[restructure/plasma] Cleanup plasma assembly

docs/physics/plasma/construction_simple_plasma.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Constructing a simple plasma"
+    "# Constructing a simple thermal plasma"
    ]
   },
   {
@@ -23,7 +23,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "bbbd27367e48465696aa4e40f25b8496",
+       "model_id": "adc8142e04de4ac4ad9fb6d9eba83286",
        "version_major": 2,
        "version_minor": 0
       },
@@ -37,7 +37,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "6830a2c86f754397999e6801ccca1001",
+       "model_id": "36b88ed7168e46c8864e17b0107f8f71",
        "version_major": 2,
        "version_minor": 0
       },
@@ -51,9 +51,20 @@
    ],
    "source": [
     "import numpy as np\n",
+    "import pandas as pd\n",
     "from astropy import units as u\n",
-    "from tardis.radiation_field.planck_rad_field import DilutePlanckianRadiationField\n",
-    "#from tardis.plasma.properties.plasma_input import T"
+    "\n",
+    "from tardis.io.atom_data import AtomData\n",
+    "from tardis.plasma.assembly.base import PlasmaSolverFactory\n",
+    "from tardis.plasma.radiation_field import DilutePlanckianRadiationField\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "In the default configuration the plasma solver assumes the conditions for a Local Thermodynamic Equilibrium meaning a planckian radiation field and a maxwellian electron velocity distribution at the same templerature"
    ]
   },
   {
@@ -62,8 +73,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "temperatures_rad = np.ones(10) * 10000 * u.K\n",
-    "dilution_factor = np.ones(10) * 0.1"
+    "NO_OF_CELLS = 1000\n",
+    "temperatures_rad = np.ones(NO_OF_CELLS) * 10000 * u.K\n",
+    "dilution_factor = np.ones(NO_OF_CELLS) * 0.1"
    ]
   },
   {
@@ -77,12 +89,141 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "base_density = 1e-15 * u.Unit('g/cm^3')\n",
+    "number_densities = pd.DataFrame(columns=range(NO_OF_CELLS), index=[1,26,28])\n",
+    "number_densities.values[:] = 0.5 * (base_density / u.u).to(1/u.cm**3).value\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
-    "test = DilutePlanckianRadFieldInput()\n",
-    "test.set_value(d_radfield)"
+    "atom_data = AtomData.from_hdf('kurucz_cd23_chianti_H_He.h5')\n",
+    "plasma_solver_factory = PlasmaSolverFactory(atom_data, selected_atomic_numbers=[1,26,28])\n",
+    "plasma_solver_factory.setup_factory()\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "SCRUN MAGIC\n"
+     ]
+    },
+    {
+     "data": {
+      "text/html": [
+       "\n",
+       "        <iframe\n",
+       "            width=\"100%\"\n",
+       "            height=\"400\"\n",
+       "            src=\"http://localhost:8182\"\n",
+       "            frameborder=\"0\"\n",
+       "            allowfullscreen\n",
+       "            \n",
+       "        ></iframe>\n",
+       "        "
+      ],
+      "text/plain": [
+       "<IPython.lib.display.IFrame at 0x31e16f5c0>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 36,
+   "metadata": {},
+   "outputs": [
+    {
+     "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></th>\n",
+       "      <th>0</th>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>atomic_number</th>\n",
+       "      <th>ion_number</th>\n",
+       "      <th></th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th rowspan=\"2\" valign=\"top\">1</th>\n",
+       "      <th>0</th>\n",
+       "      <td>2.245918e-04</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>3.011070e+08</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th rowspan=\"3\" valign=\"top\">2</th>\n",
+       "      <th>0</th>\n",
+       "      <td>1.405189e-15</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>2.206015e-03</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>3.011070e+08</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                                     0\n",
+       "atomic_number ion_number              \n",
+       "1             0           2.245918e-04\n",
+       "              1           3.011070e+08\n",
+       "2             0           1.405189e-15\n",
+       "              1           2.206015e-03\n",
+       "              2           3.011070e+08"
+      ]
+     },
+     "execution_count": 36,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "plasma_solver.ion_number_density"
    ]
   },
   {
@@ -107,7 +248,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.12.4"
   }
  },
  "nbformat": 4,

tardis/io/configuration/tests/test_config_reader.py

@@ -10,7 +10,7 @@
 from astropy.units import Quantity
 from tardis.io.configuration.config_reader import Configuration
 from tardis.plasma.exceptions import PlasmaConfigError
-from tardis.plasma.standard_plasmas import assemble_plasma
+from tardis.plasma.assembly.legacy_assembly import assemble_plasma
 
 
 def test_convergence_section_parser():

tardis/model/base.py

@@ -95,6 +95,7 @@ class SimulationState(HDFWriterMixin):
         "density",
         "r_inner",
         "time_explosion",
+        "abundance",
     ]
     hdf_name = "simulation_state"
 

tardis/opacities/opacity_solver.py

@@ -46,7 +46,9 @@ def solve(self, legacy_plasma) -> OpacityState:
                         legacy_plasma.atomic_data.lines.shape[
                             0
                         ],  # number of lines
-                        legacy_plasma.abundance.shape[1],  # number of shells
+                        legacy_plasma.number_density.shape[
+                            1
+                        ],  # number of shells
                     ),
                     dtype=np.float64,
                 ),