Added a Lorenz CellML and SED-ML files, as well as a corresponding Py…

…thon script and Jupyter notebook.

The idea of the Python script will be to test all of our Python wrappers.

models/tests/jupyter/lorenz.ipynb

@@ -0,0 +1,112 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import OpenCOR as oc"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "s = oc.openSimulation('../sedml/lorenz/lorenz.sedml')\n",
+    "s"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "s.run()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "r = s.results()\n",
+    "r"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "states = r.states()\n",
+    "states"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "x = states['main/x'].values()\n",
+    "y = states['main/y'].values()\n",
+    "z = states['main/z'].values()\n",
+    "x,y,z"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib inline\n",
+    "from mpl_toolkits import mplot3d\n",
+    "import matplotlib.pyplot as plt"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plt.axes(projection='3d').plot3D(x, y, z)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "OpenCOR",
+   "language": "python",
+   "name": "opencor"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

models/tests/python/lorenz.py

@@ -0,0 +1,47 @@
+# Open our Lorenz SED-ML document
+
+import os
+import OpenCOR as oc
+
+s = oc.openSimulation(os.path.dirname(__file__) + '/../sedml/lorenz/lorenz.sedml')
+
+print('---------------------------------------')
+print('Simulation:')
+print(s)
+
+# Run our Lorenz simulation
+
+s.run()
+
+# Retrieve our simulation results
+
+r = s.results()
+
+print('---------------------------------------')
+print('Results:')
+print(r)
+
+# Retrieve our states
+
+states = r.states()
+
+print('---------------------------------------')
+print('States:')
+print(states)
+
+# Retrieve the values for our states
+
+x = states['main/x'].values()
+y = states['main/y'].values()
+z = states['main/z'].values()
+
+print('---------------------------------------')
+print('x, y and z:')
+print(x, y, z)
+
+# Generate a 3D plot for our states
+
+from mpl_toolkits import mplot3d
+import matplotlib.pyplot as plt
+
+plt.axes(projection='3d').plot3D(x, y, z)

models/tests/sedml/lorenz/lorenz.cellml

@@ -0,0 +1,79 @@
+<?xml version='1.0'?>
+<model name="Lorenz" xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
+    <component name="main">
+        <variable initial_value="0" name="t" units="dimensionless"/>
+        <variable initial_value="1" name="x" units="dimensionless"/>
+        <variable initial_value="1" name="y" units="dimensionless"/>
+        <variable initial_value="1" name="z" units="dimensionless"/>
+        <variable initial_value="10" name="sigma" units="dimensionless"/>
+        <variable initial_value="28" name="rho" units="dimensionless"/>
+        <variable initial_value="2.66667" name="beta" units="dimensionless"/>
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+                <eq/>
+                <apply>
+                    <diff/>
+                    <bvar>
+                        <ci>t</ci>
+                    </bvar>
+                    <ci>x</ci>
+                </apply>
+                <apply>
+                    <times/>
+                    <ci>sigma</ci>
+                    <apply>
+                        <minus/>
+                        <ci>y</ci>
+                        <ci>x</ci>
+                    </apply>
+                </apply>
+            </apply>
+            <apply>
+                <eq/>
+                <apply>
+                    <diff/>
+                    <bvar>
+                        <ci>t</ci>
+                    </bvar>
+                    <ci>y</ci>
+                </apply>
+                <apply>
+                    <minus/>
+                    <apply>
+                        <times/>
+                        <ci>x</ci>
+                        <apply>
+                            <minus/>
+                            <ci>rho</ci>
+                            <ci>z</ci>
+                        </apply>
+                    </apply>
+                    <ci>y</ci>
+                </apply>
+            </apply>
+            <apply>
+                <eq/>
+                <apply>
+                    <diff/>
+                    <bvar>
+                        <ci>t</ci>
+                    </bvar>
+                    <ci>z</ci>
+                </apply>
+                <apply>
+                    <minus/>
+                    <apply>
+                        <times/>
+                        <ci>x</ci>
+                        <ci>y</ci>
+                    </apply>
+                    <apply>
+                        <times/>
+                        <ci>beta</ci>
+                        <ci>z</ci>
+                    </apply>
+                </apply>
+            </apply>
+        </math>
+    </component>
+</model>