From e2ce5b578525ce8886ba742ded597a6c84c62288 Mon Sep 17 00:00:00 2001
From: "Eric T. Johnson" <yut23@users.noreply.github.com>
Date: Wed, 13 Mar 2024 08:06:57 -0400
Subject: [PATCH] Add X(ash) as a derived variable for flame_wave (#2773)

It's fairly straightforward to calculate in C++, and this lets me
include it in small plotfiles.
---
 Exec/science/flame_wave/Problem_Derive.H   |  5 ++
 Exec/science/flame_wave/Problem_Derive.cpp | 53 ++++++++++++++++++++++
 Exec/science/flame_wave/Problem_Derives.H  |  7 +++
 3 files changed, 65 insertions(+)
 create mode 100644 Exec/science/flame_wave/Problem_Derive.H
 create mode 100644 Exec/science/flame_wave/Problem_Derive.cpp
 create mode 100644 Exec/science/flame_wave/Problem_Derives.H

diff --git a/Exec/science/flame_wave/Problem_Derive.H b/Exec/science/flame_wave/Problem_Derive.H
new file mode 100644
index 0000000000..885d730a57
--- /dev/null
+++ b/Exec/science/flame_wave/Problem_Derive.H
@@ -0,0 +1,5 @@
+void ca_derxash
+  (const amrex::Box& bx, amrex::FArrayBox& derfab, int /*dcomp*/, int /*ncomp*/,
+   const amrex::FArrayBox& datfab, const amrex::Geometry& /*geomdata*/,
+   amrex::Real /*time*/, const int* /*bcrec*/, int /*level*/);
+
diff --git a/Exec/science/flame_wave/Problem_Derive.cpp b/Exec/science/flame_wave/Problem_Derive.cpp
new file mode 100644
index 0000000000..d1736bcc36
--- /dev/null
+++ b/Exec/science/flame_wave/Problem_Derive.cpp
@@ -0,0 +1,53 @@
+#include <bitset>
+
+#include <AMReX_REAL.H>
+
+#include <Derive.H>
+#include <Castro.H>
+
+using namespace amrex;
+
+void ca_derxash(const Box& bx, FArrayBox& derfab, int /*dcomp*/, int /*ncomp*/,
+                const FArrayBox& datfab, const Geometry& /*geomdata*/,
+                Real /*time*/, const int* /*bcrec*/, int /*level*/)
+{
+
+    // determine which species should be considered ash
+
+    std::bitset<NumSpec> is_ash{};
+
+    for (int i = 0; i < NumSpec; ++i) {
+        // include all elements beyond oxygen
+        if (zion[i] > 8.0) {
+            is_ash.set(i);
+        }
+    }
+
+    // exclude all of the "ash" species from the input file; they're actually
+    // used for the star composition and hiding them helps make the flame more
+    // visible
+    for (const std::string& ash_name : {problem::ash1_name,
+                                        problem::ash2_name,
+                                        problem::ash3_name}) {
+        int i = network_spec_index(ash_name);
+        if (i != -1) {
+            is_ash.reset(i);
+        }
+    }
+
+    auto const dat = datfab.array();
+    auto const der = derfab.array();
+
+    amrex::ParallelFor(bx,
+    [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
+    {
+        Real sum = 0.0_rt;
+        for (int n = 0; n < NumSpec; ++n) {
+            if (is_ash[n]) {
+                sum += dat(i,j,k,1+n)/dat(i,j,k,0);
+            }
+        }
+        der(i,j,k,0) = sum;
+    });
+}
+
diff --git a/Exec/science/flame_wave/Problem_Derives.H b/Exec/science/flame_wave/Problem_Derives.H
new file mode 100644
index 0000000000..d7eefefae9
--- /dev/null
+++ b/Exec/science/flame_wave/Problem_Derives.H
@@ -0,0 +1,7 @@
+    //
+    // X(ash) from rhoX - sum of all mass fractions for the elements beyond oxygen,
+    // excluding the species that make up the star
+    //
+    derive_lst.add("X(ash)",IndexType::TheCellType(),1,ca_derxash,the_same_box);
+    derive_lst.addComponent("X(ash)",desc_lst,State_Type,URHO,1);
+    derive_lst.addComponent("X(ash)",desc_lst,State_Type,UFS,NumSpec);