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

Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
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. 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) {
106	<	#endif
105	>	if (worldRank == 0) {
106	>	#endif
107
108	<	int error;
108	<	error = fclose(inFile_);
108	>	delete inFile_;
109
110	<	if (error) {
111	<	sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str());
112	<	painCave.isFatal = 1;
113	<	simError();
114	<	}
110	>	#ifdef IS_MPI
111
112	<	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);
208	>	#endif // is_mpi
209
210	<	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
211	<	MPIcheckPoint();
212	<
213	<	#endif // is_mpi
214	<
215	<	isScanned_ = true;
216	<	}
217	<
218	<	void DumpReader::readFrame(int whichFrame) {
219	<	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
220	<
221	<	if (storageLayout & DataStorage::dslPosition) {
222	<	needPos_ = true;
223	<	} else {
224	<	needPos_ = 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::dslVelocity) {
263	<	needVel_ = 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	<	needVel_ = 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::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
322	<	needQuaternion_ = 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	<	needQuaternion_ = 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	<	if (storageLayout & DataStorage::dslAngularMomentum) {
343	<	needAngMom_ = true;
344	<	} else {
345	<	needAngMom_ = false;
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	<	readSet(whichFrame);
371	<	}
372	<
373	<	void DumpReader::readSet(int whichFrame) {
374	<	int i;
375	<	int nTotObjs;                  // the number of atoms
376	<	char read_buffer[maxBufferSize];  //the line buffer for reading
377	<	char * eof_test;               // ptr to see when we reach the end of the file
378	<
379	<	Molecule* mol;
258	<	StuntDouble* integrableObject;
259	<	SimInfo::MoleculeIterator mi;
260	<	Molecule::IntegrableObjectIterator ii;
261	<
262	<	#ifndef IS_MPI
263	<
264	<	fsetpos(inFile_, framePos_[whichFrame]);
265	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
266	<
267	<	if (eof_test == NULL) {
268	<	sprintf(painCave.errMsg,
269	<	"DumpReader error: error reading 1st line of \"%s\"\n",
270	<	filename_.c_str());
271	<	painCave.isFatal = 1;
272	<	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	<	nTotObjs = atoi(read_buffer);
383	<
384	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
385	<	sprintf(painCave.errMsg,
386	<	"DumpReader error. %s nIntegrable, %d, "
387	<	"does not match the meta-data file's nIntegrable, %d.\n",
388	<	filename_.c_str(),
389	<	nTotObjs,
390	<	info_->getNGlobalIntegrableObjects());
391	<
392	<	painCave.isFatal = 1;
393	<	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	<	//read the box mat from the comment line
397	<
291	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
292	<
293	<	if (eof_test == NULL) {
294	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
295	<	filename_.c_str());
296	<	painCave.isFatal = 1;
297	<	simError();
298	<	}
299	<
300	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
301	<
302	<	//parse dump lines
303	<
304	<	i = 0;
305	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
306	<
307	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
308	<	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,
319	<	i);
320	<
321	<	painCave.isFatal = 1;
322	<	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;
338	<
339	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
340	<	int haveError;
341	<
342	<	MPI_Status istatus;
343	<	int nitems;
344	<
345	<	nTotObjs = info_->getNGlobalIntegrableObjects();
346	<	haveError = 0;
347	<
348	<	if (worldRank == masterNode) {
349	<	fsetpos(inFile_, framePos_[whichFrame]);
350	<
351	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
352	<
353	<	if (eof_test == NULL) {
354	<	sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ",
355	<	filename_.c_str());
356	<	painCave.isFatal = 1;
357	<	simError();
358	<	}
359	<
360	<	nitems = atoi(read_buffer);
361	<
362	<	// Check to see that the number of integrable objects in the
363	<	// intial configuration file is the same as derived from the
364	<	// meta-data file.
365	<
366	<	if (nTotObjs != nitems) {
367	<	sprintf(painCave.errMsg,
368	<	"DumpReader Error. %s nIntegrable, %d, "
369	<	"does not match the meta-data file's nIntegrable, %d.\n",
370	<	filename_.c_str(),
371	<	nTotObjs,
372	<	info_->getNGlobalIntegrableObjects());
373	<
374	<	painCave.isFatal = 1;
375	<	simError();
376	<	}
377	<
378	<	//read the boxMat from the comment line
379	<
380	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
381	<
382	<	if (eof_test == NULL) {
383	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
384	<	filename_.c_str());
385	<	painCave.isFatal = 1;
386	<	simError();
387	<	}
388	<
389	<	//Every single processor will parse the comment line by itself
390	<	//By using this way, we might lose some efficiency, but if we want to add
391	<	//more parameters into comment line, we only need to modify function
392	<	//parseCommentLine
393	<
394	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
395	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
396	<
397	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
398	<	int which_node = info_->getMolToProc(i);
399	<
400	<	if (which_node == masterNode) {
401	<	//molecules belong to master node
402	<
403	<	mol = info_->getMoleculeByGlobalIndex(i);
404	<
405	<	if (mol == NULL) {
406	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
407	<	painCave.isFatal = 1;
408	<	simError();
409	<	}
410	<
411	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
412	<	integrableObject = mol->nextIntegrableObject(ii)){
413	<
414	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
415	<
416	<	if (eof_test == NULL) {
417	<	sprintf(painCave.errMsg,
418	<	"DumpReader Error: error in reading file %s\n"
419	<	"natoms  = %d; index = %d\n"
420	<	"error reading the line from the file.\n",
421	<	filename_.c_str(),
422	<	nTotObjs,
423	<	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	<
429	<	parseDumpLine(read_buffer, integrableObject);
430	<	}
431	<	} else {
432	<	//molecule belongs to slave nodes
433	<
434	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
435	<	MPI_COMM_WORLD, &istatus);
436	<
437	<	for(int j = 0; j < nCurObj; j++) {
438	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
439	<
440	<	if (eof_test == NULL) {
441	<	sprintf(painCave.errMsg,
442	<	"DumpReader Error: error in reading file %s\n"
443	<	"natoms  = %d; index = %d\n"
444	<	"error reading the line from the file.\n",
445	<	filename_.c_str(),
446	<	nTotObjs,
447	<	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	<
465	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
466	<	int which_node = info_->getMolToProc(i);
467	<
468	<	if (which_node == worldRank) {
469	<	//molecule with global index i belongs to this processor
470	<
471	<	mol = info_->getMoleculeByGlobalIndex(i);
472	<	if (mol == NULL) {
473	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
474	<	painCave.isFatal = 1;
475	<	simError();
476	<	}
477	<
478	<	nCurObj = mol->getNIntegrableObjects();
479	<
480	<	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
481	<	MPI_COMM_WORLD);
482	<
483	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
484	<	integrableObject = mol->nextIntegrableObject(ii)){
485	<
486	<	MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
487	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
488	<
489	<	parseDumpLine(read_buffer, integrableObject);
490	<	}
491	<
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	>	default: {
514	>	sprintf(painCave.errMsg,
515	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
516	>	painCave.isFatal = 1;
517	>	simError();
518	>	break;
519	>	}
520	>
521		}
495	–
522		}
523	<
524	<	#endif
525	<
526	<	}
527	<
528	<	void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
529	<
530	<	Vector3d pos;  // position place holders
531	<	Vector3d vel;  // velocity placeholders
532	<	Quat4d q;    // the quaternions
533	<	Vector3d ji;   // angular velocity placeholders;
534	<	StringTokenizer tokenizer(line);
535	<	int nTokens;
536	<
537	<	nTokens = tokenizer.countTokens();
538	<
539	<	if (nTokens < 14) {
540	<	sprintf(painCave.errMsg,
541	<	"DumpReader Error: Not enough Tokens.\n%s\n", line);
542	<	painCave.isFatal = 1;
543	<	simError();
544	<	}
545	<
546	<	std::string name = tokenizer.nextToken();
547	<
522	<	if (name != integrableObject->getType()) {
523	<
524	<	sprintf(painCave.errMsg,
525	<	"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
526	<	name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
527	<	painCave.isFatal = 1;
528	<	simError();
529	<	}
530	<
531	<	pos[0] = tokenizer.nextTokenAsDouble();
532	<	pos[1] = tokenizer.nextTokenAsDouble();
533	<	pos[2] = tokenizer.nextTokenAsDouble();
534	<	if (needPos_) {
535	<	integrableObject->setPos(pos);
523	>	}
524	>
525	>
526	>	void DumpReader::parseSiteLine(const std::string& line) {
527	>
528	>	StringTokenizer tokenizer(line);
529	>	int nTokens;
530	>
531	>	nTokens = tokenizer.countTokens();
532	>
533	>	if (nTokens < 2) {
534	>	sprintf(painCave.errMsg,
535	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
536	>	painCave.isFatal = 1;
537	>	simError();
538	>	}
539	>
540	>	/**
541	>	* The first token is the global integrable object index.
542	>	*/
543	>
544	>	int index = tokenizer.nextTokenAsInt();
545	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
546	>	if (sd == NULL) {
547	>	return;
548		}
549	<
550	<	vel[0] = tokenizer.nextTokenAsDouble();
551	<	vel[1] = tokenizer.nextTokenAsDouble();
552	<	vel[2] = tokenizer.nextTokenAsDouble();
553	<	if (needVel_) {
554	<	integrableObject->setVel(vel);
549	>
550	>	/**
551	>	* Test to see if the next token is an integer or not.  If not,
552	>	* we've got data on the integrable object itself.  If there is an
553	>	* integer, we're parsing data for a site on a rigid body.
554	>	*/
555	>
556	>	std::string indexTest = tokenizer.peekNextToken();
557	>	std::istringstream i(indexTest);
558	>	int siteIndex;
559	>	if (i >> siteIndex) {
560	>	// chew up this token and parse as an int:
561	>	siteIndex = tokenizer.nextTokenAsInt();
562	>
563	>	if (sd->isRigidBody()) {
564	>	RigidBody* rb = static_cast<RigidBody*>(sd);
565	>	sd = rb->getAtoms()[siteIndex];
566	>	}
567		}
568	+
569	+	/**
570	+	* The next token contains information on what follows.
571	+	*/
572	+	std::string type = tokenizer.nextToken();
573	+	int size = type.size();
574
575	<	if (integrableObject->isDirectional()) {
576	<
547	<	q[0] = tokenizer.nextTokenAsDouble();
548	<	q[1] = tokenizer.nextTokenAsDouble();
549	<	q[2] = tokenizer.nextTokenAsDouble();
550	<	q[3] = tokenizer.nextTokenAsDouble();
551	<
552	<	double qlen = q.length();
553	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
575	>	for(int i = 0; i < size; ++i) {
576	>	switch(type[i]) {
577
578	<	sprintf(painCave.errMsg,
556	<	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
557	<	painCave.isFatal = 1;
558	<	simError();
578	>	case 'u' : {
579
580	<	}
581	<
582	<	q.normalize();
583	<	if (needQuaternion_) {
564	<	integrableObject->setQ(q);
580	>	RealType particlePot;
581	>	particlePot = tokenizer.nextTokenAsDouble();
582	>	sd->setParticlePot(particlePot);
583	>	break;
584		}
585	<
586	<	ji[0] = tokenizer.nextTokenAsDouble();
587	<	ji[1] = tokenizer.nextTokenAsDouble();
588	<	ji[2] = tokenizer.nextTokenAsDouble();
589	<	if (needAngMom_) {
590	<	integrableObject->setJ(ji);
585	>	case 'c' : {
586	>
587	>	RealType flucQPos;
588	>	flucQPos = tokenizer.nextTokenAsDouble();
589	>	sd->setFlucQPos(flucQPos);
590	>	break;
591		}
592	<	}
593	<
594	<	}
592	>	case 'w' : {
593	>
594	>	RealType flucQVel;
595	>	flucQVel = tokenizer.nextTokenAsDouble();
596	>	sd->setFlucQVel(flucQVel);
597	>	break;
598	>	}
599	>	case 'g' : {
600	>
601	>	RealType flucQFrc;
602	>	flucQFrc = tokenizer.nextTokenAsDouble();
603	>	sd->setFlucQFrc(flucQFrc);
604	>	break;
605	>	}
606	>	case 'e' : {
607	>
608	>	Vector3d eField;
609	>	eField[0] = tokenizer.nextTokenAsDouble();
610	>	eField[1] = tokenizer.nextTokenAsDouble();
611	>	eField[2] = tokenizer.nextTokenAsDouble();
612	>	sd->setElectricField(eField);
613	>	break;
614	>	}
615	>	default: {
616	>	sprintf(painCave.errMsg,
617	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
618	>	painCave.isFatal = 1;
619	>	simError();
620	>	break;
621	>	}
622	>	}
623	>	}
624	>	}
625
626
627	<	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
579	<	double currTime;
580	<	Mat3x3d hmat;
581	<	double chi;
582	<	double integralOfChiDt;
583	<	Mat3x3d eta;
627	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
628
629	<	StringTokenizer tokenizer(line);
630	<	int nTokens;
629	>	inputStream.getline(buffer, bufferSize);
630	>	std::string line(buffer);
631
632	<	nTokens = tokenizer.countTokens();
633	<
634	<	//comment line should at least contain 10 tokens: current time(1 token) and  h-matrix(9 tokens)
635	<	if (nTokens < 10) {
636	<	sprintf(painCave.errMsg,
593	<	"DumpReader Error: Not enough tokens in comment line: %s", line);
594	<	painCave.isFatal = 1;
595	<	simError();
632	>	if (line.find("<StuntDoubles>") == std::string::npos) {
633	>	sprintf(painCave.errMsg,
634	>	"DumpReader Error: Missing <StuntDoubles>\n");
635	>	painCave.isFatal = 1;
636	>	simError();
637		}
638	<
639	<	//read current time
640	<	currTime = tokenizer.nextTokenAsDouble();
600	<	s->setTime(currTime);
601	<
602	<	//read h-matrix
603	<	hmat(0, 0) = tokenizer.nextTokenAsDouble();
604	<	hmat(0, 1) = tokenizer.nextTokenAsDouble();
605	<	hmat(0, 2) = tokenizer.nextTokenAsDouble();
606	<	hmat(1, 0) = tokenizer.nextTokenAsDouble();
607	<	hmat(1, 1) = tokenizer.nextTokenAsDouble();
608	<	hmat(1, 2) = tokenizer.nextTokenAsDouble();
609	<	hmat(2, 0) = tokenizer.nextTokenAsDouble();
610	<	hmat(2, 1) = tokenizer.nextTokenAsDouble();
611	<	hmat(2, 2) = tokenizer.nextTokenAsDouble();
612	<	s->setHmat(hmat);
613	<
614	<	//read chi and integralOfChidt, they should apprear in pair
615	<	if (tokenizer.countTokens() >= 2) {
616	<	chi = tokenizer.nextTokenAsDouble();
617	<	integralOfChiDt = tokenizer.nextTokenAsDouble();
638	>
639	>	while(inputStream.getline(buffer, bufferSize)) {
640	>	line = buffer;
641
642	<	s->setChi(chi);
643	<	s->setIntegralOfChiDt(integralOfChiDt);
642	>	if(line.find("</StuntDoubles>") != std::string::npos) {
643	>	break;
644	>	}
645	>
646	>	parseDumpLine(line);
647		}
648	+
649	+	}
650	+
651	+	void  DumpReader::readSiteData(std::istream& inputStream) {
652	+
653	+	std::string line(buffer);
654	+
655	+	// We already found the starting <SiteData> tag or we wouldn't be
656	+	// here, so just start parsing until we get to the ending
657	+	// </SiteData> tag:
658
659	<	//read eta (eta is 3x3 matrix)
660	<	if (tokenizer.countTokens() >= 9) {
625	<	eta(0, 0) = tokenizer.nextTokenAsDouble();
626	<	eta(0, 1) = tokenizer.nextTokenAsDouble();
627	<	eta(0, 2) = tokenizer.nextTokenAsDouble();
628	<	eta(1, 0) = tokenizer.nextTokenAsDouble();
629	<	eta(1, 1) = tokenizer.nextTokenAsDouble();
630	<	eta(1, 2) = tokenizer.nextTokenAsDouble();
631	<	eta(2, 0) = tokenizer.nextTokenAsDouble();
632	<	eta(2, 1) = tokenizer.nextTokenAsDouble();
633	<	eta(2, 2) = tokenizer.nextTokenAsDouble();
659	>	while(inputStream.getline(buffer, bufferSize)) {
660	>	line = buffer;
661
662	<	s->setEta(eta);
662	>	if(line.find("</SiteData>") != std::string::npos) {
663	>	break;
664	>	}
665	>
666	>	parseSiteLine(line);
667		}
637	–
638	–
639	–	}
668
669	<	}//end namespace oopse
669	>	}
670	>
671	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
672	>
673	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
674	>	inputStream.getline(buffer, bufferSize);
675	>	std::string line(buffer);
676	>
677	>	if (line.find("<FrameData>") == std::string::npos) {
678	>	sprintf(painCave.errMsg,
679	>	"DumpReader Error: Missing <FrameData>\n");
680	>	painCave.isFatal = 1;
681	>	simError();
682	>	}
683	>
684	>	while(inputStream.getline(buffer, bufferSize)) {
685	>	line = buffer;
686	>
687	>	if(line.find("</FrameData>") != std::string::npos) {
688	>	break;
689	>	}
690	>
691	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
692	>	if (!tokenizer.hasMoreTokens()) {
693	>	sprintf(painCave.errMsg,
694	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
695	>	painCave.isFatal = 1;
696	>	simError();
697	>	}
698	>
699	>	std::string propertyName = tokenizer.nextToken();
700	>	if (propertyName == "Time") {
701	>	RealType currTime = tokenizer.nextTokenAsDouble();
702	>	s->setTime(currTime);
703	>	} else if (propertyName == "Hmat"){
704	>	Mat3x3d hmat;
705	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
706	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
707	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
708	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
709	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
710	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
711	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
712	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
713	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
714	>	s->setHmat(hmat);
715	>	} else if (propertyName == "Thermostat") {
716	>	pair<RealType, RealType> thermostat;
717	>	thermostat.first = tokenizer.nextTokenAsDouble();
718	>	thermostat.second = tokenizer.nextTokenAsDouble();
719	>	s->setThermostat(thermostat);
720	>	} else if (propertyName == "Barostat") {
721	>	Mat3x3d eta;
722	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
723	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
724	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
725	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
726	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
727	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
728	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
729	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
730	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
731	>	s->setBarostat(eta);
732	>	} else {
733	>	sprintf(painCave.errMsg,
734	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
735	>	painCave.isFatal = 0;
736	>	simError();
737	>	}
738	>
739	>	}
740	>
741	>	}
742	>
743	>
744	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpReader.cpp (property svn:keywords):
Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

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