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$FMOXYZ group (given for FMO runs)
This group provides an analog of $DATA for $FMO, except
that no explicit basis set is given here. For DFTB and
FMO/MM runs see notes at the end of this subsection - these
runs have some specific requirements. $FMOXYZ contains any
number of lines of the following type:
A.N Q X Y Z
A is the dummy name of an atom.
N is an optional basis set number (if omitted, it will be
set to 1). N is intended for mixed basis set runs, for
example, if you want to put diffuse functions on carboxyl
groups.
Q is the atomic charge.
Z is the integer atomic charge.
X, Y and Z are Cartesian coordinates. These obey UNITS
given in $CONTRL.
There is no default, this group must always be given for
FMO runs. Alternatively, you may use the chemical symbol
instead of Q. Note that "A" is ignored in all cases, but
must be given.
Here is how $DATA is used in FMO:
Each atom given in $DATA defines the basis set for that
atom type, entirely omitting Cartesian coordinates (which
are in $FMOXYZ). There are two ways to input basis sets in
FMO.
I. easy!
This works only if you want to use the same built-in basis
set for all atoms. It is possible to use EXTFIL as usual
for externally defined basis sets.
1. Define $BASIS as usual
2. Put each atom type in $DATA, e.g. for (H2O)2,
$DATA
H2O
C1 ! FMO does not support symmetry, so always use C1
H 1
O 8
$end
II. advanced.
This allows you to mix basis sets, have multiple layers or
a non-standard without involving EXTFIL.
1. Do not define $BASIS.
2. Put each atom type in $DATA, followed by basis set,
either explicit or built in.
The names of atoms in $DATA have the following format,
where brackets indicate optional parameters:
S[.N][-L]
N and L may be omitted (taking the default value of 1),
S is the atom name (discarded upon reading),
N is the basis set ordinal number,
L is the layer.
S[.N][-L] may not exceed 8 characters.
Example: 2-layer water dimer. In the first layer, you want
to use STO-3G for the first molecule and your own basis set
for the second. In the second layer, you want to use 6-31G
and 6-31G* for the 1st and 2nd molecules, respectively.
$DATA
water dimer (H2O)2
C1
H-1 1 ! explanation: layer 1, basis 1 (STO-3G) for Hydr.
sto 3
O-1 8 ! explanation: layer 1, basis 1 (STO-3G) for Oxygen
sto 3
H.2-1 1 ! layer 1, basis 2 (manual) for hydrogen
s 1 ; 1 2.0 1
O.2-1 8 ! explanation: layer 1, basis 2 (manual) for Oxygen
s 2
1 100.0 0.8
2 10.0 0.6
l 1
1 5.0 1 1
H-2 1 ! explanation: layer 2, basis 1 (6-31G) for Hydr.
n31 6
O-2 8 ! explanation: layer 2, basis 1 (6-31G) for Oxygen
n31 6
H.2-2 1 ! layer 2, basis 2 (6-31G* = 6-31G) for Hydrogen
n31 6
O.2-2 8 ! explanation: layer 2, basis 2 (6-31G*) for Oxygen
n31 6
d 1 ; 1 0.8 1
$end
Your $FMOXYZ matching this $DATA will then look as follows:
$FMOXYZ
O 8 x y z
H 1 x y z
H 1 x y z
O.2 8 x y z
H.2 1 x y z
H.2 1 x y z
$END
Note that if you define mixed basis sets for the atoms
where bond detachment occurs (do not do this for basis sets
with diffuse functions), then you should provide all
required sets in $FMOHYB as well, and define $FMOBND
properly.
For DFTB, atom names used in $FMOXYZ should match the usage
in other places, such as $DFTBSK.
For FMO-based IMOMM (FMO/MM) atomic coordinates are given
in $TINXYZ rather than in $FMOXYZ! There are no FMO-
specific options to turn on FMO/MM (use the same style as
for regular SIMOMM, complemented by FMO groups).
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generated on 7/7/2017