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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 1796 by gezelter, Mon Sep 10 18:38:44 2012 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, 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 || storageLayout & DataStorage::dslElectroFrame) {
231	>	needQuaternion_ = true;
232	>	} else {
233	>	needQuaternion_ = false;
234	>	}
235	>
236	>	if (storageLayout & DataStorage::dslAngularMomentum) {
237	>	needAngMom_ = true;
238	>	} else {
239	>	needAngMom_ = false;
240	>	}
241	>
242	>	readSet(whichFrame);
243	>
244	>	if (needCOMprops_) {
245	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
246	>	Thermo thermo(info_);
247	>	Vector3d com;
248	>
249	>	if (needPos_ && needVel_) {
250	>	Vector3d comvel;
251	>	Vector3d comw;
252	>	thermo.getComAll(com, comvel);
253	>	comw = thermo.getAngularMomentum();
254	>	} else {
255	>	com = thermo.getCom();
256	>	}
257		}
258	<
259	<	if (storageLayout & DataStorage::dslVelocity) {
260	<	needVel_ = true;
258	>	}
259	>
260	>	void DumpReader::readSet(int whichFrame) {
261	>	std::string line;
262	>
263	>	#ifndef IS_MPI
264	>	inFile_->clear();
265	>	inFile_->seekg(framePos_[whichFrame]);
266	>
267	>	std::istream& inputStream = *inFile_;
268	>
269	>	#else
270	>	int masterNode = 0;
271	>	std::stringstream sstream;
272	>	if (worldRank == masterNode) {
273	>	std::string sendBuffer;
274	>
275	>	inFile_->clear();
276	>	inFile_->seekg(framePos_[whichFrame]);
277	>
278	>	while (inFile_->getline(buffer, bufferSize)) {
279	>
280	>	line = buffer;
281	>	sendBuffer += line;
282	>	sendBuffer += '\n';
283	>	if (line.find("</Snapshot>") != std::string::npos) {
284	>	break;
285	>	}
286	>	}
287	>
288	>	int sendBufferSize = sendBuffer.size();
289	>	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
290	>	MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize,
291	>	MPI::CHAR, masterNode);
292	>
293	>	sstream.str(sendBuffer);
294		} else {
295	<	needVel_ = false;
296	<	}
295	>	int sendBufferSize;
296	>	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
297	>	char * recvBuffer = new char[sendBufferSize+1];
298	>	assert(recvBuffer);
299	>	recvBuffer[sendBufferSize] = '\0';
300	>	MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
301	>	sstream.str(recvBuffer);
302	>	delete [] recvBuffer;
303	>	}
304	>
305	>	std::istream& inputStream = sstream;
306	>	#endif
307	>
308	>	inputStream.getline(buffer, bufferSize);
309	>
310	>	line = buffer;
311	>	if (line.find("<Snapshot>") == std::string::npos) {
312	>	sprintf(painCave.errMsg,
313	>	"DumpReader Error: can not find <Snapshot>\n");
314	>	painCave.isFatal = 1;
315	>	simError();
316	>	}
317
318	<	if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
319	<	needQuaternion_ = true;
318	>	//read frameData
319	>	readFrameProperties(inputStream);
320	>
321	>	//read StuntDoubles
322	>	readStuntDoubles(inputStream);
323	>
324	>	inputStream.getline(buffer, bufferSize);
325	>	line = buffer;
326	>
327	>	if (line.find("<SiteData>") != std::string::npos) {
328	>	//read SiteData
329	>	readSiteData(inputStream);
330		} else {
331	<	needQuaternion_ = false;
331	>	if (line.find("</Snapshot>") == std::string::npos) {
332	>	sprintf(painCave.errMsg,
333	>	"DumpReader Error: can not find </Snapshot>\n");
334	>	painCave.isFatal = 1;
335	>	simError();
336	>	}
337		}
338	<
339	<	if (storageLayout & DataStorage::dslAngularMomentum) {
340	<	needAngMom_ = true;
341	<	} else {
342	<	needAngMom_ = false;
338	>	}
339	>
340	>	void DumpReader::parseDumpLine(const std::string& line) {
341	>
342	>
343	>	StringTokenizer tokenizer(line);
344	>	int nTokens;
345	>
346	>	nTokens = tokenizer.countTokens();
347	>
348	>	if (nTokens < 2) {
349	>	sprintf(painCave.errMsg,
350	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
351	>	painCave.isFatal = 1;
352	>	simError();
353	>	}
354	>
355	>	int index = tokenizer.nextTokenAsInt();
356	>
357	>	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
358	>
359	>	if (sd == NULL) {
360	>	return;
361		}
362	+	std::string type = tokenizer.nextToken();
363	+	int size = type.size();
364	+
365	+	size_t found;
366
367	<	readSet(whichFrame);
368	<	}
369	<
370	<	void DumpReader::readSet(int whichFrame) {
371	<	int i;
372	<	int nTotObjs;                  // the number of atoms
373	<	char read_buffer[maxBufferSize];  //the line buffer for reading
374	<	char * eof_test;               // ptr to see when we reach the end of the file
375	<
376	<	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();
367	>	if (needPos_) {
368	>	found = type.find("p");
369	>	if (found == std::string::npos) {
370	>	sprintf(painCave.errMsg,
371	>	"DumpReader Error: StuntDouble %d has no Position\n"
372	>	"\tField (\"p\") specified.\n%s\n", index,
373	>	line.c_str());
374	>	painCave.isFatal = 1;
375	>	simError();
376	>	}
377		}
378
379	<	nTotObjs = atoi(read_buffer);
380	<
381	<	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
382	<	sprintf(painCave.errMsg,
383	<	"DumpReader error. %s nIntegrable, %d, "
384	<	"does not match the meta-data file's nIntegrable, %d.\n",
385	<	filename_.c_str(),
386	<	nTotObjs,
387	<	info_->getNGlobalIntegrableObjects());
388	<
389	<	painCave.isFatal = 1;
390	<	simError();
379	>	if (sd->isDirectional()) {
380	>	if (needQuaternion_) {
381	>	found = type.find("q");
382	>	if (found == std::string::npos) {
383	>	sprintf(painCave.errMsg,
384	>	"DumpReader Error: Directional StuntDouble %d has no\n"
385	>	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
386	>	line.c_str());
387	>	painCave.isFatal = 1;
388	>	simError();
389	>	}
390	>	}
391		}
392	<
393	<	//read the box mat from the comment line
394	<
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)) {
392	>
393	>	for(int i = 0; i < size; ++i) {
394	>	switch(type[i]) {
395
396	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
397	<
398	<	if (eof_test == NULL) {
399	<	sprintf(painCave.errMsg,
400	<	"DumpReader Error: error in reading file %s\n"
401	<	"natoms  = %d; index = %d\n"
402	<	"error reading the line from the file.\n",
403	<	filename_.c_str(),
404	<	nTotObjs,
319	<	i);
320	<
321	<	painCave.isFatal = 1;
322	<	simError();
396	>	case 'p': {
397	>	Vector3d pos;
398	>	pos[0] = tokenizer.nextTokenAsDouble();
399	>	pos[1] = tokenizer.nextTokenAsDouble();
400	>	pos[2] = tokenizer.nextTokenAsDouble();
401	>	if (needPos_) {
402	>	sd->setPos(pos);
403	>	}
404	>	break;
405		}
406	<
407	<	parseDumpLine(read_buffer, integrableObject);
408	<	i++;
406	>	case 'v' : {
407	>	Vector3d vel;
408	>	vel[0] = tokenizer.nextTokenAsDouble();
409	>	vel[1] = tokenizer.nextTokenAsDouble();
410	>	vel[2] = tokenizer.nextTokenAsDouble();
411	>	if (needVel_) {
412	>	sd->setVel(vel);
413	>	}
414	>	break;
415	>	}
416	>
417	>	case 'q' : {
418	>	Quat4d q;
419	>	if (sd->isDirectional()) {
420	>
421	>	q[0] = tokenizer.nextTokenAsDouble();
422	>	q[1] = tokenizer.nextTokenAsDouble();
423	>	q[2] = tokenizer.nextTokenAsDouble();
424	>	q[3] = tokenizer.nextTokenAsDouble();
425	>
426	>	RealType qlen = q.length();
427	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
428	>
429	>	sprintf(painCave.errMsg,
430	>	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
431	>	painCave.isFatal = 1;
432	>	simError();
433	>
434	>	}
435	>
436	>	q.normalize();
437	>	if (needQuaternion_) {
438	>	sd->setQ(q);
439	>	}
440	>	}
441	>	break;
442	>	}
443	>	case 'j' : {
444	>	Vector3d ji;
445	>	if (sd->isDirectional()) {
446	>	ji[0] = tokenizer.nextTokenAsDouble();
447	>	ji[1] = tokenizer.nextTokenAsDouble();
448	>	ji[2] = tokenizer.nextTokenAsDouble();
449	>	if (needAngMom_) {
450	>	sd->setJ(ji);
451	>	}
452	>	}
453	>	break;
454	>	}
455	>	case 'f': {
456	>
457	>	Vector3d force;
458	>	force[0] = tokenizer.nextTokenAsDouble();
459	>	force[1] = tokenizer.nextTokenAsDouble();
460	>	force[2] = tokenizer.nextTokenAsDouble();
461	>	sd->setFrc(force);
462	>	break;
463	>	}
464	>	case 't' : {
465	>
466	>	Vector3d torque;
467	>	torque[0] = tokenizer.nextTokenAsDouble();
468	>	torque[1] = tokenizer.nextTokenAsDouble();
469	>	torque[2] = tokenizer.nextTokenAsDouble();
470	>	sd->setTrq(torque);
471	>	break;
472	>	}
473	>	case 'u' : {
474	>
475	>	RealType particlePot;
476	>	particlePot = tokenizer.nextTokenAsDouble();
477	>	sd->setParticlePot(particlePot);
478	>	break;
479	>	}
480	>	case 'c' : {
481	>
482	>	RealType flucQPos;
483	>	flucQPos = tokenizer.nextTokenAsDouble();
484	>	sd->setFlucQPos(flucQPos);
485	>	break;
486	>	}
487	>	case 'w' : {
488	>
489	>	RealType flucQVel;
490	>	flucQVel = tokenizer.nextTokenAsDouble();
491	>	sd->setFlucQVel(flucQVel);
492	>	break;
493	>	}
494	>	case 'g' : {
495	>
496	>	RealType flucQFrc;
497	>	flucQFrc = tokenizer.nextTokenAsDouble();
498	>	sd->setFlucQFrc(flucQFrc);
499	>	break;
500	>	}
501	>	case 'e' : {
502	>
503	>	Vector3d eField;
504	>	eField[0] = tokenizer.nextTokenAsDouble();
505	>	eField[1] = tokenizer.nextTokenAsDouble();
506	>	eField[2] = tokenizer.nextTokenAsDouble();
507	>	sd->setElectricField(eField);
508	>	break;
509	>	}
510	>	default: {
511	>	sprintf(painCave.errMsg,
512	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
513	>	painCave.isFatal = 1;
514	>	simError();
515	>	break;
516	>	}
517	>
518		}
519		}
520	+
521	+	}
522	+
523	+
524	+	void DumpReader::parseSiteLine(const std::string& line) {
525	+
526	+	StringTokenizer tokenizer(line);
527	+	int nTokens;
528	+
529	+	nTokens = tokenizer.countTokens();
530	+
531	+	if (nTokens < 2) {
532	+	sprintf(painCave.errMsg,
533	+	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
534	+	painCave.isFatal = 1;
535	+	simError();
536	+	}
537	+
538	+	/**
539	+	* The first token is the global integrable object index.
540	+	*/
541	+
542	+	int index = tokenizer.nextTokenAsInt();
543	+	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
544	+	if (sd == NULL) {
545	+	return;
546	+	}
547	+
548	+	/**
549	+	* Test to see if the next token is an integer or not.  If not,
550	+	* we've got data on the integrable object itself.  If there is an
551	+	* integer, we're parsing data for a site on a rigid body.
552	+	*/
553	+
554	+	std::string indexTest = tokenizer.peekNextToken();
555	+	std::istringstream i(indexTest);
556	+	int siteIndex;
557	+	if (i >> siteIndex) {
558	+	// chew up this token and parse as an int:
559	+	siteIndex = tokenizer.nextTokenAsInt();
560	+	RigidBody* rb = static_cast<RigidBody*>(sd);
561	+	sd = rb->getAtoms()[siteIndex];
562	+	}
563	+
564	+	/**
565	+	* The next token contains information on what follows.
566	+	*/
567	+	std::string type = tokenizer.nextToken();
568	+	int size = type.size();
569
570	<	// MPI Section of code..........
571	<
572	<	#else //IS_MPI
573	<
574	<	// first thing first, suspend fatalities.
575	<	int masterNode = 0;
576	<	int nCurObj;
577	<	painCave.isEventLoop = 1;
578	<
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();
570	>	for(int i = 0; i < size; ++i) {
571	>	switch(type[i]) {
572	>
573	>	case 'u' : {
574	>
575	>	RealType particlePot;
576	>	particlePot = tokenizer.nextTokenAsDouble();
577	>	sd->setParticlePot(particlePot);
578	>	break;
579		}
580	<
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());
580	>	case 'c' : {
581
582	<	painCave.isFatal = 1;
583	<	simError();
582	>	RealType flucQPos;
583	>	flucQPos = tokenizer.nextTokenAsDouble();
584	>	sd->setFlucQPos(flucQPos);
585	>	break;
586		}
587	<
588	<	//read the boxMat from the comment line
589	<
590	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
591	<
592	<	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();
587	>	case 'w' : {
588	>
589	>	RealType flucQVel;
590	>	flucQVel = tokenizer.nextTokenAsDouble();
591	>	sd->setFlucQVel(flucQVel);
592	>	break;
593		}
594	<
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);
594	>	case 'g' : {
595
596	<	if (which_node == masterNode) {
597	<	//molecules belong to master node
598	<
599	<	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	<	}
596	>	RealType flucQFrc;
597	>	flucQFrc = tokenizer.nextTokenAsDouble();
598	>	sd->setFlucQFrc(flucQFrc);
599	>	break;
600		}
601	<	} 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);
601	>	case 'e' : {
602
603	<	if (which_node == worldRank) {
604	<	//molecule with global index i belongs to this processor
605	<
606	<	mol = info_->getMoleculeByGlobalIndex(i);
607	<	if (mol == NULL) {
608	<	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	<
603	>	Vector3d eField;
604	>	eField[0] = tokenizer.nextTokenAsDouble();
605	>	eField[1] = tokenizer.nextTokenAsDouble();
606	>	eField[2] = tokenizer.nextTokenAsDouble();
607	>	sd->setElectricField(eField);
608	>	break;
609		}
610	<
611	<	}
612	<
613	<	#endif
614	<
615	<	}
610	>	default: {
611	>	sprintf(painCave.errMsg,
612	>	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
613	>	painCave.isFatal = 1;
614	>	simError();
615	>	break;
616	>	}
617	>	}
618	>	}
619	>	}
620
621	<	void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
621	>
622	>	void  DumpReader::readStuntDoubles(std::istream& inputStream) {
623
624	<	Vector3d pos;  // position place holders
625	<	Vector3d vel;  // velocity placeholders
506	<	Quat4d q;    // the quaternions
507	<	Vector3d ji;   // angular velocity placeholders;
508	<	StringTokenizer tokenizer(line);
509	<	int nTokens;
624	>	inputStream.getline(buffer, bufferSize);
625	>	std::string line(buffer);
626
627	<	nTokens = tokenizer.countTokens();
628	<
629	<	if (nTokens < 14) {
630	<	sprintf(painCave.errMsg,
631	<	"DumpReader Error: Not enough Tokens.\n%s\n", line);
516	<	painCave.isFatal = 1;
517	<	simError();
627	>	if (line.find("<StuntDoubles>") == std::string::npos) {
628	>	sprintf(painCave.errMsg,
629	>	"DumpReader Error: Missing <StuntDoubles>\n");
630	>	painCave.isFatal = 1;
631	>	simError();
632		}
633	<
634	<	std::string name = tokenizer.nextToken();
635	<
522	<	if (name != integrableObject->getType()) {
633	>
634	>	while(inputStream.getline(buffer, bufferSize)) {
635	>	line = buffer;
636
637	<	sprintf(painCave.errMsg,
638	<	"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
639	<	name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
640	<	painCave.isFatal = 1;
641	<	simError();
637	>	if(line.find("</StuntDoubles>") != std::string::npos) {
638	>	break;
639	>	}
640	>
641	>	parseDumpLine(line);
642		}
643	+
644	+	}
645	+
646	+	void  DumpReader::readSiteData(std::istream& inputStream) {
647	+
648	+	inputStream.getline(buffer, bufferSize);
649	+	std::string line(buffer);
650
651	<	pos[0] = tokenizer.nextTokenAsDouble();
652	<	pos[1] = tokenizer.nextTokenAsDouble();
653	<	pos[2] = tokenizer.nextTokenAsDouble();
534	<	if (needPos_) {
535	<	integrableObject->setPos(pos);
651	>	if (line.find("<SiteData>") == std::string::npos) {
652	>	// site data isn't required for a simulation, so skip
653	>	return;
654		}
655	<
656	<	vel[0] = tokenizer.nextTokenAsDouble();
657	<	vel[1] = tokenizer.nextTokenAsDouble();
540	<	vel[2] = tokenizer.nextTokenAsDouble();
541	<	if (needVel_) {
542	<	integrableObject->setVel(vel);
543	<	}
544	<
545	<	if (integrableObject->isDirectional()) {
655	>
656	>	while(inputStream.getline(buffer, bufferSize)) {
657	>	line = buffer;
658
659	<	q[0] = tokenizer.nextTokenAsDouble();
660	<	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);
659	>	if(line.find("</SiteData>") != std::string::npos) {
660	>	break;
661		}
662	<
663	<	ji[0] = tokenizer.nextTokenAsDouble();
568	<	ji[1] = tokenizer.nextTokenAsDouble();
569	<	ji[2] = tokenizer.nextTokenAsDouble();
570	<	if (needAngMom_) {
571	<	integrableObject->setJ(ji);
572	<	}
662	>
663	>	parseSiteLine(line);
664		}
574	–
575	–	}
665
666	<
667	<	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
668	<	double currTime;
669	<	Mat3x3d hmat;
670	<	double chi;
671	<	double integralOfChiDt;
672	<	Mat3x3d eta;
673	<
674	<	StringTokenizer tokenizer(line);
675	<	int nTokens;
676	<
677	<	nTokens = tokenizer.countTokens();
678	<
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();
666	>	}
667	>
668	>	void DumpReader::readFrameProperties(std::istream& inputStream) {
669	>
670	>	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
671	>	inputStream.getline(buffer, bufferSize);
672	>	std::string line(buffer);
673	>
674	>	if (line.find("<FrameData>") == std::string::npos) {
675	>	sprintf(painCave.errMsg,
676	>	"DumpReader Error: Missing <FrameData>\n");
677	>	painCave.isFatal = 1;
678	>	simError();
679		}
680	<
681	<	//read current time
682	<	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();
680	>
681	>	while(inputStream.getline(buffer, bufferSize)) {
682	>	line = buffer;
683
684	<	s->setChi(chi);
685	<	s->setIntegralOfChiDt(integralOfChiDt);
686	<	}
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();
684	>	if(line.find("</FrameData>") != std::string::npos) {
685	>	break;
686	>	}
687
688	<	s->setEta(eta);
688	>	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
689	>	if (!tokenizer.hasMoreTokens()) {
690	>	sprintf(painCave.errMsg,
691	>	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
692	>	painCave.isFatal = 1;
693	>	simError();
694	>	}
695	>
696	>	std::string propertyName = tokenizer.nextToken();
697	>	if (propertyName == "Time") {
698	>	RealType currTime = tokenizer.nextTokenAsDouble();
699	>	s->setTime(currTime);
700	>	} else if (propertyName == "Hmat"){
701	>	Mat3x3d hmat;
702	>	hmat(0, 0) = tokenizer.nextTokenAsDouble();
703	>	hmat(0, 1) = tokenizer.nextTokenAsDouble();
704	>	hmat(0, 2) = tokenizer.nextTokenAsDouble();
705	>	hmat(1, 0) = tokenizer.nextTokenAsDouble();
706	>	hmat(1, 1) = tokenizer.nextTokenAsDouble();
707	>	hmat(1, 2) = tokenizer.nextTokenAsDouble();
708	>	hmat(2, 0) = tokenizer.nextTokenAsDouble();
709	>	hmat(2, 1) = tokenizer.nextTokenAsDouble();
710	>	hmat(2, 2) = tokenizer.nextTokenAsDouble();
711	>	s->setHmat(hmat);
712	>	} else if (propertyName == "Thermostat") {
713	>	pair<RealType, RealType> thermostat;
714	>	thermostat.first = tokenizer.nextTokenAsDouble();
715	>	thermostat.second = tokenizer.nextTokenAsDouble();
716	>	s->setThermostat(thermostat);
717	>	} else if (propertyName == "Barostat") {
718	>	Mat3x3d eta;
719	>	eta(0, 0) = tokenizer.nextTokenAsDouble();
720	>	eta(0, 1) = tokenizer.nextTokenAsDouble();
721	>	eta(0, 2) = tokenizer.nextTokenAsDouble();
722	>	eta(1, 0) = tokenizer.nextTokenAsDouble();
723	>	eta(1, 1) = tokenizer.nextTokenAsDouble();
724	>	eta(1, 2) = tokenizer.nextTokenAsDouble();
725	>	eta(2, 0) = tokenizer.nextTokenAsDouble();
726	>	eta(2, 1) = tokenizer.nextTokenAsDouble();
727	>	eta(2, 2) = tokenizer.nextTokenAsDouble();
728	>	s->setBarostat(eta);
729	>	} else {
730	>	sprintf(painCave.errMsg,
731	>	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
732	>	painCave.isFatal = 0;
733	>	simError();
734	>	}
735	>
736		}
737	<
638	<
737	>
738		}
739	<
740	<	}//end namespace oopse
739	>
740	>
741	>	}//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 1796 by gezelter, Mon Sep 10 18:38:44 2012 UTC

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