New functionality for generating slab consistent bulk model

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Codecov Report

Attention: Patch coverage is 98.38710% with 1 lines in your changes are missing coverage. Please review.

Project coverage is 88.23%. Comparing base (2dc2644) to head (7f9bcb2).

Files	Patch %	Lines
carmm/build/slab_consistent_bulk_generator.py	97.50%	1 Missing :warning:

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[OscarvanVuren]

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

[logsdail]

Ah OK, so perhaps my comment makes no difference. I thought it was a bonding distance cutoff.

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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.

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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:
• 1. 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.
• 2. 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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[AkashHiregange]

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.

[OscarvanVuren]

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.

[GaryLZW]

Looks good to me!