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

Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 601 by tim, Thu Sep 15 19:17:04 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.
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. 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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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		*/
41	–
42	–	#define _LARGEFILE_SOURCE64
43	–	#define _FILE_OFFSET_BITS 64
44	–
45	–	#include <sys/types.h>
46	–	#include <sys/stat.h>
47	–
48	–	#include <iostream>
49	–	#include <math.h>
50	–
51	–	#include <stdio.h>
52	–	#include <stdlib.h>
53	–	#include <string.h>
54	–
55	–	#include "io/DumpReader.hpp"
56	–	#include "primitives/Molecule.hpp"
57	–	#include "utils/simError.h"
58	–	#include "utils/MemoryUtils.hpp"
59	–	#include "utils/StringTokenizer.hpp"
60	–
61	–	#ifdef IS_MPI
62	–
63	–	#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 {
42
43	<	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
44	<	: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
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	>
53	>	#include <iostream>
54	>	#include <math.h>
55	>
56	>	#include <stdio.h>
57	>	#include <stdlib.h>
58	>	#include <string.h>
59	>
60	>	#include "io/DumpReader.hpp"
61	>	#include "primitives/Molecule.hpp"
62	>	#include "utils/simError.h"
63	>	#include "utils/MemoryUtils.hpp"
64	>	#include "utils/StringTokenizer.hpp"
65	>	#include "brains/Thermo.hpp"
66	>
67	>
68	>	namespace OpenMD {
69	>
70	>	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
71	>	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
72
73	<	#ifdef IS_MPI
73	>	#ifdef IS_MPI
74
75	<	if (worldRank == 0) {
76	<	#endif
75	>	if (worldRank == 0) {
76	>	#endif
77
78	<	inFile_ = fopen(filename_.c_str(), "r");
78	>	inFile_ = new std::ifstream(filename_.c_str(),
79	>	ifstream::in | ifstream::binary);
80
81	<	if (inFile_ == NULL) {
82	<	sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
83	<	painCave.isFatal = 1;
84	<	simError();
85	<	}
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	<	#ifdef IS_MPI
89	>	#ifdef IS_MPI
90
91	<	}
91	>	}
92
93	<	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
94	<	MPIcheckPoint();
93	>	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
94	>	errorCheckPoint();
95
96	<	#endif
96	>	#endif
97
98	<	return;
99	<	}
98	>	return;
99	>	}
100
101	<	DumpReader::~DumpReader() {
101	>	DumpReader::~DumpReader() {
102
103	<	#ifdef IS_MPI
103	>	#ifdef IS_MPI
104
105	<	if (worldRank == 0) {
105	>	if (worldRank == 0) {
106		#endif
107	+
108	+	inFile_->~istream();
109
110	<	int error;
108	<	error = fclose(inFile_);
110	>	#ifdef IS_MPI
111
112	<	if (error) {
111	<	sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str());
112	<	painCave.isFatal = 1;
113	<	simError();
114	<	}
115	<
116	<	MemoryUtils::deletePointers(framePos_);
117	<
118	<	#ifdef IS_MPI
119	<
120	<	}
112	>	}
113
114	<	strcpy(checkPointMsg, "Dump file closed successfully.");
115	<	MPIcheckPoint();
114	>	strcpy(checkPointMsg, "Dump file closed successfully.");
115	>	errorCheckPoint();
116
117	<	#endif
117	>	#endif
118
119	<	return;
120	<	}
119	>	return;
120	>	}
121
122	<	int DumpReader::getNFrames(void) {
122	>	int DumpReader::getNFrames(void) {
123	>
124	>	if (!isScanned_)
125	>	scanFile();
126	>
127	>	return nframes_;
128	>	}
129	>
130	>	void DumpReader::scanFile(void) {
131	>
132	>	std::streampos prevPos;
133	>	std::streampos  currPos;
134
135	<	if (!isScanned_)
133	<	scanFile();
135	>	#ifdef IS_MPI
136
137	<	return nframes_;
138	<	}
137	<
138	<	void DumpReader::scanFile(void) {
139	<	int i, j;
140	<	int lineNum = 0;
141	<	char readBuffer[maxBufferSize];
142	<	fpos_t * currPos;
143	<
144	<	#ifdef IS_MPI
145	<
146	<	if (worldRank == 0) {
147	<	#endif // is_mpi
137	>	if (worldRank == 0) {
138	>	#endif // is_mpi
139
140	<	rewind(inFile_);
141	<
142	<	currPos = new fpos_t;
143	<	fgetpos(inFile_, currPos);
144	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
145	<	lineNum++;
146	<
147	<	if (feof(inFile_)) {
157	<	sprintf(painCave.errMsg,
158	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
159	<	filename_.c_str(),
160	<	lineNum);
161	<	painCave.isFatal = 1;
162	<	simError();
163	<	}
164	<
165	<	while (!feof(inFile_)) {
166	<	framePos_.push_back(currPos);
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	<	i = atoi(readBuffer);
150	<
151	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
152	<	lineNum++;
153	<
154	<	if (feof(inFile_)) {
155	<	sprintf(painCave.errMsg,
156	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
157	<	filename_.c_str(),
158	<	lineNum);
159	<	painCave.isFatal = 1;
160	<	simError();
161	<	}
181	<
182	<	for(j = 0; j < i; j++) {
183	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
184	<	lineNum++;
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:<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	<	if (feof(inFile_)) {
164	<	sprintf(painCave.errMsg,
165	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d,"
166	<	" with atom %d\n", filename_.c_str(),
167	<	lineNum,
168	<	j);
169	<
193	<	painCave.isFatal = 1;
194	<	simError();
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	+	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	<
198	<	currPos = new fpos_t;
199	<	fgetpos(inFile_, currPos);
200	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
201	<	lineNum++;
182	>	prevPos = currPos;
183		}
184
185	<	delete currPos;
186	<	rewind(inFile_);
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	<	#ifdef IS_MPI
197	<	}
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
208	<	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
212	<
213	<	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
214	<	MPIcheckPoint();
215	<
216	<	#endif // is_mpi
217	<
218	<	isScanned_ = true;
219	<	}
220	<
221	<	void DumpReader::readFrame(int whichFrame) {
222	<	if (!isScanned_)
223	<	scanFile();
224	<
225	<	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
226	<
227	<	if (storageLayout & DataStorage::dslPosition) {
228	<	needPos_ = true;
229	<	} else {
230	<	needPos_ = false;
231	<	}
208	>	#endif // is_mpi
209
210	<	if (storageLayout & DataStorage::dslVelocity) {
211	<	needVel_ = true;
212	<	} else {
213	<	needVel_ = false;
210	>	isScanned_ = true;
211	>	}
212	>
213	>	void DumpReader::readFrame(int whichFrame) {
214	>	if (!isScanned_)
215	>	scanFile();
216	>
217	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
218	>
219	>	if (storageLayout & DataStorage::dslPosition) {
220	>	needPos_ = true;
221	>	} else {
222	>	needPos_ = false;
223	>	}
224	>
225	>	if (storageLayout & DataStorage::dslVelocity) {
226	>	needVel_ = true;
227	>	} else {
228	>	needVel_ = false;
229	>	}
230	>
231	>	if (storageLayout & DataStorage::dslAmat ||
232	>	storageLayout & DataStorage::dslDipole ||
233	>	storageLayout & DataStorage::dslQuadrupole) {
234	>	needQuaternion_ = true;
235	>	} else {
236	>	needQuaternion_ = false;
237	>	}
238	>
239	>	if (storageLayout & DataStorage::dslAngularMomentum) {
240	>	needAngMom_ = true;
241	>	} else {
242	>	needAngMom_ = false;
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	<	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
263	<	needQuaternion_ = true;
261	>	}
262	>
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	>	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	<	needQuaternion_ = false;
299	<	}
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: can not find <Snapshot>\n");
317	>	painCave.isFatal = 1;
318	>	simError();
319	>	}
320
321	<	if (storageLayout & DataStorage::dslAngularMomentum) {
322	<	needAngMom_ = true;
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	<	needAngMom_ = false;
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	<	readSet(whichFrame);
343	<	}
344	<
345	<	void DumpReader::readSet(int whichFrame) {
346	<	int i;
347	<	int nTotObjs;                  // the number of atoms
348	<	char read_buffer[maxBufferSize];  //the line buffer for reading
349	<	char * eof_test;               // ptr to see when we reach the end of the file
350	<
351	<	Molecule* mol;
352	<	StuntDouble* integrableObject;
353	<	SimInfo::MoleculeIterator mi;
354	<	Molecule::IntegrableObjectIterator ii;
355	<
356	<	#ifndef IS_MPI
357	<
358	<	fsetpos(inFile_, framePos_[whichFrame]);
359	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
360	<
361	<	if (eof_test == NULL) {
362	<	sprintf(painCave.errMsg,
363	<	"DumpReader error: error reading 1st line of \"%s\"\n",
273	<	filename_.c_str());
274	<	painCave.isFatal = 1;
275	<	simError();
341	>	}
342	>
343	>	void DumpReader::parseDumpLine(const std::string& line) {
344	>
345	>
346	>	StringTokenizer tokenizer(line);
347	>	int nTokens;
348	>
349	>	nTokens = tokenizer.countTokens();
350	>
351	>	if (nTokens < 2) {
352	>	sprintf(painCave.errMsg,
353	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
354	>	painCave.isFatal = 1;
355	>	simError();
356	>	}
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	<	nTotObjs = atoi(read_buffer);
371	<
372	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
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(),
377	<	nTotObjs,
378	<	info_->getNGlobalIntegrableObjects());
379	<
288	<	painCave.isFatal = 1;
289	<	simError();
370	>	if (needPos_) {
371	>	found = type.find("p");
372	>	if (found == std::string::npos) {
373	>	sprintf(painCave.errMsg,
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
382	<	//read the box mat from the comment line
383	<
384	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
385	<
386	<	if (eof_test == NULL) {
387	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
388	<	filename_.c_str());
389	<	painCave.isFatal = 1;
390	<	simError();
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	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
397	<
305	<	//parse dump lines
306	<
307	<	i = 0;
308	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
309	<
310	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
311	<	integrableObject = mol->nextIntegrableObject(ii)) {
395	>
396	>	for(int i = 0; i < size; ++i) {
397	>	switch(type[i]) {
398
399	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
400	<
401	<	if (eof_test == NULL) {
402	<	sprintf(painCave.errMsg,
403	<	"DumpReader Error: error in reading file %s\n"
404	<	"natoms  = %d; index = %d\n"
405	<	"error reading the line from the file.\n",
406	<	filename_.c_str(),
407	<	nTotObjs,
322	<	i);
323	<
324	<	painCave.isFatal = 1;
325	<	simError();
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	<
410	<	parseDumpLine(read_buffer, integrableObject);
411	<	i++;
412	<	}
413	<	}
414	<
415	<	// MPI Section of code..........
416	<
417	<	#else //IS_MPI
418	<
419	<	// first thing first, suspend fatalities.
420	<	int masterNode = 0;
421	<	int nCurObj;
422	<	painCave.isEventLoop = 1;
341	<
342	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
343	<	int haveError;
344	<
345	<	MPI_Status istatus;
346	<	int nitems;
347	<
348	<	nTotObjs = info_->getNGlobalIntegrableObjects();
349	<	haveError = 0;
350	<
351	<	if (worldRank == masterNode) {
352	<	fsetpos(inFile_, framePos_[whichFrame]);
353	<
354	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
355	<
356	<	if (eof_test == NULL) {
357	<	sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ",
358	<	filename_.c_str());
359	<	painCave.isFatal = 1;
360	<	simError();
361	<	}
362	<
363	<	nitems = atoi(read_buffer);
364	<
365	<	// Check to see that the number of integrable objects in the
366	<	// intial configuration file is the same as derived from the
367	<	// meta-data file.
368	<
369	<	if (nTotObjs != nitems) {
370	<	sprintf(painCave.errMsg,
371	<	"DumpReader Error. %s nIntegrable, %d, "
372	<	"does not match the meta-data file's nIntegrable, %d.\n",
373	<	filename_.c_str(),
374	<	nTotObjs,
375	<	info_->getNGlobalIntegrableObjects());
376	<
377	<	painCave.isFatal = 1;
378	<	simError();
379	<	}
380	<
381	<	//read the boxMat from the comment line
382	<
383	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
384	<
385	<	if (eof_test == NULL) {
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)){
416	<
417	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
418	<
419	<	if (eof_test == NULL) {
420	<	sprintf(painCave.errMsg,
421	<	"DumpReader Error: error in reading file %s\n"
422	<	"natoms  = %d; index = %d\n"
423	<	"error reading the line from the file.\n",
424	<	filename_.c_str(),
425	<	nTotObjs,
426	<	i);
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	>	break;
418	>	}
419	>
420	>	case 'q' : {
421	>	Quat4d q;
422	>	if (sd->isDirectional()) {
423
424	<	painCave.isFatal = 1;
425	<	simError();
426	<	}
427	<
432	<	parseDumpLine(read_buffer, integrableObject);
433	<	}
434	<	} else {
435	<	//molecule belongs to slave nodes
436	<
437	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
438	<	MPI_COMM_WORLD, &istatus);
439	<
440	<	for(int j = 0; j < nCurObj; j++) {
441	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
442	<
443	<	if (eof_test == NULL) {
444	<	sprintf(painCave.errMsg,
445	<	"DumpReader Error: error in reading file %s\n"
446	<	"natoms  = %d; index = %d\n"
447	<	"error reading the line from the file.\n",
448	<	filename_.c_str(),
449	<	nTotObjs,
450	<	i);
424	>	q[0] = tokenizer.nextTokenAsDouble();
425	>	q[1] = tokenizer.nextTokenAsDouble();
426	>	q[2] = tokenizer.nextTokenAsDouble();
427	>	q[3] = tokenizer.nextTokenAsDouble();
428
429	<	painCave.isFatal = 1;
430	<	simError();
431	<	}
432	<
433	<	MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
434	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
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	<	}
468	<	} else {
469	<	//actions taken at slave nodes
470	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
471	<
472	<	/**@todo*/
473	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
474	<
468	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
469	<	int which_node = info_->getMolToProc(i);
470	<
471	<	if (which_node == worldRank) {
472	<	//molecule with global index i belongs to this processor
473	<
474	<	mol = info_->getMoleculeByGlobalIndex(i);
475	<	if (mol == NULL) {
476	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
477	<	painCave.isFatal = 1;
478	<	simError();
479	<	}
480	<
481	<	nCurObj = mol->getNIntegrableObjects();
482	<
483	<	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
484	<	MPI_COMM_WORLD);
485	<
486	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
487	<	integrableObject = mol->nextIntegrableObject(ii)){
488	<
489	<	MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
490	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
491	<
492	<	parseDumpLine(read_buffer, integrableObject);
493	<	}
494	<
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	<
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		}
498	–
529		}
530	<
531	<	#endif
532	<
533	<	}
534	<
535	<	void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
536	<
537	<	Vector3d pos;  // position place holders
538	<	Vector3d vel;  // velocity placeholders
539	<	Quat4d q;    // the quaternions
540	<	Vector3d ji;   // angular velocity placeholders;
541	<	StringTokenizer tokenizer(line);
542	<	int nTokens;
543	<
544	<	nTokens = tokenizer.countTokens();
545	<
546	<	if (nTokens < 14) {
547	<	sprintf(painCave.errMsg,
548	<	"DumpReader Error: Not enough Tokens.\n%s\n", line);
549	<	painCave.isFatal = 1;
550	<	simError();
551	<	}
552	<
553	<	std::string name = tokenizer.nextToken();
554	<
525	<	if (name != integrableObject->getType()) {
526	<
527	<	sprintf(painCave.errMsg,
528	<	"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
529	<	name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
530	<	painCave.isFatal = 1;
531	<	simError();
532	<	}
533	<
534	<	pos[0] = tokenizer.nextTokenAsDouble();
535	<	pos[1] = tokenizer.nextTokenAsDouble();
536	<	pos[2] = tokenizer.nextTokenAsDouble();
537	<	if (needPos_) {
538	<	integrableObject->setPos(pos);
530	>	}
531	>
532	>
533	>	void DumpReader::parseSiteLine(const std::string& line) {
534	>
535	>	StringTokenizer tokenizer(line);
536	>	int nTokens;
537	>
538	>	nTokens = tokenizer.countTokens();
539	>
540	>	if (nTokens < 2) {
541	>	sprintf(painCave.errMsg,
542	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
543	>	painCave.isFatal = 1;
544	>	simError();
545	>	}
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	<	vel[0] = tokenizer.nextTokenAsDouble();
558	<	vel[1] = tokenizer.nextTokenAsDouble();
559	<	vel[2] = tokenizer.nextTokenAsDouble();
560	<	if (needVel_) {
561	<	integrableObject->setVel(vel);
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	<	if (integrableObject->isDirectional()) {
583	<
550	<	q[0] = tokenizer.nextTokenAsDouble();
551	<	q[1] = tokenizer.nextTokenAsDouble();
552	<	q[2] = tokenizer.nextTokenAsDouble();
553	<	q[3] = tokenizer.nextTokenAsDouble();
554	<
555	<	double qlen = q.length();
556	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
582	>	for(int i = 0; i < size; ++i) {
583	>	switch(type[i]) {
584
585	<	sprintf(painCave.errMsg,
559	<	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
560	<	painCave.isFatal = 1;
561	<	simError();
585	>	case 'u' : {
586
587	<	}
588	<
589	<	q.normalize();
590	<	if (needQuaternion_) {
567	<	integrableObject->setQ(q);
587	>	RealType particlePot;
588	>	particlePot = tokenizer.nextTokenAsDouble();
589	>	sd->setParticlePot(particlePot);
590	>	break;
591		}
592	<
593	<	ji[0] = tokenizer.nextTokenAsDouble();
594	<	ji[1] = tokenizer.nextTokenAsDouble();
595	<	ji[2] = tokenizer.nextTokenAsDouble();
596	<	if (needAngMom_) {
597	<	integrableObject->setJ(ji);
592	>	case 'c' : {
593	>
594	>	RealType flucQPos;
595	>	flucQPos = tokenizer.nextTokenAsDouble();
596	>	sd->setFlucQPos(flucQPos);
597	>	break;
598		}
599	<	}
600	<
601	<	}
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: %s is an unrecognized type\n", type.c_str());
632	>	painCave.isFatal = 1;
633	>	simError();
634	>	break;
635	>	}
636	>	}
637	>	}
638	>	}
639
640
641	<	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
582	<	double currTime;
583	<	Mat3x3d hmat;
584	<	double chi;
585	<	double integralOfChiDt;
586	<	Mat3x3d eta;
641	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
642
643	<	StringTokenizer tokenizer(line);
644	<	int nTokens;
643	>	inputStream.getline(buffer, bufferSize);
644	>	std::string line(buffer);
645
646	<	nTokens = tokenizer.countTokens();
647	<
648	<	//comment line should at least contain 10 tokens: current time(1 token) and  h-matrix(9 tokens)
649	<	if (nTokens < 10) {
650	<	sprintf(painCave.errMsg,
596	<	"DumpReader Error: Not enough tokens in comment line: %s", line);
597	<	painCave.isFatal = 1;
598	<	simError();
646	>	if (line.find("<StuntDoubles>") == std::string::npos) {
647	>	sprintf(painCave.errMsg,
648	>	"DumpReader Error: Missing <StuntDoubles>\n");
649	>	painCave.isFatal = 1;
650	>	simError();
651		}
652	<
653	<	//read current time
654	<	currTime = tokenizer.nextTokenAsDouble();
603	<	s->setTime(currTime);
604	<
605	<	//read h-matrix
606	<	hmat(0, 0) = tokenizer.nextTokenAsDouble();
607	<	hmat(0, 1) = tokenizer.nextTokenAsDouble();
608	<	hmat(0, 2) = tokenizer.nextTokenAsDouble();
609	<	hmat(1, 0) = tokenizer.nextTokenAsDouble();
610	<	hmat(1, 1) = tokenizer.nextTokenAsDouble();
611	<	hmat(1, 2) = tokenizer.nextTokenAsDouble();
612	<	hmat(2, 0) = tokenizer.nextTokenAsDouble();
613	<	hmat(2, 1) = tokenizer.nextTokenAsDouble();
614	<	hmat(2, 2) = tokenizer.nextTokenAsDouble();
615	<	s->setHmat(hmat);
616	<
617	<	//read chi and integralOfChidt, they should apprear in pair
618	<	if (tokenizer.countTokens() >= 2) {
619	<	chi = tokenizer.nextTokenAsDouble();
620	<	integralOfChiDt = tokenizer.nextTokenAsDouble();
652	>
653	>	while(inputStream.getline(buffer, bufferSize)) {
654	>	line = buffer;
655
656	<	s->setChi(chi);
657	<	s->setIntegralOfChiDt(integralOfChiDt);
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	<	//read eta (eta is 3x3 matrix)
674	<	if (tokenizer.countTokens() >= 9) {
628	<	eta(0, 0) = tokenizer.nextTokenAsDouble();
629	<	eta(0, 1) = tokenizer.nextTokenAsDouble();
630	<	eta(0, 2) = tokenizer.nextTokenAsDouble();
631	<	eta(1, 0) = tokenizer.nextTokenAsDouble();
632	<	eta(1, 1) = tokenizer.nextTokenAsDouble();
633	<	eta(1, 2) = tokenizer.nextTokenAsDouble();
634	<	eta(2, 0) = tokenizer.nextTokenAsDouble();
635	<	eta(2, 1) = tokenizer.nextTokenAsDouble();
636	<	eta(2, 2) = tokenizer.nextTokenAsDouble();
673	>	while(inputStream.getline(buffer, bufferSize)) {
674	>	line = buffer;
675
676	<	s->setEta(eta);
676	>	if(line.find("</SiteData>") != std::string::npos) {
677	>	break;
678	>	}
679	>
680	>	parseSiteLine(line);
681		}
640	–
641	–
642	–	}
682
683	<	}//end namespace oopse
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 OpenMD

Comparing trunk/src/io/DumpReader.cpp (property svn:keywords):
Revision 601 by tim, Thu Sep 15 19:17:04 2005 UTC vs.
Revision 2000 by gezelter, Sat May 31 22:35:05 2014 UTC

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