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# program that builds water boxes |
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# author = "Chris Fennell |
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< |
# version = "$Revision: 1.2 $" |
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< |
# date = "$Date: 2007-01-09 03:42:14 $" |
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> |
# version = "$Revision: 1.5 $" |
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> |
# date = "$Date: 2008-01-23 21:22:18 $" |
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# copyright = "Copyright (c) 2006 by the University of Notre Dame" |
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# license = "OOPSE" |
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# DPD waters are stand-ins for 4 water molecules |
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$density = $density * 0.25; |
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} |
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if ($waterName eq 'CG2') { |
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# CG2 waters are stand-ins for 2 water molecules |
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$density = $density * 0.5; |
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} |
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if (defined($opt_l)){ |
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$nothingSelected = 0; |
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} |
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} elsif ($lattice == 1){ |
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$crystalNumReal = ($nMol/1.0)**(1.0/3.0); |
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$crystalNum = int($crystalNumReal); |
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$crystalNum = int($crystalNumReal + $tolerance); |
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$remainder = $crystalNumReal - $crystalNum; |
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# again, if crystalNumReal wasn't an integer, we bump the crystal to the next |
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$zCorr[3] = $cell2Z; |
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# assemble the lattice |
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$counter = 0; |
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< |
for ($z = 0; $z < $nx; $z++) { |
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for ($z = 0; $z < $nz; $z++) { |
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for ($y = 0; $y < $ny; $y++) { |
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< |
for ($x = 0; $x < $nz; $x++) { |
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> |
for ($x = 0; $x < $nx; $x++) { |
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for ($uc = 0; $uc < 4; $uc++) { |
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$xCorr[$uc+$counter] = $xCorr[$uc] + $cellLengthX*$x; |
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$yCorr[$uc+$counter] = $yCorr[$uc] + $cellLengthY*$y; |
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$zCorr[0] = $cell2Z; |
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#assemble the lattice |
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$counter = 0; |
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< |
for ($z = 0; $z < $nx; $z++) { |
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> |
for ($z = 0; $z < $nz; $z++) { |
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for ($y = 0; $y < $ny; $y++) { |
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< |
for ($x = 0; $x < $nz; $x++) { |
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> |
for ($x = 0; $x < $nx; $x++) { |
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$xCorr[$counter] = $xCorr[0] + $cellLengthX*$x; |
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$yCorr[$counter] = $yCorr[0] + $cellLengthY*$y; |
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$zCorr[$counter] = $zCorr[0] + $cellLengthZ*$z; |
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printSPCE(); |
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printSPC(); |
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printDPD(); |
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printCG2(); |
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print WATERMD "\n\n#endif"; |
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} |
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}" |
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} |
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sub printCG2 { |
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print $waterFileHandle "\n\nmolecule{ |
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name = \"CG2\"; |
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atom[0]{ |
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type = \"CG2\"; |
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position(0.0, 0.0, 0.0); |
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} |
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}" |
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} |
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sub printFakeWater { |
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print $waterFileHandle "\n\nmolecule{ |
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elsif ($waterName eq 'SPCE') { $waterCase = 11; } |
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elsif ($waterName eq 'SPC') { $waterCase = 12; } |
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elsif ($waterName eq 'DPD') { $waterCase = 13; } |
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elsif ($waterName eq 'CG2') { $waterCase = 14; } |
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else { $invalidWater = 1; } |
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} |
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elsif ($waterCase == 11) { printSPCE(); } |
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elsif ($waterCase == 12) { printSPC(); } |
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elsif ($waterCase == 13) { printDPD(); } |
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elsif ($waterCase == 14) { printCG2(); } |
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} |
