[ViewVC] Diff of: OpenMD/trunk/src/applications/utilities/waterBoxer.in

Comparing trunk/src/applications/utilities/waterBoxer.in (file contents):
Revision 1034 by chrisfen, Fri Sep 1 21:08:03 2006 UTC vs.
Revision 1035 by chrisfen, Fri Sep 1 22:58:33 2006 UTC

+# program that builds water boxes
+# author    = "Chris Fennell
-<
+# version   = "$Revision: 1.1 $"
-<
+# date      = "$Date: 2006-09-01 21:08:03 $"
->
+# version   = "$Revision: 1.2 $"
->
+# date      = "$Date: 2006-09-01 22:58:33 $"
+# copyright = "Copyright (c) 2006 by the University of Notre Dame"
+# license   = "OOPSE"
+$alpha = 0.2125;
+$alphaInt = 0.5125;
+$alphaSlope = 0.025;
-+
+$invalidWater = 0;
+# get our options
-<
+getopts('hrvd:l:n:w:');
->
+getopts('hmrvd:l:n:w:');
+# if we don't have a filename, drop to -h
+$opt_h = 'true' if $#ARGV != 0;
+    print "usage: waterBoxer [-hv] [-d density] [-l lattice] [-n # waters]\n";
+    print "\t[-w water name] [file name]\n\n";
+    print "  -h : show this message\n";
-+
+    print "  -m : print out a water.md file (file with all water models)\n";
+    print "  -r : randomize orientations\n";
+    print "  -v : verbose output\n\n";
+    print "  -d real    : density in g/cm^3\n";
+} else {
+    $fileName = 'waterBox';
-+
+if ($opt_m){
-+
+  die "$fileName cannot be \"water.md\"\n\tPlease choose a different name\n" if $fileName eq 'water.md';
-+
+  $waterFileHandle = 'WATERMD';
-+
+} else {
-+
+  $waterFileHandle = 'OUTFILE';
-+
+}
+if ($opt_r){
+  $doRandomize = $opt_r;
-+
+if (defined($opt_w)){
+  $waterName = $opt_w;
+} else {
+  $waterName = 'SPCE';
-<
->
+validateWater();
+if (defined($opt_d)){
+  if ($opt_d =~ /^[0-9]/) {
+    $density = $opt_d;
+writeOutFile();
-+
+if ($opt_m || $invalidWater){
-+
+  printWaterMD();
-+
+}
-+
+# this marks the end of the main program, below is subroutines
+sub acos {
+sub printMetaData {
-<
+print OUTFILE"  <MetaData>
-<
+#include \"water.md\"
->
+  print OUTFILE "  <MetaData>\n";
-<
+component{
->
+# print the water model or includes
->
+  if ($opt_m){
->
+    print OUTFILE "#include \"water.md\"";
->
+  } else {
->
+    printWaterModel();
->
+  }
->
+  printFakeWater() if $invalidWater == 1;
->
->
+# now back to the metaData output
->
+  print OUTFILE "\n\ncomponent{
+  type = \"$waterName\";
+  nMol = $nMol;
-–
+ensemble = NVE;
+forceField = \"DUFF\";
+electrostaticSummationMethod = \"shifted_force\";
+        Time: 0
+        Hmat: {{ $boxLength, 0, 0 }, { 0, $boxLength, 0 }, { 0, 0, $boxLength }}
+    </FrameData>\n";
-+
+}
-+
-+
+sub printWaterMD{
-+
+  open(WATERMD, ">./water.md") || die "\tError: can't open file water.md\n";
-+
-+
+  print WATERMD "#ifndef _WATER_MD_\n#define _WATER_MD_\n";
-+
+  printCl();
-+
+  printNa();
-+
+  printSSD_E();
-+
+  printSSD_RF();
-+
+  printSSD();
-+
+  printSSD1();
-+
+  printTRED();
-+
+  printTIP3P();
-+
+  printTIP4P();
-+
+  printTIP4PEw();
-+
+  printTIP5P();
-+
+  printTIP5PE();
-+
+  printSPCE();
-+
+  printSPC();
-+
+  printDPD();
-+
+  print WATERMD "\n\n#endif";
-+
+}
-+
-+
+sub printCl{
-+
+  print $waterFileHandle "\n\nmolecule{
-+
+  name = \"Cl-\";
-+
-+
+  atom[0]{
-+
+    type = \"Cl-\";
-+
+    position(0.0, 0.0, 0.0);
-+
+  }
-+
+}"
-+
+}
-+
-+
+sub printNa{
-+
+  print $waterFileHandle "\n\nmolecule{
-+
+  name = \"Na+\";
-+
-+
+  atom[0]{
-+
+    type = \"Na+\";
-+
+    position(0.0, 0.0, 0.0);
-+
+  }
-+
+}"
-+
+}
-+
-+
+sub printSSD_E{
-+
+  print $waterFileHandle "\n\nmolecule{
-+
+  name = \"SSD_E\";
-+
-+
+  atom[0]{
-+
+    type = \"SSD_E\";
-+
+    position( 0.0, 0.0, 0.0 );
-+
+    orientation( 0.0, 0.0, 0.0 );
-+
+  }
-+
+}"
-+
+}
-+
-+
+sub printSSD_RF{
-+
+  print $waterFileHandle "\n\nmolecule{
-+
+  name = \"SSD_RF\";
-+
-+
+  atom[0]{
-+
+    type = \"SSD_RF\";
-+
+    position( 0.0, 0.0, 0.0 );
-+
+    orientation( 0.0, 0.0, 0.0 );
-+
+  }
-+
+}"
-+
+}
-+
-+
+sub printSSD{
-+
+  print $waterFileHandle "\n\nmolecule{
-+
+  name = \"SSD\";
-+
-+
+  atom[0]{
-+
+    type = \"SSD\";
-+
+    position( 0.0, 0.0, 0.0 );
-+
+    orientation( 0.0, 0.0, 0.0 );
-+
+  }
-+
+}"
-+
+}
-+
-+
+sub printSSD1{
-+
+  print $waterFileHandle "\n\nmolecule{
-+
+  name = \"SSD1\";
-+
-+
+  atom[0]{
-+
+    type = \"SSD1\";
-+
+    position( 0.0, 0.0, 0.0 );
-+
+    orientation( 0.0, 0.0, 0.0 );
-+
+  }
-+
+}"
-+
+}
-+
-+
+sub printTRED{
-+
+  print $waterFileHandle "\n\nmolecule{
-+
+  name = \"TRED\";
-+
-+
+  atom[0]{
-+
+    type = \"TRED\";
-+
+    position( 0.0, 0.0, 0.0 );
-+
+    orientation( 0.0, 0.0, 0.0 );
-+
+  }
-+
+  atom[1]{
-+
+    type = \"EP_TRED\";
-+
+    position( 0.0, 0.0, 0.5 );
-+
+  }
-+
-+
+  rigidBody[0]{
-+
+    members(0, 1);
-+
+  }
-+
-+
+  cutoffGroup{
-+
+    members(0, 1);
-+
+  }
-+
+}"
-+
+}
-+
-+
+sub printTIP3P{
-+
+  print $waterFileHandle "\n\nmolecule{
-+
+  name = \"TIP3P\";
-+
-+
+  atom[0]{
-+
+    type = \"O_TIP3P\";
-+
+    position( 0.0, 0.0, -0.06556 );
-+
+  }
-+
+  atom[1]{
-+
+    type = \"H_TIP3P\";
-+
+    position( 0.0, 0.75695, 0.52032 );
-+
+  }
-+
+  atom[2]{
-+
+    type = \"H_TIP3P\";
-+
+    position( 0.0, -0.75695, 0.52032 );
-+
+  }
-+
-+
+  rigidBody[0]{
-+
+    members(0, 1, 2);
-+
+  }
-+
-+
+  cutoffGroup{
-+
+    members(0, 1, 2);
-+
+  }
-+
+}"
-+
+}
-+
-+
+sub printTIP4P{
-+
+  print $waterFileHandle "\n\nmolecule{
-+
+  name = \"TIP4P\";
-+
-+
+  atom[0]{
-+
+    type = \"O_TIP4P\";
-+
+    position( 0.0, 0.0, -0.06556 );
-+
+  }
-+
+  atom[1]{
-+
+    type = \"H_TIP4P\";
-+
+    position( 0.0, 0.75695, 0.52032 );
-+
+  }
-+
+  atom[2]{
-+
+    type = \"H_TIP4P\";
-+
+    position( 0.0, -0.75695, 0.52032 );
-+
+  }
-+
+  atom[3]{
-+
+    type = \"EP_TIP4P\";
-+
+    position( 0.0, 0.0, 0.08444 );
-+
+  }
-+
-+
+  rigidBody[0]{
-+
+    members(0, 1, 2, 3);
-+
+  }
-+
-+
+  cutoffGroup{
-+
+    members(0, 1, 2, 3);
-+
+  }
-+
+}"
-+
+}
-+
-+
+sub printTIP4PEw{
-+
+  print $waterFileHandle "\n\nmolecule{
-+
+  name = \"TIP4P-Ew\";
-+
-+
+  atom[0]{
-+
+    type = \"O_TIP4P-Ew\";
-+
+    position( 0.0, 0.0, -0.06556 );
-+
+  }
-+
+  atom[1]{
-+
+    type = \"H_TIP4P-Ew\";
-+
+    position( 0.0, 0.75695, 0.52032 );
-+
+  }
-+
+  atom[2]{
-+
+    type = \"H_TIP4P-Ew\";
-+
+    position( 0.0, -0.75695, 0.52032 );
-+
+  }
-+
+  atom[3]{
-+
+    type = \"EP_TIP4P-Ew\";
-+
+    position( 0.0, 0.0, 0.05944 );
-+
+  }
-+
-+
+  rigidBody[0]{
-+
+    members(0, 1, 2, 3);
-+
+  }
-+
-+
+  cutoffGroup{
-+
+    members(0, 1, 2, 3);
-+
+  }
-+
+}"
-+
-+
+sub printTIP5P{
-+
+  print $waterFileHandle "\n\nmolecule{
-+
+  name = \"TIP5P\";
-+
-+
+  atom[0]{
-+
+    type = \"O_TIP5P\";
-+
+    position( 0.0, 0.0, -0.06556 );
-+
+  }
-+
+  atom[1]{
-+
+    type = \"H_TIP5P\";
-+
+    position( 0.0, 0.75695, 0.52032 );
-+
+  }
-+
+  atom[2]{
-+
+    type = \"H_TIP5P\";
-+
+    position( 0.0, -0.75695, 0.52032 );
-+
+  }
-+
+  atom[3]{
-+
+    type = \"EP_TIP5P\";
-+
+    position( 0.57154, 0.0, -0.46971 );
-+
+  }
-+
+  atom[4]{
-+
+    type = \"EP_TIP5P\";
-+
+    position( -0.57154, 0.0, -0.46971 );
-+
+  }
-+
-+
+  rigidBody[0]{
-+
+    members(0, 1, 2, 3, 4);
-+
+  }
-+
-+
+  cutoffGroup{
-+
+    members(0, 1, 2, 3, 4);
-+
+  }
-+
+}"
-+
+}
-+
-+
+sub printTIP5PE{
-+
+  print $waterFileHandle "\n\nmolecule{
-+
+  name = \"TIP5P-E\";
-+
-+
+  atom[0]{
-+
+    type = \"O_TIP5P-E\";
-+
+    position( 0.0, 0.0, -0.06556 );
-+
+  }
-+
+  atom[1]{
-+
+    type = \"H_TIP5P\";
-+
+    position( 0.0, 0.75695, 0.52032 );
-+
+  }
-+
+  atom[2]{
-+
+    type = \"H_TIP5P\";
-+
+    position( 0.0, -0.75695, 0.52032 );
-+
+  }
-+
+  atom[3]{
-+
+    type = \"EP_TIP5P\";
-+
+    position( 0.57154, 0.0, -0.46971 );
-+
+  }
-+
+  atom[4]{
-+
+    type = \"EP_TIP5P\";
-+
+    position( -0.57154, 0.0, -0.46971 );
-+
+  }
-+
-+
+  rigidBody[0]{
-+
+    members(0, 1, 2, 3, 4);
-+
+  }
-+
-+
+  cutoffGroup{
-+
+    members(0, 1, 2, 3, 4);
-+
+  }
-+
+}"
-+
+}
-+
-+
+sub printSPCE{
-+
+print $waterFileHandle "\n\nmolecule{
-+
+  name = \"SPCE\";
-+
-+
+  atom[0]{
-+
+    type = \"O_SPCE\";
-+
+    position( 0.0, 0.0, -0.06461 );
-+
+  }
-+
+  atom[1]{
-+
+    type = \"H_SPCE\";
-+
+    position( 0.0, 0.81649, 0.51275 );
-+
+  }
-+
+  atom[2]{
-+
+    type = \"H_SPCE\";
-+
+    position( 0.0, -0.81649, 0.51275 );
-+
+  }
-+
-+
+  rigidBody[0]{
-+
+    members(0, 1, 2);
-+
+  }
-+
-+
+  cutoffGroup{
-+
+    members(0, 1, 2);
-+
+  }
-+
+}"
-+
+}
-+
-+
+sub printSPC{
-+
+print $waterFileHandle "\n\nmolecule{
-+
+  name = \"SPC\";
-+
-+
+  atom[0]{
-+
+    type = \"O_SPC\";
-+
+    position( 0.0, 0.0, -0.06461 );
-+
+  }
-+
+  atom[1]{
-+
+    type = \"H_SPC\";
-+
+    position( 0.0, 0.81649, 0.51275 );
-+
+  }
-+
+  atom[2]{
-+
+    type = \"H_SPC\";
-+
+    position( 0.0, -0.81649, 0.51275 );
-+
+  }
-+
-+
+  rigidBody[0]{
-+
+    members(0, 1, 2);
-+
+  }
-+
-+
+  cutoffGroup{
-+
+    members(0, 1, 2);
-+
+  }
-+
+}"
-+
+}
-+
-+
+sub printDPD{
-+
+  print $waterFileHandle "\n\nmolecule{
-+
+  name = \"DPD\";
-+
-+
+  atom[0]{
-+
+    type = \"DPD\";
-+
+    position(0.0, 0.0, 0.0);
-+
+  }
-+
+}"
-+
+}
-+
-+
-+
+sub printFakeWater{
-+
+  print $waterFileHandle "\n\nmolecule{
-+
+  name = \"$waterName\";
-+
-+
+  atom[0]{
-+
+    type = \"$waterName\";
-+
+    position(0.0, 0.0, 0.0);
-+
+  }
-+
+}"
-+
+}
-+
-+
-+
+sub validateWater{
-+
+  if    ($waterName eq 'Cl-')      { $waterCase = 0;    }
-+
+  elsif ($waterName eq 'Na+')      { $waterCase = 1;    }
-+
+  elsif ($waterName eq 'SSD_E')    { $waterCase = 2;    }
-+
+  elsif ($waterName eq 'SSD_RF')   { $waterCase = 3;    }
-+
+  elsif ($waterName eq 'SSD')      { $waterCase = 4;    }
-+
+  elsif ($waterName eq 'SSD1')     { $waterCase = 5;    }
-+
+  elsif ($waterName eq 'TIP3P')    { $waterCase = 6;    }
-+
+  elsif ($waterName eq 'TIP4P')    { $waterCase = 7;    }
-+
+  elsif ($waterName eq 'TIP4P-Ew') { $waterCase = 8;    }
-+
+  elsif ($waterName eq 'TIP5P')    { $waterCase = 9;    }
-+
+  elsif ($waterName eq 'TIP5P-E')  { $waterCase = 10;   }
-+
+  elsif ($waterName eq 'SPCE')     { $waterCase = 11;   }
-+
+  elsif ($waterName eq 'SPC')      { $waterCase = 12;   }
-+
+  elsif ($waterName eq 'DPD')      { $waterCase = 13;   }
-+
+  else                             { $invalidWater = 1; }
-+
+}
-+
-+
+sub printWaterModel{
-+
+  if    ($waterCase == 0)  { printCl();      }
-+
+  elsif ($waterCase == 1)  { printNa();      }
-+
+  elsif ($waterCase == 2)  { printSSD_E();   }
-+
+  elsif ($waterCase == 3)  { printSSD_RF();  }
-+
+  elsif ($waterCase == 4)  { printSSD();     }
-+
+  elsif ($waterCase == 5)  { printSSD1();    }
-+
+  elsif ($waterCase == 6)  { printTIP3P();   }
-+
+  elsif ($waterCase == 7)  { printTIP4P();   }
-+
+  elsif ($waterCase == 8)  { printTIP4PEw(); }
-+
+  elsif ($waterCase == 9)  { printTIP5P();   }
-+
+  elsif ($waterCase == 10) { printTIP5PE();  }
-+
+  elsif ($waterCase == 11) { printSPCE();    }
-+
+  elsif ($waterCase == 12) { printSPC();     }
-+
+  elsif ($waterCase == 13) { printDPD();     }
-+
+}

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing trunk/src/applications/utilities/waterBoxer.in (file contents): Revision 1034 by chrisfen, Fri Sep 1 21:08:03 2006 UTC vs. Revision 1035 by chrisfen, Fri Sep 1 22:58:33 2006 UTC

Diff Legend

Comparing trunk/src/applications/utilities/waterBoxer.in (file contents):
Revision 1034 by chrisfen, Fri Sep 1 21:08:03 2006 UTC vs.
Revision 1035 by chrisfen, Fri Sep 1 22:58:33 2006 UTC