diff --git a/tutorials/generation/generation_tutorial.ipynb b/tutorials/generation/generation_tutorial.ipynb index 6215588..d9c0409 100644 --- a/tutorials/generation/generation_tutorial.ipynb +++ b/tutorials/generation/generation_tutorial.ipynb @@ -39,17 +39,10 @@ "warnings.filterwarnings(\"always\")\n", "warnings.filterwarnings(\"ignore\", message=\"numpy.ufunc size changed\")\n", "warnings.filterwarnings(\"ignore\", message=\"POTCAR data\")\n", -<<<<<<< HEAD - "warnings.filterwarnings(\"ignore\", message=\"Overriding the POTCAR functional\")\n", - "warnings.filterwarnings(\"ignore\", message=r\".*is a deprecated alias for the builtin.*\")\n", - "warnings.filterwarnings(\"ignore\", message=r\".*should_run_async.*\")" - ] -======= "warnings.filterwarnings(\"ignore\", message=\"Overriding the POTCAR functional\")" ], "outputs": [], "metadata": {} ->>>>>>> develop }, { "cell_type": "code", @@ -65,7 +58,7 @@ "cell_type": "markdown", "source": [ "## Generate slabs for a specified Miller index\n", - "This simple example uses the output structure from a bulk relaxation of Y$_2$Ti$_2$S$_2$O$_5$. We create a series of slabs with thickness of 20, 30 and 40 Å, and vacuum thicknesses of 20, 30, 40 and 50 Å in the (0,0,1) direction. We suppress the default behaviour of saving input files by setting `save_slabs=False`." + "This simple example uses the output structure from a bulk relaxation of $Y_2 Ti_2 S_2 O_5$. We create a series of slabs with thickness of 20, 30 and 40 Å, and vacuum thicknesses of 20, 30, 40 and 50 Å in the (0,0,1) direction. We suppress the default behaviour of saving input files by setting `save_slabs=False`." ], "metadata": {} }, @@ -92,14 +85,9 @@ { "cell_type": "markdown", "source": [ -<<<<<<< HEAD - "If you leave `thicknesses=[20,30,40], vacuums=[20,30,40,50]` you will get a warning about repeted slabs that have been removed from the final list. We can inspect one entry of the list which is a dictionary, containing details and the slab itself as a pymatgen structure:" - ] -======= "We get a warning about repeted slabs that have been removed from the final list. We can inspect one entry of the list which is a dictionary, containing details and the slab itself as a pymatgen structure:" ], "metadata": {} ->>>>>>> develop }, { "cell_type": "code", @@ -196,17 +184,6 @@ ], "metadata": {} }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "
\n", - "\n", - "**Note:** If you are running this on Binder, you may want to reduce the number of vacuum and slab thicknesses to try for it to finish in a reasonable time. Try `thicknesses=[20,40], vacuums=[20]`.\n", - "\n", - "
" - ] - }, { "cell_type": "code", "execution_count": null, @@ -226,11 +203,11 @@ { "cell_type": "markdown", "source": [ - "By default `save_slabs=True`, so the structure files are saved to files. A directory has been created locally called `Y4Ti4S4O10` and each structure has been named in the format `POSCAR_miller-index_slab-thickness_vacuum-thickness_slab-index`. The VASP POSCAR file is the default, but any other input file supported by pymatgen can be supplied as the `fmt` argument. \n", + "By default `save_slabs=True`, so the structure files are saved to files. A directory has been created locally called `Y2Ti2S2O5` and each structure has been named in the format `POSCAR_miller-index_slab-thickness_vacuum-thickness_slab-index`. The VASP POSCAR file is the default, but any other input file supported by pymatgen can be supplied as the `fmt` argument. \n", "\n", "### Make separate folders\n", "\n", - "We can get the function to organise these into directories by setting `make_fols=True`. The structure files will go into subfolders with the following structure: `hkl/slab_vacuum_index/POSCAR` in the `Y4Ti4S4O10` directory. " + "We can get the function to organise these into directories by setting `make_fols=True`. The structure files will go into subfolders with the following structure: `hkl/slab_vacuum_index/POSCAR` in the `Y2Ti2S2O5` directory. " ], "metadata": {} },