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Merged
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Nov 12, 2024
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Release for v1.2.2 #6

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2,506 changes: 1,736 additions & 770 deletions docs/poetry.lock
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6 changes: 3 additions & 3 deletions tutorials/en/1_1_welcome.ipynb
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"codemirror_mode": {
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40 changes: 20 additions & 20 deletions tutorials/en/1_2_atomistic_simulation_intro.ipynb
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"name": "stdout",
"output_type": "stream",
"text": [
" Step Time Energy fmax\n",
"BFGS: 0 01:47:51 -57.136946 0.0206\n",
"Dyn step: 0, energy: -1523.124\n",
"Dyn step: 10, energy: -1523.067\n",
"Dyn step: 20, energy: -1523.070\n",
"Dyn step: 30, energy: -1523.098\n",
"Dyn step: 40, energy: -1523.075\n",
"Dyn step: 50, energy: -1523.080\n",
"Dyn step: 60, energy: -1523.089\n",
"Dyn step: 70, energy: -1523.081\n",
"Dyn step: 80, energy: -1523.082\n",
"Dyn step: 90, energy: -1523.083\n",
"Dyn step: 100, energy: -1523.088\n"
" Step Time Energy fmax\n",
"BFGS: 0 06:22:44 -57.074789 0.015096\n",
"Dyn step: 0, energy: -1517.819\n",
"Dyn step: 10, energy: -1517.752\n",
"Dyn step: 20, energy: -1517.766\n",
"Dyn step: 30, energy: -1517.782\n",
"Dyn step: 40, energy: -1517.764\n",
"Dyn step: 50, energy: -1517.773\n",
"Dyn step: 60, energy: -1517.776\n",
"Dyn step: 70, energy: -1517.774\n",
"Dyn step: 80, energy: -1517.769\n",
"Dyn step: 90, energy: -1517.776\n",
"Dyn step: 100, energy: -1517.778\n"
]
},
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Expand All @@ -173,7 +173,7 @@
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"output_type": "stream",
"text": [
"[Parallel(n_jobs=16)]: Using backend ThreadingBackend with 16 concurrent workers.\n",
"[Parallel(n_jobs=16)]: Done 12 out of 21 | elapsed: 38.8s remaining: 29.1s\n",
"[Parallel(n_jobs=16)]: Done 21 out of 21 | elapsed: 48.8s finished\n"
"[Parallel(n_jobs=16)]: Done 12 out of 21 | elapsed: 39.4s remaining: 29.6s\n",
"[Parallel(n_jobs=16)]: Done 21 out of 21 | elapsed: 48.9s finished\n"
]
},
{
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],
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30 changes: 17 additions & 13 deletions tutorials/en/1_3_ase_basic.ipynb
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52 changes: 26 additions & 26 deletions tutorials/en/1_4_ase_structure.ipynb
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74 changes: 36 additions & 38 deletions tutorials/en/1_5_ase_calculator.ipynb
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"name": "stdout",
"output_type": "stream",
"text": [
"Total Energy : -3.853510 eV\n",
"Total Energy : -3.808640 eV\n",
"Kinetic Energy : 0.009921 eV\n",
"Potential Energy : -3.863431 eV\n"
"Potential Energy : -3.818561 eV\n"
]
}
],
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"output_type": "stream",
"text": [
"E_pot -2.2e+01 eV\n",
"charges [ 3.9643837e-08 4.6361539e-08 -3.9290802e-09 -8.2076319e-08] C\n",
"forces [[ 1.40969295e-07 -9.84009146e-07 -6.92488049e-07]\n",
" [-4.10598609e-07 2.30313659e-07 4.85817902e-07]\n",
" [ 3.25740651e-07 1.38352914e-07 1.25854928e-06]\n",
" [-5.61113370e-08 6.15342574e-07 -1.05187913e-06]] eV/A\n",
"stress [-5.88080354e-02 -5.88080333e-02 -5.88080171e-02 -7.95536639e-09\n",
" 1.62605977e-08 -1.87038475e-08] eV/A^2\n"
"charges [ 1.56390826e-07 4.79747513e-08 1.49468789e-07 -3.53834395e-07] C\n",
"forces [[ 1.21045008e-06 -1.28531060e-07 1.16374716e-06]\n",
" [-8.99028036e-07 9.10295516e-07 -7.65895014e-07]\n",
" [ 8.04090586e-07 -1.76741016e-06 1.52298933e-06]\n",
" [-1.11551263e-06 9.85645703e-07 -1.92084147e-06]] eV/A\n",
"stress [-5.98167504e-02 -5.98167416e-02 -5.98167977e-02 9.46340221e-09\n",
" -2.35475377e-08 -5.36077254e-09] eV/A^2\n"
]
}
],
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"name": "stdout",
"output_type": "stream",
"text": [
"CPU times: user 3.05 ms, sys: 337 µs, total: 3.38 ms\n",
"Wall time: 48.6 ms\n",
"CPU times: user 352 µs, sys: 39 µs, total: 391 µs\n",
"Wall time: 395 µs\n"
"CPU times: user 3.06 ms, sys: 0 ns, total: 3.06 ms\n",
"Wall time: 94 ms\n",
"CPU times: user 375 µs, sys: 61 µs, total: 436 µs\n",
"Wall time: 383 µs\n"
]
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"text": [
"----- 1st calc -----\n",
"CPU times: user 4.12 ms, sys: 0 ns, total: 4.12 ms\n",
"Wall time: 47.4 ms\n",
"After 1st calc : {'energy': -21.749338573241698, 'forces': array([[-3.52587698e-07, -3.67407246e-07, -6.28612478e-07],\n",
" [ 3.12991254e-07, -6.24721146e-07, -6.07309746e-07],\n",
" [-7.87068084e-07, 3.29968240e-07, 1.17355387e-06],\n",
" [ 8.26664527e-07, 6.62160152e-07, 6.23683523e-08]]), 'charges': array([ 2.5585669e-08, 3.7438472e-08, 9.1334904e-08, -1.5435910e-07],\n",
" dtype=float32), 'free_energy': -21.749338573241698, 'stress': array([-5.88080908e-02, -5.88081207e-02, -5.88080733e-02, -3.52897701e-08,\n",
" -7.21264163e-09, -9.03543418e-09])}\n",
"CPU times: user 3.16 ms, sys: 285 µs, total: 3.44 ms\n",
"Wall time: 90.3 ms\n",
"After 1st calc : {'energy': -21.712707825955075, 'forces': array([[-1.78798193e-07, 8.57089841e-08, -9.71775560e-07],\n",
" [-3.81674838e-07, 2.40788247e-07, 4.98792271e-07],\n",
" [ 9.00971539e-07, -2.72842101e-07, 1.12511234e-06],\n",
" [-3.40498508e-07, -5.36551305e-08, -6.52129048e-07]]), 'charges': array([-2.17493621e-07, -2.45786026e-07, -9.83995818e-09, 4.73119684e-07]), 'calc_stats': {'elapsed_usec_infer': 36693, 'elapsed_usec': 83022, 'elapsed_usec_preprocess': 3930, 'n_neighbors': 400}, 'free_energy': -21.712707825955075, 'stress': array([-5.98166255e-02, -5.98166500e-02, -5.98166300e-02, 4.26570321e-08,\n",
" -4.45518682e-08, 3.79886465e-08])}\n",
"After reset : {}\n",
"----- 2nd calc -----\n",
"CPU times: user 3.78 ms, sys: 0 ns, total: 3.78 ms\n",
"Wall time: 47.2 ms\n",
"After 2nd calc : {'energy': -21.74933875483777, 'forces': array([[-1.75533801e-07, -7.07352070e-08, -1.31710982e-07],\n",
" [ 3.94759559e-07, -1.04306302e-06, 7.94492340e-07],\n",
" [-2.85749367e-07, 3.94858442e-07, 9.49207189e-08],\n",
" [ 6.65236078e-08, 7.18939785e-07, -7.57702077e-07]]), 'charges': array([-3.10214290e-08, 3.39031700e-08, 1.06610344e-07, -1.09492071e-07],\n",
" dtype=float32), 'free_energy': -21.74933875483777, 'stress': array([-5.88080508e-02, -5.88080022e-02, -5.88080224e-02, -5.20240851e-09,\n",
" 6.77284397e-09, -7.30662162e-09])}\n"
"CPU times: user 1.66 ms, sys: 0 ns, total: 1.66 ms\n",
"Wall time: 57.7 ms\n",
"After 2nd calc : {'energy': -21.712705946017945, 'forces': array([[ 9.52835494e-08, 9.18911048e-07, -3.93850900e-07],\n",
" [-7.98279949e-07, -4.07897529e-07, 1.47059723e-06],\n",
" [-3.51072639e-07, -3.76604209e-07, 3.40857921e-07],\n",
" [ 1.05406904e-06, -1.34409311e-07, -1.41760425e-06]]), 'charges': array([-2.72528879e-08, -3.71969477e-08, -1.25965400e-07, 1.90415335e-07]), 'calc_stats': {'n_neighbors': 400, 'elapsed_usec_infer': 46355, 'elapsed_usec': 51052, 'elapsed_usec_preprocess': 3135}, 'free_energy': -21.712705946017945, 'stress': array([-5.98171226e-02, -5.98171468e-02, -5.98171011e-02, 1.97083025e-08,\n",
" -1.43127693e-08, 1.31512884e-08])}\n"
]
}
],
Expand Down Expand Up @@ -562,12 +560,12 @@
"name": "stdout",
"output_type": "stream",
"text": [
"CPU times: user 2.69 ms, sys: 281 µs, total: 2.97 ms\n",
"Wall time: 40.9 ms\n",
"CPU times: user 0 ns, sys: 3.48 ms, total: 3.48 ms\n",
"Wall time: 40.3 ms\n",
"E_pot1 -4.49 eV\n",
"E_pot2 -0.34 eV\n"
"CPU times: user 3.2 ms, sys: 0 ns, total: 3.2 ms\n",
"Wall time: 54 ms\n",
"CPU times: user 2.52 ms, sys: 0 ns, total: 2.52 ms\n",
"Wall time: 54.1 ms\n",
"E_pot1 -4.48 eV\n",
"E_pot2 -0.31 eV\n"
]
}
],
Expand Down Expand Up @@ -677,9 +675,9 @@
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Expand All @@ -691,7 +689,7 @@
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36 changes: 19 additions & 17 deletions tutorials/en/1_6_ase_playground.ipynb
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Expand All @@ -142,12 +142,12 @@
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Expand All @@ -611,9 +613,9 @@
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