Improvements for Hopfion visualisation etc.

Improved performance of GL by copying spins data etc. only if a simulation is running.
Added basis_atoms to geometry.
Added format enum for Vector Files (e.g. Spin Configurations, in order to be able to read in CSV and other formats)
Bugfix: bad file name in Neighbours.cpp.
Bugfix: Hopfion configuration now is nontrivial and has winding number 1.
Bugfix: Method_LLG now saves the effective field into the spin system after each iteration.

core/include/data/Geometry.hpp

@@ -22,7 +22,8 @@ namespace Data
 	public:
 		// Constructor
 		Geometry(const std::vector<std::vector<double>> basis, const std::vector<std::vector<double>> translation_vectors,
-			const std::vector<int> n_cells, const int n_spins_basic_domain, const std::vector<double> spin_pos);
+			const std::vector<int> n_cells, const int n_spins_basic_domain, const std::vector<std::vector<double>> basis_atoms,
+			const std::vector<double> spin_pos);
 		// Destructor
 		//~Geometry();
 
@@ -36,8 +37,8 @@ namespace Data
 		const std::vector<int> n_cells;
 		// Number of spins per basic domain
 		const int n_spins_basic_domain;
-		// TODO: array of basis atom positions [n][3]
-		// std::vector<std::vector<double>> basis_atoms;
+		// Array of basis atom positions [3][n_basis_atoms]
+		std::vector<std::vector<double>> basis_atoms;
 		// Number of Spins total
 		const int nos;
 		// number of shells -> moved to Hamiltonian

core/include/utility/IO.hpp

@@ -24,6 +24,14 @@ namespace Utility
 {
 	namespace IO
 	{
+		enum class VectorFileFormat
+		{
+			CSV_POS_SPIN,
+			CSV_SPIN,
+			WHITESPACE_POS_SPIN,
+			WHITESPACE_SPIN
+		};
+
 		// ======================== Configparser ========================
 		// Note that due to the modular structure of the input parsers, input may be given in one or in separate files.
 		// Input may be given incomplete. In this case a log entry is created and default values are used.
@@ -39,7 +47,8 @@ namespace Utility
 		std::unique_ptr<Engine::Hamiltonian_Gaussian> Hamiltonian_Gaussian_from_Config(const std::string configFile, Data::Geometry geometry);
 
 		// ========================= Fileparser =========================
-		void Read_Spin_Configuration(std::shared_ptr<Data::Spin_System> s, const std::string file);
+		void Read_Spin_Configuration_CSV(std::shared_ptr<Data::Spin_System> s, const std::string file);
+		void Read_Spin_Configuration(std::shared_ptr<Data::Spin_System> s, const std::string file, VectorFileFormat format = VectorFileFormat::CSV_POS_SPIN);
 		void Read_SpinChain_Configuration(std::shared_ptr<Data::Spin_System_Chain> c, const std::string file);
 		//External_Field_from_File ....
 		void Anisotropy_from_File(const std::string anisotropyFile, Data::Geometry geometry, int & n_indices,

core/src/data/Geometry.cpp

@@ -8,9 +8,10 @@
 namespace Data
 {
 	Geometry::Geometry(std::vector<std::vector<double>> basis_i, const std::vector<std::vector<double>> translation_vectors_i,
-		const std::vector<int> n_cells_i, const int n_spins_basic_domain_i, const std::vector<double> spin_pos_i) :
-		basis(basis_i), translation_vectors(translation_vectors_i),
-		n_cells(n_cells_i), n_spins_basic_domain(n_spins_basic_domain_i),
+		const std::vector<int> n_cells_i, const int n_spins_basic_domain_i, const std::vector<std::vector<double>> basis_atoms_i,
+		const std::vector<double> spin_pos_i) :
+		basis(basis_i), translation_vectors(translation_vectors_i), n_cells(n_cells_i),
+		n_spins_basic_domain(n_spins_basic_domain_i), basis_atoms(basis_atoms_i),
 		spin_pos(spin_pos_i), nos( n_spins_basic_domain_i * n_cells_i[0] * n_cells_i[1] * n_cells_i[2])
 	{
 		// Calculate Bounds of the System

core/src/engine/Method_LLG.cpp

@@ -82,9 +82,11 @@ namespace Engine
 
 		// --- Image Data Update
 		// Update the system's Energy
+		// ToDo: copy instead of recalculating
 		systems[0]->UpdateEnergy();
 
 		// ToDo: How to update eff_field without numerical overhead?
+		systems[0]->effective_field = F_total[0];
 		// systems[0]->UpdateEffectiveField();
 
 		// TODO: In order to update Rx with the neighbouring images etc., we need the state -> how to do this?

core/src/engine/Neighbours.cpp

@@ -299,7 +299,7 @@ namespace Engine
 		}
 		else { output_to_file.reserve(int(1E+08)); }
 
-		const int buffer_length = 80, name_length = 29;
+		const int buffer_length = 80, name_length = 35;
 		char buffer_file_name[name_length + 2];
 		char buffer_string_conversion[buffer_length + 2];
 		//------------------------ End Init ----------------------------------------
@@ -372,7 +372,7 @@ namespace Engine
 
 		for (shell = 0; shell < n_shells; ++shell)
 		{
-			snprintf(buffer_file_name, name_length, "output/neighbours_in_shell_%03i.dat", shell + 1);
+			snprintf(buffer_file_name, name_length, "output/neighbours_in_shell_%03i.dat", (shell + 1));
 			output_to_file = "List of neighbours in the ";
 			snprintf(buffer_string_conversion, buffer_length, "%03i-th shell\n Spin   Number of |List of   \n number|neighbours|neighbours", shell + 1);
 			output_to_file.append(buffer_string_conversion);

core/src/utility/Configurations.cpp

@@ -204,7 +204,7 @@ namespace Utility
 						t = sin(tmp)*sin(T);
 						t = acos(1.0 - 2.0*t*t);
 						// ...
-						F = atan2(py[n], px[n]);
+						F = atan2(py[n] - pos[1], px[n] - pos[0]);
 						if (T > M_PI / 2.0) {
 							f = F + atan(1.0 / (tan(tmp)*cos(T)));
 						}

core/src/utility/IO_Configparser.cpp

@@ -87,7 +87,7 @@ namespace Utility
 			double lattice_constant = 1.0;
 			// Basis: vector {a, b, c}
 			basis = { std::vector<double>{1,0,0}, std::vector<double>{0,1,0}, std::vector<double>{0,0,1} };
-			// Atoms in the basis
+			// Atoms in the basis [dim][n_basis_atoms]
 			basis_atoms = { std::vector<double>{0}, std::vector<double>{0}, std::vector<double>{0} };
 			// NoS in the basic domain (= unit cell for periodic lattices)
 			no_spins_basic_domain = basis_atoms[0].size();
@@ -173,7 +173,7 @@ namespace Utility
 			std::string basis_file = "";
 			// Basis: vector {a, b, c}
 			std::vector<std::vector<double>> basis = { std::vector<double>{1,0,0}, std::vector<double>{0,1,0}, std::vector<double>{0,0,1} };
-			// Atoms in the basis
+			// Atoms in the basis [dim][n_basis_atoms]
 			std::vector<std::vector<double>> basis_atoms = { std::vector<double>{0}, std::vector<double>{0}, std::vector<double>{0} };
 			// NoS in the basic domain (= unit cell for periodic lattices)
 			int no_spins_basic_domain = basis_atoms[0].size();
@@ -271,7 +271,7 @@ namespace Utility
 			Log(Log_Level::Parameter, Log_Sender::IO, "Geometry: " + std::to_string(nos) + " spins");
 
 			// Return geometry
-			auto geometry = std::unique_ptr<Data::Geometry>(new Data::Geometry(basis, translation_vectors, n_cells, no_spins_basic_domain, spin_pos));
+			auto geometry = std::unique_ptr<Data::Geometry>(new Data::Geometry(basis, translation_vectors, n_cells, no_spins_basic_domain, basis_atoms, spin_pos));
 			Log(Log_Level::Info, Log_Sender::IO, "Geometry: built");
 			return geometry;
 		}// end Geometry from Config

core/src/utility/IO_Fileparser.cpp

@@ -1,14 +1,14 @@
 #include "IO.hpp"
 #include "Vectormath.hpp"
 #include "IO_Filter_File_Handle.hpp"
+#include "Logging.hpp"
+#include "Exception.hpp"
 
 #include <iostream>
 #include <fstream>
 #include <thread>
 #include <string>
 #include <sstream>
-#include "Logging.hpp"
-#include "Exception.hpp"
 
 namespace Utility
 {
@@ -35,7 +35,7 @@ namespace Utility
 		/*
 		Reads a configuration file into an existing Spin_System
 		*/
-		void Read_Spin_Configuration(std::shared_ptr<Data::Spin_System> s, const std::string file)
+		void Read_Spin_Configuration(std::shared_ptr<Data::Spin_System> s, const std::string file, VectorFileFormat format)
 		{
 			std::ifstream myfile(file);
 			if (myfile.is_open())
@@ -45,23 +45,47 @@ namespace Utility
 				std::istringstream iss(line);
 				std::size_t found;
 				int i = 0;
-				while (getline(myfile, line))
+				if (format == VectorFileFormat::CSV_POS_SPIN)
 				{
-					if (i >= s->nos) { Log(Log_Level::Warning, Log_Sender::IO, "NOS mismatch in Read Spin Configuration - Aborting"); myfile.close(); return; }
-					found = line.find("#");
-					// Read the line if # is not found (# marks a comment)
-					if (found == std::string::npos)
+					auto& spins = *s->spins;
+					double px, py, pz;
+					while (getline(myfile, line, ','))
 					{
-						//double x, y, z;
-						iss.clear();
-						iss.str(line);
-						auto& spins = *s->spins;
-						//iss >> x >> y >> z;
-						iss >> spins[i] >> spins[1 * s->nos + i] >> spins[2 * s->nos + i];
-						++i;
-					}// endif (# not found)
-					 // discard line if # is found
-				}// endif new line (while)
+						if (i >= s->nos) { Log(Log_Level::Warning, Log_Sender::IO, "NOS mismatch in Read Spin Configuration - Aborting"); myfile.close(); return; }
+						found = line.find("#");
+						// Read the line if # is not found (# marks a comment)
+						if (found == std::string::npos)
+						{
+							//double x, y, z;
+							iss.clear();
+							iss.str(line);
+							//iss >> x >> y >> z;
+							iss >> px >> py >> pz >> spins[i] >> spins[1 * s->nos + i] >> spins[2 * s->nos + i];
+							++i;
+						}// endif (# not found)
+						 // discard line if # is found
+					}// endif new line (while)
+				}
+				else
+				{
+					auto& spins = *s->spins;
+					while (getline(myfile, line))
+					{
+						if (i >= s->nos) { Log(Log_Level::Warning, Log_Sender::IO, "NOS mismatch in Read Spin Configuration - Aborting"); myfile.close(); return; }
+						found = line.find("#");
+						// Read the line if # is not found (# marks a comment)
+						if (found == std::string::npos)
+						{
+							//double x, y, z;
+							iss.clear();
+							iss.str(line);
+							//iss >> x >> y >> z;
+							iss >> spins[i] >> spins[1 * s->nos + i] >> spins[2 * s->nos + i];
+							++i;
+						}// endif (# not found)
+						 // discard line if # is found
+					}// endif new line (while)
+				}
 				if (i < s->nos) { Log(Log_Level::Warning, Log_Sender::IO, "NOS mismatch in Read Spin Configuration"); }
 				myfile.close();
 				Log(Log_Level::Info, Log_Sender::IO, "Done");

core/src/utility/Vectormath.cpp

@@ -106,14 +106,30 @@ namespace Utility
 				}// endfor j
 			}// endfor dim
 
-			 // Check for erronous input placing two spins on the same location
-			for (i = 0; i < pos; ++i) {
-				for (j = i + 1; j < pos; ++j) {
-					if (std::abs(spin_pos[0*nos+i] - spin_pos[0*nos+j]) < 1.0E-6) {
-						if (std::abs(spin_pos[1*nos+i] - spin_pos[1*nos+j]) < 1.0E-6) {
-							if (std::abs(spin_pos[2*nos+i] - spin_pos[2*nos+j]) < 1.0E-6) {
-								Log(Utility::Log_Level::Severe, Utility::Log_Sender::All, "Unable to initialize Spin-System, since 2 spins occupy the same space.\nPlease check the config file!");
-								throw Exception::System_not_Initialized;
+			// Check for erronous input placing two spins on the same location
+			std::vector<double> sp(3);
+			for (int i = 0; i < basis_atoms[0].size(); ++i)
+			{
+				for (int j = 0; j < basis_atoms[0].size(); ++j)
+				{
+					for (int k1 = -2; k1 < 3; ++k1)
+					{
+						for (int k2 = -2; k2 < 3; ++k2)
+						{
+							for (int k3 = -2; k3 < 3; ++k3)
+							{
+								// Norm is zero if translated basis atom is at position of another basis atom
+								for (int dim = 0; dim < 3; ++dim)
+								{
+									sp[dim] = basis_atoms[dim][i] - ( basis_atoms[dim][j]
+										+ k1*translation_vectors[dim][0] + k2*translation_vectors[dim][1] + k3*translation_vectors[dim][2] );
+								}
+								if ( (i!=j || k1!=0 || k2!=0 || k3!=0) && std::abs(sp[0]) < 1e-9 && std::abs(sp[1]) < 1e-9 && std::abs(sp[2]) < 1e-9)
+								{
+									Log(Utility::Log_Level::Severe, Utility::Log_Sender::All, "Unable to initialize Spin-System, since 2 spins occupy the same space.\nPlease check the config file!");
+									Log.Append_to_File();
+									throw Exception::System_not_Initialized;
+								}
 							}
 						}
 					}

input/anisotropic/pairs-example-hopfion.txt

@@ -0,0 +1,7 @@
+i j da db dc   J
+0 0 1  0  0   1.0
+0 0 0  1  0   1.0
+0 0 0  0  1   1.0
+0 0 2  0  0   -0.24
+0 0 0  2  0   -0.24
+0 0 0  0  2   -0.24

input/example-hopfion-anisotropic.cfg

@@ -0,0 +1,126 @@
+############ Spirit Configuration ############
+
+
+
+### Hamiltonian Type (isotropic or anisotropic)
+hamiltonian anisotropic
+
+### Output Folders
+llg_output_folder output
+gneb_output_folder output
+mmf_output_folder output
+
+
+
+############### Logging Parameters ###############
+log_output_folder .
+### Levels of information
+# 0 = ALL     - Anything
+# 1 = SEVERE  - Severe error
+# 2 = ERROR   - Error which can be handled
+# 3 = WARNING - Possible unintended behaviour etc
+# 4 = PARAMETER - Status information etc
+# 5 = INFO      - Status information etc
+# 6 = DEBUG     - Deeper status, eg numerical
+### Print messages up to (including) log_print
+log_print 6
+### Accept messages up to (including) log_accept
+log_accept 6
+############## End Debug_Parameters ##############
+
+
+
+################## Geometry ##################
+### Read basis from file
+basis_from_config input/basis_sc.cfg
+
+### Keyword translation_vectors ###
+###   t1.x t1.y t1.z nCells(t1)
+###   t2.x t2.y t2.z nCells(t2)
+###   t3.x t3.y t3.z nCells(t3)
+translation_vectors
+1 0 0 30
+0 1 0 30
+0 0 1 30
+
+################# End Geometry #################
+
+
+
+################ LLG_Parameters ################
+### seed for Rendom Number Generator
+llg_seed			20006
+
+### Disable saving a seperate "Spins" configuration file after every logstep iteration
+llg_save_single_configurations 0
+
+### Number of iterations
+llg_n_iterations		2000000
+### Number of iterations after which to save
+llg_n_iterations_log    2000
+
+### temperature [K]
+llg_temperature			0
+
+### damping [none]
+llg_damping				0.3E+0
+
+### time step dt
+llg_dt					1.0E-3
+
+### Bools 0 = false || 1 = true
+llg_renorm				1
+
+### Spin transfer torque parameter proportional to injected current density
+llg_stt_magnitude			0.0
+
+### spin current polarisation normal vector
+llg_stt_polarisation_normal	1.0 0.0 0.0
+
+### Force convergence parameter
+llg_force_convergence    10e-9
+############## End LLG_Parameters ##############
+
+
+
+################ GNEB_Parameters ################
+gneb_spring_constant		1.0
+
+### Bools 0 = false || 1 = true
+gneb_renorm				1
+
+### Number of GNEB Energy interpolations
+gneb_n_energy_interpolations	10
+
+### Force convergence parameter
+gneb_force_convergence    10e-7
+
+### Number of iterations and saves
+gneb_n_iterations		200000
+gneb_n_iterations_log   200
+############## End GNEB_Parameters ##############
+
+
+
+############# Hamiltonian_Isotropic #############
+
+### boundary_conditions (in a b c) = 0(open), 1(periodical)
+boundary_conditions 1 1 1
+
+### external magnetic field vector[T]
+external_field_magnitude		0.0
+external_field_normal			0.0 0.0 1.0
+### µSpin
+mu_s= 2.0
+
+### Uniaxial anisotropy constant [meV]
+anisotropy_magnitude			0.0
+anisotropy_normal				0.0 0.0 1.0
+
+### Dipole-Dipole radius
+dd_radius		0.0
+
+### Pairs
+interaction_pairs_file input/anisotropic/pairs-example-hopfion.txt
+
+########### End Hamiltonian_Anisotropic ###########