Sync/public 1.1 code

[pkawak]

AMDAT 1.1.0

AMDAT now supports OpenMP multithreading across numerous analyses, substantially reducing execution time while preserving existing input workflows and numerical results.

Highlights

• Enables OpenMP multithreading for many commonly used analyses.
• Adds dedicated multithreading documentation.
• Adds automated GitHub Actions coverage for version metadata, analysis numerics, and memory safety.
• Fixes padded analysis storage, including allocation, copying, initialization, assignment, and cleanup.
• Improves version validation and GitHub Pages math rendering.

The multithreading implementation, benchmarking, and performance measurements were contributed by @BaoKhanhMa.

Multithreaded analyses

Analysis	Description	Maximum tested speedup
md	Mean displacement	7
msd	Mean square displacement	10
msd_2d	Two-dimensional mean square displacement	9
isfs	Incoherent scattering function	20
vhs	Self part of the Van Hove function	12
vhd	Distinct part of the Van Hove function	20
raf	Reorientation autocorrelation function	15
ngp	Non-Gaussian parameter	30
composition	Composition	7
rdf	Radial distribution function	21
rnf	Radial count	23
orientational_correlation	Orientational correlation of multibodies	6.5
neighbor_decorrelation_function	Persistence of initial neighbors over displacement time	8.5

Maximum speedups are benchmark results and may vary with the analysis, input data, thread count, and hardware.

Migration notes

No user action is required. OpenMP support is provided by the conda toolchain, and existing AMDAT input files remain compatible.

Automated testing

• Version policy: unit tests validate semantic versions, release tags, and forward version sequencing.
• Generated metadata: regression coverage verifies that the build version, Git commit, and git describe metadata refresh correctly.
• Analysis numerics: MSD, mean displacement, MSD 2D, and bond autocorrelation reproduce 97 expected output rows in both serial and four-thread runs.
• Memory lifecycle: ASan, LSan, and UBSan repeatedly exercise padded-storage construction, copying, assignment, reinitialization, and cleanup.

[BaoKhanhMa]

Hi Pierre, I checked your PR, and this is what I see:

• All supported analyses are correctly enabled with multithreading flag
• The core loop is correctly opened with #pragma and is not commented out
• You updated PADDING using array<> instead of ** (pointers to pointers)
• Added multibody_trajlist_intersection.cpp‎
• There is no leftover inside control.cpp
• Github workflow now has an automatic test system with msd, msd2d, and baf, and it accepts a small tolerance compared to the fixed result

I think your PR is ready to be merged, but do you mind if I make a small suggestion? I noticed that "tests"and "testfiles" have very similar names so I wonder if we should rename "testfiles" to something like "samples" to distinguish them? Thank you.