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root/OpenMD/trunk/src/applications/utilities/waterBoxer.in
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Comparing trunk/src/applications/utilities/waterBoxer.in (file contents):
Revision 1035 by chrisfen, Fri Sep 1 22:58:33 2006 UTC vs.
Revision 1056 by chrisfen, Mon Oct 2 23:27:40 2006 UTC

# Line 3 | Line 3
3   # program that builds water boxes
4  
5   # author    = "Chris Fennell
6 < # version   = "$Revision: 1.2 $"
7 < # date      = "$Date: 2006-09-01 22:58:33 $"
6 > # version   = "$Revision: 1.3 $"
7 > # date      = "$Date: 2006-10-02 23:27:40 $"
8   # copyright = "Copyright (c) 2006 by the University of Notre Dame"
9   # license   = "OOPSE"
10  
# Line 23 | Line 23 | $invalidWater = 0;
23   $alphaInt = 0.5125;
24   $alphaSlope = 0.025;
25   $invalidWater = 0;
26 + $waterCase = -1;
27  
28   # get our options
29   getopts('hmrvd:l:n:w:');
# Line 207 | Line 208 | sub acos {
208    return $ret;
209   }
210  
211 < sub writeOutFile{
211 > sub writeOutFile {
212    # write out the header
213    print OUTFILE "<OOPSE version=4>\n";
214    findCutoff();
# Line 267 | Line 268 | electrostaticScreeningMethod = \"damped\";
268   forceField = \"DUFF\";
269   electrostaticSummationMethod = \"shifted_force\";
270   electrostaticScreeningMethod = \"damped\";
270 – dampingAlpha = $alpha;
271   cutoffRadius = $cutoff;
272  
273   targetTemp = 300;
# Line 286 | Line 286 | statusTime = 2;
286    </MetaData>\n";
287   }
288  
289 < sub findCutoff{
289 > sub findCutoff {
290    $boxLength2 = 0.5*$boxLength;
291    if ($boxLength2 > $cutoff){
292      # the default is good
# Line 295 | Line 295 | sub findCutoff{
295    }
296   }
297  
298 < sub findAlpha{
298 > sub findAlpha {
299    $alpha = $alphaInt - $cutoff*$alphaSlope;
300   }
301  
302 < sub printFrameData{
302 > sub printFrameData {
303   print OUTFILE
304   "  <Snapshot>
305      <FrameData>
# Line 308 | Line 308 | print OUTFILE
308      </FrameData>\n";
309   }
310  
311 < sub printWaterMD{
311 > sub printWaterMD {
312    open(WATERMD, ">./water.md") || die "\tError: can't open file water.md\n";
313 +  $waterFileHandle = 'WATERMD';
314  
315    print WATERMD "#ifndef _WATER_MD_\n#define _WATER_MD_\n";
316    printCl();
# Line 330 | Line 331 | sub printWaterMD{
331    print WATERMD "\n\n#endif";
332   }
333  
334 < sub printCl{
334 > sub printCl {
335    print $waterFileHandle "\n\nmolecule{
336    name = \"Cl-\";
337    
# Line 341 | Line 342 | sub printCl{
342   }"
343   }
344  
345 < sub printNa{
345 > sub printNa {
346    print $waterFileHandle "\n\nmolecule{
347    name = \"Na+\";
348    
# Line 352 | Line 353 | sub printNa{
353   }"
354   }
355  
356 < sub printSSD_E{
356 > sub printSSD_E {
357    print $waterFileHandle "\n\nmolecule{
358    name = \"SSD_E\";
359    
# Line 364 | Line 365 | sub printSSD_E{
365   }"
366   }
367  
368 < sub printSSD_RF{
368 > sub printSSD_RF {
369    print $waterFileHandle "\n\nmolecule{
370    name = \"SSD_RF\";
371    
# Line 376 | Line 377 | sub printSSD_RF{
377   }"
378   }
379  
380 < sub printSSD{
380 > sub printSSD {
381    print $waterFileHandle "\n\nmolecule{
382    name = \"SSD\";
383    
# Line 388 | Line 389 | sub printSSD{
389   }"
390   }
391  
392 < sub printSSD1{
392 > sub printSSD1 {
393    print $waterFileHandle "\n\nmolecule{
394    name = \"SSD1\";
395    
# Line 400 | Line 401 | sub printSSD1{
401   }"
402   }
403  
404 < sub printTRED{
404 > sub printTRED {
405    print $waterFileHandle "\n\nmolecule{
406    name = \"TRED\";
407    
# Line 424 | Line 425 | sub printTRED{
425   }"
426   }
427  
428 < sub printTIP3P{
428 > sub printTIP3P {
429    print $waterFileHandle "\n\nmolecule{
430    name = \"TIP3P\";
431    
# Line 451 | Line 452 | sub printTIP3P{
452   }"
453   }
454  
455 < sub printTIP4P{
455 > sub printTIP4P {
456    print $waterFileHandle "\n\nmolecule{
457    name = \"TIP4P\";
458    
# Line 482 | Line 483 | sub printTIP4P{
483   }"
484   }
485  
486 < sub printTIP4PEw{
486 > sub printTIP4PEw {
487    print $waterFileHandle "\n\nmolecule{
488    name = \"TIP4P-Ew\";
489    
# Line 513 | Line 514 | sub printTIP4PEw{
514   }"
515   }
516  
517 < sub printTIP5P{
517 > sub printTIP5P {
518    print $waterFileHandle "\n\nmolecule{
519    name = \"TIP5P\";
520    
# Line 548 | Line 549 | sub printTIP5P{
549   }"
550   }
551  
552 < sub printTIP5PE{
552 > sub printTIP5PE {
553    print $waterFileHandle "\n\nmolecule{
554    name = \"TIP5P-E\";
555    
# Line 583 | Line 584 | sub printTIP5PE{
584   }"
585   }
586  
587 < sub printSPCE{
587 > sub printSPCE {
588   print $waterFileHandle "\n\nmolecule{
589    name = \"SPCE\";
590    
# Line 610 | Line 611 | print $waterFileHandle "\n\nmolecule{
611   }"
612   }
613  
614 < sub printSPC{
614 > sub printSPC {
615   print $waterFileHandle "\n\nmolecule{
616    name = \"SPC\";
617    
# Line 637 | Line 638 | print $waterFileHandle "\n\nmolecule{
638   }"
639   }
640  
641 < sub printDPD{
641 > sub printDPD {
642    print $waterFileHandle "\n\nmolecule{
643    name = \"DPD\";
644    
# Line 649 | Line 650 | sub printDPD{
650   }
651  
652  
653 < sub printFakeWater{
653 > sub printFakeWater {
654    print $waterFileHandle "\n\nmolecule{
655    name = \"$waterName\";
656    
# Line 661 | Line 662 | sub printFakeWater{
662   }
663  
664  
665 < sub validateWater{
665 > sub validateWater {
666    if    ($waterName eq 'Cl-')      { $waterCase = 0;    }
667    elsif ($waterName eq 'Na+')      { $waterCase = 1;    }
668    elsif ($waterName eq 'SSD_E')    { $waterCase = 2;    }
# Line 679 | Line 680 | sub validateWater{
680    else                             { $invalidWater = 1; }
681   }
682  
683 < sub printWaterModel{
683 > sub printWaterModel {
684    if    ($waterCase == 0)  { printCl();      }
685    elsif ($waterCase == 1)  { printNa();      }
686    elsif ($waterCase == 2)  { printSSD_E();   }

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