Run dftbplus_thermo in an optional isolated working directory - #55
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The DFTB+ steps read and write fixed filenames (geo_opt.gen, hessian.out, vibrations.tag, ...) in the current directory, so running more than one molecule in the same directory clobbers the previous result. Add a directory argument to dftbplus_thermo that runs the pipeline in its own directory via a context manager, restoring the previous working directory afterwards. Defaults to the current directory, so existing behaviour is unchanged.
dftbplus_thermo only runs under the DFTB+ binaries, which CI skips, so the new directory branch showed as uncovered. Add a test that mocks the calculator pipeline (Geoopt/Hessian/Modes/run_thermo) and asserts the steps run inside the given directory and the working directory is restored.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #55 +/- ##
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+ Coverage 94.27% 95.00% +0.72%
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Files 21 21
Lines 1206 1221 +15
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+ Hits 1137 1160 +23
+ Misses 69 61 -8
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galjos
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Jun 29, 2026
Implements the core screening framework from #33 (first slice). Builds on the per-job directory isolation (#55) and ASE-atoms passthrough (#52). ## What it does A \`screen()\` entry point (exported as \`ThermoScreening.screen\`) and a \`thermo screen\` CLI subcommand that, for each molecule, run the DFTB+ geometry-optimisation/Hessian/modes pipeline in its own working directory and collect the key thermochemistry into \`results.csv\` and \`results.json\`. - **Input (both):** a directory of \`.xyz\`/\`.gen\` structures (run at a global \`--charge\`), or a CSV manifest with \`path\` plus optional \`name\`/\`charge\` columns (per-molecule charge — e.g. anthraquinone at -1/-2). - **Output (both):** a CSV summary table and a JSON file (name, path, charge, status, E/H/G in Hartree, S/Cv in cal/(mol*K), error). - **Error isolation:** a molecule that fails is recorded with \`status=error\` and does not abort the run. - **Per-job isolation:** each molecule runs in \`<directory>/<name>\`. ``` # Python from ThermoScreening import screen screen("molecules.csv", out="results") # CLI thermo screen ./structures/ -o results --charge 0 thermo screen molecules.csv -o results ``` ## Tests - Job loading from a directory and a CSV manifest (per-row + default charge, relative path resolution), and rejection of empty/unknown inputs. - \`screen()\` with the pipeline mocked: collects results, writes CSV + JSON, runs each molecule in its own directory, and isolates a failing molecule. - CLI routing for the \`screen\` subcommand and the failure-count return code. - Verified locally with the real DFTB+ binaries over a directory of CH4/H2O/NH3 plus a deliberately broken structure: the three succeed (entropies 44.44 / 45.05 / 45.97 cal/(mol*K), matching literature), the broken one is isolated as an error. 152 passed, 5 skipped (no binaries); pylint 8.09/10. ## Deferred to follow-ups (not in this PR) - Resume/checkpoint (this PR always recomputes, per the agreed scope). - Parallel execution (chdir-based isolation is correct for sequential and multi-process batches; per-thread parallelism would need the calculators to thread a directory through).
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Closes #53. Re-targets the work from #54 onto main: #54 was stacked on the #52 branch and got merged into that branch instead of main (which was squash-merged separately), so the change never landed. These are the same commits, cleanly rebased onto current main.
The DFTB+ steps read and write fixed filenames (
geo_opt.gen,hessian.out,vibrations.tag,modes_in.hsd, ...) in the current directory, so running more than one molecule in the same directory clobbers the previous molecule's geometry/Hessian/frequencies. This blocks any batch/screening loop (#33).Change
directoryargument todftbplus_thermo; the pipeline runs there via a_run_in_directorycontext manager that creates the directory and restores the previous working directory afterwards (including on error).Tests
_run_in_directory: isolates into the target dir and restores the cwd, restores on exception, no-op forNone.dftbplus_thermo(..., directory=...)without the binaries, covering the directory wiring in CI (api.py coverage 87% -> 93%).144 passed, 5 skipped (no binaries); pylint 8.04/10.