{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Typical atomic data used in PHiX\n",
    "==="
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "from matplotlib import pyplot as plt\n",
    "from raysect.optical import World\n",
    "\n",
    "from cherab.phix.plasma import import_plasma\n",
    "\n",
    "plt.rcParams[\"font.size\"] = 14\n",
    "plt.rcParams[\"figure.dpi\"] = 150"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "jupyter": {
     "source_hidden": true
    }
   },
   "outputs": [],
   "source": [
    "world = World()\n",
    "plasma, eq = import_plasma(world)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The photon emission models used in PHiX are listed as follows:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "jupyter": {
     "source_hidden": true
    }
   },
   "outputs": [],
   "source": [
    "[i for i in plasma.models]"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Species taken into account are listed below as well."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "jupyter": {
     "source_hidden": true
    }
   },
   "outputs": [],
   "source": [
    "species = [i for i in plasma.composition]\n",
    "print(species)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Plotting Photon Emissivity Coefficient (PEC) vs $T_\\text{e}$ for hydrogen transitions\n",
    "----"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Plasma emissivity driven by the electron transition from $j$ to $i$ : $\\epsilon_{j\\rightarrow i}$ [$\\text{W/m}^3$] is represented by the following expression:\n",
    "\n",
    "$$\n",
    "\\epsilon_{j\\rightarrow i} = \\sum_\\rho \\text{PEC}_{\\rho, j\\rightarrow i}^\\text{(exc)}(n_\\text{e}, T_\\text{e})n_\\text{e} n_Z(\\rho) + \\sum_\\nu \\text{PEC}_{\\nu, j\\rightarrow i}^\\text{(rec)}(n_\\text{e}, T_\\text{e})n_\\text{e} n_{Z+1}(\\nu),\n",
    "$$\n",
    "\n",
    "where, $n_\\text{e}$: electron density, $T_\\text{e}$: electron temperature, $n_Z(\\rho)$: population number density $Z$ ions."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "jupyter": {
     "source_hidden": true
    },
    "tags": [
     "nbsphinx-thumbnail"
    ]
   },
   "outputs": [],
   "source": [
    "temp = [10**x for x in np.linspace(np.log10(1), np.log10(1000), num=100)]\n",
    "dens = [17, 20]  # 10^x [m^-3]\n",
    "\n",
    "pec_exc = plasma.atomic_data.impact_excitation_pec(species[0].element, species[0].charge, (3, 2))\n",
    "pec_rem = plasma.atomic_data.recombination_pec(species[0].element, species[0].charge, (3, 2))\n",
    "\n",
    "fig, ax = plt.subplots(figsize=(8, 6))\n",
    "ax.loglog(temp, [pec_exc(10 ** dens[0], te) for te in temp], \"C0\")\n",
    "ax.loglog(temp, [pec_rem(10 ** dens[0], te) for te in temp], \"C1\")\n",
    "ax.loglog(temp, [pec_exc(10 ** dens[1], te) for te in temp], \"C0\", linestyle=\"--\")\n",
    "ax.loglog(temp, [pec_rem(10 ** dens[1], te) for te in temp], \"C1\", linestyle=\"--\")\n",
    "\n",
    "dens_index1 = str(dens[0])\n",
    "dens_index2 = str(dens[1])\n",
    "ax.legend(\n",
    "    [\n",
    "        \"Excitation $n_e=10^{}$$^{}$ m$^{}$$^{}$\".format(dens_index1[0], dens_index1[1], \"-\", \"3\"),\n",
    "        \"Recombination $n_e=10^{}$$^{}$ m$^{}$$^{}$\".format(\n",
    "            dens_index1[0], dens_index1[1], \"-\", \"3\"\n",
    "        ),\n",
    "        \"Excitation $n_e=10^{}$$^{}$ m$^{}$$^{}$\".format(dens_index2[0], dens_index2[1], \"-\", \"3\"),\n",
    "        \"Recombination $n_e=10^{}$$^{}$ m$^{}$$^{}$\".format(\n",
    "            dens_index2[0], dens_index2[1], \"-\", \"3\"\n",
    "        ),\n",
    "    ]\n",
    ")\n",
    "\n",
    "ax.set_title(\"H$\\\\alpha$ emission\")\n",
    "ax.set_xlabel(\"Temperature [eV]\")\n",
    "ax.set_ylabel(\"PEC [W m$^3$]\")\n",
    "plt.grid(which=\"both\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "jupyter": {
     "source_hidden": true
    }
   },
   "outputs": [],
   "source": [
    "pec_exc = plasma.atomic_data.impact_excitation_pec(species[0].element, species[0].charge, (4, 2))\n",
    "pec_rem = plasma.atomic_data.recombination_pec(species[0].element, species[0].charge, (4, 2))\n",
    "\n",
    "fig, ax = plt.subplots(figsize=(8, 6))\n",
    "ax.loglog(temp, [pec_exc(10 ** dens[0], te) for te in temp], \"C0\")\n",
    "ax.loglog(temp, [pec_rem(10 ** dens[0], te) for te in temp], \"C1\")\n",
    "ax.loglog(temp, [pec_exc(10 ** dens[1], te) for te in temp], \"C0\", linestyle=\"--\")\n",
    "ax.loglog(temp, [pec_rem(10 ** dens[1], te) for te in temp], \"C1\", linestyle=\"--\")\n",
    "\n",
    "dens_index1 = str(dens[0])\n",
    "dens_index2 = str(dens[1])\n",
    "ax.legend(\n",
    "    [\n",
    "        \"Excitation $n_e=10^{}$$^{}$ m$^{}$$^{}$\".format(dens_index1[0], dens_index1[1], \"-\", \"3\"),\n",
    "        \"Recombination $n_e=10^{}$$^{}$ m$^{}$$^{}$\".format(\n",
    "            dens_index1[0], dens_index1[1], \"-\", \"3\"\n",
    "        ),\n",
    "        \"Excitation $n_e=10^{}$$^{}$ m$^{}$$^{}$\".format(dens_index2[0], dens_index2[1], \"-\", \"3\"),\n",
    "        \"Recombination $n_e=10^{}$$^{}$ m$^{}$$^{}$\".format(\n",
    "            dens_index2[0], dens_index2[1], \"-\", \"3\"\n",
    "        ),\n",
    "    ]\n",
    ")\n",
    "\n",
    "ax.set_title(\"H$\\\\beta$ emission\")\n",
    "ax.set_xlabel(\"Temperature [eV]\")\n",
    "ax.set_ylabel(\"PEC [W m$^3$]\")\n",
    "plt.grid(which=\"both\")"
   ]
  }
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