Clarify argument shift for SlabGenerator.get_slab

[DanielYang59]

Summary

A follow-up PR for #3691.

• Clarify misleading arg name shift for private method SlabGenerator.get_slab
• Fix typing of slab in function center_slab (should be Structure instead of Slab)

Rationale

• This method should be a private method (as per the docstring).
• The arg name shift for SlabGenerator.get_slab corresponds to the desired termination coordinate (instead of the shift vector to get the Slab), which could be misleading:

  pymatgen/pymatgen/core/surface.py

  Line 1087 in 578d29c

  shift (float): The shift value along the lattice c direction in Angstrom.

  
  Which might cause confusion in understanding the implementation:
  

  pymatgen/pymatgen/core/surface.py

  Line 1119 in 578d29c

  frac_coords = np.array(frac_coords) + np.array([0, 0, -shift])[None, :]

Clarify shift attribute of Slab

Similarly, the description of shift attribute of Slab is incorrect, it is NOT the shift but the negative shift.

pymatgen/pymatgen/core/surface.py

Lines 118 to 119 in 578d29c

	shift (float): The shift in the c-direction applied to get the
	termination.

TODO for future PRs

In future PRs

1. Function center_slab:

   pymatgen/pymatgen/core/surface.py

   Lines 759 to 788 in ad6eafe

   	# Get all site indices
   	all_indices = list(range(len(slab)))
   	# Get a reasonable cutoff radius to sample neighbors
   	bond_dists = sorted(nn[1] for nn in slab.get_neighbors(slab[0], 10) if nn[1] > 0)
   	# TODO (@DanielYang59): magic number for cutoff radius (would 3 be too large?)
   	cutoff_radius = bond_dists[0] * 3
   	# TODO (@DanielYang59): do we need the following complex method?
   	# Why don't we just calculate the center of the Slab and move it to z=0.5?
   	# Before moving we need to ensure there is only one Slab layer though
   	# If structure is case 2, shift all the sites
   	# to the other side until it is case 1
   	for site in slab: # DEBUG (@DanielYang59): Slab position changes during loop?
   	# DEBUG (@DanielYang59): sites below z=0 is not considered (only check coord > c)
   	if any(nn[1] >= slab.lattice.c for nn in slab.get_neighbors(site, cutoff_radius)):
   	# TODO (@DanielYang59): the magic offset "0.05" seems unnecessary,
   	# as the Slab would be centered later anyway
   	shift = 1 - site.frac_coords[2] + 0.05
   	slab.translate_sites(all_indices, [0, 0, shift])
   	# Now the slab is case 1, move it to the center
   	weights = [site.species.weight for site in slab]
   	center_of_mass = np.average(slab.frac_coords, weights=weights, axis=0)
   	shift = 0.5 - center_of_mass[2]
   	slab.translate_sites(all_indices, [0, 0, shift])
   	return slab

   a. During the for site in slab: loop, site coordinates would change.
   b. This method to put the Slab to the center seems overly complex, can we just calculate the z-center of the Slab, and move it to z=0.5 (fractional)?
   c. If not b, Sites with z<0 is not considered (it would only move nn[1] >= slab.lattice.c).
   d. A magic number for determining near neighbors by cutoff radius: cutoff_radius = bond_dists[0] * 3.

2. The move_to_other_side method of SlabGenerator:

   pymatgen/pymatgen/core/surface.py

   Lines 1459 to 1473 in ad6eafe

   	# Calculate Slab height
   	height: float = self._proj_height
   	# Scale height if using number of hkl planes
   	if self.in_unit_planes:
   	height /= self.parent.lattice.d_hkl(self.miller_index)
   	# Calculate the moving distance as the fractional height
   	# of the Slab inside the cell
   	# DEBUG(@DanielYang59): the use actually sizes for slab/vac
   	# instead of the input arg (min_slab/vac_size)
   	n_layers_slab: int = math.ceil(self.min_slab_size / height)
   	n_layers_vac: int = math.ceil(self.min_vac_size / height)
   	n_layers: int = n_layers_slab + n_layers_vac
   	frac_dist: float = n_layers_slab / n_layers

   Clean up core.surface comments and docstrings #3691 (comment)

3. Currently there are three very similar methods/functions that need to clarify in docstring:
   a. get_slab of SlabGenerator: The actual method to generate Slab, should be a private method (as per the docstring, but have already been used externally).
   b. get_slabs of SlabGenerator: A wrapper method on top of get_slab to generate possible shifts and then call get_slab.
   c. generate_all_slabls: A wrapper function on top of get_slabs, which generate slabs up to a given Miller index.

Next up: Fix some Slab related issues

Don't think I could resolve them in one shot, but good to collect them:

• Atom position overlap after repairing the slab #2591
• Thickness of generated slab is smaller than min_slab_size #3411
• Inconsistency in oriented_unit_cell when generating (001)/(010)/(100) surface #3412
• Create monolayer MoS2 from the bulk. #3682

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[DanielYang59]

I would need discussion/confirmation/suggestion on these proposed changes, as they more or less seem to introduce functional changes. @janosh @shyuep

Also trying to ping the original author (I guess) @CifLord in case you have any comment 😃

[janosh]

thanks @DanielYang59 and sorry for the slow reply. this all looks good. just had 1 question

[janosh]

Sorry it seems I wasn't making my intention clear enough, as I haven't actually started making changes yet. I proposed #3748 (comment) but I want to hear about your comments/suggestions before getting my hands on it, because most of them seem more or less breaking (breaking in a way to fix issues, not for enhancement).

that i understood. but i was tentatively advising against all but one of the breaking changes you suggested (the one you clearly identified as a bug). how much does that leave to change here?

[DanielYang59]

@janosh I decide to minimize (potentially) breaking changes and just clarify in the docstring.

[janosh]

thanks @DanielYang59, lgtm. just a conflict to resolve

[DanielYang59]

@janosh thanks for reviewing. Resolved

I begin to notice this CI failure about 12 hours ago:

error: Failed to download distributions
  Caused by: Failed to fetch wheel: chgnet==0.3.7
  Caused by: Failed to build: `chgnet==0.3.7`
  Caused by: Build backend failed to build wheel through `build_wheel()` with exit status: 1

--- stderr:
chgnet/graph/cygraph.c:1238:10: fatal error: fast_converter_libraries/create_graph.c: No such file or directory
 1238 | #include "fast_converter_libraries/create_graph.c"
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
error: command '/usr/bin/gcc' failed with exit code 1

Is this some issue from the latest release 0.3.7 of chgnet?