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root/OpenMD/trunk/src/applications/utilities/waterBoxer

Comparing trunk/src/applications/utilities/waterBoxer (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1962 by gezelter, Wed Jan 15 22:26:18 2014 UTC

#	Line 1 | Line 1
1	<	#!/usr/bin/env perl
1	>	#!@PERL_EXECUTABLE@
2
3		# program that builds water boxes
4
5		# author    = "Chris Fennell
6	<	# version   = "$Revision: 1.7 $"
7	<	# date      = "$Date: 2009-11-25 20:01:59 $"
6	>	# version   = "$Revision$"
7	>	# date      = "$Date$"
8		# copyright = "Copyright (c) 2006 by the University of Notre Dame"
9		# license   = "OpenMD"
10
#	Line 18 | Line 18 | $doRandomize = 0;
18		$nMol = 500;
19		$density = 1.0;
20		$doRandomize = 0;
21	<	$cutoff = 12;
22	<	$alpha = 0.2125;
23	<	$alphaInt = 0.5125;
24	<	$alphaSlope = 0.025;
21	>	$cutoff = 9;
22	>	$alpha = 0.18;
23		$invalidWater = 0;
24		$waterCase = -1;
25		$nothingSelected = 1;
#	Line 319 | Line 317 | sub writeOutFile {
317		# write out the header
318		print OUTFILE "<OpenMD version=1>\n";
319		findCutoff();
322	–	findAlpha();
320		printMetaData();
321		printFrameData();
322		print OUTFILE "    <StuntDoubles>\n";
#	Line 372 | Line 369 | ensemble = NVE;
369		}
370
371		ensemble = NVE;
372	<	forceField = \"DUFF\";
372	>	forceField = \"Amber\";
373		electrostaticSummationMethod = \"shifted_force\";
374		electrostaticScreeningMethod = \"damped\";
375		cutoffRadius = $cutoff;
376	+	switchingRadius = $cutoff;
377	+	dampingAlpha = $alpha;
378
379		targetTemp = 300;
380		targetPressure = 1.0;
#	Line 410 | Line 409 | sub findCutoff {
409		}
410		}
411
413	–	sub findAlpha {
414	–	$alpha = $alphaInt - $cutoff*$alphaSlope;
415	–	}
416	–
412		sub printFrameData {
413		print OUTFILE
414		"  <Snapshot>
#	Line 433 | Line 428 | sub printWaterMD {
428		printSSD_E();
429		printSSD_RF();
430		printSSD();
431	+	printSSDQ();
432	+	printSSDQO();
433		printSSD1();
434		printTRED();
435		printTIP3P();
#	Line 505 | Line 502 | sub printSSD {
502		}"
503		}
504
505	+	sub printSSDQ {
506	+	print $waterFileHandle "\n\nmolecule{
507	+	name = \"SSDQ\";
508	+
509	+	atom[0]{
510	+	type = \"SSDQ\";
511	+	position( 0.0, 0.0, 0.0 );
512	+	orientation( 0.0, 0.0, 0.0 );
513	+	}
514	+	}"
515	+	}
516	+
517	+	sub printSSDQO {
518	+	print $waterFileHandle "\n\nmolecule{
519	+	name = \"SSDQO\";
520	+
521	+	atom[0]{
522	+	type = \"SSDQO\";
523	+	position( 0.0, 0.0, 0.0 );
524	+	orientation( 0.0, 0.0, 0.0 );
525	+	}
526	+	}"
527	+	}
528	+
529		sub printSSD1 {
530		print $waterFileHandle "\n\nmolecule{
531		name = \"SSD1\";
#	Line 780 | Line 801 | sub validateWater {
801		elsif ($waterName eq 'SPC')      { $waterCase = 12;   }
802		elsif ($waterName eq 'DPD')      { $waterCase = 13;   }
803		elsif ($waterName eq 'CG2')      { $waterCase = 14;   }
804	+	elsif ($waterName eq 'SSDQ')     { $waterCase = 15;   }
805	+	elsif ($waterName eq 'SSDQO')    { $waterCase = 16;   }
806		else                             { $invalidWater = 1; }
807		}
808
#	Line 799 | Line 822 | sub printWaterModel {
822		elsif ($waterCase == 12) { printSPC();     }
823		elsif ($waterCase == 13) { printDPD();     }
824		elsif ($waterCase == 14) { printCG2();     }
825	+	elsif ($waterCase == 15) { printSSDQ();    }
826	+	elsif ($waterCase == 16) { printSSDQO();   }
827		}

Comparing trunk/src/applications/utilities/waterBoxer (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1962 by gezelter, Wed Jan 15 22:26:18 2014 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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