#! /bin/sh


# ADF can can calculate charge transfer integrals, that are needed in
# approximate methods that model charge transport properties. The molecular
# system typically should be build from 2 fragments. In this example charge
# transfer integrals are calculated between Adenine and Thymine. First these two
# molecules are calculated. In the fragment calculation full symmetry can be
# used. For precision reasons the ZlmFit quality is set to good.



"$ADFBIN/adf" <<eor
TITLE A fragment

ATOMS
 1 N       0.000000000000       0.656191000000       4.473450000000
 2 C       0.000000000000       1.850911000000       5.098850000000
 3 N       0.000000000000       2.094911000000       6.411070000000
 4 C       0.000000000000       0.951291000000       7.115010000000
 5 C       0.000000000000      -0.355699000000       6.611740000000
 6 C       0.000000000000      -0.487619000000       5.203330000000
 7 N       0.000000000000       0.791131000000       8.484350000000
 8 C       0.000000000000      -0.567649000000       8.729290000000
 9 N       0.000000000000      -1.292469000000       7.631450000000
10 N       0.000000000000      -1.672349000000       4.572610000000
11 H       0.000000000000       2.715551000000       4.433920000000
12 H       0.000000000000       1.540301000000       9.166150000000
13 H       0.000000000000      -0.961519000000       9.739820000000
14 H       0.000000000000      -2.515699000000       5.129900000000
15 H       0.000000000000      -1.718459000000       3.541030000000
END

ZlmFit
 Quality good
End

BASIS
 type DZ
 core None
END
eor
mv TAPE21 Adenine.t21 

"$ADFBIN/adf" <<eor
TITLE T fragment

ATOMS
 1 N       0.000000000000       0.617991000000       1.666040000000
 2 C       0.000000000000       1.851251000000       1.046260000000
 3 N       0.000000000000       1.768641000000      -0.347380000000
 4 C       0.000000000000       0.582611000000      -1.042160000000
 5 C       0.000000000000      -0.621999000000      -0.417040000000
 6 C       0.000000000000      -0.627269000000       1.045880000000
 7 O       0.000000000000      -1.670479000000       1.720780000000
 8 O       0.000000000000       2.924531000000       1.636600000000
 9 C       0.000000000000      -1.937039000000      -1.138130000000
10 H       0.000000000000       0.635221000000       2.733380000000
11 H       0.000000000000       2.660141000000      -0.830100000000
12 H       0.000000000000       0.676731000000      -2.127100000000
13 H       0.880180000000      -2.533409000000      -0.860650000000
14 H       0.000000000000      -1.793509000000      -2.225780000000
15 H      -0.880180000000      -2.533409000000      -0.860650000000
END

ZlmFit
 Quality good
End

BASIS
 type DZ
 core None
END
eor
mv TAPE21 Thymine.t21 


# Next the the base pair is calculated that consists of Adenine and Thymine. To
# calculate the charge transfer integrals, spatial overlap integrals and site
# energies, include the key TRANSFERINTEGRALS in the input for ADF. Symmetry
# NOSYM should be used.


"$ADFBIN/adf" <<eor
TITLE AT

ATOMS
 1 N       0.000000000000       0.656191000000       4.473450000000  f=Adenine
 2 C       0.000000000000       1.850911000000       5.098850000000  f=Adenine
 3 N       0.000000000000       2.094911000000       6.411070000000  f=Adenine
 4 C       0.000000000000       0.951291000000       7.115010000000  f=Adenine
 5 C       0.000000000000      -0.355699000000       6.611740000000  f=Adenine
 6 C       0.000000000000      -0.487619000000       5.203330000000  f=Adenine
 7 N       0.000000000000       0.791131000000       8.484350000000  f=Adenine
 8 C       0.000000000000      -0.567649000000       8.729290000000  f=Adenine
 9 N       0.000000000000      -1.292469000000       7.631450000000  f=Adenine
10 N       0.000000000000      -1.672349000000       4.572610000000  f=Adenine
11 H       0.000000000000       2.715551000000       4.433920000000  f=Adenine
12 H       0.000000000000       1.540301000000       9.166150000000  f=Adenine
13 H       0.000000000000      -0.961519000000       9.739820000000  f=Adenine
14 H       0.000000000000      -2.515699000000       5.129900000000  f=Adenine
15 H       0.000000000000      -1.718459000000       3.541030000000  f=Adenine
16 N       0.000000000000       0.617991000000       1.666040000000  f=Thymine
17 C       0.000000000000       1.851251000000       1.046260000000  f=Thymine
18 N       0.000000000000       1.768641000000      -0.347380000000  f=Thymine
19 C       0.000000000000       0.582611000000      -1.042160000000  f=Thymine
20 C       0.000000000000      -0.621999000000      -0.417040000000  f=Thymine
21 C       0.000000000000      -0.627269000000       1.045880000000  f=Thymine
22 O       0.000000000000      -1.670479000000       1.720780000000  f=Thymine
23 O       0.000000000000       2.924531000000       1.636600000000  f=Thymine
24 C       0.000000000000      -1.937039000000      -1.138130000000  f=Thymine
25 H       0.000000000000       0.635221000000       2.733380000000  f=Thymine
26 H       0.000000000000       2.660141000000      -0.830100000000  f=Thymine
27 H       0.000000000000       0.676731000000      -2.127100000000  f=Thymine
28 H       0.880180000000      -2.533409000000      -0.860650000000  f=Thymine
29 H       0.000000000000      -1.793509000000      -2.225780000000  f=Thymine
30 H      -0.880180000000      -2.533409000000      -0.860650000000  f=Thymine
END

ZlmFit
 Quality good
End

Fragments
    Adenine Adenine.t21 
    Thymine Thymine.t21 
end

SYMMETRY NOSYM
TRANSFERINTEGRALS
eor

# After the calculation has finished in the output one will find the charge
# transfer (overlap integrals and site energies) that are needed to calculate
# hole mobility or electron mobility calculations:

# =============================================================================================
# Electronic coupling V (also known as effective (generalized) transfer integrals J_eff)
# V = (J-S(e1+e2)/2)/(1-S^2)
# 
# V for hole transfer:           0.000 eV
# V for electron transfer:      -0.036 eV
# 
# The effective transfer integral, or electronic coupling, is calculated from these components:
# 
# e1(hole) Site energy HOMO fragment 1:      -6.88 eV
# e2(hole) Site energy HOMO fragment 2:      -6.46 eV
# J(hole) Charge transfer integral HOMO fragment 1 - HOMO fragment 2:       0.000 eV
# S(hole) Overlap integral HOMO fragment 1 - HOMO fragment 2:       0.000
# 
# e1(electron) Site energy LUMO fragment 1:      -2.24 eV
# e2(electron) Site energy LUMO fragment 2:      -2.62 eV
# J(electron) Charge transfer integral LUMO fragment 1 - LUMO fragment 2:      -0.046 eV
# S(electron) Overlap integral LUMO fragment 1 - LUMO fragment 2:       0.004
# =============================================================================================