13 |
|
|
14 |
|
|
15 |
|
InitializeFromFile :: InitializeFromFile( char *in_name ){ |
16 |
+ |
#ifdef IS_MPI |
17 |
+ |
if (worldRank == 0) { |
18 |
+ |
#endif |
19 |
|
|
20 |
|
c_in_file = fopen(in_name, "r"); |
21 |
|
if(c_in_file == NULL){ |
26 |
|
} |
27 |
|
|
28 |
|
strcpy( c_in_name, in_name); |
29 |
+ |
#ifdef IS_MPI |
30 |
+ |
} |
31 |
+ |
strcpy( checkPointMsg, "Infile opened for reading successfully." ); |
32 |
+ |
MPIcheckPoint(); |
33 |
+ |
#endif |
34 |
|
return; |
35 |
|
} |
36 |
|
|
37 |
|
InitializeFromFile :: ~InitializeFromFile( ){ |
38 |
< |
|
38 |
> |
#ifdef IS_MPI |
39 |
> |
if (worldRank == 0) { |
40 |
> |
#endif |
41 |
|
int error; |
42 |
|
error = fclose( c_in_file ); |
43 |
|
if( error ){ |
45 |
|
"Error closing %s\n", c_in_name ); |
46 |
|
simError(); |
47 |
|
} |
48 |
+ |
#ifdef IS_MPI |
49 |
+ |
} |
50 |
+ |
strcpy( checkPointMsg, "Infile closed successfully." ); |
51 |
+ |
MPIcheckPoint(); |
52 |
+ |
#endif |
53 |
+ |
|
54 |
|
return; |
55 |
|
} |
56 |
|
|
57 |
|
|
58 |
< |
void InitializeFromFile :: read_xyz( SimInfo* entry_plug ){ |
58 |
> |
void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
59 |
|
|
60 |
|
int i; // loop counter |
61 |
|
|
62 |
|
int n_atoms; // the number of atoms |
63 |
|
char read_buffer[2000]; //the line buffer for reading |
64 |
+ |
#ifdef IS_MPI |
65 |
+ |
char send_buffer[2000]; |
66 |
+ |
#endif |
67 |
+ |
|
68 |
|
char *eof_test; // ptr to see when we reach the end of the file |
69 |
|
char *foo; // the pointer to the current string token |
70 |
|
|
74 |
|
double jx, jy, jz; // angular velocity placeholders; |
75 |
|
double qSqr, qLength; // needed to normalize the quaternion vector. |
76 |
|
|
77 |
+ |
entry_plug = the_entry_plug |
78 |
+ |
|
79 |
+ |
|
80 |
+ |
#ifndef IS_MPI |
81 |
|
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
82 |
|
if( eof_test == NULL ){ |
83 |
|
std::cerr << "error reading 1st line of" << c_in_name << "\n"; |
320 |
|
atoms[i]->set_vz( vz ); |
321 |
|
|
322 |
|
} |
323 |
+ |
|
324 |
+ |
|
325 |
+ |
// MPI Section of code.......... |
326 |
+ |
#else //IS_MPI |
327 |
+ |
|
328 |
+ |
|
329 |
+ |
|
330 |
+ |
|
331 |
+ |
if (worldRank == 0) { |
332 |
+ |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
333 |
+ |
if( eof_test == NULL ){ |
334 |
+ |
sprintf( painCave.errMsg, |
335 |
+ |
"Error reading 1st line of %d \n ",c_in_name); |
336 |
+ |
painCave.isFatal = 1; |
337 |
+ |
simError(); |
338 |
+ |
} |
339 |
+ |
|
340 |
+ |
(void)sscanf(read_buffer, "%d", &n_atoms); |
341 |
+ |
|
342 |
+ |
Atom **atoms = entry_plug->atoms; |
343 |
+ |
DirectionalAtom* dAtom; |
344 |
+ |
|
345 |
+ |
if( n_atoms != entry_plug->n_atoms ){ |
346 |
+ |
sprintf( painCave.errMsg, |
347 |
+ |
"Initialize from File error. %s n_atoms, %d, " |
348 |
+ |
"does not match the BASS file's n_atoms, %d.\n", |
349 |
+ |
c_in_name, n_atoms, entry_plug->n_atoms ); |
350 |
+ |
painCave.isFatal = 1; |
351 |
+ |
simError(); |
352 |
+ |
} |
353 |
+ |
|
354 |
+ |
//read and toss the comment line |
355 |
+ |
|
356 |
+ |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
357 |
+ |
if(eof_test == NULL){ |
358 |
+ |
sprintf( painCave.errMsg, |
359 |
+ |
"error in reading commment in %s\n", c_in_name); |
360 |
+ |
painCave.isFatal = 1; |
361 |
+ |
simError(); |
362 |
+ |
} |
363 |
+ |
} |
364 |
+ |
for( i=0; i < n_atoms; i++){ |
365 |
+ |
|
366 |
+ |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
367 |
+ |
if(eof_test == NULL){ |
368 |
+ |
sprintf(painCave.errMsg, |
369 |
+ |
"error in reading file %s\n" |
370 |
+ |
"natoms = %d; index = %d\n" |
371 |
+ |
"error reading the line from the file.\n", |
372 |
+ |
c_in_name, n_atoms, i ); |
373 |
+ |
painCave.isFatal = 1; |
374 |
+ |
simError(); |
375 |
+ |
} |
376 |
+ |
|
377 |
+ |
foo = strtok(read_buffer, " ,;\t"); |
378 |
+ |
|
379 |
+ |
// check the atom name to the current atom |
380 |
+ |
|
381 |
+ |
if( strcmp( foo, atoms[i]->getType() ) ){ |
382 |
+ |
sprintf( painCave.errMsg, |
383 |
+ |
"Initialize from file error. Atom %s at index %d " |
384 |
+ |
"in file %s does not" |
385 |
+ |
" match the BASS atom %s.\n", |
386 |
+ |
foo, i, c_in_name, atoms[i]->getType() ); |
387 |
+ |
painCave.isFatal = 1; |
388 |
+ |
simError(); |
389 |
+ |
} |
390 |
+ |
|
391 |
+ |
// get the positions |
392 |
+ |
|
393 |
+ |
foo = strtok(NULL, " ,;\t"); |
394 |
+ |
if(foo == NULL){ |
395 |
+ |
sprintf( painCave.errMsg, |
396 |
+ |
"error in reading postition x from %s\n" |
397 |
+ |
"natoms = %d, index = %d\n", |
398 |
+ |
c_in_name, n_atoms, i ); |
399 |
+ |
painCave.isFatal = 1; |
400 |
+ |
simError(); |
401 |
+ |
} |
402 |
+ |
(void)sscanf( foo, "%lf", &rx ); |
403 |
+ |
|
404 |
+ |
foo = strtok(NULL, " ,;\t"); |
405 |
+ |
if(foo == NULL){ |
406 |
+ |
sprintf( painCave.errMsg, |
407 |
+ |
"error in reading postition y from %s\n" |
408 |
+ |
"natoms = %d, index = %d\n", |
409 |
+ |
c_in_name, n_atoms, i ); |
410 |
+ |
painCave.isFatal = 1; |
411 |
+ |
simError(); |
412 |
+ |
} |
413 |
+ |
(void)sscanf( foo, "%lf", &ry ); |
414 |
+ |
|
415 |
+ |
foo = strtok(NULL, " ,;\t"); |
416 |
+ |
if(foo == NULL){ |
417 |
+ |
sprintf( painCave.errMsg, |
418 |
+ |
"error in reading postition z from %s\n" |
419 |
+ |
"natoms = %d, index = %d\n", |
420 |
+ |
c_in_name, n_atoms, i ); |
421 |
+ |
painCave.isFatal = 1; |
422 |
+ |
simError(); |
423 |
+ |
} |
424 |
+ |
(void)sscanf( foo, "%lf", &rz ); |
425 |
+ |
|
426 |
+ |
// get the velocities |
427 |
+ |
|
428 |
+ |
foo = strtok(NULL, " ,;\t"); |
429 |
+ |
if(foo == NULL){ |
430 |
+ |
sprintf( painCave.errMsg, |
431 |
+ |
"error in reading velocity x from %s\n" |
432 |
+ |
"natoms = %d, index = %d\n", |
433 |
+ |
c_in_name, n_atoms, i ); |
434 |
+ |
painCave.isFatal = 1; |
435 |
+ |
simError(); |
436 |
+ |
} |
437 |
+ |
(void)sscanf( foo, "%lf", &vx ); |
438 |
+ |
|
439 |
+ |
foo = strtok(NULL, " ,;\t"); |
440 |
+ |
if(foo == NULL){ |
441 |
+ |
sprintf( painCave.errMsg, |
442 |
+ |
"error in reading velocity y from %s\n" |
443 |
+ |
"natoms = %d, index = %d\n", |
444 |
+ |
c_in_name, n_atoms, i ); |
445 |
+ |
painCave.isFatal = 1; |
446 |
+ |
simError(); |
447 |
+ |
} |
448 |
+ |
(void)sscanf( foo, "%lf", &vy ); |
449 |
+ |
|
450 |
+ |
foo = strtok(NULL, " ,;\t"); |
451 |
+ |
if(foo == NULL){ |
452 |
+ |
sprintf( painCave.errMsg, |
453 |
+ |
"error in reading velocity z from %s\n" |
454 |
+ |
"natoms = %d, index = %d\n", |
455 |
+ |
c_in_name, n_atoms, i ); |
456 |
+ |
painCave.isFatal = 1; |
457 |
+ |
simError(); |
458 |
+ |
} |
459 |
+ |
(void)sscanf( foo, "%lf", &vz ); |
460 |
+ |
|
461 |
+ |
|
462 |
+ |
// get the quaternions |
463 |
+ |
|
464 |
+ |
if( atoms[i]->isDirectional() ){ |
465 |
+ |
|
466 |
+ |
foo = strtok(NULL, " ,;\t"); |
467 |
+ |
if(foo == NULL){ |
468 |
+ |
sprintf(painCave.errMsg, |
469 |
+ |
"error in reading quaternion 0 from %s\n" |
470 |
+ |
"natoms = %d, index = %d\n", |
471 |
+ |
c_in_name, n_atoms, i ); |
472 |
+ |
painCave.isFatal = 1; |
473 |
+ |
simError(); |
474 |
+ |
} |
475 |
+ |
(void)sscanf( foo, "%lf", &q[0] ); |
476 |
+ |
|
477 |
+ |
foo = strtok(NULL, " ,;\t"); |
478 |
+ |
if(foo == NULL){ |
479 |
+ |
sprintf( painCave.errMsg, |
480 |
+ |
"error in reading quaternion 1 from %s\n" |
481 |
+ |
"natoms = %d, index = %d\n", |
482 |
+ |
c_in_name, n_atoms, i ); |
483 |
+ |
painCave.isFatal = 1; |
484 |
+ |
simError(); |
485 |
+ |
} |
486 |
+ |
(void)sscanf( foo, "%lf", &q[1] ); |
487 |
+ |
|
488 |
+ |
foo = strtok(NULL, " ,;\t"); |
489 |
+ |
if(foo == NULL){ |
490 |
+ |
sprintf( painCave.errMsg, |
491 |
+ |
"error in reading quaternion 2 from %s\n" |
492 |
+ |
"natoms = %d, index = %d\n", |
493 |
+ |
c_in_name, n_atoms, i ); |
494 |
+ |
painCave.isFatal = 1; |
495 |
+ |
simError(); |
496 |
+ |
} |
497 |
+ |
(void)sscanf( foo, "%lf", &q[2] ); |
498 |
+ |
|
499 |
+ |
foo = strtok(NULL, " ,;\t"); |
500 |
+ |
if(foo == NULL){ |
501 |
+ |
sprintf( painCave.errMsg, |
502 |
+ |
"error in reading quaternion 3 from %s\n" |
503 |
+ |
"natoms = %d, index = %d\n", |
504 |
+ |
c_in_name, n_atoms, i ); |
505 |
+ |
painCave.isFatal = 1; |
506 |
+ |
simError(); |
507 |
+ |
} |
508 |
+ |
(void)sscanf( foo, "%lf", &q[3] ); |
509 |
+ |
|
510 |
+ |
// get the angular velocities |
511 |
+ |
|
512 |
+ |
foo = strtok(NULL, " ,;\t"); |
513 |
+ |
if(foo == NULL){ |
514 |
+ |
sprintf( painCave.errMsg, |
515 |
+ |
"error in reading angular momentum jx from %s\n" |
516 |
+ |
"natoms = %d, index = %d\n", |
517 |
+ |
c_in_name, n_atoms, i ); |
518 |
+ |
painCave.isFatal = 1; |
519 |
+ |
simError(); |
520 |
+ |
} |
521 |
+ |
(void)sscanf( foo, "%lf", &jx ); |
522 |
+ |
|
523 |
+ |
foo = strtok(NULL, " ,;\t"); |
524 |
+ |
if(foo == NULL){ |
525 |
+ |
sprintf( painCave.errMsg, |
526 |
+ |
"error in reading angular momentum jy from %s\n" |
527 |
+ |
"natoms = %d, index = %d\n", |
528 |
+ |
c_in_name, n_atoms, i ); |
529 |
+ |
painCave.isFatal = 1; |
530 |
+ |
simError(); |
531 |
+ |
} |
532 |
+ |
(void)sscanf( foo, "%lf", &jy ); |
533 |
+ |
|
534 |
+ |
foo = strtok(NULL, " ,;\t"); |
535 |
+ |
if(foo == NULL){ |
536 |
+ |
sprintf( painCave.errMsg, |
537 |
+ |
"error in reading angular momentum jz from %s\n" |
538 |
+ |
"natoms = %d, index = %d\n", |
539 |
+ |
c_in_name, n_atoms, i ); |
540 |
+ |
painCave.isFatal = 1; |
541 |
+ |
simError(); |
542 |
+ |
} |
543 |
+ |
(void)sscanf( foo, "%lf", &jz ); |
544 |
+ |
|
545 |
+ |
dAtom = ( DirectionalAtom* )atoms[i]; |
546 |
+ |
|
547 |
+ |
// check that the quaternion vector is normalized |
548 |
+ |
|
549 |
+ |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
550 |
+ |
|
551 |
+ |
qLength = sqrt( qSqr ); |
552 |
+ |
q[0] = q[0] / qLength; |
553 |
+ |
q[1] = q[1] / qLength; |
554 |
+ |
q[2] = q[2] / qLength; |
555 |
+ |
q[3] = q[3] / qLength; |
556 |
+ |
|
557 |
+ |
dAtom->setQ( q ); |
558 |
+ |
|
559 |
+ |
// add the angular velocities |
560 |
+ |
|
561 |
+ |
dAtom->setJx( jx ); |
562 |
+ |
dAtom->setJy( jy ); |
563 |
+ |
dAtom->setJz( jz ); |
564 |
+ |
} |
565 |
+ |
|
566 |
+ |
// add the positions and velocities to the atom |
567 |
+ |
|
568 |
+ |
atoms[i]->setX( rx ); |
569 |
+ |
atoms[i]->setY( ry ); |
570 |
+ |
atoms[i]->setZ( rz ); |
571 |
+ |
|
572 |
+ |
atoms[i]->set_vx( vx ); |
573 |
+ |
atoms[i]->set_vy( vy ); |
574 |
+ |
atoms[i]->set_vz( vz ); |
575 |
+ |
|
576 |
+ |
} |
577 |
+ |
#endif |
578 |
|
} |
579 |
+ |
|
580 |
+ |
char* IntitializeFromFile::parseDumpLine(char* readLine); |