#!/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        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
END
SYMMETRY NOSYM
RELATIVISTIC Scalar ZORA
FRAGMENTS
    Au  Au.t21
END
XC
    LDA SCF VWN
END
OCCUPATIONS Smearq=0.001
eor
mv TAPE21 layer.t21

$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.2
    Au       -7.555589   -2.498480   -1.442498 f=left.2
    Au       -7.555589   -2.498480    1.442498 f=left.2
    Au       -7.555589    0.000000   -2.884996 f=left.2
    Au       -7.555589    0.000000    0.000000 f=left.2
    Au       -7.555589    0.000000    2.884996 f=left.2
    Au       -7.555589    2.498480   -1.442498 f=left.2
    Au       -7.555589    2.498480    1.442498 f=left.2
    Au       -7.555589    4.996959    0.000000 f=left.2
    Au       -5.200000   -3.331306    0.000000 f=left.3
    Au       -5.200000   -0.832826   -1.442498 f=left.3
    Au       -5.200000   -0.832826    1.442498 f=left.3
    Au       -5.200000    1.665653   -2.884996 f=left.3
    Au       -5.200000    1.665653    0.000000 f=left.3
    Au       -5.200000    1.665653    2.884996 f=left.3
    Au       -5.200000    4.164133   -1.442498 f=left.3
    Au       -5.200000    4.164133    1.442498 f=left.3
    Au       -5.200001    6.662612    0.000000 f=left.3
    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.3
    Au        5.200000   -4.164133   -1.442498 f=right.3
    Au        5.200000   -4.164133    1.442498 f=right.3
    Au        5.200000   -1.665653   -2.884996 f=right.3
    Au        5.200000   -1.665653    0.000000 f=right.3
    Au        5.200000   -1.665653    2.884996 f=right.3
    Au        5.200000    0.832826   -1.442498 f=right.3
    Au        5.200000    0.832826    1.442498 f=right.3
    Au        5.200000    3.331306    0.000000 f=right.3
    Au        7.555589   -4.996959    0.000000 f=right.2
    Au        7.555589   -2.498480   -1.442498 f=right.2
    Au        7.555589   -2.498480    1.442498 f=right.2
    Au        7.555589    0.000000   -2.884996 f=right.2
    Au        7.555589    0.000000    0.000000 f=right.2
    Au        7.555589    0.000000    2.884996 f=right.2
    Au        7.555589    2.498480   -1.442498 f=right.2
    Au        7.555589    2.498480    1.442498 f=right.2
    Au        7.555589    4.996959    0.000000 f=right.2
    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
    left.2      layer.t21
    left.3      layer.t21
    molecule    molecule.t21
    right.3     layer.t21
    right.2     layer.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 10000
ETA 1e-6
LEFT
    FRAGMENT left
    ETA 2e-2
END
RIGHT
    FRAGMENT right
    ETA 2e-2
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
rm molecule.t21 fock.t21