diff --git a/README.md b/README.md index aaaf5f4..b58b818 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,6 @@ anyone is welcome to contribute. | |        |          |         | | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| **[2013-01-01-Bandstructure of NiO](https://github.com/materialsvirtuallab/matgenb/blob/master/notebooks/2013-01-01-Bandstructure%20of%20NiO.ipynb)** | [![Binder]](https://mybinder.org/v2/gh/materialsvirtuallab/matgenb/master?labpath=notebooks/2013-01-01-Bandstructure%20of%20NiO.ipynb) | [![Launch Codespace]][codespace url] | [![Open in Google Colab]](https://colab.research.google.com/github/materialsvirtuallab/matgenb/blob/master/notebooks/2013-01-01-Bandstructure%20of%20NiO.ipynb) | | **[2013-01-01-Basic functionality](https://github.com/materialsvirtuallab/matgenb/blob/master/notebooks/2013-01-01-Basic%20functionality.ipynb)** | [![Binder]](https://mybinder.org/v2/gh/materialsvirtuallab/matgenb/master?labpath=notebooks/2013-01-01-Basic%20functionality.ipynb) | [![Launch Codespace]][codespace url] | [![Open in Google Colab]](https://colab.research.google.com/github/materialsvirtuallab/matgenb/blob/master/notebooks/2013-01-01-Basic%20functionality.ipynb) | | **[2013-01-01-Calculating Reaction Energies with the Materials API](https://github.com/materialsvirtuallab/matgenb/blob/master/notebooks/2013-01-01-Calculating%20Reaction%20Energies%20with%20the%20Materials%20API.ipynb)** | [![Binder]](https://mybinder.org/v2/gh/materialsvirtuallab/matgenb/master?labpath=notebooks/2013-01-01-Calculating%20Reaction%20Energies%20with%20the%20Materials%20API.ipynb) | [![Launch Codespace]][codespace url] | [![Open in Google Colab]](https://colab.research.google.com/github/materialsvirtuallab/matgenb/blob/master/notebooks/2013-01-01-Calculating%20Reaction%20Energies%20with%20the%20Materials%20API.ipynb) | | **[2013-01-01-Calculating XRD patterns](https://github.com/materialsvirtuallab/matgenb/blob/master/notebooks/2013-01-01-Calculating%20XRD%20patterns.ipynb)** | [![Binder]](https://mybinder.org/v2/gh/materialsvirtuallab/matgenb/master?labpath=notebooks/2013-01-01-Calculating%20XRD%20patterns.ipynb) | [![Launch Codespace]][codespace url] | [![Open in Google Colab]](https://colab.research.google.com/github/materialsvirtuallab/matgenb/blob/master/notebooks/2013-01-01-Calculating%20XRD%20patterns.ipynb) | diff --git a/notebooks/2013-01-01-Calculating Reaction Energies with the Materials API.ipynb b/notebooks/2013-01-01-Calculating Reaction Energies with the Materials API.ipynb index 9d8627e..70fdd28 100644 --- a/notebooks/2013-01-01-Calculating Reaction Energies with the Materials API.ipynb +++ b/notebooks/2013-01-01-Calculating Reaction Energies with the Materials API.ipynb @@ -9,7 +9,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -19,7 +19,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [ { diff --git a/notebooks/2013-01-01-Calculating XRD patterns.ipynb b/notebooks/2013-01-01-Calculating XRD patterns.ipynb index 308eb1b..97c74d2 100644 --- a/notebooks/2013-01-01-Calculating XRD patterns.ipynb +++ b/notebooks/2013-01-01-Calculating XRD patterns.ipynb @@ -11,7 +11,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -21,7 +21,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -46,7 +46,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -79,7 +79,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -108,7 +108,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -153,7 +153,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, "outputs": [ { diff --git a/notebooks/2013-01-01-Molecule.ipynb b/notebooks/2013-01-01-Molecule.ipynb index 753a65b..f527ae6 100644 --- a/notebooks/2013-01-01-Molecule.ipynb +++ b/notebooks/2013-01-01-Molecule.ipynb @@ -215,7 +215,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [ { diff --git a/notebooks/2013-01-01-Ordering Disordered Structures.ipynb b/notebooks/2013-01-01-Ordering Disordered Structures.ipynb index 9e75753..0d399e0 100644 --- a/notebooks/2013-01-01-Ordering Disordered Structures.ipynb +++ b/notebooks/2013-01-01-Ordering Disordered Structures.ipynb @@ -93,7 +93,9 @@ } ], "source": [ - "from pymatgen.transformations.standard_transformations import OrderDisorderedStructureTransformation\n", + "from pymatgen.transformations.standard_transformations import (\n", + " OrderDisorderedStructureTransformation,\n", + ")\n", "\n", "trans = OrderDisorderedStructureTransformation()\n", "\n", @@ -159,7 +161,9 @@ "metadata": {}, "outputs": [], "source": [ - "from pymatgen.transformations.advanced_transformations import EnumerateStructureTransformation\n", + "from pymatgen.transformations.advanced_transformations import (\n", + " EnumerateStructureTransformation,\n", + ")\n", "\n", "specie = {\"Cu\": 0.5, \"Au\": 0.5}\n", "cuau = Structure.from_spacegroup(\"Fm-3m\", Lattice.cubic(3.677), [specie], [[0, 0, 0]])\n", diff --git a/notebooks/2013-01-01-Plotting the electronic structure of Fe.ipynb b/notebooks/2013-01-01-Plotting the electronic structure of Fe.ipynb index 207aaf5..74c7f66 100644 --- a/notebooks/2013-01-01-Plotting the electronic structure of Fe.ipynb +++ b/notebooks/2013-01-01-Plotting the electronic structure of Fe.ipynb @@ -9,7 +9,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -20,7 +20,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -40,7 +40,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -91,13 +91,6 @@ "grid(True)\n", "show()" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { diff --git a/notebooks/2016-09-08-Data-driven First Principles Methods for the Study and Design of Alkali Superionic Conductors Part 1 - Structure Generation.ipynb b/notebooks/2016-09-08-Data-driven First Principles Methods for the Study and Design of Alkali Superionic Conductors Part 1 - Structure Generation.ipynb index f89f63b..b997654 100644 --- a/notebooks/2016-09-08-Data-driven First Principles Methods for the Study and Design of Alkali Superionic Conductors Part 1 - Structure Generation.ipynb +++ b/notebooks/2016-09-08-Data-driven First Principles Methods for the Study and Design of Alkali Superionic Conductors Part 1 - Structure Generation.ipynb @@ -36,7 +36,9 @@ "from pymatgen.core import Structure\n", "from pymatgen.io.vasp.sets import MPRelaxSet, batch_write_input\n", "from pymatgen.symmetry.analyzer import SpacegroupAnalyzer\n", - "from pymatgen.transformations.advanced_transformations import EnumerateStructureTransformation" + "from pymatgen.transformations.advanced_transformations import (\n", + " EnumerateStructureTransformation,\n", + ")" ] }, { diff --git a/notebooks/2016-09-08-Data-driven First Principles Methods for the Study and Design of Alkali Superionic Conductors Part 2 - Phase and Electrochemical Stability.ipynb b/notebooks/2016-09-08-Data-driven First Principles Methods for the Study and Design of Alkali Superionic Conductors Part 2 - Phase and Electrochemical Stability.ipynb index ae13fb3..9b33fb2 100644 --- a/notebooks/2016-09-08-Data-driven First Principles Methods for the Study and Design of Alkali Superionic Conductors Part 2 - Phase and Electrochemical Stability.ipynb +++ b/notebooks/2016-09-08-Data-driven First Principles Methods for the Study and Design of Alkali Superionic Conductors Part 2 - Phase and Electrochemical Stability.ipynb @@ -18,7 +18,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -29,7 +29,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -40,7 +40,11 @@ "\n", "import matplotlib as mpl\n", "import palettable\n", - "from pymatgen.analysis.phase_diagram import CompoundPhaseDiagram, PDPlotter, PhaseDiagram\n", + "from pymatgen.analysis.phase_diagram import (\n", + " CompoundPhaseDiagram,\n", + " PDPlotter,\n", + " PhaseDiagram,\n", + ")\n", "from pymatgen.core import Composition, Element\n", "from pymatgen.entries.compatibility import MaterialsProjectCompatibility\n", "from pymatgen.entries.computed_entries import ComputedEntry\n", @@ -60,7 +64,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -78,7 +82,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -110,7 +114,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -128,7 +132,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -157,7 +161,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -3026,7 +3030,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -4286,7 +4290,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -4315,7 +4319,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -4332,7 +4336,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -4390,7 +4394,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -4399,7 +4403,7 @@ "Text(0, 0.5, 'Li uptake per f.u.')" ] }, - "execution_count": 12, + "execution_count": null, "metadata": {}, "output_type": "execute_result" }, diff --git a/notebooks/2016-09-08-Data-driven First Principles Methods for the Study and Design of Alkali Superionic Conductors Part 3 - Diffusivity and Ionic Conductivity.ipynb b/notebooks/2016-09-08-Data-driven First Principles Methods for the Study and Design of Alkali Superionic Conductors Part 3 - Diffusivity and Ionic Conductivity.ipynb index a21ff15..6f158ce 100644 --- a/notebooks/2016-09-08-Data-driven First Principles Methods for the Study and Design of Alkali Superionic Conductors Part 3 - Diffusivity and Ionic Conductivity.ipynb +++ b/notebooks/2016-09-08-Data-driven First Principles Methods for the Study and Design of Alkali Superionic Conductors Part 3 - Diffusivity and Ionic Conductivity.ipynb @@ -18,7 +18,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -29,7 +29,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -43,7 +43,11 @@ "import matplotlib.pyplot as plt\n", "from pymatgen.analysis.diffusion.aimd.pathway import ProbabilityDensityAnalysis\n", "from pymatgen.analysis.diffusion.aimd.van_hove import VanHoveAnalysis\n", - "from pymatgen.analysis.diffusion.analyzer import DiffusionAnalyzer, get_arrhenius_plot, get_extrapolated_conductivity" + "from pymatgen.analysis.diffusion.analyzer import (\n", + " DiffusionAnalyzer,\n", + " get_arrhenius_plot,\n", + " get_extrapolated_conductivity,\n", + ")" ] }, { @@ -57,7 +61,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -74,7 +78,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -97,7 +101,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -127,7 +131,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -156,7 +160,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -189,7 +193,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -210,7 +214,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -220,7 +224,7 @@ "" ] }, - "execution_count": 9, + "execution_count": null, "metadata": {}, "output_type": "execute_result" } @@ -240,7 +244,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -256,7 +260,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -265,7 +269,7 @@ "" ] }, - "execution_count": 11, + "execution_count": null, "metadata": {}, "output_type": "execute_result" }, diff --git a/notebooks/2016-09-25-Plotting phonon bandstructure and dos.ipynb b/notebooks/2016-09-25-Plotting phonon bandstructure and dos.ipynb index eb9bd22..3974832 100644 --- a/notebooks/2016-09-25-Plotting phonon bandstructure and dos.ipynb +++ b/notebooks/2016-09-25-Plotting phonon bandstructure and dos.ipynb @@ -11,7 +11,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -22,7 +22,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -52,7 +52,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -79,7 +79,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -95,7 +95,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -114,7 +114,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -126,7 +126,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -135,7 +135,7 @@ "" ] }, - "execution_count": 7, + "execution_count": null, "metadata": {}, "output_type": "execute_result" }, @@ -173,7 +173,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -182,7 +182,7 @@ "" ] }, - "execution_count": 8, + "execution_count": null, "metadata": {}, "output_type": "execute_result" }, diff --git a/notebooks/2017-03-02-Getting data from Materials Project.ipynb b/notebooks/2017-03-02-Getting data from Materials Project.ipynb index c38f2e5..c57f87a 100644 --- a/notebooks/2017-03-02-Getting data from Materials Project.ipynb +++ b/notebooks/2017-03-02-Getting data from Materials Project.ipynb @@ -11,7 +11,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -21,7 +21,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -47,7 +47,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -100,7 +100,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -146,7 +146,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -170,7 +170,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -181,7 +181,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -211,7 +211,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -245,7 +245,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -288,7 +288,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -297,16 +297,18 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ - "m = StructureMatcher() # You can customize tolerances etc., but the defaults usually work fine." + "m = (\n", + " StructureMatcher()\n", + ") # You can customize tolerances etc., but the defaults usually work fine." ] }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -352,7 +354,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -376,7 +378,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -388,7 +390,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -406,7 +408,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": null, "metadata": {}, "outputs": [ { diff --git a/notebooks/2017-04-03-Slab generation and Wulff shape.ipynb b/notebooks/2017-04-03-Slab generation and Wulff shape.ipynb index b214a12..dd8fa23 100644 --- a/notebooks/2017-04-03-Slab generation and Wulff shape.ipynb +++ b/notebooks/2017-04-03-Slab generation and Wulff shape.ipynb @@ -22,7 +22,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -32,7 +32,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -47,7 +47,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -62,7 +62,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -93,7 +93,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -141,7 +141,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -206,7 +206,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -222,7 +222,7 @@ "" ] }, - "execution_count": 7, + "execution_count": null, "metadata": {}, "output_type": "execute_result" }, @@ -280,7 +280,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -312,7 +312,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -351,7 +351,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -374,7 +374,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -386,7 +386,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": {}, "outputs": [ { diff --git a/notebooks/2017-04-14-Inputs and Analysis of VASP runs.ipynb b/notebooks/2017-04-14-Inputs and Analysis of VASP runs.ipynb index af84ef3..2a228d1 100644 --- a/notebooks/2017-04-14-Inputs and Analysis of VASP runs.ipynb +++ b/notebooks/2017-04-14-Inputs and Analysis of VASP runs.ipynb @@ -11,17 +11,17 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# Uncomment the subsequent lines in this cell to install dependencies for Google Colab.\n", - "# !pip install pymatgen==2022.7.19\n" + "# !pip install pymatgen==2022.7.19" ] }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -36,6 +36,7 @@ "source": [ "from pymatgen.core import Structure\n", "from pymatgen.io.vasp.sets import MPRelaxSet\n", + "\n", "s = Structure.from_file(\"Al-relax/Al.cif\", primitive=True)\n", "custom_settings = {\"NELMIN\": 5} # user custom incar settings\n", "relax = MPRelaxSet(s, user_incar_settings=custom_settings)\n", @@ -51,7 +52,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -90,7 +91,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -121,7 +122,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -148,7 +149,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -189,7 +190,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -223,7 +224,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -258,7 +259,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -293,7 +294,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -302,7 +303,7 @@ "" ] }, - "execution_count": 10, + "execution_count": null, "metadata": {}, "output_type": "execute_result" }, @@ -326,13 +327,6 @@ "plt = BSPlotter(bs)\n", "plt.get_plot(vbm_cbm_marker=True)" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { diff --git a/notebooks/2017-09-03-Analyze and plot band structures.ipynb b/notebooks/2017-09-03-Analyze and plot band structures.ipynb index afa6252..907c1e8 100644 --- a/notebooks/2017-09-03-Analyze and plot band structures.ipynb +++ b/notebooks/2017-09-03-Analyze and plot band structures.ipynb @@ -16,7 +16,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -27,7 +27,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -64,7 +64,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -109,7 +109,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -118,7 +118,7 @@ "" ] }, - "execution_count": 4, + "execution_count": null, "metadata": {}, "output_type": "execute_result" }, @@ -150,7 +150,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -170,7 +170,7 @@ "
" ] }, - "execution_count": 5, + "execution_count": null, "metadata": {}, "output_type": "execute_result" } diff --git a/notebooks/2017-12-15-Plotting a Pourbaix Diagram.ipynb b/notebooks/2017-12-15-Plotting a Pourbaix Diagram.ipynb index 3ee9292..7ddd245 100644 --- a/notebooks/2017-12-15-Plotting a Pourbaix Diagram.ipynb +++ b/notebooks/2017-12-15-Plotting a Pourbaix Diagram.ipynb @@ -40,7 +40,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -58,7 +58,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -67,7 +67,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -90,7 +90,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -204,12 +204,13 @@ "metadata": {}, "outputs": [], "source": [ - "plotter.get_pourbaix_plot(limits=[[0,14], [-2,2]], # pH and E limits\n", - " title=\"Customized Pourbaix Plot\",\n", - " label_domains=True, # set True to label phases\n", - " label_fontsize=10, # font size for the phase labels\n", - " show_neutral_axes=False, # show or hide axes at pH=0, E=0\n", - " show_water_lines=False, # show or hide lines for water stability\n", + "plotter.get_pourbaix_plot(\n", + " limits=[[0, 14], [-2, 2]], # pH and E limits\n", + " title=\"Customized Pourbaix Plot\",\n", + " label_domains=True, # set True to label phases\n", + " label_fontsize=10, # font size for the phase labels\n", + " show_neutral_axes=False, # show or hide axes at pH=0, E=0\n", + " show_water_lines=False, # show or hide lines for water stability\n", ")" ] }, diff --git a/notebooks/2018-01-01-ChemEnv - How to automatically identify coordination environments in a structure.ipynb b/notebooks/2018-01-01-ChemEnv - How to automatically identify coordination environments in a structure.ipynb index 5995796..d96b177 100644 --- a/notebooks/2018-01-01-ChemEnv - How to automatically identify coordination environments in a structure.ipynb +++ b/notebooks/2018-01-01-ChemEnv - How to automatically identify coordination environments in a structure.ipynb @@ -69,7 +69,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -80,15 +80,21 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ "import logging\n", "\n", - "from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import SimplestChemenvStrategy\n", - "from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder\n", - "from pymatgen.analysis.chemenv.coordination_environments.structure_environments import LightStructureEnvironments\n", + "from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (\n", + " SimplestChemenvStrategy,\n", + ")\n", + "from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (\n", + " LocalGeometryFinder,\n", + ")\n", + "from pymatgen.analysis.chemenv.coordination_environments.structure_environments import (\n", + " LightStructureEnvironments,\n", + ")\n", "from pymatgen.ext.matproj import MPRester" ] }, @@ -109,7 +115,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -153,7 +159,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -178,7 +184,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -216,7 +222,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -321,7 +327,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -340,7 +346,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -374,12 +380,14 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# Get the strategy from D. Waroquiers et al., Chem Mater., 2017, 29, 8346.\n", - "from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import MultiWeightsChemenvStrategy\n", + "from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (\n", + " MultiWeightsChemenvStrategy,\n", + ")\n", "\n", "strategy = MultiWeightsChemenvStrategy.stats_article_weights_parameters()\n", "\n", @@ -397,7 +405,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -433,7 +441,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": {}, "outputs": [ { diff --git a/notebooks/2018-03-09-Computing the Reaction Diagram between Two Compounds.ipynb b/notebooks/2018-03-09-Computing the Reaction Diagram between Two Compounds.ipynb index 9f44e03..a2bd013 100644 --- a/notebooks/2018-03-09-Computing the Reaction Diagram between Two Compounds.ipynb +++ b/notebooks/2018-03-09-Computing the Reaction Diagram between Two Compounds.ipynb @@ -13,7 +13,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -23,7 +23,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -41,7 +41,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -61,7 +61,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -86,7 +86,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -116,7 +116,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -205,7 +205,7 @@ "for e in all_entries:\n", " if len(e.composition) == 1 and e.composition.reduced_formula in [\"C\", \"O2\"]:\n", " potcars.extend(e.parameters[\"potcar_spec\"])\n", - " \n", + "\n", "co_form_energy = -110.53 * factor\n", "\n", "co = ComputedEntry(\n", diff --git a/notebooks/2018-03-14-Plotting COHP from LOBSTER.ipynb b/notebooks/2018-03-14-Plotting COHP from LOBSTER.ipynb index 6a79933..a148ab8 100644 --- a/notebooks/2018-03-14-Plotting COHP from LOBSTER.ipynb +++ b/notebooks/2018-03-14-Plotting COHP from LOBSTER.ipynb @@ -11,7 +11,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -21,7 +21,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -57,13 +57,6 @@ "ax = cp.get_plot()\n", "ax.set_ylim([-6, 6])" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { diff --git a/notebooks/2018-07-24-Adsorption on solid surfaces.ipynb b/notebooks/2018-07-24-Adsorption on solid surfaces.ipynb index a2728c4..6f269d8 100644 --- a/notebooks/2018-07-24-Adsorption on solid surfaces.ipynb +++ b/notebooks/2018-07-24-Adsorption on solid surfaces.ipynb @@ -21,7 +21,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -31,7 +31,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -60,7 +60,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -78,7 +78,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -105,7 +105,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -114,7 +114,7 @@ "" ] }, - "execution_count": 5, + "execution_count": null, "metadata": {}, "output_type": "execute_result" }, @@ -144,7 +144,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -163,7 +163,7 @@ "" ] }, - "execution_count": 6, + "execution_count": null, "metadata": {}, "output_type": "execute_result" }, @@ -197,7 +197,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": {}, "outputs": [ { diff --git a/notebooks/2018-09-25-Structure Prediction using Pymatgen and the Materials API.ipynb b/notebooks/2018-09-25-Structure Prediction using Pymatgen and the Materials API.ipynb index d83adb9..c6b1368 100644 --- a/notebooks/2018-09-25-Structure Prediction using Pymatgen and the Materials API.ipynb +++ b/notebooks/2018-09-25-Structure Prediction using Pymatgen and the Materials API.ipynb @@ -33,11 +33,15 @@ "from pprint import pprint\n", "\n", "from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher\n", - "from pymatgen.analysis.structure_prediction.substitution_probability import SubstitutionPredictor\n", + "from pymatgen.analysis.structure_prediction.substitution_probability import (\n", + " SubstitutionPredictor,\n", + ")\n", "from pymatgen.analysis.structure_prediction.substitutor import Substitutor\n", "from pymatgen.core.periodic_table import Specie\n", "from pymatgen.ext.matproj import MPRester\n", - "from pymatgen.transformations.standard_transformations import AutoOxiStateDecorationTransformation" + "from pymatgen.transformations.standard_transformations import (\n", + " AutoOxiStateDecorationTransformation,\n", + ")" ] }, { diff --git a/notebooks/2018-11-6-Dopant suggestions using Pymatgen.ipynb b/notebooks/2018-11-6-Dopant suggestions using Pymatgen.ipynb index f341142..00f71d9 100644 --- a/notebooks/2018-11-6-Dopant suggestions using Pymatgen.ipynb +++ b/notebooks/2018-11-6-Dopant suggestions using Pymatgen.ipynb @@ -13,7 +13,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -23,7 +23,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -42,7 +42,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -62,7 +62,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -80,7 +80,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -113,7 +113,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -136,7 +136,7 @@ "PeriodicSite: O (O2-) (0.0, 3.307, 3.307) [-0.0, 0.6942, 0.6938]" ] }, - "execution_count": 6, + "execution_count": null, "metadata": {}, "output_type": "execute_result" } @@ -154,7 +154,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -177,7 +177,7 @@ "PeriodicSite: O (O2-) (0.0, 3.307, 3.307) [-0.0, 0.6942, 0.6938]" ] }, - "execution_count": 7, + "execution_count": null, "metadata": {}, "output_type": "execute_result" } @@ -195,7 +195,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -223,7 +223,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -240,7 +240,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -316,7 +316,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -332,7 +332,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": {}, "outputs": [ { diff --git a/notebooks/2019-01-11-How to plot and evaluate output files from Lobster.ipynb b/notebooks/2019-01-11-How to plot and evaluate output files from Lobster.ipynb index a53ca2d..3c36ed2 100644 --- a/notebooks/2019-01-11-How to plot and evaluate output files from Lobster.ipynb +++ b/notebooks/2019-01-11-How to plot and evaluate output files from Lobster.ipynb @@ -13,7 +13,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -38,7 +38,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -57,7 +57,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [ { diff --git a/notebooks/2019-03-11-Interface Reactions.ipynb b/notebooks/2019-03-11-Interface Reactions.ipynb index fdb211b..1f89e19 100644 --- a/notebooks/2019-03-11-Interface Reactions.ipynb +++ b/notebooks/2019-03-11-Interface Reactions.ipynb @@ -15,7 +15,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -26,7 +26,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -52,7 +52,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -79,7 +79,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -130,7 +130,7 @@ " norm=True,\n", " include_no_mixing_energy=True,\n", " pd_non_grand=pd,\n", - " use_hull_energy=False\n", + " use_hull_energy=False,\n", " )\n", "else:\n", " interface = InterfacialReactivity(\n", @@ -153,7 +153,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [ { diff --git a/notebooks/2020-07-15-How to plot a Fermi surface with Boltztrap - notest.ipynb b/notebooks/2020-07-15-How to plot a Fermi surface with Boltztrap - notest.ipynb index 642d0bc..3f3c692 100644 --- a/notebooks/2020-07-15-How to plot a Fermi surface with Boltztrap - notest.ipynb +++ b/notebooks/2020-07-15-How to plot a Fermi surface with Boltztrap - notest.ipynb @@ -23,7 +23,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -34,7 +34,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -49,7 +49,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -77,7 +77,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -87,7 +87,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [ { diff --git a/notebooks/2021-08-26-Magnetic Structure Generation as Input for Initial DFT Calculations.ipynb b/notebooks/2021-08-26-Magnetic Structure Generation as Input for Initial DFT Calculations.ipynb index 003296f..394b977 100644 --- a/notebooks/2021-08-26-Magnetic Structure Generation as Input for Initial DFT Calculations.ipynb +++ b/notebooks/2021-08-26-Magnetic Structure Generation as Input for Initial DFT Calculations.ipynb @@ -24,7 +24,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "e167481e", "metadata": {}, "outputs": [], @@ -36,7 +36,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "id": "4622d496", "metadata": {}, "outputs": [], @@ -49,7 +49,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "id": "299fd4df", "metadata": {}, "outputs": [ @@ -116,7 +116,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "id": "7c7b6ea0", "metadata": {}, "outputs": [], @@ -128,7 +128,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "id": "94b18ea1", "metadata": {}, "outputs": [], @@ -139,7 +139,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "id": "64729507", "metadata": {}, "outputs": [ @@ -192,7 +192,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "id": "56698524", "metadata": {}, "outputs": [ @@ -219,7 +219,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "id": "c3e09dbc", "metadata": {}, "outputs": [ @@ -229,7 +229,7 @@ "'2/m'" ] }, - "execution_count": 8, + "execution_count": null, "metadata": {}, "output_type": "execute_result" } @@ -241,7 +241,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "id": "10867b71", "metadata": {}, "outputs": [ @@ -251,7 +251,7 @@ "'P2_1/c'" ] }, - "execution_count": 9, + "execution_count": null, "metadata": {}, "output_type": "execute_result" } @@ -262,7 +262,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "id": "4a8ec0de", "metadata": {}, "outputs": [ @@ -272,7 +272,7 @@ "\"# generated using pymatgen\\ndata_LiFePO4\\n_symmetry_space_group_name_H-M 'P 1'\\n_cell_length_a 4.74480000\\n_cell_length_b 6.06577000\\n_cell_length_c 10.41037000\\n_cell_angle_alpha 90.50179000\\n_cell_angle_beta 90.00019000\\n_cell_angle_gamma 90.00362000\\n_symmetry_Int_Tables_number 1\\n_chemical_formula_structural LiFePO4\\n_chemical_formula_sum 'Li4 Fe4 P4 O16'\\n_cell_volume 299.60796771\\n_cell_formula_units_Z 4\\nloop_\\n _symmetry_equiv_pos_site_id\\n _symmetry_equiv_pos_as_xyz\\n 1 'x, y, z'\\nloop_\\n _atom_site_type_symbol\\n _atom_site_label\\n _atom_site_symmetry_multiplicity\\n _atom_site_fract_x\\n _atom_site_fract_y\\n _atom_site_fract_z\\n _atom_site_occupancy\\n Li Li0 1 0.00001000 0.99999000 0.99999000 1.0\\n Li Li1 1 0.99999000 0.50000000 0.00001000 1.0\\n Li Li2 1 0.49999000 0.99999000 0.50000000 1.0\\n Li Li3 1 0.50002000 0.50000000 0.50000000 1.0\\n Fe Fe4 1 0.52507000 0.25344000 0.21884000 1.0\\n Fe Fe5 1 0.02508000 0.74654000 0.28116000 1.0\\n Fe Fe6 1 0.97497000 0.25346000 0.71884000 1.0\\n Fe Fe7 1 0.47493000 0.74653000 0.78116000 1.0\\n P P8 1 0.58205000 0.75169000 0.09444000 1.0\\n P P9 1 0.08207000 0.24830000 0.40556000 1.0\\n P P10 1 0.91794000 0.75174000 0.59443000 1.0\\n P P11 1 0.41793000 0.24828000 0.90557000 1.0\\n O O12 1 0.29156000 0.25112000 0.04317000 1.0\\n O O13 1 0.25851000 0.75043000 0.09622000 1.0\\n O O14 1 0.71346000 0.95594000 0.16580000 1.0\\n O O15 1 0.71627000 0.54860000 0.16562000 1.0\\n O O16 1 0.21629000 0.45140000 0.33438000 1.0\\n O O17 1 0.21345000 0.04406000 0.33419000 1.0\\n O O18 1 0.75852000 0.24955000 0.40378000 1.0\\n O O19 1 0.79157000 0.74890000 0.45682000 1.0\\n O O20 1 0.20845000 0.25110000 0.54316000 1.0\\n O O21 1 0.24149000 0.75046000 0.59622000 1.0\\n O O22 1 0.78658000 0.95602000 0.66577000 1.0\\n O O23 1 0.78367000 0.54867000 0.66564000 1.0\\n O O24 1 0.28366000 0.45133000 0.83436000 1.0\\n O O25 1 0.28658000 0.04399000 0.83423000 1.0\\n O O26 1 0.74149000 0.24958000 0.90378000 1.0\\n O O27 1 0.70842000 0.74889000 0.95684000 1.0\\nloop_\\n _atom_site_moment_label\\n _atom_site_moment_crystalaxis_x\\n _atom_site_moment_crystalaxis_y\\n _atom_site_moment_crystalaxis_z\\n Fe4 -5.00000000 0.00000000 0.00000000\\n Fe5 -5.00000000 0.00000000 0.00000000\\n Fe6 -5.00000000 0.00000000 0.00000000\\n Fe7 -5.00000000 0.00000000 0.00000000\\n\"" ] }, - "execution_count": 10, + "execution_count": null, "metadata": {}, "output_type": "execute_result" } @@ -283,7 +283,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "id": "8703b5d7", "metadata": {}, "outputs": [ @@ -360,7 +360,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "id": "e90dcfb8", "metadata": {}, "outputs": [ @@ -431,7 +431,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "id": "eb53cc57", "metadata": {}, "outputs": [], @@ -443,7 +443,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": null, "id": "ccedc00c", "metadata": {}, "outputs": [ @@ -453,7 +453,7 @@ "True" ] }, - "execution_count": 14, + "execution_count": null, "metadata": {}, "output_type": "execute_result" } @@ -464,7 +464,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "id": "d400c9af", "metadata": {}, "outputs": [ @@ -474,7 +474,7 @@ "{'Co': [0.988, 2.739, 2.746, 2.747, 2.762, 2.768]}" ] }, - "execution_count": 15, + "execution_count": null, "metadata": {}, "output_type": "execute_result" } @@ -485,7 +485,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": null, "id": "1436c1aa", "metadata": {}, "outputs": [ @@ -495,7 +495,7 @@ "" ] }, - "execution_count": 16, + "execution_count": null, "metadata": {}, "output_type": "execute_result" } diff --git a/notebooks/2021-5-12-Explanation of Corrections.ipynb b/notebooks/2021-5-12-Explanation of Corrections.ipynb index 3804b3f..c0e9ccb 100644 --- a/notebooks/2021-5-12-Explanation of Corrections.ipynb +++ b/notebooks/2021-5-12-Explanation of Corrections.ipynb @@ -31,7 +31,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -42,7 +42,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -61,7 +61,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -96,7 +96,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -105,7 +105,7 @@ "[]" ] }, - "execution_count": 4, + "execution_count": null, "metadata": {}, "output_type": "execute_result" } @@ -132,7 +132,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -143,7 +143,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -152,7 +152,7 @@ "[]" ] }, - "execution_count": 6, + "execution_count": null, "metadata": {}, "output_type": "execute_result" } @@ -179,7 +179,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -188,7 +188,7 @@ "-4.536662329583334" ] }, - "execution_count": 7, + "execution_count": null, "metadata": {}, "output_type": "execute_result" } @@ -199,7 +199,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -208,7 +208,7 @@ "0.0" ] }, - "execution_count": 8, + "execution_count": null, "metadata": {}, "output_type": "execute_result" } @@ -219,7 +219,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -228,7 +228,7 @@ "-4.536662329583334" ] }, - "execution_count": 9, + "execution_count": null, "metadata": {}, "output_type": "execute_result" } @@ -240,7 +240,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -249,7 +249,7 @@ "0.0" ] }, - "execution_count": 10, + "execution_count": null, "metadata": {}, "output_type": "execute_result" } @@ -267,7 +267,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -294,7 +294,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -303,7 +303,7 @@ "[]" ] }, - "execution_count": 12, + "execution_count": null, "metadata": {}, "output_type": "execute_result" } diff --git a/notebooks/2023-03-10-Plotting a Pourbaix Diagram-new.ipynb b/notebooks/2023-03-10-Plotting a Pourbaix Diagram-new.ipynb index 4892f8c..24f9817 100644 --- a/notebooks/2023-03-10-Plotting a Pourbaix Diagram-new.ipynb +++ b/notebooks/2023-03-10-Plotting a Pourbaix Diagram-new.ipynb @@ -44,7 +44,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -63,7 +63,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -72,7 +72,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -102,7 +102,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -216,12 +216,13 @@ "metadata": {}, "outputs": [], "source": [ - "plotter.get_pourbaix_plot(limits=[[0,14], [-2,2]], # pH and E limits\n", - " title=\"Customized Pourbaix Plot\",\n", - " label_domains=True, # set True to label phases\n", - " label_fontsize=10, # font size for the phase labels\n", - " show_neutral_axes=False, # show or hide axes at pH=0, E=0\n", - " show_water_lines=False, # show or hide lines for water stability\n", + "plotter.get_pourbaix_plot(\n", + " limits=[[0, 14], [-2, 2]], # pH and E limits\n", + " title=\"Customized Pourbaix Plot\",\n", + " label_domains=True, # set True to label phases\n", + " label_fontsize=10, # font size for the phase labels\n", + " show_neutral_axes=False, # show or hide axes at pH=0, E=0\n", + " show_water_lines=False, # show or hide lines for water stability\n", ").show()" ] }, @@ -367,7 +368,7 @@ "source": [ "from pymatgen.entries.compatibility import MaterialsProjectAqueousCompatibility\n", "\n", - "aqcompat=MaterialsProjectAqueousCompatibility()\n", + "aqcompat = MaterialsProjectAqueousCompatibility()\n", "solid_entries = aqcompat.process_entries(solid_entries)" ] }, @@ -396,8 +397,9 @@ " continue\n", " # create a new ComputedEntry with the formation energy. Copy all other parameters\n", " # from the original ComputedEntry.\n", - " free_energy_entries.append(ComputedEntry(v.composition, pd.get_form_energy(v),\n", - " parameters=v.parameters))" + " free_energy_entries.append(\n", + " ComputedEntry(v.composition, pd.get_form_energy(v), parameters=v.parameters)\n", + " )" ] }, { @@ -414,7 +416,7 @@ "outputs": [], "source": [ "with MPRester() as m:\n", - " ion_data = m.get_ion_reference_data_for_chemsys([\"Bi\",\"V\"])" + " ion_data = m.get_ion_reference_data_for_chemsys([\"Bi\", \"V\"])" ] }, { @@ -449,7 +451,6 @@ "metadata": {}, "outputs": [], "source": [ - "\n", "pbx_entries = [PourbaixEntry(e) for e in free_energy_entries]\n", "pbx_entries.extend([PourbaixEntry(e) for e in ion_entries])" ] diff --git a/notebooks/2023-12-31-FHI-aims-example.ipynb b/notebooks/2023-12-31-FHI-aims-example.ipynb index bf154b7..c3e4914 100644 --- a/notebooks/2023-12-31-FHI-aims-example.ipynb +++ b/notebooks/2023-12-31-FHI-aims-example.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "0", "metadata": {}, "outputs": [], @@ -19,7 +19,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "id": "1", "metadata": {}, "outputs": [], @@ -32,14 +32,16 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "id": "2", "metadata": {}, "outputs": [], "source": [ "# Create test structure\n", "structure = Structure(\n", - " lattice=Lattice(np.array([[0, 2.715, 2.715], [2.715, 0, 2.715], [2.715, 2.715, 0]])),\n", + " lattice=Lattice(\n", + " np.array([[0, 2.715, 2.715], [2.715, 0, 2.715], [2.715, 2.715, 0]])\n", + " ),\n", " species=[\"Si\", \"Si\"],\n", " coords=np.array([np.zeros(3), np.ones(3) * 0.25]),\n", ")" @@ -47,7 +49,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "id": "3", "metadata": {}, "outputs": [], @@ -81,7 +83,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "id": "4", "metadata": {}, "outputs": [], @@ -96,7 +98,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "id": "5", "metadata": {}, "outputs": [], @@ -108,7 +110,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "id": "6", "metadata": {}, "outputs": [ @@ -143,14 +145,6 @@ "# Check the results\n", "print(outputs.get_results_for_image(-1))" ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "1aadaebf-f797-4733-8180-fc1850fa1069", - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { diff --git a/requirements-ci.txt b/requirements-ci.txt index c9bb416..b6328ba 100644 --- a/requirements-ci.txt +++ b/requirements-ci.txt @@ -6,4 +6,4 @@ pymatgen pymatgen-analysis-diffusion mp-api # BoltzTraP2 # Does not work because numpy not detected. -phonopy \ No newline at end of file +phonopy