fix(poly): polytrope converges to solution

first commit where the polytrope module converges to a solution. I have not yet validated if it is a correct solution

src/poly/solver/private/polySolver.cpp

@@ -9,6 +9,8 @@
 #include "polyMFEMUtils.h"
 #include "polyCoeff.h"
 
+#include "warning_control.h"
+
 
 // TODO: Come back to this and think of a better way to get the mesh file
 const std::string SPHERICAL_MESH = std::string(getenv("MESON_SOURCE_ROOT")) + "/src/resources/mesh/sphere.msh";
@@ -111,10 +113,11 @@ void PolySolver::solve(){
 
     // --- Extract the Solution ---
     mfem::Vector u_sol_view(U.GetData(), lambdaDofOffset);
-    #pragma GCC diagnostic push // MFEM is using deprecated functions, I cant do anything about it so I will ignore the warning
-    #pragma GCC diagnostic ignored "-Wdeprecated-declarations"
-    u->SetData(u_sol_view);
-    #pragma GCC diagnostic pop
+
+    DEPRECATION_WARNING_OFF // DISABLE DEPRECATION WARNING
+        u->SetData(u_sol_view);
+    DEPRECATION_WARNING_ON // REENABLE DEPRECATION WARNING
+
     double lambda = U[lambdaDofOffset];
 
     std::cout << "λ = " << lambda << std::endl;

src/poly/utils/private/polyMFEMUtils.cpp

@@ -6,6 +6,8 @@
 
 #include "polyMFEMUtils.h"
 
+#include "warning_control.h"
+
 namespace polyMFEMUtils {
   NonlinearPowerIntegrator::NonlinearPowerIntegrator(
   mfem::Coefficient &coeff,
@@ -242,7 +244,11 @@ namespace polyMFEMUtils {
       y[i] = F[i];
     }
     mfem::GridFunction u_gf(C.FESpace());
-    u_gf.SetData(u);
+
+    DEPRECATION_WARNING_OFF
+      u_gf.SetData(u);
+    DEPRECATION_WARNING_ON
+
     y[lambdaDofOffset] = C.operator()(u_gf);
 
     // add -lambda * C to the residual
@@ -275,8 +281,13 @@ namespace polyMFEMUtils {
     mfem::SparseMatrix *J_aug = new mfem::SparseMatrix(height, width);
     // Copy the original Jacobian into the augmented Jacobian
     for (int i = 0; i < Jnfl_sparse->Height(); i++) {
-      for (int j = 0; j < Jnfl_sparse->Width(); j++) {
-        J_aug->Set(i, j, Jnfl_sparse->Elem(i, j));
+      const int *J_cols = Jnfl_sparse->GetRowColumns(i); 
+      const double *J_vals = Jnfl_sparse->GetRowEntries(i);
+
+      for (int jj = 0; jj < Jnfl_sparse->RowSize(i); jj++) {
+        int j = J_cols[jj];
+        double val = J_vals[jj];
+        J_aug->Set(i, j, val);
       }
     }
 

src/poly/utils/public/polyMFEMUtils.h

@@ -5,6 +5,7 @@
 #include <string>
 
 
+
 /**
  * @file polyMFEMUtils.h
  * @brief A collection of utilities for working with MFEM and solving the lane-emden equation.