Bugfix: irregular memory error (double free).

- fixed bug in Chain API and System API where images were not locked before updating Energy arrays
- fixed bug in ControlWidget which would continuously update SettingsWidget
- improved names of energy IO methods
- added save interpolated energies to file menu

core/include/Spirit/IO.h

@@ -28,11 +28,17 @@ DLLEXPORT void IO_Chain_Write(State * state, const char * file, int idx_image=-1
 DLLEXPORT void IO_Collection_Read(State * state, const char * file, int idx_image=-1, int idx_chain=-1);
 DLLEXPORT void IO_Collection_Write(State * state, const char * file, int idx_image=-1, int idx_chain=-1);
 
-// Data
-DLLEXPORT void IO_Energy_Spins_Save(State * state, const char * file, int idx_image=-1, int idx_chain=-1);
-DLLEXPORT void IO_Energies_Save(State * state, const char * file, int idx_chain = -1);
-DLLEXPORT void IO_Energies_Spins_Save(State * state, const char * file, int idx_chain = -1);
-DLLEXPORT void IO_Energies_Interpolated_Save(State * state, const char * file, int idx_chain = -1);
+
+// Save the spin-resolved energy contributions of a spin system
+DLLEXPORT void IO_Write_System_Energy_per_Spin(State * state, const char * file, int idx_chain = -1);
+// Save the Energy contributions of a spin system
+DLLEXPORT void IO_Write_System_Energy(State * state, const char * file, int idx_image=-1, int idx_chain=-1);
+
+// Save the Energy contributions of a chain of spin systems
+DLLEXPORT void IO_Write_Chain_Energies(State * state, const char * file, int idx_chain = -1);
+// Save the interpolated energies of a chain of spin systems
+DLLEXPORT void IO_Write_Chain_Energies_Interpolated(State * state, const char * file, int idx_chain = -1);
+
 
 #include "DLL_Undefine_Export.h"
 #endif

core/include/utility/IO.hpp

@@ -96,18 +96,22 @@ namespace Utility
 		void Save_SpinChain_Configuration(std::shared_ptr<Data::Spin_System_Chain> & c, const std::string fileName);
 
 		// =========================== Saving Energies ===========================
-		void Write_Energy_Header(Data::Spin_System & s, const std::string fileName, std::vector<std::string> firstcolumns={"iteration", "E_tot"}, bool contributions=true, bool normalize_nos=true);
-		// Appends the current Energy of the current image with energy contributions, without header
-		void Append_Energy(Data::Spin_System &s, const int iteration, const std::string fileName, bool normalize_nos=true);
-		// Save energy contributions per spin
-		void Save_Energy_Spins(Data::Spin_System & s, const std::string fileName, bool normalize_nos=true);
+		void Write_Energy_Header(const Data::Spin_System & s, const std::string fileName, std::vector<std::string> firstcolumns={"iteration", "E_tot"}, bool contributions=true, bool normalize_nos=true);
+		// Appends the Energy of a spin system with energy contributions (without header)
+		void Append_System_Energy(const Data::Spin_System &s, const int iteration, const std::string fileName, bool normalize_nos=true);
+		// Save energy contributions of a spin system
+		void Write_System_Energy(const Data::Spin_System & system, const std::string fileName, bool normalize_by_nos=true);
+		// Save energy contributions of a spin system per spin
+		void Write_System_Energy_per_Spin(const Data::Spin_System & s, const std::string fileName, bool normalize_nos=true);
+		// Saves the forces on an image chain
+		void Write_System_Force(const Data::Spin_System & s, const std::string fileName);
+
 		// Saves Energies of all images with header and contributions
-		void Save_Energies(Data::Spin_System_Chain & c, const int iteration, const std::string fileName, bool normalize_nos=true);
+		void Write_Chain_Energies(const Data::Spin_System_Chain & c, const int iteration, const std::string fileName, bool normalize_nos=true);
 		// Saves the Energies interpolated by the GNEB method
-		void Save_Energies_Interpolated(Data::Spin_System_Chain & c, const std::string fileName, bool normalize_nos=true);
-		// Saves the energy contributions of every spin of an image
-		void Save_Energies_Spins(Data::Spin_System_Chain & c, const std::string fileName, bool normalize_nos=true);
-		void Save_Forces(Data::Spin_System_Chain & c, const std::string fileName);
+		void Write_Chain_Energies_Interpolated(const Data::Spin_System_Chain & c, const std::string fileName, bool normalize_nos=true);
+		// Saves the forces on an image chain
+		void Write_Chain_Forces(const Data::Spin_System_Chain & c, const std::string fileName);
 
 
 		// ========================= Saving Helpers =========================

core/src/Spirit/Chain.cpp

@@ -422,8 +422,11 @@ void Chain_Update_Data(State * state, int idx_chain_i)
     {
         //Engine::Energy::Update(*chain->images[i]);
         //chain->images[i]->E = chain->images[i]->hamiltonian_isotropichain->Energy(chain->images[i]->spins);
+
+	    image->Lock();
         chain->images[i]->UpdateEnergy();
         if (i > 0) chain->Rx[i] = chain->Rx[i-1] + Engine::Manifoldmath::dist_geodesic(*chain->images[i-1]->spins, *chain->images[i]->spins);
+	    image->Unlock();
     }
 }
 

core/src/Spirit/IO.cpp

@@ -130,46 +130,49 @@ void IO_Collection_Write(State * state, const char * file, int idx_image, int id
 /*--------------------------------------- Data --------------------------------------------------------- */
 /*------------------------------------------------------------------------------------------------------ */
 
-void IO_Energy_Spins_Save(State * state, const char * file, int idx_image, int idx_chain)
+//IO_Energies_Spins_Save
+void IO_Write_System_Energy_per_Spin(State * state, const char * file, int idx_chain)
 {
+	int idx_image = -1;
 	std::shared_ptr<Data::Spin_System> image;
 	std::shared_ptr<Data::Spin_System_Chain> chain;
 	from_indices(state, idx_image, idx_chain, image, chain);
 
 	// Write the data
-	Utility::IO::Save_Energy_Spins(*image, std::string(file));
+	Utility::IO::Write_System_Energy_per_Spin(*image, std::string(file));
 }
 
-void IO_Energies_Save(State * state, const char * file, int idx_chain)
+//IO_Energy_Spins_Save
+void IO_Write_System_Energy(State * state, const char * file, int idx_image, int idx_chain)
 {
-	int idx_image = -1;
 	std::shared_ptr<Data::Spin_System> image;
 	std::shared_ptr<Data::Spin_System_Chain> chain;
 	from_indices(state, idx_image, idx_chain, image, chain);
 
 	// Write the data
-	Utility::IO::Save_Energies(*chain, idx_chain, std::string(file));
+	Utility::IO::Write_System_Energy(*image, std::string(file));
 }
 
-
-void IO_Energies_Spins_Save(State * state, const char * file, int idx_chain)
+//IO_Energies_Save
+void IO_Write_Chain_Energies(State * state, const char * file, int idx_chain)
 {
 	int idx_image = -1;
 	std::shared_ptr<Data::Spin_System> image;
 	std::shared_ptr<Data::Spin_System_Chain> chain;
 	from_indices(state, idx_image, idx_chain, image, chain);
 
 	// Write the data
-	Utility::IO::Save_Energies_Spins(*state->active_chain, std::string(file));
+	Utility::IO::Write_Chain_Energies(*chain, idx_chain, std::string(file));
 }
 
-void IO_Energies_Interpolated_Save(State * state, const char * file, int idx_chain)
+//IO_Energies_Interpolated_Save
+void IO_Write_Chain_Energies_Interpolated(State * state, const char * file, int idx_chain)
 {
 	int idx_image = -1;
 	std::shared_ptr<Data::Spin_System> image;
 	std::shared_ptr<Data::Spin_System_Chain> chain;
 	from_indices(state, idx_image, idx_chain, image, chain);
 
 	// Write the data
-	Utility::IO::Save_Energies_Interpolated(*state->active_chain, std::string(file));
+	Utility::IO::Write_Chain_Energies_Interpolated(*chain, std::string(file));
 }

core/src/Spirit/System.cpp

@@ -88,5 +88,7 @@ void System_Update_Data(State * state, int idx_image, int idx_chain)
     std::shared_ptr<Data::Spin_System_Chain> chain;
     from_indices(state, idx_image, idx_chain, image, chain);
 
+	image->Lock();
     image->UpdateEnergy();
+	image->Unlock();
 }

core/src/engine/Method_GNEB.cpp

@@ -202,11 +202,11 @@ namespace Engine
 			{
 				// Save current Energies with reaction coordinates
 				auto energiesFile = this->chain->gneb_parameters->output_folder + "/" + starttime + "_E_Images_" + s_iter + suffix + ".txt";
-				Utility::IO::Save_Energies(*this->chain, iteration, energiesFile);
+				Utility::IO::Write_Chain_Energies(*this->chain, iteration, energiesFile);
 
 				// Save interpolated Energies
 				auto energiesInterpFile = this->chain->gneb_parameters->output_folder + "/" + starttime + "_E_interp_Images_" + s_iter + suffix + ".txt";
-				Utility::IO::Save_Energies_Interpolated(*this->chain, energiesInterpFile);
+				Utility::IO::Write_Chain_Energies_Interpolated(*this->chain, energiesInterpFile);
 			}
 
 			// Save Log

core/src/engine/Method_LLG.cpp

@@ -171,15 +171,15 @@ namespace Engine
 					std::ifstream f(energyFile);
 					if (!f.good()) Utility::IO::Write_Energy_Header(*this->systems[0], energyFile);
 					// Append Energy to File
-					Utility::IO::Append_Energy(*this->systems[0], iteration, energyFile, normalize);
+					Utility::IO::Append_System_Energy(*this->systems[0], iteration, energyFile, normalize);
 				}
 				else
 				{
 					Utility::IO::Write_Energy_Header(*this->systems[0], energyFile);
-					Utility::IO::Append_Energy(*this->systems[0], iteration, energyFile, normalize);
+					Utility::IO::Append_System_Energy(*this->systems[0], iteration, energyFile, normalize);
 					if (this->systems[0]->llg_parameters->output_energy_spin_resolved)
 					{
-						Utility::IO::Save_Energy_Spins(*this->systems[0], energyFilePerSpin, normalize);
+						Utility::IO::Write_System_Energy_per_Spin(*this->systems[0], energyFilePerSpin, normalize);
 					}
 				}
 			};

core/src/utility/IO_Filedump.cpp

@@ -61,7 +61,7 @@ namespace Utility
 		}
 		// ------------------------------------------------------------
 
-		void Write_Energy_Header(Data::Spin_System & s, const std::string fileName, std::vector<std::string> firstcolumns, bool contributions, bool normalize_by_nos)
+		void Write_Energy_Header(const Data::Spin_System & s, const std::string fileName, std::vector<std::string> firstcolumns, bool contributions, bool normalize_by_nos)
 		{
 			bool readability_toggle = true;
 
@@ -97,14 +97,14 @@ namespace Utility
 			String_to_File(header, fileName);
 		}
 
-		void Append_Energy(Data::Spin_System & s, const int iteration, const std::string fileName, bool normalize_by_nos)
+		void Append_System_Energy(const Data::Spin_System & s, const int iteration, const std::string fileName, bool normalize_by_nos)
 		{
 			bool readability_toggle = true;
 			scalar nd = 1.0; // nos divide
 			if (normalize_by_nos) nd = 1.0 / s.nos;
 			else nd = 1;
 
-			s.UpdateEnergy();
+			// s.UpdateEnergy();
 
 			std::string line = center(iteration, 0, 20) + "||" + center(s.E * nd, 10, 20) + "||";
 			bool first = true;
@@ -123,14 +123,40 @@ namespace Utility
 			Append_String_to_File(line, fileName);
 		}
 
-		void Save_Energy_Spins(Data::Spin_System & s, const std::string fileName, bool normalize_by_nos)
+		void Write_System_Energy(const Data::Spin_System & system, const std::string fileName, bool normalize_by_nos)
+		{
+			bool readability_toggle = true;
+			scalar nd = 1.0; // nos divide
+			if (normalize_by_nos) nd = 1.0 / system.nos;
+			else nd = 1;
+
+			Write_Energy_Header(system, fileName, {"E_tot"});
+
+			std::string line = center(system.E * nd, 10, 20) + "||";
+			bool first = true;
+			for (auto pair : system.E_array)
+			{
+				if (first) first = false;
+				else
+				{
+					line += "|";;
+				}
+				line += center(pair.second * nd, 10, 20);
+			}
+			line += "\n";
+
+			if (!readability_toggle) std::replace( line.begin(), line.end(), '|', ' ');
+			Append_String_to_File(line, fileName);
+		}
+
+		void Write_System_Energy_per_Spin(const Data::Spin_System & s, const std::string fileName, bool normalize_by_nos)
 		{
 			bool readability_toggle = true;
 			scalar nd = 1.0; // nos divide
 			if (normalize_by_nos) nd = 1.0 / s.nos;
 			else nd = 1;
 
-			s.UpdateEnergy();
+			// s.UpdateEnergy();
 
 			Write_Energy_Header(s, fileName, {"ispin", "E_tot"});
 
@@ -160,7 +186,11 @@ namespace Utility
 			Append_String_to_File(data, fileName);
 		}
 
-		void Save_Energies(Data::Spin_System_Chain & c, const int iteration, const std::string fileName, bool normalize_by_nos)
+		void Write_System_Force(const Data::Spin_System & s, const std::string fileName)
+		{
+		}
+
+		void Write_Chain_Energies(const Data::Spin_System_Chain & c, const int iteration, const std::string fileName, bool normalize_by_nos)
 		{
 			int isystem;
 			bool readability_toggle = true;
@@ -173,7 +203,7 @@ namespace Utility
 			for (isystem = 0; isystem < (int)c.noi; ++isystem)
 			{
 				auto& system = *c.images[isystem];
-				std::string line = center(isystem, 0, 20) + "||" + center(c.Rx[isystem], 0, 20) + "||" + center(system.E * nd, 10, 20) + "||";
+				std::string line = center(isystem, 0, 20) + "||" + center(c.Rx[isystem], 10, 20) + "||" + center(system.E * nd, 10, 20) + "||";
 				bool first = true;
 				for (auto pair : system.E_array)
 				{
@@ -191,8 +221,7 @@ namespace Utility
 			}
 		}
 
-
-		void Save_Energies_Interpolated(Data::Spin_System_Chain & c, const std::string fileName, bool normalize_by_nos)
+		void Write_Chain_Energies_Interpolated(const Data::Spin_System_Chain & c, const std::string fileName, bool normalize_by_nos)
 		{
 			int isystem, iinterp, idx;
 			bool readability_toggle = true;
@@ -209,7 +238,7 @@ namespace Utility
 				for (iinterp = 0; iinterp < c.gneb_parameters->n_E_interpolations+1; ++iinterp)
 				{
 					idx = isystem * (c.gneb_parameters->n_E_interpolations+1) + iinterp;
-					std::string line = center(isystem, 0, 20) + "||" + center(iinterp, 0, 20) + "||" + center(c.Rx_interpolated[idx], 0, 20) + "||" + center(c.E_interpolated[idx] * nd, 10, 20) + "||";
+					std::string line = center(isystem, 0, 20) + "||" + center(iinterp, 0, 20) + "||" + center(c.Rx_interpolated[idx], 10, 20) + "||" + center(c.E_interpolated[idx] * nd, 10, 20) + "||";
 
 					// TODO: interpolated Energy contributions
 					// bool first = true;
@@ -234,61 +263,7 @@ namespace Utility
 		}
 
 
-		void Save_Energies_Spins(Data::Spin_System_Chain & c, const std::string fileName, bool normalize_by_nos)
-		{
-			/////////////////
-			// TODO: rewrite like other save_energy functions
-			/////////////////
-
-			// //========================= Init local vars ================================
-			// int isystem, ispin, iE;
-			// bool readability_toggle = true;
-			// scalar nd = 1.0; // nos divide
-			// const int buffer_length = 200;
-			// std::string output_to_file = "";
-			// output_to_file.reserve(int(1E+08));
-			// char buffer_string_conversion[buffer_length + 2];
-			// snprintf(buffer_string_conversion, buffer_length, " isystem ||  ispin  ||         E_tot        ||       E_Zeeman      |       E_Aniso       |      E_Exchange     |        E_DMI        |        E_BQC        |       E_FourSC       |   E_DipoleDipole\n");
-			// if (!readability_toggle) { std::replace(buffer_string_conversion, buffer_string_conversion + strlen(buffer_string_conversion), '|', ' '); }
-			// output_to_file.append(buffer_string_conversion);
-			// snprintf(buffer_string_conversion, buffer_length, "---------++---------++----------------------++---------------------+---------------------+---------------------+---------------------+---------------------+----------------------+---------------------");
-			// if (readability_toggle) { output_to_file.append(buffer_string_conversion); }
-			// //------------------------ End Init ----------------------------------------
-
-			// int nos = (int)c.images[0]->nos;
-			// int noi = (int)c.noi;
-			// auto Energies_spins = std::vector<std::vector<scalar>>(nos, std::vector<scalar>(7, 0.0));
-			// auto E_tot_spins = std::vector<scalar>(nos, 0.0);
-			// for (isystem = 0; isystem < noi; ++isystem) {
-			// 	// Get Energies
-			// 	Energies_spins = c.images[isystem]->hamiltonian->Energy_Array_per_Spin(*c.images[isystem]->spins);
-			// 	for (ispin = 0; ispin < nos; ++ispin)
-			// 	{
-			// 		for (iE = 0; iE < 7; ++iE)
-			// 		{
-			// 			E_tot_spins[ispin] += Energies_spins[ispin][iE];
-			// 		}
-			// 	}
-			// 	// Normalise?
-			// 	if (normalize_by_nos) { nd = 1.0 / nos; }
-			// 	else { nd = 1; }
-			// 	// Write
-			// 	for (ispin = 0; ispin < nos; ++ispin)
-			// 	{
-			// 		snprintf(buffer_string_conversion, buffer_length, "\n %6i  || %6i  ||  %18.10f  ||  %18.10f |  %18.10f |  %18.10f |  %18.10f |  %18.10f |  %18.10f  |  %18.10f",
-			// 			isystem, ispin, E_tot_spins[ispin] * nd, Energies_spins[ispin][ENERGY_POS_ZEEMAN] * nd, Energies_spins[ispin][ENERGY_POS_ANISOTROPY] * nd,
-			// 			Energies_spins[ispin][ENERGY_POS_EXCHANGE] * nd, Energies_spins[ispin][ENERGY_POS_DMI] * nd,
-			// 			Energies_spins[ispin][ENERGY_POS_BQC] * nd, Energies_spins[ispin][ENERGY_POS_FSC] * nd,
-			// 			Energies_spins[ispin][ENERGY_POS_DD] * nd);
-			// 		if (!readability_toggle) { std::replace(buffer_string_conversion, buffer_string_conversion + strlen(buffer_string_conversion), '|', ' '); }
-			// 		output_to_file.append(buffer_string_conversion);
-			// 	}
-			// }
-			// Dump_to_File(output_to_file, fileName);
-		}
-
-
-		void Save_Forces(Data::Spin_System_Chain & c, const std::string fileName)
+		void Write_Chain_Forces(const Data::Spin_System_Chain & c, const std::string fileName)
 		{
 			/////////////////
 			// TODO: rewrite like save_energy functions

ui-qt/include/ControlWidget.hpp

@@ -51,6 +51,7 @@ private slots:
 	void save_EPressed();
 
 private:
+	void updateOthers();
 	void readSettings();
 	void writeSettings();
 	// State

ui-qt/include/MainWindow.hpp

@@ -65,8 +65,9 @@ private slots:
 	void load_Spin_Configuration();
 	void save_SpinChain_Configuration();
 	void load_SpinChain_Configuration();
-	void save_Energies();
-	void save_Energy_Spins();
+	void save_System_Energy_Spins();
+	void save_Chain_Energies();
+	void save_Chain_Energies_Interpolated();
 	void return_focus();
 
 private: