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charnleycharnley
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displace ethanol and structure jupyter
1 parent 097517a commit c6894fc

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+80
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‎examples/ethanol.xyz

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C -0.01917708 0.56528151 -0.01770717
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C -1.32254101 -0.25786302 0.02110478
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O 1.20740778 -0.24047001 0.05234389
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H 0.11291534 1.27230970 -0.83004524
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H 0.15881439 1.11662642 0.86968220
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H -1.08763483 -1.14951348 0.66303058
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H -2.29503737 0.28289532 0.19860290
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H -1.30572545 -0.56583718 -1.04026005
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H 1.22983760 -0.80042654 -0.73220070
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Energy: 4.5404112
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C 0.28455 0.77306 0.04413
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C -1.43338 -0.66454 0.47898
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O 1.43913 -0.01863 -0.00537
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H 0.29059 1.52268 -0.77945
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H 0.28064 1.33297 1.00319
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H -1.02799 -1.48376 1.10985
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H -2.35522 -0.26639 0.95249
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H -1.69003 -1.06899 -0.52305
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H 2.67545 0.80118 -0.04217

‎tutorial.ipynb

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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"The autoreload extension is already loaded. To reload it, use:\n",
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" %reload_ext autoreload\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"%load_ext autoreload\n",
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"%autoreload 2\n",
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"execution_count": 6,
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{
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"<IPython.core.display.HTML object>"
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]
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}
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Doesn't seem very optimized, so let us optimize it"
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"## Optimization using OQML forces\n",
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"\n",
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"Doesn't seem very optimized, so let us optimize it. We do this by"
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]
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"execution_count": 46,
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"execution_count": 7,
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"execution_count": 8,
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"metadata": {},
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"metadata": {},
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"outputs": [
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"output_type": "stream",
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"text": [
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" Step Time Energy fmax\n",
347-
"BFGS: 0 21:07:41 -34.423529 2.0469\n",
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"BFGS: 1 21:07:41 -34.638227 1.3120\n",
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"BFGS: 2 21:07:41 -34.820155 0.8899\n",
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"BFGS: 3 21:07:41 -34.879206 0.5760\n",
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"BFGS: 4 21:07:41 -34.898182 0.5022\n",
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"BFGS: 5 21:07:41 -34.918828 0.4900\n"
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"BFGS: 0 22:37:46 -30.748595 2.9513\n",
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"BFGS: 1 22:37:46 -31.014309 2.8324\n",
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"BFGS: 2 22:37:46 -31.262773 3.6434\n",
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"BFGS: 3 22:37:46 -31.505507 4.8465\n",
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"BFGS: 4 22:37:46 -31.743424 6.6610\n",
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"BFGS: 5 22:37:46 -31.971456 8.1748\n",
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"BFGS: 6 22:37:46 -32.184914 9.2098\n",
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"BFGS: 7 22:37:46 -32.382798 9.6392\n",
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"BFGS: 8 22:37:47 -32.569092 9.3728\n",
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"BFGS: 9 22:37:47 -32.734802 8.4763\n",
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"BFGS: 10 22:37:47 -32.891674 7.8435\n",
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"BFGS: 11 22:37:47 -33.054999 7.0145\n",
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"BFGS: 12 22:37:47 -33.227541 5.9866\n",
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"BFGS: 13 22:37:47 -33.403943 4.8442\n",
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"BFGS: 14 22:37:47 -33.575563 3.6585\n",
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"BFGS: 15 22:37:47 -33.719203 2.6356\n",
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"BFGS: 16 22:37:47 -33.842170 1.7739\n",
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"BFGS: 17 22:37:47 -33.948032 1.0753\n",
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"BFGS: 18 22:37:47 -34.039315 0.7158\n",
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"BFGS: 19 22:37:47 -34.119271 0.7409\n",
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"BFGS: 20 22:37:47 -34.191398 0.7695\n",
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"BFGS: 21 22:37:47 -34.258895 0.8952\n",
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"BFGS: 22 22:37:47 -34.320404 1.0367\n",
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"BFGS: 23 22:37:47 -34.372717 1.4497\n",
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"BFGS: 24 22:37:47 -34.437527 1.9175\n",
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"BFGS: 25 22:37:47 -34.526138 1.6620\n",
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"BFGS: 26 22:37:47 -34.577242 1.1807\n",
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"BFGS: 27 22:37:47 -34.600738 0.9882\n",
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"BFGS: 28 22:37:47 -34.626664 0.8059\n",
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"BFGS: 29 22:37:47 -34.640207 0.6961\n",
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"BFGS: 30 22:37:47 -34.649518 0.6129\n",
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"BFGS: 31 22:37:47 -34.657426 0.6886\n",
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"BFGS: 32 22:37:47 -34.671682 0.7980\n",
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"BFGS: 33 22:37:47 -34.687578 0.5759\n",
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"BFGS: 34 22:37:47 -34.698413 0.4056\n"
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{
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]
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"execution_count": 9,
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"metadata": {},
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"output_type": "execute_result"
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{
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" <Transform translation=\"0.03 0.58 0.02\">\n",
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"execution_count": 49,
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"execution_count": 10,
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"metadata": {},
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}

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