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# program that builds water boxes |
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# author = "Chris Fennell |
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# version = "$Revision: 1.3 $" |
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# date = "$Date: 2006-10-02 23:27:40 $" |
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# version = "$Revision: 1.4 $" |
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# date = "$Date: 2006-10-02 23:54:30 $" |
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# copyright = "Copyright (c) 2006 by the University of Notre Dame" |
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# license = "OOPSE" |
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$waterCase = -1; |
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# get our options |
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getopts('hmrvd:l:n:w:'); |
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getopts('hmrvd:l:n:o:w:'); |
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# if we don't have a filename, drop to -h |
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$opt_h = 'true' if $#ARGV != 0; |
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$opt_h = 'true' if $#ARGV != -1; |
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# our option output |
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if ($opt_h){ |
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print "waterBoxer: builds water boxes\n\n"; |
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print "usage: waterBoxer [-hv] [-d density] [-l lattice] [-n # waters]\n"; |
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print "\t[-w water name] [file name]\n\n"; |
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print "usage: waterBoxer [-hmrv] [-d density] [-l lattice] [-n # waters]\n"; |
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print "\t[-o file name] [-w water name] \n\n"; |
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print " -h : show this message\n"; |
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print " -m : print out a water.md file (file with all water models)\n"; |
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print " -r : randomize orientations\n"; |
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print " (default: 0)\n"; |
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print " -n integer : # of water molecules\n"; |
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print " (default: 500)\n"; |
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print " -o char : output file name\n"; |
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print " (default: freshWater.md)\n"; |
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print " -w char : name of the water stunt double\n"; |
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print " (default: SPCE)\n"; |
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print "Example:\n"; |
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die " waterBoxer -d 0.997 -n 864 -w SSD_RF ssdrfWater.md\n"; |
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die " waterBoxer -d 0.997 -n 864 -w SSD_RF -o ssdrfWater.md\n"; |
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} |
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# set some variables to be used in the code |
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$fileName = $ARGV[0]; |
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if (defined($fileName)){ |
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if (defined($opt_o)){ |
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$fileName = $opt_o; |
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} else { |
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$fileName = 'waterBox'; |
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$fileName = 'freshWater.md'; |
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} |
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if ($opt_m){ |
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die "$fileName cannot be \"water.md\"\n\tPlease choose a different name\n" if $fileName eq 'water.md'; |
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$waterName = 'SPCE'; |
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} |
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validateWater(); |
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if ($invalidWater == 1){ |
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print "Warning: \'$waterName\' is not a recognized water model name.\n"; |
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print " Use the \'-m\' option to generate a \'water.md\' with the\n"; |
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print " recognized water model geometries.\n"; |
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} |
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if (defined($opt_d)){ |
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if ($opt_d =~ /^[0-9]/) { |
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$density = $opt_d; |
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} |
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writeOutFile(); |
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print "Water box \"$fileName\" generated.\n"; |
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if ($opt_m || $invalidWater){ |
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if ($opt_m){ |
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printWaterMD(); |
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print "File \"water.md\" generated for inclusion in \"$fileName\"\n"; |
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} |
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# this marks the end of the main program, below is subroutines |
