Merge branch 'develop' into fixed-micromagnetic

.github/workflows/ci.yml

@@ -427,3 +427,31 @@ jobs:
         name: spirit-windows
         path: |
           ${{runner.workspace}}/build/*.zip
+
+  draft-release:
+    if: github.event_name == 'push' && startsWith( github.ref, 'refs/tags/' )
+    needs: [test, webapp-mobile, webapp-desktop, deploy-package]
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: 📄 Generate a changelog
+      id: changelog
+      uses: metcalfc/changelog-generator@v1.0.0
+      with:
+        myToken: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: 📄 Print the changelog
+      run: echo "${{ steps.changelog.outputs.changelog }}"
+
+    - name: 🎉 Create draft release
+      id: draft_release
+      uses: actions/create-release@v1
+      with:
+        tag_name: ${{ github.ref }}
+        release_name: Release ${{ github.ref }}
+        body: ${{ steps.changelog.outputs.changelog }}
+        draft: true

CMakeLists.txt

@@ -70,10 +70,6 @@ set( CMAKE_POSITION_INDEPENDENT_CODE ON )
 set( CMAKE_CXX_STANDARD 14 )
 ### Set the cmake subdirectory
 list( APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/CMake" )
-### Need to use pthread if emscripten is used
-if( SPIRIT_BUILD_FOR_JS AND SPIRIT_UI_USE_IMGUI )
-    set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -s USE_PTHREADS=1 -s PTHREAD_POOL_SIZE=2")
-endif()
 ####################################################################
 
 
@@ -207,6 +203,18 @@ endif()
 ###
 if( SPIRIT_BUILD_FOR_JS )
     set( SPIRIT_BUILD_FOR_CXX OFF )
+    set( SPIRIT_USE_CUDA      OFF )
+    set( SPIRIT_USE_OPENMP    OFF )
+    set( SPIRIT_UI_CXX_USE_QT OFF )
+    set( SPIRIT_UI_USE_IMGUI  ON  )
+
+    if( ${CMAKE_SYSTEM_NAME} MATCHES "Emscripten" )
+        message( WARNING "You set SPIRIT_BUILD_FOR_JS to ON but your are not using emscripten. That might not work" )
+    endif()
+endif()
+### Need to use pthread if emscripten is used
+if( SPIRIT_BUILD_FOR_JS AND SPIRIT_UI_USE_IMGUI )
+    set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread -s USE_PTHREADS=1 -s USE_PTHREADS=1 -s WASM=1" )
 endif()
 ####################################################################
 
@@ -226,23 +234,20 @@ endif()
 add_subdirectory( core )
 ### Web UI
 if( SPIRIT_BUILD_FOR_JS )
-    add_subdirectory( VFRendering )
     if( SPIRIT_UI_USE_IMGUI )
         add_definitions( -DSPIRIT_UI_USE_IMGUI )
-        add_subdirectory( ui-cpp )
-    else()
-        add_subdirectory( ui-web )
     endif()
+    add_subdirectory( VFRendering )
+    add_subdirectory( ui-cpp )
+    add_subdirectory( ui-web )
 ### CXX UI
 elseif( SPIRIT_BUILD_FOR_CXX )
     if( SPIRIT_UI_CXX_USE_QT )
         add_definitions( -DSPIRIT_UI_CXX_USE_QT )
-        add_subdirectory( VFRendering )
-    endif()
-    if( SPIRIT_UI_USE_IMGUI )
+    elseif( SPIRIT_UI_USE_IMGUI )
         add_definitions( -DSPIRIT_UI_USE_IMGUI )
-        add_subdirectory( VFRendering )
     endif()
+    add_subdirectory( VFRendering )
     add_subdirectory( ui-cpp )
 endif()
 ####################################################################

core/CMake/Spirit_Version.hpp.in

@@ -1,6 +1,6 @@
 #pragma once
-#ifndef SPIRIT_UTILITY_VERSION_HPP
-#define SPIRIT_UTILITY_VERSION_HPP
+#ifndef SPIRIT_CORE_UTILITY_VERSION_HPP
+#define SPIRIT_CORE_UTILITY_VERSION_HPP
 
 #include <string>
 

core/CMakeLists.txt

@@ -97,27 +97,27 @@ include( GetGitRevisionDescription )
 get_git_head_revision( GIT_REFSPEC GIT_SHA1 )
 string( SUBSTRING "${GIT_SHA1}" 0 13 GIT_REV )
 #----- Meta information about the project
-set(META_PROJECT_NAME         "Spirit")
-set(META_PROJECT_DESCRIPTION  "Optimizations and Dynamics Framework for atomistic Spin systems")
-set(META_AUTHOR_ORGANIZATION  "")
-set(META_AUTHOR_DOMAIN        "https://spirit-code.github.io")
-set(META_AUTHOR_MAINTAINER    "Gideon Mueller")
-set(META_AUTHOR_EMAIL         "g.mueller@fz-juelich.de")
-set(META_VERSION_MAJOR        "2")
-set(META_VERSION_MINOR        "1")
-set(META_VERSION_PATCH        "1")
-set(META_VERSION              "${META_VERSION_MAJOR}.${META_VERSION_MINOR}.${META_VERSION_PATCH}")
-set(META_VERSION_REVISION     "${GIT_REV}")
+set( META_PROJECT_NAME         "Spirit" )
+set( META_PROJECT_DESCRIPTION  "Optimizations and Dynamics Framework for atomistic Spin systems" )
+set( META_AUTHOR_ORGANIZATION  "" )
+set( META_AUTHOR_DOMAIN        "https://spirit-code.github.io" )
+set( META_AUTHOR_MAINTAINER    "Gideon Mueller" )
+set( META_AUTHOR_EMAIL         "g.mueller@fz-juelich.de" )
+set( META_VERSION_MAJOR        "2" )
+set( META_VERSION_MINOR        "1" )
+set( META_VERSION_PATCH        "1" )
+set( META_VERSION              "${META_VERSION_MAJOR}.${META_VERSION_MINOR}.${META_VERSION_PATCH}" )
+set( META_VERSION_REVISION     "${GIT_REV}" )
 #----- Compiler
-set(META_COMPILER             "${CMAKE_CXX_COMPILER_ID}")
-set(META_COMPILER_VERSION     "${CMAKE_CXX_COMPILER_VERSION}")
-set(META_COMPILER_FULL        "${CMAKE_CXX_COMPILER_ID} (${CMAKE_CXX_COMPILER_VERSION})")
+set( META_COMPILER             "${CMAKE_CXX_COMPILER_ID}" )
+set( META_COMPILER_VERSION     "${CMAKE_CXX_COMPILER_VERSION}" )
+set( META_COMPILER_FULL        "${CMAKE_CXX_COMPILER_ID} (${CMAKE_CXX_COMPILER_VERSION})" )
 #----- Propagate version and name_version upwards
-set(SPIRIT_META_VERSION_MAJOR ${META_VERSION_MAJOR} PARENT_SCOPE)
-set(SPIRIT_META_VERSION_MINOR ${META_VERSION_MINOR} PARENT_SCOPE)
-set(SPIRIT_META_VERSION_PATCH ${META_VERSION_PATCH} PARENT_SCOPE)
-set(SPIRIT_META_VERSION       "${META_VERSION}" PARENT_SCOPE)
-set(SPIRIT_META_NAME_VERSION  "${META_PROJECT_NAME} v${META_VERSION} (${META_VERSION_REVISION})" PARENT_SCOPE)
+set( SPIRIT_META_VERSION_MAJOR ${META_VERSION_MAJOR} PARENT_SCOPE )
+set( SPIRIT_META_VERSION_MINOR ${META_VERSION_MINOR} PARENT_SCOPE )
+set( SPIRIT_META_VERSION_PATCH ${META_VERSION_PATCH} PARENT_SCOPE )
+set( SPIRIT_META_VERSION       "${META_VERSION}" PARENT_SCOPE )
+set( SPIRIT_META_NAME_VERSION  "${META_PROJECT_NAME} v${META_VERSION} (${META_VERSION_REVISION})" PARENT_SCOPE )
 ####################################################################
 
 
@@ -439,11 +439,11 @@ if( SPIRIT_BUILD_FOR_CXX OR SPIRIT_BUILD_FOR_JS )
     message( STATUS ">> Building static C/C++ library ${META_PROJECT_NAME}_static" )
     add_library( ${META_PROJECT_NAME}_static STATIC $<TARGET_OBJECTS:${META_PROJECT_NAME}> )
     ### Forward public includes from the object library
-    target_include_directories(${META_PROJECT_NAME}_static PUBLIC
-        $<TARGET_PROPERTY:${META_PROJECT_NAME},INTERFACE_INCLUDE_DIRECTORIES>)
+    target_include_directories( ${META_PROJECT_NAME}_static PUBLIC
+        $<TARGET_PROPERTY:${META_PROJECT_NAME},INTERFACE_INCLUDE_DIRECTORIES> )
     ### Apply interface link dependencies from the object library
-    target_link_libraries(${META_PROJECT_NAME}_static PRIVATE
-        $<TARGET_PROPERTY:${META_PROJECT_NAME},INTERFACE_LINK_LIBRARIES>)
+    target_link_libraries( ${META_PROJECT_NAME}_static PRIVATE
+        $<TARGET_PROPERTY:${META_PROJECT_NAME},INTERFACE_LINK_LIBRARIES> )
     #--------------------------------------------------
 
     #--------------------------------------------------

core/docs/Input.md

@@ -476,6 +476,9 @@ llg_force_convergence   10e-9
 llg_n_iterations        2000000
 ### Number of iterations after which to save
 llg_n_iterations_log    2000
+### Number of iterations that gets run with no checks or outputs (Increasing this boosts performance, especially in CUDA builds)
+llg_n_iterations_amortize 1
+
 ```
 
 **LLG:**

core/docs/c-api/Configurations.md

@@ -151,6 +151,10 @@ void Configuration_Skyrmion(State *state, float r, float order, float phase, boo
 
 Create a skyrmion configuration
 
+
+
+### Configuration_DW_Skyrmion
+
 ```C
 void Configuration_DW_Skyrmion(State *state, float dw_radius, float dw_width, float order, float phase, bool upDown, bool achiral, bool rl, const float position[3]=defaultPos, const float r_cut_rectangular[3]=defaultRect, float r_cut_cylindrical=-1, float r_cut_spherical=-1, bool inverted=false, int idx_image=-1, int idx_chain=-1)
 ```

core/docs/c-api/HTST.md

@@ -16,7 +16,7 @@ Note that `HTST_Calculate` needs to be called before using any of the getter fun
 ### HTST_Calculate
 
 ```C
-float HTST_Calculate(State * state, int idx_image_minimum, int idx_image_sp, int n_eigenmodes_keep=0, int idx_chain=-1)
+float HTST_Calculate(State * state, int idx_image_minimum, int idx_image_sp, int n_eigenmodes_keep=0, bool sparse=false, int idx_chain=-1)
 ```
 
 Calculates the HTST transition rate prefactor for the transition from a minimum over saddle point.
@@ -26,7 +26,7 @@ Calculates the HTST transition rate prefactor for the transition from a minimum
 - `n_eigenmodes_keep`: the number of energy eigenmodes to keep in memory (0 = none, negative value = all)
 - `sparse`: when set to `true` the sparse version is used, which greatly improves speed and memory footprint, 
             but does not evaluate the eigenvectors and all single eigenvalues. 
-            The sparse version should only be used in the abscence of DDI.
+            The sparse version should only be used in the abscence of DDI
 
 Note: The Get_Eigenvalues/vectors functions only work after HTST_Calculate with sparse=false has been called.
 Note: In the sparse version zero mode checking has not been implemented yet.
@@ -39,7 +39,7 @@ respectively.
 ### HTST_Get_Info
 
 ```C
-void HTST_Get_Info( State * state, float * temperature_exponent, float * me, float * Omega_0, float * s, float * volume_min, float * volume_sp, float * prefactor_dynamical, float * prefactor, int idx_chain=-1 )
+void HTST_Get_Info( State * state, float * temperature_exponent, float * me, float * Omega_0, float * s, float * volume_min, float * volume_sp, float * prefactor_dynamical, float * prefactor, int * n_eigenmodes_keep, int idx_chain=-1 )
 ```
 
 Retrieves a set of information from HTST:

core/docs/c-api/Hamiltonian.md

@@ -165,7 +165,7 @@ Set the Dzyaloshinskii-Moriya interaction in terms of neighbour shells [meV]
 ### Hamiltonian_Set_DDI
 
 ```C
-void Hamiltonian_Set_DDI(State *state, int ddi_method, int n_periodic_images[3], float cutoff_radius=0, int idx_image=-1, int idx_chain=-1)
+void Hamiltonian_Set_DDI(State *state, int ddi_method, int n_periodic_images[3], float cutoff_radius=0, bool pb_zero_padding=true, int idx_image=-1, int idx_chain=-1)
 ```
 
 Configure the dipole-dipole interaction
@@ -176,6 +176,7 @@ Configure the dipole-dipole interaction
   boundary conditions are used
 - `cutoff_radius`: the distance at which to stop the direct summation,
   if used
+- `pb_zero_padding`: if `True` zero padding is used even for periodical directions
 
 
 
@@ -273,15 +274,14 @@ Returns the number of Dzyaloshinskii-Moriya interaction pairs
 ### Hamiltonian_Get_DDI
 
 ```C
-void Hamiltonian_Get_DDI(State *state, int * ddi_method, int n_periodic_images[3], float * cutoff_radius, int idx_image=-1, int idx_chain=-1)
+void Hamiltonian_Get_DDI(State *state, int * ddi_method, int n_periodic_images[3], float * cutoff_radius,  bool * pb_zero_padding, int idx_image=-1, int idx_chain=-1)
 ```
 
 Retrieves the dipole-dipole interaction configuration.
 
 - `ddi_method`: see integers defined above
-- `n_periodic_images`: how many repetition of the spin configuration to
-  append along the translation directions [a, b, c], if periodical
-  boundary conditions are used
-- `cutoff_radius`: the distance at which to stop the direct summation,
-  if used
+- `n_periodic_images`: how many repetitions of the spin configuration to
+  append along the translation directions [a, b, c], if periodical boundary conditions are used
+- `cutoff_radius`: the distance at which to stop the direct summation, if method_cutoff is used
+- `pb_zero_padding`: if `True` zero padding is used even for periodical directions
 

core/docs/c-api/Simulation.md

@@ -38,7 +38,7 @@ Solver_VP          0
 Solver_SIB         1
 ```
 
-`SIB`: Verlet-like velocity projection
+`SIB`: Semi-implicit midpoint method B
 
 
 
@@ -48,7 +48,7 @@ Solver_SIB         1
 Solver_Depondt     2
 ```
 
-`Depondt`: Verlet-like velocity projection
+`Depondt`: Heun method using rotations
 
 
 
@@ -58,7 +58,7 @@ Solver_Depondt     2
 Solver_Heun        3
 ```
 
-`Heun`: Verlet-like velocity projection
+`Heun`: second-order midpoint
 
 
 
@@ -68,30 +68,40 @@ Solver_Heun        3
 Solver_RungeKutta4 4
 ```
 
-`RK4`: Verlet-like velocity projection
+`RK4`: 4th order Runge-Kutta
 
 
+
+### Solver_LBFGS_OSO
+
 ```C
 Solver_LBFGS_OSO   5
 ```
 
 `LBFGS_OSO`: Limited memory Broyden-Fletcher-Goldfarb-Shanno, exponential transform
 
 
+
+### Solver_LBFGS_Atlas
+
 ```C
 Solver_LBFGS_Atlas 6
 ```
 
 `LBFGS_Atlas`: Limited memory Broyden-Fletcher-Goldfarb-Shannon, stereographic projection
 
 
+
+### Solver_VP_OSO
+
 ```C
 Solver_VP_OSO      7
 ```
 
 `Solver_VP_OSO`: Verlet-like velocity projection, exponential transform
 
 
+
 Start or stop a simulation
 --------------------------------------------------------------------
 
@@ -163,7 +173,7 @@ Otherwise, nothing will happen.
 ### Simulation_N_Shot
 
 ```C
-void Simulation_N_Shot(State *state, int N, int idx_image=-1, int idx_chain=-1);
+void Simulation_N_Shot(State *state, int N, int idx_image=-1, int idx_chain=-1)
 ```
 
 N iterations of a Method
@@ -224,6 +234,32 @@ Will only work if a GNEB simulation is running.
 
 
 
+### Simulation_Get_MaxTorqueNorm
+
+```C
+float Simulation_Get_MaxTorqueNorm(State * state, int idx_image=-1, int idx_chain=-1)
+```
+
+Get maximum torque norm.
+
+If a MC, LLG, MMF or EMA simulation is running this returns the max. torque on the current image.
+
+If a GNEB simulation is running this returns the max. torque on the current chain.
+
+
+
+### Simulation_Get_Chain_MaxTorqueNorms
+
+```C
+void Simulation_Get_Chain_MaxTorqueNorms(State * state, float * torques, int idx_chain=-1)
+```
+
+Get maximum torque norms on the images of a chain.
+
+Will only work if a GNEB simulation is running.
+
+
+
 ### Simulation_Get_IterationsPerSecond
 
 ```C

core/docs/c-api/System.md

@@ -90,13 +90,23 @@ Returns the energy of a spin system.
 
 
 
+### System_Get_Energy_Array_Names
+
+```C
+int System_Get_Energy_Array_Names(State * state, char* names, int idx_image=-1, int idx_chain=-1)
+```
+
+If 'names' is a nullptr, the required length of the char array is returned.
+
+
+
 ### System_Get_Energy_Array
 
 ```C
-void System_Get_Energy_Array(State * state, float * energies, int idx_image=-1, int idx_chain=-1)
+int System_Get_Energy_Array(State * state, float * energies, bool divide_by_nspins=true, int idx_image=-1, int idx_chain=-1)
 ```
 
-Retrieves the energy contributions of a spin system.
+If 'energies' is a nullptr, the required length of the energies array is returned.