Film Generation Algorithm (FGA)
Latest edits: Kaustubh Sawant (21st August 2022)
FGA consists of tools that can stack films ontop of atom slabs such that the strain in non-pseudomorphic, periodic overlayer films is minimized.
Requirements
Installation
Install using pip
pip install fgaAlternatively, you can just add ./fga to your $PYTHONPATH. (not recommended)
export PYTHONPATH=$PYTHONPATH:"<path_to_fga>"Examples
- All the possible overlayer structures for given set of films and substrates can be constructed using [run_fga] Please note that the film is slightly distorted to fit on the substrate since there is almost never a perfect match.
#Bash
run_fga -s <path_to_substrates_POSCAR> -f <path_to_films_POSCAR>The above command will create a folder called Generated_Films which will have a tree of folders for each possible configration.
Theoritically there are infinite possible structures. For practical purposes we have set a few constraints which are discussed in later sections.
- The best structure can be found using a simple function get_best_cell()
#python
from fga import get_best_cell
unit_substrate_path = './Substrates/POSCAR_Au'
unit_film_path = './Films/POSCAR_ZnO'
best_cell_atoms = get_best_cell(unit_substrate_path,unit_film_path)Parameters
1. Film Search Space
--film_search, -film_search, -fs,
type: int, default: 4,
Defines repetition of the film unit cell
2. Substrate Search Space
--sub_search, -sub_search, -ss,
type: int, default: 4,
Defines repetition of the substrate unit cell
3. Maximum size of cell diagonal
--max_size, -max_size, -msize,
type: float, default: 40,
Max diagonal distance of the cells that are created (a way to limit size of cell)
4. Maximum allowed atoms in the final structure
--max_num_of_atoms, -max_num_of_atoms, -matoms,
type: int, default: 200,
Maximum number of atom you want in the system -- will filter out big cells
5. Distance between film and substrate
--buffer, -buffer, -b,
type: float, default: 2,
This is the distance between the lowest atoms in your film and the highest atoms in your substrate
6. The vacuum between z images
--vacuum, -vacuum, -v,
type: float, default: 10,
7. The maximum ratio change
--max_ratio_change, -max_ratio_change, -mrc,
type: float, default: 0.5
This is the range of structures that will be looked at on each side of the sturcutre that will have the minimum strain
8. Maximum length ratio
--max_length_ratio, -max_length_ratio, -ml',
type: float, default: 1.5,
This is the max ratio between the x vector and the y vector (and its reciprocal) that is allowable.
This prevents dealing with really thin cells which are hard to work with (though they may be useful cells).
Cite
Original idea by Joseph Kubal and implemented by Kaustubh Sawant