#!/bin/bash

#
# Script to apply AMBER 10 bugfix.all
#
# Written by Ross Walker (SDSC)
#
# Version 1.0
# 10/19/2009 - Support bugfix.26 (chamber)
#

if [ $# != 1 ]; then
  echo "Usage:"
  echo "      ./apply_bugfix_all.x path_to_bugfix.all_patch_file"
  exit 1
fi

echo "Applying all bugfixes in $1"

if [ "$AMBERHOME" == "" ]; then
  echo "AMBERHOME environment variable not set."
  echo "Cannot continue."
  exit 1
fi

echo "Patching AMBER installation in $AMBERHOME"

echo "Directory exists warnings can be safely ignored."

#Specifics for bugfix.26
         cd $AMBERHOME
         mkdir test/chamber
         mkdir test/chamber/md_engine/
         cd test/chamber/md_engine/
         mkdir dhfr
         touch dhfr/inpcrd
         touch dhfr/mdout.dhfrc_charmm.min.save
         touch dhfr/mdout.dhfrc_charmm.save
         touch dhfr/prmtop
         touch dhfr/Run.dhfr_charmm.md
         touch dhfr/Run.dhfr_charmm.min

         mkdir dhfr_cmap
         touch dhfr_cmap/inpcrd
         touch dhfr_cmap/mdout.dhfr_charmm.min.save
         touch dhfr_cmap/mdout.dhfr_charmm.save
         touch dhfr_cmap/prmtop
         touch dhfr_cmap/Run.dhfr_charmm.md
         touch dhfr_cmap/Run.dhfr_charmm.min

         mkdir dhfr_cmap_pbc
         touch dhfr_cmap_pbc/inpcrd
         touch dhfr_cmap_pbc/mdout.dhfr_charmm.md.save
         touch dhfr_cmap_pbc/mdout.dhfr_charmm.min.save
         touch dhfr_cmap_pbc/mdout.dhfr_charmm_noshake.md.save
         touch dhfr_cmap_pbc/mdout.dhfr_charmm_noshake.min.save
         touch dhfr_cmap_pbc/prmtop 
         touch dhfr_cmap_pbc/Run.dhfr_cmap_pbc_charmm.md
         touch dhfr_cmap_pbc/Run.dhfr_cmap_pbc_charmm.min
         touch dhfr_cmap_pbc/Run.dhfr_cmap_pbc_charmm_noshake.md
         touch dhfr_cmap_pbc/Run.dhfr_cmap_pbc_charmm_noshake.min

         chmod 755 dhfr/Run.dhfr_charmm.md
         chmod 755 dhfr/Run.dhfr_charmm.min
         chmod 755 dhfr_cmap/Run.dhfr_charmm.md
         chmod 755 dhfr_cmap/Run.dhfr_charmm.min
         chmod 755 dhfr_cmap_pbc/Run.dhfr_cmap_pbc_charmm.md
         chmod 755 dhfr_cmap_pbc/Run.dhfr_cmap_pbc_charmm.min
         chmod 755 dhfr_cmap_pbc/Run.dhfr_cmap_pbc_charmm_noshake.md
         chmod 755 dhfr_cmap_pbc/Run.dhfr_cmap_pbc_charmm_noshake.min

         cd $AMBERHOME/src/pmemd/src/
         touch angles_ub.fpp
         touch charmm.fpp
         touch charmm_gold.fpp
         touch cmap.fpp
         touch dihedrals_imp.fpp
         touch mdin_debugf_dat.fpp

#Apply patch
         cd $AMBERHOME
         patch -p0 -N <$1

echo "Done"