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

src/polytrope/utils/public/integrators.h

@@ -0,0 +1,107 @@
+/* ***********************************************************************
+//
+//   Copyright (C) 2025 -- The 4D-STAR Collaboration
+//   File Author: Emily Boudreaux
+//   Last Modified: April 21, 2025
+//
+//   4DSSE is free software; you can use it and/or modify
+//   it under the terms and restrictions the GNU General Library Public
+//   License version 3 (GPLv3) as published by the Free Software Foundation.
+//
+//   4DSSE is distributed in the hope that it will be useful,
+//   but WITHOUT ANY WARRANTY; without even the implied warranty of
+//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+//   See the GNU Library General Public License for more details.
+//
+//   You should have received a copy of the GNU Library General Public License
+//   along with this software; if not, write to the Free Software
+//   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+//
+// *********************************************************************** */
+#pragma once
+
+#include "mfem.hpp"
+#include <string>
+#include "config.h"
+#include "probe.h"
+
+
+/**
+ * @file integrators.h
+ * @brief A collection of utilities for working with MFEM and solving the lane-emden equation.
+ */
+
+namespace serif {
+namespace polytrope {
+/**
+ * @namespace polyMFEMUtils
+ * @brief A namespace for utilities for working with MFEM and solving the lane-emden equation.
+ */
+namespace polyMFEMUtils {
+  /**
+   * @brief A class for nonlinear power integrator.
+   */
+  class NonlinearPowerIntegrator: public mfem::NonlinearFormIntegrator {
+  public:
+    /**
+     * @brief Constructor for NonlinearPowerIntegrator.
+     *
+     * @param coeff The function coefficient.
+     * @param n The polytropic index.
+     */
+    NonlinearPowerIntegrator(double n);
+
+    /**
+     * @brief Assembles the element vector.
+     *
+     * @param el The finite element.
+     * @param Trans The element transformation.
+     * @param elfun The element function.
+     * @param elvect The element vector to be assembled.
+     */
+     virtual void AssembleElementVector(const mfem::FiniteElement &el, mfem::ElementTransformation &Trans, const mfem::Vector &elfun, mfem::Vector &elvect) override;
+    /**
+     * @brief Assembles the element gradient.
+     *
+     * @param el The finite element.
+     * @param Trans The element transformation.
+     * @param elfun The element function.
+     * @param elmat The element matrix to be assembled.
+     */
+     virtual void AssembleElementGrad (const mfem::FiniteElement &el, mfem::ElementTransformation &Trans, const mfem::Vector &elfun, mfem::DenseMatrix &elmat) override;
+  private:
+    serif::config::Config& m_config = serif::config::Config::getInstance();
+    serif::probe::LogManager& m_logManager = serif::probe::LogManager::getInstance();
+    quill::Logger* m_logger = m_logManager.getLogger("log");
+    double m_polytropicIndex;
+    double m_epsilon;
+    static constexpr double m_regularizationRadius = 0.15; ///< Regularization radius for the epsilon function, used to avoid singularities in the power law.
+    static constexpr double m_regularizationCoeff = 1.0/6.0; ///< Coefficient for the regularization term, used to ensure smoothness in the power law.
+  };
+
+  inline double dfmod(const double epsilon, const double n) {
+    if (n == 0.0) {
+      return 0.0;
+    }
+    if (n == 1.0) {
+      return 1.0;
+    }
+    return n * std::pow(epsilon, n - 1.0);
+  }
+
+  inline double fmod(const double theta, const double n, const double epsilon) {
+    if (n == 0.0) {
+      return 1.0;
+    }
+    // For n != 0
+    const double y_prime_at_epsilon = dfmod(epsilon, n); // Uses the robust dfmod
+    const double y_at_epsilon = std::pow(epsilon, n);     // epsilon^n
+
+    // f_mod(theta) = y_at_epsilon + y_prime_at_epsilon * (theta - epsilon)
+    return y_at_epsilon + y_prime_at_epsilon * (theta - epsilon);
+  }
+
+
+} // namespace polyMFEMUtils
+} // namespace polytrope
+} // namespace serif