#!/bin/sh
#                      pc_setupsrc
#                     -------------
# Description:
#   Link files into a local src directory
#   Also link script files from the bin directory ==> should be renamed
#
# CVS:
#   $Id$
#
# Usage:
#   pc_setupsrc [options] [src-dir]
# Options:
#   --pencil-home <dir>   Specify the root path of the Pencil Code directory
#   --min                 Link only a minimum of files
IAM=$0
#
link_scripts()
{
  echo "Linking job submission/execution scripts."
  to_link=
  for script in $scripts
  do
    if [ -f $bindir/$script ]; then
      [ -h ./$script ] && rm -f $script
      [ ! -f ./$script ] && to_link="$to_link $bindir/$script"
    else
      echo "No such file: $bindir/$script"
    fi
  done
  [ "$to_link" ] && ln -s $to_link .
}
#
link_root_makefile()
{
## Make a link to a root Makefile to allow make from the run directory
  [ -h Makefile ] && rm -f Makefile
  [ ! -f Makefile ] && ln -s $srcdir/Makefile.parent Makefile
  echo Linked root Makefile.
}
#
#-----------------------------------------------------------------------------
make_src_dir()
{
## src subdirectory
  if [ ! -d $src ]; then
    echo "No src directory found: creating new one (`pwd`/src)."
    mkdir $src
  fi
}
#
link_src_files()
{
#
#  LINK all *.f90, *.f, *.h, *.c, *.inc, and the Makefile to local src directory
#
  echo "Linking files in '$src'."
  old_dir="`pwd`"
  cd $src
  n=0
  to_link=
  for file in $srcdir/*.f90 $srcdir/*.f $srcdir/*.c \
              $srcdir/Makefile.src $srcdir/Makefile.depend \
              $srcdir/Makefile.library $srcdir/Makefile.machine \
              $srcdir/*.h $srcdir/*.inc $srcdir/scripts $srcdir/*.sed $srcdir/.cvsignore
  do
    if [ -f $file ] || [ -d $file ]; then
      if [ -h "`basename $file`" ]; then
        rm -f "`basename $file`"
        to_link="$to_link $file"
        #ln -s $file .
      elif [ -f "`basename $file`" ] \
        || [ -d "`basename $file`" ]; then
        n="`expr $n + 1`"
        existf="$existf`basename $file` "
      else
        to_link="$to_link $file"
        #ln -s $file .
      fi
    else
      echo "No such file: $file"
    fi
  done
  [ "$to_link" ] && ln -s $to_link .
  cd $old_dir
}
#
#-----------------------------------------------------------------------------
make_special_dir()
{
## src subdirectory
  [ -h $src/special ] && rm $src/special
  if [ ! -d $src/special ]; then
    echo "No special directory found: creating new one (`pwd`/src/special)."
    mkdir $src/special
  fi
}
#
link_special_files()
{
#
#  LINK all *.f90, *.f, and the Makefile to local src directory
#
  echo "Linking files in '$src/special'."
  old_dir="`pwd`"
  cd $src/special
  n=0
  to_link=
  for file in $srcdir/special/*.f90
  do
    if [ -f $file ] || [ -d $file ]; then
      if [ -h "`basename $file`" ]; then
        rm -f "`basename $file`"
        to_link="$to_link $file"
        #ln -s $file .
      elif [ -f "`basename $file`" ] \
        || [ -d "`basename $file`" ]; then
        n="`expr $n + 1`"
        existf="$existf`basename $file` "
      else
        to_link="$to_link $file"
        #ln -s $file .
      fi
    else
      echo "No such file: $file"
    fi
  done
  [ "$to_link" ] && ln -s $to_link .
  cd $old_dir
}
#
#-----------------------------------------------------------------------------
make_pre_and_post_processing_dir()
{
## pre- and post-processing subdirectory
  [ -h $src/pre_and_post_processing ] && rm $src/pre_and_post_processing
  if [ ! -d $src/pre_and_post_processing ]; then
    echo "No pre_and_post_processing directory found: creating new one (`pwd`/src/pre_and_post_processing)."
    mkdir $src/pre_and_post_processing
  fi
}
#
link_pre_and_post_processing_files()
{
#
#  LINK all *.f90 files to the local src directory
#
  echo "Linking files in '$src/pre_and_post_processing'."
  old_dir="`pwd`"
  cd $src/pre_and_post_processing
  n=0
  to_link=
  for file in $srcdir/pre_and_post_processing/*.f90
  do
    if [ -f $file ] || [ -d $file ]; then
      if [ -h "`basename $file`" ]; then
        rm -f "`basename $file`"
        to_link="$to_link $file"
      elif [ -f "`basename $file`" ] \
        || [ -d "`basename $file`" ]; then
        n="`expr $n + 1`"
        existf="$existf`basename $file` "
      else
        to_link="$to_link $file"
      fi
    else
      echo "No such file: $file"
    fi
  done
  [ "$to_link" ] && ln -s $to_link .
  cd $old_dir
}
#
#-----------------------------------------------------------------------------
make_inactive_dir()
{
## src subdirectory
  [ -h $src/inactive ] && rm $src/inactive
  if [ ! -d $src/inactive ]; then
    echo "No inactive directory found: creating new one (`pwd`/src/inactive)."
    mkdir $src/inactive
  fi
}
#
link_inactive_files()
{
#
#  LINK all *.f90, *.f, and the Makefile to local src directory
#
  echo "Linking files in '$src/inactive'."
  old_dir="`pwd`"
  cd $src/inactive
  n=0
  to_link=
  for file in $srcdir/inactive/*.f90
  do
    if [ -f $file ] || [ -d $file ]; then
      if [ -h "`basename $file`" ]; then
        rm -f "`basename $file`"
        to_link="$to_link $file"
        #ln -s $file .
      elif [ -f "`basename $file`" ] \
        || [ -d "`basename $file`" ]; then
        n="`expr $n + 1`"
        existf="$existf`basename $file` "
      else
        to_link="$to_link $file"
        #ln -s $file .
      fi
    else
      echo "No such file: $file"
    fi
  done
  [ "$to_link" ] && ln -s $to_link .
  cd $old_dir
}
#
#-----------------------------------------------------------------------------
make_experimental_dir()
{
## src subdirectory
  [ -h $src/experimental ] && rm $src/experimental
  if [ ! -d $src/experimental ]; then
    echo "No experimental directory found: creating new one (`pwd`/src/experimental)."
    mkdir $src/experimental
  fi
}
#
link_experimental_files()
{
#
#  LINK all *.90 to the local src directory
#
  echo "Linking files in '$src/experimental'."
  old_dir="`pwd`"
  cd $src/experimental
  n=0
  to_link=
  for file in $srcdir/experimental/*.*
  do
    if [ -f $file ] || [ -d $file ]; then
      if [ -h "`basename $file`" ]; then
        rm -f "`basename $file`"
        to_link="$to_link $file"
        #ln -s $file .
      elif [ -f "`basename $file`" ] \
        || [ -d "`basename $file`" ]; then
        n="`expr $n + 1`"
        existf="$existf`basename $file` "
      else
        to_link="$to_link $file"
        #ln -s $file .
      fi
    else
      echo "No such file: $file"
    fi
  done
  [ "$to_link" ] && ln -s $to_link .
  cd $old_dir
}
#
#-----------------------------------------------------------------------------
make_magnetic_dir()
{
## src subdirectory
  [ -h $src/magnetic ] && rm $src/magnetic
  if [ ! -d $src/magnetic ]; then
    echo "No magnetic directory found: creating new one (`pwd`/src/magnetic)."
    mkdir $src/magnetic
  fi
}
#
link_magnetic_files()
{
#
#  LINK all *.* to local src directory
#
  echo "Linking files in '$src/magnetic'."
  old_dir="`pwd`"
  cd $src/magnetic
  n=0
  to_link=
  for file in $srcdir/magnetic/*.*
  do
    if [ -f $file ] || [ -d $file ]; then
      if [ -h "`basename $file`" ]; then
        rm -f "`basename $file`"
        to_link="$to_link $file"
        #ln -s $file .
      elif [ -f "`basename $file`" ] \
        || [ -d "`basename $file`" ]; then
        n="`expr $n + 1`"
        existf="$existf`basename $file` "
      else
        to_link="$to_link $file"
        #ln -s $file .
      fi
    else
      echo "No such file: $file"
    fi
  done
  [ "$to_link" ] && ln -s $to_link .
  cd $old_dir
}
#
#-----------------------------------------------------------------------------
make_test_methods_dir()
{
## src subdirectory
  [ -h $src/test_methods ] && rm $src/test_methods
  if [ ! -d $src/test_methods ]; then
    echo "No test_methods directory found: creating new one (`pwd`/src/test_methods)."
    mkdir $src/test_methods
  fi
}
#
link_test_methods_files()
{
#
#  LINK all *.* to local src directory
#
  echo "Linking files in '$src/test_methods'."
  old_dir="`pwd`"
  cd $src/test_methods
  n=0
  to_link=
  for file in $srcdir/test_methods/*.*
  do
    if [ -f $file ] || [ -d $file ]; then
      if [ -h "`basename $file`" ]; then
        rm -f "`basename $file`"
        to_link="$to_link $file"
        #ln -s $file .
      elif [ -f "`basename $file`" ] \
        || [ -d "`basename $file`" ]; then
        n="`expr $n + 1`"
        existf="$existf`basename $file` "
      else
        to_link="$to_link $file"
        #ln -s $file .
      fi
    else
      echo "No such file: $file"
    fi
  done
  [ "$to_link" ] && ln -s $to_link .
  cd $old_dir
}
#
#-----------------------------------------------------------------------------
make_initial_condition_dir()
{
## src subdirectory
  [ -h $src/initial_condition ] && rm $src/initial_condition
  if [ ! -d $src/initial_condition ]; then
    echo "No initial_condition directory found: creating new one (`pwd`/src/initial_condition)."
    mkdir $src/initial_condition
  fi
}
#
link_initial_condition_files()
{
#
#  LINK all *.f90, *.f, and the Makefile to local src directory
#
  echo "Linking files in '$src/initial_condition'."
  old_dir="`pwd`"
  cd $src/initial_condition
  n=0
  to_link=
  for file in $srcdir/initial_condition/*.f90
  do
    if [ -f $file ] || [ -d $file ]; then
      if [ -h "`basename $file`" ]; then
        rm -f "`basename $file`"
        to_link="$to_link $file"
        #ln -s $file .
      elif [ -f "`basename $file`" ] \
        || [ -d "`basename $file`" ]; then
        n="`expr $n + 1`"
        existf="$existf`basename $file` "
      else
        to_link="$to_link $file"
        #ln -s $file .
      fi
    else
      echo "No such file: $file"
    fi
  done
  [ "$to_link" ] && ln -s $to_link .
  cd $old_dir
#
#-----------------------------------------------------------------------------
#  Local initial condition subroutines can be saved in initial_condition
#  folder in run directory.
#
  if [ -d "$old_dir/initial_condition" ]; then
    echo "Linking files in '$old_dir/initial_condition'."
    ln -fs $old_dir/initial_condition/* $src/initial_condition/
  fi
}
#
make_cuda_dir()
{
## cuda subdirectory
  [ -h $src/cuda ] && rm $src/cuda
  adddir $src/cuda
## cuda/src_new subdirectory
  [ -h $src/cuda/src_new ] && rm $src/cuda/src_new
  adddir $src/cuda/src_new
## subdirectories of src_new
  adddir $src/cuda/src_new/utils
  adddir $src/cuda/src_new/common
  adddir $src/cuda/src_new/gpu
  adddir $src/cuda/src_new/diagnostics
  adddir $src/cuda/src_new/gpu/cuda
  adddir $src/cuda/src_new/gpu/cuda/core
  adddir $src/cuda/src_new/gpu/cuda/generic
}
#
make_astaroth_dir()
{
## astaroth subdirectory
  [ -h $src/astaroth ] && rm $src/astaroth
  adddir $src/astaroth
## submodule subdirectory
  [ -h $src/astaroth/submodule ] && rm $src/astaroth/submodule
  adddir $src/astaroth/submodule
## subdirectories of submodule
  adddir $src/astaroth/submodule/include
  adddir $src/astaroth/submodule/src
  adddir $src/astaroth/submodule/src/core
  adddir $src/astaroth/submodule/src/core/kernels
  adddir $src/astaroth/submodule/src/utils
#  adddir $src/astaroth/submodule/scripts
#  adddir $src/astaroth/submodule/acc
#  adddir $src/astaroth/submodule/acc/pc_mhd_solver
#  adddir $src/astaroth/submodule/acc/pencil
  adddir $src/astaroth/submodule/acc-runtime
  adddir $src/astaroth/submodule/acc-runtime/acc
  adddir $src/astaroth/submodule/acc-runtime/api
  adddir $src/astaroth/submodule/acc-runtime/Pencil
  adddir $src/astaroth/submodule/acc-runtime/stdlib
  adddir $src/astaroth/submodule/acc-runtime/samples
  adddir $src/astaroth/submodule/acc-runtime/samples/mhd
  adddir $src/astaroth/submodule/acc-runtime/samples/mhd_modular
}
#
adddir()
{
echo adddir: $1
  if [ ! -d $1 ]; then
    echo "No ${1##*/} directory found: creating new one ($1)."
    mkdir $1
  fi
}
#
link_astaroth_files()
{
#
#  LINK all sources headers and Makefiles to local src/astaroth directory
#
  echo "Linking files in '$src/astaroth'."
  old_dir="`pwd`"
  cd $src/astaroth
  to_link=
#  len=`expr match "$srcdir/cuda/astaroth/" '.*astaroth/'`
  for file in $srcdir/astaroth/*.cc $srcdir/astaroth/*.*h $srcdir/astaroth/Makefile* \
$srcdir/astaroth/submodule/CMakeLists.txt $srcdir/astaroth/submodule/include/*.*h \
$srcdir/astaroth/submodule/acc/CMakeLists.txt \
$srcdir/astaroth/submodule/acc-runtime/CMakeLists.txt \
$srcdir/astaroth/submodule/acc-runtime/acc/* \
$srcdir/astaroth/submodule/acc-runtime/api/* \
$srcdir/astaroth/submodule/acc-runtime/Pencil/prerequisites.h \
$srcdir/astaroth/submodule/acc-runtime/stdlib/*.h \
$srcdir/astaroth/submodule/acc-runtime/samples/mhd/* \
$srcdir/astaroth/submodule/acc-runtime/samples/mhd_modular/* \
$srcdir/astaroth/submodule/src/core/*.*h $srcdir/astaroth/submodule/src/core/*.cc \
$srcdir/astaroth/submodule/src/utils/*.h $srcdir/astaroth/submodule/src/utils/*.c $srcdir/astaroth/submodule/src/utils/CMakeLists.txt \
$srcdir/astaroth/submodule/src/core/CMakeLists.txt $srcdir/astaroth/submodule/src/core/kernels/* \
$srcdir/astaroth/submodule/acc/*.sh $srcdir/astaroth/submodule/acc/src/* $srcdir/astaroth/submodule/acc/pc_mhd_solver/* \
$srcdir/astaroth/submodule/acc/pencil/*.h $srcdir/astaroth/submodule/acc/stdlib/*.h
  do
    file_for_link $file
  done

  for file in $to_link
  do
#    ln -s $file ${file:$len}
    ln -s $file `echo $file | sed -r 's/^.*astaroth\///'`
  done

  cd $old_dir
}
#
link_cuda_files()
{
#
#  LINK all *.* to local src/cuda directory
#
  echo "Linking files in '$src/cuda'."
  old_dir="`pwd`"
  cd $src/cuda
  n=0
  to_link=
  for file in $srcdir/cuda/src/*.cc $srcdir/cuda/src/*.cuh $srcdir/cuda/src/*.cpp $srcdir/cuda/src/*.h $srcdir/cuda/src/makefile $srcdir/cuda/src/makefile.* $srcdir/cuda/src/*.conf 
  do
    if [ -f $file ] || [ -d $file ]; then
      if [ -h "`basename $file`" ]; then
        rm -f "`basename $file`"
        to_link="$to_link $file"
        #ln -s $file .
      elif [ -f "`basename $file`" ] \
        || [ -d "`basename $file`" ]; then
        n="`expr $n + 1`"
        existf="$existf`basename $file` "
      else
        to_link="$to_link $file"
        #ln -s $file .
      fi
    else
      echo "No such file: $file"
    fi
  done
  [ "$to_link" ] && ln -s $to_link .

  echo "Linking files in '$src/cuda/src_new'."
  cd $src/cuda/src_new
  to_link=
  len=`expr match "$srcdir/cuda/src_new/" '.*src_new/'`
  for file in $srcdir/cuda/src_new/*.cc $srcdir/cuda/src_new/*.txt $srcdir/cuda/src_new/Makefile* $srcdir/cuda/src_new/utils/*.h $srcdir/cuda/src_new/common/*.cc $srcdir/cuda/src_new/common/*.txt $srcdir/cuda/src_new/common/*.h $srcdir/cuda/src_new/gpu/*.cc $srcdir/cuda/src_new/gpu/*.txt $srcdir/cuda/src_new/gpu/*.h $srcdir/cuda/src_new/diagnostics/*.h $srcdir/cuda/src_new/diagnostics/*.cc $srcdir/cuda/src_new/gpu/cuda/*.cc* $srcdir/cuda/src_new/gpu/cuda/core/*.cc* $srcdir/cuda/src_new/gpu/cuda/generic/*.cu*
  do
    file_for_link $file
  done
  for file in $to_link
  do 
#    ln -s $file ${file:$len}
    ln -s $file `echo $file | sed -r 's/^.*src_new\///'`
  done

  cd $old_dir
}
#
file_for_link()
{
    if [ -f $1 ] || [ -d $1 ]; then
#      relname=${1:$len}
      relname=`echo $file | sed -r 's/^.*\/src_new\///' | sed -r 's/^.*\/astaroth\///'`
      if [ -h $relname ]; then
        rm -f $relname
        to_link="$to_link $1"
      elif [ ! -f $relname ] \
        && [ ! -d $relname ]; then
        to_link="$to_link $1"
      fi
    else
      echo "No such file: $1"
    fi
}
#
create_Makefile_inc()
{
#
#  Create empty src/Makefile.inc, so `make' does not complain about its
#  absence when run for the first time
#
  printf "# %s\n" "Empty" "(This file was written by 'pc_setupsrc')" \
      > src/Makefile.inc
  printf "# %s\n" "Empty" "(This file was written by 'pc_setupsrc')" \
      > src/Makefile-standard.inc
}
#
copy_local_files()
{
#
#  COPY all *.local files into local src directory
#
  echo "Creating .local files in $src (if necessary)."
  old_dir="`pwd`"
  cd $src
  n=0
  to_copy=
  for file in $srcdir/*.local
  do
    if [ -f $file ]; then
      if [ ! -f "`basename $file`" ]; then
# Warn user about copying *.local, as these should normally come
# with each run directory:
        echo "Copying default file $file to src/ -- are you sure this is OK?"
        to_copy="$to_copy $file"
        #cp $file .
      else
        # echo "`basename $file` already exists"
        n="`expr $n + 1`"
        existf="$existf`basename $file` "
      fi
    else
      echo "No such file: $file"
    fi
  done
  [ "$to_copy" ] && cp $to_copy .
  cd $old_dir
}
#
print_status()
{
  [ $n -eq 1 ] &&  echo "$existf already existed in $src"
  [ $n -gt 1 ] && echo "$n files already existed in $src"
}
#
remove_broken_links()
{
## Remove any broken links...
  find . $src -type l 2>/dev/null | perl -lne 'unlink $_ if (-l && ! -e)'
}
#
prepare_for_compile()
{
#
#  Generate Makefile
#
  echo "Rebuilding Makefile from Makefile.src."
  old_dir="`pwd`"
  cd $src
  rm -f Makefile                        # for old run directories
  rm -f makefile                        # for old run directories
  $srcdir/scripts/adapt-mkfile Makefile.src Makefile
  cd $old_dir
  hn=`hostname`
  if [ "$hn" = emil-login2.pdc.kth.se ]; then
      touch FAKE_PARALLEL_IO
  fi
}
#
scripts="start.csh start_run.csh run.csh getconf.csh"
pencil_home_path=$PENCIL_HOME
src="`pwd`/src"
link_all=1
#
while [ $# -gt 0 ]
do
  case $1 in
  -h)
    . $pencil_home_path/lib/sh/functions.sh
    usage_from_header $IAM
    exit 1
  ;;
  -?)
    . $pencil_home_path/lib/sh/functions.sh
    usage_from_header $IAM
    exit 1
  ;;
  --help)
    . $pencil_home_path/lib/sh/functions.sh
    usage_from_header $IAM
    exit 1
  ;;
  --pencil-home)
    pencil_home_path=$2
    shift
  ;;
  --min)
    link_all=0
    break
  ;;
  --)
    shift
    break
  ;;
  *)
    if [ $specified_src ]; then
      echo UNRECOGNISED PARAMETER
      usage_from_header $IAM
      exit 1
    fi
    src=$1
  ;;
  esac
  shift
done
#
. $pencil_home_path/lib/sh/functions.sh
#
if [ ! "$pencil_home_path" ]; then
  echo " You need to provide the path to the Pencil Code, either via the"
  echo " --pencil-home option or you need to set PENCIL_HOME; "
  echo " consider sourcing sourceme.{,c}sh"
  exit 1
fi
#
bindir=$pencil_home_path/bin
srcdir=$pencil_home_path/src
#
echo "Files will be linked to the root code directory '$pencil_home_path'."
#
n=0
remove_broken_links
link_scripts
link_root_makefile
#
make_src_dir
if [ "$link_all" -eq 1 ]; then link_src_files; fi
#
make_pre_and_post_processing_dir
if [ "$link_all" -eq 1 ]; then link_pre_and_post_processing_files; fi
#
make_magnetic_dir
if [ "$link_all" -eq 1 ]; then link_magnetic_files; fi

if [ -f "$src/Makefile.local" ]; then
  if [ "`grep '^[^#]*= *special' $src/Makefile.local`" != "" ]; then
    make_special_dir
    if [ "$link_all" -eq 1 ]; then link_special_files; fi
  fi
  if [ "`grep '^[^#]*= *test_methods' $src/Makefile.local`" != "" ] || [ "`grep '^[^#]*=.*testfield' $src/Makefile.local`" != "" ]; then
    make_test_methods_dir
    if [ "$link_all" -eq 1 ]; then link_test_methods_files; fi
  fi
  if [ "`grep '^[^#]*= *inactive' $src/Makefile.local`" != "" ]; then 
    make_inactive_dir
    if [ "$link_all" -eq 1 ]; then link_inactive_files; fi
  fi
  if [ "`grep '^[^#]*= *experimental' $src/Makefile.local`" != "" ]; then 
    make_experimental_dir
    if [ "$link_all" -eq 1 ]; then link_experimental_files; fi
  fi
  if [ "`grep '^[^#]*= *initial_condition' $src/Makefile.local`" != "" ]; then 
    make_initial_condition_dir
    if [ "$link_all" -eq 1 ]; then link_initial_condition_files; fi
  fi
  if [ "`grep '^[^#]*= *gpu' $src/Makefile.local`" != "" ]; then 
    make_astaroth_dir
    if [ "$link_all" -eq 1 ]; then link_astaroth_files; fi
  fi
  if [ "`grep -i '^[^#]*= *openmp' $src/Makefile.local`" != "" ]; then 
    if [ "$link_all" -eq 1 ]; then ln -s $PENCIL_HOME/src/multithread src/multithread; fi
  fi
fi
if [ "$link_all" -eq 1 ]; then create_Makefile_inc; fi
#copy_local_files
print_status
if [ "$link_all" -eq 1 ]; then prepare_for_compile; fi