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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 2069 by gezelter, Thu Mar 5 16:30:23 2015 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) {
105	>	if (worldRank == 0) {
106		#endif
107	+
108	+	delete inFile_;
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	<	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
223	<
224	<	if (storageLayout & DataStorage::dslPosition) {
225	<	needPos_ = true;
226	<	} else {
227	<	needPos_ = false;
228	<	}
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	>	Thermo thermo(info_);
249	>	Vector3d com;
250	>
251	>	if (needPos_ && needVel_) {
252	>	Vector3d comvel;
253	>	Vector3d comw;
254	>	thermo.getComAll(com, comvel);
255	>	comw = thermo.getAngularMomentum();
256	>	} else {
257	>	com = thermo.getCom();
258	>	}
259		}
260	<
261	<	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
262	<	needQuaternion_ = true;
260	>	}
261	>
262	>	void DumpReader::readSet(int whichFrame) {
263	>	std::string line;
264	>
265	>	#ifndef IS_MPI
266	>	inFile_->clear();
267	>	inFile_->seekg(framePos_[whichFrame]);
268	>
269	>	std::istream& inputStream = *inFile_;
270	>
271	>	#else
272	>	int masterNode = 0;
273	>	std::stringstream sstream;
274	>	if (worldRank == masterNode) {
275	>	std::string sendBuffer;
276	>
277	>	inFile_->clear();
278	>	inFile_->seekg(framePos_[whichFrame]);
279	>
280	>	while (inFile_->getline(buffer, bufferSize)) {
281	>
282	>	line = buffer;
283	>	sendBuffer += line;
284	>	sendBuffer += '\n';
285	>	if (line.find("</Snapshot>") != std::string::npos) {
286	>	break;
287	>	}
288	>	}
289	>
290	>	int sendBufferSize = sendBuffer.size();
291	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
292	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize,
293	>	MPI_CHAR, masterNode, MPI_COMM_WORLD);
294	>
295	>	sstream.str(sendBuffer);
296		} else {
297	<	needQuaternion_ = false;
298	<	}
297	>	int sendBufferSize;
298	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
299	>	char * recvBuffer = new char[sendBufferSize+1];
300	>	assert(recvBuffer);
301	>	recvBuffer[sendBufferSize] = '\0';
302	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
303	>	sstream.str(recvBuffer);
304	>	delete [] recvBuffer;
305	>	}
306	>
307	>	std::istream& inputStream = sstream;
308	>	#endif
309	>
310	>	inputStream.getline(buffer, bufferSize);
311	>
312	>	line = buffer;
313	>	if (line.find("<Snapshot>") == std::string::npos) {
314	>	sprintf(painCave.errMsg,
315	>	"DumpReader Error: can not find <Snapshot>\n");
316	>	painCave.isFatal = 1;
317	>	simError();
318	>	}
319
320	<	if (storageLayout & DataStorage::dslAngularMomentum) {
321	<	needAngMom_ = true;
320	>	//read frameData
321	>	readFrameProperties(inputStream);
322	>
323	>	//read StuntDoubles
324	>	readStuntDoubles(inputStream);
325	>
326	>	inputStream.getline(buffer, bufferSize);
327	>	line = buffer;
328	>
329	>	if (line.find("<SiteData>") != std::string::npos) {
330	>	//read SiteData
331	>	readSiteData(inputStream);
332		} else {
333	<	needAngMom_ = false;
333	>	if (line.find("</Snapshot>") == std::string::npos) {
334	>	sprintf(painCave.errMsg,
335	>	"DumpReader Error: can not find </Snapshot>\n");
336	>	painCave.isFatal = 1;
337	>	simError();
338	>	}
339		}
340	<
341	<	readSet(whichFrame);
342	<	}
343	<
344	<	void DumpReader::readSet(int whichFrame) {
345	<	int i;
346	<	int nTotObjs;                  // the number of atoms
347	<	char read_buffer[maxBufferSize];  //the line buffer for reading
348	<	char * eof_test;               // ptr to see when we reach the end of the file
349	<
350	<	Molecule* mol;
351	<	StuntDouble* integrableObject;
352	<	SimInfo::MoleculeIterator mi;
353	<	Molecule::IntegrableObjectIterator ii;
354	<
355	<	#ifndef IS_MPI
356	<
357	<	fsetpos(inFile_, framePos_[whichFrame]);
358	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
359	<
360	<	if (eof_test == NULL) {
361	<	sprintf(painCave.errMsg,
362	<	"DumpReader error: error reading 1st line of \"%s\"\n",
270	<	filename_.c_str());
271	<	painCave.isFatal = 1;
272	<	simError();
340	>	}
341	>
342	>	void DumpReader::parseDumpLine(const std::string& line) {
343	>
344	>
345	>	StringTokenizer tokenizer(line);
346	>	int nTokens;
347	>
348	>	nTokens = tokenizer.countTokens();
349	>
350	>	if (nTokens < 2) {
351	>	sprintf(painCave.errMsg,
352	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
353	>	painCave.isFatal = 1;
354	>	simError();
355	>	}
356	>
357	>	int index = tokenizer.nextTokenAsInt();
358	>
359	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
360	>
361	>	if (sd == NULL) {
362	>	return;
363		}
364	+	std::string type = tokenizer.nextToken();
365	+	int size = type.size();
366	+
367	+	size_t found;
368
369	<	nTotObjs = atoi(read_buffer);
370	<
371	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
372	<	sprintf(painCave.errMsg,
373	<	"DumpReader error. %s nIntegrable, %d, "
374	<	"does not match the meta-data file's nIntegrable, %d.\n",
375	<	filename_.c_str(),
376	<	nTotObjs,
377	<	info_->getNGlobalIntegrableObjects());
378	<
285	<	painCave.isFatal = 1;
286	<	simError();
369	>	if (needPos_) {
370	>	found = type.find("p");
371	>	if (found == std::string::npos) {
372	>	sprintf(painCave.errMsg,
373	>	"DumpReader Error: StuntDouble %d has no Position\n"
374	>	"\tField (\"p\") specified.\n%s\n", index,
375	>	line.c_str());
376	>	painCave.isFatal = 1;
377	>	simError();
378	>	}
379		}
380
381	<	//read the box mat 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();
381	>	if (sd->isDirectional()) {
382	>	if (needQuaternion_) {
383	>	found = type.find("q");
384	>	if (found == std::string::npos) {
385	>	sprintf(painCave.errMsg,
386	>	"DumpReader Error: Directional StuntDouble %d has no\n"
387	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
388	>	line.c_str());
389	>	painCave.isFatal = 1;
390	>	simError();
391	>	}
392	>	}
393		}
394	<
395	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
396	<
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)) {
394	>
395	>	for(int i = 0; i < size; ++i) {
396	>	switch(type[i]) {
397
398	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
399	<
400	<	if (eof_test == NULL) {
401	<	sprintf(painCave.errMsg,
402	<	"DumpReader Error: error in reading file %s\n"
403	<	"natoms  = %d; index = %d\n"
404	<	"error reading the line from the file.\n",
405	<	filename_.c_str(),
406	<	nTotObjs,
319	<	i);
320	<
321	<	painCave.isFatal = 1;
322	<	simError();
398	>	case 'p': {
399	>	Vector3d pos;
400	>	pos[0] = tokenizer.nextTokenAsDouble();
401	>	pos[1] = tokenizer.nextTokenAsDouble();
402	>	pos[2] = tokenizer.nextTokenAsDouble();
403	>	if (needPos_) {
404	>	sd->setPos(pos);
405	>	}
406	>	break;
407		}
408	<
409	<	parseDumpLine(read_buffer, integrableObject);
410	<	i++;
411	<	}
412	<	}
413	<
414	<	// MPI Section of code..........
415	<
416	<	#else //IS_MPI
417	<
418	<	// first thing first, suspend fatalities.
419	<	int masterNode = 0;
420	<	int nCurObj;
421	<	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);
408	>	case 'v' : {
409	>	Vector3d vel;
410	>	vel[0] = tokenizer.nextTokenAsDouble();
411	>	vel[1] = tokenizer.nextTokenAsDouble();
412	>	vel[2] = tokenizer.nextTokenAsDouble();
413	>	if (needVel_) {
414	>	sd->setVel(vel);
415	>	}
416	>	break;
417	>	}
418	>
419	>	case 'q' : {
420	>	Quat4d q;
421	>	if (sd->isDirectional()) {
422
423	<	painCave.isFatal = 1;
424	<	simError();
425	<	}
426	<
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);
423	>	q[0] = tokenizer.nextTokenAsDouble();
424	>	q[1] = tokenizer.nextTokenAsDouble();
425	>	q[2] = tokenizer.nextTokenAsDouble();
426	>	q[3] = tokenizer.nextTokenAsDouble();
427
428	<	painCave.isFatal = 1;
429	<	simError();
430	<	}
431	<
432	<	MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
433	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
428	>	RealType qlen = q.length();
429	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
430	>
431	>	sprintf(painCave.errMsg,
432	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
433	>	painCave.isFatal = 1;
434	>	simError();
435	>
436	>	}
437	>
438	>	q.normalize();
439	>	if (needQuaternion_) {
440	>	sd->setQ(q);
441	>	}
442	>	}
443	>	break;
444	>	}
445	>	case 'j' : {
446	>	Vector3d ji;
447	>	if (sd->isDirectional()) {
448	>	ji[0] = tokenizer.nextTokenAsDouble();
449	>	ji[1] = tokenizer.nextTokenAsDouble();
450	>	ji[2] = tokenizer.nextTokenAsDouble();
451	>	if (needAngMom_) {
452	>	sd->setJ(ji);
453	>	}
454		}
455	+	break;
456	+	}
457	+	case 'f': {
458	+
459	+	Vector3d force;
460	+	force[0] = tokenizer.nextTokenAsDouble();
461	+	force[1] = tokenizer.nextTokenAsDouble();
462	+	force[2] = tokenizer.nextTokenAsDouble();
463	+	sd->setFrc(force);
464	+	break;
465		}
466	<	}
467	<	} else {
468	<	//actions taken at slave nodes
469	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
470	<
471	<	/**@todo*/
472	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
473	<
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	<
466	>	case 't' : {
467	>
468	>	Vector3d torque;
469	>	torque[0] = tokenizer.nextTokenAsDouble();
470	>	torque[1] = tokenizer.nextTokenAsDouble();
471	>	torque[2] = tokenizer.nextTokenAsDouble();
472	>	sd->setTrq(torque);
473	>	break;
474		}
475	<
475	>	case 'u' : {
476	>
477	>	RealType particlePot;
478	>	particlePot = tokenizer.nextTokenAsDouble();
479	>	sd->setParticlePot(particlePot);
480	>	break;
481	>	}
482	>	case 'c' : {
483	>
484	>	RealType flucQPos;
485	>	flucQPos = tokenizer.nextTokenAsDouble();
486	>	sd->setFlucQPos(flucQPos);
487	>	break;
488	>	}
489	>	case 'w' : {
490	>
491	>	RealType flucQVel;
492	>	flucQVel = tokenizer.nextTokenAsDouble();
493	>	sd->setFlucQVel(flucQVel);
494	>	break;
495	>	}
496	>	case 'g' : {
497	>
498	>	RealType flucQFrc;
499	>	flucQFrc = tokenizer.nextTokenAsDouble();
500	>	sd->setFlucQFrc(flucQFrc);
501	>	break;
502	>	}
503	>	case 'e' : {
504	>
505	>	Vector3d eField;
506	>	eField[0] = tokenizer.nextTokenAsDouble();
507	>	eField[1] = tokenizer.nextTokenAsDouble();
508	>	eField[2] = tokenizer.nextTokenAsDouble();
509	>	sd->setElectricField(eField);
510	>	break;
511	>	}
512	>	case 's' : {
513	>
514	>	RealType sPot;
515	>	sPot = tokenizer.nextTokenAsDouble();
516	>	sd->setSitePotential(sPot);
517	>	break;
518	>	}
519	>	default: {
520	>	sprintf(painCave.errMsg,
521	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
522	>	painCave.isFatal = 1;
523	>	simError();
524	>	break;
525	>	}
526	>
527		}
495	–
528		}
529	<
530	<	#endif
531	<
532	<	}
533	<
534	<	void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
535	<
536	<	Vector3d pos;  // position place holders
537	<	Vector3d vel;  // velocity placeholders
538	<	Quat4d q;    // the quaternions
539	<	Vector3d ji;   // angular velocity placeholders;
540	<	StringTokenizer tokenizer(line);
541	<	int nTokens;
542	<
543	<	nTokens = tokenizer.countTokens();
544	<
545	<	if (nTokens < 14) {
546	<	sprintf(painCave.errMsg,
547	<	"DumpReader Error: Not enough Tokens.\n%s\n", line);
548	<	painCave.isFatal = 1;
549	<	simError();
550	<	}
551	<
552	<	std::string name = tokenizer.nextToken();
553	<
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);
529	>	}
530	>
531	>
532	>	void DumpReader::parseSiteLine(const std::string& line) {
533	>
534	>	StringTokenizer tokenizer(line);
535	>	int nTokens;
536	>
537	>	nTokens = tokenizer.countTokens();
538	>
539	>	if (nTokens < 2) {
540	>	sprintf(painCave.errMsg,
541	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
542	>	painCave.isFatal = 1;
543	>	simError();
544	>	}
545	>
546	>	/**
547	>	* The first token is the global integrable object index.
548	>	*/
549	>
550	>	int index = tokenizer.nextTokenAsInt();
551	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
552	>	if (sd == NULL) {
553	>	return;
554		}
555	<
556	<	vel[0] = tokenizer.nextTokenAsDouble();
557	<	vel[1] = tokenizer.nextTokenAsDouble();
558	<	vel[2] = tokenizer.nextTokenAsDouble();
559	<	if (needVel_) {
560	<	integrableObject->setVel(vel);
555	>
556	>	/**
557	>	* Test to see if the next token is an integer or not.  If not,
558	>	* we've got data on the integrable object itself.  If there is an
559	>	* integer, we're parsing data for a site on a rigid body.
560	>	*/
561	>
562	>	std::string indexTest = tokenizer.peekNextToken();
563	>	std::istringstream i(indexTest);
564	>	int siteIndex;
565	>	if (i >> siteIndex) {
566	>	// chew up this token and parse as an int:
567	>	siteIndex = tokenizer.nextTokenAsInt();
568	>
569	>	if (sd->isRigidBody()) {
570	>	RigidBody* rb = static_cast<RigidBody*>(sd);
571	>	sd = rb->getAtoms()[siteIndex];
572	>	}
573		}
574	+
575	+	/**
576	+	* The next token contains information on what follows.
577	+	*/
578	+	std::string type = tokenizer.nextToken();
579	+	int size = type.size();
580
581	<	if (integrableObject->isDirectional()) {
582	<
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
581	>	for(int i = 0; i < size; ++i) {
582	>	switch(type[i]) {
583
584	<	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();
584	>	case 'u' : {
585
586	<	}
587	<
588	<	q.normalize();
589	<	if (needQuaternion_) {
564	<	integrableObject->setQ(q);
586	>	RealType particlePot;
587	>	particlePot = tokenizer.nextTokenAsDouble();
588	>	sd->setParticlePot(particlePot);
589	>	break;
590		}
591	<
592	<	ji[0] = tokenizer.nextTokenAsDouble();
593	<	ji[1] = tokenizer.nextTokenAsDouble();
594	<	ji[2] = tokenizer.nextTokenAsDouble();
595	<	if (needAngMom_) {
596	<	integrableObject->setJ(ji);
591	>	case 'c' : {
592	>
593	>	RealType flucQPos;
594	>	flucQPos = tokenizer.nextTokenAsDouble();
595	>	sd->setFlucQPos(flucQPos);
596	>	break;
597		}
598	<	}
599	<
600	<	}
598	>	case 'w' : {
599	>
600	>	RealType flucQVel;
601	>	flucQVel = tokenizer.nextTokenAsDouble();
602	>	sd->setFlucQVel(flucQVel);
603	>	break;
604	>	}
605	>	case 'g' : {
606	>
607	>	RealType flucQFrc;
608	>	flucQFrc = tokenizer.nextTokenAsDouble();
609	>	sd->setFlucQFrc(flucQFrc);
610	>	break;
611	>	}
612	>	case 'e' : {
613	>
614	>	Vector3d eField;
615	>	eField[0] = tokenizer.nextTokenAsDouble();
616	>	eField[1] = tokenizer.nextTokenAsDouble();
617	>	eField[2] = tokenizer.nextTokenAsDouble();
618	>	sd->setElectricField(eField);
619	>	break;
620	>	}
621	>	case 's' : {
622	>
623	>	RealType sPot;
624	>	sPot = tokenizer.nextTokenAsDouble();
625	>	sd->setSitePotential(sPot);
626	>	break;
627	>	}
628	>	default: {
629	>	sprintf(painCave.errMsg,
630	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
631	>	painCave.isFatal = 1;
632	>	simError();
633	>	break;
634	>	}
635	>	}
636	>	}
637	>	}
638
639
640	<	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
579	<	double currTime;
580	<	Mat3x3d hmat;
581	<	double chi;
582	<	double integralOfChiDt;
583	<	Mat3x3d eta;
640	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
641
642	<	StringTokenizer tokenizer(line);
643	<	int nTokens;
642	>	inputStream.getline(buffer, bufferSize);
643	>	std::string line(buffer);
644
645	<	nTokens = tokenizer.countTokens();
646	<
647	<	//comment line should at least contain 10 tokens: current time(1 token) and  h-matrix(9 tokens)
648	<	if (nTokens < 10) {
649	<	sprintf(painCave.errMsg,
593	<	"DumpReader Error: Not enough tokens in comment line: %s", line);
594	<	painCave.isFatal = 1;
595	<	simError();
645	>	if (line.find("<StuntDoubles>") == std::string::npos) {
646	>	sprintf(painCave.errMsg,
647	>	"DumpReader Error: Missing <StuntDoubles>\n");
648	>	painCave.isFatal = 1;
649	>	simError();
650		}
651	<
652	<	//read current time
653	<	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();
651	>
652	>	while(inputStream.getline(buffer, bufferSize)) {
653	>	line = buffer;
654
655	<	s->setChi(chi);
656	<	s->setIntegralOfChiDt(integralOfChiDt);
655	>	if(line.find("</StuntDoubles>") != std::string::npos) {
656	>	break;
657	>	}
658	>
659	>	parseDumpLine(line);
660		}
661	+
662	+	}
663	+
664	+	void  DumpReader::readSiteData(std::istream& inputStream) {
665	+
666	+	std::string line(buffer);
667	+
668	+	// We already found the starting <SiteData> tag or we wouldn't be
669	+	// here, so just start parsing until we get to the ending
670	+	// </SiteData> tag:
671
672	<	//read eta (eta is 3x3 matrix)
673	<	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();
672	>	while(inputStream.getline(buffer, bufferSize)) {
673	>	line = buffer;
674
675	<	s->setEta(eta);
675	>	if(line.find("</SiteData>") != std::string::npos) {
676	>	break;
677	>	}
678	>
679	>	parseSiteLine(line);
680		}
637	–
638	–
639	–	}
681
682	<	}//end namespace oopse
682	>	}
683	>
684	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
685	>
686	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
687	>	inputStream.getline(buffer, bufferSize);
688	>	std::string line(buffer);
689	>
690	>	if (line.find("<FrameData>") == std::string::npos) {
691	>	sprintf(painCave.errMsg,
692	>	"DumpReader Error: Missing <FrameData>\n");
693	>	painCave.isFatal = 1;
694	>	simError();
695	>	}
696	>
697	>	while(inputStream.getline(buffer, bufferSize)) {
698	>	line = buffer;
699	>
700	>	if(line.find("</FrameData>") != std::string::npos) {
701	>	break;
702	>	}
703	>
704	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
705	>	if (!tokenizer.hasMoreTokens()) {
706	>	sprintf(painCave.errMsg,
707	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
708	>	painCave.isFatal = 1;
709	>	simError();
710	>	}
711	>
712	>	std::string propertyName = tokenizer.nextToken();
713	>	if (propertyName == "Time") {
714	>	RealType currTime = tokenizer.nextTokenAsDouble();
715	>	s->setTime(currTime);
716	>	} else if (propertyName == "Hmat"){
717	>	Mat3x3d hmat;
718	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
719	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
720	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
721	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
722	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
723	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
724	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
725	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
726	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
727	>	s->setHmat(hmat);
728	>	} else if (propertyName == "Thermostat") {
729	>	pair<RealType, RealType> thermostat;
730	>	thermostat.first = tokenizer.nextTokenAsDouble();
731	>	thermostat.second = tokenizer.nextTokenAsDouble();
732	>	s->setThermostat(thermostat);
733	>	} else if (propertyName == "Barostat") {
734	>	Mat3x3d eta;
735	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
736	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
737	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
738	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
739	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
740	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
741	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
742	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
743	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
744	>	s->setBarostat(eta);
745	>	} else {
746	>	sprintf(painCave.errMsg,
747	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
748	>	painCave.isFatal = 0;
749	>	simError();
750	>	}
751	>
752	>	}
753	>
754	>	}
755	>
756	>
757	>	}//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 2069 by gezelter, Thu Mar 5 16:30:23 2015 UTC

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