atat-mirror/glue/castep/runstruct_castep

#!/bin/csh

# This script makes use of a wrap file (located in either the current directory
# or up to 3 directories up) as well as an "str.out" file (in the current directory)
# generated from MAPS. With these files we run CASTEP and then extract the energy of
# the structure which is placed in a file called "energy" in the current directory.
# If the calculation fails, an empty file called "error" will be created instead.

# Initial version created: 11/08/2011.  Author: Aaron Hopkinson (a.hopkinson89@gmail.com)
# This script is heavily based on the runstruct_abinit and runstruct_vasp scripts
# provided with ATAT.
#
# Revision: 14/10/2011. Updated extract_castep (change of variable names, division of
# energy by total number of ions) and fixed typo in the comment above.

source ~/.atat.rc
set strout = "str.out"
set wrapfilename = "castep.wrap"
set seedname = "temp"
set cellfile = "$seedname.cell"
set paramfile = "$seedname.param"
set extractfilename = "$seedname.castep"

# Loop over command line arguments to set script mode.
while ( $#argv != 0 )
  switch ( "$1" )
    case "-h":
      cat - <<EOF
runstruct_castep [-w file1] [-nr] [-ex file2] [-clean] cmdprefix
  Where file1 is an optional alternate wrap file (default: castep.wrap)
  and file2 is the .castep file for energy to be extracted from.
    If the wrap file is not found in the current directory,
    it searches in the parent directories .. and ../.. and ../../..
  -nr means do not run castep, just generate input files.
  -ex means do not generate cell and param files, do not run CASTEP, but extract info from a CASTEP output file.
  -clean deletes ALL CASTEP output files: CAUTION.
  cmdprefix is the prefix needed for CASTEP to run on a remote machine,
            such as "node -s node2" 
  Script contributed by Matt Probert matt.probert@york.ac.uk
EOF
      exit 1
      breaksw
    case "-w":
      set wrapfilename="$2"
      shift
    breaksw;
    case "-nr":
      set notruncastep
    breaksw;
    case "-ex":
      set extractonly
      set extractfilename="$2"
      shift
    breaksw;
    case "-clean":
      set clean
    breaksw;
    default:
      break;
  endsw
  shift
end

# Look for ~/.runstruct_castep.rc file to get necessary command to run CASTEP.
# If this does not exist, create a new one.
if ( -e ~/.runstruct_castep.rc ) then
  source ~/.runstruct_castep.rc
else
  cat - >! ~/.runstruct_castep.rc <<EOF
#!/bin/csh
# Enter the name of the CASTEP executable here.
set CASTEPCMD = castep
EOF
  echo "A default ~/.runstruct_castep.rc file has been created. Please edit this to match your configuration."
  exit 1
endif

# Look for str.out file (current dir), give error if it cannot be found.
if ( ! -e $strout ) then
  echo "str.out does not exist."
  echo "Please restart the program from a directory containing str.out."
  exit 1
endif

# Look for wrap file containing necessary CASTEP parameters.
# Check current directory or up to 3 levels up. If it cannot be found, print error.
set wrapfile="$wrapfilename"
if ( ! -e $wrapfile ) then
  set wrapfile="../$wrapfilename"
  if ( ! -e $wrapfile ) then
    set wrapfile="../../$wrapfilename"
    if ( ! -e $wrapfile ) then
      set wrapfile="../../../$wrapfilename"
      if ( ! -e $wrapfile ) then
        echo "You need a $wrapfilename file in $PWD , $PWD/.. , $PWD/../.. or $PWD/../../.."
        echo "Please restart the program from a directory where $wrapfilename can be found."
        exit 1
      endif
    endif
  endif
endif

# MAPS requires this for CASTEP to run on a remote machine.
set CMDPREFIX = "$1"

# Not in extract only mode:
if ( ! $?extractonly ) then
  echo "Generating input files.."

  # Generate the .param file from the .wrap file.
  set paramlines = `grep -n "\[param\]" $wrapfile | sed -e 's/\([0-9]*\)\(.*\)/\1/g'`
  tail -n +`expr $paramlines + 1` $wrapfile >! $paramfile

  # Now generate the .cell file. Firstly by extracting the coordinates from str.out
  # and using cellcvrt (included with ATAT) to convert to necessary format for CASTEP.
  echo "%block lattice_cart" >! $cellfile
  cat $strout | cellcvrt -c -ns=1 -sig=9 | head -n 6 | tail -n 3 >>! $cellfile
  echo "%endblock lattice_cart" >>! $cellfile
  echo "" >>! $cellfile
  echo "%block positions_abs" >>! $cellfile
  cat $strout | cellcvrt -c -ns=1 -sig=9 | tail -n +7 | sed -e 's/\([-0-9\.]*[ ]*[-0-9\.]*[ ]*[-0-9\.]*\)\([ ]*\)\([A-Za-z]*\)/\3\2\1/g' >>! $cellfile
  echo "%endblock positions_abs" >>! $cellfile

  # Add in the extra parameters from the .wrap file.
  echo "" >>! $cellfile
  head -n `expr $paramlines - 1` $wrapfile | tail -n +2 >>! $cellfile

  # If not-not running CASTEP: ie: We ARE running CASTEP..
  if ( ! $?notruncastep ) then
    # Run CASTEP:
    echo "Running CASTEP Geometry Optimisation.."
    $CMDPREFIX $CASTEPCMD $seedname

    # Use external script to extract the energy and check for errors. (External because it is used below as well)
    source $atatdir/glue/castep/extract_castep
    
    # $run == 3 when extract_castep is finished - explained in there.
    if ( $run == 3 ) then
      # If we don't want to clean, at least move CASTEP output to a new directory for neatness.
      # Default action in case people want to analyse runs.
      if ( ! $?clean ) then
        echo "Moving CASTEP output files to $PWD/castep_files.."
        mkdir castep_files >& /dev/null
        mv $seedname.* *.usp castep_files
      else
        # Otherwise, delete output.
        echo "Removing CASTEP output files.."
        rm -f $seedname.* *.usp
      endif
    endif
  endif
else
  # Extract energy from a previously generated .castep file.
  source $atatdir/glue/castep/extract_castep
  exit
endif