Merge pull request #4 from temken/dev

Dev

Author: temken

.github/workflows/main.yml

@@ -77,10 +77,10 @@ jobs:
 
     # # TESTS
     # - name: Test installed executable
-    #   working-directory: ${{runner.workspace}}/graphene/bin
+    #   working-directory: ${{runner.workspace}}/Darphene/bin
     #   shell: bash
     #   # Execute the executable from the /bin/ directory.
-    #   run: ./graphene config.cfg
+    #   run: ./Darphene config.cfg
 
     - name: Unit tests
       working-directory: ${{runner.workspace}}/build

CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.12)
 
-project(graphene VERSION "0.1.0")
+project(Darphene VERSION "0.1.0")
 
 # Use C++-14
 set(CMAKE_CXX_STANDARD 14)
@@ -37,7 +37,7 @@ include(FetchContent)
 set(OBSCURA_DIR ${EXTERNAL_DIR}/obscura)
 FetchContent_Declare(obscura
   GIT_REPOSITORY https://github.com/temken/obscura.git
-  GIT_TAG origin/dev
+  GIT_TAG v1.0.3
   SOURCE_DIR "${OBSCURA_DIR}"
   CMAKE_ARGS "-DCMAKE_BUILD_TYPE=Release -DCODE_COVERAGE=OFF")
 FetchContent_GetProperties(obscura)
@@ -60,7 +60,7 @@ 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 ""

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2020 Timon Emken
+Copyright (c) 2023 Timon Emken
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,12 +1,186 @@
-[![Build Status](https://github.com/temken/graphene/workflows/Build%20Status/badge.svg)](https://github.com/temken/graphene/actions)
-[![codecov](https://codecov.io/gh/temken/graphene/branch/main/graph/badge.svg)](https://codecov.io/gh/temken/template_cpp_cmake_obscura)
+[![Build Status](https://github.com/temken/Darphene/workflows/Build%20Status/badge.svg)](https://github.com/temken/Darphene/actions)
+[![codecov](https://codecov.io/gh/temken/Darphene/branch/main/graph/badge.svg)](https://codecov.io/gh/temken/template_cpp_cmake_obscura)
 [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
 
-# Graphene
+# Darphene - Modelling general dark matter - electron interactions in graphene targets
 
+[![DOI](https://zenodo.org/badge/xxx.svg)](https://zenodo.org/badge/latestdoi/xxx)
+[![arXiv](https://img.shields.io/badge/arXiv-2303.xxxxx-B31B1B.svg)](https://arxiv.org/abs/2303.xxxxx)
 
-- build with [CMake](https://cmake.org/)
-- continuous integration with [Github Actions](https://github.com/actions)
-- unit testing with [googletest](https://github.com/google/googletest)
-- code coverage with [codecov](https://codecov.io/).
-- imports the static library [obscura](https://github.com/temken/obscura) and thereby also [libphysica](https://github.com/temken/libphysica) and [libconfig](https://github.com/hyperrealm/libconfig)
+
+<img width="500" src="https://user-images.githubusercontent.com/29034913/227547647-9d2825dd-9cfd-4fde-9573-04d6c885a99f.png">
+
+*Darphene* calculates predicted signal rates for dark matter detection experiments using graphene as target material using the [tight-binding approximation](https://en.wikipedia.org/wiki/Tight_binding). Details on the physics can be found in [the corresponding publication](https://arxiv.org/abs/2303.XXXXX).
+
+<img width="250" src="https://user-images.githubusercontent.com/29034913/226607786-762d3a59-88d8-4927-bd16-eb2a577391d2.png">
+
+## General notes
+
+- The material properties of the graphene target are modeled using the tight-binding approxmation, which uses atomic orbitals of carbon as a basis for the initial wavefunction of the electrons in graphene.
+- The final electron states are approximated as plane-waves.
+- *Darphene* is written in C++ and build using CMake.
+- Parts of the calculations, in particular tabulation of event rates, are parallelized using MPI.
+
+<details><summary>Repository content</summary>
+<p>
+
+The included folders are:
+
+- *bin/*: This folder contains the executable after successful installation together with the configuration files.
+- *data/*: Contains additional data necessary for the simulations, e.g. the solar model tables.
+- *external/*: This folder will only be created and filled during the build with CMake and will contain the [obscura](https://github.com/temken/obscura) library necessary for all direct detection computations.
+- *include/*: All header files of Darphene can be found here.
+- *results/*: Each run of Darphene generates result files in a dedicated sub-folder named after the run's simulation ID string, which is specified in the configuration file.
+- *src/*: Here you find the source code of Darphene.
+- *tests/*: All code and executable files of the unit tests are stored here.
+
+</p>
+</details>
+
+
+## Getting started
+
+<details><summary>1. Dependencies</summary>
+<p>
+
+Before we can install *Darphene*, we need to make sure that a few dependencies are taken care of.
+
+- [arb](https://arblib.org/): For the evaluation of hypergeometric functions.
+- [boost](https://www.boost.org/): For numerical integration (used by *libphysica*).
+- [CMake](https://cmake.org/): *Darphene* as well as the libraries *libphysica* and *obscura* are built with CMake.
+- [eigen](https://eigen.tuxfamily.org): For the numerical procedure to find eigenvalues and eigenvectors of the generalized eigen problem.
+- [libconfig](https://github.com/hyperrealm/libconfig): For the configuration files, *Darphene* uses the *libconfig* library (required version at least 1.6). This will be installed by *libphysica*, if it is not already installed.
+- [libphysica](https://github.com/temken/libphysica): Automatically downloaded to */external/obscura/external/*, compiled, and linked by *CMake*.
+- [MPI](https://www.mpi-forum.org/): The tabulation of DM observables is accelerated via parallelization using MPI.
+- [obscura](https://github.com/temken/obscura): Automatically downloaded to */external/*, compiled, and linked by *CMake*.
+
+On macOS, the dependencies can be installed using [homebrew](https://brew.sh/).
+
+```
+>brew install arb boost cmake eigen libconfig open-mpi
+```
+
+On Linux machines, we can use APT:
+
+```
+>sudo apt-get update -y
+>sudo apt-get install -y arb libboost-all-dev libeigen3-dev libconfig-dev openmpi-bin openmpi-doc libopenmpi-dev
+```
+
+<details><summary>Notes on libconfig</summary>
+<p>
+
+The installation of `libconfig` is optional, since `libphysica` will install it automatically, if it is not available. Alternatively, it can be built from the source files via
+
+```
+>wget https://hyperrealm.github.io/libconfig/dist/libconfig-1.7.2.tar.gz
+>tar -xvzf libconfig-1.7.2.tar.gz
+>pushd libconfig-1.7.2
+>./configure
+>make
+>sudo make install
+>popd
+```
+</p>
+</details>
+
+</p>
+</details>
+
+<details><summary>2. Download & Installation</summary>
+<p>
+The *Darphene* source code can be downloaded by cloning this git repository:
+
+```
+>git clone https://github.com/temken/Darphene.git 
+>cd Darphene
+```
+
+The code is compiled and the executable is created using CMake.
+
+```
+>cmake -E make_directory build
+>cd build
+>cmake -DCMAKE_BUILD_TYPE=Release -DCODE_COVERAGE=OFF ..
+>cmake --build . --config Release
+>cmake --install .
+```
+
+If everything worked well, there should be the executable *Darphene* in the */bin/* folder.
+
+</p>
+</details>
+
+<details><summary>3. Usage</summary>
+<p>
+Once *Darphene* is installed, it can run by running the following command from the */bin/* folder:
+
+```
+>./Darphene Darphene.cfg
+```
+
+Alternative, one can use MPI to speed up calculations.
+
+```
+>mpirun -n N Darphene Darphene.cfg
+```
+
+where *N* is the number of desired MPI processes.
+
+</p>
+</details>
+
+## Version History
+
+- 27.03.2023: Release of version 0.1.0
+
+## Everything else
+
+<details><summary>Citing Darphene</summary>
+<p>
+
+If you decide to use this code, please cite the latest archived version,
+
+> Emken, T., 2023, Darphene [Code, v0.1.0], [[DOI:10.5281/zenodo.xxxxxxx]](https://doi.org/10.5281/zenodo.xxxxxxx)
+
+<details><summary>BibTeX entry</summary>
+<p>
+
+```
+@software{Darphene,
+  author = {Emken, Timon},
+  title = {{Darphene [Code, v0.1.0]}},
+  year         = {2023},
+  publisher    = {Zenodo},
+  version      = {v0.1.0},
+  doi          = {DOI:10.5281/zenodo.xxxxxxx},
+  url          = {https://doi.org/10.5281/zenodo.xxxxxxx},
+  howpublished={The code can be found under \url{https://github.com/temken/Darphene}. Version 0.1.0 is archived as \href{https://doi.org/10.5281/zenodo.xxxxxxx}{DOI:10.5281/zenodo.xxxxxxx}}
+}
+```
+</p>
+</details>
+
+As well as the original publication,
+
+> R. Catena, T. Emken, M. Matas, N.A. Spaldin, E. Urdshals , 2023,  **Direct searches for general dark matter-electron interactions with graphene detectors: Part I. Electronic structure calculations**, [[arXiv:2303.xxxxx]](https://arxiv.org/abs/2303.xxxxx).
+
+</p>
+</details>
+
+<details><summary>Author & Contact</summary>
+<p>
+
+The author of *Darphene* is Timon Emken.
+
+For questions, bug reports or other suggestions please open an [issue](https://github.com/temken/Darphene/issues).
+</p>
+</details>
+
+<details><summary>License</summary>
+<p>
+
+This project is licensed under the MIT License - see the LICENSE file.
+
+</p>
+</details>

bin/Darphene.cfg

@@ -0,0 +1,54 @@
+//Darphene - Configuration File
+
+//ID
+	ID		    =	"result_ID";
+
+// Run modus
+    run_modus   =	"Graphene"; 	//Options: "Energy-Spectrum", "Total-Rate" "Directional-Spectrum", "Daily-Modulation", "Graphene", "Exclusion-Limit" "Custom"
+    MC_points   =	1000;
+    grid_points =	10;
+
+// Graphene Options
+	carbon_wave_functions	= "RHF"; 		// Options: "Hydrogenic" and "Roothaan-Hartree-Fock"/"RHF"
+											// Recommended: "RHF"
+    work_function 			= 4.3; 			// in eV
+
+//Dark matter particle
+	DM_mass		  				=	100.0;		// in MeV
+	DM_spin		  				=	0.5;
+	DM_fraction					=	1.0;		// the DM particle's fractional abundance (set to 1.0 for 100%)
+
+	DM_interaction				=	"NREFT";		// Options: "Dark-Photon", "NREFT", "Electric-Dipole", "Magnetic-Dipole", "Anapole"
+
+// Options for "Dark-Photon"
+	DM_cross_section_electron	=	1.0e-37;	//in cm^2 (only relevant for dark photon model)
+	DM_form_factor				=	"Contact";	// Options: "Contact", "Long-Range", "General"
+	DM_mediator_mass			=	0.0;		// in MeV (only relevant if 'DM_form_factor' is "General")
+
+// Options for "NREFT" (operator, effective coupling, form factor, parameter e.g. mediator mass [MeV])
+    NREFT_couplings =   (
+                        (1, 1.0, "Contact", 3.0),   
+                        # (5, 1.0, "Contact", 3.0)        
+    );
+// Options for "Electric-Dipole", "Magnetic-Dipole", "Anapole"
+    DM_coupling     =  1.0;		// either in GeV^-1 or GeV^-2 (depending on the interaction)
+
+//Dark matter distribution
+	DM_distribution 	=	"SHM";		//Options: "SHM", "SHM++"
+	DM_local_density	=	0.4;		//in GeV / cm^3
+	time 				=	6.0; 		// in hr.  t = 0 corresponds to the DM wind coming from the top.
+	
+	//Options for "SHM" and "SHM++"
+		SHM_v0			=	238.0;					//in km/sec
+		SHM_vObserver	=	(0.0, 0.0, 250.552);	//in km/sec
+		SHM_vEscape		=	544.0;					//in km/sec
+	//Options for "SHM++"
+		SHMpp_eta		=	0.2;
+		SHMpp_beta		=	0.9;
+
+//Computation of exclusion limits (relevant for "Exclusion-Limit" mode)
+	exposure				=	1.0;	//in gram*year
+	constraints_certainty	=	0.95;	//Certainty level
+	constraints_mass_min	=	20.0;	//in MeV										
+	constraints_mass_max	=	1000.0;	//in MeV
+	constraints_masses		=	10;										

data/README.md

@@ -0,0 +1,5 @@
+## Reference for Roothaan-Hartree-Fock ground state atomic wave functions
+
+The coefficients for the RHF wavefunctions of carbons are taken from
+
+> C. F. Bunge, J. A. Barrientos, and A. V. Bunge, **Roothaan-Hartree-Fock Ground-State Atomic Wave Functions: Slater-Type Orbital Expansions and Expectation Values for Z = 2-54", [Atom. Data Nucl. Data Tabl. 53, 113–162 (1993)](https://www.sciencedirect.com/science/article/pii/S0092640X8371003X)

include/graphene/Carbon_Wavefunctions.hpp include/Darphene/Carbon_Wavefunctions.hppinclude/graphene/Carbon_Wavefunctions.hpp renamed to include/Darphene/Carbon_Wavefunctions.hpp

@@ -6,14 +6,15 @@
 #include <string>
 #include <vector>
 
-namespace graphene
+namespace Darphene
 {
 
 // 1. Base class for atomic wavefunctions of carbon
 class Carbon_Wavefunctions
 {
   protected:
   public:
+	std::string name;
 	Carbon_Wavefunctions() {};
 
 	// Position space wavefunctions
@@ -35,7 +36,7 @@ class Hydrogenic : public Carbon_Wavefunctions
 
   public:
 	Hydrogenic(double Z2s, double Z2pxpy, double Z2pz)
-	: Zeff_2s(Z2s), Zeff_2pxpy(Z2pxpy), Zeff_2pz(Z2pz) {};
+	: Zeff_2s(Z2s), Zeff_2pxpy(Z2pxpy), Zeff_2pz(Z2pz) { name = "Hydrogenic"; };
 
 	// Position space wavefunctions
 	virtual double Wavefunction_Position(const Eigen::Vector3d& xVec, const std::string& orbital) override;
@@ -45,10 +46,16 @@ class Hydrogenic : public Carbon_Wavefunctions
 };
 
 // 3. Roothaan-Hartree-Fock wavefunctions
+extern std::complex<double> Hypergeometric_2F1(double a, double b, double c, double z);
+extern double Slate_Type_Orbital_Position(double r, double Z, double n);
+extern std::complex<double> Slate_Type_Orbital_Momentum(double k, double Z, double n, int l);
+
 class Roothaan_Hartree_Fock : public Carbon_Wavefunctions
 {
   protected:
 	std::vector<std::vector<double>> C_nlj, Z_lj, n_lj;
+
+  public:
 	void Import_RHF_Coefficients();
 
 	double Radial_Wavefunction_Position(double r, const std::string& orbital) const;
@@ -64,6 +71,6 @@ class Roothaan_Hartree_Fock : public Carbon_Wavefunctions
 	virtual std::complex<double> Wavefunction_Momentum(const Eigen::Vector3d& kVec, const std::string& orbital) override;
 };
 
-}	// namespace graphene
+}	// namespace Darphene
 
 #endif

include/graphene/Configuration.hpp include/Darphene/Configuration.hppinclude/graphene/Configuration.hpp renamed to include/Darphene/Configuration.hpp

@@ -3,10 +3,10 @@
 
 #include "obscura/Configuration.hpp"
 
-#include "graphene/DM_Particle_NREFT.hpp"
-#include "graphene/Graphene.hpp"
+#include "Darphene/DM_Particle_NREFT.hpp"
+#include "Darphene/Graphene.hpp"
 
-namespace graphene
+namespace Darphene
 {
 // 1. Configuration class for input file, which extends the obscura::Configuration class.
 
@@ -31,12 +31,15 @@ class Configuration : public obscura::Configuration
 	double graphene_work_function, time;
 	std::string run_modus, carbon_wavefunctions;
 	unsigned int MC_points, grid_points;
+	// For constraints
+	double exposure, constraints_certainty, constraints_mass_min, constraints_mass_max;
+	unsigned int constraints_masses;
 
 	explicit Configuration(std::string cfg_filename, int MPI_rank = 0);
 
 	void Print_Summary(int mpi_rank = 0) override;
 };
 
-}	// namespace graphene
+}	// namespace Darphene
 
 #endif