xtb_step Phase F – File Drop Notes#

Three real bugs from your last test run, all fixed:

  1. KeyError: 'optimization frame' and the analogous 'frequencies frame' error when opening the Optimization / Frequencies edit dialogs. Root cause: my Phase E TkEnergy.create_dialog ended with self.reset_dialog(), which Python’s MRO dispatched to the subclass reset_dialog – but at that point the subclass create_dialog had not yet built its own frames, so the lookup blew up.

  2. (Same bug, fixed by the same removal in TkOptimization.create_dialog and TkFrequencies.create_dialog.)

  3. xtbopt.xyz and xtbtopo.mol were not coming back from the work directory because return_files only listed ["xtbout.json", "xtbrestart"]. Extended to glob over the commonly-written xtb output files.

Files in this drop#

Replace existing#

xtb_step/tk_energy.py

One-line change: removed the self.reset_dialog() call at the end of create_dialog, and added a comment explaining why it must not go there. Detailed reasoning below.

xtb_step/tk_optimization.py

Same one-line removal at the end of create_dialog.

xtb_step/tk_frequencies.py

Same one-line removal at the end of create_dialog.

xtb_step/energy.py

Changed return_files from ["xtbout.json", "xtbrestart"] to:

return_files = [
    "xtbout.json",
    "xtbrestart",
    "*.xyz",          # xtbopt.xyz and any other xyz files
    "*.mol",          # xtbtopo.mol topology file
    "*.log",          # xtbopt.log optimization trajectory
    "vibspectrum",    # Turbomole-format IR spectrum
    "hessian",        # Turbomole-format Hessian matrix
    "g98.out",        # Gaussian-98 output for visualization
]

Modeled on the Gaussian step’s use of ["*.cube"] / ["*"] glob patterns in its CubeGen invocations.

Why the dialog bug happened#

The flow when the user double-clicks an Optimization step:

  1. seamm.tk_node.edit() calls self.create_dialog().

  2. Python’s MRO dispatches to TkOptimization.create_dialog().

  3. TkOptimization.create_dialog calls super().create_dialog(), which goes to TkEnergy.create_dialog().

  4. TkEnergy.create_dialog builds self["energy frame"], creates the energy widgets, binds the solvation-model widget, and (in Phase E) called self.reset_dialog() at the end.

  5. self.reset_dialog() is also MRO-dispatched, so it goes to TkOptimization.reset_dialog().

  6. TkOptimization.reset_dialog does row = super().reset_dialog() (which lays out the energy frame fine) then tries self["optimization frame"].grid(...) – but the optimization frame doesn’t exist yet. Subclass create_dialog has not built it. KeyError.

The MOPAC pattern (which I should have copied more carefully) ends each create_dialog with self.logger.debug("Finished creating the dialog") and return frame, and never calls self.reset_dialog from within create_dialog. The seamm framework’s tk_node.edit() calls reset_dialog itself, after create_dialog has fully unwound through all the subclass and parent calls, so by the time reset_dialog runs every frame exists.

This is now noted in the comments at the bottom of each create_dialog.

Why the missing files happened#

Your directory listing for step 3.2 (Optimization) showed:

coord.xyz, stderr.txt, stdout.txt, step.out,
xtb.err, xtb.out, xtbout.json, xtbrestart

xtb’s own log (the xtb.out file you sent) reports:

Writing topology from bond orders to xtbtopo.mol
optimized geometry written to: xtbopt.xyz

So xtb did write both files into the working directory, but the seamm executor’s “return files” mechanism only copies back the files listed in return_files to the long-term step directory. The defaults in Phase D were too restrictive.

The new globs are deliberately permissive – *.xyz / *.mol / *.log will pick up anything xtb might write under those extensions in any future xtb release, plus the explicit names for the Turbomole-format files (vibspectrum, hessian) and the Gaussian-format file (g98.out).

Not in this drop#

All the other files from Phase D / Phase E (substep.py, metadata.py, frequencies.py, optimization.py, energy_parameters.py, optimization_parameters.py, frequencies_parameters.py, xtb.py, __init__.py, setup.py, the data files, the installer) are unchanged.

Test plan after copying#

  1. make lint && make install && make test – still pass.

  2. Open the Optimization step’s edit dialog. It should now open without a KeyError, and show two frames: the Hamiltonian Parameters frame at the top with the dynamic solvent visibility, and the Optimization frame below with optimization level / max iterations / structure handling.

  3. Open the Frequencies step’s edit dialog. Three frames now: Hamiltonian, Optimization, Frequencies / Thermochemistry.

  4. Re-run the water flowchart. After the run, the Optimization step directory should contain xtbopt.xyz, xtbopt.log, and xtbtopo.mol in addition to the Phase E files. The Frequencies step directory should additionally contain vibspectrum, hessian, and g98.out.

  5. The WARNING: xtbopt.xyz not found log messages from Optimization._handle_optimized_structure should now be silent for the optimization step (we have the file) and may still appear for the frequency step if xtb under --ohess writes the optimized geometry to a different filename. If the latter persists, check what filename xtb actually used (likely xtbopt.xyz still – --ohess is just opt + hess in one invocation – but worth confirming).

Code style#

All four files compile cleanly, all lines <= 88 chars. The diffs against the previous phase are minimal (a 4-line block removed in each tk_*.py, a 9-line list extension in energy.py).