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"""
Grid search for accessible positions
This script is heavily adapted from the `DAC-SIM <https://github.com/hspark1212/DAC-SIM>`_ package. Please cite the original work if you use this script.
References
~~~~~~~~~~~
- Lim, Y., Park, H., Walsh, A., & Kim, J. (2024). Accelerating CO₂ Direct Air Capture Screening for Metal-Organic Frameworks with a Transferable Machine Learning Force Field.
"""
import MDAnalysis as mda
import numpy as np
from ase import Atoms
def get_accessible_positions(
structure: Atoms,
grid_spacing: float = 0.5,
cutoff_distance: float = 10.0,
min_interplanar_distance: float = 2.0,
) -> dict:
# get the supercell structure
cell_volume = structure.get_volume()
cell_vectors = np.array(structure.cell)
dist_a = cell_volume / np.linalg.norm(np.cross(cell_vectors[1], cell_vectors[2]))
dist_b = cell_volume / np.linalg.norm(np.cross(cell_vectors[2], cell_vectors[0]))
dist_c = cell_volume / np.linalg.norm(np.cross(cell_vectors[0], cell_vectors[1]))
plane_distances = np.array([dist_a, dist_b, dist_c])
supercell = np.ceil(min_interplanar_distance / plane_distances).astype(int)
if np.any(supercell > 1):
print(
f"Making supercell: {supercell} to prevent interplanar distance < {min_interplanar_distance}"
)
structure = structure.repeat(supercell)
# get position for grid
grid_size = np.ceil(np.array(structure.cell.cellpar()[:3]) / grid_spacing).astype(
int
)
indices = np.indices(grid_size).reshape(3, -1).T # (G, 3)
pos_grid = indices.dot(cell_vectors / grid_size) # (G, 3)
# get positions for atoms
pos_atoms = structure.get_positions() # (N, 3)
# distance matrix
dist_matrix = mda.lib.distances.distance_array(
pos_grid, pos_atoms, box=structure.cell.cellpar()
) # (G, N) # TODO: check if we could use other packages instead of mda
# calculate the accessible positions
min_dist = np.min(dist_matrix, axis=1) # (G,)
idx_accessible_pos = np.where(min_dist > cutoff_distance)[0]
# result
return {
"pos_grid": pos_grid,
"idx_accessible_pos": idx_accessible_pos,
"accessible_pos": pos_grid[idx_accessible_pos],
"structure": structure,
}
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