2. Input file description¶

fromage uses input files at two points of its execution. During the preparatory calculation (using fro_prep_calc.py), the config file is required. During the actual geometry optimisation (run_fromage.py), the file fromage.in is read if present.

2.1. config file¶

All fromage input files follow the same input structure. The order of the keywords is irrelevant and blank lines are ignored. The keyword is stated and then its value(s) after any number of whitespaces. Therefore:

bond_thresh 1.9

Is the same as:

bond_thresh      1.9

Below are listed the most important keywords available.

name: The name of your calculation. Default: fromage_calc
a_vec, b_vec and c_vec: The lattice vectors in Angstrom. This section has no default value. Example:

a_vec        8.9638004303         0.0000000000         0.0000000000
b_vec        0.0000000000        10.5200004578         0.0000000000
c_vec       -3.8748910079         0.0000000000        10.7924653741

vectors_file: Alternatively the vectors can be stored in a file (called e.g. vectors) of the form:

8.9638004303         0.0000000000         0.0000000000
0.0000000000        10.5200004578         0.0000000000
-3.8748910079         0.0000000000         10.7924653741

In which case the file name should be specified in the config file:

vectors_file vectors

cell_file: The file containing the atomic positions in the unit cell in .xyz format. Default: cell.xyz
high_pop_file: The file containing the population analysis used for the embedding of mh. Default: gaussian_h.log
high_pop_program: The program used to calculate the above file. Default: gaussian
high_pop_method: The method of population analysis. “Mulliken” or “ESP”. Default: ESP
low_pop_file: The file containing the population analysis used for the embedding of ml. Default: gaussian_l.log
low_pop_program: The program used to calculate the above file. Default: gaussian
low_pop_method: The method of population analysis. “Mulliken” or “ESP”. Default: ESP
bond_thresh: The distance between two atoms in Angsrom below which fromage will consider the atoms to be bonded together. The definition of bond_thresh can be altered by using the keyword bonding. Default: 1.7
bonding: The method which determines whether two atoms are bonded. The options are dis, cov and vdw. dis measures the distance between two nuclei whereas cov measures the distance from the edge of the spheres of covalent radius and vdw from the edge of the sphere of van der Waals radius. Default: dis
atom_label: The number of the atom in the cell_file which belongs to the molecule which will become the model system. Several atoms can be specified and must be separated by whitespaces, however they must not belong to the same molecule. Default: 1
ewald: Whether or not to use the Ewald embedding. To turn off, use “false”, “no”, “off”, “zero”, “none” or “nan” or any capitalisations. Default: off
nchk: The number of random points sampled around the model system by Ewald to check the accuracy of the fit. Default: 1000
nat: The number of atoms included in the fixed charge region generated spherically by Ewald. Default: 500
an, bn and cn: Multiplications of the unit cell along each cell direction to generate the Ewald supercell. The cell is multiplied 2N times per direction (N positive and N negative). Default: 2, 2 and 2
clust_rad: The radius in Angstrom used to generate the cluster which will constitute the real system. The cluster includes all molecules which fall within the threshold distance from any of the atoms of the central region. Default: 5
self_consistent: Whether or not to use the Self Consistent Ewald Embedding. Be sure to also turn on ewald. Default: off
sc_temp: The template file for the self consistent population analyses. Default: sc_temp.template
dev_tol: The convergence threshold for the self consistent loop. This corresponds to the average deviation between two successive steps of the loop. Units in \(e^-\) Default: 0.001
damping: Damping factor for the self-consistent loop to solve certain convergence problems. Choose a value between 0 to 1 with 0 being no damping and 1 being complete damping (won’t get you anywhere). Default: 0
print_tweak: Whether or not to print the tweaked version of the cell with the selected molecule(s) completed and the whole cell centred around its centroid. This is useful for debugging and more involved analysis. Default: off

2.2. fromage.in file¶

The input structure is the same as for config.

mol_file: File name for the .xyz file containing the inital position of the model system. Default: mol.init.xyz
shell_file: File name for the .xyz file containing the molecules surrounding the model system. Default: shell.xyz
out_file: File name for the output file containing the geometry optimisation information. Default: fromage.out
bool_ci: Whether or not to optimise for MECI. “1” for yes “0 for no. Default: 0
sigma: The Lagrangian multiplier for the penalty function method for the location of MECI. Only use if bool_ci is on. Defualt: 3.5
high_level: The program used for the high level calculation. The options are gaussian, dftb, turbomole and molcas. Default: gaussian
low_level: The program used for the low level calculation. The options are gaussian, dftb, turbomole and molcas. Default: gaussian