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cleanup plotting module
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@ireaml
ireaml committed Dec 25, 2023
1 parent 45ef3be commit b54e322
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3 changes: 3 additions & 0 deletions docs/TODO.md
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[ ] Tests
1. Check coverage of main functions

[ ] Code
* Cleanup plotting module. The function `plot_active_plane` is limited to only specific planes.

[ ] Tutorials
* Add tutorial for all main functions (currently missing `plot_variation_along_vector`, `plot_on_site_potential`)
62 changes: 31 additions & 31 deletions docs/tutorials/Porous/Porous.ipynb
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"6. Sample the potential from the pore centre"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/tmp/ipykernel_7455/391802285.py:7: DeprecationWarning: the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses\n",
" import imp\n"
]
}
],
"source": [
"%matplotlib inline\n",
"%load_ext autoreload\n",
"%autoreload 2\n",
"\n",
"import sys\n",
"sys.path.append('../../')\n",
"import imp\n",
"import macrodensity as md\n",
"import math\n",
"import numpy as np\n",
"import matplotlib.pyplot as plt\n",
"import os"
]
},
{
"cell_type": "markdown",
"metadata": {},
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},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 19,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"The autoreload extension is already loaded. To reload it, use:\n",
" %reload_ext autoreload\n"
]
}
],
"source": [
"%matplotlib inline\n",
"%load_ext autoreload\n",
"%autoreload 2\n",
"\n",
"import sys\n",
"sys.path.append('../../')\n",
"import imp\n",
"import macrodensity as md\n",
"import math\n",
"import numpy as np\n",
"import matplotlib.pyplot as plt\n",
"import os"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [
{
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},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 21,
"metadata": {},
"outputs": [
{
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88 changes: 88 additions & 0 deletions docs/tutorials/Slab/Bi2O3_slab.POSCAR
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89 changes: 83 additions & 6 deletions docs/tutorials/Slab/SlabCalculation.ipynb
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},
{
"cell_type": "code",
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"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
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},
{
"cell_type": "code",
"execution_count": 25,
"execution_count": 3,
"metadata": {},
"outputs": [
{
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},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 8,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"bunzip2: Can't open input file LOCPOT_Bi2O3.vasp.bz2: No such file or directory.\n"
]
}
],
"source": [
"if os.path.isfile('LOCPOT.BiO3.vasp'):\n",
" print('LOCPOT already exists')\n",
"else:\n",
" os.system('bunzip2 LOCPOT_Bi2O3.vasp.bz2')"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {},
"outputs": [],
"source": [
"import pymatgen\n",
"from pymatgen.core.structure import Structure\n",
"from pymatgen.core.surface import Slab\n",
"\n",
"\n",
"def get_layer_sites(\n",
" structure: Structure,\n",
" epsilon: float=1.5,\n",
"):\n",
" \"\"\"\n",
" Returns sites in top and bottom layer of slab. These are selected as those whose\n",
" z coordinate lies between the top/bottom of slab and top-epsilon/bottom+epsilon.\n",
"\n",
" Args:\n",
" structure (pymatgen.core.structure.Structure):\n",
" pymatgen Structure object of slab\n",
" epsilon (float):\n",
" Length from top/bottom of slab to select the sites that lie within\n",
" (i.e. sites within top/bottom surface of slab +- epsilon).\n",
" Defaults to 1.5 A.\n",
"\n",
" Returns:\n",
" [dict]: dict with top_layer and bottom_layer sites\n",
" \"\"\"\n",
" max_z = max(site.coords[2] for site in structure)\n",
" min_z = min(site.coords[2] for site in structure)\n",
" top_layer = [site for site in structure if site.coords[2] >= max_z - epsilon]\n",
" bottom_layer = [site for site in structure if site.coords[2] <= min_z + epsilon]\n",
" # print(f\"Number of sites in top layer: {len(top_layer)}\")\n",
" return {\"top_layer\": top_layer, \"bottom_layer\": bottom_layer}"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {},
"outputs": [
{
"data": {
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"[array([0.346566, 0.311911, 0.977977]),\n",
" array([0.112189, 0.94876 , 0.979416]),\n",
" array([0.257093, 0.532772, 0.997718])]"
]
},
"execution_count": 31,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from pymatgen.core.structure import Structure\n",
"\n",
"slab_struc = Structure.from_file(\"Bi2O3_slab.POSCAR\")\n",
"\n",
"# Get sites in surface layer\n",
"layers = get_layer_sites(slab_struc, 1.3)\n",
"layers[\"top_layer\"]\n",
"# Get fractional coordinates as points\n",
"top_layer_points = [site.frac_coords for site in layers[\"top_layer\"]]\n",
"top_layer_points"
]
},
{
"cell_type": "markdown",
"metadata": {},
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},
{
"cell_type": "code",
"execution_count": 19,
"execution_count": 13,
"metadata": {},
"outputs": [
{
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},
{
"cell_type": "code",
"execution_count": 30,
"execution_count": 14,
"metadata": {},
"outputs": [
{
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