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zincware · Sep 16, 2024 · c48b455 · c48b455
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diff --git a/docs/source/examples/01_Data_Loading_and_Selection.ipynb b/docs/source/examples/01_Data_Loading_and_Selection.ipynb
@@ -33,21 +33,22 @@
     }
    ],
    "source": [
-    "import ipsuite as ips\n",
     "from zntrack.utils import cwd_temp_dir\n",
     "\n",
+    "import ipsuite as ips\n",
+    "\n",
     "temp_dir = cwd_temp_dir()\n",
     "\n",
-    "import ipsuite as ips\n",
     "\n",
     "import os\n",
+    "\n",
     "from ase import units\n",
     "from ase.calculators.emt import EMT\n",
     "from ase.io.trajectory import TrajectoryWriter\n",
     "from ase.lattice.cubic import FaceCenteredCubic\n",
-    "from ase.md.velocitydistribution import MaxwellBoltzmannDistribution\n",
     "from ase.md.langevin import Langevin\n",
-    "from ase.visualize import view\n"
+    "from ase.md.velocitydistribution import MaxwellBoltzmannDistribution\n",
+    "from ase.visualize import view"
    ]
   },
   {
@@ -119,10 +120,10 @@
     "# Set up a crystal\n",
     "atoms = FaceCenteredCubic(\n",
     "    directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],\n",
-    "    symbol='Cu',\n",
+    "    symbol=\"Cu\",\n",
     "    size=(size, size, size),\n",
-    "    pbc=True\n",
-    ")\n"
+    "    pbc=True,\n",
+    ")"
    ]
   },
   {
@@ -225,7 +226,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "trajectory.load() # requires the project to have been run"
+    "trajectory.load()  # requires the project to have been run"
    ]
   },
   {
@@ -296,9 +297,19 @@
    ],
    "source": [
     "with project:\n",
-    "    random_test_selection = ips.configuration_selection.RandomSelection(data=trajectory, n_configurations=10, name=\"random_test_selection\")\n",
-    "    random_val_selection = ips.configuration_selection.RandomSelection(data=random_test_selection.excluded_atoms, n_configurations=15, name=\"random_val_selection\")\n",
-    "    random_train_selection = ips.configuration_selection.RandomSelection(data=random_val_selection.excluded_atoms, n_configurations=75, name=\"random_train_selection\")\n",
+    "    random_test_selection = ips.configuration_selection.RandomSelection(\n",
+    "        data=trajectory, n_configurations=10, name=\"random_test_selection\"\n",
+    "    )\n",
+    "    random_val_selection = ips.configuration_selection.RandomSelection(\n",
+    "        data=random_test_selection.excluded_atoms,\n",
+    "        n_configurations=15,\n",
+    "        name=\"random_val_selection\",\n",
+    "    )\n",
+    "    random_train_selection = ips.configuration_selection.RandomSelection(\n",
+    "        data=random_val_selection.excluded_atoms,\n",
+    "        n_configurations=75,\n",
+    "        name=\"random_train_selection\",\n",
+    "    )\n",
     "project.run()"
    ]
   },
@@ -415,13 +426,23 @@
    "source": [
     "with ips.Project(remove_existing_graph=True) as project:\n",
     "    trajectory = ips.AddData(file=traj_path, name=\"trajectory\")\n",
-    "    test_split = ips.configuration_selection.SplitSelection(data=trajectory, split=0.1, name=\"test_split\")\n",
-    "    val_split = ips.configuration_selection.SplitSelection(data=test_split.excluded_atoms, split=0.17, name=\"val_split\") # 0.15 / 0.9 * 1.0 \\approx 0.17\n",
-    "    train_split = val_split.excluded_atoms # 0.8 of the total data\n",
+    "    test_split = ips.configuration_selection.SplitSelection(\n",
+    "        data=trajectory, split=0.1, name=\"test_split\"\n",
+    "    )\n",
+    "    val_split = ips.configuration_selection.SplitSelection(\n",
+    "        data=test_split.excluded_atoms, split=0.17, name=\"val_split\"\n",
+    "    )  # 0.15 / 0.9 * 1.0 \\approx 0.17\n",
+    "    train_split = val_split.excluded_atoms  # 0.8 of the total data\n",
     "\n",
-    "    test_data = ips.configuration_selection.UniformTemporalSelection(data=test_split, n_configurations=10, name=\"test_data\")\n",
-    "    val_data = ips.configuration_selection.UniformTemporalSelection(data=val_split, n_configurations=15, name=\"val_data\")\n",
-    "    train_data = ips.configuration_selection.UniformEnergeticSelection(data=train_split, n_configurations=80, name=\"train_data\")\n",
+    "    test_data = ips.configuration_selection.UniformTemporalSelection(\n",
+    "        data=test_split, n_configurations=10, name=\"test_data\"\n",
+    "    )\n",
+    "    val_data = ips.configuration_selection.UniformTemporalSelection(\n",
+    "        data=val_split, n_configurations=15, name=\"val_data\"\n",
+    "    )\n",
+    "    train_data = ips.configuration_selection.UniformEnergeticSelection(\n",
+    "        data=train_split, n_configurations=80, name=\"train_data\"\n",
+    "    )\n",
     "\n",
     "project.run()"
    ]

diff --git a/docs/source/examples/03_Analysing_Datasets_and_Model_Predictions.ipynb b/docs/source/examples/03_Analysing_Datasets_and_Model_Predictions.ipynb
@@ -42,21 +42,19 @@
     }
    ],
    "source": [
-    "import ipsuite as ips\n",
     "from zntrack.utils import cwd_temp_dir\n",
     "\n",
     "temp_dir = cwd_temp_dir()\n",
     "\n",
-    "import ipsuite as ips\n",
     "\n",
     "import os\n",
+    "\n",
     "from ase import units\n",
     "from ase.calculators.emt import EMT\n",
     "from ase.io.trajectory import TrajectoryWriter\n",
     "from ase.lattice.cubic import FaceCenteredCubic\n",
-    "from ase.md.velocitydistribution import MaxwellBoltzmannDistribution\n",
     "from ase.md.langevin import Langevin\n",
-    "from ase.visualize import view\n"
+    "from ase.md.velocitydistribution import MaxwellBoltzmannDistribution"
    ]
   },
   {
@@ -115,9 +113,9 @@
     "# Set up a crystal\n",
     "atoms = FaceCenteredCubic(\n",
     "    directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],\n",
-    "    symbol='Cu',\n",
+    "    symbol=\"Cu\",\n",
     "    size=(size, size, size),\n",
-    "    pbc=True\n",
+    "    pbc=True,\n",
     ")"
    ]
   },

diff --git a/docs/source/examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb b/docs/source/examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb
@@ -13,9 +13,7 @@
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": [
-    "import ipsuite as ips"
-   ]
+   "source": []
   }
  ],
  "metadata": {

diff --git a/docs/source/examples/05_Labeling_with_Calculators.ipynb b/docs/source/examples/05_Labeling_with_Calculators.ipynb
@@ -13,9 +13,7 @@
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": [
-    "import ipsuite as ips"
-   ]
+   "source": []
   }
  ],
  "metadata": {

diff --git a/docs/source/examples/06_Bootstrapping_Datasets.ipynb b/docs/source/examples/06_Bootstrapping_Datasets.ipynb
@@ -49,12 +49,12 @@
     }
    ],
    "source": [
-    "import ipsuite as ips\n",
-    "import znflow\n",
     "import matplotlib.pyplot as plt\n",
-    "\n",
+    "import znflow\n",
     "from zntrack.utils import cwd_temp_dir\n",
     "\n",
+    "import ipsuite as ips\n",
+    "\n",
     "temp_dir = cwd_temp_dir()"
    ]
   },
@@ -376,7 +376,9 @@
     "        data=[water.atoms], count=[10], density=997\n",
     "    )\n",
     "\n",
-    "    opt_calc = ips.calculators.xTBSinglePoint(data=packmol, method=\"gfn1-xtb\", name=\"opt_calc\")\n",
+    "    opt_calc = ips.calculators.xTBSinglePoint(\n",
+    "        data=packmol, method=\"gfn1-xtb\", name=\"opt_calc\"\n",
+    "    )\n",
     "\n",
     "    geopt = ips.calculators.ASEGeoOpt(\n",
     "        model=opt_calc,\n",
@@ -390,27 +392,29 @@
     "        data=geopt.atoms,\n",
     "        data_id=-1,\n",
     "        n_configurations=n_configs,\n",
-    "        maximum=0.08, # Ang max atomic displacement\n",
-    "        include_original=True\n",
+    "        maximum=0.08,  # Ang max atomic displacement\n",
+    "        include_original=True,\n",
     "    )\n",
     "    rotate = ips.bootstrap.RotateMolecules(\n",
     "        data=geopt.atoms,\n",
     "        data_id=-1,\n",
     "        n_configurations=n_configs,\n",
     "        maximum=15,  # deg max rotation\n",
-    "        include_original=False\n",
+    "        include_original=False,\n",
     "    )\n",
     "    translate = ips.bootstrap.TranslateMolecules(\n",
     "        data=geopt.atoms,\n",
     "        data_id=-1,\n",
     "        n_configurations=n_configs,\n",
-    "        maximum=0.3, # Ang max molecular displacement\n",
-    "        include_original=False\n",
+    "        maximum=0.3,  # Ang max molecular displacement\n",
+    "        include_original=False,\n",
     "    )\n",
     "\n",
     "    bootstrap_configurations = rattle.atoms + rotate.atoms + translate.atoms\n",
     "\n",
-    "    labeling_calc = ips.calculators.xTBSinglePoint(data=bootstrap_configurations, method=\"gfn1-xtb\", name=\"label_calc\")\n",
+    "    labeling_calc = ips.calculators.xTBSinglePoint(\n",
+    "        data=bootstrap_configurations, method=\"gfn1-xtb\", name=\"label_calc\"\n",
+    "    )\n",
     "    volume_scan = ips.analysis.BoxScale(\n",
     "        data=rattle.atoms,\n",
     "        data_id=0,\n",
@@ -473,7 +477,7 @@
     "plt.xlabel(energy_hist.xlabel)\n",
     "plt.ylabel(energy_hist.ylabel)\n",
     "plt.yscale(\"log\")\n",
-    "plt.show()\n"
+    "plt.show()"
    ]
   },
   {