From fc7531d97cddb7272f94ef6a867b9def9ffe6c82 Mon Sep 17 00:00:00 2001 From: Matteo Giantomassi Date: Sun, 27 Oct 2024 17:20:33 +0100 Subject: [PATCH] Fix typos --- .github/workflows/tests.yml | 8 ++++---- abipy_book/_config.yml | 2 ++ abipy_book/abinit_input.md | 2 +- abipy_book/ddb.md | 12 ++++++------ abipy_book/structure.md | 2 +- requirements.txt | 1 + 6 files changed, 15 insertions(+), 12 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index bfbe7d1..ae985a5 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -18,7 +18,7 @@ jobs: # This job tests that the CC works test-and-jb-build: # prevent this action from running on forks - #if: github.repository == 'abinit/abipy' + if: github.repository == 'abinit/abipy_book' defaults: run: shell: bash -l {0} # enables conda/mamba env activation by reading bash profile @@ -28,11 +28,11 @@ jobs: matrix: config: - os: ubuntu-latest - python: '3.11' + python: '3.12' runs-on: ${{ matrix.config.os }} - #env: - # PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }} + env: + PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }} # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages permissions: diff --git a/abipy_book/_config.yml b/abipy_book/_config.yml index 10ca6f6..8d4ca0e 100644 --- a/abipy_book/_config.yml +++ b/abipy_book/_config.yml @@ -7,6 +7,7 @@ # Book settings title : AbiPy Book # The title of the book. Will be placed in the left navbar. author : M. Giantomassi and the AbiPy group # The author of the book +language: en copyright : "2024" # Copyright year to be placed in the footer logo : "images/abipy_logo.png" # A path to the book logo # Patterns to skip when building the book. Can be glob-style (e.g. "*skip.ipynb") @@ -22,6 +23,7 @@ execute: #execute_notebooks: cache #execute_notebooks: auto execute_notebooks: force + timeout: 120 # Set the timeout to 120 # Define the name of the latex output file for PDF builds latex: diff --git a/abipy_book/abinit_input.md b/abipy_book/abinit_input.md index 96eef7e..b5d1bbb 100644 --- a/abipy_book/abinit_input.md +++ b/abipy_book/abinit_input.md @@ -289,7 +289,7 @@ inp.set_structure(abilab.Structure.from_mpid("mp-149")) ``` Remember to set the `PMG_MAPI_KEY` in ~/.pmgrc.yaml as described -[here](https://pymatgen.org/usage.html#setting-the-pmg-mapi-key-in-the-config-file). +[here](https://pymatgen.org/usage.html#setting-the-pmg_mapi_key-in-the-config-file) +++ diff --git a/abipy_book/ddb.md b/abipy_book/ddb.md index f68b8c4..506f8ef 100644 --- a/abipy_book/ddb.md +++ b/abipy_book/ddb.md @@ -49,7 +49,7 @@ ddb = abilab.DdbFile.from_mpid("mp-1009129")
Remember to set the `PMG_MAPI_KEY` in your ~/.pmgrc.yaml as described -[here](http://pymatgen.org/usage.html#setting-the-pmg-mapi-key-in-the-config-file). +[here](https://pymatgen.org/usage.html#setting-the-pmg_mapi_key-in-the-config-file) ## How to create a DdbFile object @@ -362,15 +362,15 @@ Unfortunately, all the terms that are evaluated on the real-space FFT mesh The error depends on several factors: the density of the FFT mesh, pseudopotentials with hard model core charges, XC functional, etc.) Note that it is not always possible to reduce the error to zero by just increasing the convergence parameters -but fortunately it is possible to restore the acoustic sum rule via the {{asr_anaddb}} input variable. +but fortunately it is possible to restore the acoustic sum rule via the {{asr@anaddb}} input variable. -One can easily compare the phonons bands obtained with different values of {{asr_anaddb}} with: +One can easily compare the phonons bands obtained with different values of {{asr@anaddb}} with: ```{code-cell} asr_plotter = ddb.anacompare_asr() ``` -This method invokes anaddb with different values of {{asr_anaddb}} and returns a plotter object +This method invokes anaddb with different values of {{asr@anaddb}} and returns a plotter object we can call to compare the phonon band structures: ```{code-cell} @@ -382,7 +382,7 @@ asr_plotter.combiplotly(); ``` Now we can perform a similar test for the treatment of the non-analytical term in the $q \rightarrow 0$ limit. -We compute the phonon band dispersion for {{dipdip_anaddb} in [0, 1] and the compare the +We compute the phonon band dispersion for {{dipdip@anaddb} in [0, 1] and the compare the results on the same figure with the commands: ```{code-cell} @@ -404,7 +404,7 @@ in polar semiconductors. The correct description of this long-range term without dipdip = 1 would require using an extremely dense q-point mesh in the DFPT calculation. -With {{dipdip_anaddb} = 1, on the other hand, we can model this long-range behavior in terms of a dipole-dipole +With {{dipdip@anaddb} = 1, on the other hand, we can model this long-range behavior in terms of a dipole-dipole interaction involving the Born effective charges and the macroscopic dielectric tensor. This allows us to decompose the full dynamical matrix into: diff --git a/abipy_book/structure.md b/abipy_book/structure.md index 085065c..cd4f38d 100644 --- a/abipy_book/structure.md +++ b/abipy_book/structure.md @@ -67,7 +67,7 @@ structure = Structure.from_file(abidata.cif_file("si.cif")) print(structure) ``` -```{include} abidata_note.md +```{include} snippets/abidata_note.md ``` To read the structure from an Abinit netcdf file, use: diff --git a/requirements.txt b/requirements.txt index 5a00179..307d23d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -3,4 +3,5 @@ abipy jupyter-book graphviz scikit-image +mp-api #ghp-import