#!/bin/sh

cp $ADFHOME/examples/adf/green_Al/Au.5p .
cp $ADFHOME/examples/adf/green_Al/Au.5p.dirac .

$ADFBIN/dirac < Au.5p.dirac
mv TAPE12 t12.rel

$ADFBIN/adf -n1 << eor
CREATE Au   file=Au.5p
RELATIVISTIC Scalar ZORA

COREPOTENTIALS t12.rel
End

XC
    LDA SCF VWN
END
eor
mv TAPE21 t21.Au

$ADFBIN/adf << eor
TITLE Gold atom
ATOMS
    Au        0.000000    0.000000    0.000000
END
RELATIVISTIC Scalar ZORA
FRAGMENTS
    Au  t21.Au
END
XC
    LDA SCF VWN
END
eor
mv TAPE21 Au.t21

$ADFBIN/adf << eor
TITLE Principal layer
ATOMS
    Au       -2.355588   -6.662612    0.000000
    Au       -2.355589   -4.164133   -1.442498
    Au       -2.355589   -4.164133    1.442498
    Au       -2.355589   -1.665653   -2.884996
    Au       -2.355589   -1.665653    0.000000
    Au       -2.355589   -1.665653    2.884996
    Au       -2.355589    0.832826   -1.442498
    Au       -2.355589    0.832826    1.442498
    Au       -2.355589    3.331306    0.000000
    Au        0.000000   -4.996959    0.000000
    Au        0.000000   -2.498480   -1.442498
    Au        0.000000   -2.498480    1.442498
    Au        0.000000    0.000000   -2.884996
    Au        0.000000    0.000000    0.000000
    Au        0.000000    0.000000    2.884996
    Au        0.000000    2.498480   -1.442498
    Au        0.000000    2.498480    1.442498
    Au        0.000000    4.996959    0.000000
    Au        2.355589   -3.331306    0.000000
    Au        2.355589   -0.832826   -1.442498
    Au        2.355589   -0.832826    1.442498
    Au        2.355589    1.665653   -2.884996
    Au        2.355589    1.665653    0.000000
    Au        2.355589    1.665653    2.884996
    Au        2.355589    4.164133   -1.442498
    Au        2.355589    4.164133    1.442498
    Au        2.355588    6.662612    0.000000
END
SYMMETRY NOSYM
RELATIVISTIC Scalar ZORA
FRAGMENTS
    Au  Au.t21
END
XC
    LDA SCF VWN
END
eor
mv TAPE21 layer.t21

$ADFBIN/adf << eor
TITLE Bulk gold
ATOMS
    Au       -9.422355  -11.659571    0.000000 f=left
    Au       -9.422356   -9.161092   -1.442498 f=left
    Au       -9.422356   -9.161092    1.442498 f=left
    Au       -9.422356   -6.662612   -2.884996 f=left
    Au       -9.422356   -6.662612    0.000000 f=left
    Au       -9.422356   -6.662612    2.884996 f=left
    Au       -9.422356   -4.164133   -1.442498 f=left
    Au       -9.422356   -4.164133    1.442498 f=left
    Au       -9.422356   -1.665653    0.000000 f=left
    Au       -7.066767   -9.993918    0.000000 f=left
    Au       -7.066767   -7.495439   -1.442498 f=left
    Au       -7.066767   -7.495439    1.442498 f=left
    Au       -7.066767   -4.996959   -2.884996 f=left
    Au       -7.066767   -4.996959    0.000000 f=left
    Au       -7.066767   -4.996959    2.884996 f=left
    Au       -7.066767   -2.498479   -1.442498 f=left
    Au       -7.066767   -2.498479    1.442498 f=left
    Au       -7.066767    0.000000    0.000000 f=left
    Au       -4.711178   -8.328265    0.000000 f=left
    Au       -4.711178   -5.829785   -1.442498 f=left
    Au       -4.711178   -5.829785    1.442498 f=left
    Au       -4.711178   -3.331306   -2.884996 f=left
    Au       -4.711178   -3.331306    0.000000 f=left
    Au       -4.711178   -3.331306    2.884996 f=left
    Au       -4.711178   -0.832826   -1.442498 f=left
    Au       -4.711178   -0.832826    1.442498 f=left
    Au       -4.711179    1.665653    0.000000 f=left
    Au       -2.355588   -6.662612    0.000000 f=center
    Au       -2.355589   -4.164133   -1.442498 f=center
    Au       -2.355589   -4.164133    1.442498 f=center
    Au       -2.355589   -1.665653   -2.884996 f=center
    Au       -2.355589   -1.665653    0.000000 f=center
    Au       -2.355589   -1.665653    2.884996 f=center
    Au       -2.355589    0.832826   -1.442498 f=center
    Au       -2.355589    0.832826    1.442498 f=center
    Au       -2.355589    3.331306    0.000000 f=center
    Au        0.000000   -4.996959    0.000000 f=center
    Au        0.000000   -2.498480   -1.442498 f=center
    Au        0.000000   -2.498480    1.442498 f=center
    Au        0.000000    0.000000   -2.884996 f=center
    Au        0.000000    0.000000    0.000000 f=center
    Au        0.000000    0.000000    2.884996 f=center
    Au        0.000000    2.498480   -1.442498 f=center
    Au        0.000000    2.498480    1.442498 f=center
    Au        0.000000    4.996959    0.000000 f=center
    Au        2.355589   -3.331306    0.000000 f=center
    Au        2.355589   -0.832826   -1.442498 f=center
    Au        2.355589   -0.832826    1.442498 f=center
    Au        2.355589    1.665653   -2.884996 f=center
    Au        2.355589    1.665653    0.000000 f=center
    Au        2.355589    1.665653    2.884996 f=center
    Au        2.355589    4.164133   -1.442498 f=center
    Au        2.355589    4.164133    1.442498 f=center
    Au        2.355588    6.662612    0.000000 f=center
    Au        4.711179   -1.665653    0.000000 f=right
    Au        4.711178    0.832826   -1.442498 f=right
    Au        4.711178    0.832826    1.442498 f=right
    Au        4.711178    3.331306   -2.884996 f=right
    Au        4.711178    3.331306    0.000000 f=right
    Au        4.711178    3.331306    2.884996 f=right
    Au        4.711178    5.829785   -1.442498 f=right
    Au        4.711178    5.829785    1.442498 f=right
    Au        4.711178    8.328265    0.000000 f=right
    Au        7.066767    0.000000    0.000000 f=right
    Au        7.066767    2.498479   -1.442498 f=right
    Au        7.066767    2.498479    1.442498 f=right
    Au        7.066767    4.996959   -2.884996 f=right
    Au        7.066767    4.996959    0.000000 f=right
    Au        7.066767    4.996959    2.884996 f=right
    Au        7.066767    7.495439   -1.442498 f=right
    Au        7.066767    7.495439    1.442498 f=right
    Au        7.066767    9.993918    0.000000 f=right
    Au        9.422356    1.665653    0.000000 f=right
    Au        9.422356    4.164133   -1.442498 f=right
    Au        9.422356    4.164133    1.442498 f=right
    Au        9.422356    6.662612   -2.884996 f=right
    Au        9.422356    6.662612    0.000000 f=right
    Au        9.422356    6.662612    2.884996 f=right
    Au        9.422356    9.161092   -1.442498 f=right
    Au        9.422356    9.161092    1.442498 f=right
    Au        9.422355   11.659571    0.000000 f=right
END
SYMMETRY NOSYM
RELATIVISTIC Scalar ZORA
FRAGMENTS
    left    layer.t21
    center  layer.t21
    right   layer.t21
END
XC
    LDA SCF VWN
END
eor
mv TAPE21 bulk.t21

$ADFBIN/green << eor
SURFACE bulk.t21
    FRAGMENTS center right
END
EPS -0.5 0 1000
ETA 1e-6
eor
mv SURFACE left.kf

$ADFBIN/green << eor
SURFACE bulk.t21
    FRAGMENTS center left
END
EPS -0.5 0 1000
ETA 1e-6
eor
mv SURFACE right.kf

$ADFBIN/adf << eor
TITLE Benzenedithiol
ATOMS
    C        -1.400000    0.000000    0.000000
    C        -0.700000    0.000000   -1.200000
    C        -0.700000    0.000000    1.200000
    C         0.700000    0.000000   -1.200000
    C         0.700000    0.000000    1.200000
    C         1.400000    0.000000    0.000000
    H        -1.200000    0.000000   -2.200000
    H        -1.200000    0.000000    2.200000
    H         1.200000    0.000000   -2.200000
    H         1.200000    0.000000    2.200000
    S        -3.200000    0.000000    0.000000
    S         3.200000    0.000000    0.000000
END
SYMMETRY NOSYM
RELATIVISTIC Scalar ZORA
BASIS
    type DZP
    core Large
    createOutput None
END
XC
    LDA SCF VWN
END
eor
mv TAPE21 molecule.t21

$ADFBIN/adf << eor
TITLE Benzenedithiol
ATOMS
    Au       -9.911177   -6.662612    0.000000 f=left
    Au       -9.911178   -4.164133   -1.442498 f=left
    Au       -9.911178   -4.164133    1.442498 f=left
    Au       -9.911178   -1.665653   -2.884996 f=left
    Au       -9.911178   -1.665653    0.000000 f=left
    Au       -9.911178   -1.665653    2.884996 f=left
    Au       -9.911178    0.832826   -1.442498 f=left
    Au       -9.911178    0.832826    1.442498 f=left
    Au       -9.911178    3.331306    0.000000 f=left
    Au       -7.555589   -4.996959    0.000000 f=left
    Au       -7.555589   -2.498480   -1.442498 f=left
    Au       -7.555589   -2.498480    1.442498 f=left
    Au       -7.555589    0.000000   -2.884996 f=left
    Au       -7.555589    0.000000    0.000000 f=left
    Au       -7.555589    0.000000    2.884996 f=left
    Au       -7.555589    2.498480   -1.442498 f=left
    Au       -7.555589    2.498480    1.442498 f=left
    Au       -7.555589    4.996959    0.000000 f=left
    Au       -5.200000   -3.331306    0.000000 f=left
    Au       -5.200000   -0.832826   -1.442498 f=left
    Au       -5.200000   -0.832826    1.442498 f=left
    Au       -5.200000    1.665653   -2.884996 f=left
    Au       -5.200000    1.665653    0.000000 f=left
    Au       -5.200000    1.665653    2.884996 f=left
    Au       -5.200000    4.164133   -1.442498 f=left
    Au       -5.200000    4.164133    1.442498 f=left
    Au       -5.200001    6.662612    0.000000 f=left
    C        -1.400000    0.000000    0.000000 f=molecule
    C        -0.700000    0.000000   -1.200000 f=molecule
    C        -0.700000    0.000000    1.200000 f=molecule
    C         0.700000    0.000000   -1.200000 f=molecule
    C         0.700000    0.000000    1.200000 f=molecule
    C         1.400000    0.000000    0.000000 f=molecule
    H        -1.200000    0.000000   -2.200000 f=molecule
    H        -1.200000    0.000000    2.200000 f=molecule
    H         1.200000    0.000000   -2.200000 f=molecule
    H         1.200000    0.000000    2.200000 f=molecule
    S        -3.200000    0.000000    0.000000 f=molecule
    S         3.200000    0.000000    0.000000 f=molecule
    Au        5.200001   -6.662612    0.000000 f=right
    Au        5.200000   -4.164133   -1.442498 f=right
    Au        5.200000   -4.164133    1.442498 f=right
    Au        5.200000   -1.665653   -2.884996 f=right
    Au        5.200000   -1.665653    0.000000 f=right
    Au        5.200000   -1.665653    2.884996 f=right
    Au        5.200000    0.832826   -1.442498 f=right
    Au        5.200000    0.832826    1.442498 f=right
    Au        5.200000    3.331306    0.000000 f=right
    Au        7.555589   -4.996959    0.000000 f=right
    Au        7.555589   -2.498480   -1.442498 f=right
    Au        7.555589   -2.498480    1.442498 f=right
    Au        7.555589    0.000000   -2.884996 f=right
    Au        7.555589    0.000000    0.000000 f=right
    Au        7.555589    0.000000    2.884996 f=right
    Au        7.555589    2.498480   -1.442498 f=right
    Au        7.555589    2.498480    1.442498 f=right
    Au        7.555589    4.996959    0.000000 f=right
    Au        9.911178   -3.331306    0.000000 f=right
    Au        9.911178   -0.832826   -1.442498 f=right
    Au        9.911178   -0.832826    1.442498 f=right
    Au        9.911178    1.665653   -2.884996 f=right
    Au        9.911178    1.665653    0.000000 f=right
    Au        9.911178    1.665653    2.884996 f=right
    Au        9.911178    4.164133   -1.442498 f=right
    Au        9.911178    4.164133    1.442498 f=right
    Au        9.911177    6.662612    0.000000 f=right
END
SYMMETRY NOSYM
RELATIVISTIC Scalar ZORA
FRAGMENTS
    left        layer.t21
    molecule    molecule.t21
    right       layer.t21
END
XC
    LDA SCF VWN
END
eor
mv TAPE21 fock.t21

$ADFBIN/green << eor
DOS fock.t21
TRANS fock.t21
EPS -0.5 0 1000
ETA 1e-6
LEFT left.kf
    FRAGMENT left
END
RIGHT right.kf
    FRAGMENT right
END
NOSAVE DOS_B, TRANS_B
eor

echo ""
echo "Contents of DOS_A:"
cat DOS_A
echo "END"
echo ""
echo "Contents of TRANS_A:"
cat TRANS_A
echo "END"

rm logfile
rm t12.rel
rm t21.Au
rm Au.t21 layer.t21 bulk.t21
rm left.kf right.kf
rm molecule.t21 fock.t21