{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# The sGFRD Method"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The `numpy-stl` module is required for visualizations of a STL mesh."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/kaizu/.local/share/virtualenvs/python-eSbFG-Wg/lib/python3.7/importlib/_bootstrap.py:219: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
" return f(*args, **kwds)\n"
]
}
],
"source": [
"# !pip install numpy-stl\n",
"import stl"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Set Plotly as the default backend."
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/kaizu/.local/share/virtualenvs/python-eSbFG-Wg/lib/python3.7/site-packages/xarray/core/merge.py:18: FutureWarning: The Panel class is removed from pandas. Accessing it from the top-level namespace will also be removed in the next version\n",
" PANDAS_TYPES = (pd.Series, pd.DataFrame, pd.Panel)\n",
"/home/kaizu/.local/share/virtualenvs/python-eSbFG-Wg/lib/python3.7/site-packages/xarray/core/dataarray.py:1829: FutureWarning: The Panel class is removed from pandas. Accessing it from the top-level namespace will also be removed in the next version\n",
" 'DataArray', pd.Series, pd.DataFrame, pd.Panel]:\n"
]
}
],
"source": [
"from ecell4.prelude import *"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"import ecell4.plotting\n",
"import ecell4.plotting._plotly\n",
"ecell4.plotting.BACKEND = ecell4.plotting._plotly\n",
"from ecell4.plotting._plotly import plot_stl"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"f = sgfrd.Factory()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Diffusion on a Triangle Mesh"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Here is a STL-format file named [stanford_bunny.stl](https://github.com/kaizu/ecell4_docs/blob/latest/en/examples/stanford_bunny.stl):"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
" \n",
" "
]
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