Add a native-xtb engine with implicit solvation for open-shell species - #70
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The tblite xTB engine (in-process) can't do solvation (tblite's ASE calculator exposes no ALPB/GBSA), and running xTB through DFTB+ can't do open-shell (a known DFTB+ limitation). The native xtb binary does all of it, so add it as the "xtb-cli" engine -- covering charged radicals in solution with method-consistent parameters. - calculator/xtb_cli.py: run `xtb --ohess --gfn <n> --chrg <c> --uhf <2S> [--alpb <solvent>]`, then parse the energy (xtbopt.xyz), optimised geometry, and frequencies (vibspectrum), feeding them into run_thermo like the other engines. The xtb executable is found via $XTB_COMMAND or PATH; nothing is imported from xtb, so the package still imports without it. - thermo/api.py: `xtb_cli_thermo`, resolving spin to --uhf so radicals run open-shell automatically; solvent -> --alpb. - thermo/screening.py, cli/thermo.py: `screen(engine="xtb-cli")` / `--engine xtb-cli`; solvent now applies to dftb+ and xtb-cli. Validated against the real xtb 6.7.1: gas-phase water S = 45.05 cal/mol/K (experiment ~45.1); an OH radical runs open-shell and is stabilised by ~6.5 kcal/mol in water (--alpb). Frequencies/energy match the tblite path.
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Follow-up to the xtb engines (#68, #70): `thermo doctor` only checked the DFTB+ toolchain. Now it also reports the xTB backends, so `doctor` reflects all three engines. ## What it reports - **`xtb`** — the native binary for `--engine xtb-cli` (resolved via `$XTB_COMMAND`, then PATH). - **`tblite`** — the Python package for `--engine xtb`. ``` dftb+ found /.../bin/dftb+ modes found /.../bin/modes DFTB_PREFIX found /.../3ob/skfiles C-C.skf found /.../3ob/skfiles/C-C.skf xtb found /.../xtbcli/bin/xtb tblite found importable ``` When missing, the detail line gives the fix: ``` xtb missing not found (set XTB_COMMAND or `conda install -c conda-forge xtb`; needed for --engine xtb-cli) (optional) tblite missing not importable (`conda install -c conda-forge tblite-python`; needed for --engine xtb) (optional) ``` ## Design: optional, so DFTB+-only users are unaffected - The xTB checks are marked `(optional)` and **do not change the doctor exit code** — it still fails only on a missing *required* DFTB+ backend (`dftb+`/`modes`/`DFTB_PREFIX`/`C-C.skf`). - `Diagnostic` gains an `optional` flag; `run_doctor` filters optional items from the pass/fail decision. This is a small step toward the "helpful doctor" idea — the detail now includes the exact `conda install` command for whatever's missing. ## Note This was originally committed onto the #70 branch, but #70 merged before its CI picked up the extra commit — so it's re-based here as its own PR off the current main. Offline suite: 252 passed / 11 skipped.
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`environment.yml` already installed DFTB+ but predates the xTB engines (#68, #70). Add the xTB backends so `conda env create -f environment.yml` provisions **every** calculation engine in one command. ```yaml dependencies: - python>=3.12 - dftbplus # DFTB+ engine: `dftb+` and `modes` - xtb # native xtb binary, for --engine xtb-cli - tblite-python # GFN-xTB via tblite, for --engine xtb - pip - pip: - "-e .[test,lint]" ``` After `conda env create -f environment.yml && conda activate thermoscreening`, `thermo doctor` reports every backend as found (pairs with #71). README updated to say the env covers all backends. Verified the three backends resolve on conda-forge (dftbplus-25.1 nompi, xtb-6.6.1, tblite-python-0.3.0); YAML validated. This is the "installable through the project" follow-up: the compiled backends (DFTB+/modes/xtb/tblite) can't be pip-installed, so the conda env is how the project bundles them, while `thermo setup-dftb` handles the Slater-Koster and GBSA parameter files.
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Closes the gap the last two discussions surfaced: neither prior xTB path can do open-shell + solvation together.
The native
xtbbinary does all of it, so this adds it as thextb-cliengine — covering charged radicals in solution with method-consistent parameters.Usage
What changed
calculator/xtb_cli.py(new) — runsxtb --ohess --gfn <n> --chrg <c> --uhf <2S> [--alpb <solvent>], then parses the energy (xtbopt.xyz), optimised geometry, and frequencies (vibspectrum, wavenumber = 3rd-from-last token). The executable is found via$XTB_COMMANDor PATH; nothing is imported from xtb, so the package still imports without it.thermo/api.py—xtb_cli_thermo, resolving the electron-count spin guess to--uhf(radicals open-shell automatically) andsolvent→--alpb.thermo/screening.py,cli/thermo.py—screen(engine="xtb-cli")/--engine xtb-cli;solventnow applies to both dftb+ and xtb-cli.Validation
Real xtb 6.7.1: gas-phase water S = 45.05 cal/mol/K (experiment ~45.1); an OH radical runs open-shell and is stabilised by ~6.5 kcal/mol in water (
--alpb) —ΔG_solvon an open-shell radical, the exact case that motivated this. Energy/frequencies match the tblite path.Offline suite 223 passed / 6 skipped; real DFTB+ + xtb integration 45 passed. CI-safe tests cover parsing, command construction (mocked subprocess), dispatch, and the missing-binary error; a real end-to-end test runs when
xtbis present and skips otherwise. Patch coverage verified without the xtb binary (0 uncovered).Dependency
xtb-clineeds the nativextbbinary (optional):conda install -c conda-forge xtb. Without it, the other engines work unchanged and the xtb-cli tests skip.