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

Comparing:
trunk/src/io/DumpReader.cpp (file contents), Revision 601 by tim, Thu Sep 15 19:17:04 2005 UTC vs.
branches/development/src/io/DumpReader.cpp (file contents), Revision 1794 by gezelter, Thu Sep 6 19:44:06 2012 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	>	bool foundOpenSiteDataTag = false;
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_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
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	<	if (!isScanned_)
219	<	scanFile();
220	<
221	<	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
222	<
223	<	if (storageLayout & DataStorage::dslPosition) {
224	<	needPos_ = true;
225	<	} else {
226	<	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_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
292	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
293	>
294	>	sstream.str(sendBuffer);
295		} else {
296	<	needVel_ = false;
297	<	}
296	>	int sendBufferSize;
297	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
298	>	char * recvBuffer = new char[sendBufferSize+1];
299	>	assert(recvBuffer);
300	>	recvBuffer[sendBufferSize] = '\0';
301	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
302	>	sstream.str(recvBuffer);
303	>	delete [] recvBuffer;
304	>	}
305	>
306	>	std::istream& inputStream = sstream;
307	>	#endif
308	>
309	>	inputStream.getline(buffer, bufferSize);
310	>
311	>	line = buffer;
312	>	if (line.find("<Snapshot>") == std::string::npos) {
313	>	sprintf(painCave.errMsg,
314	>	"DumpReader Error: can not find <Snapshot>\n");
315	>	painCave.isFatal = 1;
316	>	simError();
317	>	}
318
319	<	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
320	<	needQuaternion_ = true;
319	>	//read frameData
320	>	readFrameProperties(inputStream);
321	>
322	>	//read StuntDoubles
323	>	readStuntDoubles(inputStream);
324	>
325	>	inputStream.getline(buffer, bufferSize);
326	>	line = buffer;
327	>
328	>	if (line.find("<SiteData>") != std::string::npos) {
329	>	//read SiteData
330	>	readSiteData(inputStream);
331		} else {
332	<	needQuaternion_ = false;
332	>	if (line.find("</Snapshot>") == std::string::npos) {
333	>	sprintf(painCave.errMsg,
334	>	"DumpReader Error: can not find </Snapshot>\n");
335	>	painCave.isFatal = 1;
336	>	simError();
337	>	}
338		}
339	<
340	<	if (storageLayout & DataStorage::dslAngularMomentum) {
341	<	needAngMom_ = true;
342	<	} else {
343	<	needAngMom_ = false;
339	>	}
340	>
341	>	void DumpReader::parseDumpLine(const std::string& line) {
342	>
343	>
344	>	StringTokenizer tokenizer(line);
345	>	int nTokens;
346	>
347	>	nTokens = tokenizer.countTokens();
348	>
349	>	if (nTokens < 2) {
350	>	sprintf(painCave.errMsg,
351	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
352	>	painCave.isFatal = 1;
353	>	simError();
354	>	}
355	>
356	>	int index = tokenizer.nextTokenAsInt();
357	>
358	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
359	>
360	>	if (sd == NULL) {
361	>	return;
362		}
363	+	std::string type = tokenizer.nextToken();
364	+	int size = type.size();
365	+
366	+	size_t found;
367
368	<	readSet(whichFrame);
369	<	}
370	<
371	<	void DumpReader::readSet(int whichFrame) {
372	<	int i;
373	<	int nTotObjs;                  // the number of atoms
374	<	char read_buffer[maxBufferSize];  //the line buffer for reading
375	<	char * eof_test;               // ptr to see when we reach the end of the file
376	<
377	<	Molecule* mol;
261	<	StuntDouble* integrableObject;
262	<	SimInfo::MoleculeIterator mi;
263	<	Molecule::IntegrableObjectIterator ii;
264	<
265	<	#ifndef IS_MPI
266	<
267	<	fsetpos(inFile_, framePos_[whichFrame]);
268	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
269	<
270	<	if (eof_test == NULL) {
271	<	sprintf(painCave.errMsg,
272	<	"DumpReader error: error reading 1st line of \"%s\"\n",
273	<	filename_.c_str());
274	<	painCave.isFatal = 1;
275	<	simError();
368	>	if (needPos_) {
369	>	found = type.find("p");
370	>	if (found == std::string::npos) {
371	>	sprintf(painCave.errMsg,
372	>	"DumpReader Error: StuntDouble %d has no Position\n"
373	>	"\tField (\"p\") specified.\n%s\n", index,
374	>	line.c_str());
375	>	painCave.isFatal = 1;
376	>	simError();
377	>	}
378		}
379
380	<	nTotObjs = atoi(read_buffer);
381	<
382	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
383	<	sprintf(painCave.errMsg,
384	<	"DumpReader error. %s nIntegrable, %d, "
385	<	"does not match the meta-data file's nIntegrable, %d.\n",
386	<	filename_.c_str(),
387	<	nTotObjs,
388	<	info_->getNGlobalIntegrableObjects());
389	<
390	<	painCave.isFatal = 1;
391	<	simError();
380	>	if (sd->isDirectional()) {
381	>	if (needQuaternion_) {
382	>	found = type.find("q");
383	>	if (found == std::string::npos) {
384	>	sprintf(painCave.errMsg,
385	>	"DumpReader Error: Directional StuntDouble %d has no\n"
386	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
387	>	line.c_str());
388	>	painCave.isFatal = 1;
389	>	simError();
390	>	}
391	>	}
392		}
393	<
394	<	//read the box mat from the comment line
395	<
294	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
295	<
296	<	if (eof_test == NULL) {
297	<	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
298	<	filename_.c_str());
299	<	painCave.isFatal = 1;
300	<	simError();
301	<	}
302	<
303	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
304	<
305	<	//parse dump lines
306	<
307	<	i = 0;
308	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
309	<
310	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
311	<	integrableObject = mol->nextIntegrableObject(ii)) {
393	>
394	>	for(int i = 0; i < size; ++i) {
395	>	switch(type[i]) {
396
397	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
398	<
399	<	if (eof_test == NULL) {
400	<	sprintf(painCave.errMsg,
401	<	"DumpReader Error: error in reading file %s\n"
402	<	"natoms  = %d; index = %d\n"
403	<	"error reading the line from the file.\n",
404	<	filename_.c_str(),
405	<	nTotObjs,
322	<	i);
323	<
324	<	painCave.isFatal = 1;
325	<	simError();
397	>	case 'p': {
398	>	Vector3d pos;
399	>	pos[0] = tokenizer.nextTokenAsDouble();
400	>	pos[1] = tokenizer.nextTokenAsDouble();
401	>	pos[2] = tokenizer.nextTokenAsDouble();
402	>	if (needPos_) {
403	>	sd->setPos(pos);
404	>	}
405	>	break;
406		}
407	<
408	<	parseDumpLine(read_buffer, integrableObject);
409	<	i++;
407	>	case 'v' : {
408	>	Vector3d vel;
409	>	vel[0] = tokenizer.nextTokenAsDouble();
410	>	vel[1] = tokenizer.nextTokenAsDouble();
411	>	vel[2] = tokenizer.nextTokenAsDouble();
412	>	if (needVel_) {
413	>	sd->setVel(vel);
414	>	}
415	>	break;
416	>	}
417	>
418	>	case 'q' : {
419	>	Quat4d q;
420	>	if (sd->isDirectional()) {
421	>
422	>	q[0] = tokenizer.nextTokenAsDouble();
423	>	q[1] = tokenizer.nextTokenAsDouble();
424	>	q[2] = tokenizer.nextTokenAsDouble();
425	>	q[3] = tokenizer.nextTokenAsDouble();
426	>
427	>	RealType qlen = q.length();
428	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
429	>
430	>	sprintf(painCave.errMsg,
431	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
432	>	painCave.isFatal = 1;
433	>	simError();
434	>
435	>	}
436	>
437	>	q.normalize();
438	>	if (needQuaternion_) {
439	>	sd->setQ(q);
440	>	}
441	>	}
442	>	break;
443	>	}
444	>	case 'j' : {
445	>	Vector3d ji;
446	>	if (sd->isDirectional()) {
447	>	ji[0] = tokenizer.nextTokenAsDouble();
448	>	ji[1] = tokenizer.nextTokenAsDouble();
449	>	ji[2] = tokenizer.nextTokenAsDouble();
450	>	if (needAngMom_) {
451	>	sd->setJ(ji);
452	>	}
453	>	}
454	>	break;
455	>	}
456	>	case 'f': {
457	>
458	>	Vector3d force;
459	>	force[0] = tokenizer.nextTokenAsDouble();
460	>	force[1] = tokenizer.nextTokenAsDouble();
461	>	force[2] = tokenizer.nextTokenAsDouble();
462	>	sd->setFrc(force);
463	>	break;
464	>	}
465	>	case 't' : {
466	>
467	>	Vector3d torque;
468	>	torque[0] = tokenizer.nextTokenAsDouble();
469	>	torque[1] = tokenizer.nextTokenAsDouble();
470	>	torque[2] = tokenizer.nextTokenAsDouble();
471	>	sd->setTrq(torque);
472	>	break;
473	>	}
474	>	case 'u' : {
475	>
476	>	RealType particlePot;
477	>	particlePot = tokenizer.nextTokenAsDouble();
478	>	sd->setParticlePot(particlePot);
479	>	break;
480	>	}
481	>	case 'c' : {
482	>
483	>	RealType flucQPos;
484	>	flucQPos = tokenizer.nextTokenAsDouble();
485	>	sd->setFlucQPos(flucQPos);
486	>	break;
487	>	}
488	>	case 'w' : {
489	>
490	>	RealType flucQVel;
491	>	flucQVel = tokenizer.nextTokenAsDouble();
492	>	sd->setFlucQVel(flucQVel);
493	>	break;
494	>	}
495	>	case 'g' : {
496	>
497	>	RealType flucQFrc;
498	>	flucQFrc = tokenizer.nextTokenAsDouble();
499	>	sd->setFlucQFrc(flucQFrc);
500	>	break;
501	>	}
502	>	case 'e' : {
503	>
504	>	Vector3d eField;
505	>	eField[0] = tokenizer.nextTokenAsDouble();
506	>	eField[1] = tokenizer.nextTokenAsDouble();
507	>	eField[2] = tokenizer.nextTokenAsDouble();
508	>	sd->setElectricField(eField);
509	>	break;
510	>	}
511	>	default: {
512	>	sprintf(painCave.errMsg,
513	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
514	>	painCave.isFatal = 1;
515	>	simError();
516	>	break;
517	>	}
518	>
519		}
520		}
521	+
522	+	}
523	+
524	+
525	+	void DumpReader::parseSiteLine(const std::string& line) {
526	+
527	+	StringTokenizer tokenizer(line);
528	+	int nTokens;
529	+
530	+	nTokens = tokenizer.countTokens();
531	+
532	+	if (nTokens < 2) {
533	+	sprintf(painCave.errMsg,
534	+	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
535	+	painCave.isFatal = 1;
536	+	simError();
537	+	}
538	+
539	+	/**
540	+	* The first token is the global integrable object index.
541	+	*/
542	+
543	+	int index = tokenizer.nextTokenAsInt();
544	+	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
545	+	if (sd == NULL) {
546	+	return;
547	+	}
548	+
549	+	/**
550	+	* Test to see if the next token is an integer or not.  If not,
551	+	* we've got data on the integrable object itself.  If there is an
552	+	* integer, we're parsing data for a site on a rigid body.
553	+	*/
554	+
555	+	std::string indexTest = tokenizer.peekNextToken();
556	+	std::istringstream i(indexTest);
557	+	int siteIndex;
558	+	if (i >> siteIndex) {
559	+	// chew up this token and parse as an int:
560	+	siteIndex = tokenizer.nextTokenAsInt();
561	+	RigidBody* rb = static_cast<RigidBody*>(sd);
562	+	sd = rb->getAtoms()[siteIndex];
563	+	}
564	+
565	+	/**
566	+	* The next token contains information on what follows.
567	+	*/
568	+	std::string type = tokenizer.nextToken();
569	+	int size = type.size();
570
571	<	// MPI Section of code..........
572	<
573	<	#else //IS_MPI
574	<
575	<	// first thing first, suspend fatalities.
576	<	int masterNode = 0;
577	<	int nCurObj;
578	<	painCave.isEventLoop = 1;
579	<
342	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
343	<	int haveError;
344	<
345	<	MPI_Status istatus;
346	<	int nitems;
347	<
348	<	nTotObjs = info_->getNGlobalIntegrableObjects();
349	<	haveError = 0;
350	<
351	<	if (worldRank == masterNode) {
352	<	fsetpos(inFile_, framePos_[whichFrame]);
353	<
354	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
355	<
356	<	if (eof_test == NULL) {
357	<	sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ",
358	<	filename_.c_str());
359	<	painCave.isFatal = 1;
360	<	simError();
571	>	for(int i = 0; i < size; ++i) {
572	>	switch(type[i]) {
573	>
574	>	case 'u' : {
575	>
576	>	RealType particlePot;
577	>	particlePot = tokenizer.nextTokenAsDouble();
578	>	sd->setParticlePot(particlePot);
579	>	break;
580		}
581	<
363	<	nitems = atoi(read_buffer);
364	<
365	<	// Check to see that the number of integrable objects in the
366	<	// intial configuration file is the same as derived from the
367	<	// meta-data file.
368	<
369	<	if (nTotObjs != nitems) {
370	<	sprintf(painCave.errMsg,
371	<	"DumpReader Error. %s nIntegrable, %d, "
372	<	"does not match the meta-data file's nIntegrable, %d.\n",
373	<	filename_.c_str(),
374	<	nTotObjs,
375	<	info_->getNGlobalIntegrableObjects());
581	>	case 'c' : {
582
583	<	painCave.isFatal = 1;
584	<	simError();
583	>	RealType flucQPos;
584	>	flucQPos = tokenizer.nextTokenAsDouble();
585	>	sd->setFlucQPos(flucQPos);
586	>	break;
587		}
588	<
589	<	//read the boxMat from the comment line
590	<
591	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
592	<
593	<	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();
588	>	case 'w' : {
589	>
590	>	RealType flucQVel;
591	>	flucQVel = tokenizer.nextTokenAsDouble();
592	>	sd->setFlucQVel(flucQVel);
593	>	break;
594		}
595	<
392	<	//Every single processor will parse the comment line by itself
393	<	//By using this way, we might lose some efficiency, but if we want to add
394	<	//more parameters into comment line, we only need to modify function
395	<	//parseCommentLine
396	<
397	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
398	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
399	<
400	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
401	<	int which_node = info_->getMolToProc(i);
595	>	case 'g' : {
596
597	<	if (which_node == masterNode) {
598	<	//molecules belong to master node
599	<
600	<	mol = info_->getMoleculeByGlobalIndex(i);
407	<
408	<	if (mol == NULL) {
409	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
410	<	painCave.isFatal = 1;
411	<	simError();
412	<	}
413	<
414	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
415	<	integrableObject = mol->nextIntegrableObject(ii)){
416	<
417	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
418	<
419	<	if (eof_test == NULL) {
420	<	sprintf(painCave.errMsg,
421	<	"DumpReader Error: error in reading file %s\n"
422	<	"natoms  = %d; index = %d\n"
423	<	"error reading the line from the file.\n",
424	<	filename_.c_str(),
425	<	nTotObjs,
426	<	i);
427	<
428	<	painCave.isFatal = 1;
429	<	simError();
430	<	}
431	<
432	<	parseDumpLine(read_buffer, integrableObject);
433	<	}
434	<	} else {
435	<	//molecule belongs to slave nodes
436	<
437	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
438	<	MPI_COMM_WORLD, &istatus);
439	<
440	<	for(int j = 0; j < nCurObj; j++) {
441	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
442	<
443	<	if (eof_test == NULL) {
444	<	sprintf(painCave.errMsg,
445	<	"DumpReader Error: error in reading file %s\n"
446	<	"natoms  = %d; index = %d\n"
447	<	"error reading the line from the file.\n",
448	<	filename_.c_str(),
449	<	nTotObjs,
450	<	i);
451	<
452	<	painCave.isFatal = 1;
453	<	simError();
454	<	}
455	<
456	<	MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
457	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
458	<	}
459	<	}
597	>	RealType flucQFrc;
598	>	flucQFrc = tokenizer.nextTokenAsDouble();
599	>	sd->setFlucQFrc(flucQFrc);
600	>	break;
601		}
602	<	} else {
462	<	//actions taken at slave nodes
463	<	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
464	<
465	<	/**@todo*/
466	<	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
467	<
468	<	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
469	<	int which_node = info_->getMolToProc(i);
602	>	case 'e' : {
603
604	<	if (which_node == worldRank) {
605	<	//molecule with global index i belongs to this processor
606	<
607	<	mol = info_->getMoleculeByGlobalIndex(i);
608	<	if (mol == NULL) {
609	<	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
477	<	painCave.isFatal = 1;
478	<	simError();
479	<	}
480	<
481	<	nCurObj = mol->getNIntegrableObjects();
482	<
483	<	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
484	<	MPI_COMM_WORLD);
485	<
486	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
487	<	integrableObject = mol->nextIntegrableObject(ii)){
488	<
489	<	MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
490	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
491	<
492	<	parseDumpLine(read_buffer, integrableObject);
493	<	}
494	<
495	<	}
496	<
604	>	Vector3d eField;
605	>	eField[0] = tokenizer.nextTokenAsDouble();
606	>	eField[1] = tokenizer.nextTokenAsDouble();
607	>	eField[2] = tokenizer.nextTokenAsDouble();
608	>	sd->setElectricField(eField);
609	>	break;
610		}
611	<
612	<	}
613	<
614	<	#endif
615	<
616	<	}
611	>	default: {
612	>	sprintf(painCave.errMsg,
613	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
614	>	painCave.isFatal = 1;
615	>	simError();
616	>	break;
617	>	}
618	>	}
619	>	}
620	>	}
621
622	<	void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
622	>
623	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
624
625	<	Vector3d pos;  // position place holders
626	<	Vector3d vel;  // velocity placeholders
509	<	Quat4d q;    // the quaternions
510	<	Vector3d ji;   // angular velocity placeholders;
511	<	StringTokenizer tokenizer(line);
512	<	int nTokens;
625	>	inputStream.getline(buffer, bufferSize);
626	>	std::string line(buffer);
627
628	<	nTokens = tokenizer.countTokens();
629	<
630	<	if (nTokens < 14) {
631	<	sprintf(painCave.errMsg,
632	<	"DumpReader Error: Not enough Tokens.\n%s\n", line);
519	<	painCave.isFatal = 1;
520	<	simError();
628	>	if (line.find("<StuntDoubles>") == std::string::npos) {
629	>	sprintf(painCave.errMsg,
630	>	"DumpReader Error: Missing <StuntDoubles>\n");
631	>	painCave.isFatal = 1;
632	>	simError();
633		}
634	<
635	<	std::string name = tokenizer.nextToken();
636	<
525	<	if (name != integrableObject->getType()) {
634	>
635	>	while(inputStream.getline(buffer, bufferSize)) {
636	>	line = buffer;
637
638	<	sprintf(painCave.errMsg,
639	<	"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
640	<	name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
641	<	painCave.isFatal = 1;
642	<	simError();
638	>	if(line.find("</StuntDoubles>") != std::string::npos) {
639	>	break;
640	>	}
641	>
642	>	parseDumpLine(line);
643		}
644	+
645	+	}
646	+
647	+	void  DumpReader::readSiteData(std::istream& inputStream) {
648	+
649	+	inputStream.getline(buffer, bufferSize);
650	+	std::string line(buffer);
651
652	<	pos[0] = tokenizer.nextTokenAsDouble();
653	<	pos[1] = tokenizer.nextTokenAsDouble();
654	<	pos[2] = tokenizer.nextTokenAsDouble();
537	<	if (needPos_) {
538	<	integrableObject->setPos(pos);
652	>	if (line.find("<SiteData>") == std::string::npos) {
653	>	// site data isn't required for a simulation, so skip
654	>	return;
655		}
656	<
657	<	vel[0] = tokenizer.nextTokenAsDouble();
658	<	vel[1] = tokenizer.nextTokenAsDouble();
543	<	vel[2] = tokenizer.nextTokenAsDouble();
544	<	if (needVel_) {
545	<	integrableObject->setVel(vel);
546	<	}
547	<
548	<	if (integrableObject->isDirectional()) {
656	>
657	>	while(inputStream.getline(buffer, bufferSize)) {
658	>	line = buffer;
659
660	<	q[0] = tokenizer.nextTokenAsDouble();
661	<	q[1] = tokenizer.nextTokenAsDouble();
552	<	q[2] = tokenizer.nextTokenAsDouble();
553	<	q[3] = tokenizer.nextTokenAsDouble();
554	<
555	<	double qlen = q.length();
556	<	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
557	<
558	<	sprintf(painCave.errMsg,
559	<	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
560	<	painCave.isFatal = 1;
561	<	simError();
562	<
563	<	}
564	<
565	<	q.normalize();
566	<	if (needQuaternion_) {
567	<	integrableObject->setQ(q);
660	>	if(line.find("</SiteData>") != std::string::npos) {
661	>	break;
662		}
663	<
664	<	ji[0] = tokenizer.nextTokenAsDouble();
571	<	ji[1] = tokenizer.nextTokenAsDouble();
572	<	ji[2] = tokenizer.nextTokenAsDouble();
573	<	if (needAngMom_) {
574	<	integrableObject->setJ(ji);
575	<	}
663	>
664	>	parseSiteLine(line);
665		}
577	–
578	–	}
666
667	<
668	<	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
669	<	double currTime;
670	<	Mat3x3d hmat;
671	<	double chi;
672	<	double integralOfChiDt;
673	<	Mat3x3d eta;
674	<
675	<	StringTokenizer tokenizer(line);
676	<	int nTokens;
677	<
678	<	nTokens = tokenizer.countTokens();
679	<
593	<	//comment line should at least contain 10 tokens: current time(1 token) and  h-matrix(9 tokens)
594	<	if (nTokens < 10) {
595	<	sprintf(painCave.errMsg,
596	<	"DumpReader Error: Not enough tokens in comment line: %s", line);
597	<	painCave.isFatal = 1;
598	<	simError();
667	>	}
668	>
669	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
670	>
671	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
672	>	inputStream.getline(buffer, bufferSize);
673	>	std::string line(buffer);
674	>
675	>	if (line.find("<FrameData>") == std::string::npos) {
676	>	sprintf(painCave.errMsg,
677	>	"DumpReader Error: Missing <FrameData>\n");
678	>	painCave.isFatal = 1;
679	>	simError();
680		}
681	<
682	<	//read current time
683	<	currTime = tokenizer.nextTokenAsDouble();
603	<	s->setTime(currTime);
604	<
605	<	//read h-matrix
606	<	hmat(0, 0) = tokenizer.nextTokenAsDouble();
607	<	hmat(0, 1) = tokenizer.nextTokenAsDouble();
608	<	hmat(0, 2) = tokenizer.nextTokenAsDouble();
609	<	hmat(1, 0) = tokenizer.nextTokenAsDouble();
610	<	hmat(1, 1) = tokenizer.nextTokenAsDouble();
611	<	hmat(1, 2) = tokenizer.nextTokenAsDouble();
612	<	hmat(2, 0) = tokenizer.nextTokenAsDouble();
613	<	hmat(2, 1) = tokenizer.nextTokenAsDouble();
614	<	hmat(2, 2) = tokenizer.nextTokenAsDouble();
615	<	s->setHmat(hmat);
616	<
617	<	//read chi and integralOfChidt, they should apprear in pair
618	<	if (tokenizer.countTokens() >= 2) {
619	<	chi = tokenizer.nextTokenAsDouble();
620	<	integralOfChiDt = tokenizer.nextTokenAsDouble();
681	>
682	>	while(inputStream.getline(buffer, bufferSize)) {
683	>	line = buffer;
684
685	<	s->setChi(chi);
686	<	s->setIntegralOfChiDt(integralOfChiDt);
687	<	}
625	<
626	<	//read eta (eta is 3x3 matrix)
627	<	if (tokenizer.countTokens() >= 9) {
628	<	eta(0, 0) = tokenizer.nextTokenAsDouble();
629	<	eta(0, 1) = tokenizer.nextTokenAsDouble();
630	<	eta(0, 2) = tokenizer.nextTokenAsDouble();
631	<	eta(1, 0) = tokenizer.nextTokenAsDouble();
632	<	eta(1, 1) = tokenizer.nextTokenAsDouble();
633	<	eta(1, 2) = tokenizer.nextTokenAsDouble();
634	<	eta(2, 0) = tokenizer.nextTokenAsDouble();
635	<	eta(2, 1) = tokenizer.nextTokenAsDouble();
636	<	eta(2, 2) = tokenizer.nextTokenAsDouble();
685	>	if(line.find("</FrameData>") != std::string::npos) {
686	>	break;
687	>	}
688
689	<	s->setEta(eta);
689	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
690	>	if (!tokenizer.hasMoreTokens()) {
691	>	sprintf(painCave.errMsg,
692	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
693	>	painCave.isFatal = 1;
694	>	simError();
695	>	}
696	>
697	>	std::string propertyName = tokenizer.nextToken();
698	>	if (propertyName == "Time") {
699	>	RealType currTime = tokenizer.nextTokenAsDouble();
700	>	s->setTime(currTime);
701	>	} else if (propertyName == "Hmat"){
702	>	Mat3x3d hmat;
703	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
704	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
705	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
706	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
707	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
708	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
709	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
710	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
711	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
712	>	s->setHmat(hmat);
713	>	} else if (propertyName == "Thermostat") {
714	>	pair<RealType, RealType> thermostat;
715	>	thermostat.first = tokenizer.nextTokenAsDouble();
716	>	thermostat.second = tokenizer.nextTokenAsDouble();
717	>	s->setThermostat(thermostat);
718	>	} else if (propertyName == "Barostat") {
719	>	Mat3x3d eta;
720	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
721	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
722	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
723	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
724	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
725	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
726	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
727	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
728	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
729	>	s->setBarostat(eta);
730	>	} else {
731	>	sprintf(painCave.errMsg,
732	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
733	>	painCave.isFatal = 0;
734	>	simError();
735	>	}
736	>
737		}
738	<
641	<
738	>
739		}
740	<
741	<	}//end namespace oopse
740	>
741	>
742	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpReader.cpp (property svn:keywords), Revision 601 by tim, Thu Sep 15 19:17:04 2005 UTC vs.
branches/development/src/io/DumpReader.cpp (property svn:keywords), Revision 1794 by gezelter, Thu Sep 6 19:44:06 2012 UTC

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