adding spatial birth death model, shows error for #78

examples/tests/Spatial_Birth_Death.ipynb

@@ -0,0 +1,255 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import numpy\n",
+    "import matplotlib.pyplot as plt"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'../../spatialpy/__init__.py'"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "import sys\n",
+    "sys.path.insert(0,'../..')\n",
+    "import spatialpy\n",
+    "spatialpy.__file__"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "model = spatialpy.Model('Spatial Birth-Death')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "model.mesh = spatialpy.Mesh.create_3D_domain([0,1],[0,1],[0,0.1], 10,10,1, fixed=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rabbits = model.add_species(spatialpy.Species('rabbits', D=0.1))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "model.add_initial_condition(spatialpy.ScatterInitialCondition(rabbits, 100, types=None))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[<spatialpy.Model.Parameter at 0x7f6ade4d9280>,\n",
+       " <spatialpy.Model.Parameter at 0x7f6ade4d98e0>]"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "kb=spatialpy.Parameter('k_birth',10)\n",
+    "kd=spatialpy.Parameter('k_death',0.1)\n",
+    "model.add_parameter([kb,kd])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "model.add_reaction(spatialpy.Reaction(\n",
+    "    'birth',\n",
+    "    reactants={},\n",
+    "    products={rabbits:1},\n",
+    "    rate=kb))\n",
+    "#model.add_reaction(spatialpy.Reaction(\n",
+    "#    'death',\n",
+    "#    reactants={rabbits:1},\n",
+    "#    products={},\n",
+    "#    rate=kd))\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "model.staticDomain"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "model.timespan(numpy.arange(0,10,1))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "model.timestep_size = 1"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Reading stdout/stderr from process:\n",
+      "\n",
+      "make: *** No rule to make target 'Birth-Death_generated_model.c'.  Stop.\n",
+      "\n"
+     ]
+    },
+    {
+     "ename": "SimulationError",
+     "evalue": "Compilation of solver failed, return_code=2",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mSimulationError\u001b[0m                           Traceback (most recent call last)",
+      "\u001b[0;32m<timed exec>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n",
+      "\u001b[0;32m~/Desktop/research/SpatialPy/spatialpy/Model.py\u001b[0m in \u001b[0;36mrun\u001b[0;34m(self, number_of_trajectories, seed, timeout, number_of_threads, debug_level, debug, profile)\u001b[0m\n\u001b[1;32m    103\u001b[0m         \u001b[0msol\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mSolver\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdebug_level\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdebug_level\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    104\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 105\u001b[0;31m         return sol.run(number_of_trajectories=number_of_trajectories, seed=seed, timeout=timeout,\n\u001b[0m\u001b[1;32m    106\u001b[0m                        number_of_threads=number_of_threads, debug=debug, profile=profile)\n\u001b[1;32m    107\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/Desktop/research/SpatialPy/spatialpy/Solver.py\u001b[0m in \u001b[0;36mrun\u001b[0;34m(self, number_of_trajectories, seed, timeout, number_of_threads, debug, profile)\u001b[0m\n\u001b[1;32m    131\u001b[0m         \u001b[0;31m# Check if compiled, call compile() if not.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    132\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mis_compiled\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 133\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcompile\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdebug\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdebug\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mprofile\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mprofile\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    134\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    135\u001b[0m         \u001b[0;31m# Execute the solver\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/Desktop/research/SpatialPy/spatialpy/Solver.py\u001b[0m in \u001b[0;36mcompile\u001b[0;34m(self, debug, profile)\u001b[0m\n\u001b[1;32m    103\u001b[0m             \u001b[0;32mexcept\u001b[0m \u001b[0mException\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0me\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    104\u001b[0m                 \u001b[0;32mpass\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 105\u001b[0;31m             raise SimulationError(\n\u001b[0m\u001b[1;32m    106\u001b[0m                 \"Compilation of solver failed, return_code={0}\".format(return_code))\n\u001b[1;32m    107\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mSimulationError\u001b[0m: Compilation of solver failed, return_code=2"
+     ]
+    }
+   ],
+   "source": [
+    "%time result = model.run()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "NameError",
+     "evalue": "name 'result' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-14-baaa9e3c3437>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mresult\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplot_property\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'type'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "\u001b[0;31mNameError\u001b[0m: name 'result' is not defined"
+     ]
+    }
+   ],
+   "source": [
+    "result.plot_property('type')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "result.plot_species('rabbits', animated=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}