Some cleanup and figuring out environment issues

espressomd · Sep 9, 2024 · f1a3c1b · f1a3c1b
1 parent 2a99c0d
commit f1a3c1b
Showing 1 changed file with 65 additions and 17 deletions.
diff --git a/doc/tutorials/mlip/mlip.ipynb b/doc/tutorials/mlip/mlip.ipynb
@@ -29,6 +29,26 @@
     "We can use "
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# packmol"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# import os\n",
+    "# os.environ[\"PATH\"] = f\"{os.environ['PATH']}:/tikhome/ess_delme/Documents/test_for_ml_tutorial/espresso/build\"\n",
+    "# os.environ[\"CUDA_VISIBLE_DEVICES\"] = \"-1\""
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -58,7 +78,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "For MLIP the typical unit system is energies in eV, distances in Angstrom, time in fs and mass in atomic units. This is also the default unit system within ASE. We will use pint to ensure correct unit usage within ESPResSo. For setting the simulation temperature, we will also convert the boltzmann constant `boltzmann_k` to our desired unit system."
+    "For MLIP the typical unit system is energies in eV, distances in Angstrom, time in fs and mass in atomic units. This is also the default unit system within ASE. We will use pint to ensure correct unit usage within ESPResSo."
    ]
   },
   {
@@ -67,9 +87,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ureg = pint.UnitRegistry()\n",
-    "boltzmann_k = 1.380649e-23 * ureg.J / ureg.K\n",
-    "boltzmann_k = boltzmann_k.to(ureg.eV / ureg.K)"
+    "ureg = pint.UnitRegistry()"
    ]
   },
   {
@@ -148,9 +166,8 @@
    "source": [
     "system = espressomd.System(box_l=[16] * 3) # A cubic box of 16 Angstroms\n",
     "system.time_step = (\n",
-    "    (0.05 * ureg.fs)\n",
-    "    .to(((1 * ureg.u * ureg.angstrom**2) / ureg.electron_volt) ** 0.5)\n",
-    "    .magnitude\n",
+    "    (0.5 * ureg.fs)\n",
+    "    .m_as(((1 * ureg.u * ureg.angstrom**2) / ureg.electron_volt) ** 0.5)\n",
     ") # we convert the time units from fs to be in line with our other units for mass, distance and energy.\n",
     "system.cell_system.skin = 0.4"
    ]
@@ -210,7 +227,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "tbar = tqdm.trange(500, ncols=120)\n",
+    "tbar = tqdm.trange(10, ncols=120)\n",
     "for idx in tbar:\n",
     "    forces = mace_mp_calc.get_forces(system.ase.get())\n",
     "    system.part.all().ext_force = forces\n",
@@ -230,7 +247,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### MD Simulations of Sulfuric Acid and Water"
+    "# MD Simulations of Sulfuric Acid and Water"
    ]
   },
   {
@@ -284,7 +301,7 @@
    "source": [
     "system.box_l = box_of_atoms.get_cell().diagonal()\n",
     "system.time_step = (\n",
-    "    (0.05 * ureg.fs)\n",
+    "    (0.25 * ureg.fs)\n",
     "    .to(((1 * ureg.u * ureg.angstrom**2) / ureg.electron_volt) ** 0.5)\n",
     "    .magnitude\n",
     ")\n",
@@ -313,9 +330,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "del vis.zndraw[:]\n",
@@ -330,7 +345,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "tbar = tqdm.trange(500, ncols=120)\n",
+    "vis.zndraw.config.scene.vector_scale = 0"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tbar = tqdm.trange(50, ncols=120)\n",
     "for _ in tbar:\n",
     "    atoms = system.ase.get()\n",
     "    atoms.calc = mace_mp_calc\n",
@@ -367,7 +391,7 @@
    "source": [
     "# Langevin dynamics at 400 K\n",
     "system.integrator.set_vv()\n",
-    "system.thermostat.set_langevin(kT=(400 * ureg.K * boltzmann_k).magnitude, gamma=2, seed=42)"
+    "system.thermostat.set_langevin(kT=(400 * ureg.K * ureg.boltzmann_constant).m_as(\"eV\"), gamma=2, seed=42)"
    ]
   },
   {
@@ -376,7 +400,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "tbar = tqdm.trange(5000, ncols=120)\n",
+    "tbar = tqdm.trange(500, ncols=120)\n",
     "for idx in tbar:\n",
     "    atoms = system.ase.get()\n",
     "    atoms.calc = mace_mp_calc\n",
@@ -402,9 +426,11 @@
    "source": [
     "OH_1 = []\n",
     "OH_2 = []\n",
+    "energies = []\n",
     "for atoms in vis.zndraw:\n",
     "    OH_1.append(atoms.get_distance(300, 305, mic=True))\n",
     "    OH_2.append(atoms.get_distance(304, 306, mic=True))\n",
+    "    energies.append(atoms.get_potential_energy())\n",
     "\n",
     "df = pd.DataFrame({\"OH_1\": OH_1, \"OH_2\": OH_2})\n",
     "fig = px.line(df, y=[\"OH_1\", \"OH_2\"])"
@@ -426,6 +452,28 @@
     "vis.zndraw.figures = {\"distance\": fig.to_json()}"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "fig"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df = pd.DataFrame({\"Energies\": energies})\n",
+    "fig = px.line(df, y=\"Energies\")\n",
+    "fig"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -467,7 +515,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,