data.oc.scripts.precompute_sample_structures#
This submodule contains the scripts that the we used to sample the adsorption structures.
Note that some of these scripts were taken from [GASpy](ulissigroup/GASpy) with permission of author.
Attributes#
Functions#
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Enumerate all the symmetrically distinct surfaces of a bulk structure. It |
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There are many ways to define a bulk unit cell. If you change the unit cell |
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This function figures out whether or not an pymatgen.Structure object has |
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Flips an atoms object upside down. Normally used to flip surfaces. |
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Module Contents#
- data.oc.scripts.precompute_sample_structures.__authors__ = ['Kevin Tran', 'Aini Palizhati', 'Siddharth Goyal', 'Zachary Ulissi']#
- data.oc.scripts.precompute_sample_structures.__email__ = ['ktran@andrew.cmu.edu']#
- data.oc.scripts.precompute_sample_structures.BULK_PKL = '/fill/this/in/with/path/to/bulk/pkl/file'#
- data.oc.scripts.precompute_sample_structures.MAX_MILLER = 2#
- data.oc.scripts.precompute_sample_structures.enumerate_surfaces_for_saving(bulk_atoms, max_miller=MAX_MILLER)#
Enumerate all the symmetrically distinct surfaces of a bulk structure. It will not enumerate surfaces with Miller indices above the max_miller argument. Note that we also look at the bottoms of surfaces if they are distinct from the top. If they are distinct, we flip the surface so the bottom is pointing upwards.
- Parameters:
enumerate (bulk_atoms ase.Atoms object of the bulk you want to) – surfaces from.
surfaces (max_miller An integer indicating the maximum Miller index of the) – you are willing to enumerate. Increasing this argument will increase the number of surfaces, but the surfaces will generally become larger.
- Returns:
- pymatgen.Structure
objects for surfaces we have enumerated, the Miller indices, floats for the shifts, and Booleans for “top”.
- Return type:
all_slabs_info A list of 4-tuples containing
- data.oc.scripts.precompute_sample_structures.standardize_bulk(atoms)#
There are many ways to define a bulk unit cell. If you change the unit cell itself but also change the locations of the atoms within the unit cell, you can get effectively the same bulk structure. To address this, there is a standardization method used to reduce the degrees of freedom such that each unit cell only has one “true” configuration. This function will align a unit cell you give it to fit within this standardization.
- Arg:
atoms ase.Atoms object of the bulk you want to standardize
- Returns:
standardized_struct pymatgen.Structure of the standardized bulk
- data.oc.scripts.precompute_sample_structures.is_structure_invertible(structure)#
This function figures out whether or not an pymatgen.Structure object has symmetricity. In this function, the affine matrix is a rotation matrix that is multiplied with the XYZ positions of the crystal. If the z,z component of that is negative, it means symmetry operation exist, it could be a mirror operation, or one that involves multiple rotations/etc. Regardless, it means that the top becomes the bottom and vice-versa, and the structure is the symmetric. i.e. structure_XYZ = structure_XYZ*M.
In short: If this function returns False, then the input structure can be flipped in the z-direction to create a new structure.
- Arg:
structure A pymatgen.Structure object.
- Returns
A boolean indicating whether or not your ase.Atoms object is symmetric in z-direction (i.e. symmetric with respect to x-y plane).
- data.oc.scripts.precompute_sample_structures.flip_struct(struct)#
Flips an atoms object upside down. Normally used to flip surfaces.
- Arg:
atoms pymatgen.Structure object
- Returns:
- flipped_struct The same ase.Atoms object that was fed as an
argument, but flipped upside down.
- data.oc.scripts.precompute_sample_structures.precompute_enumerate_surface(bulk_database, bulk_index, opfile)#
- data.oc.scripts.precompute_sample_structures.s#