$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                       
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                     
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,                             
C1 ! FMO does not support symmetry, so always use C1                            
H 1                                                                             
O 8                                                                             
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:                                    
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.                         
water dimer (H2O)2                                                              
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                                                                   
Your $FMOXYZ matching this $DATA will then look as follows:                     
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                                                                     
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                            
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