Polishing the docs

[henry2004y]

• docs: fix latex display
• add BATL AMR description

[gemini-code-assist]

Code Review

This pull request updates the documentation for analysis and logging, including detailed explanations of the BATL AMR grid structure and potential VTK conversion strategies. It also refines docstrings and modifies the retrieval of current density vector indices in src/select.jl. Feedback was provided regarding the robustness of the index retrieval for :J, as the new implementation assumes contiguous storage of components and may not align with documentation for derived quantities.

[github-actions]

Benchmark Results (Julia v1)

Time benchmarks

	master	2155cf4...	master / 2155cf4...
amrex/load	25.3 ± 0.57 μs	25.7 ± 0.56 μs	0.984 ± 0.031
amrex/phase_space_3d	6.54 ± 1.3 ms	6.55 ± 1.3 ms	0.999 ± 0.28
amrex/select_region	0.226 ± 0.012 ms	0.226 ± 0.012 ms	0.997 ± 0.075
amrex/select_region_from_files	0.865 ± 0.15 ms	0.873 ± 0.16 ms	0.991 ± 0.26
read/ASCII	0.665 ± 0.014 ms	0.67 ± 0.015 ms	0.992 ± 0.03
read/Anisotropy	7.56 ± 0.24 μs	9.04 ± 1.5 μs	0.837 ± 0.15
read/Current density	9.58 ± 0.44 μs	9.71 ± 0.44 μs	0.987 ± 0.064
read/Current density 3D	10.4 ± 0.38 μs	10.4 ± 0.35 μs	1 ± 0.05
read/Current density 3D Jx	5.31 ± 0.13 μs	5.32 ± 0.11 μs	0.998 ± 0.032
read/Current density Jz	7.52 ± 0.11 μs	7.54 ± 0.081 μs	0.997 ± 0.018
read/Cutdir	2.27 ± 0.2 μs	2.26 ± 0.19 μs	1 ± 0.12
read/Cutdir subset	3.11 ± 0.28 μs	3.1 ± 0.26 μs	1 ± 0.12
read/Extract Bmag	0.511 ± 0.1 μs	0.512 ± 0.1 μs	0.998 ± 0.28
read/HDF5	0.113 ± 0.0033 ms	0.109 ± 0.0027 ms	1.03 ± 0.039
read/HDF5 extract	14.2 ± 0.44 μs	13.4 ± 0.35 μs	1.07 ± 0.043
read/Interp2d	0.831 ± 0.22 μs	0.831 ± 0.19 μs	1 ± 0.35
read/Load binary structured	0.0463 ± 0.0053 ms	0.0464 ± 0.0049 ms	0.999 ± 0.15
time_to_load	1.27 ± 0.021 s	1.26 ± 0.008 s	1.01 ± 0.018

Memory benchmarks

	master	2155cf4...	master / 2155cf4...
amrex/load	0.212 k allocs: 9.67 kB	0.212 k allocs: 9.67 kB	1
amrex/phase_space_3d	0.059 k allocs: 18.3 MB	0.059 k allocs: 18.3 MB	1
amrex/select_region	3 allocs: 1.07 MB	3 allocs: 1.07 MB	1
amrex/select_region_from_files	0.05 k allocs: 7.48 MB	0.05 k allocs: 7.48 MB	1
read/ASCII	0.395 k allocs: 0.109 MB	0.395 k allocs: 0.109 MB	1
read/Anisotropy	3 allocs: 4.84 kB	3 allocs: 4.84 kB	1
read/Current density	10 allocs: 12.5 kB	10 allocs: 12.5 kB	1
read/Current density 3D	10 allocs: 6.65 kB	10 allocs: 6.65 kB	1
read/Current density 3D Jx	4 allocs: 2.23 kB	4 allocs: 2.23 kB	1
read/Current density Jz	4 allocs: 4.18 kB	4 allocs: 4.18 kB	1
read/Cutdir	0.137 k allocs: 5.98 kB	0.137 k allocs: 5.98 kB	1
read/Cutdir subset	0.159 k allocs: 8.89 kB	0.159 k allocs: 8.89 kB	1
read/Extract Bmag	3 allocs: 4.09 kB	3 allocs: 4.09 kB	1
read/HDF5	0.1 k allocs: 3.67 kB	0.1 k allocs: 3.67 kB	1
read/HDF5 extract	17 allocs: 4.55 kB	17 allocs: 4.55 kB	1
read/Interp2d	12 allocs: 4.45 kB	12 allocs: 4.45 kB	1
read/Load binary structured	0.144 k allocs: 0.0743 MB	0.144 k allocs: 0.0743 MB	1
time_to_load	0.149 k allocs: 11.1 kB	0.149 k allocs: 11.1 kB	1

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 82.83%. Comparing base (0bf2055) to head (2155cf4).

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #162   +/-   ##
=======================================
  Coverage   82.82%   82.83%           
=======================================
  Files          21       21           
  Lines        4001     4002    +1     
=======================================
+ Hits         3314     3315    +1     
  Misses        687      687           

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