refactor(serif): refactored entire codebase into serif and sub namespaces

src/polytrope/utils/public/utilities.h

@@ -0,0 +1,62 @@
+#pragma once
+
+#include "mfem.hpp"
+
+namespace serif::utilities {
+    [[nodiscard]] mfem::SparseMatrix build_reduced_matrix(
+        const mfem::SparseMatrix& matrix,
+        const mfem::Array<int>& trialEssentialDofs,
+        const mfem::Array<int>& testEssentialDofs
+    );
+
+    /**
+     * @brief Generate a vector of 1s and 0s where 1 elemetns cooresponds to queried dofs. Useful for degugging
+     * @param allDofs array, counding from 0, of all dofs in the system
+     * @param highlightDofs the dofs that you want to identify
+     * @return
+     *
+     * *Example Usage:*
+     * One could use this to identify, for example, which dofs are being identified as the central dofs
+     * @code
+     * ...
+     * mfem::Array<int> phiDofs, thetaDofs;
+     * phiDofs.SetSize(m_fePhi->GetNDofs());
+     * thetaDofs.SetSize(m_feTheta->GetNDofs());
+     * const mfem::Vector phiHighlightVector = serif::utilities::build_dof_identification_vector(phiDofs, phiCenterDofs);
+     * const mfem::Vector thetaHighlightVector = serif::utilities::build_dof_identification_vector(thetaDofs, thetaCenterDofs);
+     * Probe::glVisView(
+     *     const_cast<mfem::Vector&>(phiHighlightVector),
+     *     *m_fePhi,
+     *     "Phi Center Dofs"
+     *     );
+     * Probe::glVisView(
+     *     const_cast<mfem::Vector&>(thetaHighlightVector),
+     *     *m_feTheta,
+     *     "Theta Center Dofs"
+     *     );
+     * @endcode
+     */
+    mfem::Vector build_dof_identification_vector(
+        const mfem::Array<int>& allDofs,
+        const::mfem::Array<int>& highlightDofs
+        );
+
+    /**
+     * @brief Computes the curl of a given H(div) grid function (e.g., from an RT space).
+     *
+     * This function is crucial for diagnosing spurious, non-physical modes in mixed FEM
+     * formulations where the curl of a gradient field is expected to be zero.
+     *
+     * @param phi_gf The GridFunction representing the vector field (e.g., φ). It is expected
+     * to be in an H(div)-conforming space like Raviart-Thomas (RT).
+     * @return A std::pair containing two new grid functions:
+     * - pair.first: A unique_ptr to the vector curl field (∇ × φ). This field will
+     * be in an H(curl)-conforming Nedelec (ND) space.
+     * - pair.second: A unique_ptr to the scalar magnitude of the curl (||∇ × φ||).
+     * This field will be in an L2 space.
+     *
+     * @note The returned unique_ptrs manage the lifetime of the new GridFunctions and their
+     * associated FiniteElementSpaces and FECollections, preventing memory leaks.
+     */
+    mfem::GridFunction compute_curl(mfem::GridFunction& phi_gf);
+}