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Clarify argument shift for SlabGenerator.get_slab #3748

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Jun 3, 2024
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65e3ec8
put `is_symmetric/polar` next to `property`
DanielYang59 Apr 12, 2024
90ef691
BREAKING: reverse `get_slab` shift direction
DanielYang59 Apr 12, 2024
185a79c
clarify `shift` for single atom
DanielYang59 Apr 12, 2024
f1d5433
use `isclose` to determine overlap atoms
DanielYang59 Apr 12, 2024
86bbc34
correct tolerance unit
DanielYang59 Apr 12, 2024
34c05e7
Merge branch 'master' into core-surface
DanielYang59 Apr 12, 2024
a7f7dc0
Revert "put `is_symmetric/polar` next to `property`"
DanielYang59 Apr 13, 2024
8c78e43
reapply docstring changes
DanielYang59 Apr 13, 2024
a787580
Merge branch 'master' into core-surface
DanielYang59 Apr 13, 2024
e57fc99
Merge branch 'master' into core-surface
DanielYang59 Apr 20, 2024
7c0a13d
Merge branch 'master' into core-surface
DanielYang59 Apr 21, 2024
c7420cf
use `isclose` to check close
DanielYang59 Apr 22, 2024
b4627e9
fix typo in tag
DanielYang59 Apr 22, 2024
dbd5d3a
Merge branch 'master' into core-surface
DanielYang59 Apr 23, 2024
6ac9530
Merge branch 'master' into core-surface
DanielYang59 Apr 29, 2024
93ef095
Merge branch 'master' into core-surface
DanielYang59 May 1, 2024
4be466c
remove debug tag
DanielYang59 May 1, 2024
16b1999
pre-commit auto-fixes
pre-commit-ci[bot] May 1, 2024
28a7c93
Merge branch 'master' into core-surface
DanielYang59 May 2, 2024
c7f0d32
make `center_slab` very simple
DanielYang59 May 3, 2024
f45c386
Failed: make center_slab and get_slab_regions methods for `Slab`
DanielYang59 May 3, 2024
8009dd7
Merge branch 'master' into core-surface
DanielYang59 May 3, 2024
4e801cf
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DanielYang59 May 4, 2024
81f441a
Merge branch 'master' into core-surface
DanielYang59 May 12, 2024
7d0871c
revert deprecation of `center_slab` function
DanielYang59 May 12, 2024
50bf70a
revert "overlap position check with isclose"
DanielYang59 May 12, 2024
8541a83
revert deprecation of center_slab and get_slab_regions
DanielYang59 May 12, 2024
60271c3
revert changes for `center_slab` function
DanielYang59 May 12, 2024
b138d18
recover docstring
DanielYang59 May 12, 2024
20aca0b
rename slab to struct (type is Structure)
DanielYang59 May 13, 2024
6c2803c
revert adding minus sign
DanielYang59 May 13, 2024
df7f0f9
fix slab type
DanielYang59 May 13, 2024
bb85596
Merge branch 'master' into core-surface
DanielYang59 May 13, 2024
06b2410
keep shift def consistent (need clarify)
DanielYang59 May 13, 2024
7f552c8
unify usage of shift outside Slab
DanielYang59 May 13, 2024
01a9458
fix unit test
DanielYang59 May 13, 2024
0a33ada
add missing minus sign for single atom shift
DanielYang59 May 13, 2024
d75ee61
[need confirm] fix test for coh-interface
DanielYang59 May 13, 2024
a77d6bd
add TODO tag
DanielYang59 May 13, 2024
71e102f
clarify shift definition
DanielYang59 May 13, 2024
3d664d2
revert ALL change related to the direction of shift
DanielYang59 May 13, 2024
adc6e60
rename arg shift to termination
DanielYang59 May 13, 2024
6703c95
tweak comments
DanielYang59 May 13, 2024
e0fc5f3
clarify `shift` attrib in `Slab`
DanielYang59 May 13, 2024
9cc5a04
clarify magic number
DanielYang59 May 13, 2024
79430a6
simplify doc
DanielYang59 May 13, 2024
d50328a
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DanielYang59 May 14, 2024
33fbd3e
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DanielYang59 May 14, 2024
b72ab44
Merge branch 'master' into core-surface
DanielYang59 May 14, 2024
28e20b1
Merge branch 'master' into core-surface
DanielYang59 May 16, 2024
b607536
reuse `center_slab` func
DanielYang59 May 16, 2024
191b959
remove unneeded TODO tag
DanielYang59 May 16, 2024
5384a27
Merge branch 'master' into core-surface
DanielYang59 May 17, 2024
e38efdb
Merge branch 'master' into core-surface
DanielYang59 May 18, 2024
ba4f83a
revert shift to termination rename
DanielYang59 May 18, 2024
c4f871b
remove finished TODO tag
DanielYang59 May 18, 2024
b887a5b
Merge branch 'master' into core-surface
DanielYang59 May 25, 2024
8413745
Merge branch 'master' into core-surface
DanielYang59 Jun 1, 2024
b423716
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DanielYang59 Jun 1, 2024
b0b4ac8
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janosh Jun 3, 2024
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8 changes: 4 additions & 4 deletions pymatgen/analysis/interfaces/coherent_interfaces.py
Original file line number Diff line number Diff line change
Expand Up @@ -133,11 +133,11 @@ def _find_terminations(self):
film_slabs = film_sg.get_slabs()
sub_slabs = sub_sg.get_slabs()

film_shifts = [s.shift for s in film_slabs]
film_terminations = [label_termination(s) for s in film_slabs]
film_shifts = [slab.shift for slab in film_slabs]
film_terminations = [label_termination(slab) for slab in film_slabs]

sub_shifts = [s.shift for s in sub_slabs]
sub_terminations = [label_termination(s) for s in sub_slabs]
sub_shifts = [slab.shift for slab in sub_slabs]
sub_terminations = [label_termination(slab) for slab in sub_slabs]

self._terminations = {
(film_label, sub_label): (film_shift, sub_shift)
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