
206	+
207		#endif // is_mpi
208	<
208	>
209		isScanned_ = true;
210		}
211
#	Line 225 | Line 227 | namespace oopse {
227		needVel_ = false;
228		}
229
230	<	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
230	>	if (storageLayout & DataStorage::dslAmat ||
231	>	storageLayout & DataStorage::dslDipole ||
232	>	storageLayout & DataStorage::dslQuadrupole) {
233		needQuaternion_ = true;
234		} else {
235		needQuaternion_ = false;
#	Line 238 | Line 242 | namespace oopse {
242		}
243
244		readSet(whichFrame);
245	+
246	+	if (needCOMprops_) {
247	+	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
248	+	Thermo thermo(info_);
249	+	Vector3d com;
250	+
251	+	if (needPos_ && needVel_) {
252	+	Vector3d comvel;
253	+	Vector3d comw;
254	+	thermo.getComAll(com, comvel);
255	+	comw = thermo.getAngularMomentum();
256	+	} else {
257	+	com = thermo.getCom();
258	+	}
259	+	}
260		}
261
262	<	void DumpReader::readSet(int whichFrame) {
263	<	int i;
264	<	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	<
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::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
292	>	MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize,
293	>	MPI::CHAR, masterNode);
294	>
295	>	sstream.str(sendBuffer);
296	>	} else {
297	>	int sendBufferSize;
298	>	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
299	>	char * recvBuffer = new char[sendBufferSize+1];
300	>	assert(recvBuffer);
301	>	recvBuffer[sendBufferSize] = '\0';
302	>	MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
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	+	//read frameData
321	+	readFrameProperties(inputStream);
322	+
323	+	//read StuntDoubles
324	+	readStuntDoubles(inputStream);
325	+
326	+	inputStream.getline(buffer, bufferSize);
327	+	line = buffer;
328	+
329	+	if (line.find("<SiteData>") != std::string::npos) {
330	+	//read SiteData
331	+	readSiteData(inputStream);
332	+	} else {
333	+	if (line.find("</Snapshot>") == std::string::npos) {
334	+	sprintf(painCave.errMsg,
335	+	"DumpReader Error: can not find </Snapshot>\n");
336	+	painCave.isFatal = 1;
337	+	simError();
338	+	}
339	+	}
340	+	}
341	+
342	+	void DumpReader::parseDumpLine(const std::string& line) {
343	+
344	+
345	+	StringTokenizer tokenizer(line);
346	+	int nTokens;
347
348	<	nTotObjs = atoi(read_buffer);
348	>	nTokens = tokenizer.countTokens();
349
350	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
350	>	if (nTokens < 2) {
351		sprintf(painCave.errMsg,
352	<	"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	<
352	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
353		painCave.isFatal = 1;
354		simError();
355		}
356	<
357	<	//read the box mat from the comment line
358	<
359	<
360	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
361	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
362	<	filename_.c_str());
363	<	painCave.isFatal = 1;
364	<	simError();
365	<	}
366	<
367	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
368	<
369	<	//parse dump lines
370	<
371	<	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	>
357	>	int index = tokenizer.nextTokenAsInt();
358	>
359	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
360	>
361	>	if (sd == NULL) {
362	>	return;
363	>	}
364	>	std::string type = tokenizer.nextToken();
365	>	int size = type.size();
366	>
367	>	size_t found;
368	>
369	>	if (needPos_) {
370	>	found = type.find("p");
371	>	if (found == std::string::npos) {
372		sprintf(painCave.errMsg,
373	<	"DumpReader Error. %s nIntegrable, %d, "
374	<	"does not match the meta-data file's nIntegrable, %d.\n",
375	<	filename_.c_str(),
360	<	nTotObjs,
361	<	info_->getNGlobalIntegrableObjects());
362	<
373	>	"DumpReader Error: StuntDouble %d has no Position\n"
374	>	"\tField (\"p\") specified.\n%s\n", index,
375	>	line.c_str());
376		painCave.isFatal = 1;
377		simError();
378	<	}
379	<
380	<	//read the boxMat from the comment line
381	<
382	<
383	<
384	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
385	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
386	<	filename_.c_str());
387	<	painCave.isFatal = 1;
388	<	simError();
389	<	}
390	<
391	<	//Every single processor will parse the comment line by itself
392	<	//By using this way, we might lose some efficiency, but if we want to add
393	<	//more parameters into comment line, we only need to modify function
394	<	//parseCommentLine
395	<
396	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
397	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
398	<
399	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
400	<	int which_node = info_->getMolToProc(i);
401	<
402	<	if (which_node == masterNode) {
403	<	//molecules belong to master node
404	<
405	<	mol = info_->getMoleculeByGlobalIndex(i);
406	<
407	<	if (mol == NULL) {
408	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
409	<	painCave.isFatal = 1;
410	<	simError();
411	<	}
412	<
413	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
414	<	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();
378	>	}
379	>	}
380	>
381	>	if (sd->isDirectional()) {
382	>	if (needQuaternion_) {
383	>	found = type.find("q");
384	>	if (found == std::string::npos) {
385	>	sprintf(painCave.errMsg,
386	>	"DumpReader Error: Directional StuntDouble %d has no\n"
387	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
388	>	line.c_str());
389	>	painCave.isFatal = 1;
390	>	simError();
391	>	}
392	>	}
393	>	}
394	>
395	>	for(int i = 0; i < size; ++i) {
396	>	switch(type[i]) {
397	>
398	>	case 'p': {
399	>	Vector3d pos;
400	>	pos[0] = tokenizer.nextTokenAsDouble();
401	>	pos[1] = tokenizer.nextTokenAsDouble();
402	>	pos[2] = tokenizer.nextTokenAsDouble();
403	>	if (needPos_) {
404	>	sd->setPos(pos);
405	>	}
406	>	break;
407	>	}
408	>	case 'v' : {
409	>	Vector3d vel;
410	>	vel[0] = tokenizer.nextTokenAsDouble();
411	>	vel[1] = tokenizer.nextTokenAsDouble();
412	>	vel[2] = tokenizer.nextTokenAsDouble();
413	>	if (needVel_) {
414	>	sd->setVel(vel);
415		}
416	<
417	<	parseDumpLine(read_buffer, integrableObject);
418	<	}
419	<	} else {
420	<	//molecule belongs to slave nodes
421	<
422	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
423	<	MPI_COMM_WORLD, &istatus);
424	<
425	<	for(int j = 0; j < nCurObj; j++) {
426	<
427	<
428	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
429	<	sprintf(painCave.errMsg,
430	<	"DumpReader Error: error in reading file %s\n"
431	<	"natoms  = %d; index = %d\n"
432	<	"error reading the line from the file.\n",
433	<	filename_.c_str(),
434	<	nTotObjs,
435	<	i);
436	<
437	<	painCave.isFatal = 1;
438	<	simError();
439	<	}
440	<
441	<	MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
442	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
443	<	}
444	<	}
445	<	}
446	<	} else {
447	<	//actions taken at slave nodes
448	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
449	<
450	<	/**@todo*/
451	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
452	<
453	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
454	<	int which_node = info_->getMolToProc(i);
455	<
456	<	if (which_node == worldRank) {
457	<	//molecule with global index i belongs to this processor
458	<
459	<	mol = info_->getMoleculeByGlobalIndex(i);
460	<	if (mol == NULL) {
461	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
462	<	painCave.isFatal = 1;
463	<	simError();
464	<	}
465	<
466	<	nCurObj = mol->getNIntegrableObjects();
467	<
468	<	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
469	<	MPI_COMM_WORLD);
470	<
471	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
472	<	integrableObject = mol->nextIntegrableObject(ii)){
473	<
474	<	MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
475	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
476	<
477	<	parseDumpLine(read_buffer, integrableObject);
478	<	}
479	<
480	<	}
481	<
482	<	}
483	<
484	<	}
416	>	break;
417	>	}
418	>
419	>	case 'q' : {
420	>	Quat4d q;
421	>	if (sd->isDirectional()) {
422	>
423	>	q[0] = tokenizer.nextTokenAsDouble();
424	>	q[1] = tokenizer.nextTokenAsDouble();
425	>	q[2] = tokenizer.nextTokenAsDouble();
426	>	q[3] = tokenizer.nextTokenAsDouble();
427	>
428	>	RealType qlen = q.length();
429	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
430	>
431	>	sprintf(painCave.errMsg,
432	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
433	>	painCave.isFatal = 1;
434	>	simError();
435	>
436	>	}
437	>
438	>	q.normalize();
439	>	if (needQuaternion_) {
440	>	sd->setQ(q);
441	>	}
442	>	}
443	>	break;
444	>	}
445	>	case 'j' : {
446	>	Vector3d ji;
447	>	if (sd->isDirectional()) {
448	>	ji[0] = tokenizer.nextTokenAsDouble();
449	>	ji[1] = tokenizer.nextTokenAsDouble();
450	>	ji[2] = tokenizer.nextTokenAsDouble();
451	>	if (needAngMom_) {
452	>	sd->setJ(ji);
453	>	}
454	>	}
455	>	break;
456	>	}
457	>	case 'f': {
458	>
459	>	Vector3d force;
460	>	force[0] = tokenizer.nextTokenAsDouble();
461	>	force[1] = tokenizer.nextTokenAsDouble();
462	>	force[2] = tokenizer.nextTokenAsDouble();
463	>	sd->setFrc(force);
464	>	break;
465	>	}
466	>	case 't' : {
467	>
468	>	Vector3d torque;
469	>	torque[0] = tokenizer.nextTokenAsDouble();
470	>	torque[1] = tokenizer.nextTokenAsDouble();
471	>	torque[2] = tokenizer.nextTokenAsDouble();
472	>	sd->setTrq(torque);
473	>	break;
474	>	}
475	>	case 'u' : {
476	>
477	>	RealType particlePot;
478	>	particlePot = tokenizer.nextTokenAsDouble();
479	>	sd->setParticlePot(particlePot);
480	>	break;
481	>	}
482	>	case 'c' : {
483	>
484	>	RealType flucQPos;
485	>	flucQPos = tokenizer.nextTokenAsDouble();
486	>	sd->setFlucQPos(flucQPos);
487	>	break;
488	>	}
489	>	case 'w' : {
490	>
491	>	RealType flucQVel;
492	>	flucQVel = tokenizer.nextTokenAsDouble();
493	>	sd->setFlucQVel(flucQVel);
494	>	break;
495	>	}
496	>	case 'g' : {
497	>
498	>	RealType flucQFrc;
499	>	flucQFrc = tokenizer.nextTokenAsDouble();
500	>	sd->setFlucQFrc(flucQFrc);
501	>	break;
502	>	}
503	>	case 'e' : {
504	>
505	>	Vector3d eField;
506	>	eField[0] = tokenizer.nextTokenAsDouble();
507	>	eField[1] = tokenizer.nextTokenAsDouble();
508	>	eField[2] = tokenizer.nextTokenAsDouble();
509	>	sd->setElectricField(eField);
510	>	break;
511	>	}
512	>	default: {
513	>	sprintf(painCave.errMsg,
514	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
515	>	painCave.isFatal = 1;
516	>	simError();
517	>	break;
518	>	}
519	>
520	>	}
521	>	}
522
487	–	#endif
488	–
523		}
524
525	<	void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
526	<
527	<	Vector3d pos;  // position place holders
494	<	Vector3d vel;  // velocity placeholders
495	<	Quat4d q;    // the quaternions
496	<	Vector3d ji;   // angular velocity placeholders;
525	>
526	>	void DumpReader::parseSiteLine(const std::string& line) {
527	>
528		StringTokenizer tokenizer(line);
529		int nTokens;
530
531		nTokens = tokenizer.countTokens();
532
533	<	if (nTokens < 14) {
533	>	if (nTokens < 2) {
534		sprintf(painCave.errMsg,
535	<	"DumpReader Error: Not enough Tokens.\n%s\n", line);
535	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
536		painCave.isFatal = 1;
537		simError();
538		}
539	<
540	<	std::string name = tokenizer.nextToken();
541	<
542	<	if (name != integrableObject->getType()) {
543	<
544	<	sprintf(painCave.errMsg,
545	<	"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
546	<	name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
547	<	painCave.isFatal = 1;
548	<	simError();
549	<	}
550	<
551	<	pos[0] = tokenizer.nextTokenAsDouble();
552	<	pos[1] = tokenizer.nextTokenAsDouble();
553	<	pos[2] = tokenizer.nextTokenAsDouble();
554	<	if (needPos_) {
555	<	integrableObject->setPos(pos);
556	<	}
557	<
558	<	vel[0] = tokenizer.nextTokenAsDouble();
559	<	vel[1] = tokenizer.nextTokenAsDouble();
560	<	vel[2] = tokenizer.nextTokenAsDouble();
561	<	if (needVel_) {
562	<	integrableObject->setVel(vel);
563	<	}
564	<
565	<	if (integrableObject->isDirectional()) {
566	<
567	<	q[0] = tokenizer.nextTokenAsDouble();
568	<	q[1] = tokenizer.nextTokenAsDouble();
569	<	q[2] = tokenizer.nextTokenAsDouble();
570	<	q[3] = tokenizer.nextTokenAsDouble();
571	<
572	<	double qlen = q.length();
573	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
574	<
539	>
540	>	/**
541	>	* The first token is the global integrable object index.
542	>	*/
543	>
544	>	int index = tokenizer.nextTokenAsInt();
545	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
546	>	if (sd == NULL) {
547	>	return;
548	>	}
549	>
550	>	/**
551	>	* Test to see if the next token is an integer or not.  If not,
552	>	* we've got data on the integrable object itself.  If there is an
553	>	* integer, we're parsing data for a site on a rigid body.
554	>	*/
555	>
556	>	std::string indexTest = tokenizer.peekNextToken();
557	>	std::istringstream i(indexTest);
558	>	int siteIndex;
559	>	if (i >> siteIndex) {
560	>	// chew up this token and parse as an int:
561	>	siteIndex = tokenizer.nextTokenAsInt();
562	>	RigidBody* rb = static_cast<RigidBody*>(sd);
563	>	sd = rb->getAtoms()[siteIndex];
564	>	}
565	>
566	>	/**
567	>	* The next token contains information on what follows.
568	>	*/
569	>	std::string type = tokenizer.nextToken();
570	>	int size = type.size();
571	>
572	>	for(int i = 0; i < size; ++i) {
573	>	switch(type[i]) {
574	>
575	>	case 'u' : {
576	>
577	>	RealType particlePot;
578	>	particlePot = tokenizer.nextTokenAsDouble();
579	>	sd->setParticlePot(particlePot);
580	>	break;
581	>	}
582	>	case 'c' : {
583	>
584	>	RealType flucQPos;
585	>	flucQPos = tokenizer.nextTokenAsDouble();
586	>	sd->setFlucQPos(flucQPos);
587	>	break;
588	>	}
589	>	case 'w' : {
590	>
591	>	RealType flucQVel;
592	>	flucQVel = tokenizer.nextTokenAsDouble();
593	>	sd->setFlucQVel(flucQVel);
594	>	break;
595	>	}
596	>	case 'g' : {
597	>
598	>	RealType flucQFrc;
599	>	flucQFrc = tokenizer.nextTokenAsDouble();
600	>	sd->setFlucQFrc(flucQFrc);
601	>	break;
602	>	}
603	>	case 'e' : {
604	>
605	>	Vector3d eField;
606	>	eField[0] = tokenizer.nextTokenAsDouble();
607	>	eField[1] = tokenizer.nextTokenAsDouble();
608	>	eField[2] = tokenizer.nextTokenAsDouble();
609	>	sd->setElectricField(eField);
610	>	break;
611	>	}
612	>	default: {
613		sprintf(painCave.errMsg,
614	<	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0\n");
614	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
615		painCave.isFatal = 1;
616		simError();
617	<
618	<	}
619	<
620	<	q.normalize();
552	<	if (needQuaternion_) {
553	<	integrableObject->setQ(q);
554	<	}
555	<
556	<	ji[0] = tokenizer.nextTokenAsDouble();
557	<	ji[1] = tokenizer.nextTokenAsDouble();
558	<	ji[2] = tokenizer.nextTokenAsDouble();
559	<	if (needAngMom_) {
560	<	integrableObject->setJ(ji);
561	<	}
562	<	}
563	<
617	>	break;
618	>	}
619	>	}
620	>	}
621		}
622	<
623	<
624	<	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
625	<	double currTime;
626	<	Mat3x3d hmat;
627	<	double chi;
628	<	double integralOfChiDt;
629	<	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) {
622	>
623	>
624	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
625	>
626	>	inputStream.getline(buffer, bufferSize);
627	>	std::string line(buffer);
628	>
629	>	if (line.find("<StuntDoubles>") == std::string::npos) {
630		sprintf(painCave.errMsg,
631	<	"DumpReader Error: Not enough tokens in comment line: %s", line);
631	>	"DumpReader Error: Missing <StuntDoubles>\n");
632		painCave.isFatal = 1;
633	<	simError();
634	<	}
635	<
636	<	//read current time
637	<	currTime = tokenizer.nextTokenAsDouble();
638	<	s->setTime(currTime);
639	<
640	<	//read h-matrix
641	<	hmat(0, 0) = tokenizer.nextTokenAsDouble();
642	<	hmat(0, 1) = tokenizer.nextTokenAsDouble();
643	<	hmat(0, 2) = tokenizer.nextTokenAsDouble();
644	<	hmat(1, 0) = tokenizer.nextTokenAsDouble();
645	<	hmat(1, 1) = tokenizer.nextTokenAsDouble();
646	<	hmat(1, 2) = tokenizer.nextTokenAsDouble();
647	<	hmat(2, 0) = tokenizer.nextTokenAsDouble();
648	<	hmat(2, 1) = tokenizer.nextTokenAsDouble();
649	<	hmat(2, 2) = tokenizer.nextTokenAsDouble();
650	<	s->setHmat(hmat);
651	<
652	<	//read chi and integralOfChidt, they should apprear in pair
653	<	if (tokenizer.countTokens() >= 2) {
654	<	chi = tokenizer.nextTokenAsDouble();
655	<	integralOfChiDt = tokenizer.nextTokenAsDouble();
656	<
657	<	s->setChi(chi);
658	<	s->setIntegralOfChiDt(integralOfChiDt);
659	<	}
660	<
661	<	//read eta (eta is 3x3 matrix)
662	<	if (tokenizer.countTokens() >= 9) {
663	<	eta(0, 0) = tokenizer.nextTokenAsDouble();
664	<	eta(0, 1) = tokenizer.nextTokenAsDouble();
665	<	eta(0, 2) = tokenizer.nextTokenAsDouble();
666	<	eta(1, 0) = tokenizer.nextTokenAsDouble();
667	<	eta(1, 1) = tokenizer.nextTokenAsDouble();
668	<	eta(1, 2) = tokenizer.nextTokenAsDouble();
669	<	eta(2, 0) = tokenizer.nextTokenAsDouble();
670	<	eta(2, 1) = tokenizer.nextTokenAsDouble();
671	<	eta(2, 2) = tokenizer.nextTokenAsDouble();
672	<
673	<	s->setEta(eta);
674	<	}
675	<
676	<
677	<	}
633	>	simError();
634	>	}
635	>
636	>	while(inputStream.getline(buffer, bufferSize)) {
637	>	line = buffer;
638	>
639	>	if(line.find("</StuntDoubles>") != std::string::npos) {
640	>	break;
641	>	}
642	>
643	>	parseDumpLine(line);
644	>	}
645	>
646	>	}
647	>
648	>	void  DumpReader::readSiteData(std::istream& inputStream) {
649	>
650	>	inputStream.getline(buffer, bufferSize);
651	>	std::string line(buffer);
652	>
653	>	if (line.find("<SiteData>") == std::string::npos) {
654	>	// site data isn't required for a simulation, so skip
655	>	return;
656	>	}
657	>
658	>	while(inputStream.getline(buffer, bufferSize)) {
659	>	line = buffer;
660	>
661	>	if(line.find("</SiteData>") != std::string::npos) {
662	>	break;
663	>	}
664	>
665	>	parseSiteLine(line);
666	>	}
667	>
668	>	}
669	>
670	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
671	>
672	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
673	>	inputStream.getline(buffer, bufferSize);
674	>	std::string line(buffer);
675	>
676	>	if (line.find("<FrameData>") == std::string::npos) {
677	>	sprintf(painCave.errMsg,
678	>	"DumpReader Error: Missing <FrameData>\n");
679	>	painCave.isFatal = 1;
680	>	simError();
681	>	}
682	>
683	>	while(inputStream.getline(buffer, bufferSize)) {
684	>	line = buffer;
685	>
686	>	if(line.find("</FrameData>") != std::string::npos) {
687	>	break;
688	>	}
689	>
690	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
691	>	if (!tokenizer.hasMoreTokens()) {
692	>	sprintf(painCave.errMsg,
693	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
694	>	painCave.isFatal = 1;
695	>	simError();
696	>	}
697	>
698	>	std::string propertyName = tokenizer.nextToken();
699	>	if (propertyName == "Time") {
700	>	RealType currTime = tokenizer.nextTokenAsDouble();
701	>	s->setTime(currTime);
702	>	} else if (propertyName == "Hmat"){
703	>	Mat3x3d hmat;
704	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
705	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
706	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
707	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
708	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
709	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
710	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
711	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
712	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
713	>	s->setHmat(hmat);
714	>	} else if (propertyName == "Thermostat") {
715	>	pair<RealType, RealType> thermostat;
716	>	thermostat.first = tokenizer.nextTokenAsDouble();
717	>	thermostat.second = tokenizer.nextTokenAsDouble();
718	>	s->setThermostat(thermostat);
719	>	} else if (propertyName == "Barostat") {
720	>	Mat3x3d eta;
721	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
722	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
723	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
724	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
725	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
726	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
727	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
728	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
729	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
730	>	s->setBarostat(eta);
731	>	} else {
732	>	sprintf(painCave.errMsg,
733	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
734	>	painCave.isFatal = 0;
735	>	simError();
736	>	}
737	>
738	>	}
739	>
740	>	}
741	>
742
743	<	}//end namespace oopse
743	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpReader.cpp (property svn:keywords), Revision 721 by chrisfen, Tue Nov 8 13:32:27 2005 UTC vs.
branches/development/src/io/DumpReader.cpp (property svn:keywords), Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 UTC

#	Line 0 | Line 1
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