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.
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
andvdw
.dis
measures the distance between two nuclei whereascov
measures the distance from the edge of the spheres of covalent radius andvdw
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 :term:`model system<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
and2
- clust_rad
- The radius in Angstrom used to generate the cluster which will constitute the
:term:`real system<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
The input structure is the same as for config
.
- mol_file
- File name for the .xyz file containing the inital position of the :term:`model
system<Model system>`. Default:
mol.init.xyz
- shell_file
- File name for the .xyz file containing the molecules surrounding the
:term:`model system<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 :term:`MECI`. "1" for yes "0 for no. Default:
0
- sigma
- The Lagrangian multiplier for the penalty function method for the location of
:term:`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
andmolcas
. Default:gaussian
- low_level
- The program used for the low level calculation. The options are
gaussian
,dftb
,turbomole
andmolcas
. Default:gaussian