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[pre-commit.ci] pre-commit autoupdate #323

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merged 2 commits into from
Aug 20, 2024
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[pre-commit.ci] pre-commit autoupdate #323

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a7b37f5
[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot] Aug 19, 2024
9c3ef9a
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 19, 2024
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2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ repos:

- repo: https://github.com/astral-sh/ruff-pre-commit
# Ruff version.
rev: v0.5.6
rev: v0.6.1
hooks:
# Run the linter.
- id: ruff
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13 changes: 7 additions & 6 deletions examples/01_Model_Training.ipynb
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Expand Up @@ -7,6 +7,7 @@
"outputs": [],
"source": [
"import warnings\n",
"\n",
"warnings.simplefilter('ignore')"
]
},
Expand All @@ -31,7 +32,8 @@
"outputs": [],
"source": [
"from pathlib import Path\n",
"from apax.utils.datasets import mod_md_datasets, download_etoh_ccsdt\n",
"\n",
"from apax.utils.datasets import download_etoh_ccsdt, mod_md_datasets\n",
"\n",
"data_path = Path(\"project\")\n",
"\n",
Expand Down Expand Up @@ -187,9 +189,9 @@
"metadata": {},
"outputs": [],
"source": [
"from apax.utils.helpers import mod_config\n",
"import yaml\n",
"\n",
"from apax.utils.helpers import mod_config\n",
"\n",
"config_path = Path(\"config.yaml\")\n",
"\n",
Expand Down Expand Up @@ -311,7 +313,6 @@
"from apax.train.run import run\n",
"from apax.utils.helpers import mod_config\n",
"\n",
"\n",
"config_path = Path(\"config.yaml\")\n",
"\n",
"config_updates = {\n",
Expand Down Expand Up @@ -342,9 +343,9 @@
}
],
"source": [
"import csv\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"\n",
"from apax.utils.helpers import load_csv_metrics\n",
"\n",
"metrics_path = \"project/models/ethanol_ccsd_t_script/log.csv\"\n",
Expand All @@ -354,7 +355,7 @@
"\n",
"fig, axes = plt.subplots(2, 2, constrained_layout=True)\n",
"axes = axes.ravel()\n",
"fig.suptitle(f'Metrics', fontsize=16)\n",
"fig.suptitle('Metrics', fontsize=16)\n",
"\n",
"for id, key in enumerate(keys):\n",
" val = np.array(data_dict[f\"val_{key}\"])\n",
Expand Down Expand Up @@ -440,7 +441,7 @@
"\n",
"fig, axes = plt.subplots(1, 4, constrained_layout=True)\n",
"axes = axes.ravel()\n",
"fig.suptitle(f'Metrics', fontsize=16)\n",
"fig.suptitle('Metrics', fontsize=16)\n",
"\n",
"for id, key in enumerate(keys):\n",
" test = np.array(data_dict[f\"test_{key}\"])\n",
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17 changes: 10 additions & 7 deletions examples/02_Molecular_Dynamics.ipynb
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Expand Up @@ -7,6 +7,7 @@
"outputs": [],
"source": [
"import warnings\n",
"\n",
"warnings.simplefilter('ignore')"
]
},
Expand Down Expand Up @@ -55,11 +56,12 @@
],
"source": [
"from pathlib import Path\n",
"from apax.utils.datasets import download_etoh_ccsdt, mod_md_datasets\n",
"from apax.train.run import run\n",
"from apax.utils.helpers import mod_config\n",
"\n",
"import yaml\n",
"\n",
"from apax.train.run import run\n",
"from apax.utils.datasets import download_etoh_ccsdt, mod_md_datasets\n",
"from apax.utils.helpers import mod_config\n",
"\n",
"# Download and modify the dataset\n",
"data_path = Path(\"project\")\n",
Expand Down Expand Up @@ -118,12 +120,12 @@
"metadata": {},
"outputs": [],
"source": [
"from ase.io import read\n",
"from apax.md import ASECalculator\n",
"from ase.md.langevin import Langevin\n",
"from ase import units\n",
"from ase.io import read\n",
"from ase.io.trajectory import Trajectory\n",
"from ase.md.langevin import Langevin\n",
"\n",
"from apax.md import ASECalculator\n",
"\n",
"# read starting structure and define modelpath\n",
"atoms = read(train_file_path, index=0)\n",
Expand Down Expand Up @@ -164,6 +166,7 @@
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"\n",
"\n",
"def plot_bondlength_distribution(traj, indices: list, bins: int=25):\n",
" oh_dist = []\n",
" for atoms in traj:\n",
Expand Down Expand Up @@ -253,9 +256,9 @@
"metadata": {},
"outputs": [],
"source": [
"from apax.utils.helpers import mod_config\n",
"import yaml\n",
"\n",
"from apax.utils.helpers import mod_config\n",
"\n",
"md_config_path = Path(\"md_config.yaml\")\n",
"\n",
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12 changes: 9 additions & 3 deletions examples/03_Transfer_Learning.ipynb
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Expand Up @@ -53,9 +53,15 @@
"outputs": [],
"source": [
"from pathlib import Path\n",
"from apax.utils.datasets import download_md22_benzene_CCSDT, mod_md_datasets, download_benzene_DFT\n",
"from apax.utils.helpers import mod_config\n",
"import yaml"
"\n",
"import yaml\n",
"\n",
"from apax.utils.datasets import (\n",
" download_benzene_DFT,\n",
" download_md22_benzene_CCSDT,\n",
" mod_md_datasets,\n",
")\n",
"from apax.utils.helpers import mod_config"
]
},
{
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13 changes: 6 additions & 7 deletions examples/04_Batch_Data_Selection.ipynb
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Expand Up @@ -21,17 +21,16 @@
"outputs": [],
"source": [
"from pathlib import Path\n",
"import yaml\n",
"\n",
"from ase.md.velocitydistribution import MaxwellBoltzmannDistribution\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import yaml\n",
"from ase import units\n",
"from ase.io import read\n",
"from ase.io.trajectory import TrajectoryWriter\n",
"from ase.md.langevin import Langevin\n",
"from ase.md.velocitydistribution import MaxwellBoltzmannDistribution\n",
"from ase.optimize.fire import FIRE\n",
"from ase.io.trajectory import TrajectoryWriter\n",
"from ase.io import read\n",
"import numpy as np\n",
"import matplotlib.pyplot as plt\n",
"\n",
"\n",
"from apax.bal import api\n",
"from apax.md import ASECalculator\n",
Expand Down
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