added a nlte excitation case rate matrix block

tardis/plasma/properties/nlte_excitation_matrix.py

@@ -0,0 +1,95 @@
+import pandas as pd
+import numpy as np
+
+from tardis.plasma.properties.nlte_rate_equation_solver import (
+    NLTERateEquationsSolver,
+)
+
+
+def create_nlte_excitation_rate_matrix_block(
+    atomic_number,
+    ion_number,
+    gamma,
+    alpha_sp,
+    alpha_stim,
+    coll_ion_coeff,
+    coll_recomb_coeff,
+    coll_exc_coeff,
+    coll_deexc_coeff,
+    electron_density,
+    nlte_excitation_species,
+    j_blues,
+    nlte_data,
+    beta_sobolev,
+):
+    number_of_levels = gamma.loc[(atomic_number, ion_number)].size
+    number_of_shells = 1
+    ionization_coeff = gamma + coll_ion_coeff * electron_density
+    recombination_coeff = (
+        alpha_sp + alpha_stim
+    ) * electron_density + coll_recomb_coeff * electron_density**2
+    diagonal_block = np.diag(
+        -ionization_coeff.loc[(atomic_number, ion_number)]
+        - recombination_coeff.loc[(atomic_number, ion_number)]
+    )
+    ion_recomb_block = np.zeros(
+        (diagonal_block.shape[0] + 1, diagonal_block.shape[1] + 1)
+    )
+    if ion_number > 0:
+        try:
+            ion_recomb_block[1:-1, 0] = ionization_coeff.loc[
+                (atomic_number, ion_number - 1)
+            ]
+        except:
+            ion_recomb_block[1:-1, 0] = 0
+        try:
+            ionization_coeff[0, 1:-1] = recombination_coeff.loc[
+                (atomic_number, ion_number - 1)
+            ]
+        except:
+            ionization_coeff[0, 1:-1] = 0
+    if ion_number < atomic_number:
+        try:
+            ion_recomb_block[-1, 1:-1] = ionization_coeff.loc[
+                (atomic_number, ion_number)
+            ]
+        except:
+            ion_recomb_block[-1, 1:-1] = 0
+        try:
+            ion_recomb_block[1:-1, -1] = recombination_coeff
+        except:
+            ion_recomb_block[1:-1, -1] = 0
+
+    coll_exc_deexc_block = (
+        NLTERateEquationsSolver.create_coll_exc_deexc_block(
+            coll_exc_coeff, coll_deexc_coeff, number_of_levels
+        )
+        * electron_density
+    )
+
+    (
+        lines_index,
+        r_ul_index,
+        r_ul_matrix,
+        r_lu_index,
+        r_lu_matrix,
+    ) = NLTERateEquationsSolver.prepare_r_uls_r_lus(
+        number_of_levels,
+        number_of_shells,
+        j_blues,
+        nlte_excitation_species,
+        nlte_data,
+    )
+    bound_bound_block = NLTERateEquationsSolver.prepare_bound_bound_rate_matrix(
+        number_of_levels,
+        lines_index,
+        r_ul_index,
+        r_ul_matrix,
+        r_lu_index,
+        r_lu_matrix,
+        beta_sobolev,
+    )
+    excitation_block = bound_bound_block + coll_exc_deexc_block
+    rate_matrix_block = ion_recomb_block
+    rate_matrix_block[1:-1, 1:-1] = excitation_block
+    return rate_matrix_block