Add hybrid modeling with neural-network-based binding models

CMakeLists.txt

@@ -78,6 +78,7 @@ set(CMAKE_C_VISIBILITY_PRESET hidden)
 set(CMAKE_CXX_VISIBILITY_PRESET hidden)
 set(CMAKE_VISIBILITY_INLINES_HIDDEN ON)
 
+
 # Enable folders for IDEs
 set_property(GLOBAL PROPERTY USE_FOLDERS ON)
 

CMakeSettings.json

@@ -2,22 +2,24 @@
   // See https://go.microsoft.com//fwlink//?linkid=834763 for more information about this file.
   "environments": [
     {
-      "TBB_DIR": "C:/Program Files (x86)/IntelSWTools/compilers_and_libraries/windows/tbb",
-      "BLAS_DIR": "C:/Program Files (x86)/IntelSWTools/compilers_and_libraries/windows/mkl/lib/intel64_win",
-      "SUNDIALS_DIR": "${projectDir}/../../libs/sundials",
-      "HDF5_DIR": "${projectDir}/../../libs/hdf5",
-      "ZLIB": "${projectDir}/../../libs/hdf5/lib/zlib.lib",
-      "SZLIB": "${projectDir}/../../libs/hdf5/lib/szip.lib",
+      "TBB_DIR": "C:/Users/hassan/Desktop/Libs/tbb",
+      "BLAS_DIR": "C:/Program Files (x86)/IntelSWTools/compilers_and_libraries_2020/windows/mkl/lib/intel64_win",
+      "SUNDIALS_DIR": "C:/Users/hassan/Desktop/CADET_All/CADET_Jazib/Libs/sundials",
+      "HDF5_DIR": "C:/Users/hassan/Desktop/CADET_All/CADET_Jazib/Libs/hdf5_src/build/_CPack_Packages/win64/ZIP/HDF5-1.12.0-win64",
+      "ZLIB": "C:/Users/hassan/Desktop/CADET_All/CADET_Jazib/Libs/hdf5_src/build/_CPack_Packages/win64/ZIP/HDF5-1.12.0-win64/lib/zlib.lib",
+      "SZLIB": "C:/Users/hassan/Desktop/CADET_All/CADET_Jazib/Libs/hdf5_src/build/_CPack_Packages/win64/ZIP/HDF5-1.12.0-win64/lib/szip.lib",
       "INSTALL_DIR": "${projectDir}/../cadet/${name}",
       "BLAS_DEBUG": "Intel10_64lp_seq",
       "BLAS_RELEASE": "Intel10_64lp_seq",
       "BUILDROOT": "${env.USERPROFILE}\\CMakeBuild\\${workspaceHash}\\build\\${name}"
     }
   ],
+
+
   "configurations": [
     {
       "name": "MS_MKL_DEBUG",
-      "generator": "Visual Studio 15 2017 Win64",
+      "generator": "Visual Studio 16 2019 Win64",
       "configurationType": "Debug",
       "buildRoot": "${env.BUILDROOT}",
       "cmakeCommandArgs": "",
@@ -64,7 +66,7 @@
           "value": "${env.BLAS_DEBUG}"
         },
         {
-          "name": "CMAKE_INSTALL_PREFIX",
+          "name": "remoteInstallRoot",
           "value": "${env.INSTALL_DIR}"
         },
         {
@@ -76,7 +78,7 @@
     },
     {
       "name": "MS_MKL_RELEASE",
-      "generator": "Visual Studio 15 2017 Win64",
+      "generator": "Visual Studio 16 2019 Win64",
       "configurationType": "Release",
       "buildRoot": "${env.BUILDROOT}",
       "cmakeCommandArgs": "",
@@ -127,7 +129,7 @@
           "value": "${env.BLAS_RELEASE}"
         },
         {
-          "name": "CMAKE_INSTALL_PREFIX",
+          "name": "remoteInstallRoot",
           "value": "${env.INSTALL_DIR}"
         },
         {
@@ -138,7 +140,7 @@
     },
     {
       "name": "MS_MKL_RELDEBINFO",
-      "generator": "Visual Studio 15 2017 Win64",
+      "generator": "Visual Studio 16 2019",
       "configurationType": "RelWithDebInfo",
       "buildRoot": "${env.BUILDROOT}",
       "cmakeCommandArgs": "",
@@ -189,7 +191,7 @@
           "value": "${env.BLAS_RELEASE}"
         },
         {
-          "name": "CMAKE_INSTALL_PREFIX",
+          "name": "remoteInstallRoot",
           "value": "${env.INSTALL_DIR}"
         },
         {
@@ -200,7 +202,7 @@
     },
     {
       "name": "MS_SMKL_DEBUG",
-      "generator": "Visual Studio 15 2017 Win64",
+      "generator": "Visual Studio 16 2019",
       "configurationType": "Debug",
       "buildRoot": "${env.BUILDROOT}",
       "cmakeCommandArgs": "",
@@ -247,7 +249,7 @@
           "value": "${env.BLAS_DEBUG}"
         },
         {
-          "name": "CMAKE_INSTALL_PREFIX",
+          "name": "remoteInstallRoot",
           "value": "${env.INSTALL_DIR}"
         },
         {
@@ -257,13 +259,18 @@
         {
           "name": "BLA_STATIC",
           "value": "1"
+        },
+        {
+          "name": "BUILD_CADET_MEX",
+          "value": "False",
+          "type": "BOOL"
         }
       ]
 
     },
     {
       "name": "MS_SMKL_RELEASE",
-      "generator": "Visual Studio 15 2017 Win64",
+      "generator": "Visual Studio 16 2019",
       "configurationType": "Release",
       "buildRoot": "${env.BUILDROOT}",
       "cmakeCommandArgs": "",
@@ -314,7 +321,7 @@
           "value": "${env.BLAS_RELEASE}"
         },
         {
-          "name": "CMAKE_INSTALL_PREFIX",
+          "name": "remoteInstallRoot",
           "value": "${env.INSTALL_DIR}"
         },
         {
@@ -329,7 +336,7 @@
     },
     {
       "name": "MS_SMKL_RELDEBINFO",
-      "generator": "Visual Studio 15 2017 Win64",
+      "generator": "Visual Studio 16 2019",
       "configurationType": "RelWithDebInfo",
       "buildRoot": "${env.BUILDROOT}",
       "cmakeCommandArgs": "",
@@ -380,7 +387,7 @@
           "value": "${env.BLAS_RELEASE}"
         },
         {
-          "name": "CMAKE_INSTALL_PREFIX",
+          "name": "remoteInstallRoot",
           "value": "${env.INSTALL_DIR}"
         },
         {

src/libcadet/BindingModelFactory.cpp

@@ -38,6 +38,11 @@ namespace cadet
 			void registerMultiComponentSpreadingModel(std::unordered_map<std::string, std::function<model::IBindingModel*()>>& bindings);
 			void registerGeneralizedIonExchangeModel(std::unordered_map<std::string, std::function<model::IBindingModel*()>>& bindings);
 			void registerColloidalModel(std::unordered_map<std::string, std::function<model::IBindingModel*()>>& bindings);
+			void registerMachineLearningModel(std::unordered_map<std::string, std::function<model::IBindingModel* ()>>& bindings);
+			void registerSplineModel(std::unordered_map<std::string, std::function<model::IBindingModel* ()>>& bindings);
+			void registerFreundlichLDFModel(std::unordered_map<std::string, std::function<model::IBindingModel* ()>>& bindings);
+			void registerEFunctionModel(std::unordered_map<std::string, std::function<model::IBindingModel* ()>>& bindings);
+			void registerGPRModel(std::unordered_map<std::string, std::function<model::IBindingModel* ()>>& bindings);
 		}
 	}
 
@@ -61,6 +66,11 @@ namespace cadet
 		model::binding::registerMultiComponentSpreadingModel(_bindingModels);
 		model::binding::registerGeneralizedIonExchangeModel(_bindingModels);
 		model::binding::registerColloidalModel(_bindingModels);
+		model::binding::registerMachineLearningModel(_bindingModels);
+		model::binding::registerSplineModel(_bindingModels);
+		model::binding::registerFreundlichLDFModel(_bindingModels);
+		model::binding::registerEFunctionModel(_bindingModels);
+		model::binding::registerGPRModel(_bindingModels);
 		registerModel<model::SimplifiedMultiStateStericMassActionBinding>();
 	}
 

src/libcadet/CMakeLists.txt

@@ -94,6 +94,11 @@ set(LIBCADET_BINDINGMODEL_SOURCES
 	${CMAKE_SOURCE_DIR}/src/libcadet/model/binding/MultiComponentSpreadingBinding.cpp
 	${CMAKE_SOURCE_DIR}/src/libcadet/model/binding/GeneralizedIonExchangeBinding.cpp
 	${CMAKE_SOURCE_DIR}/src/libcadet/model/binding/ColloidalBinding.cpp
+	${CMAKE_SOURCE_DIR}/src/libcadet/model/binding/MachineLearningBinding.cpp
+	${CMAKE_SOURCE_DIR}/src/libcadet/model/binding/SplineBinding.cpp
+	${CMAKE_SOURCE_DIR}/src/libcadet/model/binding/FreundlichLDFBinding.cpp
+	${CMAKE_SOURCE_DIR}/src/libcadet/model/binding/EFunctionBinding.cpp
+	${CMAKE_SOURCE_DIR}/src/libcadet/model/binding/GuassianProcessRegressionBinding.cpp
 )
 
 # LIBCADET_REACTIONMODEL_SOURCES holds all source files of reaction models
@@ -218,7 +223,7 @@ if (LAPACK_FOUND)
 	set(LIB_LAPACK_DEFINE "CADET_LAPACK_TRAILING_UNDERSCORE")
 
 	# Add the build target for the static nonlinalg library
-	add_library(libcadet_nonlinalg_static STATIC ${LIBCADET_NONLINALG_SOURCES} ${LIBCADET_NONLINALG_SPARSE_SOURCES})
+	add_library(libcadet_nonlinalg_static STATIC ${LIBCADET_NONLINALG_SOURCES} ${LIBCADET_NONLINALG_SPARSE_SOURCES} "model/binding/MachineLearningBinding.cpp" "model/binding/SplineBinding.cpp" "model/binding/EFunctionBinding.cpp"   "model/binding/Class_ANN.h" "model/binding/GuassianProcessRegressionBinding.cpp")
 	set_target_properties(libcadet_nonlinalg_static PROPERTIES OUTPUT_NAME cadet_nonlinalg_static)
 	target_compile_definitions(libcadet_nonlinalg_static PRIVATE libcadet_nonlinalg_static_EXPORTS ${LIB_LAPACK_DEFINE})
 	target_link_libraries(libcadet_nonlinalg_static PUBLIC CADET::CompileOptions PRIVATE SUNDIALS::sundials_idas ${SUNDIALS_NVEC_TARGET} ${LAPACK_LIBRARIES})
@@ -234,7 +239,7 @@ if (LAPACK_FOUND)
 
 
 	# Add the build target for CADET object library
-	add_library(libcadet_object OBJECT ${LIBCADET_SOURCES})
+	add_library(libcadet_object OBJECT ${LIBCADET_SOURCES} "model/binding/MachineLearningBinding.cpp" "model/binding/SplineBinding.cpp" "model/binding/EFunctionBinding.cpp"   "model/binding/Class_ANN.h" "model/binding/GuassianProcessRegressionBinding.cpp")
 	target_compile_definitions(libcadet_object PRIVATE libcadet_EXPORTS ${LIB_LAPACK_DEFINE})
 	target_link_libraries(libcadet_object PUBLIC CADET::CompileOptions CADET::LibOptions PRIVATE CADET::AD libcadet_nonlinalg_static SUNDIALS::sundials_idas ${SUNDIALS_NVEC_TARGET} ${TBB_TARGET})
 
@@ -280,7 +285,7 @@ if (ENABLE_CADET_MEX)
 	endif()
 
 	# Add the build target for the mex nonlinalg library
-	add_library(libcadet_nonlinalg_mex STATIC ${LIBCADET_NONLINALG_SOURCES} ${LIBCADET_NONLINALG_MEX_SOURCES})
+	add_library(libcadet_nonlinalg_mex STATIC ${LIBCADET_NONLINALG_SOURCES} ${LIBCADET_NONLINALG_MEX_SOURCES} "model/binding/MachineLearningBinding.cpp" "model/binding/SplineBinding.cpp" "model/binding/EFunctionBinding.cpp"   "model/binding/Class_ANN.h" "model/binding/GuassianProcessRegressionBinding.cpp")
 	set_target_properties(libcadet_nonlinalg_mex PROPERTIES 
 		OUTPUT_NAME cadet_nonlinalg_mex
 		LINK_SEARCH_START_STATIC ON
@@ -309,7 +314,7 @@ if (ENABLE_CADET_MEX)
 	endif()
 
 	# Add the build target for the mex CADET library
-	add_library(libcadet_mex STATIC ${LIBCADET_SOURCES})
+	add_library(libcadet_mex STATIC ${LIBCADET_SOURCES} "model/binding/MachineLearningBinding.cpp" "model/binding/SplineBinding.cpp" "model/binding/EFunctionBinding.cpp"   "model/binding/Class_ANN.h" "model/binding/GuassianProcessRegressionBinding.cpp")
 	set_target_properties(libcadet_mex PROPERTIES 
 		OUTPUT_NAME cadet_mex
 		LINK_SEARCH_START_STATIC ON