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@certik
Created March 1, 2014 00:17
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{
"metadata": {
"name": ""
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "code",
"collapsed": false,
"input": [
"%pylab inline"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Populating the interactive namespace from numpy and matplotlib\n"
]
}
],
"prompt_number": 1
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Run `opium` for our `Sn` test case:"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!opium sn.param sn.log all rpt"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 2
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"It saves the pseudopotentials into the file:"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!head sn.vs_plt"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
" 2.714417617e-05 4.476987772 0.0\r\n",
" 2.749935411e-05 4.476987772 0.0\r\n",
" 2.785917951e-05 4.476987772 0.0\r\n",
" 2.822371318e-05 4.476987772 0.0\r\n",
" 2.859301672e-05 4.476987772 0.0\r\n",
" 2.896715255e-05 4.476987772 0.0\r\n",
" 2.93461839e-05 4.476987772 0.0\r\n",
" 2.973017483e-05 4.476987772 0.0\r\n",
" 3.011919022e-05 4.476987772 0.0\r\n",
" 3.051329583e-05 4.476987772 0.0\r\n"
]
}
],
"prompt_number": 3
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Load the 4 potentials from the file, they are separated using `@`, so we load it to one 3D array `V`:"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"t = open(\"sn.vs_plt\").read().split(\"@\")\n",
"V = []\n",
"for n in range(4):\n",
" V.append(fromstring(t[n], sep=\" \").reshape([-1, 3]))\n",
"V = array(V)\n",
"# For the potential number n=0, 1, 2, 3:\n",
"# R = V[n, :, 0]\n",
"# V(R) = V[n, :, 1]\n",
"# V[n, :, 2] is radius"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 4
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Plot the first 3 of them:"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"for n in range(3):\n",
" semilogx(V[n, :, 0], V[n, :, 1], label=\"$V_%d$\" % n)\n",
"legend(loc=\"best\")\n",
"title(\"Pseudopotentials\")\n",
"xlabel(\"r [a.u.]\")\n",
"ylabel(\"V(r) [a.u.]\");"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "display_data",
"png": 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tWzJp0iSHnrm0cuVKmjdvzpYtW+jXrx99+vQBYNOmTXTq1Im4uDiGDh3Ku+++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\n",
"text": [
"<matplotlib.figure.Figure at 0x2c1f1d0>"
]
}
],
"prompt_number": 5
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The 4th one is numerically equivalent to the 1st one:"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"max(abs(V[0, :, 1] - V[3, :, 1]))"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 6,
"text": [
"1.0800000005417587e-07"
]
}
],
"prompt_number": 6
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"So we'll just ignore it for now. The first 3 potentials are probably for the `s`, `p` and `d` states."
]
}
],
"metadata": {}
}
]
}
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