#!/bin/sh
#set -xv

command="$0 $*"

# configure script for amber: creates config_amber.h

#------------------------------------------------------------------------------
#  set up usage statement:
#------------------------------------------------------------------------------
usage(){
cat<<EOD

Usage: ./configure [flags] [compiler/architecture]

    where <compiler/architecture> is one of:

    compaqf90, hpf90, ifort, pgf90, sgi_altix, sgi_mips, 
    sparc, xlf90_aix, xlf90_suse, xlf90_macosx, xlf90_bluegene, 
    ifort_macosx, g95, gfortran, pathscale

    Parallel option flags:
      -mpi        Use native MPI (assumes that the proper path will be searched)
      -mpi2       Like -mpi, but assumes mpi2 compatibility
      -nopar      Explicit request of no MPI, the default
      -lamsource  Use LAM/MPI   (compile from source code)
      -lam        Use (existing) LAM/MPI   (MPI_HOME must be set)
      -mpich      Use MPICH     (MPI_HOME must be set)
      -mpich2     Use MPICH2    (MPI_HOME must be set)
      -openmpi    Use OpenMPI   (MPI_HOME must be set)
      -intelmpi   Use Intel MPI (MPI_HOME must be set, 
                                 e.g. to /opt/intel/mpi/2.0)
      -scali      Use scali MPI (MPI_HOME must be set, e.g. to /opt/scali)

    Platform option flags:
      -gnucompat  Add a second underscore to some symbols to maintain
                    GNU link compatibility (g95, gfortran, pgf90).
      -p4         Optimize for Pentium 4 processor (pgf90,g95,
                    gfortran, pathscale).  Adds SSE1, SSE2 vectorisation 
                    where available.
      -cygwin     Add CygWin flags for Windows (g95, gfortran).

    General flags:
      -mmtsb       Request building sander for MMTSB.
      -static      Static linking, i.e., prevent linking with shared libraries.
      -verbose     Add verbose compiler comment and warning flags.
      -nobintraj   Do not include support for binary (netCDF) trajectory files
      -nolfs       Remove compile flags for Large File Support
      -nosanderidc Do not include support for IDC>0 in Sander.

    Environment variables:
      MKL_HOME     Root directory of the Intel Math Kernel Library
                     for example, /opt/intel/mkl/8.0.
                     The MKL helps some with performance, but it is generally
                     not a big deal if you leave this variable empty.
      GOTO         Location for the "Goto" optimized blas library; this is
                     used if MKL_HOME is *not* defined.

===============================================================================
EOD

exit 1;
}

#------------------------------------------------------------------------------
#  Process commandline configuration options:
#------------------------------------------------------------------------------
arch='unknown'
cygwin='no'
# This controls GNU's second underscore fortran external symbol convention.
# Our default is no second underscore.
# This is a good default because by default ifort and pgf90 (which can
# link to gnu object files) do not add a second underscore.
gnucompat='no'
mmtsb='no'
parallel='none'
p4='no'
bintraj='yes'
sfx=''
sgimips='unknown'
static='no'
verbose='no'
verbosity=''
lm='-lm'
lfs='yes'
libdivcon='../dcqtp/src/qmmm/libdivcon.a'
incdivcon='divcon'
testsanderDIVCON='test.sander.DIVCON'
nosanderidc='false'
openmp='no'
openmp_flag=''

while [ $# -gt 0 ]; do
    case "$1" in
    -lam)     parallel="lam" ;;
    -lamsource)  parallel="lamsource" ;;
    -mpi)     parallel="mpi" ;;
    -mpi2)    parallel="mpi2" ;;
    -mpich)   parallel="mpich" ;;
    -mpich2)  parallel="mpich2" ;;
    -intelmpi)  parallel="intelmpi" ;;
    -openmpi) parallel="openmpi" ;;
    -scali)   parallel="scali" ;;
    -nopar)   parallel="none" ;;

    -gnucompat)  gnucompat="yes" ;;
    -p4)      p4="yes" ;;
    -cygwin)  cygwin="yes" ; lfs="no"; sfx=".exe" ;;

    -mmtsb)   mmtsb="yes" ;;
    -static)  static="yes" ;;
    -verbose) verbose="yes" ;;
    -nobintraj) bintraj="no" ;;
    -nolfs)   lfs="no";;
    -nosanderidc)   nosanderidc="true";;

#OpenMP is currently experimental - it is not currently documented as an
#available option. It has only been tested with ifort and gfortran. This is currently
#only used for parts of the QMMM code and is expected to also be used
#with an MPI run. - This will turn on -DQMMM_OMP
    -openmp)   openmp="yes";;

    -help) usage ;;
    --help)  usage ;;
    -h)  usage ;;

    -*) echo ""; echo "unknown flag $1";  usage ;;

    *) if [ $# -gt 1 ]; then
         usage
       fi
       arch=$1 ;;

    esac
    shift
done

#------------------------------------------------------------------------------
#  Set up defaults that work for most machines:
#------------------------------------------------------------------------------

workdir=`pwd`
AMBERHOME=`dirname $workdir`
echo "Setting AMBERHOME to $AMBERHOME"
echo " "

#-------------------
#  Platform specific: 
#-------------------
x86_64='no'

machine=`uname -m`
if [ "$machine" = "em64t" ] || [ "$machine" = "x86_64" ]; then
       x86_64='yes';
       if [ $arch = "ifort" ]; then
          arch="ifort_x86_64"
       fi

elif [ "$machine" = "i686" ] && [ $arch = "ifort" ]; then
    arch="ifort_ia32"

elif [ "$machine" = "ia64" ] && [ $arch = "ifort" ]; then
    arch="ifort_ia64"
fi

if [ "$arch" = "xlf90_aix" ]; then
#dcqtp (idc) compilation is broken on xlf90_aix.
    nosanderidc="true"
fi

#-------------------
#  Program specific: 
#-------------------
localflags=

#-------------------
# preprocessor:
#-------------------
fpp="cpp -traditional"
fppflags="-P"
if [ $mmtsb = "yes" ]; then
    fppflags="$fppflags -DMMTSB"
fi

#-----------------------------------
# Remove Divcon support from sander?
#-----------------------------------
if [ $nosanderidc = "true" ]; then
    fppflags="$fppflags -DNO_SANDER_DIVCON"
    libdivcon=" "
    incdivcon=" "
    testsanderDIVCON="skipsanderDIVCON"
fi
moduledir="-I"

#-------------------
#  C compilation:
#-------------------
cpp=cpp
cc=cc
cplusplus=CC
cppflags=
if [ $mmtsb = "yes" ]; then
    cppflags="$cppflags -DMMTSB"
fi
cflags=
if [ $lfs = "yes" ]; then
    cflags="$cflags -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE"
fi

#-------------------
#  Fortran compilation:
#-------------------
fc=f90
fflags="-O0 -132"
foptflags=-O2
freeformat_flag=

#-------------------
#  Loading:
#-------------------
loadcc="$cc"
loadlib=
if [ $static = "yes" ]; then
    static_flag='-static'
else
    static_flag=
fi

#-------------------
#  Libraries:
#-------------------
m4='m4'
use_blas=SOURCE_COMPILED
use_lapack=SOURCE_COMPILED

xhome='/usr/X11R6'
xlibs="-L$xhome/lib"
if [ "$x86_64" = "yes" ]; then
    xlibs="-L$xhome/lib64 $xlibs"
fi

#-------------------
#  Auxiliary programs:
#-------------------
ar='ar rv'
ranlib=ranlib

#  NetCDF variables:
netcdf=netcdf.mod
netcdflib="../netcdf/lib/libnetcdf.a"

par_error () {
cat <<EOD
**********************************************************
  ERROR:  MPI_HOME is not set

  set the MPI_HOME environment variable to the
  location of the include/ and lib/ subdirectories
  containing $FILES for your $PAR distribution.

  For example, with csh/tcsh:
      setenv MPI_HOME $EXAMPLE
  or with sh/bash:
      export MPI_HOME=$EXAMPLE

**********************************************************
EOD
exit 1
}

echo "Setting up Amber configuration file for architecture: $arch"
echo "Using parallel communications library: $parallel"

#------------------------------------------------------------------------------
#  Case statement identifying the architecture/compilers:
#------------------------------------------------------------------------------

case "$arch" in

############ IA64 Intel compilers ################
ifort_ia64|sgi_altix)
    fppflags="$fppflags "
    freeformat_flag='-FR'
    fflags=" -w95 -ftz "
    static_flag='-i-static'
    verbosity=''
    if [ $verbose = "yes" ]; then
        verbosity='-vec_report3 -opt_report -opt_report_level max -opt_report_phase all -V -v'
    fi
    fflags="$fflags $verbosity"

    #   First check for the SGI scs library; if that is not present,
    #   check for installation of the Intel Math Kernel library:

    usrlib=/usr/lib
    if [ -e $usrlib/libscs.so ]; then

        # Assume that .a's also exist if static has been requested.
        use_lapack=VENDOR_SUPPLIED
        use_blas=VENDOR_SUPPLIED
        loadlib="$loadlib -lscs"
        echo "Using LAPACK and BLAS from SCSL."

    else
        mkll='no'
        if [ -z "$MKL_HOME" ]; then
            echo "The MKL_HOME environment variable is not defined."
        else
            echo "MKL_HOME is set to $MKL_HOME"
            if [ -d $MKL_HOME/lib/64 ]; then
                mkll=$MKL_HOME/lib/64
                echo "Using MKL libraries from $mkll"
            else
                echo "MKL libraries were not found !"
            fi
        fi
        if [ $mkll != 'no' ]; then
            use_lapack=VENDOR_SUPPLIED
            use_blas=VENDOR_SUPPLIED
            # MKL Technical Notes: Itanium static linking of LAPACK and kernels
            loadlib="$loadlib $mkll/libmkl_lapack.a $mkll/libmkl_ipf.a -L$mkll -lguide -lpthread -ldl"
            fppflags="$fppflags -DMKL"
        fi
    fi

    fc=ifort
    foptflags="$fflags -O3 -IPF_fma -IPF_fp_relaxed -ip"
    cc=icc
    cplusplus=icpc

    fflags="$fflags -O2"
    cflags="$cflags -O2"
    loadcc="$cc $static_flag"

#openMP support for QMMM Density build.
    if [ $openmp = "yes" ]; then
        foptflags="$foptflags -openmp"
        fflags="$fflags -openmp"
        fppflags="$fppflags -DQMMM_OMP"
        openmp_flag="-openmp"
    fi

    ;;

############ IA32 Intel compilers;  ################
ifort_ia32)
    cc="gcc -m32"
    cplusplus=g++
    cflags="$cflags -O2"
    loadcc="$cc $static_flag"
    fppflags="$fppflags"
    freeformat_flag='-FR'
    fflags=" -w95 "
    verbosity='-vec_report0'
    if [ $verbose = "yes" ]; then
        verbosity='-sox -vec_report3 -opt_report -opt_report_level max -opt_report_phase all -V -v -Wl,-verbose,-M'
    fi
    fflags="$fflags $verbosity"

    foptflags="$fflags -mp1 -ip -O3 -axNP"
    fflags="$fflags -mp1 -O0"
    loadlib="$loadlib -lsvml"

    fc=ifort

    #   check for installation of the Intel Math Kernel library:

    mkll='no'
    goto='no'
    if [ -z "$MKL_HOME" ]; then
        echo "The MKL_HOME environment variable is not defined."
        echo "    The MKL is recommended for optimal performance."
        if [ -z "$GOTO" ]; then
            goto='no'
        else
            goto='yes'
            echo "Using Goto BLAS routines from $GOTO"
        fi
    else
        echo "MKL_HOME is set to $MKL_HOME"
        if [ -d $MKL_HOME/lib/32 ]; then
            mkll=$MKL_HOME/lib/32
            echo "Using MKL libraries from $mkll"
        else
            echo "MKL libraries were not found !"
        fi
    fi
    if [ $mkll != 'no' ]; then
        use_lapack=VENDOR_SUPPLIED
        use_blas=VENDOR_SUPPLIED
        if [ $static = "yes" ]; then
            # Intel® Math Kernel Library 6.1 for Linux Technical User Notes
            #  IA-32 static linking of LAPACK and kernels
            loadlib="$loadlib $mkll/libmkl_lapack.a $mkll/libmkl_ia32.a -L$mkll -lguide -lpthread"
        else
            # Intel® Math Kernel Library 6.1 for Linux Technical User Notes
            #  IA-32 dynamic linking of double-precision-LAPACK and kernels
            loadlib="$loadlib -L$mkll -lvml -lmkl_lapack -lmkl -lguide -lpthread"
        fi
        fppflags="$fppflags -DMKL"
    fi

    if [ $goto = "yes" ]; then
        use_lapack=SOURCE_COMPILED
        use_blas=VENDOR_SUPPLIED
        loadlib="$loadlib \$(GOTO) -lpthread"
    fi

#openMP support for QMMM Density build.
    if [ $openmp = "yes" ]; then
        foptflags="$foptflags -openmp"
        fflags="$fflags -openmp"
        fppflags="$fppflags -DQMMM_OMP"
        openmp_flag="-openmp"
    fi

    ;;

############ EM64T Intel compilers;  ################
ifort_x86_64)
    cc=gcc
    cplusplus=g++
    cflags="$cflags -m64 -O2"
    loadcc="$cc $static_flag"
    fppflags="$fppflags"
    freeformat_flag='-FR'
    fflags=" -w95 "
    verbosity='-vec_report0'
    if [ $verbose = "yes" ]; then
        verbosity='-sox -vec_report3 -opt_report -opt_report_level max -opt_report_phase all -V -v -Wl,-verbose,-M'
    fi

    fflags="$fflags $verbosity"
    foptflags="$fflags -mp1 -ip -O3 -axWP"
    fflags="$fflags -mp1 -O0"

    fc=ifort

    #   check for installation of the Intel Math Kernel library:

    mkll='no'
    if [ -z "$MKL_HOME" ]; then
        echo "The MKL_HOME environment variable is not defined."
        echo "    The MKL is recommended for optimal performance."
    else
        echo "MKL_HOME is set to $MKL_HOME"
        if [ -d $MKL_HOME/lib/em64t ]; then
            mkll=$MKL_HOME/lib/em64t
            echo "Using MKL libraries from $mkll"
        else
            echo "MKL libraries were not found !"
        fi
    fi
    if [ $mkll != 'no' ]; then
        use_lapack=VENDOR_SUPPLIED
        use_blas=VENDOR_SUPPLIED
        if [ $static = "yes" ]; then
            #  EM64T static linking of LAPACK and kernels
            loadlib="$loadlib $mkll/libmkl_lapack.a $mkll/libmkl_em64t.a -L$mkll -lguide -lpthread"
        else
            #  EM64T dynamic linking of double-precision-LAPACK and kernels
            loadlib="$loadlib -L$mkll -lvml -lmkl_lapack -lmkl -lguide -lpthread"
        fi
        fppflags="$fppflags -DMKL"
    fi

    fc=ifort

#openMP support for QMMM Density build.
    if [ $openmp = "yes" ]; then
        foptflags="$foptflags -openmp"
        fflags="$fflags -openmp"
        fppflags="$fppflags -DQMMM_OMP"
        openmp_flag="-openmp"
    fi

    ;;

#################### PathScale Compiler #####################
pathscale)
    if [ "$static" = "yes" ]; then
       static_flag='-static'
    fi

    if [ "$verbose" = "yes" ]; then
       verbosity='-Wall'
    fi

    if [ "$ACML_DIR" != "" ]; then
       if [ ! -d "$ACML_DIR" ]; then
          echo "ERROR: invalid \$ACML_DIR directory" 2>&1
          exit 1
       fi
       use_lapack=VENDER_SUPPLIED
       use_blas=VENDER_SUPPLIED
       loadlib="$loadlib -L$ACML_DIR -lacml"

       echo "Using optimized AMD Core Math Library (ACML)"
    fi

    fc="pathf90"
    fpp="$fc -cpp -E"
    if [ "$set_foptflags" != "" ]; then
       foptflags="$set_foptflags"
       fflags="$set_foptflags"
    elif [ "$p4" = "yes" ]; then
       foptflags="-O3 -m32 -msse2"
       fflags="-O0 -m32 -msse2"
    else
       foptflags="-O3"
       fflags="-O0"
    fi

    intr_flags="-intrinsic=PGI -intrinsic=fdate"
    fflags="$fflags $intr_flags $verbosity -fno-unsafe-math-optimizations"
    foptflags="$foptflags $intr_flags $verbosity -fno-unsafe-math-optimizations"
    freeformat_flag='-freeform'

    cc="pathcc"
    cplusplus="pathCC"
    cpp="$pathcc -E"
    if [ "$set_cflags" != "" ]; then
       cflags="$cflags $set_cflags"
    elif [ "$p4" = "yes" ]; then
       cflags="$cflags -O3 -m32 -msse2"
    else
       cflags="$cflags -O1"
    fi

    cflags="$cflags $verbosity"
    loadcc="$cc $static_flag"

    ;;


#################### g95 or gfortran compiler (Linux/cygwin/Macintosh only) #######
g95|gfortran)
    cc=gcc
    cplusplus=g++
    cflags="$cflags -O2"
    if [ $arch = "g95" ]; then
        fc=g95
        fppflags="$fppflags -xassembler-with-cpp"
        fflags="-O0 "
        foptflags="-O3 "
    else
        fc=gfortran
        fppflags="$fppflags -xassembler-with-cpp -Dsecond=ambsecond"
        fflags="-O0 -fno-range-check"
        foptflags="-O3 -fno-range-check"
    fi

    if [ $gnucompat = "yes" ]; then
        gnucompatibility="-fsecond-underscore"
    else
        gnucompatibility="-fno-second-underscore"
    fi
    fflags="$fflags $gnucompatibility"
    foptflags="$foptflags $gnucompatibility"

    if [ $p4 = "yes" ]; then
       fflags="$fflags -march=pentium4 -mfpmath=sse -msse -msse2 -malign-double"
       foptflags="$foptflags -march=pentium4 -mfpmath=sse -msse -msse2 -malign-double"
    fi
    if [ $x86_64 = "yes" ]; then
       cflags="$cflags -m64"
    elif [ "$machine" = "ia64" ]; then
       cflags="$cflags"
    elif [ "$machine" = "Power Macintosh" ]; then
       cflags="$cflags"
    else
       cflags="$cflags -m32"
    fi
    freeformat_flag=-ffree-form
    loadcc="$cc $static_flag"

    #   check for installation of the Intel Math Kernel library:

    mkll='no'
    if [ -z "$MKL_HOME" -a "$OSTYPE" = "darwin" -a "$VENDOR" = "apple" ]; then
        echo "Using Apple Accelerate Framework for g95."
        use_lapack=VENDOR_SUPPLIED
        use_blas=VENDOR_SUPPLIED
        loadlib="$loadlib -framework Accelerate"
    elif [ -z "$MKL_HOME" ]; then
        echo "The MKL_HOME environment variable is not defined."
    elif [ $x86_64 = "yes" ]; then
        echo "MKL_HOME is set to $MKL_HOME"
        if [ -d $MKL_HOME/lib/em64t ]; then
            mkll=$MKL_HOME/lib/em64t
            echo "Using MKL libraries from $mkll"
        else
            echo "MKL libraries were not found !"
        fi
    else
        echo "MKL_HOME is set to $MKL_HOME"
        if [ -d $MKL_HOME/lib/32 ]; then
            mkll=$MKL_HOME/lib/32
            echo "Using MKL libraries from $mkll"
        else
            echo "MKL libraries were not found !"
        fi
    fi
    if [ $mkll != 'no' ]; then
        use_lapack=VENDOR_SUPPLIED
        use_blas=VENDOR_SUPPLIED
        if [ $static = "yes" ]; then
            if [ $x86_64 = "yes" ]; then
                loadlib="$loadlib $mkll/libmkl_lapack.a $mkll/libmkl_em64t.a -L$mkll -lguide -lpthread"
            else
                loadlib="$loadlib $mkll/libmkl_lapack.a $mkll/libmkl_ia32.a -L$mkll -lguide -lpthread"
            fi
        else
                loadlib="$loadlib -L$mkll -lvml -lmkl_lapack -lmkl -lguide -lpthread"
        fi
        fppflags="$fppflags -DMKL"
    fi

#openMP support for QMMM Density build. - only gfortran supports it at present - no g95.
    if [ $openmp = "yes" ]; then
        if [ $arch = "gfortran" ]; then
          foptflags="$foptflags -openmp"
          fflags="$fflags -openmp"
          fppflags="$fppflags -DQMMM_OMP"
          openmp_flag="-fopenmp"
        else
          echo "WARNING: Openmp is not supported with g95 - the -openmp option will be ignored."
        fi
    fi
    ;;

#################### Portland Compiler #####################
pgf90)

    cc=gcc
    cplusplus=g++
    cflags="$cflags -O2"
    loadcc="$cc $static_flag"

    fc=pgf90
    fflags="-O1"
    foptflags="-fast -O3"
    if [ $p4 = "yes" ]; then
       fflags="-tp p7 $fflags"
       foptflags="-tp p7 -fastsse $foptflags"
    fi

    moduledir='-module $(EMPTY)'
    if [ $static = "yes" ]; then
        static_flag='-Bstatic'
    fi

    if [ -e /usr/pgi/linux86/lib/liblapack.a ]; then
        use_lapack=VENDOR_SUPPLIED
        use_blas=VENDOR_SUPPLIED
        loadlib="$loadlib -llapack -lblas"
        echo "Using Portland Group LAPACK and BLAS."
    fi

    if [ $gnucompat = "yes" ]; then
        gnucompatibility='-Msecond_underscore'
        # cflags="$cflags $gnucompatibility"
        fflags="$fflags $gnucompatibility"
        foptflags="$foptflags $gnucompatibility"
    fi

    if [ $verbose = "yes" ]; then
        verbosity='-v -V -Minfo=all -Minform=inform -Mneginfo'
    fi
    fflags="$fflags $verbosity"
    foptflags="$foptflags $verbosity"

    freeformat_flag='-Mfree'
    ;;

#################### Absoft Windows #####################
absoft)
#                   (absoft-Linux, tested on with Absoft V10.0)
    cc=gcc
    cplusplus='g++'
    cflags="$cflags -DCLINK_CAPS"
    fc=f95
    loadcc=$cc
    loadlib="$loadlib -lU77 "
    fflags=" -O1 -safefp"
    foptflags=" -O1 -safefp"
    if [ $verbose = "yes" ]; then
        echo "verbose option is not implemented yet."
    fi
    fflags="$fflags $verbosity"
    foptflags="$foptflags $verbosity"
    freeformat_flag='-f free'
    if [ $x86_64 = "yes" ]; then
       cflags="$cflags -m64"
    else
       cflags="$cflags -m32"
    fi
#   use_lapack=VENDOR_SUPPLIED
#   use_blas=VENDOR_SUPPLIED

    moduledir="-p "
    ;;

##################### SGI IRIX 32-bit ###############
sgi_mips|IRIX64)

    sgi_abi='-n32'
    fpp='/lib/cpp'
    fppflags="$fppflags -DSGI -DnoVDINVSQRT"
    if [ -e /usr/lib32/mips4/libscs.so ]; then
        use_lapack=VENDOR_SUPPLIED
        use_blas=VENDOR_SUPPLIED
        loadlib="$loadlib -lscs"
    fi

    sgi_cpuarch=` hinv -t cpu | awk ' { print $3 }  ' | head -1 `
    sgi_Rdigit=` echo $sgi_cpuarch | sed s/R// `
    if [ $sgi_Rdigit -lt 4000 ]; then
        # R3k machines, those less than R4000 are not supported.
        echo "The $sgi_cpuarch Processor is no longer supported."
        exit 1
    elif [ $sgi_Rdigit -lt 5000 ]; then
        # R4k machines: only ones with -mips3
        sgi_mips='-mips3'
    else
        # All others are now -mips4
        sgi_mips="-mips4 -r$sgi_Rdigit"
    fi
    if [ $sgi_cpuarch = R5000 ]; then
        # R5k machines
        sgi_options='-OPT:roundoff=3:IEEE_arithmetic=3 -TENV:X=1 -SWP:strict_ivdep=OFF:if_conversion=OFF -WK,-dr=ACK,-o=1,-so=1,-r=3'
        # -WK options should be removed in a year; SRB Apr 2003.
        loadlib="$loadlib -lm"
    elif [ $sgi_cpuarch = R8000 ]; then
        # R8k machines
        sgi_options='-OPT:cis=off:roundoff=3:IEEE_arithmetic=3 -TENV:X=3 -SWP:strict_ivdep=OFF -WK,-dr=AKC'
        # -WK options should be removed in a year; SRB Apr 2003.
        loadlib="$loadlib -lfastm"
    else
        # The following line causes problems with at least the 7.3 MIPSpro
        # compiler suite.  If you turn it back on, please test carefully,
        # especially for QM/MM:
        # sgi_options='-OPT:roundoff=3:IEEE_arithmetic=3 -TENV:X=1'
        sgi_options=""
        loadlib="$loadlib -lfastm"
    fi

    cflags="$cflags $sgi_abi $sgi_mips $sgi_options -O2 -DSYSV"
    cppflags="-LANG:std $cflags"
    fflags="$sgi_abi $sgi_mips $sgi_options -O0"
    foptflags="$sgi_abi $sgi_mips $sgi_options -O3"
    if [ $verbose = "yes" ]; then
        # include -S to get a software pipelining report,
        # delete the .s files later else the build will not be up to date.
        verbosity="-LIST:notes=ON:software_names=ON -LIST:all_options=ON:cite=ON:symbols=ON"
    fi
    cflags="$cflags "
    fflags="$fflags $verbosity"
    foptflags="$foptflags $verbosity"
    load="$fc $sgi_abi $sgi_mips"    #Note: not used!
    loadcc="$cc $sgi_abi $sgi_mips"
    if [ $static = "yes" ]; then
        echo "Warning: static linking is not supported; option ignored."
    fi
    freeformat_flag='-freeform'
    ar='ar rvs $(EMPTY)'
    ranlib=/bin/true
    m4='m4 -B50000'

    xhome='/usr/lib32'
    xlibs="-L$xhome"
    ;;

####################### HP ############################
hpf90|HP-UX)
    fpp='/lib/cpp'
    if [ $parallel = "mpi" ]; then
        fppflags="$fppflags -I/opt/mpi/include"
        fc='mpif90'
    else
        fc=f90
    fi
    cplusplus=aCC
    use_lapack=VENDOR_SUPPLIED
    use_blas=VENDOR_SUPPLIED
    loadlib="$loadlib -lveclib -llapack -lm "
    if [ $static = "yes" ]; then
        # +noshared is preferred over -N which is ignored by ld.
        # But it is not clear that +noshared is working; so use archive_shared.
        static_flag='+noshared -Wl,-aarchive_shared'
    fi
    loadcc="$cc $static_flag"

    fppflags="$fppflags -DHP "
    cppflags="-DCLINK_PLAIN"
    cflags="$cflags -Ae -DSYSV"
    # no postpending underscores (ppu) to link Fortran and C.
    # U77 library contains: etime, getarg, iargc.
    fflags='+noppu +U77 +Ofast'
    # +Ofaster is ~10% faster (JAC) but build is very slow
    # and in Sep 2003 for unknown reasons suddenly produces link errors
    foptflags='+noppu +U77 +Ofast'
    if [ $verbose = "yes" ]; then
        verbosity='-v +Oinfo -Wl,-v,-m'
    fi
    cflags="$cflags "
    fflags="$fflags $verbosity"
    foptflags="$foptflags $verbosity"
    freeformat_flag='+source=free'
    ar='ar rvs $(EMPTY)'
    ranlib=/bin/true
    m4='m4 -B50000'
    ;;

####################### IBM AIX ############################
xlf90_aix|AIX)

    libpath=/usr/lib
    if [ -e $libpath/libmassv.a ]; then
        loadlib="$loadlib -L$libpath -lmassv -lmass"
        fppflags="$fppflags -DMASSLIB"
    fi
    if [ -e $libpath/libblas.a ]; then
        loadlib="$loadlib -L$libpath -lblas"
        use_blas=VENDOR_SUPPLIED
    fi
    fppflags="$fppflags -DNMLEQ -DCLINK_PLAIN -DXLF90"
    fpp='/lib/cpp'

    # if you are in AIX 5.2 add -I/usr/lpp/ppe.poe/include/thread64:
    # fpp="$fpp -I/usr/lpp/ppe.poe/include/thread64"

    if [ $parallel = "mpi" ]; then
        if [ -e /usr/lpp/ppe.poe/include/mpif.h ]; then
            AIXMPIFDIR=/usr/lpp/ppe.poe/include/mpif.h
        else
            echo " ***** CANNOT FIND mpif.h ******** "
            echo using: \"mpxlf90 -v -c bogus.f\" to find mpif.h directory
        cat > tmp.awk << EEEOF
                {CT=1; 
                 while( CT <= NF){
                     if(substr( \$CT,1,2)=="-I"){print \$CT; exit;}
                     CT++;
                 }}
EEEOF
        AIXMPIFINC=`mpxlf90 -v -c bogus.f 2>1 | head -1 | awk -f tmp.awk`
        AIXMPIFDIR=`echo $AIXMPIFINC | sed s/-I//`
            /bin/rm tmp.awk
        if [ -e $AIXMPIFDIR/mpif.h  ]; then        
               echo "Found in $AIXMPIFDIR"
        else
           echo "**** FAILED to find mpif.h, ask sys admin person"
               exit 1
            fi
        fi
        fppflags="$fppflags -DPOE"
        fpp="$fpp $AIXMPIFINC"
echo $fpp
        fc='mpxlf90_r -bmaxdata:0x80000000'
        #  (for 64-bit environments, rmove the -bmaxdata flag above)
    else
        fc=xlf90
    fi
    cc="xlc -qlanglvl=stdc99"
    cppflags="-DCLINK_PLAIN"
    cflags="$cflags -O2"
    cplusplus=xlC
    if [ $static = "yes" ]; then
        static_flag='-bstatic'
    fi
    loadcc="$cc $static_flag"
    fflags="-qfixed"
    foptflags="-qfixed -O3 -qmaxmem=-1 -qarch=auto -qtune=auto"
    if [ $verbose = "yes" ]; then
        verbosity='-qsource -qreport=hotlist'
    fi
    fflags="$fflags $verbosity"
    foptflags="$foptflags $verbosity"
    freeformat_flag='-qfree=f90'
    ar='ar rvs $(EMPTY)'
    ranlib=/bin/true
    m4='m4 -B50000'
    ;;

####################### IBM XLF90 AIX ############################
xlf90_bluegene)

    #libpath=/bgl/BlueLight/ppcfloor/bglsys/lib 
    libpath=/usr/local/apps/lib
    #if [ -e $libpath/libmassv.a ]; then
    #    loadlib="$loadlib -L$libpath -lmassv -lmass"
    #    fppflags="$fppflags -DMASSLIB"
    #fi
    #if [ -e $libpath/libblas.a ]; then
    #    loadlib="$loadlib -L$libpath -lblas"
    #    use_blas=VENDOR_SUPPLIED
    #fi
    fppflags="$fppflags -DNMLEQ -DCLINK_PLAIN -DXLF90 -I/bgl/BlueLight/ppcfloor/bglsys/include/"
    fpp='/opt/ibmcmp/xlf/9.1/exe/cpp'
    
    if [ $parallel = "mpi" ]; then
        fppflags="$fppflags -DPOE"
        fpp="$fpp $AIXMPIFINC"
        fc='mpxlf90 -qarch=440 -qtune=440'
        echo " ***** Blue Gene support is currently experimental. It may be necessary *****"
        echo " ***** to manually edit the config_amber.h file to insert the correct paths.  *****"
    else
        echo " ***** ERROR - ONLY PARALLEL MPI COMPILATION SUPPORTED ON BLUE GENE ***** "
        exit 1
    fi
    cc="mpcc -qlanglvl=stdc99 -qarch=440 -qtune=440"
    cppflags="-DCLINK_PLAIN"
    cflags="$cflags -O2"
    cplusplus="mpCC -qarch=440 -qtune=440"
    loadcc="$cc"
    fflags="-qfixed"
    foptflags="-qfixed -O3 -qmaxmem=-1 -qarch=auto -qtune=auto"
    freeformat_flag='-qfree=f90'
    ar='ar rvs $(EMPTY)'
    ranlib=/bin/true
    m4='m4 -B50000'
    ;;

####################### PowerPC SUSE Linux ############################
xlf90_suse)

    libpath=/usr/lib
    if [ -e $libpath/libmass.a ]; then
        loadlib="$loadlib -L$libpath "
    fi
    if [ -e $libpath/libblas.a ]; then
        loadlib="$loadlib -L$libpath -lblas"
        use_blas=VENDOR_SUPPLIED
    fi
    if [ -e $libpath/libessl.a ]; then
        loadlib="$loadlib -L$libpath -lessl"
        use_lapack=VENDOR_SUPPLIED
    fi

    fc=xlf90
    fppflags="$fppflags -DCLINK_PLAIN -DXLF90"
    fpp='/opt/ibmcmp/xlf/8.1/exe/cpp '
    cc=cc
    cppflags="-DCLINK_PLAIN"
    cflags="$cflags -O2"
    cplusplus=xlC
    if [ $static = "yes" ]; then
        static_flag='-bstatic'
    fi
    loadcc="$cc $static_flag"
    fflags="-qfixed"
    foptflags="-qfixed -O3 -qmaxmem=-1 -qarch=auto -qtune=auto"
    if [ $verbose = "yes" ]; then
        verbosity='-qsource -qreport=hotlist'
    fi
    fflags="$fflags $verbosity"
    foptflags="$foptflags $verbosity"
    freeformat_flag='-qfree=f90'
    ar='ar rvs $(EMPTY)'
    ranlib=/bin/true
    ;;

####################### Compaq DEC Alpha OSF1 ##########################
compaqf90|OSF1)

    use_lapack=VENDOR_SUPPLIED
    use_blas=VENDOR_SUPPLIED

    # -C prevents striping of C-style AND C++-style comments;
    # some format statements contain //
    fppflags="-C $fppflags"
    fpp='/lib/cpp -traditional'

    fflags="-tune host -arch host"
    foptflags="-fast -O3 -tune host -arch host"
    cplusplus=cxx
    cflags="$cflags -O -std1"
    if [ $verbose = "yes" ]; then
        verbosity='-source_listing -annotations all -Wl,-v,-m,-M'
    fi
    fflags="$fflags $verbosity"
    foptflags="$foptflags $verbosity"

    if [ $static = "yes" ]; then
        static_flag='-non_shared'
    fi
    loadcc="$cc $static_flag"
    loadlib="$loadlib -ldxml -lm"
    freeformat_flag='-free'
    ranlib=/bin/true
    m4='m4 -B50000'
    ;;

####################### Sun ############################
sparc|SunOS)

    xhome='/usr/openwin'
    fpp='/lib/cpp'
    fppflags="$fppflags"
    if [ -f /opt/SUNWspro/lib/libsunperf.so ]; then
        use_lapack=VENDOR_SUPPLIED
        use_blas=VENDOR_SUPPLIED
        loadlib="$loadlib -xlic_lib=sunperf"
        # Note that the Sun Performance Library has FFT routines.
        # Sun Performance Library User's Guide,
        # http://docs.sun.com/source/806-3566/index.html
    fi
    loadlib="$loadlib -lm"

    fflags='-O1'
    foptflags='-O2'
    if [ $verbose = "yes" ]; then
        echo "verbose option is not implemented yet."
    fi
    fflags="$fflags $verbosity"
    foptflags="$foptflags $verbosity"
    if [ $static = "yes" ]; then
        static_flag='-Bstatic'
    fi
    loadcc="$cc $static_flag"
    cflags="$cflags -DSYSV "
    freeformat_flag='-free'
    m4='m4 -B50000'
    moduledir="-M"
    ;;

####################### Mac OS X ############################
xlf90_macosx)

    xhome='/usr/X11R6'
    libpath=/System/Library/Frameworks/Accelerate.framework
    if [ -e $libpath/Accelerate ]; then
        loadlib="$loadlib -Wl,-framework -Wl,Accelerate"
        use_blas=VENDOR_SUPPLIED
        use_lapack=VENDOR_SUPPLIED
        fflags="-qextname=ddot:fdate:flush:lsame:dscal:dnrm2:idamax:drot:dswap:dspmv:daxpy:dspr2:dgemm:dcopy:dgemv:dtrmv:dtrmm:dger:lsame:dspev:dgeev:dspevd:dsyev:dppsv:dspsv:dlamch:dsteqr:dgeqr2:dorm2r:dlacpy:dlarnv:dlascl:dlaset:dlartg:dlanst:dlaev2:dlapy2:dlasr"
        foptflags="-qextname=ddot:fdate:flush:lsame:dscal:dnrm2:idamax:drot:dswap:dspmv:daxpy:dspr2:dgemm:dcopy:dgemv:dtrmv:dtrmm:dger:lsame:dspev:dgeev:dspevd:dsyev:dppsv:dspsv:dlamch:dsteqr:dgeqr2:dorm2r:dlacpy:dlarnv:dlascl:dlaset:dlartg:dlanst:dlaev2:dlapy2:dlasr"
    fi
    fppflags="$fppflags -DNMLEQ -DCLINK_PLAIN -DXLF90 -DHASSECOND"
    fpp='/opt/ibmcmp/xlf/8.1/exe/cpp'
    if [ $parallel = "mpi" ]; then
        fppflags="$fppflags -DPOE"
        fpp="$fpp -I/usr/lpp/ppe.poe/include"
        fc='mpxlf90_r -bmaxdata:0x80000000'
    else
        fc=xlf90
    fi
    cc="xlc -qlanglvl=stdc99"
    cppflags="-DCLINK_PLAIN -I/usr/include/malloc"
    cflags="$cflags -O0 -Ddspev=dspev_"
    cplusplus=g++
    if [ $static = "yes" ]; then
        static_flag='-bstatic'
    fi
    loadcc="$cc $static_flag"

    fflags="$fflags -qfloat=nomaf -qfixed"
    foptflags="$foptflags -qfloat=nomaf -qfixed -O3 -qmaxmem=-1 -qarch=auto -qtune=auto"
    if [ $verbose = "yes" ]; then
        verbosity='-qsource -qreport=hotlist'
    fi
    fflags="$fflags $verbosity"
    foptflags="$foptflags $verbosity"
    freeformat_flag='-qfree=f90'
    ar='ar rvs $(EMPTY)'
    ranlib=ranlib
    m4='m4 -B50000'
    ;;

ifort_macosx)
    cc="gcc -m32"
    cplusplus=g++
    cflags="$cflags -O2"
    loadcc="$cc $static_flag"
    fppflags="$fppflags"
    freeformat_flag='-FR'
    fflags=" -w95 "
    verbosity='-vec_report0'
    if [ $verbose = "yes" ]; then
        verbosity='-sox -vec_report3 -opt_report -opt_report_level max -opt_report_phase all -V -v -Wl,-verbose,-M'
    fi

    fflags="$fflags $verbosity"
    foptflags="$fflags -mp1 -ip -O3"
    fflags="$fflags -mp1 -O0"

    if [ $static = "yes" ]; then
       static_flag='-i-static'
    else
       static_flag=
    fi
    fc=ifort

    #   check for installation of the Intel Math Kernel library:
    mkll='no'
    if [ -z "$MKL_HOME" ]; then
        echo "The MKL_HOME environment variable is not defined."
        echo "    The MKL is recommended for optimal performance."
    else
        echo "MKL_HOME is set to $MKL_HOME"
        if [ -d $MKL_HOME/lib/32 ]; then
            mkll=$MKL_HOME/lib/32
            echo "Using MKL libraries from $mkll"
        else
            echo "MKL libraries were not found !"
        fi
    fi
    if [ $mkll != 'no' ]; then
        use_lapack=VENDOR_SUPPLIED
        use_blas=VENDOR_SUPPLIED

        if [ $static = "yes" ]; then
            #  IA-32 static linking of LAPACK and kernels
            loadlib="$loadlib $mkll/libmkl_lapack.a $mkll/libmkl_ia32.a -L$mkll -lguide -lpthread"
        else
            #  IA-32 dynamic linking of double-precision-LAPACK and kernels
            loadlib="$loadlib -L$mkll -lmkl_lapack -lmkl_ia32 -lguide -lpthread"
        fi
        fppflags="$fppflags -DMKL"
    fi

    ;;

*)
    echo "Architecture/compiler $arch is not supported (?)" 1>&2
    usage
    ;;

esac

#--------------------------------------------------------------------------
#  Test if the compilers work:
#--------------------------------------------------------------------------

cat <<EOF >testp.c
#include <stdio.h>
int main()
{
   printf( "testing a C program\n" );
}
EOF

echo ""
echo "Testing the C compiler:"
echo "      $cc $cflags -o testp testp.c"
$cc $cflags -o testp testp.c
./testp | grep "testing a C program" > /dev/null
status=$?

if [ "$status" -gt 0 ]; then
    echo "Unable to compile a C program using $cc $cflags"
    echo "Please check your compiler settings or configure flags."
    exit 1
fi
/bin/rm -f testp.c testp.o testp
echo "OK"

cat <<EOF >testp.f
      program testf
      write(6,*) 'testing a Fortran program'
      end program testf
EOF

echo ""
echo "Testing the Fortran compiler:"
echo "     $fc $fflags -o testp testp.f"
$fc $fflags -o testp testp.f
./testp | grep "testing a Fortran program" > /dev/null
status=$?

if [ "$status" -gt 0 ]; then
    echo "Unable to compile a Fortran program using $fc $fflags"
    echo "Please check your compiler settings or configure flags."
    exit 1
fi
/bin/rm -f testp.f testp.o testp
echo "OK"

#--------------------------------------------------------------------------
#  Set configuration for netcdf:
#  This comes before the "parallel" section as we don't want to use the mpi wrapped $fc
#--------------------------------------------------------------------------

if [ $bintraj = "yes" ]; then

    fncflags=
    f90ncflags=
    case "$fc" in
    *xlf90*)
        fncflags='-O3 -qmaxmem=-1 -qarch=auto -qtune=auto'
        f90ncflags=' -qsuffix=f=f90'
        ;;
    *)
        fncflags="$foptflags"
        f90ncflags="$foptflags"
        ;;
    esac

    echo ""
    echo "  ------   Configuring the netCDF libraries:   --------"
    echo ""

    netcdfflag="--prefix=$AMBERHOME/src/netcdf --disable-cxx" 
    if [ $arch = 'sgi_altix' ] ; then
         netcdfflag="$netcdfflag --enable-64bit"
    fi

    echo "Configuring netcdf; (may be time-consuming)"

    cd netcdf/src && \
    env FC="$fc" F90="$fc" FFLAGS="$static_flag $fncflags" \
            F90FLAGS="$static_flag $f90ncflags" CC="$cc" \
            CFLAGS="$cflags" CPPFLAGS="-DNDEBUG" ./configure $netcdfflag \
            > ../../netcdf_config.log
    ncerror=$?
    if [ "$ncerror" -gt 0 ]; then
        echo "netcdf configure returned $ncerror"
        echo "NETCDF configure failed!  Check the netcdf_config.log file"
        exit 1
    else
        echo "NETCDF configure succeeded."
    fi
    cd ../..

    fppflags="$fppflags -DBINTRAJ"
    cppflags="$cppflags -DBINTRAJ -I../netcdf/include"
else
    netcdf=
    netcdflib=
fi

#------------------------------------------------------------------------------
#  Case statement identifying the parallel options:
#------------------------------------------------------------------------------

case "$parallel" in

mpi)
    loadlib="-lmpi $loadlib"
    fppflags="$fppflags -DMPI "
    ;;

mpi2)
    loadlib="-lmpi $loadlib"
    fppflags="$fppflags -DMPI -DUSE_MPI_INPLACE"
    ;;

lamsource)
    export MPI_HOME=$AMBERHOME
    echo "MPI_HOME is set to $MPI_HOME"
    fppflags="-I$MPI_HOME/include $fppflags -DMPI"

    echo ""
    echo "  ------   Configuring the lam libraries:   --------"
    echo ""

cat <<EOF > configure_lam
#!/bin/sh

cd lam-7.1.3 && \\
./configure --prefix=$AMBERHOME --disable-tv-queue --without-mpi2cpp \\
            --without-profiling --without-romio FC="$fc" FFLAGS="$fflags" \\
            CXX="$cplusplus"
lamcerror=\$?
if [ "\$lamcerror" -gt 0 ]; then
    echo "lam configure returned \$lamcerror"
    echo "LAM configure failed!  Check the above messages."
    exit 1
else
    echo "LAM configure succeeded."
fi
make clean
make install
cd ..
EOF

    chmod +x ./configure_lam
    echo ""
    echo " Creating a 'configure_lam' script "
    echo ""
	echo " Please execute './configure_lam' before 'make parallel'"
	echo "   (You only need to execute configure_lam once, unless you)"
    echo "    change compilers.)"
    echo ""
    fc=$MPI_HOME/bin/mpif77
    ;;

lam)
    if [ -z "$MPI_HOME" ]; then
        PAR="LAM"
        FILES="mpif.h and libmpi.a, liblam.a or liblamf77mpi.a"
        EXAMPLE="/opt/lam"
        par_error
    fi
    echo "MPI_HOME is set to $MPI_HOME"
    fppflags="-I$MPI_HOME/include $fppflags -DMPI"
    fc=$MPI_HOME/bin/mpif77
    ;;

openmpi)
    if [ -z "$MPI_HOME" ]; then
        PAR="OPENMPI"
        FILES="mpif.h and libmpi.a"
        EXAMPLE="/usr/local/openmpi-1.0"
        par_error
    fi
    echo "MPI_HOME is set to $MPI_HOME"
    fppflags="-I$MPI_HOME/include $fppflags -DMPI"
    fc=$MPI_HOME/bin/mpif90
    ;;

scali)
    if [ -z "$MPI_HOME" ]; then
        PAR="SCALI"
        FILES="mpif.h and libmpi.a or libfmpi.a"
        EXAMPLE="/opt/scali"
        par_error
    fi
    echo "MPI_HOME is set to $MPI_HOME"
    loadlib="$loadlib -L$MPI_HOME/lib -lfmpi -lmpi"
    fppflags="-I$MPI_HOME/include $fppflags -DMPI"
    ;;

mpich)
    if [ -z "$MPI_HOME" ]; then
        PAR="MPICH"
        FILES="mpif.h and libmpi.a or libmpich.a"
        EXAMPLE="/usr/local/src/mpich/build/LINUX/ch_pentium4"
        par_error
    fi
    echo "MPI_HOME is set to $MPI_HOME"
    fppflags="-I$MPI_HOME/include $fppflags -DMPI"
    fc=$MPI_HOME/bin/mpif90
    ;;

mpich2)
    if [ -z "$MPI_HOME" ]; then
        PAR="MPICH2"
        FILES="mpif.h and libmpi.a or libmpich.a"
        EXAMPLE="/usr/local/src/mpich/build/LINUX/ch_pentium4"
        par_error
    fi
    echo "MPI_HOME is set to $MPI_HOME"
    #MPICH 2 is supposed to be MPI v2 complient so must support MPI_IN_PLACE.
    fppflags="-I$MPI_HOME/include $fppflags -DMPI -DUSE_MPI_IN_PLACE"
    fc=$MPI_HOME/bin/mpif90
    ;;

intelmpi)
    if [ -z "$MPI_HOME" ]; then
        PAR="INTELMPI"
        FILES="mpif.h and libmpi.a"
        EXAMPLE="/opt/intel/mpi/2.0"
        par_error
    fi
    echo "MPI_HOME is set to $MPI_HOME"
    loadlib2="-L$MPI_HOME/lib -lmpi -lmpiif -lmpigi"
    fppflags="-I$MPI_HOME/include $fppflags -DMPI"
    if [  "$machine" = "x86_64" ] || [ "$x86_64" = "yes" ]; then
       loadlib2="-L$MPI_HOME/lib64 -lmpi -lmpiif -lmpigi -lrt"
       fppflags="-I$MPI_HOME/include64 $fppflags -DMPI"
    else
        loadlib2="-L$MPI_HOME/lib -lmpi -lmpiif -lmpigi -lrt"
        fppflags="-I$MPI_HOME/include $fppflags -DMPI"
    fi
    loadlib="$loadlib $loadlib2"
    ;;

none) # Nothing to do
    ;;

*)
    echo "FIXME: add support for parallel flag $parallel"
    exit 1
    ;;

esac

#------------------------------------------------------------------------------
#  Make some needed directories
#------------------------------------------------------------------------------
cd ..
if [ ! -x bin ]; then
	mkdir bin
fi
if [ ! -x lib ]; then
	mkdir lib
fi
if [ ! -x include ]; then
	mkdir include
fi
if [ ! -x exe ]; then
	ln -s bin exe
fi
cd src

#------------------------------------------------------------------------------
#  Finally, write out the config_amber.h file:
#------------------------------------------------------------------------------

cat <<EOD > config_amber.h
#==============================================================================
# AMBER Makefile configuration for compiler/architecture: $arch
# Generated via command: $command
#
# Configuration script written mainly by Joe Krahn, Scott Brozell, and
# Dave Case, with contributions from lots of people.
#==============================================================================

#------------------------------------------------------------------------------
# AMBERBUILDFLAGS provides a hook into the build process for installers;
# for example, to build debug versions of the amber programs
# make -e AMBERBUILDFLAGS="-DDEBUG -g"
#------------------------------------------------------------------------------
AMBERBUILDFLAGS=

#------------------------------------------------------------------------------
# LOCALFLAGS is intended for program specific modifications to the
# Fortran build process and may be modified by the program's local makefile
#------------------------------------------------------------------------------
LOCALFLAGS=$localflags

#------------------------------------------------------------------------------
# Availability and method of delivery of math and optional libraries
#------------------------------------------------------------------------------
USE_BLASLIB=\$($use_blas)
USE_LAPACKLIB=\$($use_lapack)

#------------------------------------------------------------------------------
# C compiler
#------------------------------------------------------------------------------
CC= $cc
CPLUSPLUS=$cplusplus
CFLAGS=$cflags \$(AMBERBUILDFLAGS)
CPPFLAGS=$cppflags \$(AMBERBUILDFLAGS)

#------------------------------------------------------------------------------
# Fortran preprocessing and compiler.
# FPPFLAGS holds the main Fortran options, such as whether MPI is used.
#------------------------------------------------------------------------------
FPPFLAGS= $fppflags \$(AMBERBUILDFLAGS)
FPP= $fpp \$(FPPFLAGS)
FC= $fc
FFLAGS= $fflags \$(LOCALFLAGS) \$(AMBERBUILDFLAGS)
FOPTFLAGS= $foptflags \$(LOCALFLAGS) \$(AMBERBUILDFLAGS)
FREEFORMAT_FLAG= $freeformat_flag

#------------------------------------------------------------------------------
# Loader:
#------------------------------------------------------------------------------
LOAD= $fc $static_flag $openmp_flag \$(LOCALFLAGS) \$(AMBERBUILDFLAGS)
LOADCC= $loadcc \$(LOCALFLAGS) \$(AMBERBUILDFLAGS)
LOADLIB= $loadlib
LM= $lm
XHOME= $xhome
XLIBS= $xlibs

#------------------------------------------------------------------------------
#  Other stuff:
#------------------------------------------------------------------------------
.SUFFIXES:  .f90
EMPTY=
AR=$ar
M4=$m4
RANLIB=$ranlib
SFX=$sfx
NETCDF=$netcdf
NETCDFLIB=$netcdflib
MODULEDIR=$moduledir
testsanderDIVCON=$testsanderDIVCON
INCDIVCON=$incdivcon
LIBDIVCON=$libdivcon

#  Location for executables, etc:

BINDIR=$AMBERHOME/bin
LIBDIR=$AMBERHOME/lib
INCDIR=$AMBERHOME/include
DATDIR=$AMBERHOME/dat

#  default rules for Fortran and C compilation:

.f.o:   \$<
	\$(FPP) \$< > _\$<
	\$(FC) -c \$(FFLAGS) -o \$@ _\$<

.c.o:
	\$(CC) -c \$(CFLAGS) \$(CPPFLAGS) -o \$@ \$<

EOD

echo " "
echo "The configuration file, config_amber.h, was successfully created."
echo " "
exit