From 6bb9e95146a561c0c153fb6c7128a1530472adc4 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 10 Sep 2025 08:35:13 -0700
Subject: [PATCH] external_apar: Add component to modify Apar_flutter

Reads a variable "external_apar" from the mesh file, then
adds it to the "Apar_flutter" state variable in the `transform`
function.
---
 CMakeLists.txt            |  2 ++
 hermes-3.cxx              |  1 +
 include/external_apar.hxx | 29 +++++++++++++++++++++++++++
 src/electromagnetic.cxx   |  2 +-
 src/external_apar.cxx     | 41 +++++++++++++++++++++++++++++++++++++++
 5 files changed, 74 insertions(+), 1 deletion(-)
 create mode 100644 include/external_apar.hxx
 create mode 100644 src/external_apar.cxx

diff --git a/CMakeLists.txt b/CMakeLists.txt
index c70322c9b..360571a72 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -65,6 +65,7 @@ set(HERMES_SOURCES
     src/evolve_energy.cxx
     src/evolve_pressure.cxx
     src/evolve_momentum.cxx
+    src/external_apar.cxx
     src/isothermal.cxx
     src/quasineutral.cxx
     src/diamagnetic_drift.cxx
@@ -122,6 +123,7 @@ set(HERMES_SOURCES
     include/evolve_energy.hxx
     include/evolve_momentum.hxx
     include/evolve_pressure.hxx
+    include/external_apar.hxx
     include/fixed_density.hxx
     include/fixed_fraction_ions.hxx
     include/fixed_velocity.hxx
diff --git a/hermes-3.cxx b/hermes-3.cxx
index 9893fa6c6..0997b8daa 100644
--- a/hermes-3.cxx
+++ b/hermes-3.cxx
@@ -41,6 +41,7 @@
 #include "include/evolve_energy.hxx"
 #include "include/evolve_momentum.hxx"
 #include "include/evolve_pressure.hxx"
+#include "include/external_apar.hxx"
 #include "include/fixed_density.hxx"
 #include "include/fixed_fraction_ions.hxx"
 #include "include/fixed_fraction_radiation.hxx"
diff --git a/include/external_apar.hxx b/include/external_apar.hxx
new file mode 100644
index 000000000..e19516393
--- /dev/null
+++ b/include/external_apar.hxx
@@ -0,0 +1,29 @@
+#pragma once
+#ifndef EXTERNAL_APAR_H
+#define EXTERNAL_APAR_H
+
+#include "component.hxx"
+
+/// Adds an external contribution to the Apar flutter
+///
+struct ExternalApar : public Component {
+  ExternalApar(std::string name, Options& alloptions, Solver* UNUSED(solver));
+
+  /// Adds to the Apar_flutter field
+  ///
+  /// - fields
+  ///   - Apar_flutter
+  void transform(Options& state) override;
+
+  /// Saves the added field to output
+  void outputVars(Options& state) override;
+
+private:
+  Field3D external_apar; ///< The external field
+};
+
+namespace {
+RegisterComponent<ExternalApar> registercomponentexternalapar("external_apar");
+}
+
+#endif // EXTERNAL_APAR_H
diff --git a/src/electromagnetic.cxx b/src/electromagnetic.cxx
index 3bb7386be..fc188d06d 100644
--- a/src/electromagnetic.cxx
+++ b/src/electromagnetic.cxx
@@ -214,7 +214,7 @@ void Electromagnetic::transform(Options &state) {
     // Ensure that guard cells are communicated
     Apar.getMesh()->communicate(Apar_flutter);
 
-    set(state["fields"]["Apar_flutter"], Apar_flutter);
+    add(state["fields"]["Apar_flutter"], Apar_flutter);
 
 #if 0
     // Create a vector A from covariant components
diff --git a/src/external_apar.cxx b/src/external_apar.cxx
new file mode 100644
index 000000000..661634bb1
--- /dev/null
+++ b/src/external_apar.cxx
@@ -0,0 +1,41 @@
+#include "../include/external_apar.hxx"
+
+#include <bout/constants.hxx>
+#include <bout/mesh.hxx>
+
+ExternalApar::ExternalApar(std::string name, Options& alloptions,
+                           Solver* UNUSED(solver)) {
+  AUTO_TRACE();
+
+  // Read a 3D field from the input e.g. mesh file
+  // Store in member variable
+  bout::globals::mesh->get(external_apar, "external_apar");
+
+  // Normalise
+  const Options& units = alloptions["units"];
+  const BoutReal rho_s0 = units["meters"];
+  const BoutReal Bnorm = units["Tesla"];
+  external_apar /= Bnorm * rho_s0;
+}
+
+void ExternalApar::transform(Options& state) {
+  AUTO_TRACE();
+
+  // Add the field member variable to Apar_flutter
+  add(state["fields"]["Apar_flutter"], external_apar);
+}
+
+void ExternalApar::outputVars(Options& state) {
+  AUTO_TRACE();
+
+  // Normalisations
+  auto Bnorm = get<BoutReal>(state["Bnorm"]);
+  auto rho_s0 = get<BoutReal>(state["rho_s0"]);
+
+  set_with_attrs(state["external_apar"], external_apar,
+                 {{"units", "Tm"},
+                  {"conversion", Bnorm * rho_s0},
+                  {"standard_name", "External Apar"},
+                  {"long_name", "External Apar"},
+                  {"source", "external_apar"}});
+}