Symmetry Operations on Cell not working

[atbug]

I have already avoided using spglib_jll 2.2.0. The following code is directly copied from tests.

pkg> add Spglib spglib_jll@2.1.0
   Resolving package versions...
  [f761d5c5] + Spglib v0.9.3
⌃ [ac4a9f1e] + spglib_jll v2.1.0+0
⌅ [80545937] + CrystallographyCore v0.3.3
  [f761d5c5] + Spglib v0.9.3
  [6ec83bb0] + StructEquality v2.1.0
  [8e1ec7a9] + SumTypes v0.5.5
⌃ [ac4a9f1e] + spglib_jll v2.1.0+0
        Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`
Precompiling project...
  2 dependencies successfully precompiled in 3 seconds. 92 already precompiled.

julia> using Spglib

julia> lattice = [[7.17851431, 0, 0], [0, 3.99943947, 0], [0, 0, 8.57154746]]
3-element Vector{Vector{Float64}}:

 [7.17851431, 0.0, 0.0]
 [0.0, 3.99943947, 0.0]
 [0.0, 0.0, 8.57154746]

julia> positions = [
           [0.0, 0.84688439, 0.1203133],
           [0.0, 0.65311561, 0.6203133],
           [0.0, 0.34688439, 0.3796867],
           [0.0, 0.15311561, 0.8796867],
           [0.5, 0.34688439, 0.1203133],
           [0.5, 0.15311561, 0.6203133],
           [0.5, 0.84688439, 0.3796867],
           [0.5, 0.65311561, 0.8796867],
       ]
8-element Vector{Vector{Float64}}:
 [0.0, 0.84688439, 0.1203133]
 [0.0, 0.65311561, 0.6203133]
 [0.0, 0.34688439, 0.3796867]
 [0.0, 0.15311561, 0.8796867]
 [0.5, 0.34688439, 0.1203133]
 [0.5, 0.15311561, 0.6203133]
 [0.5, 0.84688439, 0.3796867]
 [0.5, 0.65311561, 0.8796867]

julia> atoms = fill(8, length(positions))
8-element Vector{Int64}:
 8
 8
 8
 8
 8
 8
 8
 8

julia> cell = Cell(lattice, positions, atoms)
SpglibCell{Float64, Float64, Int64, Any}
 lattice:
   7.17851431  0.0  0.0
   0.0  3.99943947  0.0
   0.0  0.0  8.57154746
 8 atomic positions:
   0.0  0.84688439  0.1203133
   0.0  0.65311561  0.6203133
   0.0  0.34688439  0.3796867
   0.0  0.15311561  0.8796867
   0.5  0.34688439  0.1203133
   0.5  0.15311561  0.6203133
   0.5  0.84688439  0.3796867
   0.5  0.65311561  0.8796867
 8 atoms:
   8  8  8  8  8  8  8  8


julia> primitive_cell = find_primitive(cell)
Unreachable reached at 0x7fa4b5c87ac3

Julia info:

julia> versioninfo()
Julia Version 1.10.0
Commit 3120989f39b (2023-12-25 18:01 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 40 × Intel(R) Xeon(R) Gold 6230 CPU @ 2.10GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, cascadelake)
  Threads: 1 on 40 virtual cores
Environment:
  JULIA_PKG_USE_CLI_GIT = true

[singularitti]

Hi @atbug, I am having no issue running this example:

julia> find_primitive(cell)
SpglibCell{Float64, Float64, Int64, Any}
 lattice:
   3.589257155  3.589257155  0.0
   -1.999719735  1.999719735  0.0
   0.0  0.0  8.57154746
 4 atomic positions:
   0.15311560999999996  0.84688439  0.1203133
   0.34688439000000004  0.65311561  0.6203133
   0.65311561  0.34688439000000004  0.3796867
   0.84688439  0.15311560999999996  0.8796867
 4 atoms:
   8  8  8  8

So I guess it may be some problem with spglib itself. Let use debug it step by step:

1. Have you tried uninstalling and reinstalling Spglib.jl and spglib_jll.jl?
2. Have you tried installing the Python Spglib and run the same example?
3. Can you run julia --bug-report=rr-local <your code script> to let us see the detailed bug report?

You can use this package also for debugging your own Julia code locally. Use --bug-report=rr-local to record a trace, and replay() to replay the latest trace.

For example, if you have a script in a project that you'd like to trace, run julia --bug-report=rr -- --project=foo run.jl.

[atbug]

1. I tried again in a clean new environment where only Spglib.jl and spglib_jll.jl were installed and can reproduce what I reported. But I agree that I cannot reproduce the issue on my Mac laptop.

2. I can use Python version of spglib by PyCall on the machine where the reported issue can be reproduced.

julia> using Cells, PyCall

julia> spglib = pyimport("spglib")
PyObject <module 'spglib' from '/path/to/myhome/.julia/conda/3/lib/python3.9/site-packages/spglib/__init__.py'>

julia> lattice = [[7.17851431, 0, 0], [0, 3.99943947, 0], [0, 0, 8.57154746]]
3-element Vector{Vector{Float64}}:
 [7.17851431, 0.0, 0.0]
 [0.0, 3.99943947, 0.0]
 [0.0, 0.0, 8.57154746]

julia> positions = [
          [0.0, 0.84688439, 0.1203133],
          [0.0, 0.65311561, 0.6203133],
          [0.0, 0.34688439, 0.3796867],
          [0.0, 0.15311561, 0.8796867],
          [0.5, 0.34688439, 0.1203133],
          [0.5, 0.15311561, 0.6203133],
          [0.5, 0.84688439, 0.3796867],
          [0.5, 0.65311561, 0.8796867],
       ]
8-element Vector{Vector{Float64}}:
 [0.0, 0.84688439, 0.1203133]
 [0.0, 0.65311561, 0.6203133]
 [0.0, 0.34688439, 0.3796867]
 [0.0, 0.15311561, 0.8796867]
 [0.5, 0.34688439, 0.1203133]
 [0.5, 0.15311561, 0.6203133]
 [0.5, 0.84688439, 0.3796867]
 [0.5, 0.65311561, 0.8796867]

julia> atoms = [8 for i in 1:length(positions)]
8-element Vector{Int64}:
 8
 8
 8
 8
 8
 8
 8
 8

julia> spglib.get_spacegroup(
           (lattice,
           positions,
           atoms),
           symprec=1.0e-3
       )
"Cmce (64)"

3. I am trying to get an rr trace, but am now stucked at Downloading artifact: Python. I'll get back to you when I have the trace, probably at a time when the cluster is not crowded and the IO is faster.

Thank you for the quick response.

[atbug]

Here is the rr trace:
https://julialang-dumps.s3.amazonaws.com/reports/2024-01-24T05-50-27-atbug.tar.zst

I don't really understand how to use rr. Let me know if it is not what you want.

[singularitti]

Hi @atbug, may I ask which version of Spglib.jl were you using? Could it be the same bug we are having as in #183? Can you try v0.9.2?

[atbug]

I was using 0.9.3.

I can now confirm the issue is not reproducible for 0.9.2 and seems to be fixed on current main branch. Thank you.

[singularitti]

Thank you for your bug report! A new release will be released immediately!