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

Comparing:
trunk/src/io/DumpReader.cpp (file contents), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 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, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
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	>	#include <sys/types.h>
47	>	#include <sys/stat.h>
48	>
49	>	#include <iostream>
50	>	#include <math.h>
51	>
52	>	#include <stdio.h>
53	>	#include <stdlib.h>
54	>	#include <string.h>
55	>
56	>	#include "io/DumpReader.hpp"
57	>	#include "primitives/Molecule.hpp"
58	>	#include "utils/simError.h"
59	>	#include "utils/MemoryUtils.hpp"
60	>	#include "utils/StringTokenizer.hpp"
61	>	#include "brains/Thermo.hpp"
62	>
63	>	#ifdef IS_MPI
64	>	#include <mpi.h>
65	>	#endif
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	>	int lineNo = 0;
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	<
156	<	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	>	while(inFile_->getline(buffer, bufferSize)) {
146	>	++lineNo;
147
148	<	i = atoi(readBuffer);
149	<
150	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
151	<	lineNum++;
152	<
153	<	if (feof(inFile_)) {
154	<	sprintf(painCave.errMsg,
155	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
156	<	filename_.c_str(),
157	<	lineNum);
158	<	painCave.isFatal = 1;
159	<	simError();
160	<	}
181	<
182	<	for(j = 0; j < i; j++) {
183	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
184	<	lineNum++;
148	>	std::string line = buffer;
149	>	currPos = inFile_->tellg();
150	>	if (line.find("<Snapshot>")!= std::string::npos) {
151	>	if (foundOpenSnapshotTag) {
152	>	sprintf(painCave.errMsg,
153	>	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
154	>	filename_.c_str());
155	>	painCave.isFatal = 1;
156	>	simError();
157	>	}
158	>	foundOpenSnapshotTag = true;
159	>	foundClosedSnapshotTag = false;
160	>	framePos_.push_back(prevPos);
161
162	<	if (feof(inFile_)) {
163	<	sprintf(painCave.errMsg,
164	<	"DumpReader Error: File \"%s\" ended unexpectedly at line %d,"
165	<	" with atom %d\n", filename_.c_str(),
166	<	lineNum,
167	<	j);
168	<
193	<	painCave.isFatal = 1;
194	<	simError();
162	>	} else if (line.find("</Snapshot>") != std::string::npos){
163	>	if (!foundOpenSnapshotTag) {
164	>	sprintf(painCave.errMsg,
165	>	"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
166	>	filename_.c_str());
167	>	painCave.isFatal = 1;
168	>	simError();
169		}
170	+
171	+	if (foundClosedSnapshotTag) {
172	+	sprintf(painCave.errMsg,
173	+	"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
174	+	filename_.c_str());
175	+	painCave.isFatal = 1;
176	+	simError();
177	+	}
178	+	foundClosedSnapshotTag = true;
179	+	foundOpenSnapshotTag = false;
180		}
181	<
198	<	currPos = new fpos_t;
199	<	fgetpos(inFile_, currPos);
200	<	fgets(readBuffer, sizeof(readBuffer), inFile_);
201	<	lineNum++;
181	>	prevPos = currPos;
182		}
183
184	<	delete currPos;
185	<	rewind(inFile_);
184	>	// only found <Snapshot> for the last frame means the file is corrupted, we should discard
185	>	// it and give a warning message
186	>	if (foundOpenSnapshotTag) {
187	>	sprintf(painCave.errMsg,
188	>	"DumpReader: last frame in %s is invalid\n", filename_.c_str());
189	>	painCave.isFatal = 0;
190	>	simError();
191	>	framePos_.pop_back();
192	>	}
193
194	<	nframes_ = framePos_.size();
195	<	#ifdef IS_MPI
196	<	}
194	>	nframes_ = framePos_.size();
195	>
196	>	if (nframes_ == 0) {
197	>	sprintf(painCave.errMsg,
198	>	"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
199	>	painCave.isFatal = 1;
200	>	simError();
201	>	}
202	>	#ifdef IS_MPI
203	>	}
204	>
205	>	MPI::COMM_WORLD.Bcast(&nframes_, 1, MPI::INT, 0);
206
207	<	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
207	>	#endif // is_mpi
208
209	<	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
210	<	MPIcheckPoint();
211	<
212	<	#endif // is_mpi
213	<
214	<	isScanned_ = true;
215	<	}
216	<
217	<	void DumpReader::readFrame(int whichFrame) {
218	<	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
219	<
220	<	if (storageLayout & DataStorage::dslPosition) {
221	<	needPos_ = true;
222	<	} else {
223	<	needPos_ = false;
209	>	isScanned_ = true;
210	>	}
211	>
212	>	void DumpReader::readFrame(int whichFrame) {
213	>	if (!isScanned_)
214	>	scanFile();
215	>
216	>	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
217	>
218	>	if (storageLayout & DataStorage::dslPosition) {
219	>	needPos_ = true;
220	>	} else {
221	>	needPos_ = false;
222	>	}
223	>
224	>	if (storageLayout & DataStorage::dslVelocity) {
225	>	needVel_ = true;
226	>	} else {
227	>	needVel_ = false;
228	>	}
229	>
230	>	if (storageLayout & DataStorage::dslAmat ||
231	>	storageLayout & DataStorage::dslDipole ||
232	>	storageLayout & DataStorage::dslQuadrupole) {
233	>	needQuaternion_ = true;
234	>	} else {
235	>	needQuaternion_ = false;
236	>	}
237	>
238	>	if (storageLayout & DataStorage::dslAngularMomentum) {
239	>	needAngMom_ = true;
240	>	} else {
241	>	needAngMom_ = false;
242	>	}
243	>
244	>	readSet(whichFrame);
245	>
246	>	if (needCOMprops_) {
247	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
248	>	Thermo thermo(info_);
249	>	Vector3d com;
250	>
251	>	if (needPos_ && needVel_) {
252	>	Vector3d comvel;
253	>	Vector3d comw;
254	>	thermo.getComAll(com, comvel);
255	>	comw = thermo.getAngularMomentum();
256	>	} else {
257	>	com = thermo.getCom();
258	>	}
259		}
260	<
261	<	if (storageLayout & DataStorage::dslVelocity) {
262	<	needVel_ = 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::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
292	>	MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize,
293	>	MPI::CHAR, masterNode);
294	>
295	>	sstream.str(sendBuffer);
296		} else {
297	<	needVel_ = false;
298	<	}
297	>	int sendBufferSize;
298	>	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
299	>	char * recvBuffer = new char[sendBufferSize+1];
300	>	assert(recvBuffer);
301	>	recvBuffer[sendBufferSize] = '\0';
302	>	MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
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::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
321	<	needQuaternion_ = 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	<	needQuaternion_ = 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	<	if (storageLayout & DataStorage::dslAngularMomentum) {
342	<	needAngMom_ = true;
343	<	} else {
344	<	needAngMom_ = false;
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	<	readSet(whichFrame);
370	<	}
371	<
372	<	void DumpReader::readSet(int whichFrame) {
373	<	int i;
374	<	int nTotObjs;                  // the number of atoms
375	<	char read_buffer[maxBufferSize];  //the line buffer for reading
376	<	char * eof_test;               // ptr to see when we reach the end of the file
377	<
378	<	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();
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	<	nTotObjs = atoi(read_buffer);
382	<
383	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
384	<	sprintf(painCave.errMsg,
385	<	"DumpReader error. %s nIntegrable, %d, "
386	<	"does not match the meta-data file's nIntegrable, %d.\n",
387	<	filename_.c_str(),
388	<	nTotObjs,
389	<	info_->getNGlobalIntegrableObjects());
390	<
391	<	painCave.isFatal = 1;
392	<	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	<	//read the box mat from the comment line
396	<
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)) {
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++;
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	>	q[0] = tokenizer.nextTokenAsDouble();
424	>	q[1] = tokenizer.nextTokenAsDouble();
425	>	q[2] = tokenizer.nextTokenAsDouble();
426	>	q[3] = tokenizer.nextTokenAsDouble();
427	>
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	>	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	>	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	>	default: {
513	>	sprintf(painCave.errMsg,
514	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
515	>	painCave.isFatal = 1;
516	>	simError();
517	>	break;
518	>	}
519	>
520		}
521		}
522	+
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	+	/**
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	+	RigidBody* rb = static_cast<RigidBody*>(sd);
563	+	sd = rb->getAtoms()[siteIndex];
564	+	}
565	+
566	+	/**
567	+	* The next token contains information on what follows.
568	+	*/
569	+	std::string type = tokenizer.nextToken();
570	+	int size = type.size();
571
572	<	// MPI Section of code..........
573	<
574	<	#else //IS_MPI
575	<
576	<	// first thing first, suspend fatalities.
577	<	int masterNode = 0;
578	<	int nCurObj;
579	<	painCave.isEventLoop = 1;
580	<
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();
572	>	for(int i = 0; i < size; ++i) {
573	>	switch(type[i]) {
574	>
575	>	case 'u' : {
576	>
577	>	RealType particlePot;
578	>	particlePot = tokenizer.nextTokenAsDouble();
579	>	sd->setParticlePot(particlePot);
580	>	break;
581		}
582	<
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());
582	>	case 'c' : {
583
584	<	painCave.isFatal = 1;
585	<	simError();
584	>	RealType flucQPos;
585	>	flucQPos = tokenizer.nextTokenAsDouble();
586	>	sd->setFlucQPos(flucQPos);
587	>	break;
588		}
589	<
590	<	//read the boxMat from the comment line
591	<
592	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
593	<
594	<	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();
589	>	case 'w' : {
590	>
591	>	RealType flucQVel;
592	>	flucQVel = tokenizer.nextTokenAsDouble();
593	>	sd->setFlucQVel(flucQVel);
594	>	break;
595		}
596	<
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);
596	>	case 'g' : {
597
598	<	if (which_node == masterNode) {
599	<	//molecules belong to master node
600	<
601	<	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);
424	<
425	<	painCave.isFatal = 1;
426	<	simError();
427	<	}
428	<
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);
448	<
449	<	painCave.isFatal = 1;
450	<	simError();
451	<	}
452	<
453	<	MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
454	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
455	<	}
456	<	}
598	>	RealType flucQFrc;
599	>	flucQFrc = tokenizer.nextTokenAsDouble();
600	>	sd->setFlucQFrc(flucQFrc);
601	>	break;
602		}
603	<	} else {
459	<	//actions taken at slave nodes
460	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
461	<
462	<	/**@todo*/
463	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
464	<
465	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
466	<	int which_node = info_->getMolToProc(i);
603	>	case 'e' : {
604
605	<	if (which_node == worldRank) {
606	<	//molecule with global index i belongs to this processor
607	<
608	<	mol = info_->getMoleculeByGlobalIndex(i);
609	<	if (mol == NULL) {
610	<	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	<
492	<	}
493	<
605	>	Vector3d eField;
606	>	eField[0] = tokenizer.nextTokenAsDouble();
607	>	eField[1] = tokenizer.nextTokenAsDouble();
608	>	eField[2] = tokenizer.nextTokenAsDouble();
609	>	sd->setElectricField(eField);
610	>	break;
611		}
612	<
613	<	}
614	<
615	<	#endif
616	<
617	<	}
612	>	default: {
613	>	sprintf(painCave.errMsg,
614	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
615	>	painCave.isFatal = 1;
616	>	simError();
617	>	break;
618	>	}
619	>	}
620	>	}
621	>	}
622
623	<	void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
623	>
624	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
625
626	<	Vector3d pos;  // position place holders
627	<	Vector3d vel;  // velocity placeholders
506	<	Quat4d q;    // the quaternions
507	<	Vector3d ji;   // angular velocity placeholders;
508	<	StringTokenizer tokenizer(line);
509	<	int nTokens;
626	>	inputStream.getline(buffer, bufferSize);
627	>	std::string line(buffer);
628
629	<	nTokens = tokenizer.countTokens();
630	<
631	<	if (nTokens < 14) {
632	<	sprintf(painCave.errMsg,
633	<	"DumpReader Error: Not enough Tokens.\n%s\n", line);
516	<	painCave.isFatal = 1;
517	<	simError();
629	>	if (line.find("<StuntDoubles>") == std::string::npos) {
630	>	sprintf(painCave.errMsg,
631	>	"DumpReader Error: Missing <StuntDoubles>\n");
632	>	painCave.isFatal = 1;
633	>	simError();
634		}
635	<
636	<	std::string name = tokenizer.nextToken();
637	<
522	<	if (name != integrableObject->getType()) {
635	>
636	>	while(inputStream.getline(buffer, bufferSize)) {
637	>	line = buffer;
638
639	<	sprintf(painCave.errMsg,
640	<	"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
641	<	name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
642	<	painCave.isFatal = 1;
643	<	simError();
639	>	if(line.find("</StuntDoubles>") != std::string::npos) {
640	>	break;
641	>	}
642	>
643	>	parseDumpLine(line);
644		}
645	+
646	+	}
647	+
648	+	void  DumpReader::readSiteData(std::istream& inputStream) {
649	+
650	+	inputStream.getline(buffer, bufferSize);
651	+	std::string line(buffer);
652
653	<	pos[0] = tokenizer.nextTokenAsDouble();
654	<	pos[1] = tokenizer.nextTokenAsDouble();
655	<	pos[2] = tokenizer.nextTokenAsDouble();
534	<	if (needPos_) {
535	<	integrableObject->setPos(pos);
653	>	if (line.find("<SiteData>") == std::string::npos) {
654	>	// site data isn't required for a simulation, so skip
655	>	return;
656		}
657	<
658	<	vel[0] = tokenizer.nextTokenAsDouble();
659	<	vel[1] = tokenizer.nextTokenAsDouble();
540	<	vel[2] = tokenizer.nextTokenAsDouble();
541	<	if (needVel_) {
542	<	integrableObject->setVel(vel);
543	<	}
544	<
545	<	if (integrableObject->isDirectional()) {
657	>
658	>	while(inputStream.getline(buffer, bufferSize)) {
659	>	line = buffer;
660
661	<	q[0] = tokenizer.nextTokenAsDouble();
662	<	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
554	<
555	<	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();
559	<
560	<	}
561	<
562	<	q.normalize();
563	<	if (needQuaternion_) {
564	<	integrableObject->setQ(q);
661	>	if(line.find("</SiteData>") != std::string::npos) {
662	>	break;
663		}
664	<
665	<	ji[0] = tokenizer.nextTokenAsDouble();
568	<	ji[1] = tokenizer.nextTokenAsDouble();
569	<	ji[2] = tokenizer.nextTokenAsDouble();
570	<	if (needAngMom_) {
571	<	integrableObject->setJ(ji);
572	<	}
664	>
665	>	parseSiteLine(line);
666		}
574	–
575	–	}
667
668	<
669	<	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
670	<	double currTime;
671	<	Mat3x3d hmat;
672	<	double chi;
673	<	double integralOfChiDt;
674	<	Mat3x3d eta;
675	<
676	<	StringTokenizer tokenizer(line);
677	<	int nTokens;
678	<
679	<	nTokens = tokenizer.countTokens();
680	<
590	<	//comment line should at least contain 10 tokens: current time(1 token) and  h-matrix(9 tokens)
591	<	if (nTokens < 10) {
592	<	sprintf(painCave.errMsg,
593	<	"DumpReader Error: Not enough tokens in comment line: %s", line);
594	<	painCave.isFatal = 1;
595	<	simError();
668	>	}
669	>
670	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
671	>
672	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
673	>	inputStream.getline(buffer, bufferSize);
674	>	std::string line(buffer);
675	>
676	>	if (line.find("<FrameData>") == std::string::npos) {
677	>	sprintf(painCave.errMsg,
678	>	"DumpReader Error: Missing <FrameData>\n");
679	>	painCave.isFatal = 1;
680	>	simError();
681		}
682	<
683	<	//read current time
684	<	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();
682	>
683	>	while(inputStream.getline(buffer, bufferSize)) {
684	>	line = buffer;
685
686	<	s->setChi(chi);
687	<	s->setIntegralOfChiDt(integralOfChiDt);
688	<	}
622	<
623	<	//read eta (eta is 3x3 matrix)
624	<	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();
686	>	if(line.find("</FrameData>") != std::string::npos) {
687	>	break;
688	>	}
689
690	<	s->setEta(eta);
690	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
691	>	if (!tokenizer.hasMoreTokens()) {
692	>	sprintf(painCave.errMsg,
693	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
694	>	painCave.isFatal = 1;
695	>	simError();
696	>	}
697	>
698	>	std::string propertyName = tokenizer.nextToken();
699	>	if (propertyName == "Time") {
700	>	RealType currTime = tokenizer.nextTokenAsDouble();
701	>	s->setTime(currTime);
702	>	} else if (propertyName == "Hmat"){
703	>	Mat3x3d hmat;
704	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
705	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
706	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
707	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
708	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
709	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
710	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
711	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
712	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
713	>	s->setHmat(hmat);
714	>	} else if (propertyName == "Thermostat") {
715	>	pair<RealType, RealType> thermostat;
716	>	thermostat.first = tokenizer.nextTokenAsDouble();
717	>	thermostat.second = tokenizer.nextTokenAsDouble();
718	>	s->setThermostat(thermostat);
719	>	} else if (propertyName == "Barostat") {
720	>	Mat3x3d eta;
721	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
722	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
723	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
724	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
725	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
726	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
727	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
728	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
729	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
730	>	s->setBarostat(eta);
731	>	} else {
732	>	sprintf(painCave.errMsg,
733	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
734	>	painCave.isFatal = 0;
735	>	simError();
736	>	}
737	>
738		}
739	<
638	<
739	>
740		}
741	<
742	<	}//end namespace oopse
741	>
742	>
743	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpReader.cpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/io/DumpReader.cpp (property svn:keywords), Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 UTC

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