Command Line Tools

We have created simple command line tools as a wrapper to the Add Modifiers so they can be used independently.

Add Mono

add_mono -s <path_to_surface> -a <adsorbate|path> -sc <surface coordination> -aa <adsorbate identity>

# Example: Only unconstrained atoms are used as surface atoms. For complex surface determination, use py API
add_mono -s POSCAR_Pt -a OH -sc 1 2 3 -aa O

Add Bi

Base: Add Bidentate

add_bi -s <path_to_surface> -a <adsorbate|path> -sc <surface coordination> -aa <adsorbate identity>

# Example: Only unconstrained atoms are used as surface atoms. For complex surface determination, use py API
add_bi -s POSCAR_Pt -a HCOO -sc 1 2 3 -aa O

Args for add_bi
-surface / -s	str	Path to surface atoms objects to adsorb
-adsorbate / -a	str	Adsorbate name or path to atoms object
-ads_atom / -aa	str	Atom through which the adsorbate attaches to the surface
-surf_coord / -sc	int	Coordination of surface atoms: e.g., 1-top, 2-bridge, …
-surf_sym / -ss	str	Symbols of atoms that can adsorb
-unique / -u	str	Whether to check if the structures are repeated
-max_bond_ratio / -mbr	float	Allowable tolerance between bonds
-max_bond / -mb	float	Fixed allowable bond distance
–add_ads_error / -ads_err	float	Allowable distance between two sites for adsorption
–norm_method / -norm_method	str	Method to calculate normals