$FMO group             (optional, activates FMO option)                         
    The presence of this group activates the Fragment                           
Molecular Orbital option, which divides large molecules                         
(think proteins or clusters) into smaller regions for                           
faster computation.  The small pieces are termed 'monomers'                     
no matter how many atoms they contain.  Calculations within                     
monomers, then 'dimer' pairs, and optionally 'trimer' sets                      
act so as to approximate the wavefunction of the full                           
system.  The quantum model may be SCF, DFT, DFTB, MP2, CC,                      
MCSCF, TDDFT, or CI.                                                            
     Sample inputs, and auxiliary programs, and other                           
information may be found in the GAMESS source distribution                      
in the directory ~/gamess/tools/fmo.                                            
NBODY  = n-body FMO expansion:                                                  
         0 only run initial monomer guess (maybe remotely                       
           useful to create the restart file, or as an                          
           alternative to EXETYP=CHECK).                                        
         1 run up to monomer SCF                                                
         2 run up to dimers (FMO2, the default)                                 
         3 run up to trimers (FMO3)                                             
IEFMO  = switch to turn on EFMO (effective fragment                             
         potential based Fragment Molecular Orbital)                            
         0 = use FMO (default)                                                  
         1 = use EFMO                                                           
MODEFM   array of five values controlling EFMO, each                            
         allows a bit-wise combination of several options.                      
         Default is MODEFM(1)=0,0,0,0,0                                         
       The first element is control over electrostatics                         
            0 no screening of electrostatics                                    
            1 exponential screening of electrostatics by                        
              fixed value to fit the classical potential to                     
              the QM-potential, set SCREEN(1)=-1 in $FMO.                       
            2 Add octupole energy into electrostatic energy                     
            4 use Hui Li's density based multipole                              
            8 ignore torque contributions to the gradient                       
           16 generate electrostatics on bond midpoints too                     
       The second element controls polarizabilities.                            
            0 Tang-Toenis type screening                                        
            1 do not include any polarization at all                            
            4 add percentage discrimination based on                            
              distance to atoms                                                 
            8 ignore torque contributions to the gradient                       
           16 use full polarization tensors                                     
           32 move polarizability tensors to nearest atom                       
              before induction                                                  
           64 do not evaluate electrostatic field, induced                      
              dipoles or gradient contributions from                            
              neighbouring fragments.  This assumes                             
              fragments are made in a sequential fashion.                       
          128 use Ruedenberg localization for localization                      
              of orbitals                                                       
       The third element affects dispersion                                     
            0 no dispersion interactions                                        
            1 include dispersion                                                
       The fourth element affects charge transfer                               
            0 no charge transfer interactions                                   
            1 include charge transfer                                           
       The fifth element affects exchange repulsion                             
            0 no exchange interactions                                          
            1 include exchange repulsion                                        
MODFD  = switch to freeze the electronic state of some                          
         fragments. FMO/FD and FMO/FDD require                                  
         RUNTYP=OPTIMIZE and two layers in FMO.                                 
         0 = regular FMO                                                        
         1 = FMO/FD (frozen domain)                                             
         3 = FMO/FDD (frozen domain and dimers)                                 
NDUALB = switch to use dual basis approach with                                 
         auxilliary polarization, AP, (i.e., a different                        
         basis set is used to estimate the polarization).                       
         The two basis sets in FMO/AP are entered in                            
         the multibasis fashion (not in the multilayer),                        
         i.e., as H.1 and H.2 in $DATA, not as H-1 and H-2.                     
         The dual basis set has some restrictions.                              
         Gradient (but not Hessian) is available.                               
         0 = usual FMO                                                          
         1 = dual basis FMO/AP                                                  
       I. The following parameters define layers.                               
NLAYER = the number of layers (default: 1)                                      
MPLEVL = an array specifying n in MPn PT for each layer,                        
         n=0 or 2. (default: all 0s).                                           
         Note that MCQDPT is not available and therefore                        
         one may not choose this for MCSCF.                                     
DFTTYP = an array specifying the DFT functional type for                        
         each layer. (default: DFTTYP in $DFT).                                 
         See $DFT for possible functionals. All functionals                     
         except dual hybrids may be used.                                       
         Only grid-based DFT is supported.                                      
SCFTYP = an array specifying SCF type for each layer.                           
         At present the only valid choices are RHF, ROHF,                       
         UHF, and MCSCF.                                                        
         (default: SCFTYP in $CONTRL for all layers).                           
CCTYP  = an array specifying CC type for each layer, which                      
         may be only the following choices from $CONTRL:                        
             LCCD, CCD, CCSD, CCSD(T), CCSD(T), CCSD(TQ),                       
             CR-CCL, or non-size extensive R-CC or CR-CC.                       
         Since FMO's CC methods involve adding corrections                      
         from pairs of monomers together, it is better to                       
         choose a size extensive method.                                        
TDTYP  = an array specifying TDDFT type for each layer,                         
         of the same kind as TDDFT in $CONTRL.                                  
         Default: TDDFT in $CONTRL for all layers.                              
CITYP  = an array specifying CI type for each layer, see                        
         CITYP in $CONTRL.  At present, only CIS may be                         
         used (FMO1-CIS energy only, i.e., nbody=1).                            
         Default: CITYP from $CONTRL, for all layers.                           
       II. Parameters defining FMO fragments:                                   
NFRAG  = the number of FMO fragments (default: 1)                               
LAYER  = an array defining the layer for each fragment.                         
         Default: all fragments in layer 1, i.e.,                               
FRGNAM = an array of names for each fragment (each 1-8                          
         character long) (default: FRG00001,FRG00002...).                       
INDAT  = an array assigning atoms to fragments. Two styles                      
         are supported (the choice is made based on                             
         INDAT(1): if it is nonzero, choice (a) is taken,                       
         otherwise INDAT(1) is ignored and choice (b) is                        
         a) INDAT(i)=m assigns atom i is to fragment m.                         
            INDAT(i) must be given for each atom.                               
         b) the style is                                                        
            a1 a2 ... ak 0                                                      
            b1 b2 ... bm 0                                                      
            Elements a1...ak are assigned to fragment 1,                        
            then b1...bm are assigned to fragment 2,etc.                        
            An element is one of the following:                                 
                I    or   I -J                                                  
            where I means atom I, and a pair I,-J means                         
            the range of atoms I-J.  There must be no space                     
            after the "-"!                                                      
         indat(1)=1,1,1,2,2,1 is equivalent to                                  
         indat(1)=0, 1,-3,6,0, 4,5,0                                            
         Both assign atoms 1,2,3 and 6 to fragment 1,                           
         and 4,5 to fragment 2.                                                 
ICHARG = an array of charges on the fragments                                   
         (default: all 0 charges)                                               
MULT   = an array of multiplicities for each fragment.                          
         For MCSCF only the unique MCSCF fragment may be                        
         something other than a singlet.                                        
         For ROHF and UHF multiple open-shell fragments                         
         are allowed, which may have any multiplicity;                          
         for dimers the high spin coupling will be used.                        
         (default: all 1's)                                                     
SCFFRG = an array giving the SCF type for each fragment.                        
         For MCSCF, only one fragment may be MCSCF and                          
         the rest should be RHF. For ROHF, UHF and U-DFT                        
         multiple open-shell fragments are allowed, but                         
         for ground state runs only.                                            
         The values in SCFTYP overwrite SCFFRG, that is, if                     
         you want to do a 2-layer calculation, the first                        
         layer being RHF and the other MCSCF, then you                          
         would use SCFTYP(1)=RHF,MCSCF and SCFFRG(N)=MCSCF,                     
         where you should replace N by your MCSCF fragment                      
         number. Then the first layer will be all RHF and                       
         the other will have one MCSCF fragment. In special                     
         cases, some SCFFRG values may be set to NONE, in                       
         which case SCF is not performed. This is useful in                     
         conjunction with ATCHRG.                                               
         (default: SCFTYP in $CONTRL).                                          
MOLFRG = an array listing fragments for selective FMO,                          
         where not all dimers (and/or trimers) are                              
         computed. Setting MOLFRG imposes various                               
         restrictions, such as RUNTYP=ENERGY only.                              
         See MODMOL. For subsystem analysis (MODMOL=8),                         
         MOLFRG(i) defines which subsystem fragment i                           
         belongs to.  Default: all 0.                                           
MODMUL   Use the multipole expansion to compute                                 
         electrostatic interactions exactly, bit additive.                      
       1 Compute individual contributions for each ES                           
       2 Compute the sums for all ES dimer contributions                        
         and add them to the energy and gradient.                               
       8 Compute one-electron ESP gradients (implemented                        
         for RESPPC<=0 only).                                                   
         Only one of bits 1 or 2 may be turned on.                              
         Default: 0                                                             
IACTFG = array specifying fragments in the active domain in                     
         FMO/FD(D). Ranges can be specified as in INDAT, so                     
         INDAT(1)=1,2,-5,8 means fragments 1,2,3,4,5,8.                         
         All IACTFG fragments should be in the 2nd layer,                       
         and the interfragment distance between fragments                       
         in IACTFG and the 1st layer's fragments should not                     
         be zero (i.e., no detached bonds between them).                        
         Default: all zeroes.                                                   
NOPFRG = printing and other additive options, specified for                     
         each fragment,                                                         
       1 set the equivalent of $CONTRL NPRINT=7 (printing                       
         option).  Useful if you want to print orbitals                         
         only for a few selected monomers.                                      
       2 set MVOQ to +6 to obtain better virtual orbitals                       
         (ENERGY runs only, useful mostly to prepare good                       
         initial orbitals for MCSCF).                                           
       4 generate cube file for the specified fragment,                         
         the grid being chosen automatically.                                   
         (default: all 0s)                                                      
      64 use frozen atomic charges (defined in ATCHRG)                          
         instead of the variational ones to compute                             
         converged fragment densities, to describe the                          
         electrostastic field from a fragment acting upon                       
         other fragments.                                                       
     128 apply options 1 and 4 above only at the final SCF                      
         iteration (correlation or GRADIENT only).                              
NACUT  = automatically divides a molecule into fragments by                     
         assigning NACUT atoms to each fragment (useful for                     
         something like water clusters).  This sets FRGNAM                      
         and INDAT, so they need not be given.  If 0, the                       
         automatic option is disabled. (default: 0)                             
IEXCIT = options for FMO based TDHF, TDDFT, or CI                               
IEXCIT(1): ordinal number for the excited state fragment.                       
           There is no default for IEXCIT(1), you should                        
           always set it.                                                       
IEXCIT(2): chooses the many-body level excitation n, e.g.                       
           for FMOn-TDDFT.                                                      
           n=1 means only the fragment given in IEXCIT(1)                       
           will be excited.                                                     
           n=2 adds dimer corrections (from fragment                            
           pairs involving IEXCIT(1)).                                          
           IEXCIT(2) must not exceed NBODY.  Default: 1.                        
IEXCIT(3): (relevant for FMO2-TDDFT only)                                       
           = 0 economic mode: only TDDFT dimer calculations                     
               are performed (skipping all other dimers).                       
           = 1 all dimer calculations are performed to                          
               obtain not just the excitation but also the                      
               total excited state energy.                                      
           Default: 0.                                                          
IEXCIT(4): excited state matching method in FMO2-TDDFT used                     
           to determine which excitations in dimers                             
           correspond to those in the TDDFT fragment given                      
           in IEXCIT(1).  Default=2.                                            
           = 0 trivial or identity matching (assume the                         
               same order of the excited states in monomers                     
               and dimers.                                                      
           = 1 match the dominant orbital pair (aka DRF)                        
           = 2 match the whole excitation vector.                               
     Methods 1 and 2 try to match monomer dimer orbitals                        
     first, and then use DRF coefficients. In difficult                         
     cases (i.e., if the orbitals in a dimer are very                           
     delocalised), methods 1 and 2 may not be able to find                      
     the right transition, so some visual checking is                           
ATCHRG = array of atomic charges, to be used with NOPFRG,                       
         set for some fragments to 64 (i.e., to freeze some                     
         of fragment electrostatic potentials during SCC).                      
Nota bene: the order of atoms in ATCHRG is not the same as                      
in FMOXYZ. In ATCHRG, you should specify atomic charges for                     
all atoms in fragment 1, then for fragment 2 etc, as a                          
single array. For covalently connected fragments there are                      
formally divided atoms (some redundant), and ATCHRG should                      
then list charges for them as well, all in the exact order                      
of atoms in which fragments are defined in FMO. The number                      
of entries in ATCHRG is NATFMO+NBDFG, where NATFMO is the                       
number of atoms in $FMOXYZ and NBDFG is the number of bonds                     
defined in $FMOBND.                                                             
NATCHA = option applicable to molecular clusters made                           
         exclusively of the same molecules. Only NATCHA                         
         atoms are then specified in ATCHRG, and the rest                       
         are copied from the first set.                                         
RAFO   = array of three thresholds defining model systems                       
         in FMO/AFO. All of them are multiplicative factors                     
         applied to distances. Two atoms are considered                         
         covalently bonded if they are separated by the                         
         predefined distance determined by their van der                        
         Waals radii.  Larger RAFO values make further                          
         separated atoms to be considered as bonded.                            
All atoms within RAFO(1) distance from BDA or BAA are                           
included into the model system in AFO ($FMOBND lists BDAs                       
and BAAs in this order as -BDA BAA).  Atoms within RAFO(2)                      
from the set defined by RAFO(1) are replaced by hydrogens.                      
AO coefficients expanding localized orbitals to be frozen                       
are saved for use in FMO for atoms within  RAFO(3) from BDA                     
or BAA. A nonzero RAFO(1) turns on FMO/AFO, else FMO/HOP is                     
used. Default: 0,0,0.                                                           
MODMOL  = additive options for dimers and trimers in the                        
          selective FMO based on MOLFRG.                                        
        1 limits correlated calculations to a) dimers/                          
          trimers including one fragments in MOLFRG, and                        
          b) monomers appearing in such dimers/trimers.                         
          In other words, this is a cross option, to study                      
          interactions between MOLFRG and the rest.                             
        2 modifies the choice of dimers/trimers to those                        
          in which all fragments are listed in MOLFRG                           
          (i.e., option 2 requires also 1, resulting in 3).                     
          In other words, this is an intra option, to study                     
          interactions within MOLFRG.                                           
        4 do not store NFRAG**3 arrays in FMO3, to be used                      
          with MODMOL=2, to reduce memory in very special                       
          cases. No property summary will be provided, just                     
          whatever is printed in SCF for each trimer.                           
        8 do subsystem analysis. See MOLFRG.                                    
                 Default: 0 (do not use MOLFRG)                                 
NFRND   = additive options controlling interface and                            
          compatibility of GAMESS' FMO with other programs.                     
        2 output basis set for each n-mer.  Such an FMO                         
          output can be split with tools/fmo/misc/frgout,                       
          and thus obtained fragment output files can be                        
          read into various GUIs (e.g., MacMolPlt), for                         
          example to plot MOs of individual n-mers (but not                     
          of the whole system), e.g., to help understand an                     
          excited state calculation.                                            
        4 punch normal modes in RUNTYP=FMOHESS for                              
          GUIs (e.g., MacMolPlt) to visualize vibrations.                       
          This also prints a frequency table in the output.                     
        8 write out coordinates                                                 
       III. Parameters defining FMO approximations                              
MODESP = options for ESP calculations.                                          
       0 the original distance definition (uniform),                            
       1 an improved distance definition (many-body                             
         consistent, applied to unconnected n-mers),                            
       2 an improved distance definition (many-body                             
         consistent, applied to all n-mers).                                    
         (default: 0 (FMO2) or 1 (FMO3))                                        
MODGRD =  0 subtract the external potential from the                            
            Lagrangian (default).                                               
          1 do not do that.                                                     
          2 add ESP derivatives (MODESP should be 0)                            
          8 add Mulliken charge derivatives to MODGRD=2                         
         16 do not add HOP derivatives (required for AFO)                       
         32 add CPHF-related terms (known as SCZV) needed                       
            for the fully analytic gradient, which may                          
            be combined with EFP or PCM<1>.                                     
            This option requires MODESP=0 and for MP2                           
            also RESPPC=0.                                                      
            Note that 2+8 terms should be added, too,                           
            so MODGRD=42 (=2+8+32) gives the fully analytic                     
      There are three main usages (some further limitations                     
      are not listed below, e.g., for combinations with PCM                     
      or EFP):                                                                  
         MODGRD=0  gives the least accurate gradient,                           
                   available for almost any FMO method                          
                   (except CIS and when ab initio gradient                      
                   in GAMESS is not available, e.g., CC).                       
         MODGRD=10 is medium accurate, unavailable for CI,                      
                   CC, ROHF and MCSCF.                                          
         MODGRD=42 is analytic, only for RHF, UHF, ROHF,                        
                   RDFT, UDFT, and RMP2.  RMP2 requires                         
      Note that RUNTYP=FMOHESS should use MODGRD=2, and                         
      such runs cannot calculate analytic gradient.                             
      Default: 10 (=2+8, for FMO2) or 0 (for FMO3).                             
RESPAP = cutoff for Mulliken atomic population approx,                          
         namely, usage of only diagonal terms in ESPs.                          
         It is applied if the distance between two monomers                     
         is less than RESPAP, the distance is relative to                       
         van der Waals radii; e.g. two atoms A and B                            
         separated by R are defined to have the distance                        
         equal to R/(RA+RB), where RA and RB are van                            
         der Waals radii of A and B).  RESPAP has no units,                     
         as may be deduced from the formula.                                    
         RESPAP=0.0 disables this approximation.                                
         (default: 0.0)                                                         
RESPPC = cutoff for Mulliken atomic point charge                                
         approximation, namely replacing 2e integral                            
         contributions in ESPs by effective 1e terms).                          
         See RESPAP. (default: 2.0 (FMO2) or 2.5 (FMO3))                        
RESDIM = cutoff for approximating the SCF energy by                             
         electrostatic interaction (1e terms), see RESPAP.                      
         This parameter must be nonzero for ab initio                           
         electron correlation methods. RESDIM=0 disables                        
         this approximation. (default: 2.0 (FMO2) or                            
         RITRIM(1)+RITRIM(3) for FMO3 energy, 0 for FMO3                        
RCORSD = cutoff that is compared to the distance between                        
         two monomers and all dynamic electron correlation                      
         during the dimer run is turned off if the                              
         distance is larger than this cutoff.  RCORSD must                      
         be less than or equal to RESDIM and it affects                         
         only MP2, CC, CI, and TDDFT.                                           
         (default: 2.0 (FMO2), RITRIM(1)+RITRIM(4) for                          
         FMO3 energy, 0 for FMO3 gradient)                                      
RITRIM = an array of 4 thresholds determining neglect of                        
         3-body terms (FMO3 only). The first three are for                      
         uncorrelated trimers and the exact definition can                      
         be found in the source code.  The fourth one                           
         neglects correlated trimers with the separation                        
         larger than the threshold value. RITRIM(4) should                      
         not exceed RITRIM(3).                                                  
         (default: 1.25,-1.0,2.0,2.0, which corresponds to                      
         the medium accuracy with medium basis sets, see                        
SCREEN  = an array of two elements, alpha and beta, giving                      
          the exponent and the multiplicative factor                            
          defining the damping function                                         
          This damping function is used to screen the                           
          potential due to point charges of bond detached                       
          atoms and it can only be applied for RESPPC=-1,                       
          i.e., when ESP is approximated by point charges.                      
          Default: 0,0 (no screening). Other sensible                           
          values are 1,1.                                                       
ORSHFT = orbital shift, the universal constant that                             
         multiplies all projection operators.  The value of                     
         1e+8 was sometimes erroneously quoted instead of                       
         the actual value of 1e+6 in some FMO publications.                     
         (default: 1e+6).                                                       
MAXKND = the maximum number of hybrid orbital sets (one set                     
         is given for each basis set located at the atoms                       
         where bonds are detached).  See also $FMOHYB.                          
         (default: 10)                                                          
MAXCAO = the maximum number of hybrid orbitals in an LMO                        
         set.  (default: 5)                                                     
MAXBND = the maximum number of detached bonds.                                  
         (default: NFG*2+1)                                                     

generated on 7/7/2017