$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). ========================================================== ==========================================================

generated on 7/7/2017