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

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trunk/src/io/DumpReader.cpp (file contents), Revision 996 by chrisfen, Wed Jun 28 14:35:14 2006 UTC vs.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1794 by gezelter, Thu Sep 6 19:44:06 2012 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) {
71	>	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
72
73		#ifdef IS_MPI
74
75		if (worldRank == 0) {
76		#endif
77
78	<	inFile_ = new std::ifstream(filename_.c_str());
78	>	inFile_ = new std::ifstream(filename_.c_str(),
79	>	ifstream::in | ifstream::binary);
80
81		if (inFile_->fail()) {
82		sprintf(painCave.errMsg,
#	Line 92 | Line 91 | namespace oopse {
91		}
92
93		strcpy(checkPointMsg, "Dump file opened for reading successfully.");
94	<	MPIcheckPoint();
94	>	errorCheckPoint();
95
96		#endif
97
#	Line 113 | Line 112 | namespace oopse {
112		}
113
114		strcpy(checkPointMsg, "Dump file closed successfully.");
115	<	MPIcheckPoint();
115	>	errorCheckPoint();
116
117		#endif
118
#	Line 129 | Line 128 | namespace oopse {
128		}
129
130		void DumpReader::scanFile(void) {
131	<	int i, j;
132	<	int lineNum = 0;
134	<	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);
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()) {
139	>
140	>	currPos = inFile_->tellg();
141	>	prevPos = currPos;
142	>	bool foundOpenSnapshotTag = false;
143	>	bool foundClosedSnapshotTag = false;
144	>	bool foundOpenSiteDataTag = 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 227 | 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 240 | 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
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	+	//read frameData
320	+	readFrameProperties(inputStream);
321	+
322	+	//read StuntDoubles
323	+	readStuntDoubles(inputStream);
324	+
325	+	inputStream.getline(buffer, bufferSize);
326	+	line = buffer;
327	+
328	+	if (line.find("<SiteData>") != std::string::npos) {
329	+	//read SiteData
330	+	readSiteData(inputStream);
331	+	} else {
332	+	if (line.find("</Snapshot>") == std::string::npos) {
333	+	sprintf(painCave.errMsg,
334	+	"DumpReader Error: can not find </Snapshot>\n");
335	+	painCave.isFatal = 1;
336	+	simError();
337	+	}
338	+	}
339	+	}
340	+
341	+	void DumpReader::parseDumpLine(const std::string& line) {
342	+
343	+
344	+	StringTokenizer tokenizer(line);
345	+	int nTokens;
346
347	<	nTotObjs = atoi(read_buffer);
347	>	nTokens = tokenizer.countTokens();
348
349	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
349	>	if (nTokens < 2) {
350		sprintf(painCave.errMsg,
351	<	"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	<
351	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
352		painCave.isFatal = 1;
353		simError();
354		}
355	<
356	<	//read the box mat from the comment line
357	<
358	<
359	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
360	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
361	<	filename_.c_str());
362	<	painCave.isFatal = 1;
363	<	simError();
364	<	}
365	<
366	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
367	<
368	<	//parse dump lines
369	<
370	<	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) {
355	>
356	>	int index = tokenizer.nextTokenAsInt();
357	>
358	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
359	>
360	>	if (sd == NULL) {
361	>	return;
362	>	}
363	>	std::string type = tokenizer.nextToken();
364	>	int size = type.size();
365	>
366	>	size_t found;
367	>
368	>	if (needPos_) {
369	>	found = type.find("p");
370	>	if (found == std::string::npos) {
371		sprintf(painCave.errMsg,
372	<	"DumpReader Error. %s nIntegrable, %d, "
373	<	"does not match the meta-data file's nIntegrable, %d.\n",
374	<	filename_.c_str(),
362	<	nTotObjs,
363	<	info_->getNGlobalIntegrableObjects());
364	<
372	>	"DumpReader Error: StuntDouble %d has no Position\n"
373	>	"\tField (\"p\") specified.\n%s\n", index,
374	>	line.c_str());
375		painCave.isFatal = 1;
376		simError();
377	<	}
378	<
379	<	//read the boxMat from the comment line
380	<
381	<
382	<
383	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
384	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
385	<	filename_.c_str());
386	<	painCave.isFatal = 1;
387	<	simError();
388	<	}
389	<
390	<	//Every single processor will parse the comment line by itself
391	<	//By using this way, we might lose some efficiency, but if we want to add
392	<	//more parameters into comment line, we only need to modify function
393	<	//parseCommentLine
394	<
395	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
396	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
397	<
398	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
399	<	int which_node = info_->getMolToProc(i);
400	<
401	<	if (which_node == masterNode) {
402	<	//molecules belong to master node
403	<
404	<	mol = info_->getMoleculeByGlobalIndex(i);
405	<
406	<	if (mol == NULL) {
407	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
408	<	painCave.isFatal = 1;
409	<	simError();
410	<	}
411	<
412	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
413	<	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();
377	>	}
378	>	}
379	>
380	>	if (sd->isDirectional()) {
381	>	if (needQuaternion_) {
382	>	found = type.find("q");
383	>	if (found == std::string::npos) {
384	>	sprintf(painCave.errMsg,
385	>	"DumpReader Error: Directional StuntDouble %d has no\n"
386	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
387	>	line.c_str());
388	>	painCave.isFatal = 1;
389	>	simError();
390	>	}
391	>	}
392	>	}
393	>
394	>	for(int i = 0; i < size; ++i) {
395	>	switch(type[i]) {
396	>
397	>	case 'p': {
398	>	Vector3d pos;
399	>	pos[0] = tokenizer.nextTokenAsDouble();
400	>	pos[1] = tokenizer.nextTokenAsDouble();
401	>	pos[2] = tokenizer.nextTokenAsDouble();
402	>	if (needPos_) {
403	>	sd->setPos(pos);
404	>	}
405	>	break;
406	>	}
407	>	case 'v' : {
408	>	Vector3d vel;
409	>	vel[0] = tokenizer.nextTokenAsDouble();
410	>	vel[1] = tokenizer.nextTokenAsDouble();
411	>	vel[2] = tokenizer.nextTokenAsDouble();
412	>	if (needVel_) {
413	>	sd->setVel(vel);
414		}
415	<
416	<	parseDumpLine(read_buffer, integrableObject);
417	<	}
418	<	} else {
419	<	//molecule belongs to slave nodes
420	<
421	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
422	<	MPI_COMM_WORLD, &istatus);
423	<
424	<	for(int j = 0; j < nCurObj; j++) {
425	<
426	<
427	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
428	<	sprintf(painCave.errMsg,
429	<	"DumpReader Error: error in reading file %s\n"
430	<	"natoms  = %d; index = %d\n"
431	<	"error reading the line from the file.\n",
432	<	filename_.c_str(),
433	<	nTotObjs,
434	<	i);
435	<
436	<	painCave.isFatal = 1;
437	<	simError();
438	<	}
439	<
440	<	MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
441	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
442	<	}
443	<	}
444	<	}
445	<	} else {
446	<	//actions taken at slave nodes
447	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
448	<
449	<	/**@todo*/
450	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
451	<
452	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
453	<	int which_node = info_->getMolToProc(i);
454	<
455	<	if (which_node == worldRank) {
456	<	//molecule with global index i belongs to this processor
457	<
458	<	mol = info_->getMoleculeByGlobalIndex(i);
459	<	if (mol == NULL) {
460	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
461	<	painCave.isFatal = 1;
462	<	simError();
463	<	}
464	<
465	<	nCurObj = mol->getNIntegrableObjects();
466	<
467	<	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
468	<	MPI_COMM_WORLD);
469	<
470	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
471	<	integrableObject = mol->nextIntegrableObject(ii)){
472	<
473	<	MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
474	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
475	<
476	<	parseDumpLine(read_buffer, integrableObject);
477	<	}
478	<
479	<	}
480	<
481	<	}
482	<
483	<	}
415	>	break;
416	>	}
417	>
418	>	case 'q' : {
419	>	Quat4d q;
420	>	if (sd->isDirectional()) {
421	>
422	>	q[0] = tokenizer.nextTokenAsDouble();
423	>	q[1] = tokenizer.nextTokenAsDouble();
424	>	q[2] = tokenizer.nextTokenAsDouble();
425	>	q[3] = tokenizer.nextTokenAsDouble();
426	>
427	>	RealType qlen = q.length();
428	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
429	>
430	>	sprintf(painCave.errMsg,
431	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
432	>	painCave.isFatal = 1;
433	>	simError();
434	>
435	>	}
436	>
437	>	q.normalize();
438	>	if (needQuaternion_) {
439	>	sd->setQ(q);
440	>	}
441	>	}
442	>	break;
443	>	}
444	>	case 'j' : {
445	>	Vector3d ji;
446	>	if (sd->isDirectional()) {
447	>	ji[0] = tokenizer.nextTokenAsDouble();
448	>	ji[1] = tokenizer.nextTokenAsDouble();
449	>	ji[2] = tokenizer.nextTokenAsDouble();
450	>	if (needAngMom_) {
451	>	sd->setJ(ji);
452	>	}
453	>	}
454	>	break;
455	>	}
456	>	case 'f': {
457	>
458	>	Vector3d force;
459	>	force[0] = tokenizer.nextTokenAsDouble();
460	>	force[1] = tokenizer.nextTokenAsDouble();
461	>	force[2] = tokenizer.nextTokenAsDouble();
462	>	sd->setFrc(force);
463	>	break;
464	>	}
465	>	case 't' : {
466	>
467	>	Vector3d torque;
468	>	torque[0] = tokenizer.nextTokenAsDouble();
469	>	torque[1] = tokenizer.nextTokenAsDouble();
470	>	torque[2] = tokenizer.nextTokenAsDouble();
471	>	sd->setTrq(torque);
472	>	break;
473	>	}
474	>	case 'u' : {
475	>
476	>	RealType particlePot;
477	>	particlePot = tokenizer.nextTokenAsDouble();
478	>	sd->setParticlePot(particlePot);
479	>	break;
480	>	}
481	>	case 'c' : {
482	>
483	>	RealType flucQPos;
484	>	flucQPos = tokenizer.nextTokenAsDouble();
485	>	sd->setFlucQPos(flucQPos);
486	>	break;
487	>	}
488	>	case 'w' : {
489	>
490	>	RealType flucQVel;
491	>	flucQVel = tokenizer.nextTokenAsDouble();
492	>	sd->setFlucQVel(flucQVel);
493	>	break;
494	>	}
495	>	case 'g' : {
496	>
497	>	RealType flucQFrc;
498	>	flucQFrc = tokenizer.nextTokenAsDouble();
499	>	sd->setFlucQFrc(flucQFrc);
500	>	break;
501	>	}
502	>	case 'e' : {
503	>
504	>	Vector3d eField;
505	>	eField[0] = tokenizer.nextTokenAsDouble();
506	>	eField[1] = tokenizer.nextTokenAsDouble();
507	>	eField[2] = tokenizer.nextTokenAsDouble();
508	>	sd->setElectricField(eField);
509	>	break;
510	>	}
511	>	default: {
512	>	sprintf(painCave.errMsg,
513	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
514	>	painCave.isFatal = 1;
515	>	simError();
516	>	break;
517	>	}
518	>
519	>	}
520	>	}
521
489	–	#endif
490	–
522		}
523
524	<	void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
525	<
526	<	Vector3d pos;  // position place holders
496	<	Vector3d vel;  // velocity placeholders
497	<	Quat4d q;    // the quaternions
498	<	Vector3d ji;   // angular velocity placeholders;
524	>
525	>	void DumpReader::parseSiteLine(const std::string& line) {
526	>
527		StringTokenizer tokenizer(line);
528		int nTokens;
529
530		nTokens = tokenizer.countTokens();
531
532	<	if (nTokens < 14) {
532	>	if (nTokens < 2) {
533		sprintf(painCave.errMsg,
534	<	"DumpReader Error: Not enough Tokens.\n%s\n", line);
534	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
535		painCave.isFatal = 1;
536		simError();
537		}
538	<
539	<	std::string name = tokenizer.nextToken();
540	<
541	<	if (name != integrableObject->getType()) {
542	<
543	<	sprintf(painCave.errMsg,
544	<	"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
545	<	name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
546	<	painCave.isFatal = 1;
547	<	simError();
548	<	}
549	<
550	<	pos[0] = tokenizer.nextTokenAsDouble();
551	<	pos[1] = tokenizer.nextTokenAsDouble();
552	<	pos[2] = tokenizer.nextTokenAsDouble();
553	<	if (needPos_) {
554	<	integrableObject->setPos(pos);
555	<	}
556	<
557	<	vel[0] = tokenizer.nextTokenAsDouble();
558	<	vel[1] = tokenizer.nextTokenAsDouble();
559	<	vel[2] = tokenizer.nextTokenAsDouble();
560	<	if (needVel_) {
561	<	integrableObject->setVel(vel);
562	<	}
563	<
564	<	if (integrableObject->isDirectional()) {
565	<
566	<	q[0] = tokenizer.nextTokenAsDouble();
567	<	q[1] = tokenizer.nextTokenAsDouble();
568	<	q[2] = tokenizer.nextTokenAsDouble();
569	<	q[3] = tokenizer.nextTokenAsDouble();
570	<
571	<	RealType qlen = q.length();
572	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
573	<
538	>
539	>	/**
540	>	* The first token is the global integrable object index.
541	>	*/
542	>
543	>	int index = tokenizer.nextTokenAsInt();
544	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
545	>	if (sd == NULL) {
546	>	return;
547	>	}
548	>
549	>	/**
550	>	* Test to see if the next token is an integer or not.  If not,
551	>	* we've got data on the integrable object itself.  If there is an
552	>	* integer, we're parsing data for a site on a rigid body.
553	>	*/
554	>
555	>	std::string indexTest = tokenizer.peekNextToken();
556	>	std::istringstream i(indexTest);
557	>	int siteIndex;
558	>	if (i >> siteIndex) {
559	>	// chew up this token and parse as an int:
560	>	siteIndex = tokenizer.nextTokenAsInt();
561	>	RigidBody* rb = static_cast<RigidBody*>(sd);
562	>	sd = rb->getAtoms()[siteIndex];
563	>	}
564	>
565	>	/**
566	>	* The next token contains information on what follows.
567	>	*/
568	>	std::string type = tokenizer.nextToken();
569	>	int size = type.size();
570	>
571	>	for(int i = 0; i < size; ++i) {
572	>	switch(type[i]) {
573	>
574	>	case 'u' : {
575	>
576	>	RealType particlePot;
577	>	particlePot = tokenizer.nextTokenAsDouble();
578	>	sd->setParticlePot(particlePot);
579	>	break;
580	>	}
581	>	case 'c' : {
582	>
583	>	RealType flucQPos;
584	>	flucQPos = tokenizer.nextTokenAsDouble();
585	>	sd->setFlucQPos(flucQPos);
586	>	break;
587	>	}
588	>	case 'w' : {
589	>
590	>	RealType flucQVel;
591	>	flucQVel = tokenizer.nextTokenAsDouble();
592	>	sd->setFlucQVel(flucQVel);
593	>	break;
594	>	}
595	>	case 'g' : {
596	>
597	>	RealType flucQFrc;
598	>	flucQFrc = tokenizer.nextTokenAsDouble();
599	>	sd->setFlucQFrc(flucQFrc);
600	>	break;
601	>	}
602	>	case 'e' : {
603	>
604	>	Vector3d eField;
605	>	eField[0] = tokenizer.nextTokenAsDouble();
606	>	eField[1] = tokenizer.nextTokenAsDouble();
607	>	eField[2] = tokenizer.nextTokenAsDouble();
608	>	sd->setElectricField(eField);
609	>	break;
610	>	}
611	>	default: {
612		sprintf(painCave.errMsg,
613	<	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
613	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
614		painCave.isFatal = 1;
615		simError();
616	<
617	<	}
618	<
619	<	q.normalize();
554	<	if (needQuaternion_) {
555	<	integrableObject->setQ(q);
556	<	}
557	<
558	<	ji[0] = tokenizer.nextTokenAsDouble();
559	<	ji[1] = tokenizer.nextTokenAsDouble();
560	<	ji[2] = tokenizer.nextTokenAsDouble();
561	<	if (needAngMom_) {
562	<	integrableObject->setJ(ji);
563	<	}
564	<	}
565	<
616	>	break;
617	>	}
618	>	}
619	>	}
620		}
621	<
622	<
623	<	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
624	<	RealType currTime;
625	<	Mat3x3d hmat;
626	<	RealType chi;
627	<	RealType integralOfChiDt;
628	<	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) {
621	>
622	>
623	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
624	>
625	>	inputStream.getline(buffer, bufferSize);
626	>	std::string line(buffer);
627	>
628	>	if (line.find("<StuntDoubles>") == std::string::npos) {
629		sprintf(painCave.errMsg,
630	<	"DumpReader Error: Not enough tokens in comment line: %s", line);
630	>	"DumpReader Error: Missing <StuntDoubles>\n");
631		painCave.isFatal = 1;
632	<	simError();
633	<	}
634	<
635	<	//read current time
636	<	currTime = tokenizer.nextTokenAsDouble();
637	<	s->setTime(currTime);
638	<
639	<	//read h-matrix
640	<	hmat(0, 0) = tokenizer.nextTokenAsDouble();
641	<	hmat(0, 1) = tokenizer.nextTokenAsDouble();
642	<	hmat(0, 2) = tokenizer.nextTokenAsDouble();
643	<	hmat(1, 0) = tokenizer.nextTokenAsDouble();
644	<	hmat(1, 1) = tokenizer.nextTokenAsDouble();
645	<	hmat(1, 2) = tokenizer.nextTokenAsDouble();
646	<	hmat(2, 0) = tokenizer.nextTokenAsDouble();
647	<	hmat(2, 1) = tokenizer.nextTokenAsDouble();
648	<	hmat(2, 2) = tokenizer.nextTokenAsDouble();
649	<	s->setHmat(hmat);
650	<
651	<	//read chi and integralOfChidt, they should apprear in pair
652	<	if (tokenizer.countTokens() >= 2) {
653	<	chi = tokenizer.nextTokenAsDouble();
654	<	integralOfChiDt = tokenizer.nextTokenAsDouble();
655	<
656	<	s->setChi(chi);
657	<	s->setIntegralOfChiDt(integralOfChiDt);
658	<	}
659	<
660	<	//read eta (eta is 3x3 matrix)
661	<	if (tokenizer.countTokens() >= 9) {
662	<	eta(0, 0) = tokenizer.nextTokenAsDouble();
663	<	eta(0, 1) = tokenizer.nextTokenAsDouble();
664	<	eta(0, 2) = tokenizer.nextTokenAsDouble();
665	<	eta(1, 0) = tokenizer.nextTokenAsDouble();
666	<	eta(1, 1) = tokenizer.nextTokenAsDouble();
667	<	eta(1, 2) = tokenizer.nextTokenAsDouble();
668	<	eta(2, 0) = tokenizer.nextTokenAsDouble();
669	<	eta(2, 1) = tokenizer.nextTokenAsDouble();
670	<	eta(2, 2) = tokenizer.nextTokenAsDouble();
671	<
672	<	s->setEta(eta);
673	<	}
674	<
675	<
676	<	}
632	>	simError();
633	>	}
634	>
635	>	while(inputStream.getline(buffer, bufferSize)) {
636	>	line = buffer;
637	>
638	>	if(line.find("</StuntDoubles>") != std::string::npos) {
639	>	break;
640	>	}
641	>
642	>	parseDumpLine(line);
643	>	}
644	>
645	>	}
646	>
647	>	void  DumpReader::readSiteData(std::istream& inputStream) {
648	>
649	>	inputStream.getline(buffer, bufferSize);
650	>	std::string line(buffer);
651	>
652	>	if (line.find("<SiteData>") == std::string::npos) {
653	>	// site data isn't required for a simulation, so skip
654	>	return;
655	>	}
656	>
657	>	while(inputStream.getline(buffer, bufferSize)) {
658	>	line = buffer;
659	>
660	>	if(line.find("</SiteData>") != std::string::npos) {
661	>	break;
662	>	}
663	>
664	>	parseSiteLine(line);
665	>	}
666	>
667	>	}
668	>
669	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
670	>
671	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
672	>	inputStream.getline(buffer, bufferSize);
673	>	std::string line(buffer);
674	>
675	>	if (line.find("<FrameData>") == std::string::npos) {
676	>	sprintf(painCave.errMsg,
677	>	"DumpReader Error: Missing <FrameData>\n");
678	>	painCave.isFatal = 1;
679	>	simError();
680	>	}
681	>
682	>	while(inputStream.getline(buffer, bufferSize)) {
683	>	line = buffer;
684	>
685	>	if(line.find("</FrameData>") != std::string::npos) {
686	>	break;
687	>	}
688	>
689	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
690	>	if (!tokenizer.hasMoreTokens()) {
691	>	sprintf(painCave.errMsg,
692	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
693	>	painCave.isFatal = 1;
694	>	simError();
695	>	}
696	>
697	>	std::string propertyName = tokenizer.nextToken();
698	>	if (propertyName == "Time") {
699	>	RealType currTime = tokenizer.nextTokenAsDouble();
700	>	s->setTime(currTime);
701	>	} else if (propertyName == "Hmat"){
702	>	Mat3x3d hmat;
703	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
704	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
705	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
706	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
707	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
708	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
709	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
710	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
711	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
712	>	s->setHmat(hmat);
713	>	} else if (propertyName == "Thermostat") {
714	>	pair<RealType, RealType> thermostat;
715	>	thermostat.first = tokenizer.nextTokenAsDouble();
716	>	thermostat.second = tokenizer.nextTokenAsDouble();
717	>	s->setThermostat(thermostat);
718	>	} else if (propertyName == "Barostat") {
719	>	Mat3x3d eta;
720	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
721	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
722	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
723	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
724	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
725	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
726	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
727	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
728	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
729	>	s->setBarostat(eta);
730	>	} else {
731	>	sprintf(painCave.errMsg,
732	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
733	>	painCave.isFatal = 0;
734	>	simError();
735	>	}
736	>
737	>	}
738	>
739	>	}
740	>
741
742	<	}//end namespace oopse
742	>	}//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.
branches/development/src/io/DumpReader.cpp (property svn:keywords), Revision 1794 by gezelter, Thu Sep 6 19:44:06 2012 UTC

#	Line 0 | Line 1
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