Update stable with main - #3001
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correct_binding_energy walks each surface site to apply the linear scaling relationship, but assumed every bonded site had a covalent (single/double/triple/quadruple) bond. A physisorbed site is attached by a van der Waals bond of order 0.0, which fell through to the else branch and raised NotImplementedError. This crashed RMG whenever a family such as Surface_Dissociation_vdWBidentate_Beta produced a vdW-bonded species (e.g. [Pt]~[O]=C[O][Pt]), as reported in #2987. A van der Waals contact is not covalently bound to the surface, so it correctly contributes nothing to the LSR correction (bond order 0). This mirrors the existing vdW handling in Molecule.desorb_molecule. Closes #2987 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Changed syntax seperator in JULIA_CPU_TARGET
Two unpinned dependencies moved and took CI down. Both are fixed here because neither can be verified on its own: the Julia fix cannot go green while openbabel hangs the test step, and an openbabel fix branched off main cannot go green while Julia segfaults. Julia. All the RMS jobs and the regression test were failing at install_rms.sh, where `from juliacall import Main` died with a segmentation fault before RMG-Py was built. Pinning pyjuliacall alone was not enough -- with it pinned the Julia package set at the point of the import is identical to the last green run, all 22 packages, and it still segfaulted. That left julia itself: 1.10.11 on 16 Aug, 1.10.12 on 17 Aug, because both the workflow and the Dockerfile asked juliaup for the floating '1.10' channel. Ask for 1.10.11 in both, and keep pyjuliacall pinned exactly rather than capped, since 0.9.28 with 1.10.11 is the only combination there is evidence for. openbabel. The Python 3.10 and 3.11 jobs then hung in `make test-all` and were killed at the 6 hour limit, with and without RMS, on four consecutive attempts. They stop after pytest prints its plugin list and before a single test is collected, which is where test/conftest.py imports pybel. Comparing a green run from 10 Aug against a hanging one, openbabel is the only package that differs in the whole environment, 3.1.1 against 3.2.1. Python 3.9 is unaffected only because conda-forge has no py39 build of 3.2.1, so it still resolves to 3.1.1. Cap it below 3.2 in both environment.yml and .conda/meta.yaml.
to clarify that Ag111 thermochemistry and kinetics libraries are used specifically for this example.
[echem] Updated CO2RR example input file
see same patch on database here: ReactionMechanismGenerator/RMG-database#745
…load fix conda upload logic
…l_version Pin Julia and openbabel to unbreak CI
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Post release of v4 we introduced a number of small fixes that need to be reflected in
stableMore importantly, I also just fixed a bug that was causing the
rmgbinaries onconda-forgeto be overwritten. Merging this PR will cause the correct ones to be uploaded