From df174947ce2cd521709a958689ce134ac662b3f7 Mon Sep 17 00:00:00 2001
From: Habeeb Idris <habeebidris247@gmail.com>
Date: Wed, 2 Oct 2024 02:16:11 -0400
Subject: [PATCH] Got the optimization running and all tes passingts with
 minimal changes

---
 src/common/data_logging.hpp                       | 11 +++++++----
 src/physics/CMakeLists.txt                        |  9 +++++----
 src/physics/electromagnetics/CMakeLists.txt       |  6 ++++++
 src/physics/electromagnetics/electromag_integ.cpp |  6 +++---
 src/physics/physics.hpp                           |  2 ++
 src/physics/thermal/temp_integ.hpp                |  2 +-
 6 files changed, 24 insertions(+), 12 deletions(-)

diff --git a/src/common/data_logging.hpp b/src/common/data_logging.hpp
index ea6144fe..c9afab9a 100644
--- a/src/common/data_logging.hpp
+++ b/src/common/data_logging.hpp
@@ -120,10 +120,13 @@ class ParaViewLogger
                   double time,
                   int rank)
    {
-      fields.at(fieldname)->SetFromTrueDofs(state);
-      pv.SetCycle(timestep);
-      pv.SetTime(time);
-      pv.Save();
+      if (fields.count(fieldname) > 0)
+      {
+         fields.at(fieldname)->SetFromTrueDofs(state);
+         pv.SetCycle(timestep);
+         pv.SetTime(time);
+         pv.Save();
+      }
    }
 
    void registerField(const std::string &name, mfem::ParGridFunction &field)
diff --git a/src/physics/CMakeLists.txt b/src/physics/CMakeLists.txt
index fcff6613..af681064 100644
--- a/src/physics/CMakeLists.txt
+++ b/src/physics/CMakeLists.txt
@@ -13,6 +13,7 @@ set(MISO_PHYSICS_HEADERS
    physics.hpp
 )
 
+
 target_sources(miso
    PRIVATE
       common_outputs.cpp
@@ -27,10 +28,10 @@ target_sources(miso
       ${MISO_PHYSICS_HEADERS}
 )
 
-# get_target_property(MACH_PUBLIC_HEADERS mach PUBLIC_HEADER)
-# set(MACH_PUBLIC_HEADERS ${MACH_PUBLIC_HEADERS} ${MACH_PHYSICS_HEADERS})
-# set_target_properties(mach PROPERTIES
-#    PUBLIC_HEADER "${MACH_PUBLIC_HEADERS}"
+# get_target_property(MISO_PUBLIC_HEADERS miso PUBLIC_HEADER)
+# set(MISO_PUBLIC_HEADERS ${MISO_PUBLIC_HEADERS} ${MISO_PHYSICS_HEADERS})
+# set_target_properties(miso PROPERTIES
+#    PUBLIC_HEADER "${MISO_PUBLIC_HEADERS}"
 # )
 
 add_public_headers_to_target(miso "${MISO_PHYSICS_HEADERS}")
diff --git a/src/physics/electromagnetics/CMakeLists.txt b/src/physics/electromagnetics/CMakeLists.txt
index badc9479..7ec17e08 100644
--- a/src/physics/electromagnetics/CMakeLists.txt
+++ b/src/physics/electromagnetics/CMakeLists.txt
@@ -38,6 +38,12 @@ target_sources(miso
       ${MISO_PHYSICS_ELECTROMAGNETICS_HEADERS}
 )
 
+# get_target_property(MISO_PUBLIC_HEADERS miso PUBLIC_HEADER)
+# set(MISO_PUBLIC_HEADERS ${MISO_PUBLIC_HEADERS} ${MISO_PHYSICS_ELECTROMAGNETICS_HEADERS})
+# set_target_properties(miso PROPERTIES
+#    PUBLIC_HEADER "${MISO_PUBLIC_HEADERS}"
+# )
+
 add_public_headers_to_target(miso "${MISO_PHYSICS_ELECTROMAGNETICS_HEADERS}")
 
 target_include_directories(miso
diff --git a/src/physics/electromagnetics/electromag_integ.cpp b/src/physics/electromagnetics/electromag_integ.cpp
index e9988cac..c435debe 100644
--- a/src/physics/electromagnetics/electromag_integ.cpp
+++ b/src/physics/electromagnetics/electromag_integ.cpp
@@ -404,7 +404,7 @@ void NonlinearDiffusionIntegratorMeshRevSens::AssembleRHSElementVect(
 
       /// const double pointflux_norm = pointflux.Norml2();
       pointflux_bar = 0.0;
-      if (fabs(pointflux_norm) > 1e-14)
+      if (fabs(pointflux_norm) > 1e-16)
       {
          add(pointflux_bar,
              pointflux_norm_bar / pointflux_norm,
@@ -1651,14 +1651,14 @@ void DGInteriorFaceDiffusionIntegratorMeshRevSens::AssembleRHSElementVect(
 
       /// const double ip_flux2_norm = ip_flux2.Norml2();
       ip_flux2_bar = 0.0;
-      if (fabs(ip_flux2_norm) > 1e-14)
+      if (fabs(ip_flux2_norm) > 1e-16)
       {
          ip_flux2_bar.Add(ip_flux2_norm_bar / ip_flux2_norm, ip_flux2);
       }
 
       /// const double ip_flux1_norm = ip_flux1.Norml2();
       ip_flux1_bar = 0.0;
-      if (fabs(ip_flux1_norm) > 1e-14)
+      if (fabs(ip_flux1_norm) > 1e-16)
       {
          ip_flux1_bar.Add(ip_flux1_norm_bar / ip_flux1_norm, ip_flux1);
       }
diff --git a/src/physics/physics.hpp b/src/physics/physics.hpp
index 845ce32d..01a225b9 100644
--- a/src/physics/physics.hpp
+++ b/src/physics/physics.hpp
@@ -4,8 +4,10 @@
 #include "electromagnetics/electromagnetics.hpp"
 #include "fluidflow/fluidflow.hpp"
 #include "thermal/thermal.hpp"
+#include "joule/joule.hpp"
 #include "diag_mass_integ.hpp"
 #include "miso_input.hpp"
 #include "miso_integrator.hpp"
+#include "solver.hpp"
 
 #endif
\ No newline at end of file
diff --git a/src/physics/thermal/temp_integ.hpp b/src/physics/thermal/temp_integ.hpp
index c61b1d7f..1bf68e39 100644
--- a/src/physics/thermal/temp_integ.hpp
+++ b/src/physics/thermal/temp_integ.hpp
@@ -2,7 +2,7 @@
 #define MISO_TEMP_INTEGRATOR
 
 #include "mfem.hpp"
-//#include "solver.hpp"
+#include "solver.hpp"
 
 namespace miso
 {