$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. (experimental) 2 Add octupole energy into electrostatic energy 4 use Hui Li's density based multipole expansion 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., LAYER(1)=1,1,1,...,1 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 taken): 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 "-"! Example: 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 dimer. 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 calculations: 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) coefficient. = 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 recommended. 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 gradient. 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 RESPCC=0. 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 gradient) 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 REFS.DOC). SCREEN = an array of two elements, alpha and beta, giving the exponent and the multiplicative factor defining the damping function 1-beta*exp(-alpha*R**2). 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