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

src/network/private/approx8.cpp

@@ -72,7 +72,7 @@ The coefficients to the fit are from reaclib.jinaweb.org .
 
 */
 
-namespace nnApprox8{
+namespace serif::network::approx8{
 
 	// using namespace std;
 	using namespace boost::numeric::odeint;
@@ -245,7 +245,7 @@ namespace nnApprox8{
 	// a Jacobian matrix for implicit solvers
 
     void Jacobian::operator() ( const vector_type &y, matrix_type &J, double /* t */, vector_type &dfdt ) {
-        Constants& constants = Constants::getInstance();
+        serif::constant::Constants& constants = serif::constant::Constants::getInstance();
         const double avo = constants.get("N_a").value;
         const double clight = constants.get("c").value;
         // EOS
@@ -350,7 +350,7 @@ namespace nnApprox8{
     } 
 
 	void ODE::operator() ( const vector_type &y, vector_type &dydt, double /* t */) {
-		Constants& constants = Constants::getInstance();
+		serif::constant::Constants& constants = serif::constant::Constants::getInstance();
 		const double avo = constants.get("N_a").value;
 		const double clight = constants.get("c").value;
 
@@ -444,7 +444,7 @@ namespace nnApprox8{
 		dydt[Net::iener] = -enuc*avo*clight*clight;
 	} 
 
-	nuclearNetwork::NetOut Approx8Network::evaluate(const nuclearNetwork::NetIn &netIn) {
+	NetOut Approx8Network::evaluate(const NetIn &netIn) {
 		m_y = convert_netIn(netIn);
 		m_tmax = netIn.tmax;
 		m_dt0 = netIn.dt0;
@@ -488,7 +488,7 @@ namespace nnApprox8{
 			m_y[i] /= ysum;
 		}
 
-		nuclearNetwork::NetOut netOut;
+		NetOut netOut;
 		std::vector<double> outComposition;
 		outComposition.reserve(Net::nvar);
 
@@ -506,7 +506,7 @@ namespace nnApprox8{
 		m_stiff = stiff;
 	}
 
-	vector_type Approx8Network::convert_netIn(const nuclearNetwork::NetIn &netIn) {
+	vector_type Approx8Network::convert_netIn(const NetIn &netIn) {
 		if (netIn.composition.size() != Net::niso) {
 			LOG_ERROR(m_logger, "Error: composition size mismatch in convert_netIn");
 			throw std::runtime_error("Error: composition size mismatch in convert_netIn");

src/network/private/network.cpp

@@ -22,13 +22,13 @@
 #include "probe.h"
 #include "quill/LogMacros.h"
 
-namespace nuclearNetwork {
+namespace serif::network {
     Network::Network() :
-        m_config(Config::getInstance()),
-        m_logManager(Probe::LogManager::getInstance()),
+        m_config(serif::config::Config::getInstance()),
+        m_logManager(serif::probe::LogManager::getInstance()),
         m_logger(m_logManager.getLogger("log")) {
     }
-    nuclearNetwork::NetOut nuclearNetwork::Network::evaluate(const NetIn &netIn) {
+    NetOut Network::evaluate(const NetIn &netIn) {
         // You can throw an exception here or log a warning if it should never be used.
         LOG_ERROR(m_logger, "nuclearNetwork::Network::evaluate() is not implemented");
         throw std::runtime_error("nuclearNetwork::Network::evaluate() is not implemented");

src/network/public/approx8.h

@@ -53,7 +53,7 @@ typedef boost::numeric::ublas::matrix< double > matrix_type;
  */
 typedef std::array<double,7> vec7;
 
-namespace nnApprox8{
+namespace serif::network::approx8{
 
     using namespace boost::numeric::odeint;
 
@@ -294,14 +294,14 @@ namespace nnApprox8{
      * @class Approx8Network
      * @brief Class for the Approx8 nuclear reaction network.
      */
-    class Approx8Network : public nuclearNetwork::Network {
+    class Approx8Network : public Network {
     public:
         /**
          * @brief Evaluates the nuclear network.
          * @param netIn Input parameters for the network.
          * @return Output results from the network.
          */
-        virtual nuclearNetwork::NetOut evaluate(const nuclearNetwork::NetIn &netIn);
+        virtual NetOut evaluate(const NetIn &netIn);
 
         /**
          * @brief Sets whether the solver should use a stiff method.
@@ -325,7 +325,7 @@ namespace nnApprox8{
          * @param netIn Input parameters for the network.
          * @return Internal state vector.
          */
-        vector_type convert_netIn(const nuclearNetwork::NetIn &netIn);
+        vector_type convert_netIn(const NetIn &netIn);
     };
 
 } // namespace nnApprox8

src/network/public/network.h

@@ -26,7 +26,7 @@
 #include "config.h"
 #include "quill/Logger.h"
 
-namespace nuclearNetwork {
+namespace serif::network {
 
     /**
      * @struct NetIn
@@ -102,8 +102,8 @@ namespace nuclearNetwork {
             virtual NetOut evaluate(const NetIn &netIn);
 
         protected:
-            Config& m_config; ///< Configuration instance
-            Probe::LogManager& m_logManager; ///< Log manager instance
+            serif::config::Config& m_config; ///< Configuration instance
+            serif::probe::LogManager& m_logManager; ///< Log manager instance
             quill::Logger* m_logger; ///< Logger instance
     };