From ad53e1353a1eddf110f5fda327c7a4ee0d6ee6c6 Mon Sep 17 00:00:00 2001
From: ChongChong He <chongchong.he@anu.edu.au>
Date: Fri, 6 Sep 2024 09:28:33 +1000
Subject: [PATCH] cleanup

---
 src/radiation/radiation_system.cpp         | 10 ----------
 src/radiation/radiation_system.hpp         | 14 +++++++-------
 src/radiation/source_terms_multi_group.hpp |  6 ++----
 3 files changed, 9 insertions(+), 21 deletions(-)
 delete mode 100644 src/radiation/radiation_system.cpp

diff --git a/src/radiation/radiation_system.cpp b/src/radiation/radiation_system.cpp
deleted file mode 100644
index 7fc1608df..000000000
--- a/src/radiation/radiation_system.cpp
+++ /dev/null
@@ -1,10 +0,0 @@
-//==============================================================================
-// TwoMomentRad - a radiation transport library for patch-based AMR codes
-// Copyright 2020 Benjamin Wibking.
-// Released under the MIT license. See LICENSE file included in the GitHub repo.
-//==============================================================================
-/// \file radiation_system.cpp
-/// \brief Implements methods for solving the (1d) radiation moment equations.
-///
-
-#include "radiation/radiation_system.hpp" // IWYU pragma: keep
diff --git a/src/radiation/radiation_system.hpp b/src/radiation/radiation_system.hpp
index 86bcdb94b..36101eecd 100644
--- a/src/radiation/radiation_system.hpp
+++ b/src/radiation/radiation_system.hpp
@@ -103,13 +103,13 @@ template <typename problem_t> struct NewtonIterationResult {
 
 // A struct to hold the results of ComputeJacobianForPureGas or ComputeJacobianForGasAndDust
 template <typename problem_t> struct JacobianResult {
-	double J00;
-	quokka::valarray<double, Physics_Traits<problem_t>::nGroups> J0g;
-	quokka::valarray<double, Physics_Traits<problem_t>::nGroups> Jg0;
-	quokka::valarray<double, Physics_Traits<problem_t>::nGroups> Jgg;
-	double F0;
-	quokka::valarray<double, Physics_Traits<problem_t>::nGroups> Fg;
-	double Fg_abs_sum;
+	double J00; // (0, 0) component of the Jacobian matrix
+	double F0; // (0) component of the residual
+	double Fg_abs_sum; // sum of the absolute values of the (g) components of the residual, g = 1, 2, ..., nGroups, and tau(g) > 0	
+	quokka::valarray<double, Physics_Traits<problem_t>::nGroups> J0g; // (0, g) components of the Jacobian matrix, g = 1, 2, ..., nGroups
+	quokka::valarray<double, Physics_Traits<problem_t>::nGroups> Jg0; // (g, 0) components of the Jacobian matrix, g = 1, 2, ..., nGroups
+	quokka::valarray<double, Physics_Traits<problem_t>::nGroups> Jgg; // (g, g) components of the Jacobian matrix, g = 1, 2, ..., nGroups
+	quokka::valarray<double, Physics_Traits<problem_t>::nGroups> Fg; // (g) components of the residual, g = 1, 2, ..., nGroups
 };
 
 [[nodiscard]] AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE static auto minmod_func(double a, double b) -> double
diff --git a/src/radiation/source_terms_multi_group.hpp b/src/radiation/source_terms_multi_group.hpp
index 6aa811d62..127d4901e 100644
--- a/src/radiation/source_terms_multi_group.hpp
+++ b/src/radiation/source_terms_multi_group.hpp
@@ -534,8 +534,6 @@ void RadSystem<problem_t>::AddSourceTermsMultiGroup(array_t &consVar, arrayconst
 		for (; ite < max_ite; ++ite) {
 			quokka::valarray<double, nGroups_> Rvec{};
 			quokka::valarray<double, nGroups_> fourPiBoverC{};
-			double T_gas = NAN;
-			double T_d = NAN;
 			quokka::valarray<double, nGroups_> kappaPVec{};
 			quokka::valarray<double, nGroups_> kappaEVec{};
 			quokka::valarray<double, nGroups_> kappaFVec{};
@@ -591,8 +589,8 @@ void RadSystem<problem_t>::AddSourceTermsMultiGroup(array_t &consVar, arrayconst
 
 			} else { // not constexpr (gamma_ != 1.0)
 
-				T_gas = quokka::EOS<problem_t>::ComputeTgasFromEint(rho, Egas0, massScalars);
-				T_d = T_gas;
+				const double T_gas = quokka::EOS<problem_t>::ComputeTgasFromEint(rho, Egas0, massScalars);
+				const double T_d = T_gas;
 				if constexpr (opacity_model_ == OpacityModel::piecewise_constant_opacity) {
 					kappa_expo_and_lower_value = DefineOpacityExponentsAndLowerValues(radBoundaries_g_copy, rho, T_d);
 					for (int g = 0; g < nGroups_; ++g) {