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Update the docs for abTEM 1.0.11 - #45
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- Config reference: cupy.fft-cache-size defaults to auto (it was ignored in 1.0.10), and the configuration files that are read are ~/.config/abtem (or $ABTEM_CONFIG) and dask's directories, not /etc/abtem. - Parallelization walkthrough: the cupy FFT plan cache is bounded to 25 % of the device memory by default, not set to zero. - Partial coherence tutorial: distribution weights are probabilities applied by reduce_ensemble (text and code from #32), outputs re-executed with 1.0.11. - Charge density tutorial: GPAW(mode="fd") is required by GPAW 26 and is the default of earlier versions. - Changelog: the 1.0.11 entry of the abTEM repository, as the fallback of the changelog mirroring. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
The tutorial runs on abTEM 1.0.11 with GPAW 26 and matplotlib 3.11 (the plots of the overlaid measurements and the filtered sites needed the fixes of abTEM#615), and its outputs are refreshed. The core-loss corrections of 1.0.11 (abTEM#364, #368, #468) change the numbers, and the number of transitions that remain after filter_by_intensity is 10 instead of 9. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Python 3.12 and later warn about the invalid escape sequences of these labels (\e, \ , \i, \m), and the warnings were stored in the outputs. The strings are raw now and give the same labels; the stored warnings are removed. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
- multislice: the "Slice thickness" tip is an admonition with that title. - contrast_transfer_function: \mathrm for the image and exit subscripts of Eq. 4. - blochwave: typo. - frozen_phonons: the thermal average of the intensities is taken with reduce_ensemble, which averages the ensemble axes that are meant to be averaged (the default of FrozenPhonons); explained in the text. - parallelization: no repr output of the compute calls, and the multiple GPUs section says that the configuration of the session reaches the workers (1.0.11). - orthogonal_cells: smaller atoms in the show_atoms plots, and the final cell of the twisted bilayer (it was tagged remove-cell) is shown. - charge_density: larger spots in the diffraction spot plot. The outputs of the executed notebooks are refreshed. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
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Summary
Documentation fixes found by running every notebook of the stable docs (the 1.0.10 tree on
main) against abTEM 1.0.11 (release/1.0.11, abTEM/abTEM#615), and by comparing with the same run on v1.0.10.default_config.yaml,config.md):cupy.fft-cache-sizeisautoand now takes effect; the files that are read are~/.config/abtem(or$ABTEM_CONFIG) and dask's directories, not/etc/abtem.reduce_ensemble(abTEM#466, in 1.0.11). Text and code from Document probability-weighted ensemble reduction (abTEM#466) #32, outputs re-executed with 1.0.11; the incoherent and quasi-coherent images now agree as the text says, and.sum(0)/.mean(0)no longer warn.GPAW(mode="fd", ...); GPAW 26 requiresmode, andfdis the default of earlier versions. The notebook now runs on GPAW 26.CHANGELOG.mdas the committed fallback of the build-time mirroring (scripts/fetch_changelog.pyreplaces it once abTEM'smainhas the file).What the run showed
_toc.yml(ensembles,potential_integrals,visualizations,custom_simulation_objects,plasmons,epie) or not linked (animations), the private_create_ctf_images, and notebooks that need packages or settings missing from my environment (xarray,bokeh,ipycytoscape, GPAW, and forreal_spacea numba threading-layer abort on macOS that the synchronous scheduler avoids; it then runs).show()panel spacing changed (abTEM#354), and noise realisations changed (abTEM#464/#475), so most stored figures differ in size or pixels from what 1.0.11 produces; the content is the same. Only the partial coherence tutorial needed new outputs.Core-loss tutorial
core_loss.ipynbneeded two library fixes that are in abTEM/abTEM#615 (commit f70e691a and earlier):filter_sitesreturns the keptAtomsagain, and the line labels of overlaid ensembles have the right count (matplotlib 3.11 raises otherwise). With them the tutorial runs without errors on GPAW 26 and matplotlib 3.11, and its outputs are re-executed with 1.0.11: the core-loss corrections of 1.0.11 change the numbers, andfilter_by_intensitynow leaves 10 transitions instead of 9 (the text is updated). Needs abTEM#615 as released.🤖 Generated with Claude Code