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To assist in tests
Previously it was in setter, and we would get a report every time rxn.multiplicity is called. Now we should only get one report of the reaction multiplicity, after it is determined.
copy other only once consider aromatic structures in other as well
And improved the logic of get_angle_in_180_range()
Added more tests to get_angle_in_180_range() Also, added a minor test to is_str_float
So that species can be used in dictionaries and sets
Streamlines the execution commands for xtb_gsm and sella Also uses `set -euo pipefail` to ensure scripts fail on errors. Also, it adds an explicit error message when a conda environment manager isn't found.
To avoid the warning:
invalid value encountered in divide
v2_x_v1 /= float(np.linalg.norm(v2_x_v1))
Adds error handling to capture and display information when a Sella run fails. This includes the return code, command, last parts of standard error and standard output, and the tail of the ts.log file. Also adds error handling to display information when the output.yml file is missing.
to save a YAML file of the thermo data from an Arkane run
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This is a large PR that fundamentally adds the Molecule class internally in ARC. Now ARC is compatible with Py 3.12
This PR follows the work done in #754 where ARC were given capabilities to work directly with the RMG-database without using the RMG API. Now, finally, ARC does not depend on Julia.
The major change made in this PR required additional modifications. Although we appreciate small and smart PR's it is very hard to decouple these changes. The main modifications are as follows:
parsermodule in ARC with adapters for each ESS.species/xyz_to_2dandspecies/xyz_to_smiles, falling back to a single bond version of the molecule if it cannot be perceived). Now we have a newspecies/perceivealgorithm, with a fallback tospecies/xyz_to_smilesif needed. Success rates are higher, and we always return a molecule with bond orders. This might be the end of theallow_nonisomorphic_2dflag in ARC. We'll keep it around for a while, but may deprecate it in the future.data/elements.yml.devtoolsfor all the external dependencies, and the CI was updated as well, along with the Makefile. A big thanks to @calvinp0 for the endless hours he invested in this.Tests were of course added. We still need to updated the docs, specifically for the installation instructions, and check the installation scripts again, they were mainly tested in the context of the CI.
With this merged, we should soon tag a new version of ARC.