Merge pull request #43 from temken/dev

Dev

CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.11)
 
-project(obscura VERSION "1.0.2")
+project(obscura VERSION "1.0.3")
 
 # Use C++-11
 set(CMAKE_CXX_STANDARD 11)
@@ -30,7 +30,7 @@ include(FetchContent)
 set(LIBPHYSICA_DIR ${EXTERNAL_DIR}/libphysica)
 FetchContent_Declare(libphysica
   GIT_REPOSITORY https://github.com/temken/libphysica.git
-  GIT_TAG origin/dev
+  GIT_TAG v0.1.5
   SOURCE_DIR "${LIBPHYSICA_DIR}"
   CMAKE_ARGS "-DCMAKE_BUILD_TYPE=Release -DCODE_COVERAGE=OFF")
 FetchContent_GetProperties(libphysica)
@@ -53,7 +53,7 @@ endif()
 set(GTEST_DIR ${EXTERNAL_DIR}/googletest)
 FetchContent_Declare(googletest
   GIT_REPOSITORY https://github.com/google/googletest.git
-  GIT_TAG release-1.10.0
+  GIT_TAG release-1.12.1
   SOURCE_DIR "${GTEST_DIR}/src"
   BINARY_DIR "${GTEST_DIR}/build"
   CONFIGURE_COMMAND ""

include/obscura/DM_Distribution.hpp

@@ -20,17 +20,17 @@ class DM_Distribution
 	void Print_Summary_Base();
 
   public:
-	double DM_density;	 //Local DM density
+	double DM_density;	 // Local DM density
 	bool DD_use_eta_function;
 
-	//Constructors:
+	// Constructors:
 	DM_Distribution();
 	DM_Distribution(std::string label, double rhoDM, double vMin, double vMax);
 
 	double Minimum_DM_Speed() const;
 	double Maximum_DM_Speed() const;
 
-	//Distribution functions
+	// Distribution functions
 	virtual double PDF_Velocity(libphysica::Vector vel) { return 0.0; };
 	virtual double PDF_Speed(double v);
 	virtual double CDF_Speed(double v);
@@ -39,11 +39,11 @@ class DM_Distribution
 	virtual double Differential_DM_Flux(double v, double mDM);
 	virtual double Total_DM_Flux(double mDM);
 
-	//Averages
+	// Averages
 	virtual libphysica::Vector Average_Velocity();
 	virtual double Average_Speed(double vMin = -1.0);
 
-	//Eta-function for direct detection
+	// Eta-function for direct detection
 	virtual double Eta_Function(double vMin);
 
 	virtual void Print_Summary(int mpi_rank = 0);
@@ -65,6 +65,7 @@ class Imported_DM_Distribution : public DM_Distribution
 
   public:
 	Imported_DM_Distribution(double rho, const std::string& filepath);
+	Imported_DM_Distribution(std::vector<std::vector<double>>& pdf_table, double rho = 1.0);
 
 	virtual double PDF_Speed(double v) override;
 

include/version.hpp.in

@@ -1,7 +1,7 @@
 #ifndef VERSION_HPP
 #define VERSION_HPP
 
-#define OBSCURA_LOGO "       _                              \n      | |                             \n  ___ | |__  ___  ___ _   _ _ __ __ _ \n / _ \\| '_ \\/ __|/ __| | | | '__/ _` |\n| (_) | |_) \\__ \\ (__| |_| | | | (_| |\n \\___/|_.__/|___/\\___|\\__,_|_|  \\__,_|\n       developed by " AUTHOR " (" YEAR ")\n"
+#define OBSCURA_LOGO "       _                              \n      | |                             \n  ___ | |__  ___  ___ _   _ _ __ __ _ \n / _ \\| '_ \\/ __|/ __| | | | '__/ _` |\n| (_) | |_) \\__ \\ (__| |_| | | | (_| |\n \\___/|_.__/|___/\\___|\\__,_|_|  \\__,_|\n                 by " AUTHOR " (" YEAR ")\n"
 #define SEPARATOR "\n##############################################################\n"
 
 #define AUTHOR "Timon Emken"

src/Configuration.cpp

@@ -57,7 +57,7 @@ void Configuration::Initialize_Result_Folder(int MPI_rank)
 	}
 	catch(const SettingNotFoundException& nfex)
 	{
-		std::cerr << "Error in obscura::Configuration::Initialize_Result_Folder(): No 'ID' setting in configuration file." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in obscura::Configuration::Initialize_Result_Folder(): No 'ID' setting in configuration file." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 	results_path = TOP_LEVEL_DIR "results/" + ID + "/";
@@ -137,12 +137,12 @@ void Configuration::Read_Config_File()
 	}
 	catch(const FileIOException& fioex)
 	{
-		std::cerr << "Error in obscura::Configuration::Read_Config_File(): I/O error while reading configuration file." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in obscura::Configuration::Read_Config_File(): I/O error while reading configuration file." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 	catch(const ParseException& pex)
 	{
-		std::cerr << "Error in obscura::Configuration::Read_Config_File(): Configurate file parse error at " << pex.getFile() << ":" << pex.getLine() << " - " << pex.getError() << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in obscura::Configuration::Read_Config_File(): Configurate file parse error at " << pex.getFile() << ":" << pex.getLine() << " - " << pex.getError() << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 }
@@ -207,7 +207,7 @@ void Configuration::Construct_DM_Particle()
 		Configuration::Construct_DM_Particle_Standard(DM_interaction);
 	else
 	{
-		std::cerr << "Error in obscura::Configuration::Construct_DM_Particle(): 'DM_interaction' setting " << DM_interaction << " in configuration file not recognized." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in obscura::Configuration::Construct_DM_Particle(): 'DM_interaction' setting " << DM_interaction << " in configuration file not recognized." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 
@@ -233,7 +233,7 @@ void Configuration::Construct_DM_Particle_Standard(std::string DM_interaction)
 		}
 		catch(const SettingNotFoundException& nfex)
 		{
-			std::cerr << "Error in Configuration::Construct_DM_Particle_Standard(): No 'DM_form_factor' setting in configuration file." << std::endl;
+			std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Configuration::Construct_DM_Particle_Standard(): No 'DM_form_factor' setting in configuration file." << std::endl;
 			std::exit(EXIT_FAILURE);
 		}
 		if(DM_form_factor == "General")
@@ -244,14 +244,14 @@ void Configuration::Construct_DM_Particle_Standard(std::string DM_interaction)
 				DM_mediator_mass *= MeV;
 				if(DM_mediator_mass < 1e-60)
 				{
-					std::cout << "Error in Configuration::Construct_DM_Particle_Standard:\tMediator mass for \"General\" form factor needs to be positive. (DM_mediator_mass = " << DM_mediator_mass / MeV << " MeV)\n"
+					std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Configuration::Construct_DM_Particle_Standard:\tMediator mass for \"General\" form factor needs to be positive. (DM_mediator_mass = " << DM_mediator_mass / MeV << " MeV)\n"
 							  << std::endl;
 					std::exit(EXIT_FAILURE);
 				}
 			}
 			catch(const SettingNotFoundException& nfex)
 			{
-				std::cerr << "Error in Configuration::Construct_DM_Particle_Standard(): No 'DM_mediator_mass' setting in configuration file." << std::endl;
+				std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Configuration::Construct_DM_Particle_Standard(): No 'DM_mediator_mass' setting in configuration file." << std::endl;
 				std::exit(EXIT_FAILURE);
 			}
 		}
@@ -272,7 +272,7 @@ void Configuration::Construct_DM_Particle_Standard(std::string DM_interaction)
 	}
 	catch(const SettingNotFoundException& nfex)
 	{
-		std::cerr << "Error in Configuration::Construct_DM_Particle_Standard(): No 'DM_isospin_conserved' setting in configuration file." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Configuration::Construct_DM_Particle_Standard(): No 'DM_isospin_conserved' setting in configuration file." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 	double fp_rel, fn_rel;
@@ -290,7 +290,7 @@ void Configuration::Construct_DM_Particle_Standard(std::string DM_interaction)
 		}
 		catch(const SettingNotFoundException& nfex)
 		{
-			std::cerr << "Error in Configuration::Construct_DM_Particle_Standard(): No 'DM_relative_couplings' setting in configuration file." << std::endl;
+			std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Configuration::Construct_DM_Particle_Standard(): No 'DM_relative_couplings' setting in configuration file." << std::endl;
 			std::exit(EXIT_FAILURE);
 		}
 	}
@@ -304,7 +304,7 @@ void Configuration::Construct_DM_Particle_Standard(std::string DM_interaction)
 	}
 	catch(const SettingNotFoundException& nfex)
 	{
-		std::cerr << "Error in Configuration::Construct_DM_Particle_Standard(): No 'DM_cross_section_nucleon' setting in configuration file." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Configuration::Construct_DM_Particle_Standard(): No 'DM_cross_section_nucleon' setting in configuration file." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 	DM->Set_Interaction_Parameter(DM_cross_section_nucleon, "Nuclei");
@@ -317,7 +317,7 @@ void Configuration::Construct_DM_Particle_Standard(std::string DM_interaction)
 	}
 	catch(const SettingNotFoundException& nfex)
 	{
-		std::cerr << "Error in Configuration::Construct_DM_Particle_Standard(): No 'DM_cross_section_electron' setting in configuration file." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Configuration::Construct_DM_Particle_Standard(): No 'DM_cross_section_electron' setting in configuration file." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 	DM->Set_Sigma_Electron(DM_cross_section_electron);
@@ -342,7 +342,7 @@ void Configuration::Construct_DM_Distribution()
 		Construct_Imported_Distribution();
 	else
 	{
-		std::cerr << "Error in obscura::Configuration::Construct_DM_Distribution(): 'DM_distribution' setting " << DM_distribution << " in configuration file not recognized." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in obscura::Configuration::Construct_DM_Distribution(): 'DM_distribution' setting " << DM_distribution << " in configuration file not recognized." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 }
@@ -358,7 +358,7 @@ void Configuration::Construct_DM_Halo_Model(std::string model_label)
 	}
 	catch(const SettingNotFoundException& nfex)
 	{
-		std::cerr << "Error in Construct_DM_Distribution_SHM(): No 'DM_local_density' setting in configuration file." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Construct_DM_Distribution_SHM(): No 'DM_local_density' setting in configuration file." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 	try
@@ -368,15 +368,15 @@ void Configuration::Construct_DM_Halo_Model(std::string model_label)
 	}
 	catch(const SettingNotFoundException& nfex)
 	{
-		std::cerr << "Error in Construct_DM_Distribution_SHM(): No 'SHM_v0' setting in configuration file." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Construct_DM_Distribution_SHM(): No 'SHM_v0' setting in configuration file." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 	try
 	{
 		int entries = config.lookup("SHM_vObserver").getLength();
 		if(entries != 3)
 		{
-			std::cerr << "Error in Construct_DM_Distribution_SHM(): 'SHM_vObserver' is a " << entries << "-dimensional vector, not 3." << std::endl;
+			std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Construct_DM_Distribution_SHM(): 'SHM_vObserver' is a " << entries << "-dimensional vector, not 3." << std::endl;
 			std::exit(EXIT_FAILURE);
 		}
 		for(int i = 0; i < 3; i++)
@@ -385,7 +385,7 @@ void Configuration::Construct_DM_Halo_Model(std::string model_label)
 	}
 	catch(const SettingNotFoundException& nfex)
 	{
-		std::cerr << "Error in Construct_DM_Distribution_SHM(): No 'SHM_vObserver' setting in configuration file." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Construct_DM_Distribution_SHM(): No 'SHM_vObserver' setting in configuration file." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 	try
@@ -395,7 +395,7 @@ void Configuration::Construct_DM_Halo_Model(std::string model_label)
 	}
 	catch(const SettingNotFoundException& nfex)
 	{
-		std::cerr << "Error in Construct_DM_Distribution_SHM(): No 'SHM_vEscape' setting in configuration file." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Construct_DM_Distribution_SHM(): No 'SHM_vEscape' setting in configuration file." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 	if(model_label == "SHM")
@@ -409,7 +409,7 @@ void Configuration::Construct_DM_Halo_Model(std::string model_label)
 		}
 		catch(const SettingNotFoundException& nfex)
 		{
-			std::cerr << "Error in Construct_DM_Distribution_SHM(): No 'SHMpp_eta' setting in configuration file." << std::endl;
+			std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Construct_DM_Distribution_SHM(): No 'SHMpp_eta' setting in configuration file." << std::endl;
 			std::exit(EXIT_FAILURE);
 		}
 		try
@@ -418,7 +418,7 @@ void Configuration::Construct_DM_Halo_Model(std::string model_label)
 		}
 		catch(const SettingNotFoundException& nfex)
 		{
-			std::cerr << "Error in Construct_DM_Distribution_SHM(): No 'SHMpp_beta' setting in configuration file." << std::endl;
+			std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Construct_DM_Distribution_SHM(): No 'SHMpp_beta' setting in configuration file." << std::endl;
 			std::exit(EXIT_FAILURE);
 		}
 		DM_distr = new SHM_Plus_Plus(DM_local_density, SHM_v0, vel_observer, SHM_vEscape, eta, beta);
@@ -435,7 +435,7 @@ void Configuration::Construct_Imported_Distribution()
 	}
 	catch(const SettingNotFoundException& nfex)
 	{
-		std::cerr << "Error in Construct_DM_Distribution_SHM(): No 'DM_local_density' setting in configuration file." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Construct_DM_Distribution_SHM(): No 'DM_local_density' setting in configuration file." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 	std::string file_path;
@@ -515,7 +515,7 @@ void Configuration::Construct_DM_Detector()
 
 	else
 	{
-		std::cerr << "Error in obscura::Configuration::Construct_DM_Detector(): Experiment " << DD_experiment << " not recognized." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in obscura::Configuration::Construct_DM_Detector(): Experiment " << DD_experiment << " not recognized." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 }
@@ -766,7 +766,7 @@ void Configuration::Initialize_Parameters()
 	}
 	catch(const SettingNotFoundException& nfex)
 	{
-		std::cerr << "Error in Configuration::Initialize_Parameters(): No 'constraints_certainty' setting in configuration file." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Configuration::Initialize_Parameters(): No 'constraints_certainty' setting in configuration file." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 
@@ -776,7 +776,7 @@ void Configuration::Initialize_Parameters()
 	}
 	catch(const SettingNotFoundException& nfex)
 	{
-		std::cerr << "Error in Configuration::Initialize_Parameters(): No 'constraints_mass_min' setting in configuration file." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Configuration::Initialize_Parameters(): No 'constraints_mass_min' setting in configuration file." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 
@@ -786,7 +786,7 @@ void Configuration::Initialize_Parameters()
 	}
 	catch(const SettingNotFoundException& nfex)
 	{
-		std::cerr << "Error in Configuration::Initialize_Parameters(): No 'constraints_mass_max' setting in configuration file." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Configuration::Initialize_Parameters(): No 'constraints_mass_max' setting in configuration file." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 
@@ -796,7 +796,7 @@ void Configuration::Initialize_Parameters()
 	}
 	catch(const SettingNotFoundException& nfex)
 	{
-		std::cerr << "Error in Configuration::Initialize_Parameters(): No 'constraints_masses' setting in configuration file." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in Configuration::Initialize_Parameters(): No 'constraints_masses' setting in configuration file." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 }

src/DM_Distribution.cpp

@@ -13,7 +13,7 @@ namespace obscura
 using namespace libphysica::natural_units;
 
 // 1. Abstract base class for DM distributions that can be used to compute direct detection recoil spectra.
-//Constructors:
+// Constructors:
 DM_Distribution::DM_Distribution()
 : name("DM base distribution"), v_domain(std::vector<double> {0.0, 1.0}), DM_density(0.0), DD_use_eta_function(false)
 {
@@ -101,7 +101,7 @@ double DM_Distribution::Average_Speed(double vMin)
 	}
 	else if(vMin < v_domain[0] || vMin >= v_domain[1])
 	{
-		std::cerr << "Error in DM_Distribution::Average_Speed(): vMin = " << In_Units(vMin, km / sec) << "lies outside the domain [" << In_Units(v_domain[0], km / sec) << "," << In_Units(v_domain[1], km / sec) << "]" << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in DM_Distribution::Average_Speed(): vMin = " << In_Units(vMin, km / sec) << "lies outside the domain [" << In_Units(v_domain[0], km / sec) << "," << In_Units(v_domain[1], km / sec) << "]" << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 
@@ -122,7 +122,7 @@ double DM_Distribution::Eta_Function_Base(double vMin)
 {
 	if(vMin < v_domain[0])
 	{
-		std::cerr << "Error in obscura::DM_Distribution::Eta_Function_Base(): vMin = " << In_Units(vMin, km / sec) << "km/sec lies below the domain [" << In_Units(v_domain[0], km / sec) << "km/sec," << In_Units(v_domain[1], km / sec) << "km/sec]." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in obscura::DM_Distribution::Eta_Function_Base(): vMin = " << In_Units(vMin, km / sec) << "km/sec lies below the domain [" << In_Units(v_domain[0], km / sec) << "km/sec," << In_Units(v_domain[1], km / sec) << "km/sec]." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 	else if(vMin >= v_domain[1])
@@ -184,7 +184,7 @@ void Imported_DM_Distribution::Check_Normalization()
 {
 	double norm = pdf_speed.Integrate(v_domain[0], v_domain[1]);
 	if(libphysica::Relative_Difference(norm, 1.0) > 1.0e-3)
-		std::cout << "Warning in obscura::Imported_DM_Distribution::Check_Normalization(): Imported pdf is not normalized (norm = " << norm << ")." << std::endl
+		std::cerr << libphysica::Formatted_String("Warning", "Yellow", true) << " in obscura::Imported_DM_Distribution::Check_Normalization(): Imported pdf is not normalized (norm = " << norm << ")." << std::endl
 				  << std::endl;
 }
 
@@ -208,6 +208,15 @@ Imported_DM_Distribution::Imported_DM_Distribution(double rho, const std::string
 	Interpolate_Eta();
 }
 
+Imported_DM_Distribution::Imported_DM_Distribution(std::vector<std::vector<double>>& pdf_table, double rho)
+: DM_Distribution("Tabulated DM distribution", rho, 0.0, 1.0), file_path("-")
+{
+	pdf_speed = libphysica::Interpolation(pdf_table);
+	v_domain  = pdf_speed.domain;
+	Check_Normalization();
+	Interpolate_Eta();
+}
+
 double Imported_DM_Distribution::PDF_Speed(double v)
 {
 	if(v < v_domain[0] || v > v_domain[1])
@@ -220,7 +229,7 @@ double Imported_DM_Distribution::Eta_Function(double vMin)
 {
 	if(vMin < v_domain[0])
 	{
-		std::cerr << "Error in obscura::Imported_DM_Distribution::Eta_Function(): vMin = " << In_Units(vMin, km / sec) << "km/sec lies below the domain [" << In_Units(v_domain[0], km / sec) << "km/sec," << In_Units(v_domain[1], km / sec) << "km/sec]." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in obscura::Imported_DM_Distribution::Eta_Function(): vMin = " << In_Units(vMin, km / sec) << "km/sec lies below the domain [" << In_Units(v_domain[0], km / sec) << "km/sec," << In_Units(v_domain[1], km / sec) << "km/sec]." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 	else if(vMin > v_domain[1])

src/DM_Halo_Models.cpp

@@ -321,7 +321,7 @@ double SHM_Plus_Plus::Eta_Function(double vMin)
 {
 	if(vMin < v_domain[0])
 	{
-		std::cerr << "Error in obscura::SHM_Plus_Plus::Eta_Function: vMin = " << In_Units(vMin, km / sec) << "km/sec lies below the domain [" << In_Units(v_domain[0], km / sec) << "km/sec," << In_Units(v_domain[1], km / sec) << "km/sec]." << std::endl;
+		std::cerr << libphysica::Formatted_String("Error", "Red", true) << " in obscura::SHM_Plus_Plus::Eta_Function: vMin = " << In_Units(vMin, km / sec) << "km/sec lies below the domain [" << In_Units(v_domain[0], km / sec) << "km/sec," << In_Units(v_domain[1], km / sec) << "km/sec]." << std::endl;
 		std::exit(EXIT_FAILURE);
 	}
 	else if(vMin > v_domain[1])