Input File Format¶

“Skeleton-RHF”
OpenFMO

“Skeleton-RHF”¶

Here, we show an example of a “skeleton-RHF” input file used for the RHF energy calculation of one water molecule with the 6-31G(d) basis sets:

6-31G*
0 3
O  10.438  -22.339  1.220
H  11.395  -22.339  1.220
H  10.198  -21.412  1.220

The input file format is schematically written by

Name_of_Basis_Sets
Molecular_Charge Number_of_Atoms
Atomic_Name X Y Z
Atomic_Name X Y Z
Atomic_Name X Y Z
...

**Table 2.** Explanation of Input File Format of “Skeleton-RHF” Code¶
Line	Column	Description	Acceptable Variables	Note
1	1	Name of Basis Sets	sto-3g, 6-31g, 6-31g, 6-31g*	Both capital and lower-case letters are O.K.
2	1	Molecular charge	Integer values	Only closed-shell
2	2	Number of atoms of molecule	Integer values
4-	1	Atomic name	Up to Third-row Atoms (namely, H - Ar)	Both capital and lower-case letters are O.K.
4-	2-4	Cartesian coordinates	Floating-point numbers	In Angstrom

OpenFMO adopts the same input-file format as the FMO calculations implemented in GAMESS ab initio quantum chemistry package. Since some of the input groups used in GAMESS are directory used in the OpenFMO, the GAMESS documentations, Input Description and Further Information , are also useful for the users of OpenFMO. Table 3 lists the input groups used in OpenFMO. Both lower-case and capital letters can be used to write the input groups and their options in the input files for OpenFMO.

**Table 3.** Input Groups and Their Options Used in OpenFMO¶
name	function	options
$CONTRL	chemical control data	maxit, nprint, itol, icut
$BASIS	basis set	ngauss, gbasis, ndfunc, npfunc
$INTGRL	two-electron integrals	nintmx, nintic
$GDDI	MPI dynamic process management	ngroup, niogroup, nioprocs
$SCF	SCF control	diis, npunch, conv
$FMOPRP	FMO convergers	sccconv, maxscc
$FMOXYZ	atomic coordinates for FMO	Name, ZNUC, X, Y, Z
$FMO	Define FMO fragments	nfrag, icharg, indat
$FMOLMO	localized MO for FMO boundaries	Refer to “HMOs.txt” distributed by GAMESS
$FMOBND	FMO bond cleavage definition

Simple Example (Glycylglycine)¶

Here, we show an example of an OpenFMO input file used for the FMO-RHF/STO-3G energy calculation of one glycylglycine. Figure 2 illustrates the structure and its fragmentation points:

Fragment 1 includes N1, H2, H3, C4, H5, and H6 atoms
Fragment 2 includes C7, O8, N9, H10, C11, H12, and H13 atoms.
Fragment 3 includes C14, O15, O16, and H17 atoms.
The alpha-carbon atoms (C4 and C11) are treated as bond-detached atoms (BDAs).
Thus, the detached bonds are assigned to the atoms on the other side (C7 and C14), which are called bond-attached atoms (BAAs).

$FMOBND group in the input file tells OpenFMO program the way of the bond detachments. In the input file, the number of server groups (See Figure 1) is set to 1 through the niogroup option in $GDDI group. As mentioned in Command Line Options, the command-line argument -niogroup can also set up the number of server groups. Similarly, the command-line argument -nioprocs can also set up the size of each server groups, which is defined by the nioprocs option in $GDDI group.

Figure 2. Glycylglycine: (a) Structure and Atom Numbering (b) Fragmentation

$gddi niogroup=1 nioprocs=1 $end
$fmo nfrag=3 ICHARG(1)= 0,0,0
INDAT(1)=0, 1, -6, 0, 7, -13, 0, 14, -17,0  $end
$basis gbasis=sto ngauss=3 $end
$fmoxyz
N  7.0   3.5584    0.0170    0.1638
H  1.0   3.6446   -0.8687   -0.3332
H  1.0   3.4912   -0.2124    1.1546
C  6.0   2.3540    0.7121   -0.2674
H  1.0   2.2350    1.6486    0.2858
H  1.0   2.4304    0.9444   -1.3339
C  6.0   1.1558   -0.1725    0.0097
O  8.0   1.1192   -0.9807    0.9350
N  7.0   0.1194    0.0665   -0.8809
H  1.0   0.2322    0.7805   -1.5946
C  6.0  -1.1505   -0.6217   -0.8231
H  1.0  -0.9953   -1.6290   -0.4254
H  1.0  -1.5383   -0.6729   -1.8442
C  6.0  -2.1620    0.0850    0.0422
O  8.0  -3.2962   -0.3376    0.2304
O  8.0  -1.6980    1.2320    0.5903
H  1.0  -2.3743    1.6726    1.1478
$end
$FMOLMO
STO-3G 5 5
1 0  -0.117784    0.542251    0.000000    0.000000    0.850774
0 1  -0.117787    0.542269    0.802107    0.000000   -0.283586
0 1  -0.117787    0.542269   -0.401054   -0.694646   -0.283586
0 1  -0.117787    0.542269   -0.401054    0.694646   -0.283586
0 1   1.003621   -0.015003    0.000000    0.000000    0.000000
$end
$FMOBND
  -4    7 STO-3G
 -11   14 STO-3G
$end

$CONTRL Group ¶

**Table 4.** Options of $CONTRL Group¶
Option	Acceptable Variables	Explanation	Note
maxit =	positive integer	Maximum number of SCF iteration cycles	default: maxit = 30
nprint =	integer value	Print control flag	default: nprint = 0
itol =	positive integer	primitive cutoff factor 10**(-n)	default: itol = 20
icut =	positive integer	2e-integral cutoff factor 10**(-n)	default: icut = 12

$BASIS Group ¶

OpenFMO can treat minimum and double-zeta Gaussian basis functions of up to third-row atoms, including STO-3G, 6-31G, 6-31G(d) and 6-31G(d,p).

**Table 5.** Options of $BASIS Group¶
Option	Acceptable Variables	Explanation	Note
ngauss =	3 (for STO-3G) or 6 (for 6-31G)	the number of Gaussians	default: ngauss = 3
gbasis =	sto (STO-3G) or n31 (for 6-31G)	basis function	default: gbasis=sto
ndfunc =	0 (for STO-3G and 6-31G) or 1 ( for 6-31G* and 6-31G**)	number of heavy atom polarization functions to be used	default: ndfunc = 0
npfunc =	0 (for STO-3G, 6-31G, and 6-31G) or 1 (for 6-31G*)	number of light atom, p type polarization	default: npfunc = 1

$INTGRL Group ¶

**Table 6.** Options of $INTGRL Group¶
Option	Acceptable Variables	Explanation	Note
nintmx =	positive integer	Maximum no. of integrals in a record block	default: nintmx = 15000
nintic =	0 or positive integer	buffer size / processes in MB	default: nintic = 512; See the command-line argument -B in Command Line Options.

$GDDI Group ¶

$GDDI group tells the OpenFMO program how to manage the MPI dynamic processes in FMO calculations. However, as described in Command Line Options, users had better use the command-line options, -ng, -niogroup, and -nioprocs rather than $GDDI group in the input file in order to manage the MPI dynamic processes.

**Table 7.** Options of $GDDI Group¶
Option	Acceptable Variables	Explanation	Note
ngroup	positive integer	Number of worker groups	default: ngroup = 1; OpenFMO prefers this option to the -ng command-line argument
niogroup	positive integer	Number of server groups	default: niogroup=1; OpenFMO prefers this option to the -niogroup command-line argument
nioprocs	positive integer	Size of each server group	default: nioprocs=1; OpenFMO prefers this option to the -nioprocs command-line argument

$SCF Group ¶

**Table 8.** Options of $SCF Group¶
Option	Acceptable Variables	Explanation	Note
diis =	false or true	Pulay’s DIIS interpolation	default: diis=true
npunch =	0, 1, or 2	option for output
conv =	positive integer	SCF density convergence criteria 10**(-n)	default: conv=7

$FMOPRP Group ¶

**Table 9.** Options of $FMOPRP Group¶
Option	Acceptable Variables	Explanation	Note
sccconv =	positive integer	monomer SCF energy convergence criterion; 10**(-n)	default: sccconf = 7
maxscc =	positive integer	the maximum number of monomer SCF iterations	default: maxscc=30

$FMOXYZ Group ¶

$FMOXYZ group defines the molecular data as follows:

$fmoxyz
Name ZNUC X Y Z
Name ZNUC X Y Z
Name ZNUC X Y Z
...
$end

NAME = atomic name
ZNUNC = nuclear charge
X, Y, Z = Cartesian coordinates in Angstrom

$FMO Group ¶

**Table 10.** Options of $FMO Group¶
Option	Acceptable Variables	Explanation	Note
nfrag =	positive integer	number of distinct fragments present	default: nfrag = 1
icharg(1) =	an array of positive integers	an array of charges on the fragments	default: all 0 charges
indat(1) =	Described below	an array assigning atoms to fragments

The indat option in $FMO group tells OpenFMO program an array assigning atoms to fragments. We would like to cite its explanation from the GAMESS documentation, Input Description :

INDAT(i)=m assigns atom i is to fragment m.

INDAT(i) must be given for each atom.

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.

$FMOBND Group ¶

The atom indices involved in the bond detachment are given, in pairs for each bond. Bonds are always detached between fragments.

$fmobnd
-I1  J1  NAM1
-I2  J2  NAM2
-I3  J3  NAM3
...
$end

I and J are positive integers giving absolute atom indices. NAMs are hybrid orbital set names, defined in $FMOLMO group. Each line is allowed to have different set of NAMs, which can happen if different type of bonds are detached.

Note that OpenFMO code definitely reads $FMOBND group. If your FMO calculation does NOT need any bond detachement, its input file has to include a blank line sandwiched between $fmobnd and $end keywords (see subsection TCNE-(Benzene)8-TCNE in Samples.):

$fmobnd

$end

$FMOLMO or $FMOHYB Group ¶

Hybrid orbitals are used to describe bond detachment when dividing a molecule into fragments. These are the familiar sp3 orbitals for Carbon atom, plus the 1s core orbital.

OpenFMO can treat STO-3G, 6-31G, 6-31G(d), and 6-31G(d,p) basis sets. Therefore, you can extract the orbitals (NAM=STO-3G, 6-31G, 6-31G*, or 6-31G**) to be put into $FMOLMO group taken from “HMOs.txt” distributed by GAMESS.

Note that OpenFMO code definitely reads $FMOLMO or $FMOHYB group. Even if your FMO calculation does NOT need any bond detachement, you have to write some hybrid molecular orbitals (HMOs) taken from “HMOs.txt” for $FMOLMO/$FMOHYB group in its input file. However, the HMOs are anything O.K. and the OpenFMO code does not use them in the FMO calculation. See subsection TCNE-(Benzene)8-TCNE in Samples.