1 |
#define _LARGEFILE_SOURCE64 |
2 |
#define _FILE_OFFSET_BITS 64 |
3 |
|
4 |
#include <sys/types.h> |
5 |
#include <sys/stat.h> |
6 |
|
7 |
#include <iostream> |
8 |
#include <math.h> |
9 |
|
10 |
#include <stdio.h> |
11 |
#include <stdlib.h> |
12 |
#include <string.h> |
13 |
|
14 |
|
15 |
#include "io/ReadWrite.hpp" |
16 |
#include "utils/simError.h" |
17 |
|
18 |
#ifdef IS_MPI |
19 |
#include <mpi.h> |
20 |
#include "brains/mpiSimulation.hpp" |
21 |
#define TAKE_THIS_TAG_CHAR 0 |
22 |
#define TAKE_THIS_TAG_INT 1 |
23 |
#endif // is_mpi |
24 |
|
25 |
|
26 |
DumpReader :: DumpReader(const char *in_name ){ |
27 |
|
28 |
isScanned = false; |
29 |
|
30 |
#ifdef IS_MPI |
31 |
if (worldRank == 0) { |
32 |
#endif |
33 |
|
34 |
inFile = fopen(in_name, "r"); |
35 |
if(inFile == NULL){ |
36 |
sprintf(painCave.errMsg, |
37 |
"Cannot open file: %s\n", in_name); |
38 |
painCave.isFatal = 1; |
39 |
simError(); |
40 |
} |
41 |
|
42 |
inFileName = in_name; |
43 |
#ifdef IS_MPI |
44 |
} |
45 |
strcpy( checkPointMsg, "Dump file opened for reading successfully." ); |
46 |
MPIcheckPoint(); |
47 |
#endif |
48 |
return; |
49 |
} |
50 |
|
51 |
DumpReader :: ~DumpReader( ){ |
52 |
#ifdef IS_MPI |
53 |
if (worldRank == 0) { |
54 |
#endif |
55 |
vector<fpos_t*>::iterator i; |
56 |
|
57 |
int error; |
58 |
error = fclose( inFile ); |
59 |
if( error ){ |
60 |
sprintf( painCave.errMsg, |
61 |
"Error closing %s\n", inFileName.c_str()); |
62 |
simError(); |
63 |
} |
64 |
|
65 |
for(i = framePos.begin(); i != framePos.end(); ++i) |
66 |
delete *i; |
67 |
framePos.clear(); |
68 |
|
69 |
#ifdef IS_MPI |
70 |
} |
71 |
strcpy( checkPointMsg, "Dump file closed successfully." ); |
72 |
MPIcheckPoint(); |
73 |
#endif |
74 |
|
75 |
return; |
76 |
} |
77 |
|
78 |
int DumpReader::getNframes( void ){ |
79 |
|
80 |
if( !isScanned ) |
81 |
scanFile(); |
82 |
return framePos.size(); |
83 |
} |
84 |
|
85 |
void DumpReader::scanFile( void ){ |
86 |
|
87 |
int i, j; |
88 |
int lineNum = 0; |
89 |
char readBuffer[2000]; |
90 |
fpos_t *currPos; |
91 |
|
92 |
#ifdef IS_MPI |
93 |
if( worldRank == 0 ){ |
94 |
#endif // is_mpi |
95 |
|
96 |
rewind( inFile ); |
97 |
|
98 |
currPos = new fpos_t; |
99 |
fgetpos( inFile, currPos ); |
100 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
101 |
lineNum++; |
102 |
if( feof( inFile ) ){ |
103 |
sprintf( painCave.errMsg, |
104 |
"File \"%s\" ended unexpectedly at line %d\n", |
105 |
inFileName.c_str(), |
106 |
lineNum ); |
107 |
painCave.isFatal = 1; |
108 |
simError(); |
109 |
} |
110 |
|
111 |
while( !feof( inFile ) ){ |
112 |
|
113 |
framePos.push_back(currPos); |
114 |
|
115 |
i = atoi(readBuffer); |
116 |
|
117 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
118 |
lineNum++; |
119 |
if( feof( inFile ) ){ |
120 |
sprintf( painCave.errMsg, |
121 |
"File \"%s\" ended unexpectedly at line %d\n", |
122 |
inFileName.c_str(), |
123 |
lineNum ); |
124 |
painCave.isFatal = 1; |
125 |
simError(); |
126 |
} |
127 |
|
128 |
for(j=0; j<i; j++){ |
129 |
|
130 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
131 |
lineNum++; |
132 |
if( feof( inFile ) ){ |
133 |
sprintf( painCave.errMsg, |
134 |
"File \"%s\" ended unexpectedly at line %d," |
135 |
" with atom %d\n", |
136 |
inFileName.c_str(), |
137 |
lineNum, |
138 |
j ); |
139 |
painCave.isFatal = 1; |
140 |
simError(); |
141 |
} |
142 |
|
143 |
} |
144 |
|
145 |
currPos = new fpos_t; |
146 |
fgetpos( inFile, currPos ); |
147 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
148 |
lineNum++; |
149 |
} |
150 |
|
151 |
delete currPos; |
152 |
rewind( inFile ); |
153 |
|
154 |
isScanned = true; |
155 |
|
156 |
#ifdef IS_MPI |
157 |
} |
158 |
strcpy( checkPointMsg, "Successfully scanned DumpFile\n" ); |
159 |
MPIcheckPoint(); |
160 |
#endif // is_mpi |
161 |
} |
162 |
|
163 |
void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){ |
164 |
|
165 |
simnfo = the_simnfo; |
166 |
|
167 |
this->readSet( whichFrame ); |
168 |
} |
169 |
|
170 |
|
171 |
|
172 |
void DumpReader :: readSet( int whichFrame ){ |
173 |
|
174 |
int i; |
175 |
unsigned int j; |
176 |
|
177 |
#ifdef IS_MPI |
178 |
int done, which_node, which_atom; // loop counter |
179 |
#endif //is_mpi |
180 |
|
181 |
const int BUFFERSIZE = 2000; // size of the read buffer |
182 |
int nTotObjs; // the number of atoms |
183 |
char read_buffer[BUFFERSIZE]; //the line buffer for reading |
184 |
|
185 |
char *eof_test; // ptr to see when we reach the end of the file |
186 |
char *parseErr; |
187 |
|
188 |
vector<StuntDouble*> integrableObjects; |
189 |
|
190 |
|
191 |
#ifndef IS_MPI |
192 |
|
193 |
fsetpos(inFile, framePos[whichFrame]); |
194 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
195 |
if( eof_test == NULL ){ |
196 |
sprintf( painCave.errMsg, |
197 |
"DumpReader error: error reading 1st line of \"%s\"\n", |
198 |
inFileName.c_str() ); |
199 |
painCave.isFatal = 1; |
200 |
simError(); |
201 |
} |
202 |
|
203 |
nTotObjs = atoi( read_buffer ); |
204 |
|
205 |
if( nTotObjs != simnfo->getTotIntegrableObjects() ){ |
206 |
sprintf( painCave.errMsg, |
207 |
"DumpReader error. %s nIntegrable, %d, " |
208 |
"does not match the meta-data file's nIntegrable, %d.\n", |
209 |
inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects()); |
210 |
painCave.isFatal = 1; |
211 |
simError(); |
212 |
} |
213 |
|
214 |
//read the box mat from the comment line |
215 |
|
216 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
217 |
if(eof_test == NULL){ |
218 |
sprintf( painCave.errMsg, |
219 |
"error in reading commment in %s\n", inFileName.c_str()); |
220 |
painCave.isFatal = 1; |
221 |
simError(); |
222 |
} |
223 |
|
224 |
parseErr = parseCommentLine( read_buffer, simnfo); |
225 |
if( parseErr != NULL ){ |
226 |
strcpy( painCave.errMsg, parseErr ); |
227 |
painCave.isFatal = 1; |
228 |
simError(); |
229 |
} |
230 |
|
231 |
//parse dump lines |
232 |
|
233 |
for( i=0; i < simnfo->n_mol; i++){ |
234 |
|
235 |
integrableObjects = (simnfo->molecules[i]).getIntegrableObjects(); |
236 |
|
237 |
for(j = 0; j < integrableObjects.size(); j++){ |
238 |
|
239 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
240 |
if(eof_test == NULL){ |
241 |
sprintf(painCave.errMsg, |
242 |
"error in reading file %s\n" |
243 |
"natoms = %d; index = %d\n" |
244 |
"error reading the line from the file.\n", |
245 |
inFileName.c_str(), nTotObjs, i ); |
246 |
painCave.isFatal = 1; |
247 |
simError(); |
248 |
} |
249 |
|
250 |
parseErr = parseDumpLine( read_buffer, integrableObjects[j]); |
251 |
if( parseErr != NULL ){ |
252 |
strcpy( painCave.errMsg, parseErr ); |
253 |
painCave.isFatal = 1; |
254 |
simError(); |
255 |
} |
256 |
} |
257 |
} |
258 |
|
259 |
// MPI Section of code.......... |
260 |
#else //IS_MPI |
261 |
|
262 |
// first thing first, suspend fatalities. |
263 |
painCave.isEventLoop = 1; |
264 |
|
265 |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
266 |
int haveError; |
267 |
|
268 |
MPI_Status istatus; |
269 |
int *MolToProcMap = mpiSim->getMolToProcMap(); |
270 |
int localIndex; |
271 |
int nCurObj; |
272 |
int nitems; |
273 |
|
274 |
nTotObjs = simnfo->getTotIntegrableObjects(); |
275 |
haveError = 0; |
276 |
if (worldRank == 0) { |
277 |
fsetpos(inFile, framePos[whichFrame]); |
278 |
|
279 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
280 |
if( eof_test == NULL ){ |
281 |
sprintf( painCave.errMsg, |
282 |
"Error reading 1st line of %s \n ",inFileName.c_str()); |
283 |
haveError = 1; |
284 |
simError(); |
285 |
} |
286 |
|
287 |
nitems = atoi( read_buffer ); |
288 |
|
289 |
// Check to see that the number of integrable objects in the |
290 |
// intial configuration file is the same as derived from the |
291 |
// meta-data file. |
292 |
|
293 |
if( nTotObjs != nitems){ |
294 |
sprintf( painCave.errMsg, |
295 |
"DumpReader Error. %s nIntegrable, %d, " |
296 |
"does not match the meta-data file's nIntegrable, %d.\n", |
297 |
inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects()); |
298 |
haveError= 1; |
299 |
simError(); |
300 |
} |
301 |
|
302 |
//read the boxMat from the comment line |
303 |
|
304 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
305 |
if(eof_test == NULL){ |
306 |
sprintf( painCave.errMsg, |
307 |
"error in reading commment in %s\n", inFileName.c_str()); |
308 |
haveError = 1; |
309 |
simError(); |
310 |
} |
311 |
|
312 |
//Every single processor will parse the comment line by itself |
313 |
//By using this way, we might lose some efficiency, but if we want to add |
314 |
//more parameters into comment line, we only need to modify function |
315 |
//parseCommentLine |
316 |
|
317 |
MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
318 |
|
319 |
parseErr = parseCommentLine( read_buffer, simnfo); |
320 |
|
321 |
if( parseErr != NULL ){ |
322 |
strcpy( painCave.errMsg, parseErr ); |
323 |
haveError = 1; |
324 |
simError(); |
325 |
} |
326 |
|
327 |
for (i=0 ; i < mpiSim->getNMolGlobal(); i++) { |
328 |
which_node = MolToProcMap[i]; |
329 |
if(which_node == 0){ |
330 |
//molecules belong to master node |
331 |
|
332 |
localIndex = mpiSim->getGlobalToLocalMol(i); |
333 |
|
334 |
if(localIndex == -1) { |
335 |
strcpy(painCave.errMsg, "Molecule not found on node 0!"); |
336 |
haveError = 1; |
337 |
simError(); |
338 |
} |
339 |
|
340 |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
341 |
for(j=0; j < integrableObjects.size(); j++){ |
342 |
|
343 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
344 |
if(eof_test == NULL){ |
345 |
sprintf(painCave.errMsg, |
346 |
"error in reading file %s\n" |
347 |
"natoms = %d; index = %d\n" |
348 |
"error reading the line from the file.\n", |
349 |
inFileName.c_str(), nTotObjs, i ); |
350 |
haveError= 1; |
351 |
simError(); |
352 |
} |
353 |
|
354 |
if(haveError) nodeZeroError(); |
355 |
|
356 |
parseDumpLine(read_buffer, integrableObjects[j]); |
357 |
|
358 |
} |
359 |
|
360 |
|
361 |
} |
362 |
else{ |
363 |
//molecule belongs to slave nodes |
364 |
|
365 |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, |
366 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
367 |
|
368 |
for(j=0; j < nCurObj; j++){ |
369 |
|
370 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
371 |
if(eof_test == NULL){ |
372 |
sprintf(painCave.errMsg, |
373 |
"error in reading file %s\n" |
374 |
"natoms = %d; index = %d\n" |
375 |
"error reading the line from the file.\n", |
376 |
inFileName.c_str(), nTotObjs, i ); |
377 |
haveError= 1; |
378 |
simError(); |
379 |
} |
380 |
|
381 |
if(haveError) nodeZeroError(); |
382 |
|
383 |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
384 |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
385 |
|
386 |
} |
387 |
|
388 |
} |
389 |
|
390 |
} |
391 |
|
392 |
} |
393 |
else{ |
394 |
//actions taken at slave nodes |
395 |
MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
396 |
|
397 |
parseErr = parseCommentLine( read_buffer, simnfo); |
398 |
|
399 |
if( parseErr != NULL ){ |
400 |
strcpy( painCave.errMsg, parseErr ); |
401 |
haveError = 1; |
402 |
simError(); |
403 |
} |
404 |
|
405 |
for (i=0 ; i < mpiSim->getNMolGlobal(); i++) { |
406 |
which_node = MolToProcMap[i]; |
407 |
|
408 |
if(which_node == worldRank){ |
409 |
//molecule with global index i belongs to this processor |
410 |
|
411 |
localIndex = mpiSim->getGlobalToLocalMol(i); |
412 |
|
413 |
if(localIndex == -1) { |
414 |
sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank); |
415 |
haveError = 1; |
416 |
simError(); |
417 |
} |
418 |
|
419 |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
420 |
|
421 |
nCurObj = integrableObjects.size(); |
422 |
|
423 |
MPI_Send(&nCurObj, 1, MPI_INT, 0, |
424 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
425 |
|
426 |
for(j = 0; j < integrableObjects.size(); j++){ |
427 |
|
428 |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
429 |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
430 |
|
431 |
parseErr = parseDumpLine(read_buffer, integrableObjects[j]); |
432 |
|
433 |
if( parseErr != NULL ){ |
434 |
strcpy( painCave.errMsg, parseErr ); |
435 |
simError(); |
436 |
} |
437 |
|
438 |
} |
439 |
|
440 |
} |
441 |
|
442 |
} |
443 |
|
444 |
} |
445 |
|
446 |
#endif |
447 |
} |
448 |
|
449 |
char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){ |
450 |
|
451 |
char *foo; // the pointer to the current string token |
452 |
|
453 |
double pos[3]; // position place holders |
454 |
double vel[3]; // velocity placeholders |
455 |
double q[4]; // the quaternions |
456 |
double ji[3]; // angular velocity placeholders; |
457 |
double qSqr, qLength; // needed to normalize the quaternion vector. |
458 |
|
459 |
|
460 |
// set the string tokenizer |
461 |
|
462 |
foo = strtok(readLine, " ,;\t"); |
463 |
|
464 |
// check the atom name to the current atom |
465 |
|
466 |
if( strcmp( foo, sd->getType() ) ){ |
467 |
sprintf( painCave.errMsg, |
468 |
"DumpReader error. Does not" |
469 |
" match the meta-data atom %s.\n", |
470 |
sd->getType() ); |
471 |
return strdup( painCave.errMsg ); |
472 |
} |
473 |
|
474 |
// get the positions |
475 |
|
476 |
foo = strtok(NULL, " ,;\t"); |
477 |
if(foo == NULL){ |
478 |
sprintf( painCave.errMsg, |
479 |
"error in reading postition x from %s\n", |
480 |
inFileName.c_str()); |
481 |
return strdup( painCave.errMsg ); |
482 |
} |
483 |
pos[0] = atof( foo ); |
484 |
|
485 |
foo = strtok(NULL, " ,;\t"); |
486 |
if(foo == NULL){ |
487 |
sprintf( painCave.errMsg, |
488 |
"error in reading postition y from %s\n", |
489 |
inFileName.c_str()); |
490 |
return strdup( painCave.errMsg ); |
491 |
} |
492 |
pos[1] = atof( foo ); |
493 |
|
494 |
foo = strtok(NULL, " ,;\t"); |
495 |
if(foo == NULL){ |
496 |
sprintf( painCave.errMsg, |
497 |
"error in reading postition z from %s\n", |
498 |
inFileName.c_str()); |
499 |
return strdup( painCave.errMsg ); |
500 |
} |
501 |
pos[2] = atof( foo ); |
502 |
|
503 |
|
504 |
// get the velocities |
505 |
|
506 |
foo = strtok(NULL, " ,;\t"); |
507 |
if(foo == NULL){ |
508 |
sprintf( painCave.errMsg, |
509 |
"error in reading velocity x from %s\n", |
510 |
inFileName.c_str() ); |
511 |
return strdup( painCave.errMsg ); |
512 |
} |
513 |
vel[0] = atof( foo ); |
514 |
|
515 |
foo = strtok(NULL, " ,;\t"); |
516 |
if(foo == NULL){ |
517 |
sprintf( painCave.errMsg, |
518 |
"error in reading velocity x from %s\n", |
519 |
inFileName.c_str() ); |
520 |
return strdup( painCave.errMsg ); |
521 |
} |
522 |
vel[1] = atof( foo ); |
523 |
|
524 |
foo = strtok(NULL, " ,;\t"); |
525 |
if(foo == NULL){ |
526 |
sprintf( painCave.errMsg, |
527 |
"error in reading velocity x from %s\n", |
528 |
inFileName.c_str() ); |
529 |
return strdup( painCave.errMsg ); |
530 |
} |
531 |
vel[2] = atof( foo ); |
532 |
|
533 |
|
534 |
// add the positions and velocities to the atom |
535 |
|
536 |
sd->setPos( pos ); |
537 |
sd->setVel( vel ); |
538 |
|
539 |
if (!sd->isDirectional()) |
540 |
return NULL; |
541 |
|
542 |
// get the quaternions |
543 |
|
544 |
if( sd->isDirectional() ){ |
545 |
|
546 |
foo = strtok(NULL, " ,;\t"); |
547 |
if(foo == NULL){ |
548 |
sprintf( painCave.errMsg, |
549 |
"error in reading velocity x from %s\n", |
550 |
inFileName.c_str() ); |
551 |
return strdup( painCave.errMsg ); |
552 |
} |
553 |
q[0] = atof( foo ); |
554 |
|
555 |
foo = strtok(NULL, " ,;\t"); |
556 |
if(foo == NULL){ |
557 |
sprintf( painCave.errMsg, |
558 |
"error in reading velocity x from %s\n", |
559 |
inFileName.c_str() ); |
560 |
return strdup( painCave.errMsg ); |
561 |
} |
562 |
q[1] = atof( foo ); |
563 |
|
564 |
foo = strtok(NULL, " ,;\t"); |
565 |
if(foo == NULL){ |
566 |
sprintf( painCave.errMsg, |
567 |
"error in reading velocity x from %s\n", |
568 |
inFileName.c_str() ); |
569 |
return strdup( painCave.errMsg ); |
570 |
} |
571 |
q[2] = atof( foo ); |
572 |
|
573 |
foo = strtok(NULL, " ,;\t"); |
574 |
if(foo == NULL){ |
575 |
sprintf( painCave.errMsg, |
576 |
"error in reading velocity x from %s\n", |
577 |
inFileName.c_str() ); |
578 |
return strdup( painCave.errMsg ); |
579 |
} |
580 |
q[3] = atof( foo ); |
581 |
|
582 |
// get the angular velocities |
583 |
|
584 |
foo = strtok(NULL, " ,;\t"); |
585 |
if(foo == NULL){ |
586 |
sprintf( painCave.errMsg, |
587 |
"error in reading velocity x from %s\n", |
588 |
inFileName.c_str() ); |
589 |
return strdup( painCave.errMsg ); |
590 |
} |
591 |
ji[0] = atof( foo ); |
592 |
|
593 |
foo = strtok(NULL, " ,;\t"); |
594 |
if(foo == NULL){ |
595 |
sprintf( painCave.errMsg, |
596 |
"error in reading velocity x from %s\n", |
597 |
inFileName.c_str() ); |
598 |
return strdup( painCave.errMsg ); |
599 |
} |
600 |
ji[1] = atof(foo ); |
601 |
|
602 |
foo = strtok(NULL, " ,;\t"); |
603 |
if(foo == NULL){ |
604 |
sprintf( painCave.errMsg, |
605 |
"error in reading velocity x from %s\n", |
606 |
inFileName.c_str() ); |
607 |
return strdup( painCave.errMsg ); |
608 |
} |
609 |
ji[2] = atof( foo ); |
610 |
|
611 |
|
612 |
// check that the quaternion vector is normalized |
613 |
|
614 |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
615 |
|
616 |
if (fabs(qSqr) < 1e-6) { |
617 |
sprintf(painCave.errMsg, |
618 |
"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n"); |
619 |
return strdup(painCave.errMsg); |
620 |
} |
621 |
|
622 |
qLength = sqrt( qSqr ); |
623 |
q[0] = q[0] / qLength; |
624 |
q[1] = q[1] / qLength; |
625 |
q[2] = q[2] / qLength; |
626 |
q[3] = q[3] / qLength; |
627 |
|
628 |
// add quaternion and angular velocities |
629 |
|
630 |
sd->setQ( q ); |
631 |
sd->setJ( ji ); |
632 |
} |
633 |
|
634 |
|
635 |
|
636 |
return NULL; |
637 |
} |
638 |
|
639 |
|
640 |
char* DumpReader::parseCommentLine(char* readLine, SimInfo* entry_plug){ |
641 |
|
642 |
double currTime; |
643 |
double boxMat[9]; |
644 |
double theBoxMat3[3][3]; |
645 |
double chi; |
646 |
double integralOfChidt; |
647 |
double eta[9]; |
648 |
|
649 |
char *foo; // the pointer to the current string token |
650 |
|
651 |
// set the string tokenizer |
652 |
|
653 |
foo = strtok(readLine, " ,;\t"); |
654 |
// set the timeToken. |
655 |
|
656 |
if(foo == NULL){ |
657 |
sprintf( painCave.errMsg, |
658 |
"error in reading Time from %s\n", |
659 |
inFileName.c_str() ); |
660 |
return strdup( painCave.errMsg ); |
661 |
} |
662 |
|
663 |
currTime = atof( foo ); |
664 |
entry_plug->setTime( currTime ); |
665 |
|
666 |
//get H-Matrix |
667 |
|
668 |
for(int i = 0 ; i < 9; i++){ |
669 |
foo = strtok(NULL, " ,;\t"); |
670 |
if(foo == NULL){ |
671 |
sprintf( painCave.errMsg, |
672 |
"error in reading H[%d] from %s\n", i, inFileName.c_str() ); |
673 |
return strdup( painCave.errMsg ); |
674 |
} |
675 |
boxMat[i] = atof( foo ); |
676 |
} |
677 |
|
678 |
for(int i=0;i<3;i++) |
679 |
for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
680 |
|
681 |
//set H-Matrix |
682 |
entry_plug->setBoxM( theBoxMat3 ); |
683 |
|
684 |
//get chi and integralOfChidt, they should appear by pair |
685 |
|
686 |
if( entry_plug->useInitXSstate ){ |
687 |
foo = strtok(NULL, " ,;\t\n"); |
688 |
if(foo != NULL){ |
689 |
chi = atof(foo); |
690 |
|
691 |
foo = strtok(NULL, " ,;\t\n"); |
692 |
if(foo == NULL){ |
693 |
sprintf( painCave.errMsg, |
694 |
"chi and integralOfChidt should appear by pair in %s\n", inFileName.c_str() ); |
695 |
return strdup( painCave.errMsg ); |
696 |
} |
697 |
integralOfChidt = atof( foo ); |
698 |
|
699 |
//push chi and integralOfChidt into SimInfo::properties which can be |
700 |
//retrieved by integrator later |
701 |
DoubleData* chiValue = new DoubleData(); |
702 |
chiValue->setID(CHIVALUE_ID); |
703 |
chiValue->setData(chi); |
704 |
entry_plug->addProperty(chiValue); |
705 |
|
706 |
DoubleData* integralOfChidtValue = new DoubleData(); |
707 |
integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); |
708 |
integralOfChidtValue->setData(integralOfChidt); |
709 |
entry_plug->addProperty(integralOfChidtValue); |
710 |
|
711 |
} |
712 |
else |
713 |
return NULL; |
714 |
|
715 |
//get eta |
716 |
foo = strtok(NULL, " ,;\t\n"); |
717 |
if(foo != NULL ){ |
718 |
|
719 |
for(int i = 0 ; i < 9; i++){ |
720 |
|
721 |
if(foo == NULL){ |
722 |
sprintf( painCave.errMsg, |
723 |
"error in reading eta[%d] from %s\n", i, inFileName.c_str() ); |
724 |
return strdup( painCave.errMsg ); |
725 |
} |
726 |
eta[i] = atof( foo ); |
727 |
foo = strtok(NULL, " ,;\t\n"); |
728 |
} |
729 |
} |
730 |
else |
731 |
return NULL; |
732 |
|
733 |
//push eta into SimInfo::properties which can be |
734 |
//retrieved by integrator later |
735 |
//entry_plug->setBoxM( theBoxMat3 ); |
736 |
DoubleArrayData* etaValue = new DoubleArrayData(); |
737 |
etaValue->setID(ETAVALUE_ID); |
738 |
etaValue->setData(eta, 9); |
739 |
entry_plug->addProperty(etaValue); |
740 |
} |
741 |
|
742 |
return NULL; |
743 |
} |
744 |
|
745 |
#ifdef IS_MPI |
746 |
void DumpReader::nodeZeroError( void ){ |
747 |
int j, myStatus; |
748 |
|
749 |
myStatus = 0; |
750 |
for (j = 0; j < mpiSim->getNProcessors(); j++) { |
751 |
MPI_Send( &myStatus, 1, MPI_INT, j, |
752 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
753 |
} |
754 |
|
755 |
|
756 |
MPI_Finalize(); |
757 |
exit (0); |
758 |
|
759 |
} |
760 |
|
761 |
void DumpReader::anonymousNodeDie( void ){ |
762 |
|
763 |
MPI_Finalize(); |
764 |
exit (0); |
765 |
} |
766 |
#endif |