feat: structured trajectory output + visualization tutorial#331
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HaoZeke wants to merge 30 commits intoTheochemUI:mainfrom
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feat: structured trajectory output + visualization tutorial#331HaoZeke wants to merge 30 commits intoTheochemUI:mainfrom
HaoZeke wants to merge 30 commits intoTheochemUI:mainfrom
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eOn Documentation PreviewDownload: documentation.zip Unzip and open |
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Raw asv-spyglass output |
Add per-iteration .dat output for minimization and saddle search:
- HelperFunctions.cpp: writes {prefix}.dat TSV (iteration, step_size,
convergence, energy) alongside movie .con when write_movies=true
- MinModeSaddleSearch.cpp: writes climb.dat TSV (iteration, step_size,
delta_e, convergence, eigenvalue, torque, angle, rotations)
Add visualization tutorial (tutorials/visualization.md) with 8 figures
generated from real eOn runs:
- Minimization: profile, convergence, landscape (Pt heptamer, Morse)
- Saddle search: profile, convergence, landscape (Pt heptamer, dimer)
- NEB: profile, 2D landscape (Diels-Alder, PET-MAD via eOn+metatomic)
Update user guide output sections for minimization and saddle search.
Add ira>=2 to pixi docs environment for IRA-based RMSD in landscapes.
Convert tutorial from static markdown + pre-committed PNGs to a MyST-NB executable notebook that runs on CI: - Downloads PET-MAD xs v1.5.0 from HuggingFace - Runs eonclient for minimization + NEB on HCN isomerization - Generates all figures via rgpycrumbs at build time - Only initial .con structures are committed (960 bytes) CI changes: - ci_docs.yml: uses docs-mta env (has eonclient + metatomic) - Builds eonclient before sphinx-build - sphinx-build -W catches broken references Config changes: - conf.py: myst_nb replaces myst_parser, nb_execution_mode="auto" - pixi.toml: docs-mta env, myst-nb + rgpycrumbs + chemparseplot deps
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readcon-core subproject requires cbindgen to generate C headers.
…ras for docs The visualization tutorial imports modules that need polars, ase, matplotlib.
eonclient reads ini.Get("Metatomic", "model_path", "") -- the wrong key
name caused an empty path passed to torch, crashing with SIGABRT.
- Replace ase.io.read/write(format="eon") with readcon.read_con_as_ase() and readcon.write_con() in visualization tutorial - Bump readcon pin from >=0.4.2 to >=0.7.0 for read_con_as_ase API - Set RGPYCRUMBS_AUTO_DEPS=1 for runtime dep auto-resolution
readcon 0.7 renamed the Atom constructor kwarg from is_fixed (bool) to fixed ([bool, bool, bool]) for per-direction constraints. Update both the write path (_atoms_to_frame) and read path (_frame_to_atoms).
eonclient links against libmetatensor.so from PyPI packages at build time, but the dynamic linker can't find them at runtime without LD_LIBRARY_PATH.
Add all relevant lib dirs from torch, metatensor.torch, and metatomic.torch packages. Log LD_LIBRARY_PATH and ldd check.
libmetatensor.so is installed by the metatensor conda package into CONDA_PREFIX/lib, which isn't on LD_LIBRARY_PATH when subprocess.run() spawns eonclient from a jupyter kernel.
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Add per-iteration
.datoutput for minimization and saddle search whenwrite_movies=true:HelperFunctions.cpp: Writes{prefix}.datTSV alongside movie.confiles. Columns: iteration, step_size, convergence, energy.MinModeSaddleSearch.cpp: Writesclimb.datTSV alongsideclimb.con. Columns: iteration, step_size, delta_e, convergence, eigenvalue, torque, angle, rotations.Add visualization tutorial (
tutorials/visualization.md) with figures:Figures generated from real eOn runs, however given the newest con-file spec this may be reworked after #307.
Needs: