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feature/SOF-8102 Feature: AFIR for a molecule on a surface with ALCHEMI #409

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Merged
VsevolodX merged 31 commits into from
Nov 9, 2026
Merged

feature/SOF-8102 Feature: AFIR for a molecule on a surface with ALCHEMI #409

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b35a922
afir_molecule_surface_alchemi.ipynb: random placements of a molecule …
VsevolodX Nov 2, 2026
5778d09
afir_molecule_surface_alchemi.ipynb: two steps, configurations with m…
VsevolodX Nov 3, 2026
0eda0bf
afir_molecule_surface_alchemi.ipynb: take the AFIR subworkflow from t…
VsevolodX Nov 3, 2026
b7a2f5b
SOF-8102: afir_molecule_surface_alchemi.ipynb: step 3 saves the lowes…
VsevolodX Nov 3, 2026
635bcdd
SOF-8102: afir_molecule_surface_alchemi.ipynb: final-structure reques…
VsevolodX Nov 3, 2026
bbbe44c
SOF-8102: afir_molecule_surface_alchemi.ipynb: AFIR unit declares fin…
VsevolodX Nov 3, 2026
2c50c8c
SOF-8102: afir_molecule_surface_alchemi.ipynb: review round 3 nits
VsevolodX Nov 3, 2026
af6d002
SOF-8102: afir_molecule_surface_alchemi.ipynb: save the final structu…
VsevolodX Nov 3, 2026
e39e9ad
SOF-8102: afir_molecule_surface_alchemi.ipynb: pin matplotlib==3.11.2…
VsevolodX Nov 3, 2026
1735d52
SOF-8102: afir_molecule_surface_alchemi.ipynb: drop the matplotlib li…
VsevolodX Nov 3, 2026
66889d7
SOF-8102: afir_molecule_surface_alchemi.ipynb: save the lowest final …
VsevolodX Nov 3, 2026
88d6078
SOF-8102: AFIR script default keeps one final structure
VsevolodX Nov 3, 2026
d4ae051
SOF-8102: step 3 saves the final structure under its own unit; AFIR s…
VsevolodX Nov 4, 2026
f351219
SOF-8102: final-structure loop runs until every request is sent; cell…
VsevolodX Nov 4, 2026
ebc0a63
SOF-8102: AFIR step runs NVIDIA's ALCHEMI pre-release with cuEquivari…
VsevolodX Nov 9, 2026
13b4996
SOF-8102: workflow, steps, units, script and result files renamed; AF…
VsevolodX Nov 9, 2026
15044dc
SOF-8102: AFIR wording in the introduction and step 2's header; job n…
VsevolodX Nov 9, 2026
17ce4f2
SOF-8102: step 3 named Save Final Structures; script files back to sh…
VsevolodX Nov 9, 2026
bad13dd
SOF-8102: introduction notes the ALCHEMI 0.3.0 pre-release from a Git…
VsevolodX Nov 9, 2026
8005987
SOF-8102: requirements explained above their cell, ALCHEMI pre-releas…
VsevolodX Nov 9, 2026
4a41222
SOF-8102: AFIR step's requirements without the made and commented ind…
VsevolodX Nov 9, 2026
10fbd86
SOF-8102: step scripts and requirements as files beside the notebook,…
VsevolodX Nov 9, 2026
b30fda1
SOF-8102: AFIR step's ALCHEMI from the PyPI 0.3.0 release instead of …
VsevolodX Nov 9, 2026
0f5cea7
SOF-8102: drop the measured build time from the requirements note
VsevolodX Nov 9, 2026
f840f69
SOF-8102: the step files get their own heading, 4.4
VsevolodX Nov 9, 2026
d2308ab
SOF-8102: steps 1 and 3 share a Python environment, step 2 has its own
VsevolodX Nov 9, 2026
b026b8a
SOF-8102: the introduction says steps 1 and 3 share a Python environment
VsevolodX Nov 9, 2026
2514210
SOF-8102: step files in one folder per step, each with its requiremen…
VsevolodX Nov 9, 2026
705f86c
SOF-8102: step folders named after the workflow's subworkflows
VsevolodX Nov 9, 2026
057ba63
SOF-8102: introduction and step-files note reworded for the folder la…
VsevolodX Nov 9, 2026
f3ad038
SOF-8102: requirements file names stated as the platform gives them; …
VsevolodX Nov 9, 2026
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