Sept 8th, 2010

 
#!/usr/bin/perl -w
 
print "\nChecking files:\n";
 
if ( -e "equi.namd" )
  {
    print "   Found: equi.namd\n";
  }
else
  {
    print "   Missing equi.namd. Aborting now.\n";
    exit;
  }
 
if ( -e "LOG" )
  {
    print "   Found: LOG\n";
  }
else
  {
    print "   Missing LOG. Aborting now.\n";
    exit;
  }
 
if ( -e "output/equi_out.dcd" )
  {
    print "   Found: output/equi_out.dcd\n";
  }
else
  {
    print "   Missing output/equi_out.dcd. Aborting now.\n";
    exit;
  }
 
if ( -e "output/equi_out.xst" )
  {
    print "   Found: output/equi_out.xst\n";
  }
else
  {
    print "   Missing output/equi_out.xst. Aborting now.\n";
    exit;
  }
 
if ( -e "output/restart.coor" )
  {
    print "   Found: output/restart.coor\n";
  }
else
  {
    print "   Missing output/restart.coor. Aborting now.\n";
    exit;
  }
 
if ( -e "output/restart.vel" )
  {
    print "   Found: output/restart.vel\n";
  }
else
  {
    print "   Missing output/restart.vel. Aborting now.\n";
    exit;
  }
 
if ( -e "output/restart.xsc" )
  {
    print "   Found: output/restart.xsc\n";
  }
else
  {
    print "   Missing output/restart.xsc. Aborting now.\n";
    exit;
  }
 
$count = `grep -c -i "heat_out.vel" equi.namd`;
 
if ( $count == 1 )
  {
    print "\nThis appears to be the first restart.\n\n";
 
    $count = `grep -c -i "restart.coor" equi.namd`;
 
    if ( $count > 0 )
      {
        print "Both restart.coor and heat_out.coor used in equi.namd ?\n";
        print "Aborting now.\n";
        exit;
      }
 
    if ( -e "LOG.1" )
      {
        print "But a LOG.1 exists ? Abort.\n";
        exit;
      }
    if ( -e "equi.namd.1" )
      {
        print "But a equi.namd.1 exists ? Abort.\n";
        exit;
      }
    if ( -e "output/RUN_1.dcd" )
      {
        print "But an output/RUN_1.dcd exists ? Abort.\n";
        exit;
      }
 
    print "Renaming/moving/removing files:\n";
    system("mv LOG LOG.1");
    print "   Renamed LOG to LOG.1\n";
    system("mv equi.namd equi.namd.1");
    print "   Renamed equi.namd to equi.namd.1\n";
    system("mv output/restart.coor ./restart.coor");
    print "   Moved output/restart.coor to current directory\n";
    system("mv output/restart.vel ./restart.vel");
    print "   Moved output/restart.vel to current directory\n";
    system("mv output/restart.xsc ./restart.xsc");
    print "   Moved output/restart.xsc to current directory\n";
    system("mv output/equi_out.dcd output/RUN_1.dcd");
    print "   Renamed output/equi_out.dcd to output/RUN_1.dcd\n";
    system("rm -rf output/equi_out.xst");
    print "   Removed output/equi_out.xst\n";
    system("rm -rf output/restart*.old");
    print "   Removed output/restart*.old\n";
 
 
    #
    # Starting timestep
    #
    open XSC, "restart.xsc" or die "Can not open restart.xsc for reading ? Abort.\n";
    $line = <XSC>;
    $line = <XSC>;
    $line = <XSC>;
    @words = split( ' ', $line );
    $starting_timestep = $words[0];
    if ( ! $starting_timestep =~ /^(\d+\.?\d*|\.\d+)$/ )
      {
        print "Starting timestep not a number ? Abort now.\n";
        exit;
      }
    close( XSC );
    print "\nStarting timestep is $starting_timestep\n";
    print "Modifying equi.namd ...\n\n";
 
 
    #
    # Add restart stuff & new timestep
    #
    open IN_NAMD, "equi.namd.1" or die "Can not open equi.namd.1 for reading ? Abort.\n";
    open OUT_NAMD, ">equi.namd" or die "Can not open equi.namd file for writing. Abort.\n";
 
    while( $line = <IN_NAMD> )
    {
      if ( $line =~ /coordinates\s+heat_out.coor/ )
        {
          print OUT_NAMD "coordinates             heat_out.coor\n";
          print OUT_NAMD "bincoordinates          restart.coor\n";
          print OUT_NAMD "binvelocities           restart.vel\n";
          print OUT_NAMD "extendedSystem          restart.xsc\n";
        }
      elsif ( $line =~ /velocities\s+heat_out.vel/ )
        { }
      elsif ( $line =~ /extendedSystem\s+heat_out.xsc/ )
        { }
      elsif ( $line =~ /velocities\s+heat_out.vel/ )
        { }
      elsif ( $line =~ /firsttimestep\s+\d+/ )
        {
          print OUT_NAMD "firsttimestep           $starting_timestep\n";
        }
      else
          {
            print OUT_NAMD $line;
          }
    }
 
    print "All done.\n\n";
 
    exit;  
  }
 
$count = `grep -c -i "restart.vel" equi.namd`;
 
if ( $count == 1 )
  {
    $count = `ls -1 | grep 'LOG.*' | wc -l`;
    chomp( $count );
    print "\nThis will be restart number $count\n\n";
 
    $check = `grep -c -i "heat_out.vel" equi.namd`;
 
    if ( $check > 0 )
      {
        print "Both restart.vel and heat_out.vel used in equi.namd ?\n";
        print "Aborting now.\n";
        exit;
      }
 
    if ( -e "LOG.$count" )
      {
        print "But a LOG.$count exists ? Abort.\n";
        exit;
      }
    if ( -e "equi.namd.$count" )
      {
        print "But a equi.namd.$count exists ? Abort.\n";
        exit;
      }
    if ( -e "output/RUN_$count.dcd" )
      {
        print "But an output/RUN_1.dcd exists ? Abort.\n";
        exit;
      }
 
    print "Renaming/moving/removing files:\n";
    system("mv LOG LOG.$count");
    print "   Renamed LOG to LOG.$count\n";
    system("mv equi.namd equi.namd.$count");
    print "   Renamed equi.namd to equi.namd.$count\n";
    system("mv output/restart.coor ./restart.coor");
    print "   Moved output/restart.coor to current directory\n";
    system("mv output/restart.vel ./restart.vel");
    print "   Moved output/restart.vel to current directory\n";
    system("mv output/restart.xsc ./restart.xsc");
    print "   Moved output/restart.xsc to current directory\n";
    system("mv output/equi_out.dcd output/RUN_$count.dcd");
    print "   Renamed output/equi_out.dcd to output/RUN_$count.dcd\n";
    system("rm -rf output/equi_out.xst");
    print "   Removed output/equi_out.xst\n";
    system("rm -rf output/restart*.old");
    print "   Removed output/restart*.old\n";
 
 
    #
    # Starting timestep
    #
    open XSC, "restart.xsc" or die "Can not open restart.xsc for reading ? Abort.\n";
    $line = <XSC>;
    $line = <XSC>;
    $line = <XSC>;
    @words = split( ' ', $line );
    $starting_timestep = $words[0];
    if ( ! $starting_timestep =~ /^(\d+\.?\d*|\.\d+)$/ )
      {
        print "Starting timestep not a number ? Abort now.\n";
        exit;
      }
    close( XSC );
    print "\nStarting timestep is $starting_timestep\n";
    print "Modifying equi.namd ...\n\n";
 
 
    #
    # Add restart stuff & new timestep
    #
    open IN_NAMD, "equi.namd.$count" or die "Can not open equi.namd.1 for reading ? Abort.\n";
    open OUT_NAMD, ">equi.namd" or die "Can not open equi.namd file for writing. Abort.\n";
 
    while( $line = <IN_NAMD> )
    {
      if ( $line =~ /firsttimestep\s+\d+/ )
        {
          print OUT_NAMD "firsttimestep           $starting_timestep\n";
        }
      else
          {
            print OUT_NAMD $line;
          }
    }
 
    print "All done.\n\n";
 
    exit;
 
  }
 
print "Something is wrong. No heat_out.coor, nor restart.coor used ?\n";
print "Aborting now.\n";
 
exit;