Closed AkashHiregange closed 6 months ago
Surely there must be a Numpy function to check if a float is close to an integer within tolerance? Perhaps I expect too much from Numpy though
Ah OK, so perhaps my comment makes no difference. I thought it was a bonding distance cutoff.
From: AkashHiregange @.> Sent: 14 November 2023 15:13 To: logsdail/carmm @.> Cc: Andrew Logsdail @.>; Comment @.> Subject: Re: [logsdail/carmm] New functionality for generating slab consistent bulk model (PR #134)
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@AkashHiregange commented on this pull request.
In carmm/build/slab_consistent_bulk_generator.pyhttps://github.com/logsdail/carmm/pull/134#discussion_r1392759720:
- bulk atoms in a slab structure. This new bulk structure will be consistent with the slab model and the
- computed bulk energy for this structure will help to obtain surface energies that are convergent with
- increasing slab thickness. Further detailed information is available in the following literature article.
- Schultz, Peter A.
- "First-principles calculations of metal surfaces. I. Slab-consistent bulk reference for convergent surface
- properties." Physical Review B 103.19 (2021): 195426.
- How this functionality works:
- the difference between the x,y and z coordinates of an atom and its corresponding periodic image will be a linear
- combination of the cell vectors a,b and c.
- This idea is extended here in case of a slab model where the linear combination check
- is considered only w.r.t to the a and b vectors
- Args:
- slab: ASE Atoms object representing the slab structure
- cutoff_distance: Cutoff distance for identifying neighboring atoms (default is 10.0). This will be used to
This is the distance that is used to check the co-ordination environment of a given atom. For example, the distances between a given atom and all other atoms that lie within a 10 angstrom radius is checked. But since the atoms at the bottom of the slab have no atoms below it, I had to force it check for atoms that have a z-coordinate value great than current atom that is being checked (dist <= cutoff_distance and slab[ind].position[2] / atom_i.position[2] >= 0.9999]). But, I will have a chat with Harry to look into it
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Surely there must be a Numpy function to check if a float is close to an integer within tolerance? Perhaps I expect too much from Numpy though
I tried to search for such functionality within numpy, but couldn't find one.
I tried to search for such functionality within numpy, but couldn't find one.
Fair. I had a look too and failed to find such a routine.
Looks good to me!
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