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_ = fopen(filename_.c_str(), "r"); |
81 |
< |
|
82 |
< |
if (inFile_ == NULL) { |
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 |
< |
int error; |
108 |
< |
error = fclose(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 |
< |
} |
115 |
< |
|
116 |
< |
MemoryUtils::deletePointers(framePos_); |
117 |
< |
|
118 |
< |
#ifdef IS_MPI |
119 |
< |
|
120 |
< |
} |
121 |
< |
|
122 |
< |
strcpy(checkPointMsg, "Dump file closed successfully."); |
123 |
< |
MPIcheckPoint(); |
124 |
< |
|
125 |
< |
#endif |
126 |
< |
|
127 |
< |
return; |
128 |
< |
} |
129 |
< |
|
130 |
< |
int DumpReader::getNFrames(void) { |
131 |
< |
|
132 |
< |
if (!isScanned_) |
133 |
< |
scanFile(); |
134 |
< |
|
135 |
< |
return nframes_; |
136 |
< |
} |
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 |
148 |
< |
|
149 |
< |
rewind(inFile_); |
150 |
< |
|
151 |
< |
currPos = new fpos_t; |
152 |
< |
fgetpos(inFile_, currPos); |
153 |
< |
fgets(readBuffer, sizeof(readBuffer), inFile_); |
154 |
< |
lineNum++; |
155 |
< |
|
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); |
167 |
< |
|
168 |
< |
i = atoi(readBuffer); |
169 |
< |
|
170 |
< |
fgets(readBuffer, sizeof(readBuffer), inFile_); |
171 |
< |
lineNum++; |
172 |
< |
|
173 |
< |
if (feof(inFile_)) { |
174 |
< |
sprintf(painCave.errMsg, |
175 |
< |
"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", |
176 |
< |
filename_.c_str(), |
177 |
< |
lineNum); |
178 |
< |
painCave.isFatal = 1; |
179 |
< |
simError(); |
180 |
< |
} |
181 |
< |
|
182 |
< |
for(j = 0; j < i; j++) { |
183 |
< |
fgets(readBuffer, sizeof(readBuffer), inFile_); |
184 |
< |
lineNum++; |
185 |
< |
|
186 |
< |
if (feof(inFile_)) { |
187 |
< |
sprintf(painCave.errMsg, |
188 |
< |
"DumpReader Error: File \"%s\" ended unexpectedly at line %d," |
189 |
< |
" with atom %d\n", filename_.c_str(), |
190 |
< |
lineNum, |
191 |
< |
j); |
192 |
< |
|
193 |
< |
painCave.isFatal = 1; |
194 |
< |
simError(); |
195 |
< |
} |
196 |
< |
} |
197 |
< |
|
198 |
< |
currPos = new fpos_t; |
199 |
< |
fgetpos(inFile_, currPos); |
200 |
< |
fgets(readBuffer, sizeof(readBuffer), inFile_); |
201 |
< |
lineNum++; |
202 |
< |
} |
203 |
< |
|
204 |
< |
delete currPos; |
205 |
< |
rewind(inFile_); |
206 |
< |
|
207 |
< |
nframes_ = framePos_.size(); |
208 |
< |
#ifdef IS_MPI |
209 |
< |
} |
210 |
< |
|
211 |
< |
MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD); |
212 |
< |
|
213 |
< |
strcpy(checkPointMsg, "Successfully scanned DumpFile\n"); |
214 |
< |
MPIcheckPoint(); |
215 |
< |
|
216 |
< |
#endif // is_mpi |
217 |
< |
|
218 |
< |
isScanned_ = true; |
219 |
< |
} |
220 |
< |
|
221 |
< |
void DumpReader::readFrame(int whichFrame) { |
222 |
< |
int storageLayout = info_->getSnapshotManager()->getStorageLayout(); |
223 |
< |
|
224 |
< |
if (storageLayout & DataStorage::dslPosition) { |
225 |
< |
needPos_ = true; |
226 |
< |
} else { |
227 |
< |
needPos_ = false; |
228 |
< |
} |
229 |
< |
|
230 |
< |
if (storageLayout & DataStorage::dslVelocity) { |
231 |
< |
needVel_ = true; |
232 |
< |
} else { |
233 |
< |
needVel_ = false; |
234 |
< |
} |
235 |
< |
|
236 |
< |
if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) { |
237 |
< |
needQuaternion_ = true; |
238 |
< |
} else { |
239 |
< |
needQuaternion_ = false; |
240 |
< |
} |
241 |
< |
|
242 |
< |
if (storageLayout & DataStorage::dslAngularMomentum) { |
243 |
< |
needAngMom_ = true; |
244 |
< |
} else { |
245 |
< |
needAngMom_ = false; |
246 |
< |
} |
247 |
< |
|
248 |
< |
readSet(whichFrame); |
249 |
< |
} |
250 |
< |
|
251 |
< |
void DumpReader::readSet(int whichFrame) { |
252 |
< |
int i; |
253 |
< |
int nTotObjs; // the number of atoms |
254 |
< |
char read_buffer[maxBufferSize]; //the line buffer for reading |
255 |
< |
char * eof_test; // ptr to see when we reach the end of the file |
256 |
< |
|
257 |
< |
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(); |
273 |
< |
} |
274 |
< |
|
275 |
< |
nTotObjs = atoi(read_buffer); |
276 |
< |
|
277 |
< |
if (nTotObjs != info_->getNGlobalIntegrableObjects()) { |
278 |
< |
sprintf(painCave.errMsg, |
279 |
< |
"DumpReader error. %s nIntegrable, %d, " |
280 |
< |
"does not match the meta-data file's nIntegrable, %d.\n", |
281 |
< |
filename_.c_str(), |
282 |
< |
nTotObjs, |
283 |
< |
info_->getNGlobalIntegrableObjects()); |
284 |
< |
|
285 |
< |
painCave.isFatal = 1; |
286 |
< |
simError(); |
287 |
< |
} |
288 |
< |
|
289 |
< |
//read the box mat from the comment line |
290 |
< |
|
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)) { |
309 |
< |
|
310 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
311 |
< |
|
312 |
< |
if (eof_test == NULL) { |
313 |
< |
sprintf(painCave.errMsg, |
314 |
< |
"DumpReader Error: error in reading file %s\n" |
315 |
< |
"natoms = %d; index = %d\n" |
316 |
< |
"error reading the line from the file.\n", |
317 |
< |
filename_.c_str(), |
318 |
< |
nTotObjs, |
319 |
< |
i); |
320 |
< |
|
321 |
< |
painCave.isFatal = 1; |
322 |
< |
simError(); |
323 |
< |
} |
324 |
< |
|
325 |
< |
parseDumpLine(read_buffer, integrableObject); |
326 |
< |
i++; |
327 |
< |
} |
328 |
< |
} |
329 |
< |
|
330 |
< |
// MPI Section of code.......... |
331 |
< |
|
332 |
< |
#else //IS_MPI |
333 |
< |
|
334 |
< |
// first thing first, suspend fatalities. |
335 |
< |
int masterNode = 0; |
336 |
< |
int nCurObj; |
337 |
< |
painCave.isEventLoop = 1; |
338 |
< |
|
339 |
< |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
340 |
< |
int haveError; |
341 |
< |
|
342 |
< |
MPI_Status istatus; |
343 |
< |
int nitems; |
344 |
< |
|
345 |
< |
nTotObjs = info_->getNGlobalIntegrableObjects(); |
346 |
< |
haveError = 0; |
347 |
< |
|
348 |
< |
if (worldRank == masterNode) { |
349 |
< |
fsetpos(inFile_, framePos_[whichFrame]); |
350 |
< |
|
351 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
352 |
< |
|
353 |
< |
if (eof_test == NULL) { |
354 |
< |
sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ", |
355 |
< |
filename_.c_str()); |
356 |
< |
painCave.isFatal = 1; |
357 |
< |
simError(); |
358 |
< |
} |
359 |
< |
|
360 |
< |
nitems = atoi(read_buffer); |
361 |
< |
|
362 |
< |
// Check to see that the number of integrable objects in the |
363 |
< |
// intial configuration file is the same as derived from the |
364 |
< |
// meta-data file. |
365 |
< |
|
366 |
< |
if (nTotObjs != nitems) { |
367 |
< |
sprintf(painCave.errMsg, |
368 |
< |
"DumpReader Error. %s nIntegrable, %d, " |
369 |
< |
"does not match the meta-data file's nIntegrable, %d.\n", |
370 |
< |
filename_.c_str(), |
371 |
< |
nTotObjs, |
372 |
< |
info_->getNGlobalIntegrableObjects()); |
373 |
< |
|
374 |
< |
painCave.isFatal = 1; |
375 |
< |
simError(); |
376 |
< |
} |
377 |
< |
|
378 |
< |
//read the boxMat from the comment line |
379 |
< |
|
380 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
381 |
< |
|
382 |
< |
if (eof_test == NULL) { |
383 |
< |
sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", |
384 |
< |
filename_.c_str()); |
385 |
< |
painCave.isFatal = 1; |
386 |
< |
simError(); |
387 |
< |
} |
388 |
< |
|
389 |
< |
//Every single processor will parse the comment line by itself |
390 |
< |
//By using this way, we might lose some efficiency, but if we want to add |
391 |
< |
//more parameters into comment line, we only need to modify function |
392 |
< |
//parseCommentLine |
393 |
< |
|
394 |
< |
MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
395 |
< |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
396 |
< |
|
397 |
< |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
398 |
< |
int which_node = info_->getMolToProc(i); |
399 |
< |
|
400 |
< |
if (which_node == masterNode) { |
401 |
< |
//molecules belong to master node |
402 |
< |
|
403 |
< |
mol = info_->getMoleculeByGlobalIndex(i); |
404 |
< |
|
405 |
< |
if (mol == NULL) { |
406 |
< |
sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
407 |
< |
painCave.isFatal = 1; |
408 |
< |
simError(); |
409 |
< |
} |
410 |
< |
|
411 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
412 |
< |
integrableObject = mol->nextIntegrableObject(ii)){ |
413 |
< |
|
414 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
415 |
< |
|
416 |
< |
if (eof_test == NULL) { |
417 |
< |
sprintf(painCave.errMsg, |
418 |
< |
"DumpReader Error: error in reading file %s\n" |
419 |
< |
"natoms = %d; index = %d\n" |
420 |
< |
"error reading the line from the file.\n", |
421 |
< |
filename_.c_str(), |
422 |
< |
nTotObjs, |
423 |
< |
i); |
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 |
< |
} |
457 |
< |
} |
458 |
< |
} 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); |
467 |
< |
|
468 |
< |
if (which_node == worldRank) { |
469 |
< |
//molecule with global index i belongs to this processor |
470 |
< |
|
471 |
< |
mol = info_->getMoleculeByGlobalIndex(i); |
472 |
< |
if (mol == NULL) { |
473 |
< |
sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
474 |
< |
painCave.isFatal = 1; |
475 |
< |
simError(); |
476 |
< |
} |
477 |
< |
|
478 |
< |
nCurObj = mol->getNIntegrableObjects(); |
479 |
< |
|
480 |
< |
MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT, |
481 |
< |
MPI_COMM_WORLD); |
482 |
< |
|
483 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
484 |
< |
integrableObject = mol->nextIntegrableObject(ii)){ |
485 |
< |
|
486 |
< |
MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode, |
487 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
488 |
< |
|
489 |
< |
parseDumpLine(read_buffer, integrableObject); |
490 |
< |
} |
491 |
< |
|
492 |
< |
} |
493 |
< |
|
494 |
< |
} |
495 |
< |
|
496 |
< |
} |
497 |
< |
|
498 |
< |
#endif |
499 |
< |
|
500 |
< |
} |
501 |
< |
|
502 |
< |
void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) { |
503 |
< |
|
504 |
< |
Vector3d pos; // position place holders |
505 |
< |
Vector3d vel; // velocity placeholders |
506 |
< |
Quat4d q; // the quaternions |
507 |
< |
Vector3d ji; // angular velocity placeholders; |
508 |
< |
StringTokenizer tokenizer(line); |
509 |
< |
int nTokens; |
510 |
< |
|
511 |
< |
nTokens = tokenizer.countTokens(); |
512 |
< |
|
513 |
< |
if (nTokens < 14) { |
514 |
< |
sprintf(painCave.errMsg, |
515 |
< |
"DumpReader Error: Not enough Tokens.\n%s\n", line); |
516 |
< |
painCave.isFatal = 1; |
517 |
< |
simError(); |
518 |
< |
} |
519 |
< |
|
520 |
< |
std::string name = tokenizer.nextToken(); |
521 |
< |
|
522 |
< |
if (name != integrableObject->getType()) { |
523 |
< |
|
524 |
< |
sprintf(painCave.errMsg, |
525 |
< |
"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n", |
526 |
< |
name.c_str(), filename_.c_str(), integrableObject->getType().c_str()); |
527 |
< |
painCave.isFatal = 1; |
528 |
< |
simError(); |
529 |
< |
} |
530 |
< |
|
531 |
< |
pos[0] = tokenizer.nextTokenAsDouble(); |
532 |
< |
pos[1] = tokenizer.nextTokenAsDouble(); |
533 |
< |
pos[2] = tokenizer.nextTokenAsDouble(); |
534 |
< |
if (needPos_) { |
535 |
< |
integrableObject->setPos(pos); |
536 |
< |
} |
537 |
< |
|
538 |
< |
vel[0] = tokenizer.nextTokenAsDouble(); |
539 |
< |
vel[1] = tokenizer.nextTokenAsDouble(); |
540 |
< |
vel[2] = tokenizer.nextTokenAsDouble(); |
541 |
< |
if (needVel_) { |
542 |
< |
integrableObject->setVel(vel); |
543 |
< |
} |
544 |
< |
|
545 |
< |
if (integrableObject->isDirectional()) { |
546 |
< |
|
547 |
< |
q[0] = tokenizer.nextTokenAsDouble(); |
548 |
< |
q[1] = tokenizer.nextTokenAsDouble(); |
549 |
< |
q[2] = tokenizer.nextTokenAsDouble(); |
550 |
< |
q[3] = tokenizer.nextTokenAsDouble(); |
551 |
< |
|
552 |
< |
double qlen = q.length(); |
553 |
< |
if (qlen < oopse::epsilon) { //check quaternion is not equal to 0 |
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); |
565 |
< |
} |
566 |
< |
|
567 |
< |
ji[0] = tokenizer.nextTokenAsDouble(); |
568 |
< |
ji[1] = tokenizer.nextTokenAsDouble(); |
569 |
< |
ji[2] = tokenizer.nextTokenAsDouble(); |
570 |
< |
if (needAngMom_) { |
571 |
< |
integrableObject->setJ(ji); |
572 |
< |
} |
573 |
< |
} |
574 |
< |
|
575 |
< |
} |
576 |
< |
|
577 |
< |
|
578 |
< |
void DumpReader::parseCommentLine(char* line, Snapshot* s) { |
579 |
< |
double currTime; |
580 |
< |
Mat3x3d hmat; |
581 |
< |
double chi; |
582 |
< |
double integralOfChiDt; |
583 |
< |
Mat3x3d eta; |
584 |
< |
|
585 |
< |
StringTokenizer tokenizer(line); |
586 |
< |
int nTokens; |
587 |
< |
|
588 |
< |
nTokens = tokenizer.countTokens(); |
589 |
< |
|
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(); |
596 |
< |
} |
597 |
< |
|
598 |
< |
//read current time |
599 |
< |
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(); |
618 |
< |
|
619 |
< |
s->setChi(chi); |
620 |
< |
s->setIntegralOfChiDt(integralOfChiDt); |
621 |
< |
} |
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(); |
634 |
< |
|
635 |
< |
s->setEta(eta); |
636 |
< |
} |
637 |
< |
|
638 |
< |
|
639 |
< |
} |
640 |
< |
|
641 |
< |
}//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, "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(readBuffer, sizeof(readBuffer))) { |
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(readBuffer, sizeof(readBuffer))) { |
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(readBuffer, sizeof(readBuffer))) { |
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(readBuffer, sizeof(readBuffer))) { |
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 |