{ "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": [], "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", " " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.plotly.v1+json": { "config": { "linkText": "Export to plot.ly", "plotlyServerURL": "https://plot.ly", "showLink": false }, "data": [ { "flatshading": true, "i": [ 133, 137, 113, 137, 137, 134, 74, 134, 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