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epassaro/osc_example_blog.ipynb

Created June 2, 2019 20:38
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osc_example_blog.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"import pandas as pd\n",
"import warnings"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"def find_row(fname, string1, string2='', num_row=False):\n",
" \"\"\" Description \"\"\"\n",
" with open(fname, encoding='ISO-8859-1') as f:\n",
" n = 0\n",
" for line in f: \n",
" n += 1\n",
" if string1 in line and string2 in line:\n",
" break\n",
" \n",
" if num_row:\n",
" return n-1\n",
" \n",
" else: \n",
" return line"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"def oscillator_strengths(fname):\n",
" \"\"\" Description \"\"\"\n",
" args = {}\n",
" args['header'] = None\n",
" args['index_col'] = False\n",
" args['sep'] = '\\s*\\|\\s*|-?\\s+-?|(?<=[^ED\\s])-(?=[^\\s])'\n",
" args['skiprows'] = find_row(fname, \"Transition\", \"Lam\", num_row=True) +1\n",
" \n",
" n = find_row(fname, \"Number of transitions\").split()[0]\n",
" args['nrows'] = int(n)\n",
"\n",
" columns = ['State A', 'State B', 'f', 'A', 'Lam(A)', 'i', 'j', 'Lam(obs)', '% Acc']\n",
" \n",
" \n",
" try:\n",
" data = pd.read_csv(fname, **args)\n",
" \n",
" except pd.errors.EmptyDataError:\n",
" data = pd.DataFrame(columns=columns)\n",
" warnings.warn('Empty table')\n",
" \n",
" \n",
" # Assign column names by file content\n",
" if data.shape[1] == 9:\n",
" data.columns = columns\n",
" \n",
" elif data.shape[1] == 10: # This shouldn't happen (e.g. si2_osc_kurucz)\n",
" data.columns = columns + ['?']\n",
" data = data.drop(columns=['?'])\n",
" \n",
" elif data.shape[1] == 8:\n",
" data.columns = columns[:-2] + ['#']\n",
" data = data.drop(columns=['#'])\n",
" data['Lam(obs)'] = np.nan\n",
" data['% Acc'] = np.nan\n",
" \n",
" else:\n",
" warnings.warn('Inconsistent number of columns')\n",
" \n",
" \n",
" # Fix for Fortran float type 'D'\n",
" if data.shape[0] > 0 and 'D' in str(data['f'][0]):\n",
" data['f'] = data['f'].str.replace('D', 'E').map(np.float)\n",
" data['A'] = data['A'].str.replace('D', 'E').map(np.float)\n",
" \n",
" \n",
" return data"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/epassaro/miniconda3/envs/carsus/lib/python3.6/site-packages/ipykernel_launcher.py:16: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
" app.launch_new_instance()\n"
]
},
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>State A</th>\n",
" <th>State B</th>\n",
" <th>f</th>\n",
" <th>A</th>\n",
" <th>Lam(A)</th>\n",
" <th>i</th>\n",
" <th>j</th>\n",
" <th>Lam(obs)</th>\n",
" <th>% Acc</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(3F)4p4Go[5/2]</td>\n",
" <td>1.940000e-02</td>\n",
" <td>9.870800e+08</td>\n",
" <td>295.634</td>\n",
" <td>1</td>\n",
" <td>36</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(3F)4p4Fo[3/2]</td>\n",
" <td>9.065000e-02</td>\n",
" <td>6.971100e+09</td>\n",
" <td>294.516</td>\n",
" <td>1</td>\n",
" <td>38</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(3F)4p4Fo[5/2]</td>\n",
" <td>1.765000e-02</td>\n",
" <td>9.091600e+08</td>\n",
" <td>293.820</td>\n",
" <td>1</td>\n",
" <td>39</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(3F)4p2Fo[5/2]</td>\n",
" <td>8.831000e-04</td>\n",
" <td>4.608600e+07</td>\n",
" <td>291.910</td>\n",
" <td>1</td>\n",
" <td>43</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(3F)4p4Do[3/2]</td>\n",
" <td>4.965000e-03</td>\n",
" <td>3.901100e+08</td>\n",
" <td>291.366</td>\n",
" <td>1</td>\n",
" <td>45</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(3F)4p4Do[1/2]</td>\n",
" <td>4.875000e-02</td>\n",
" <td>7.679100e+09</td>\n",
" <td>291.020</td>\n",
" <td>1</td>\n",
" <td>47</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(3F)4p4Do[5/2]</td>\n",
" <td>1.425000e-04</td>\n",
" <td>7.510700e+06</td>\n",
" <td>290.467</td>\n",
" <td>1</td>\n",
" <td>48</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(3F)4p2Do[3/2]</td>\n",
" <td>1.100000e-02</td>\n",
" <td>8.715800e+08</td>\n",
" <td>290.147</td>\n",
" <td>1</td>\n",
" <td>49</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(3F)4p2Do[5/2]</td>\n",
" <td>6.520000e-04</td>\n",
" <td>3.469200e+07</td>\n",
" <td>289.095</td>\n",
" <td>1</td>\n",
" <td>51</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(3P)4p2So[1/2]</td>\n",
" <td>9.018000e-07</td>\n",
" <td>1.489000e+05</td>\n",
" <td>284.248</td>\n",
" <td>1</td>\n",
" <td>54</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(3P)4p4So[3/2]</td>\n",
" <td>5.648000e-07</td>\n",
" <td>4.765500e+04</td>\n",
" <td>281.170</td>\n",
" <td>1</td>\n",
" <td>55</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(1D)4p2Po[3/2]</td>\n",
" <td>3.171000e-06</td>\n",
" <td>2.707200e+05</td>\n",
" <td>279.521</td>\n",
" <td>1</td>\n",
" <td>56</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(1D)4p2Fo[5/2]</td>\n",
" <td>3.056000e-06</td>\n",
" <td>1.745000e+05</td>\n",
" <td>279.069</td>\n",
" <td>1</td>\n",
" <td>57</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(1D)4p2Po[1/2]</td>\n",
" <td>1.381000e-02</td>\n",
" <td>2.375800e+09</td>\n",
" <td>278.475</td>\n",
" <td>1</td>\n",
" <td>58</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(3P)4p4Do[1/2]</td>\n",
" <td>2.123000e-03</td>\n",
" <td>3.658300e+08</td>\n",
" <td>278.245</td>\n",
" <td>1</td>\n",
" <td>59</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(3P)4p4Do[3/2]</td>\n",
" <td>6.141000e-03</td>\n",
" <td>5.302300e+08</td>\n",
" <td>277.947</td>\n",
" <td>1</td>\n",
" <td>60</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(3P)4p4Do[5/2]</td>\n",
" <td>4.470000e-04</td>\n",
" <td>2.586300e+07</td>\n",
" <td>277.233</td>\n",
" <td>1</td>\n",
" <td>62</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(1D)4p2Do[3/2]</td>\n",
" <td>3.288000e-04</td>\n",
" <td>2.871800e+07</td>\n",
" <td>276.351</td>\n",
" <td>1</td>\n",
" <td>63</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(1D)4p2Do[5/2]</td>\n",
" <td>4.944000e-05</td>\n",
" <td>2.890700e+06</td>\n",
" <td>275.784</td>\n",
" <td>1</td>\n",
" <td>65</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>3d3(3)4Fe[3/2]</td>\n",
" <td>3d2(3P)4p4Po[1/2]</td>\n",
" <td>3.412000e-06</td>\n",
" <td>6.029200e+05</td>\n",
" <td>274.766</td>\n",
" <td>1</td>\n",
" <td>66</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" State A State B f A Lam(A) i \\\n",
"0 3d3(3)4Fe[3/2] 3d2(3F)4p4Go[5/2] 1.940000e-02 9.870800e+08 295.634 1 \n",
"1 3d3(3)4Fe[3/2] 3d2(3F)4p4Fo[3/2] 9.065000e-02 6.971100e+09 294.516 1 \n",
"2 3d3(3)4Fe[3/2] 3d2(3F)4p4Fo[5/2] 1.765000e-02 9.091600e+08 293.820 1 \n",
"3 3d3(3)4Fe[3/2] 3d2(3F)4p2Fo[5/2] 8.831000e-04 4.608600e+07 291.910 1 \n",
"4 3d3(3)4Fe[3/2] 3d2(3F)4p4Do[3/2] 4.965000e-03 3.901100e+08 291.366 1 \n",
"5 3d3(3)4Fe[3/2] 3d2(3F)4p4Do[1/2] 4.875000e-02 7.679100e+09 291.020 1 \n",
"6 3d3(3)4Fe[3/2] 3d2(3F)4p4Do[5/2] 1.425000e-04 7.510700e+06 290.467 1 \n",
"7 3d3(3)4Fe[3/2] 3d2(3F)4p2Do[3/2] 1.100000e-02 8.715800e+08 290.147 1 \n",
"8 3d3(3)4Fe[3/2] 3d2(3F)4p2Do[5/2] 6.520000e-04 3.469200e+07 289.095 1 \n",
"9 3d3(3)4Fe[3/2] 3d2(3P)4p2So[1/2] 9.018000e-07 1.489000e+05 284.248 1 \n",
"10 3d3(3)4Fe[3/2] 3d2(3P)4p4So[3/2] 5.648000e-07 4.765500e+04 281.170 1 \n",
"11 3d3(3)4Fe[3/2] 3d2(1D)4p2Po[3/2] 3.171000e-06 2.707200e+05 279.521 1 \n",
"12 3d3(3)4Fe[3/2] 3d2(1D)4p2Fo[5/2] 3.056000e-06 1.745000e+05 279.069 1 \n",
"13 3d3(3)4Fe[3/2] 3d2(1D)4p2Po[1/2] 1.381000e-02 2.375800e+09 278.475 1 \n",
"14 3d3(3)4Fe[3/2] 3d2(3P)4p4Do[1/2] 2.123000e-03 3.658300e+08 278.245 1 \n",
"15 3d3(3)4Fe[3/2] 3d2(3P)4p4Do[3/2] 6.141000e-03 5.302300e+08 277.947 1 \n",
"16 3d3(3)4Fe[3/2] 3d2(3P)4p4Do[5/2] 4.470000e-04 2.586300e+07 277.233 1 \n",
"17 3d3(3)4Fe[3/2] 3d2(1D)4p2Do[3/2] 3.288000e-04 2.871800e+07 276.351 1 \n",
"18 3d3(3)4Fe[3/2] 3d2(1D)4p2Do[5/2] 4.944000e-05 2.890700e+06 275.784 1 \n",
"19 3d3(3)4Fe[3/2] 3d2(3P)4p4Po[1/2] 3.412000e-06 6.029200e+05 274.766 1 \n",
"\n",
" j Lam(obs) % Acc \n",
"0 36 NaN NaN \n",
"1 38 NaN NaN \n",
"2 39 NaN NaN \n",
"3 43 NaN NaN \n",
"4 45 NaN NaN \n",
"5 47 NaN NaN \n",
"6 48 NaN NaN \n",
"7 49 NaN NaN \n",
"8 51 NaN NaN \n",
"9 54 NaN NaN \n",
"10 55 NaN NaN \n",
"11 56 NaN NaN \n",
"12 57 NaN NaN \n",
"13 58 NaN NaN \n",
"14 59 NaN NaN \n",
"15 60 NaN NaN \n",
"16 62 NaN NaN \n",
"17 63 NaN NaN \n",
"18 65 NaN NaN \n",
"19 66 NaN NaN "
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"oscillator_strengths('../CMFGEN/atomic/FE/VI/8may97/fevi_osc_kb_rk.dat').head(20)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.7"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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