Fix temperature units and add ASE-type functionality back into notebook

IRL2 · Aug 27, 2024 · d19d960 · d19d960
1 parent cc85812
commit d19d960
Showing 1 changed file with 39 additions and 8 deletions.
diff --git a/examples/ase/ase_openmm_graphene.ipynb b/examples/ase/ase_openmm_graphene.ipynb
@@ -226,10 +226,43 @@
     "graphene_ase_omm_sim = ASEOpenMMSimulation.from_simulation(simulation)\n",
     "graphene_ase_omm_sim.time_step = 0.05\n",
     "\n",
-    "# Pass the simulation to the OmniRunner\n",
-    "runner = OmniRunner.with_basic_server(graphene_ase_omm_sim, name=\"graphene-ase-omm-server\", port=0)"
+    "# Pass the simulation to the OmniRunner, load the simulation and pause it\n",
+    "runner = OmniRunner.with_basic_server(graphene_ase_omm_sim, name=\"graphene-ase-omm-server\", port=0)\n",
+    "runner.next()\n",
+    "runner.pause()"
    ]
   },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "Let's run a few steps and check that everything is working as expected."
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "graphene_ase_omm_sim.dynamics.run(10)"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "graphene_ase_omm_sim.dynamics.get_number_of_steps()"
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "Let's check the potential energy too."
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "graphene_ase_omm_sim.atoms.get_potential_energy()"
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -249,7 +282,7 @@
    "outputs": [],
    "source": [
     "# Start running the simulation\n",
-    "runner.next()"
+    "runner.play()"
    ]
   },
   {
@@ -319,7 +352,7 @@
     "\n",
     "    if not temp_min_val <= temperature <= temp_max_val:\n",
     "        raise ValueError(f'Temperature must be in range {temp_min_val} - {temp_max_val} Kelvin.')\n",
-    "    graphene_ase_omm_sim.dynamics.set_temperature(temperature_K=temperature * units.kB)\n",
+    "    graphene_ase_omm_sim.dynamics.set_temperature(temperature_K=temperature)\n",
     "\n",
     "\n",
     "def set_friction(friction=1):\n",
@@ -634,11 +667,9 @@
    ]
   },
   {
-   "cell_type": "markdown",
    "metadata": {},
-   "source": [
-    "With this functionality, you could write your own UI in Unity with our [libraries](https://github.com/IRL2/NarupaUnityPlugin/blob/2f5565608d9c0e1e9366a61d7c146b34eae84231/Grpc/GrpcClient.cs#L54), a python web app, or even C++."
-   ]
+   "cell_type": "markdown",
+   "source": "With this functionality, you could write your own UI in Unity with our [libraries](https://github.com/IRL2/NarupaUnityPlugin/blob/2f5565608d9c0e1e9366a61d7c146b34eae84231/Grpc/GrpcClient.cs#L54), a python web app, or even C++."
   },
   {
    "cell_type": "markdown",