Run dftbplus_thermo in an optional isolated working directory - #54
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galjos merged 2 commits intoJun 26, 2026
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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.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## feed-ase-atoms-to-run-thermo #54 +/- ##
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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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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.
galjos
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Jun 26, 2026
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 - Add a `directory` argument to `dftbplus_thermo`; the pipeline runs there via a `_run_in_directory` context manager that creates the directory and restores the previous working directory afterwards (including on error). - Backward-compatible: defaults to the current directory, so existing single-molecule workflows are unchanged. - chdir-based, so correct for sequential and multi-process batches; per-thread parallelism within one process would need the calculators to thread a directory through (follow-up). ## Tests - Unit tests for `_run_in_directory`: isolates into the target dir and restores the cwd, restores on exception, no-op for `None`. - A mocked-pipeline test drives `dftbplus_thermo(..., directory=...)` without the binaries, covering the directory wiring in CI (api.py coverage 87% -> 93%). - Verified locally with the real DFTB+ binaries: two molecules run into separate directories, the cwd is untouched, results independent and physically sensible (H2O 45.05, NH3 45.97 cal/(mol*K)). 144 passed, 5 skipped (no binaries); pylint 8.04/10.
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Closes #53. Stacked on #52 (retargets to main once that merges) — it depends on #52 because the pipeline now runs on the in-memory optimized atoms rather than re-reading a file from the working directory.
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, and is a no-op forNone.148 passed, 0 skipped (suite run with DFTB+ binaries); pylint 8.04/10.