docs(laneEmdenVariationalForm): updated to match MFEM sign convention more closley

src/poly/utils/private/polytropeOperator.cpp

@@ -58,38 +58,50 @@ void PolytropeOperator::finalize(const mfem::Vector &initTheta) {
     m_Qmat = std::make_unique<mfem::SparseMatrix>(m_Q->SpMat());
     m_Dmat = std::make_unique<mfem::SparseMatrix>(m_D->SpMat());
 
+    saveSparseMatrixBinary(*m_Mmat, "MmatRawO2.bin");
+    saveSparseMatrixBinary(*m_Qmat, "QmatRawO2.bin");
+    saveSparseMatrixBinary(*m_Dmat, "DmatRawO2.bin");
+
     // Remove the essential dofs from the constant matrices
     for (const auto& dof: m_theta_ess_tdofs.first) {
+        std::cout << "Eliminating dof: " << dof << std::endl;
         m_Mmat->EliminateRow(dof);
         m_Qmat->EliminateCol(dof);
     }
 
+    saveSparseMatrixBinary(*m_Mmat, "MmatBCThetaO2.bin");
+    saveSparseMatrixBinary(*m_Qmat, "QmatBCThetaO2.bin");
+    saveSparseMatrixBinary(*m_Dmat, "DmatBCThetaO2.bin");
+
     for (const auto& dof: m_phi_ess_tdofs.first) {
         m_Mmat->EliminateCol(dof);
         m_Qmat->EliminateRow(dof);
         m_Dmat->EliminateRowCol(dof);
     }
+    saveSparseMatrixBinary(*m_Mmat, "MmatBCO2.bin");
+    saveSparseMatrixBinary(*m_Qmat, "QmatBCO2.bin");
+    saveSparseMatrixBinary(*m_Dmat, "DmatBCO2.bin");
 
     m_negM_mat = std::make_unique<mfem::ScaledOperator>(m_Mmat.get(), -1.0);
     m_negQ_mat = std::make_unique<mfem::ScaledOperator>(m_Qmat.get(), -1.0);
 
-    m_schurCompliment = std::make_unique<SchurCompliment>(*m_Qmat, *m_Dmat, *m_Mmat);
+    // m_schurCompliment = std::make_unique<SchurCompliment>(*m_Qmat, *m_Dmat, *m_Mmat);
 
     // Set up the constant parts of the jacobian now
 
     // We use the assembled matrices with their boundary conditions already removed for the jacobian
     m_jacobian = std::make_unique<mfem::BlockOperator>(m_blockOffsets);
-    m_jacobian->SetBlock(0, 1, m_negM_mat.get()); //<- -M (constant)
+    m_jacobian->SetBlock(0, 1, m_Mmat.get());     //<- M (constant)
     m_jacobian->SetBlock(1, 0, m_negQ_mat.get()); //<- -Q (constant)
     m_jacobian->SetBlock(1, 1, m_Dmat.get());     //<-  D (constant)
 
-    m_invSchurCompliment = std::make_unique<GMRESInverter>(*m_schurCompliment);
+    // m_invSchurCompliment = std::make_unique<GMRESInverter>(*m_schurCompliment);
 
     m_isFinalized = true;
 
     // Build the initial preconditioner based on some initial guess
     const auto &grad = m_f->GetGradient(initTheta);
-    updatePreconditioner(grad);
+    // updatePreconditioner(grad);
 
 }
 
@@ -137,7 +149,7 @@ void PolytropeOperator::Mult(const mfem::Vector &x, mfem::Vector &y) const {
     mfem::Vector Qtheta_term(phi_size);
 
     // Calculate R0 and R1 terms
-    // R0 = f(θ) - Mɸ
+    // R0 = f(θ) + Mɸ
     // R1 = Dɸ - Qθ
 
     MFEM_ASSERT(m_f.get() != nullptr, "NonlinearForm m_f is null in PolytropeOperator::Mult");
@@ -147,7 +159,7 @@ void PolytropeOperator::Mult(const mfem::Vector &x, mfem::Vector &y) const {
     m_D->Mult(x_phi, Dphi_term);
     m_Q->Mult(x_theta, Qtheta_term);
 
-    subtract(f_term, Mphi_term, y_R0);
+    add(f_term, Mphi_term, y_R0);
     subtract(Dphi_term, Qtheta_term, y_R1);
 
     // -- Apply essential boundary conditions --
@@ -211,7 +223,7 @@ mfem::Operator& PolytropeOperator::GetGradient(const mfem::Vector &x) const {
     const mfem::Vector& x_theta = x_block.GetBlock(0);
 
     auto &grad = m_f->GetGradient(x_theta);
-    updatePreconditioner(grad);
+    // updatePreconditioner(grad);
 
     m_jacobian->SetBlock(0, 0, &grad);
 

src/poly/utils/private/utilities.cpp

@@ -0,0 +1,5 @@
+//
+// Created by Emily Boudreaux on 6/4/25.
+//
+
+#include "utilities.h"