3 |
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# program that builds water boxes |
4 |
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|
5 |
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# author = "Chris Fennell |
6 |
< |
# version = "$Revision: 1.1 $" |
7 |
< |
# date = "$Date: 2006-09-01 21:08:03 $" |
6 |
> |
# version = "$Revision: 1.2 $" |
7 |
> |
# date = "$Date: 2006-09-01 22:58:33 $" |
8 |
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# copyright = "Copyright (c) 2006 by the University of Notre Dame" |
9 |
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# license = "OOPSE" |
10 |
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|
22 |
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$alpha = 0.2125; |
23 |
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$alphaInt = 0.5125; |
24 |
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$alphaSlope = 0.025; |
25 |
+ |
$invalidWater = 0; |
26 |
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|
27 |
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# get our options |
28 |
< |
getopts('hrvd:l:n:w:'); |
28 |
> |
getopts('hmrvd:l:n:w:'); |
29 |
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|
30 |
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# if we don't have a filename, drop to -h |
31 |
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$opt_h = 'true' if $#ARGV != 0; |
36 |
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print "usage: waterBoxer [-hv] [-d density] [-l lattice] [-n # waters]\n"; |
37 |
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print "\t[-w water name] [file name]\n\n"; |
38 |
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print " -h : show this message\n"; |
39 |
+ |
print " -m : print out a water.md file (file with all water models)\n"; |
40 |
|
print " -r : randomize orientations\n"; |
41 |
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print " -v : verbose output\n\n"; |
42 |
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print " -d real : density in g/cm^3\n"; |
57 |
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} else { |
58 |
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$fileName = 'waterBox'; |
59 |
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} |
60 |
+ |
if ($opt_m){ |
61 |
+ |
die "$fileName cannot be \"water.md\"\n\tPlease choose a different name\n" if $fileName eq 'water.md'; |
62 |
+ |
$waterFileHandle = 'WATERMD'; |
63 |
+ |
} else { |
64 |
+ |
$waterFileHandle = 'OUTFILE'; |
65 |
+ |
} |
66 |
|
if ($opt_r){ |
67 |
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$doRandomize = $opt_r; |
68 |
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} |
69 |
+ |
|
70 |
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if (defined($opt_w)){ |
71 |
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$waterName = $opt_w; |
72 |
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} else { |
73 |
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$waterName = 'SPCE'; |
74 |
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} |
75 |
< |
|
75 |
> |
validateWater(); |
76 |
|
if (defined($opt_d)){ |
77 |
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if ($opt_d =~ /^[0-9]/) { |
78 |
|
$density = $opt_d; |
195 |
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|
196 |
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writeOutFile(); |
197 |
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|
198 |
+ |
if ($opt_m || $invalidWater){ |
199 |
+ |
printWaterMD(); |
200 |
+ |
} |
201 |
+ |
|
202 |
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# this marks the end of the main program, below is subroutines |
203 |
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|
204 |
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sub acos { |
247 |
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} |
248 |
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|
249 |
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sub printMetaData { |
250 |
< |
print OUTFILE" <MetaData> |
238 |
< |
#include \"water.md\" |
250 |
> |
print OUTFILE " <MetaData>\n"; |
251 |
|
|
252 |
< |
component{ |
252 |
> |
# print the water model or includes |
253 |
> |
if ($opt_m){ |
254 |
> |
print OUTFILE "#include \"water.md\""; |
255 |
> |
} else { |
256 |
> |
printWaterModel(); |
257 |
> |
} |
258 |
> |
printFakeWater() if $invalidWater == 1; |
259 |
> |
|
260 |
> |
# now back to the metaData output |
261 |
> |
print OUTFILE "\n\ncomponent{ |
262 |
|
type = \"$waterName\"; |
263 |
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nMol = $nMol; |
264 |
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} |
265 |
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|
245 |
– |
|
266 |
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ensemble = NVE; |
267 |
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forceField = \"DUFF\"; |
268 |
|
electrostaticSummationMethod = \"shifted_force\"; |
306 |
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Time: 0 |
307 |
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Hmat: {{ $boxLength, 0, 0 }, { 0, $boxLength, 0 }, { 0, 0, $boxLength }} |
308 |
|
</FrameData>\n"; |
309 |
+ |
} |
310 |
+ |
|
311 |
+ |
sub printWaterMD{ |
312 |
+ |
open(WATERMD, ">./water.md") || die "\tError: can't open file water.md\n"; |
313 |
+ |
|
314 |
+ |
print WATERMD "#ifndef _WATER_MD_\n#define _WATER_MD_\n"; |
315 |
+ |
printCl(); |
316 |
+ |
printNa(); |
317 |
+ |
printSSD_E(); |
318 |
+ |
printSSD_RF(); |
319 |
+ |
printSSD(); |
320 |
+ |
printSSD1(); |
321 |
+ |
printTRED(); |
322 |
+ |
printTIP3P(); |
323 |
+ |
printTIP4P(); |
324 |
+ |
printTIP4PEw(); |
325 |
+ |
printTIP5P(); |
326 |
+ |
printTIP5PE(); |
327 |
+ |
printSPCE(); |
328 |
+ |
printSPC(); |
329 |
+ |
printDPD(); |
330 |
+ |
print WATERMD "\n\n#endif"; |
331 |
+ |
} |
332 |
+ |
|
333 |
+ |
sub printCl{ |
334 |
+ |
print $waterFileHandle "\n\nmolecule{ |
335 |
+ |
name = \"Cl-\"; |
336 |
+ |
|
337 |
+ |
atom[0]{ |
338 |
+ |
type = \"Cl-\"; |
339 |
+ |
position(0.0, 0.0, 0.0); |
340 |
+ |
} |
341 |
+ |
}" |
342 |
+ |
} |
343 |
+ |
|
344 |
+ |
sub printNa{ |
345 |
+ |
print $waterFileHandle "\n\nmolecule{ |
346 |
+ |
name = \"Na+\"; |
347 |
+ |
|
348 |
+ |
atom[0]{ |
349 |
+ |
type = \"Na+\"; |
350 |
+ |
position(0.0, 0.0, 0.0); |
351 |
+ |
} |
352 |
+ |
}" |
353 |
+ |
} |
354 |
+ |
|
355 |
+ |
sub printSSD_E{ |
356 |
+ |
print $waterFileHandle "\n\nmolecule{ |
357 |
+ |
name = \"SSD_E\"; |
358 |
+ |
|
359 |
+ |
atom[0]{ |
360 |
+ |
type = \"SSD_E\"; |
361 |
+ |
position( 0.0, 0.0, 0.0 ); |
362 |
+ |
orientation( 0.0, 0.0, 0.0 ); |
363 |
+ |
} |
364 |
+ |
}" |
365 |
+ |
} |
366 |
+ |
|
367 |
+ |
sub printSSD_RF{ |
368 |
+ |
print $waterFileHandle "\n\nmolecule{ |
369 |
+ |
name = \"SSD_RF\"; |
370 |
+ |
|
371 |
+ |
atom[0]{ |
372 |
+ |
type = \"SSD_RF\"; |
373 |
+ |
position( 0.0, 0.0, 0.0 ); |
374 |
+ |
orientation( 0.0, 0.0, 0.0 ); |
375 |
+ |
} |
376 |
+ |
}" |
377 |
+ |
} |
378 |
+ |
|
379 |
+ |
sub printSSD{ |
380 |
+ |
print $waterFileHandle "\n\nmolecule{ |
381 |
+ |
name = \"SSD\"; |
382 |
+ |
|
383 |
+ |
atom[0]{ |
384 |
+ |
type = \"SSD\"; |
385 |
+ |
position( 0.0, 0.0, 0.0 ); |
386 |
+ |
orientation( 0.0, 0.0, 0.0 ); |
387 |
+ |
} |
388 |
+ |
}" |
389 |
+ |
} |
390 |
+ |
|
391 |
+ |
sub printSSD1{ |
392 |
+ |
print $waterFileHandle "\n\nmolecule{ |
393 |
+ |
name = \"SSD1\"; |
394 |
+ |
|
395 |
+ |
atom[0]{ |
396 |
+ |
type = \"SSD1\"; |
397 |
+ |
position( 0.0, 0.0, 0.0 ); |
398 |
+ |
orientation( 0.0, 0.0, 0.0 ); |
399 |
+ |
} |
400 |
+ |
}" |
401 |
+ |
} |
402 |
+ |
|
403 |
+ |
sub printTRED{ |
404 |
+ |
print $waterFileHandle "\n\nmolecule{ |
405 |
+ |
name = \"TRED\"; |
406 |
+ |
|
407 |
+ |
atom[0]{ |
408 |
+ |
type = \"TRED\"; |
409 |
+ |
position( 0.0, 0.0, 0.0 ); |
410 |
+ |
orientation( 0.0, 0.0, 0.0 ); |
411 |
+ |
} |
412 |
+ |
atom[1]{ |
413 |
+ |
type = \"EP_TRED\"; |
414 |
+ |
position( 0.0, 0.0, 0.5 ); |
415 |
+ |
} |
416 |
+ |
|
417 |
+ |
rigidBody[0]{ |
418 |
+ |
members(0, 1); |
419 |
+ |
} |
420 |
+ |
|
421 |
+ |
cutoffGroup{ |
422 |
+ |
members(0, 1); |
423 |
+ |
} |
424 |
+ |
}" |
425 |
+ |
} |
426 |
+ |
|
427 |
+ |
sub printTIP3P{ |
428 |
+ |
print $waterFileHandle "\n\nmolecule{ |
429 |
+ |
name = \"TIP3P\"; |
430 |
+ |
|
431 |
+ |
atom[0]{ |
432 |
+ |
type = \"O_TIP3P\"; |
433 |
+ |
position( 0.0, 0.0, -0.06556 ); |
434 |
+ |
} |
435 |
+ |
atom[1]{ |
436 |
+ |
type = \"H_TIP3P\"; |
437 |
+ |
position( 0.0, 0.75695, 0.52032 ); |
438 |
+ |
} |
439 |
+ |
atom[2]{ |
440 |
+ |
type = \"H_TIP3P\"; |
441 |
+ |
position( 0.0, -0.75695, 0.52032 ); |
442 |
+ |
} |
443 |
+ |
|
444 |
+ |
rigidBody[0]{ |
445 |
+ |
members(0, 1, 2); |
446 |
+ |
} |
447 |
+ |
|
448 |
+ |
cutoffGroup{ |
449 |
+ |
members(0, 1, 2); |
450 |
+ |
} |
451 |
+ |
}" |
452 |
+ |
} |
453 |
+ |
|
454 |
+ |
sub printTIP4P{ |
455 |
+ |
print $waterFileHandle "\n\nmolecule{ |
456 |
+ |
name = \"TIP4P\"; |
457 |
+ |
|
458 |
+ |
atom[0]{ |
459 |
+ |
type = \"O_TIP4P\"; |
460 |
+ |
position( 0.0, 0.0, -0.06556 ); |
461 |
+ |
} |
462 |
+ |
atom[1]{ |
463 |
+ |
type = \"H_TIP4P\"; |
464 |
+ |
position( 0.0, 0.75695, 0.52032 ); |
465 |
+ |
} |
466 |
+ |
atom[2]{ |
467 |
+ |
type = \"H_TIP4P\"; |
468 |
+ |
position( 0.0, -0.75695, 0.52032 ); |
469 |
+ |
} |
470 |
+ |
atom[3]{ |
471 |
+ |
type = \"EP_TIP4P\"; |
472 |
+ |
position( 0.0, 0.0, 0.08444 ); |
473 |
+ |
} |
474 |
+ |
|
475 |
+ |
rigidBody[0]{ |
476 |
+ |
members(0, 1, 2, 3); |
477 |
+ |
} |
478 |
+ |
|
479 |
+ |
cutoffGroup{ |
480 |
+ |
members(0, 1, 2, 3); |
481 |
+ |
} |
482 |
+ |
}" |
483 |
+ |
} |
484 |
+ |
|
485 |
+ |
sub printTIP4PEw{ |
486 |
+ |
print $waterFileHandle "\n\nmolecule{ |
487 |
+ |
name = \"TIP4P-Ew\"; |
488 |
+ |
|
489 |
+ |
atom[0]{ |
490 |
+ |
type = \"O_TIP4P-Ew\"; |
491 |
+ |
position( 0.0, 0.0, -0.06556 ); |
492 |
+ |
} |
493 |
+ |
atom[1]{ |
494 |
+ |
type = \"H_TIP4P-Ew\"; |
495 |
+ |
position( 0.0, 0.75695, 0.52032 ); |
496 |
+ |
} |
497 |
+ |
atom[2]{ |
498 |
+ |
type = \"H_TIP4P-Ew\"; |
499 |
+ |
position( 0.0, -0.75695, 0.52032 ); |
500 |
+ |
} |
501 |
+ |
atom[3]{ |
502 |
+ |
type = \"EP_TIP4P-Ew\"; |
503 |
+ |
position( 0.0, 0.0, 0.05944 ); |
504 |
+ |
} |
505 |
+ |
|
506 |
+ |
rigidBody[0]{ |
507 |
+ |
members(0, 1, 2, 3); |
508 |
+ |
} |
509 |
+ |
|
510 |
+ |
cutoffGroup{ |
511 |
+ |
members(0, 1, 2, 3); |
512 |
+ |
} |
513 |
+ |
}" |
514 |
|
} |
515 |
+ |
|
516 |
+ |
sub printTIP5P{ |
517 |
+ |
print $waterFileHandle "\n\nmolecule{ |
518 |
+ |
name = \"TIP5P\"; |
519 |
+ |
|
520 |
+ |
atom[0]{ |
521 |
+ |
type = \"O_TIP5P\"; |
522 |
+ |
position( 0.0, 0.0, -0.06556 ); |
523 |
+ |
} |
524 |
+ |
atom[1]{ |
525 |
+ |
type = \"H_TIP5P\"; |
526 |
+ |
position( 0.0, 0.75695, 0.52032 ); |
527 |
+ |
} |
528 |
+ |
atom[2]{ |
529 |
+ |
type = \"H_TIP5P\"; |
530 |
+ |
position( 0.0, -0.75695, 0.52032 ); |
531 |
+ |
} |
532 |
+ |
atom[3]{ |
533 |
+ |
type = \"EP_TIP5P\"; |
534 |
+ |
position( 0.57154, 0.0, -0.46971 ); |
535 |
+ |
} |
536 |
+ |
atom[4]{ |
537 |
+ |
type = \"EP_TIP5P\"; |
538 |
+ |
position( -0.57154, 0.0, -0.46971 ); |
539 |
+ |
} |
540 |
+ |
|
541 |
+ |
rigidBody[0]{ |
542 |
+ |
members(0, 1, 2, 3, 4); |
543 |
+ |
} |
544 |
+ |
|
545 |
+ |
cutoffGroup{ |
546 |
+ |
members(0, 1, 2, 3, 4); |
547 |
+ |
} |
548 |
+ |
}" |
549 |
+ |
} |
550 |
+ |
|
551 |
+ |
sub printTIP5PE{ |
552 |
+ |
print $waterFileHandle "\n\nmolecule{ |
553 |
+ |
name = \"TIP5P-E\"; |
554 |
+ |
|
555 |
+ |
atom[0]{ |
556 |
+ |
type = \"O_TIP5P-E\"; |
557 |
+ |
position( 0.0, 0.0, -0.06556 ); |
558 |
+ |
} |
559 |
+ |
atom[1]{ |
560 |
+ |
type = \"H_TIP5P\"; |
561 |
+ |
position( 0.0, 0.75695, 0.52032 ); |
562 |
+ |
} |
563 |
+ |
atom[2]{ |
564 |
+ |
type = \"H_TIP5P\"; |
565 |
+ |
position( 0.0, -0.75695, 0.52032 ); |
566 |
+ |
} |
567 |
+ |
atom[3]{ |
568 |
+ |
type = \"EP_TIP5P\"; |
569 |
+ |
position( 0.57154, 0.0, -0.46971 ); |
570 |
+ |
} |
571 |
+ |
atom[4]{ |
572 |
+ |
type = \"EP_TIP5P\"; |
573 |
+ |
position( -0.57154, 0.0, -0.46971 ); |
574 |
+ |
} |
575 |
+ |
|
576 |
+ |
rigidBody[0]{ |
577 |
+ |
members(0, 1, 2, 3, 4); |
578 |
+ |
} |
579 |
+ |
|
580 |
+ |
cutoffGroup{ |
581 |
+ |
members(0, 1, 2, 3, 4); |
582 |
+ |
} |
583 |
+ |
}" |
584 |
+ |
} |
585 |
+ |
|
586 |
+ |
sub printSPCE{ |
587 |
+ |
print $waterFileHandle "\n\nmolecule{ |
588 |
+ |
name = \"SPCE\"; |
589 |
+ |
|
590 |
+ |
atom[0]{ |
591 |
+ |
type = \"O_SPCE\"; |
592 |
+ |
position( 0.0, 0.0, -0.06461 ); |
593 |
+ |
} |
594 |
+ |
atom[1]{ |
595 |
+ |
type = \"H_SPCE\"; |
596 |
+ |
position( 0.0, 0.81649, 0.51275 ); |
597 |
+ |
} |
598 |
+ |
atom[2]{ |
599 |
+ |
type = \"H_SPCE\"; |
600 |
+ |
position( 0.0, -0.81649, 0.51275 ); |
601 |
+ |
} |
602 |
+ |
|
603 |
+ |
rigidBody[0]{ |
604 |
+ |
members(0, 1, 2); |
605 |
+ |
} |
606 |
+ |
|
607 |
+ |
cutoffGroup{ |
608 |
+ |
members(0, 1, 2); |
609 |
+ |
} |
610 |
+ |
}" |
611 |
+ |
} |
612 |
+ |
|
613 |
+ |
sub printSPC{ |
614 |
+ |
print $waterFileHandle "\n\nmolecule{ |
615 |
+ |
name = \"SPC\"; |
616 |
+ |
|
617 |
+ |
atom[0]{ |
618 |
+ |
type = \"O_SPC\"; |
619 |
+ |
position( 0.0, 0.0, -0.06461 ); |
620 |
+ |
} |
621 |
+ |
atom[1]{ |
622 |
+ |
type = \"H_SPC\"; |
623 |
+ |
position( 0.0, 0.81649, 0.51275 ); |
624 |
+ |
} |
625 |
+ |
atom[2]{ |
626 |
+ |
type = \"H_SPC\"; |
627 |
+ |
position( 0.0, -0.81649, 0.51275 ); |
628 |
+ |
} |
629 |
+ |
|
630 |
+ |
rigidBody[0]{ |
631 |
+ |
members(0, 1, 2); |
632 |
+ |
} |
633 |
+ |
|
634 |
+ |
cutoffGroup{ |
635 |
+ |
members(0, 1, 2); |
636 |
+ |
} |
637 |
+ |
}" |
638 |
+ |
} |
639 |
+ |
|
640 |
+ |
sub printDPD{ |
641 |
+ |
print $waterFileHandle "\n\nmolecule{ |
642 |
+ |
name = \"DPD\"; |
643 |
+ |
|
644 |
+ |
atom[0]{ |
645 |
+ |
type = \"DPD\"; |
646 |
+ |
position(0.0, 0.0, 0.0); |
647 |
+ |
} |
648 |
+ |
}" |
649 |
+ |
} |
650 |
+ |
|
651 |
+ |
|
652 |
+ |
sub printFakeWater{ |
653 |
+ |
print $waterFileHandle "\n\nmolecule{ |
654 |
+ |
name = \"$waterName\"; |
655 |
+ |
|
656 |
+ |
atom[0]{ |
657 |
+ |
type = \"$waterName\"; |
658 |
+ |
position(0.0, 0.0, 0.0); |
659 |
+ |
} |
660 |
+ |
}" |
661 |
+ |
} |
662 |
+ |
|
663 |
+ |
|
664 |
+ |
sub validateWater{ |
665 |
+ |
if ($waterName eq 'Cl-') { $waterCase = 0; } |
666 |
+ |
elsif ($waterName eq 'Na+') { $waterCase = 1; } |
667 |
+ |
elsif ($waterName eq 'SSD_E') { $waterCase = 2; } |
668 |
+ |
elsif ($waterName eq 'SSD_RF') { $waterCase = 3; } |
669 |
+ |
elsif ($waterName eq 'SSD') { $waterCase = 4; } |
670 |
+ |
elsif ($waterName eq 'SSD1') { $waterCase = 5; } |
671 |
+ |
elsif ($waterName eq 'TIP3P') { $waterCase = 6; } |
672 |
+ |
elsif ($waterName eq 'TIP4P') { $waterCase = 7; } |
673 |
+ |
elsif ($waterName eq 'TIP4P-Ew') { $waterCase = 8; } |
674 |
+ |
elsif ($waterName eq 'TIP5P') { $waterCase = 9; } |
675 |
+ |
elsif ($waterName eq 'TIP5P-E') { $waterCase = 10; } |
676 |
+ |
elsif ($waterName eq 'SPCE') { $waterCase = 11; } |
677 |
+ |
elsif ($waterName eq 'SPC') { $waterCase = 12; } |
678 |
+ |
elsif ($waterName eq 'DPD') { $waterCase = 13; } |
679 |
+ |
else { $invalidWater = 1; } |
680 |
+ |
} |
681 |
+ |
|
682 |
+ |
sub printWaterModel{ |
683 |
+ |
if ($waterCase == 0) { printCl(); } |
684 |
+ |
elsif ($waterCase == 1) { printNa(); } |
685 |
+ |
elsif ($waterCase == 2) { printSSD_E(); } |
686 |
+ |
elsif ($waterCase == 3) { printSSD_RF(); } |
687 |
+ |
elsif ($waterCase == 4) { printSSD(); } |
688 |
+ |
elsif ($waterCase == 5) { printSSD1(); } |
689 |
+ |
elsif ($waterCase == 6) { printTIP3P(); } |
690 |
+ |
elsif ($waterCase == 7) { printTIP4P(); } |
691 |
+ |
elsif ($waterCase == 8) { printTIP4PEw(); } |
692 |
+ |
elsif ($waterCase == 9) { printTIP5P(); } |
693 |
+ |
elsif ($waterCase == 10) { printTIP5PE(); } |
694 |
+ |
elsif ($waterCase == 11) { printSPCE(); } |
695 |
+ |
elsif ($waterCase == 12) { printSPC(); } |
696 |
+ |
elsif ($waterCase == 13) { printDPD(); } |
697 |
+ |
} |