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1 | < | /* |
2 | < | * Copyright (c) 2005 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 |
19 | < | * notice, this list of conditions and the following disclaimer. |
20 | < | * |
21 | < | * 3. Redistributions in binary form must reproduce the above copyright |
22 | < | * notice, this list of conditions and the following disclaimer in the |
23 | < | * documentation and/or other materials provided with the |
24 | < | * distribution. |
25 | < | * |
26 | < | * This software is provided "AS IS," without a warranty of any |
27 | < | * kind. All express or implied conditions, representations and |
28 | < | * warranties, including any implied warranty of merchantability, |
29 | < | * fitness for a particular purpose or non-infringement, are hereby |
30 | < | * excluded. The University of Notre Dame and its licensors shall not |
31 | < | * be liable for any damages suffered by licensee as a result of |
32 | < | * using, modifying or distributing the software or its |
33 | < | * derivatives. In no event will the University of Notre Dame or its |
34 | < | * licensors be liable for any lost revenue, profit or data, or for |
35 | < | * direct, indirect, special, consequential, incidental or punitive |
36 | < | * damages, however caused and regardless of the theory of liability, |
37 | < | * arising out of the use of or inability to use software, even if the |
38 | < | * University of Notre Dame has been advised of the possibility of |
39 | < | * such damages. |
40 | < | */ |
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 { |
71 | < | |
72 | < | DumpReader::DumpReader(SimInfo* info, const std::string& filename) |
73 | < | : info_(info), filename_(filename), isScanned_(false), nframes_(0) { |
74 | < | |
75 | < | #ifdef IS_MPI |
76 | < | |
77 | < | if (worldRank == 0) { |
78 | < | #endif |
79 | < | |
80 | < | inFile_ = new std::ifstream(filename_.c_str()); |
81 | < | |
82 | < | if (inFile_->fail()) { |
83 | < | sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str()); |
84 | < | painCave.isFatal = 1; |
85 | < | simError(); |
86 | < | } |
87 | < | |
88 | < | #ifdef IS_MPI |
89 | < | |
90 | < | } |
91 | < | |
92 | < | strcpy(checkPointMsg, "Dump file opened for reading successfully."); |
93 | < | MPIcheckPoint(); |
94 | < | |
95 | < | #endif |
96 | < | |
97 | < | return; |
98 | < | } |
99 | < | |
100 | < | DumpReader::~DumpReader() { |
101 | < | |
102 | < | #ifdef IS_MPI |
103 | < | |
104 | < | if (worldRank == 0) { |
105 | < | #endif |
106 | < | |
107 | < | delete inFile_; |
108 | < | |
109 | < | #ifdef IS_MPI |
110 | < | |
111 | < | } |
112 | < | |
113 | < | strcpy(checkPointMsg, "Dump file closed successfully."); |
114 | < | MPIcheckPoint(); |
115 | < | |
116 | < | #endif |
117 | < | |
118 | < | return; |
119 | < | } |
120 | < | |
121 | < | int DumpReader::getNFrames(void) { |
122 | < | |
123 | < | if (!isScanned_) |
124 | < | scanFile(); |
125 | < | |
126 | < | return nframes_; |
127 | < | } |
128 | < | |
129 | < | void DumpReader::scanFile(void) { |
130 | < | int i, j; |
131 | < | int lineNum = 0; |
132 | < | char readBuffer[maxBufferSize]; |
133 | < | std::streampos currPos; |
134 | < | |
135 | < | #ifdef IS_MPI |
136 | < | |
137 | < | if (worldRank == 0) { |
138 | < | #endif // is_mpi |
139 | < | |
140 | < | inFile_->seekg (0, std::ios::beg); |
141 | < | |
142 | < | |
143 | < | currPos = inFile_->tellg(); |
144 | < | inFile_->getline(readBuffer, sizeof(readBuffer)); |
145 | < | lineNum++; |
146 | < | |
147 | < | if (inFile_->eof()) { |
148 | < | sprintf(painCave.errMsg, |
149 | < | "DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", |
150 | < | filename_.c_str(), |
151 | < | lineNum); |
152 | < | painCave.isFatal = 1; |
153 | < | simError(); |
154 | < | } |
155 | < | |
156 | < | while (!inFile_->eof()) { |
157 | < | framePos_.push_back(currPos); |
158 | < | |
159 | < | i = atoi(readBuffer); |
160 | < | |
161 | < | inFile_->getline(readBuffer, sizeof(readBuffer)); |
162 | < | lineNum++; |
163 | < | |
164 | < | if (inFile_->eof()) { |
165 | < | sprintf(painCave.errMsg, |
166 | < | "DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", |
167 | < | filename_.c_str(), |
168 | < | lineNum); |
169 | < | painCave.isFatal = 1; |
170 | < | simError(); |
171 | < | } |
172 | < | |
173 | < | for(j = 0; j < i; j++) { |
174 | < | inFile_->getline(readBuffer, sizeof(readBuffer)); |
175 | < | lineNum++; |
176 | < | |
177 | < | if (inFile_->eof()) { |
178 | < | sprintf(painCave.errMsg, |
179 | < | "DumpReader Error: File \"%s\" ended unexpectedly at line %d," |
180 | < | " with atom %d\n", filename_.c_str(), |
181 | < | lineNum, |
182 | < | j); |
183 | < | |
184 | < | painCave.isFatal = 1; |
185 | < | simError(); |
186 | < | } |
187 | < | } |
188 | < | |
189 | < | currPos = inFile_->tellg(); |
190 | < | inFile_->getline(readBuffer, sizeof(readBuffer)); |
191 | < | lineNum++; |
192 | < | } |
193 | < | |
194 | < | inFile_->seekg (0, std::ios::beg); |
195 | < | |
196 | < | nframes_ = framePos_.size(); |
197 | < | #ifdef IS_MPI |
198 | < | } |
199 | < | |
200 | < | MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD); |
201 | < | |
202 | < | strcpy(checkPointMsg, "Successfully scanned DumpFile\n"); |
203 | < | MPIcheckPoint(); |
204 | < | |
205 | < | #endif // is_mpi |
206 | < | |
207 | < | isScanned_ = true; |
208 | < | } |
209 | < | |
210 | < | void DumpReader::readFrame(int whichFrame) { |
211 | < | if (!isScanned_) |
212 | < | scanFile(); |
213 | < | |
214 | < | int storageLayout = info_->getSnapshotManager()->getStorageLayout(); |
215 | < | |
216 | < | if (storageLayout & DataStorage::dslPosition) { |
217 | < | needPos_ = true; |
218 | < | } else { |
219 | < | needPos_ = false; |
220 | < | } |
221 | < | |
222 | < | if (storageLayout & DataStorage::dslVelocity) { |
223 | < | needVel_ = true; |
224 | < | } else { |
225 | < | needVel_ = false; |
226 | < | } |
227 | < | |
228 | < | if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) { |
229 | < | needQuaternion_ = true; |
230 | < | } else { |
231 | < | needQuaternion_ = false; |
232 | < | } |
233 | < | |
234 | < | if (storageLayout & DataStorage::dslAngularMomentum) { |
235 | < | needAngMom_ = true; |
236 | < | } else { |
237 | < | needAngMom_ = false; |
238 | < | } |
239 | < | |
240 | < | readSet(whichFrame); |
241 | < | } |
242 | < | |
243 | < | void DumpReader::readSet(int whichFrame) { |
244 | < | int i; |
245 | < | int nTotObjs; // the number of atoms |
246 | < | char read_buffer[maxBufferSize]; //the line buffer for reading |
247 | < | char * eof_test; // ptr to see when we reach the end of the file |
248 | < | |
249 | < | Molecule* mol; |
250 | < | StuntDouble* integrableObject; |
251 | < | SimInfo::MoleculeIterator mi; |
252 | < | Molecule::IntegrableObjectIterator ii; |
253 | < | |
254 | < | #ifndef IS_MPI |
255 | < | inFile_->clear(); |
256 | < | inFile_->seekg(framePos_[whichFrame]); |
257 | < | |
258 | < | if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
259 | < | sprintf(painCave.errMsg, |
260 | < | "DumpReader error: error reading 1st line of \"%s\"\n", |
261 | < | filename_.c_str()); |
262 | < | painCave.isFatal = 1; |
263 | < | simError(); |
264 | < | } |
265 | < | |
266 | < | nTotObjs = atoi(read_buffer); |
267 | < | |
268 | < | if (nTotObjs != info_->getNGlobalIntegrableObjects()) { |
269 | < | sprintf(painCave.errMsg, |
270 | < | "DumpReader error. %s nIntegrable, %d, " |
271 | < | "does not match the meta-data file's nIntegrable, %d.\n", |
272 | < | filename_.c_str(), |
273 | < | nTotObjs, |
274 | < | info_->getNGlobalIntegrableObjects()); |
275 | < | |
276 | < | painCave.isFatal = 1; |
277 | < | simError(); |
278 | < | } |
279 | < | |
280 | < | //read the box mat from the comment line |
281 | < | |
282 | < | |
283 | < | if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
284 | < | sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", |
285 | < | filename_.c_str()); |
286 | < | painCave.isFatal = 1; |
287 | < | simError(); |
288 | < | } |
289 | < | |
290 | < | parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
291 | < | |
292 | < | //parse dump lines |
293 | < | |
294 | < | i = 0; |
295 | < | for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
296 | < | |
297 | < | for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
298 | < | integrableObject = mol->nextIntegrableObject(ii)) { |
299 | < | |
300 | < | |
301 | < | |
302 | < | if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
303 | < | sprintf(painCave.errMsg, |
304 | < | "DumpReader Error: error in reading file %s\n" |
305 | < | "natoms = %d; index = %d\n" |
306 | < | "error reading the line from the file.\n", |
307 | < | filename_.c_str(), |
308 | < | nTotObjs, |
309 | < | i); |
310 | < | |
311 | < | painCave.isFatal = 1; |
312 | < | simError(); |
313 | < | } |
314 | < | |
315 | < | parseDumpLine(read_buffer, integrableObject); |
316 | < | i++; |
317 | < | } |
318 | < | } |
319 | < | |
320 | < | // MPI Section of code.......... |
321 | < | |
322 | < | #else //IS_MPI |
323 | < | |
324 | < | // first thing first, suspend fatalities. |
325 | < | int masterNode = 0; |
326 | < | int nCurObj; |
327 | < | painCave.isEventLoop = 1; |
328 | < | |
329 | < | int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
330 | < | int haveError; |
331 | < | |
332 | < | MPI_Status istatus; |
333 | < | int nitems; |
334 | < | |
335 | < | nTotObjs = info_->getNGlobalIntegrableObjects(); |
336 | < | haveError = 0; |
337 | < | |
338 | < | if (worldRank == masterNode) { |
339 | < | inFile_->clear(); |
340 | < | inFile_->seekg(framePos_[whichFrame]); |
341 | < | |
342 | < | if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
343 | < | sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ", |
344 | < | filename_.c_str()); |
345 | < | painCave.isFatal = 1; |
346 | < | simError(); |
347 | < | } |
348 | < | |
349 | < | nitems = atoi(read_buffer); |
350 | < | |
351 | < | // Check to see that the number of integrable objects in the |
352 | < | // intial configuration file is the same as derived from the |
353 | < | // meta-data file. |
354 | < | |
355 | < | if (nTotObjs != nitems) { |
356 | < | sprintf(painCave.errMsg, |
357 | < | "DumpReader Error. %s nIntegrable, %d, " |
358 | < | "does not match the meta-data file's nIntegrable, %d.\n", |
359 | < | filename_.c_str(), |
360 | < | nTotObjs, |
361 | < | info_->getNGlobalIntegrableObjects()); |
362 | < | |
363 | < | painCave.isFatal = 1; |
364 | < | simError(); |
365 | < | } |
366 | < | |
367 | < | //read the boxMat from the comment line |
368 | < | |
369 | < | |
370 | < | |
371 | < | if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
372 | < | sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", |
373 | < | filename_.c_str()); |
374 | < | painCave.isFatal = 1; |
375 | < | simError(); |
376 | < | } |
377 | < | |
378 | < | //Every single processor will parse the comment line by itself |
379 | < | //By using this way, we might lose some efficiency, but if we want to add |
380 | < | //more parameters into comment line, we only need to modify function |
381 | < | //parseCommentLine |
382 | < | |
383 | < | MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
384 | < | parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
385 | < | |
386 | < | for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
387 | < | int which_node = info_->getMolToProc(i); |
388 | < | |
389 | < | if (which_node == masterNode) { |
390 | < | //molecules belong to master node |
391 | < | |
392 | < | mol = info_->getMoleculeByGlobalIndex(i); |
393 | < | |
394 | < | if (mol == NULL) { |
395 | < | sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
396 | < | painCave.isFatal = 1; |
397 | < | simError(); |
398 | < | } |
399 | < | |
400 | < | for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
401 | < | integrableObject = mol->nextIntegrableObject(ii)){ |
402 | < | |
403 | < | |
404 | < | |
405 | < | if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
406 | < | sprintf(painCave.errMsg, |
407 | < | "DumpReader Error: error in reading file %s\n" |
408 | < | "natoms = %d; index = %d\n" |
409 | < | "error reading the line from the file.\n", |
410 | < | filename_.c_str(), |
411 | < | nTotObjs, |
412 | < | i); |
413 | < | |
414 | < | painCave.isFatal = 1; |
415 | < | simError(); |
416 | < | } |
417 | < | |
418 | < | parseDumpLine(read_buffer, integrableObject); |
419 | < | } |
420 | < | } else { |
421 | < | //molecule belongs to slave nodes |
422 | < | |
423 | < | MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
424 | < | MPI_COMM_WORLD, &istatus); |
425 | < | |
426 | < | for(int j = 0; j < nCurObj; j++) { |
427 | < | |
428 | < | |
429 | < | if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
430 | < | sprintf(painCave.errMsg, |
431 | < | "DumpReader Error: error in reading file %s\n" |
432 | < | "natoms = %d; index = %d\n" |
433 | < | "error reading the line from the file.\n", |
434 | < | filename_.c_str(), |
435 | < | nTotObjs, |
436 | < | i); |
437 | < | |
438 | < | painCave.isFatal = 1; |
439 | < | simError(); |
440 | < | } |
441 | < | |
442 | < | MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node, |
443 | < | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
444 | < | } |
445 | < | } |
446 | < | } |
447 | < | } else { |
448 | < | //actions taken at slave nodes |
449 | < | MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
450 | < | |
451 | < | /**@todo*/ |
452 | < | parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
453 | < | |
454 | < | for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
455 | < | int which_node = info_->getMolToProc(i); |
456 | < | |
457 | < | if (which_node == worldRank) { |
458 | < | //molecule with global index i belongs to this processor |
459 | < | |
460 | < | mol = info_->getMoleculeByGlobalIndex(i); |
461 | < | if (mol == NULL) { |
462 | < | sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
463 | < | painCave.isFatal = 1; |
464 | < | simError(); |
465 | < | } |
466 | < | |
467 | < | nCurObj = mol->getNIntegrableObjects(); |
468 | < | |
469 | < | MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT, |
470 | < | MPI_COMM_WORLD); |
471 | < | |
472 | < | for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
473 | < | integrableObject = mol->nextIntegrableObject(ii)){ |
474 | < | |
475 | < | MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode, |
476 | < | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
477 | < | |
478 | < | parseDumpLine(read_buffer, integrableObject); |
479 | < | } |
480 | < | |
481 | < | } |
482 | < | |
483 | < | } |
484 | < | |
485 | < | } |
486 | < | |
487 | < | #endif |
488 | < | |
489 | < | } |
490 | < | |
491 | < | void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) { |
492 | < | |
493 | < | Vector3d pos; // position place holders |
494 | < | Vector3d vel; // velocity placeholders |
495 | < | Quat4d q; // the quaternions |
496 | < | Vector3d ji; // angular velocity placeholders; |
497 | < | StringTokenizer tokenizer(line); |
498 | < | int nTokens; |
499 | < | |
500 | < | nTokens = tokenizer.countTokens(); |
501 | < | |
502 | < | if (nTokens < 14) { |
503 | < | sprintf(painCave.errMsg, |
504 | < | "DumpReader Error: Not enough Tokens.\n%s\n", line); |
505 | < | painCave.isFatal = 1; |
506 | < | simError(); |
507 | < | } |
508 | < | |
509 | < | std::string name = tokenizer.nextToken(); |
510 | < | |
511 | < | if (name != integrableObject->getType()) { |
512 | < | |
513 | < | sprintf(painCave.errMsg, |
514 | < | "DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n", |
515 | < | name.c_str(), filename_.c_str(), integrableObject->getType().c_str()); |
516 | < | painCave.isFatal = 1; |
517 | < | simError(); |
518 | < | } |
519 | < | |
520 | < | pos[0] = tokenizer.nextTokenAsDouble(); |
521 | < | pos[1] = tokenizer.nextTokenAsDouble(); |
522 | < | pos[2] = tokenizer.nextTokenAsDouble(); |
523 | < | if (needPos_) { |
524 | < | integrableObject->setPos(pos); |
525 | < | } |
526 | < | |
527 | < | vel[0] = tokenizer.nextTokenAsDouble(); |
528 | < | vel[1] = tokenizer.nextTokenAsDouble(); |
529 | < | vel[2] = tokenizer.nextTokenAsDouble(); |
530 | < | if (needVel_) { |
531 | < | integrableObject->setVel(vel); |
532 | < | } |
533 | < | |
534 | < | if (integrableObject->isDirectional()) { |
535 | < | |
536 | < | q[0] = tokenizer.nextTokenAsDouble(); |
537 | < | q[1] = tokenizer.nextTokenAsDouble(); |
538 | < | q[2] = tokenizer.nextTokenAsDouble(); |
539 | < | q[3] = tokenizer.nextTokenAsDouble(); |
540 | < | |
541 | < | double qlen = q.length(); |
542 | < | if (qlen < oopse::epsilon) { //check quaternion is not equal to 0 |
543 | < | |
544 | < | sprintf(painCave.errMsg, |
545 | < | "DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n"); |
546 | < | painCave.isFatal = 1; |
547 | < | simError(); |
548 | < | |
549 | < | } |
550 | < | |
551 | < | q.normalize(); |
552 | < | if (needQuaternion_) { |
553 | < | integrableObject->setQ(q); |
554 | < | } |
555 | < | |
556 | < | ji[0] = tokenizer.nextTokenAsDouble(); |
557 | < | ji[1] = tokenizer.nextTokenAsDouble(); |
558 | < | ji[2] = tokenizer.nextTokenAsDouble(); |
559 | < | if (needAngMom_) { |
560 | < | integrableObject->setJ(ji); |
561 | < | } |
562 | < | } |
563 | < | |
564 | < | } |
565 | < | |
566 | < | |
567 | < | void DumpReader::parseCommentLine(char* line, Snapshot* s) { |
568 | < | double currTime; |
569 | < | Mat3x3d hmat; |
570 | < | double chi; |
571 | < | double integralOfChiDt; |
572 | < | Mat3x3d eta; |
573 | < | |
574 | < | StringTokenizer tokenizer(line); |
575 | < | int nTokens; |
576 | < | |
577 | < | nTokens = tokenizer.countTokens(); |
578 | < | |
579 | < | //comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens) |
580 | < | if (nTokens < 10) { |
581 | < | sprintf(painCave.errMsg, |
582 | < | "DumpReader Error: Not enough tokens in comment line: %s", line); |
583 | < | painCave.isFatal = 1; |
584 | < | simError(); |
585 | < | } |
586 | < | |
587 | < | //read current time |
588 | < | currTime = tokenizer.nextTokenAsDouble(); |
589 | < | s->setTime(currTime); |
590 | < | |
591 | < | //read h-matrix |
592 | < | hmat(0, 0) = tokenizer.nextTokenAsDouble(); |
593 | < | hmat(0, 1) = tokenizer.nextTokenAsDouble(); |
594 | < | hmat(0, 2) = tokenizer.nextTokenAsDouble(); |
595 | < | hmat(1, 0) = tokenizer.nextTokenAsDouble(); |
596 | < | hmat(1, 1) = tokenizer.nextTokenAsDouble(); |
597 | < | hmat(1, 2) = tokenizer.nextTokenAsDouble(); |
598 | < | hmat(2, 0) = tokenizer.nextTokenAsDouble(); |
599 | < | hmat(2, 1) = tokenizer.nextTokenAsDouble(); |
600 | < | hmat(2, 2) = tokenizer.nextTokenAsDouble(); |
601 | < | s->setHmat(hmat); |
602 | < | |
603 | < | //read chi and integralOfChidt, they should apprear in pair |
604 | < | if (tokenizer.countTokens() >= 2) { |
605 | < | chi = tokenizer.nextTokenAsDouble(); |
606 | < | integralOfChiDt = tokenizer.nextTokenAsDouble(); |
607 | < | |
608 | < | s->setChi(chi); |
609 | < | s->setIntegralOfChiDt(integralOfChiDt); |
610 | < | } |
611 | < | |
612 | < | //read eta (eta is 3x3 matrix) |
613 | < | if (tokenizer.countTokens() >= 9) { |
614 | < | eta(0, 0) = tokenizer.nextTokenAsDouble(); |
615 | < | eta(0, 1) = tokenizer.nextTokenAsDouble(); |
616 | < | eta(0, 2) = tokenizer.nextTokenAsDouble(); |
617 | < | eta(1, 0) = tokenizer.nextTokenAsDouble(); |
618 | < | eta(1, 1) = tokenizer.nextTokenAsDouble(); |
619 | < | eta(1, 2) = tokenizer.nextTokenAsDouble(); |
620 | < | eta(2, 0) = tokenizer.nextTokenAsDouble(); |
621 | < | eta(2, 1) = tokenizer.nextTokenAsDouble(); |
622 | < | eta(2, 2) = tokenizer.nextTokenAsDouble(); |
623 | < | |
624 | < | s->setEta(eta); |
625 | < | } |
626 | < | |
627 | < | |
628 | < | } |
629 | < | |
630 | < | }//end namespace oopse |
1 | > | /* |
2 | > | * Copyright (c) 2005 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 |
19 | > | * notice, this list of conditions and the following disclaimer. |
20 | > | * |
21 | > | * 3. Redistributions in binary form must reproduce the above copyright |
22 | > | * notice, this list of conditions and the following disclaimer in the |
23 | > | * documentation and/or other materials provided with the |
24 | > | * distribution. |
25 | > | * |
26 | > | * This software is provided "AS IS," without a warranty of any |
27 | > | * kind. All express or implied conditions, representations and |
28 | > | * warranties, including any implied warranty of merchantability, |
29 | > | * fitness for a particular purpose or non-infringement, are hereby |
30 | > | * excluded. The University of Notre Dame and its licensors shall not |
31 | > | * be liable for any damages suffered by licensee as a result of |
32 | > | * using, modifying or distributing the software or its |
33 | > | * derivatives. In no event will the University of Notre Dame or its |
34 | > | * licensors be liable for any lost revenue, profit or data, or for |
35 | > | * direct, indirect, special, consequential, incidental or punitive |
36 | > | * damages, however caused and regardless of the theory of liability, |
37 | > | * arising out of the use of or inability to use software, even if the |
38 | > | * University of Notre Dame has been advised of the possibility of |
39 | > | * such damages. |
40 | > | */ |
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 { |
71 | > | |
72 | > | DumpReader::DumpReader(SimInfo* info, const std::string& filename) |
73 | > | : info_(info), filename_(filename), isScanned_(false), nframes_(0) { |
74 | > | |
75 | > | #ifdef IS_MPI |
76 | > | |
77 | > | if (worldRank == 0) { |
78 | > | #endif |
79 | > | |
80 | > | inFile_ = new std::ifstream(filename_.c_str()); |
81 | > | |
82 | > | if (inFile_->fail()) { |
83 | > | sprintf(painCave.errMsg, |
84 | > | "DumpReader: Cannot open file: %s\n", |
85 | > | filename_.c_str()); |
86 | > | painCave.isFatal = 1; |
87 | > | simError(); |
88 | > | } |
89 | > | |
90 | > | #ifdef IS_MPI |
91 | > | |
92 | > | } |
93 | > | |
94 | > | strcpy(checkPointMsg, "Dump file opened for reading successfully."); |
95 | > | MPIcheckPoint(); |
96 | > | |
97 | > | #endif |
98 | > | |
99 | > | return; |
100 | > | } |
101 | > | |
102 | > | DumpReader::~DumpReader() { |
103 | > | |
104 | > | #ifdef IS_MPI |
105 | > | |
106 | > | if (worldRank == 0) { |
107 | > | #endif |
108 | > | |
109 | > | delete inFile_; |
110 | > | |
111 | > | #ifdef IS_MPI |
112 | > | |
113 | > | } |
114 | > | |
115 | > | strcpy(checkPointMsg, "Dump file closed successfully."); |
116 | > | MPIcheckPoint(); |
117 | > | |
118 | > | #endif |
119 | > | |
120 | > | return; |
121 | > | } |
122 | > | |
123 | > | int DumpReader::getNFrames(void) { |
124 | > | |
125 | > | if (!isScanned_) |
126 | > | scanFile(); |
127 | > | |
128 | > | return nframes_; |
129 | > | } |
130 | > | |
131 | > | void DumpReader::scanFile(void) { |
132 | > | int i, j; |
133 | > | int lineNum = 0; |
134 | > | char readBuffer[maxBufferSize]; |
135 | > | std::streampos currPos; |
136 | > | |
137 | > | #ifdef IS_MPI |
138 | > | |
139 | > | if (worldRank == 0) { |
140 | > | #endif // is_mpi |
141 | > | |
142 | > | inFile_->seekg (0, std::ios::beg); |
143 | > | |
144 | > | |
145 | > | currPos = inFile_->tellg(); |
146 | > | inFile_->getline(readBuffer, sizeof(readBuffer)); |
147 | > | lineNum++; |
148 | > | |
149 | > | if (inFile_->eof()) { |
150 | > | sprintf(painCave.errMsg, |
151 | > | "DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", |
152 | > | filename_.c_str(), |
153 | > | lineNum); |
154 | > | painCave.isFatal = 1; |
155 | > | simError(); |
156 | > | } |
157 | > | |
158 | > | while (!inFile_->eof()) { |
159 | > | framePos_.push_back(currPos); |
160 | > | |
161 | > | i = atoi(readBuffer); |
162 | > | |
163 | > | inFile_->getline(readBuffer, sizeof(readBuffer)); |
164 | > | lineNum++; |
165 | > | |
166 | > | if (inFile_->eof()) { |
167 | > | sprintf(painCave.errMsg, |
168 | > | "DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", |
169 | > | filename_.c_str(), |
170 | > | lineNum); |
171 | > | painCave.isFatal = 1; |
172 | > | simError(); |
173 | > | } |
174 | > | |
175 | > | for(j = 0; j < i; j++) { |
176 | > | inFile_->getline(readBuffer, sizeof(readBuffer)); |
177 | > | lineNum++; |
178 | > | |
179 | > | if (inFile_->eof()) { |
180 | > | sprintf(painCave.errMsg, |
181 | > | "DumpReader Error: File \"%s\" ended unexpectedly at line %d," |
182 | > | " with atom %d\n", filename_.c_str(), |
183 | > | lineNum, |
184 | > | j); |
185 | > | |
186 | > | painCave.isFatal = 1; |
187 | > | simError(); |
188 | > | } |
189 | > | } |
190 | > | |
191 | > | currPos = inFile_->tellg(); |
192 | > | inFile_->getline(readBuffer, sizeof(readBuffer)); |
193 | > | lineNum++; |
194 | > | } |
195 | > | |
196 | > | inFile_->seekg (0, std::ios::beg); |
197 | > | |
198 | > | nframes_ = framePos_.size(); |
199 | > | #ifdef IS_MPI |
200 | > | } |
201 | > | |
202 | > | MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD); |
203 | > | |
204 | > | strcpy(checkPointMsg, "Successfully scanned DumpFile\n"); |
205 | > | MPIcheckPoint(); |
206 | > | |
207 | > | #endif // is_mpi |
208 | > | |
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 | > | |
245 | > | void DumpReader::readSet(int whichFrame) { |
246 | > | int i; |
247 | > | int nTotObjs; // the number of atoms |
248 | > | char read_buffer[maxBufferSize]; //the line buffer for reading |
249 | > | char * eof_test; // ptr to see when we reach the end of the file |
250 | > | |
251 | > | Molecule* mol; |
252 | > | StuntDouble* integrableObject; |
253 | > | SimInfo::MoleculeIterator mi; |
254 | > | Molecule::IntegrableObjectIterator ii; |
255 | > | |
256 | > | #ifndef IS_MPI |
257 | > | inFile_->clear(); |
258 | > | inFile_->seekg(framePos_[whichFrame]); |
259 | > | |
260 | > | if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
261 | > | sprintf(painCave.errMsg, |
262 | > | "DumpReader error: error reading 1st line of \"%s\"\n", |
263 | > | filename_.c_str()); |
264 | > | painCave.isFatal = 1; |
265 | > | simError(); |
266 | > | } |
267 | > | |
268 | > | nTotObjs = atoi(read_buffer); |
269 | > | |
270 | > | if (nTotObjs != info_->getNGlobalIntegrableObjects()) { |
271 | > | sprintf(painCave.errMsg, |
272 | > | "DumpReader error. %s nIntegrable, %d, " |
273 | > | "does not match the meta-data file's nIntegrable, %d.\n", |
274 | > | filename_.c_str(), |
275 | > | nTotObjs, |
276 | > | info_->getNGlobalIntegrableObjects()); |
277 | > | |
278 | > | painCave.isFatal = 1; |
279 | > | simError(); |
280 | > | } |
281 | > | |
282 | > | //read the box mat from the comment line |
283 | > | |
284 | > | |
285 | > | if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
286 | > | sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", |
287 | > | filename_.c_str()); |
288 | > | painCave.isFatal = 1; |
289 | > | simError(); |
290 | > | } |
291 | > | |
292 | > | parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
293 | > | |
294 | > | //parse dump lines |
295 | > | |
296 | > | i = 0; |
297 | > | for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
298 | > | |
299 | > | for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
300 | > | integrableObject = mol->nextIntegrableObject(ii)) { |
301 | > | |
302 | > | |
303 | > | |
304 | > | if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
305 | > | sprintf(painCave.errMsg, |
306 | > | "DumpReader Error: error in reading file %s\n" |
307 | > | "natoms = %d; index = %d\n" |
308 | > | "error reading the line from the file.\n", |
309 | > | filename_.c_str(), |
310 | > | nTotObjs, |
311 | > | i); |
312 | > | |
313 | > | painCave.isFatal = 1; |
314 | > | simError(); |
315 | > | } |
316 | > | |
317 | > | parseDumpLine(read_buffer, integrableObject); |
318 | > | i++; |
319 | > | } |
320 | > | } |
321 | > | |
322 | > | // MPI Section of code.......... |
323 | > | |
324 | > | #else //IS_MPI |
325 | > | |
326 | > | // first thing first, suspend fatalities. |
327 | > | int masterNode = 0; |
328 | > | int nCurObj; |
329 | > | painCave.isEventLoop = 1; |
330 | > | |
331 | > | int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
332 | > | int haveError; |
333 | > | |
334 | > | MPI_Status istatus; |
335 | > | int nitems; |
336 | > | |
337 | > | nTotObjs = info_->getNGlobalIntegrableObjects(); |
338 | > | haveError = 0; |
339 | > | |
340 | > | if (worldRank == masterNode) { |
341 | > | inFile_->clear(); |
342 | > | inFile_->seekg(framePos_[whichFrame]); |
343 | > | |
344 | > | if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
345 | > | sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ", |
346 | > | filename_.c_str()); |
347 | > | painCave.isFatal = 1; |
348 | > | simError(); |
349 | > | } |
350 | > | |
351 | > | nitems = atoi(read_buffer); |
352 | > | |
353 | > | // Check to see that the number of integrable objects in the |
354 | > | // intial configuration file is the same as derived from the |
355 | > | // meta-data file. |
356 | > | |
357 | > | if (nTotObjs != nitems) { |
358 | > | sprintf(painCave.errMsg, |
359 | > | "DumpReader Error. %s nIntegrable, %d, " |
360 | > | "does not match the meta-data file's nIntegrable, %d.\n", |
361 | > | filename_.c_str(), |
362 | > | nTotObjs, |
363 | > | info_->getNGlobalIntegrableObjects()); |
364 | > | |
365 | > | painCave.isFatal = 1; |
366 | > | simError(); |
367 | > | } |
368 | > | |
369 | > | //read the boxMat from the comment line |
370 | > | |
371 | > | |
372 | > | |
373 | > | if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
374 | > | sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", |
375 | > | filename_.c_str()); |
376 | > | painCave.isFatal = 1; |
377 | > | simError(); |
378 | > | } |
379 | > | |
380 | > | //Every single processor will parse the comment line by itself |
381 | > | //By using this way, we might lose some efficiency, but if we want to add |
382 | > | //more parameters into comment line, we only need to modify function |
383 | > | //parseCommentLine |
384 | > | |
385 | > | MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
386 | > | parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
387 | > | |
388 | > | for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
389 | > | int which_node = info_->getMolToProc(i); |
390 | > | |
391 | > | if (which_node == masterNode) { |
392 | > | //molecules belong to master node |
393 | > | |
394 | > | mol = info_->getMoleculeByGlobalIndex(i); |
395 | > | |
396 | > | if (mol == NULL) { |
397 | > | sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
398 | > | painCave.isFatal = 1; |
399 | > | simError(); |
400 | > | } |
401 | > | |
402 | > | for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
403 | > | integrableObject = mol->nextIntegrableObject(ii)){ |
404 | > | |
405 | > | |
406 | > | |
407 | > | if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
408 | > | sprintf(painCave.errMsg, |
409 | > | "DumpReader Error: error in reading file %s\n" |
410 | > | "natoms = %d; index = %d\n" |
411 | > | "error reading the line from the file.\n", |
412 | > | filename_.c_str(), |
413 | > | nTotObjs, |
414 | > | i); |
415 | > | |
416 | > | painCave.isFatal = 1; |
417 | > | simError(); |
418 | > | } |
419 | > | |
420 | > | parseDumpLine(read_buffer, integrableObject); |
421 | > | } |
422 | > | } else { |
423 | > | //molecule belongs to slave nodes |
424 | > | |
425 | > | MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
426 | > | MPI_COMM_WORLD, &istatus); |
427 | > | |
428 | > | for(int j = 0; j < nCurObj; j++) { |
429 | > | |
430 | > | |
431 | > | if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
432 | > | sprintf(painCave.errMsg, |
433 | > | "DumpReader Error: error in reading file %s\n" |
434 | > | "natoms = %d; index = %d\n" |
435 | > | "error reading the line from the file.\n", |
436 | > | filename_.c_str(), |
437 | > | nTotObjs, |
438 | > | i); |
439 | > | |
440 | > | painCave.isFatal = 1; |
441 | > | simError(); |
442 | > | } |
443 | > | |
444 | > | MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node, |
445 | > | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
446 | > | } |
447 | > | } |
448 | > | } |
449 | > | } else { |
450 | > | //actions taken at slave nodes |
451 | > | MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
452 | > | |
453 | > | /**@todo*/ |
454 | > | parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
455 | > | |
456 | > | for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
457 | > | int which_node = info_->getMolToProc(i); |
458 | > | |
459 | > | if (which_node == worldRank) { |
460 | > | //molecule with global index i belongs to this processor |
461 | > | |
462 | > | mol = info_->getMoleculeByGlobalIndex(i); |
463 | > | if (mol == NULL) { |
464 | > | sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
465 | > | painCave.isFatal = 1; |
466 | > | simError(); |
467 | > | } |
468 | > | |
469 | > | nCurObj = mol->getNIntegrableObjects(); |
470 | > | |
471 | > | MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT, |
472 | > | MPI_COMM_WORLD); |
473 | > | |
474 | > | for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
475 | > | integrableObject = mol->nextIntegrableObject(ii)){ |
476 | > | |
477 | > | MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode, |
478 | > | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
479 | > | |
480 | > | parseDumpLine(read_buffer, integrableObject); |
481 | > | } |
482 | > | |
483 | > | } |
484 | > | |
485 | > | } |
486 | > | |
487 | > | } |
488 | > | |
489 | > | #endif |
490 | > | |
491 | > | } |
492 | > | |
493 | > | void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) { |
494 | > | |
495 | > | Vector3d pos; // position place holders |
496 | > | Vector3d vel; // velocity placeholders |
497 | > | Quat4d q; // the quaternions |
498 | > | Vector3d ji; // angular velocity placeholders; |
499 | > | StringTokenizer tokenizer(line); |
500 | > | int nTokens; |
501 | > | |
502 | > | nTokens = tokenizer.countTokens(); |
503 | > | |
504 | > | if (nTokens < 14) { |
505 | > | sprintf(painCave.errMsg, |
506 | > | "DumpReader Error: Not enough Tokens.\n%s\n", line); |
507 | > | painCave.isFatal = 1; |
508 | > | simError(); |
509 | > | } |
510 | > | |
511 | > | std::string name = tokenizer.nextToken(); |
512 | > | |
513 | > | if (name != integrableObject->getType()) { |
514 | > | |
515 | > | sprintf(painCave.errMsg, |
516 | > | "DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n", |
517 | > | name.c_str(), filename_.c_str(), integrableObject->getType().c_str()); |
518 | > | painCave.isFatal = 1; |
519 | > | simError(); |
520 | > | } |
521 | > | |
522 | > | pos[0] = tokenizer.nextTokenAsDouble(); |
523 | > | pos[1] = tokenizer.nextTokenAsDouble(); |
524 | > | pos[2] = tokenizer.nextTokenAsDouble(); |
525 | > | if (needPos_) { |
526 | > | integrableObject->setPos(pos); |
527 | > | } |
528 | > | |
529 | > | vel[0] = tokenizer.nextTokenAsDouble(); |
530 | > | vel[1] = tokenizer.nextTokenAsDouble(); |
531 | > | vel[2] = tokenizer.nextTokenAsDouble(); |
532 | > | if (needVel_) { |
533 | > | integrableObject->setVel(vel); |
534 | > | } |
535 | > | |
536 | > | if (integrableObject->isDirectional()) { |
537 | > | |
538 | > | q[0] = tokenizer.nextTokenAsDouble(); |
539 | > | q[1] = tokenizer.nextTokenAsDouble(); |
540 | > | q[2] = tokenizer.nextTokenAsDouble(); |
541 | > | q[3] = tokenizer.nextTokenAsDouble(); |
542 | > | |
543 | > | RealType qlen = q.length(); |
544 | > | if (qlen < oopse::epsilon) { //check quaternion is not equal to 0 |
545 | > | |
546 | > | sprintf(painCave.errMsg, |
547 | > | "DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n"); |
548 | > | painCave.isFatal = 1; |
549 | > | simError(); |
550 | > | |
551 | > | } |
552 | > | |
553 | > | q.normalize(); |
554 | > | if (needQuaternion_) { |
555 | > | integrableObject->setQ(q); |
556 | > | } |
557 | > | |
558 | > | ji[0] = tokenizer.nextTokenAsDouble(); |
559 | > | ji[1] = tokenizer.nextTokenAsDouble(); |
560 | > | ji[2] = tokenizer.nextTokenAsDouble(); |
561 | > | if (needAngMom_) { |
562 | > | integrableObject->setJ(ji); |
563 | > | } |
564 | > | } |
565 | > | |
566 | > | } |
567 | > | |
568 | > | |
569 | > | void DumpReader::parseCommentLine(char* line, Snapshot* s) { |
570 | > | RealType currTime; |
571 | > | Mat3x3d hmat; |
572 | > | RealType chi; |
573 | > | RealType integralOfChiDt; |
574 | > | Mat3x3d eta; |
575 | > | |
576 | > | StringTokenizer tokenizer(line); |
577 | > | int nTokens; |
578 | > | |
579 | > | nTokens = tokenizer.countTokens(); |
580 | > | |
581 | > | //comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens) |
582 | > | if (nTokens < 10) { |
583 | > | sprintf(painCave.errMsg, |
584 | > | "DumpReader Error: Not enough tokens in comment line: %s", line); |
585 | > | painCave.isFatal = 1; |
586 | > | simError(); |
587 | > | } |
588 | > | |
589 | > | //read current time |
590 | > | currTime = tokenizer.nextTokenAsDouble(); |
591 | > | s->setTime(currTime); |
592 | > | |
593 | > | //read h-matrix |
594 | > | hmat(0, 0) = tokenizer.nextTokenAsDouble(); |
595 | > | hmat(0, 1) = tokenizer.nextTokenAsDouble(); |
596 | > | hmat(0, 2) = tokenizer.nextTokenAsDouble(); |
597 | > | hmat(1, 0) = tokenizer.nextTokenAsDouble(); |
598 | > | hmat(1, 1) = tokenizer.nextTokenAsDouble(); |
599 | > | hmat(1, 2) = tokenizer.nextTokenAsDouble(); |
600 | > | hmat(2, 0) = tokenizer.nextTokenAsDouble(); |
601 | > | hmat(2, 1) = tokenizer.nextTokenAsDouble(); |
602 | > | hmat(2, 2) = tokenizer.nextTokenAsDouble(); |
603 | > | s->setHmat(hmat); |
604 | > | |
605 | > | //read chi and integralOfChidt, they should apprear in pair |
606 | > | if (tokenizer.countTokens() >= 2) { |
607 | > | chi = tokenizer.nextTokenAsDouble(); |
608 | > | integralOfChiDt = tokenizer.nextTokenAsDouble(); |
609 | > | |
610 | > | s->setChi(chi); |
611 | > | s->setIntegralOfChiDt(integralOfChiDt); |
612 | > | } |
613 | > | |
614 | > | //read eta (eta is 3x3 matrix) |
615 | > | if (tokenizer.countTokens() >= 9) { |
616 | > | eta(0, 0) = tokenizer.nextTokenAsDouble(); |
617 | > | eta(0, 1) = tokenizer.nextTokenAsDouble(); |
618 | > | eta(0, 2) = tokenizer.nextTokenAsDouble(); |
619 | > | eta(1, 0) = tokenizer.nextTokenAsDouble(); |
620 | > | eta(1, 1) = tokenizer.nextTokenAsDouble(); |
621 | > | eta(1, 2) = tokenizer.nextTokenAsDouble(); |
622 | > | eta(2, 0) = tokenizer.nextTokenAsDouble(); |
623 | > | eta(2, 1) = tokenizer.nextTokenAsDouble(); |
624 | > | eta(2, 2) = tokenizer.nextTokenAsDouble(); |
625 | > | |
626 | > | s->setEta(eta); |
627 | > | } |
628 | > | |
629 | > | |
630 | > | } |
631 | > | |
632 | > | }//end namespace oopse |
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