linting

espressomd · Aug 16, 2024 · 8f5d3e6 · 8f5d3e6
1 parent 3c967af
commit 8f5d3e6
Showing 1 changed file with 28 additions and 33 deletions.
diff --git a/doc/tutorials/mlip/mlip.ipynb b/doc/tutorials/mlip/mlip.ipynb
@@ -33,26 +33,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from rdkit2ase import smiles2atoms\n",
-    "from mace.calculators import mace_mp\n",
-    "import numpy as np\n",
-    "from espressomd.zn import Visualizer\n",
     "import espressomd\n",
-    "from espressomd.plugins.ase import ASEInterface\n",
-    "import ase.io\n",
-    "import tqdm\n",
-    "import pint\n",
     "import ipsuite as ips\n",
-    "from rdkit2ase import smiles2atoms\n",
-    "from mace.calculators import mace_mp\n",
-    "import espressomd\n",
-    "from espressomd.plugins.ase import ASEInterface\n",
-    "import ase.io\n",
-    "import tqdm\n",
     "import numpy as np\n",
-    "from espressomd.zn import Visualizer\n",
+    "import pandas as pd\n",
+    "import pint\n",
     "import plotly.express as px\n",
-    "import pandas as pd"
+    "import tqdm\n",
+    "from espressomd.plugins.ase import ASEInterface\n",
+    "from espressomd.zn import Visualizer\n",
+    "from mace.calculators import mace_mp\n",
+    "from rdkit2ase import smiles2atoms"
    ]
   },
   {
@@ -69,8 +60,8 @@
    "outputs": [],
    "source": [
     "ureg = pint.UnitRegistry()\n",
-    "boltmk=1.380649e-23*ureg.J/ureg.K\n",
-    "boltmk = boltmk.to(ureg.eV/ureg.K)"
+    "boltmk = 1.380649e-23 * ureg.J / ureg.K\n",
+    "boltmk = boltmk.to(ureg.eV / ureg.K)"
    ]
   },
   {
@@ -165,7 +156,7 @@
    ],
    "source": [
     "print(etoh.get_potential_energy() * ureg.eV)\n",
-    "print(etoh.get_forces() * ureg.eV/ureg.angstrom)"
+    "print(etoh.get_forces() * ureg.eV / ureg.angstrom)"
    ]
   },
   {
@@ -182,7 +173,11 @@
    "outputs": [],
    "source": [
     "system = espressomd.System(box_l=[16] * 3)\n",
-    "system.time_step = (0.05 * ureg.fs).to(((1 * ureg.u * ureg.angstrom**2) / ureg.electron_volt)**0.5).magnitude\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",
+    ")\n",
     "system.cell_system.skin = 0.4"
    ]
   },
@@ -287,11 +282,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "system.integrator.set_steepest_descent(\n",
-    "        f_max=0.1,\n",
-    "        gamma=4, \n",
-    "        max_displacement=0.001\n",
-    "    )"
+    "system.integrator.set_steepest_descent(f_max=0.1, gamma=4, max_displacement=0.001)"
    ]
   },
   {
@@ -371,7 +362,9 @@
    "source": [
     "water = smiles2atoms(\"O\")\n",
     "sulfuric_acid = smiles2atoms(\"OS(=O)(=O)O\")\n",
-    "packmol = ips.nodes.Packmol(data=[[water], [sulfuric_acid]], count=[100, 1], density=1000)"
+    "packmol = ips.nodes.Packmol(\n",
+    "    data=[[water], [sulfuric_acid]], count=[100, 1], density=1000\n",
+    ")"
    ]
   },
   {
@@ -624,7 +617,11 @@
    "outputs": [],
    "source": [
     "system.box_l = packmol.atoms[0].get_cell().diagonal()\n",
-    "system.time_step = (0.05 * ureg.fs).to(((1 * ureg.u * ureg.angstrom**2) / ureg.electron_volt)**0.5).magnitude\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",
+    ")\n",
     "system.cell_system.skin = 0.4"
    ]
   },
@@ -637,11 +634,7 @@
     "system.ase = ASEInterface(type_mapping={x: x for x in set(packmol.atoms[0].numbers)})\n",
     "for atom in packmol.atoms[0]:\n",
     "    system.part.add(pos=atom.position, type=atom.number, mass=atom.mass)\n",
-    "system.integrator.set_steepest_descent(\n",
-    "        f_max=0.1,\n",
-    "        gamma=4, \n",
-    "        max_displacement=0.001\n",
-    "    )"
+    "system.integrator.set_steepest_descent(f_max=0.1, gamma=4, max_displacement=0.001)"
    ]
   },
   {
@@ -703,7 +696,9 @@
     "    system.part.all().ext_force = atoms.get_forces()\n",
     "    vis.zndraw.append(atoms)\n",
     "    system.integrator.run(1)\n",
-    "    tbar.set_description(f\"fmax: {np.linalg.norm(atoms.get_forces(), axis=0).max():.3f}\")"
+    "    tbar.set_description(\n",
+    "        f\"fmax: {np.linalg.norm(atoms.get_forces(), axis=0).max():.3f}\"\n",
+    "    )"
    ]
   },
   {