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

Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 721 by chrisfen, Tue Nov 8 13:32:27 2005 UTC vs.
Revision 2000 by gezelter, Sat May 31 22:35:05 2014 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, 234107 (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
45
46	+	#ifdef IS_MPI
47	+	#include <mpi.h>
48	+	#endif
49	+
50		#include <sys/types.h>
51		#include <sys/stat.h>
52
#	Line 57 | Line 62
62		#include "utils/simError.h"
63		#include "utils/MemoryUtils.hpp"
64		#include "utils/StringTokenizer.hpp"
65	+	#include "brains/Thermo.hpp"
66
61	–	#ifdef IS_MPI
67
68	<	#include <mpi.h>
64	<	#define TAKE_THIS_TAG_CHAR 0
65	<	#define TAKE_THIS_TAG_INT 1
66	<
67	<	#endif // is_mpi
68	<
69	<
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	<
108	<	delete inFile_;
109	<
106	>	#endif
107	>
108	>	inFile_->~istream();
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	>
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	>	int lineNo = 0;
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 225 | Line 228 | namespace oopse {
228		needVel_ = false;
229		}
230
231	<	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
231	>	if (storageLayout & DataStorage::dslAmat ||
232	>	storageLayout & DataStorage::dslDipole ||
233	>	storageLayout & DataStorage::dslQuadrupole) {
234		needQuaternion_ = true;
235		} else {
236		needQuaternion_ = false;
#	Line 238 | Line 243 | namespace oopse {
243		}
244
245		readSet(whichFrame);
246	+
247	+	if (needCOMprops_) {
248	+	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
249	+	Thermo thermo(info_);
250	+	Vector3d com;
251	+
252	+	if (needPos_ && needVel_) {
253	+	Vector3d comvel;
254	+	Vector3d comw;
255	+	thermo.getComAll(com, comvel);
256	+	comw = thermo.getAngularMomentum();
257	+	} else {
258	+	com = thermo.getCom();
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,
294	>	MPI_CHAR, masterNode, MPI_COMM_WORLD);
295	>
296	>	sstream.str(sendBuffer);
297	>	} else {
298	>	int sendBufferSize;
299	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
300	>	char * recvBuffer = new char[sendBufferSize+1];
301	>	assert(recvBuffer);
302	>	recvBuffer[sendBufferSize] = '\0';
303	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
304	>	sstream.str(recvBuffer);
305	>	delete [] recvBuffer;
306	>	}
307	>
308	>	std::istream& inputStream = sstream;
309	>	#endif
310	>
311	>	inputStream.getline(buffer, bufferSize);
312	>
313	>	line = buffer;
314	>	if (line.find("<Snapshot>") == std::string::npos) {
315		sprintf(painCave.errMsg,
316	<	"DumpReader error: error reading 1st line of \"%s\"\n",
261	<	filename_.c_str());
316	>	"DumpReader Error: can not find <Snapshot>\n");
317		painCave.isFatal = 1;
318		simError();
319		}
320	+
321	+	//read frameData
322	+	readFrameProperties(inputStream);
323	+
324	+	//read StuntDoubles
325	+	readStuntDoubles(inputStream);
326	+
327	+	inputStream.getline(buffer, bufferSize);
328	+	line = buffer;
329	+
330	+	if (line.find("<SiteData>") != std::string::npos) {
331	+	//read SiteData
332	+	readSiteData(inputStream);
333	+	} else {
334	+	if (line.find("</Snapshot>") == std::string::npos) {
335	+	sprintf(painCave.errMsg,
336	+	"DumpReader Error: can not find </Snapshot>\n");
337	+	painCave.isFatal = 1;
338	+	simError();
339	+	}
340	+	}
341	+	}
342	+
343	+	void DumpReader::parseDumpLine(const std::string& line) {
344	+
345	+
346	+	StringTokenizer tokenizer(line);
347	+	int nTokens;
348
349	<	nTotObjs = atoi(read_buffer);
349	>	nTokens = tokenizer.countTokens();
350
351	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
351	>	if (nTokens < 2) {
352		sprintf(painCave.errMsg,
353	<	"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	<
353	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
354		painCave.isFatal = 1;
355		simError();
356		}
357	<
358	<	//read the box mat from the comment line
359	<
360	<
361	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
362	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
363	<	filename_.c_str());
364	<	painCave.isFatal = 1;
365	<	simError();
366	<	}
367	<
368	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
369	<
370	<	//parse dump lines
371	<
372	<	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) {
357	>
358	>	int index = tokenizer.nextTokenAsInt();
359	>
360	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
361	>
362	>	if (sd == NULL) {
363	>	return;
364	>	}
365	>	std::string type = tokenizer.nextToken();
366	>	int size = type.size();
367	>
368	>	size_t found;
369	>
370	>	if (needPos_) {
371	>	found = type.find("p");
372	>	if (found == std::string::npos) {
373		sprintf(painCave.errMsg,
374	<	"DumpReader Error. %s nIntegrable, %d, "
375	<	"does not match the meta-data file's nIntegrable, %d.\n",
376	<	filename_.c_str(),
360	<	nTotObjs,
361	<	info_->getNGlobalIntegrableObjects());
362	<
374	>	"DumpReader Error: StuntDouble %d has no Position\n"
375	>	"\tField (\"p\") specified.\n%s\n", index,
376	>	line.c_str());
377		painCave.isFatal = 1;
378		simError();
379	<	}
380	<
381	<	//read the boxMat from the comment line
382	<
383	<
384	<
385	<	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
386	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
387	<	filename_.c_str());
388	<	painCave.isFatal = 1;
389	<	simError();
390	<	}
391	<
392	<	//Every single processor will parse the comment line by itself
393	<	//By using this way, we might lose some efficiency, but if we want to add
394	<	//more parameters into comment line, we only need to modify function
395	<	//parseCommentLine
396	<
397	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
398	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
399	<
400	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
401	<	int which_node = info_->getMolToProc(i);
402	<
403	<	if (which_node == masterNode) {
404	<	//molecules belong to master node
405	<
406	<	mol = info_->getMoleculeByGlobalIndex(i);
407	<
408	<	if (mol == NULL) {
409	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
410	<	painCave.isFatal = 1;
411	<	simError();
412	<	}
413	<
414	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
415	<	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();
379	>	}
380	>	}
381	>
382	>	if (sd->isDirectional()) {
383	>	if (needQuaternion_) {
384	>	found = type.find("q");
385	>	if (found == std::string::npos) {
386	>	sprintf(painCave.errMsg,
387	>	"DumpReader Error: Directional StuntDouble %d has no\n"
388	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
389	>	line.c_str());
390	>	painCave.isFatal = 1;
391	>	simError();
392	>	}
393	>	}
394	>	}
395	>
396	>	for(int i = 0; i < size; ++i) {
397	>	switch(type[i]) {
398	>
399	>	case 'p': {
400	>	Vector3d pos;
401	>	pos[0] = tokenizer.nextTokenAsDouble();
402	>	pos[1] = tokenizer.nextTokenAsDouble();
403	>	pos[2] = tokenizer.nextTokenAsDouble();
404	>	if (needPos_) {
405	>	sd->setPos(pos);
406	>	}
407	>	break;
408	>	}
409	>	case 'v' : {
410	>	Vector3d vel;
411	>	vel[0] = tokenizer.nextTokenAsDouble();
412	>	vel[1] = tokenizer.nextTokenAsDouble();
413	>	vel[2] = tokenizer.nextTokenAsDouble();
414	>	if (needVel_) {
415	>	sd->setVel(vel);
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	<
417	>	break;
418	>	}
419	>
420	>	case 'q' : {
421	>	Quat4d q;
422	>	if (sd->isDirectional()) {
423	>
424	>	q[0] = tokenizer.nextTokenAsDouble();
425	>	q[1] = tokenizer.nextTokenAsDouble();
426	>	q[2] = tokenizer.nextTokenAsDouble();
427	>	q[3] = tokenizer.nextTokenAsDouble();
428	>
429	>	RealType qlen = q.length();
430	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
431	>
432	>	sprintf(painCave.errMsg,
433	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
434	>	painCave.isFatal = 1;
435	>	simError();
436	>
437	>	}
438	>
439	>	q.normalize();
440	>	if (needQuaternion_) {
441	>	sd->setQ(q);
442	>	}
443	>	}
444	>	break;
445	>	}
446	>	case 'j' : {
447	>	Vector3d ji;
448	>	if (sd->isDirectional()) {
449	>	ji[0] = tokenizer.nextTokenAsDouble();
450	>	ji[1] = tokenizer.nextTokenAsDouble();
451	>	ji[2] = tokenizer.nextTokenAsDouble();
452	>	if (needAngMom_) {
453	>	sd->setJ(ji);
454	>	}
455	>	}
456	>	break;
457	>	}
458	>	case 'f': {
459	>
460	>	Vector3d force;
461	>	force[0] = tokenizer.nextTokenAsDouble();
462	>	force[1] = tokenizer.nextTokenAsDouble();
463	>	force[2] = tokenizer.nextTokenAsDouble();
464	>	sd->setFrc(force);
465	>	break;
466	>	}
467	>	case 't' : {
468	>
469	>	Vector3d torque;
470	>	torque[0] = tokenizer.nextTokenAsDouble();
471	>	torque[1] = tokenizer.nextTokenAsDouble();
472	>	torque[2] = tokenizer.nextTokenAsDouble();
473	>	sd->setTrq(torque);
474	>	break;
475	>	}
476	>	case 'u' : {
477	>
478	>	RealType particlePot;
479	>	particlePot = tokenizer.nextTokenAsDouble();
480	>	sd->setParticlePot(particlePot);
481	>	break;
482	>	}
483	>	case 'c' : {
484	>
485	>	RealType flucQPos;
486	>	flucQPos = tokenizer.nextTokenAsDouble();
487	>	sd->setFlucQPos(flucQPos);
488	>	break;
489	>	}
490	>	case 'w' : {
491	>
492	>	RealType flucQVel;
493	>	flucQVel = tokenizer.nextTokenAsDouble();
494	>	sd->setFlucQVel(flucQVel);
495	>	break;
496	>	}
497	>	case 'g' : {
498	>
499	>	RealType flucQFrc;
500	>	flucQFrc = tokenizer.nextTokenAsDouble();
501	>	sd->setFlucQFrc(flucQFrc);
502	>	break;
503	>	}
504	>	case 'e' : {
505	>
506	>	Vector3d eField;
507	>	eField[0] = tokenizer.nextTokenAsDouble();
508	>	eField[1] = tokenizer.nextTokenAsDouble();
509	>	eField[2] = tokenizer.nextTokenAsDouble();
510	>	sd->setElectricField(eField);
511	>	break;
512	>	}
513	>	case 's' : {
514	>
515	>	RealType sPot;
516	>	sPot = tokenizer.nextTokenAsDouble();
517	>	sd->setSitePotential(sPot);
518	>	break;
519	>	}
520	>	default: {
521	>	sprintf(painCave.errMsg,
522	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
523	>	painCave.isFatal = 1;
524	>	simError();
525	>	break;
526	>	}
527	>
528	>	}
529	>	}
530		}
531
532	<	void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
533	<
534	<	Vector3d pos;  // position place holders
494	<	Vector3d vel;  // velocity placeholders
495	<	Quat4d q;    // the quaternions
496	<	Vector3d ji;   // angular velocity placeholders;
532	>
533	>	void DumpReader::parseSiteLine(const std::string& line) {
534	>
535		StringTokenizer tokenizer(line);
536		int nTokens;
537	<
537	>
538		nTokens = tokenizer.countTokens();
539
540	<	if (nTokens < 14) {
540	>	if (nTokens < 2) {
541		sprintf(painCave.errMsg,
542	<	"DumpReader Error: Not enough Tokens.\n%s\n", line);
542	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
543		painCave.isFatal = 1;
544		simError();
545		}
546	<
547	<	std::string name = tokenizer.nextToken();
548	<
549	<	if (name != integrableObject->getType()) {
550	<
551	<	sprintf(painCave.errMsg,
552	<	"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
553	<	name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
554	<	painCave.isFatal = 1;
555	<	simError();
556	<	}
557	<
558	<	pos[0] = tokenizer.nextTokenAsDouble();
559	<	pos[1] = tokenizer.nextTokenAsDouble();
560	<	pos[2] = tokenizer.nextTokenAsDouble();
561	<	if (needPos_) {
562	<	integrableObject->setPos(pos);
563	<	}
564	<
565	<	vel[0] = tokenizer.nextTokenAsDouble();
566	<	vel[1] = tokenizer.nextTokenAsDouble();
567	<	vel[2] = tokenizer.nextTokenAsDouble();
568	<	if (needVel_) {
569	<	integrableObject->setVel(vel);
570	<	}
571	<
572	<	if (integrableObject->isDirectional()) {
573	<
574	<	q[0] = tokenizer.nextTokenAsDouble();
575	<	q[1] = tokenizer.nextTokenAsDouble();
576	<	q[2] = tokenizer.nextTokenAsDouble();
577	<	q[3] = tokenizer.nextTokenAsDouble();
578	<
579	<	double qlen = q.length();
580	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
581	<
546	>
547	>	/**
548	>	* The first token is the global integrable object index.
549	>	*/
550	>
551	>	int index = tokenizer.nextTokenAsInt();
552	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
553	>	if (sd == NULL) {
554	>	return;
555	>	}
556	>
557	>	/**
558	>	* Test to see if the next token is an integer or not.  If not,
559	>	* we've got data on the integrable object itself.  If there is an
560	>	* integer, we're parsing data for a site on a rigid body.
561	>	*/
562	>
563	>	std::string indexTest = tokenizer.peekNextToken();
564	>	std::istringstream i(indexTest);
565	>	int siteIndex;
566	>	if (i >> siteIndex) {
567	>	// chew up this token and parse as an int:
568	>	siteIndex = tokenizer.nextTokenAsInt();
569	>
570	>	if (sd->isRigidBody()) {
571	>	RigidBody* rb = static_cast<RigidBody*>(sd);
572	>	sd = rb->getAtoms()[siteIndex];
573	>	}
574	>	}
575	>
576	>	/**
577	>	* The next token contains information on what follows.
578	>	*/
579	>	std::string type = tokenizer.nextToken();
580	>	int size = type.size();
581	>
582	>	for(int i = 0; i < size; ++i) {
583	>	switch(type[i]) {
584	>
585	>	case 'u' : {
586	>
587	>	RealType particlePot;
588	>	particlePot = tokenizer.nextTokenAsDouble();
589	>	sd->setParticlePot(particlePot);
590	>	break;
591	>	}
592	>	case 'c' : {
593	>
594	>	RealType flucQPos;
595	>	flucQPos = tokenizer.nextTokenAsDouble();
596	>	sd->setFlucQPos(flucQPos);
597	>	break;
598	>	}
599	>	case 'w' : {
600	>
601	>	RealType flucQVel;
602	>	flucQVel = tokenizer.nextTokenAsDouble();
603	>	sd->setFlucQVel(flucQVel);
604	>	break;
605	>	}
606	>	case 'g' : {
607	>
608	>	RealType flucQFrc;
609	>	flucQFrc = tokenizer.nextTokenAsDouble();
610	>	sd->setFlucQFrc(flucQFrc);
611	>	break;
612	>	}
613	>	case 'e' : {
614	>
615	>	Vector3d eField;
616	>	eField[0] = tokenizer.nextTokenAsDouble();
617	>	eField[1] = tokenizer.nextTokenAsDouble();
618	>	eField[2] = tokenizer.nextTokenAsDouble();
619	>	sd->setElectricField(eField);
620	>	break;
621	>	}
622	>	case 's' : {
623	>
624	>	RealType sPot;
625	>	sPot = tokenizer.nextTokenAsDouble();
626	>	sd->setSitePotential(sPot);
627	>	break;
628	>	}
629	>	default: {
630		sprintf(painCave.errMsg,
631	<	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0\n");
631	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
632		painCave.isFatal = 1;
633		simError();
634	<
635	<	}
636	<
637	<	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	<
634	>	break;
635	>	}
636	>	}
637	>	}
638		}
639	<
640	<
641	<	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
642	<	double currTime;
643	<	Mat3x3d hmat;
644	<	double chi;
645	<	double integralOfChiDt;
646	<	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) {
639	>
640	>
641	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
642	>
643	>	inputStream.getline(buffer, bufferSize);
644	>	std::string line(buffer);
645	>
646	>	if (line.find("<StuntDoubles>") == std::string::npos) {
647		sprintf(painCave.errMsg,
648	<	"DumpReader Error: Not enough tokens in comment line: %s", line);
648	>	"DumpReader Error: Missing <StuntDoubles>\n");
649		painCave.isFatal = 1;
650	<	simError();
651	<	}
652	<
653	<	//read current time
654	<	currTime = tokenizer.nextTokenAsDouble();
655	<	s->setTime(currTime);
656	<
657	<	//read h-matrix
658	<	hmat(0, 0) = tokenizer.nextTokenAsDouble();
659	<	hmat(0, 1) = tokenizer.nextTokenAsDouble();
660	<	hmat(0, 2) = tokenizer.nextTokenAsDouble();
661	<	hmat(1, 0) = tokenizer.nextTokenAsDouble();
662	<	hmat(1, 1) = tokenizer.nextTokenAsDouble();
663	<	hmat(1, 2) = tokenizer.nextTokenAsDouble();
664	<	hmat(2, 0) = tokenizer.nextTokenAsDouble();
665	<	hmat(2, 1) = tokenizer.nextTokenAsDouble();
666	<	hmat(2, 2) = tokenizer.nextTokenAsDouble();
667	<	s->setHmat(hmat);
668	<
669	<	//read chi and integralOfChidt, they should apprear in pair
670	<	if (tokenizer.countTokens() >= 2) {
671	<	chi = tokenizer.nextTokenAsDouble();
672	<	integralOfChiDt = tokenizer.nextTokenAsDouble();
673	<
674	<	s->setChi(chi);
675	<	s->setIntegralOfChiDt(integralOfChiDt);
676	<	}
677	<
678	<	//read eta (eta is 3x3 matrix)
679	<	if (tokenizer.countTokens() >= 9) {
680	<	eta(0, 0) = tokenizer.nextTokenAsDouble();
681	<	eta(0, 1) = tokenizer.nextTokenAsDouble();
682	<	eta(0, 2) = tokenizer.nextTokenAsDouble();
683	<	eta(1, 0) = tokenizer.nextTokenAsDouble();
684	<	eta(1, 1) = tokenizer.nextTokenAsDouble();
685	<	eta(1, 2) = tokenizer.nextTokenAsDouble();
686	<	eta(2, 0) = tokenizer.nextTokenAsDouble();
687	<	eta(2, 1) = tokenizer.nextTokenAsDouble();
688	<	eta(2, 2) = tokenizer.nextTokenAsDouble();
689	<
690	<	s->setEta(eta);
691	<	}
692	<
693	<
694	<	}
650	>	simError();
651	>	}
652	>
653	>	while(inputStream.getline(buffer, bufferSize)) {
654	>	line = buffer;
655	>
656	>	if(line.find("</StuntDoubles>") != std::string::npos) {
657	>	break;
658	>	}
659	>
660	>	parseDumpLine(line);
661	>	}
662	>
663	>	}
664	>
665	>	void  DumpReader::readSiteData(std::istream& inputStream) {
666	>
667	>	std::string line(buffer);
668	>
669	>	// We already found the starting <SiteData> tag or we wouldn't be
670	>	// here, so just start parsing until we get to the ending
671	>	// </SiteData> tag:
672	>
673	>	while(inputStream.getline(buffer, bufferSize)) {
674	>	line = buffer;
675	>
676	>	if(line.find("</SiteData>") != std::string::npos) {
677	>	break;
678	>	}
679	>
680	>	parseSiteLine(line);
681	>	}
682	>
683	>	}
684	>
685	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
686	>
687	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
688	>	inputStream.getline(buffer, bufferSize);
689	>	std::string line(buffer);
690	>
691	>	if (line.find("<FrameData>") == std::string::npos) {
692	>	sprintf(painCave.errMsg,
693	>	"DumpReader Error: Missing <FrameData>\n");
694	>	painCave.isFatal = 1;
695	>	simError();
696	>	}
697	>
698	>	while(inputStream.getline(buffer, bufferSize)) {
699	>	line = buffer;
700	>
701	>	if(line.find("</FrameData>") != std::string::npos) {
702	>	break;
703	>	}
704	>
705	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
706	>	if (!tokenizer.hasMoreTokens()) {
707	>	sprintf(painCave.errMsg,
708	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
709	>	painCave.isFatal = 1;
710	>	simError();
711	>	}
712	>
713	>	std::string propertyName = tokenizer.nextToken();
714	>	if (propertyName == "Time") {
715	>	RealType currTime = tokenizer.nextTokenAsDouble();
716	>	s->setTime(currTime);
717	>	} else if (propertyName == "Hmat"){
718	>	Mat3x3d hmat;
719	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
720	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
721	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
722	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
723	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
724	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
725	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
726	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
727	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
728	>	s->setHmat(hmat);
729	>	} else if (propertyName == "Thermostat") {
730	>	pair<RealType, RealType> thermostat;
731	>	thermostat.first = tokenizer.nextTokenAsDouble();
732	>	thermostat.second = tokenizer.nextTokenAsDouble();
733	>	s->setThermostat(thermostat);
734	>	} else if (propertyName == "Barostat") {
735	>	Mat3x3d eta;
736	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
737	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
738	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
739	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
740	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
741	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
742	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
743	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
744	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
745	>	s->setBarostat(eta);
746	>	} else {
747	>	sprintf(painCave.errMsg,
748	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
749	>	painCave.isFatal = 0;
750	>	simError();
751	>	}
752	>
753	>	}
754	>
755	>	}
756	>
757
758	<	}//end namespace oopse
758	>	}//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.
Revision 2000 by gezelter, Sat May 31 22:35:05 2014 UTC

#	Line 0 | Line 1
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