Fixes for MRB model (#22)

* fixed reaction volume unit in RB model

* fix to allow appending elements to the database

* added automatic tests for RB model, thermofun v0.3.5

* test for appending elements

* removed old functions

CMakeLists.txt

@@ -1,8 +1,8 @@
 # Require a certain version of cmake
-cmake_minimum_required(VERSION 3.0)
+cmake_minimum_required(VERSION 3.9)
 
 # Set the name of the project
-project(ThermoFun VERSION 0.3.3 LANGUAGES CXX)
+project(ThermoFun VERSION 0.3.5 LANGUAGES CXX)
 
 # Set the cmake module path of the project
 set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules")
@@ -13,15 +13,6 @@ include(CCache)
 # Define variables with the GNU standard installation directories
 include(GNUInstallDirs)
 
-# Ensure proper configuration if in a conda environment
-include(CondaAware)
-
-# Define which types of libraries to build
-option(TFUN_BUILD_SHARED_LIBS "Build shared libraries." ON)
-option(TFUN_BUILD_STATIC_LIBS "Build static libraries." ON)
-#option(TFUN_BUILD_TESTS "Build tests." OFF)
-option(TFUN_BUILD_PYTHON "Build the python wrappers and python package thermofun." ON)
-
 # Modify the TFUN_BUILD_* variables accordingly to BUILD_ALL
 if(TFUN_BUILD_ALL MATCHES ON)
     set(TFUN_BUILD_SHARED_LIBS          ON)
@@ -30,6 +21,27 @@ if(TFUN_BUILD_ALL MATCHES ON)
     set(TFUN_BUILD_PYTHON               ON)
 endif()
 
+if (TFUN_WASM MATCHES ON)
+    # Define which types of libraries to build
+    option(TFUN_BUILD_STATIC_LIBS "Build static libraries." ON)
+    set(TFUN_BUILD_PYTHON               OFF)
+    # Set the list of compiler flags for Clang compiler
+    if(${CMAKE_CXX_COMPILER_ID} MATCHES "Clang")
+    add_compile_options(-std=c++11 -Wall -Wno-ignored-attributes -Wno-pedantic -Wno-variadic-macros -Wno-deprecated -fcxx-exceptions -frtti)
+    endif()
+else()
+    # Ensure proper configuration if in a conda environment
+    include(CondaAware)
+    option(TFUN_BUILD_SHARED_LIBS "Build shared libraries." ON)
+    option(TFUN_BUILD_STATIC_LIBS "Build static libraries." ON)
+    #option(TFUN_BUILD_TESTS "Build tests." OFF)
+    option(TFUN_BUILD_PYTHON "Build the python wrappers and python package thermofun." ON)
+    # Define if shared library should be build instead of static.
+    option(BUILD_SHARED_LIBS "Build shared libraries." ON)
+
+    # Set libraries to be compiled with position independent code mode (i.e., fPIC option in GNU compilers)
+    set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+endif()
 
 # Set the default build type to Release
 if(NOT CMAKE_BUILD_TYPE)
@@ -40,12 +52,6 @@ if(NOT CMAKE_BUILD_TYPE)
     set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS Debug Release MinSizeRel RelWithDebInfo)
 endif()
 
-# Define if shared library should be build instead of static.
-option(BUILD_SHARED_LIBS "Build shared libraries." ON)
-
-# Set libraries to be compiled with position independent code mode (i.e., fPIC option in GNU compilers)
-set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-
 # Set the C++ standard
 set(CMAKE_CXX_STANDARD 14)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)

ThermoFun/CMakeLists.txt

@@ -4,16 +4,27 @@ file(GLOB_RECURSE HEADER_FILES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.hpp *.h)
 # Recursively collect all source files from the current directory
 file(GLOB_RECURSE SOURCE_FILES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.cpp)
 
-# The name of the shared and static libraries
-set(THERMOFUN_SHARED_LIB ${PROJECT_NAME}${SUFFIX_SHARED_LIBS})
-set(THERMOFUN_STATIC_LIB ${PROJECT_NAME}${SUFFIX_STATIC_LIBS})
+if(TFUN_BUILD_SHARED_LIBS)
+    set(THERMOFUN_SHARED_LIB ${PROJECT_NAME}${SUFFIX_SHARED_LIBS})
+    # Enable automatic creation of a module definition (.def) file for a SHARED library on Windows.
+    set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
+    #add_library(XGEMS_SHARED SHARED $<TARGET_OBJECTS:XGEMS_OBJECT>)
+    #target_link_libraries(XGEMS_SHARED GEMS3K-static)
+    #set_target_properties(XGEMS_SHARED PROPERTIES OUTPUT_NAME xGEMS)
+    #install(TARGETS XGEMS_SHARED DESTINATION "lib" COMPONENT libraries)
+endif()
 
-# Enable automatic creation of a module definition (.def) file for a SHARED library on Windows.
-set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
+# Check if a static library must be built
+if(TFUN_BUILD_STATIC_LIBS)
+    set(THERMOFUN_STATIC_LIB ${PROJECT_NAME}${SUFFIX_STATIC_LIBS})
+    #add_library(XGEMS_STATIC STATIC $<TARGET_OBJECTS:XGEMS_OBJECT>)
+    #target_link_libraries(XGEMS_STATIC GEMS3K-static)
+    #set_target_properties(XGEMS_STATIC PROPERTIES OUTPUT_NAME xGEMS)
+    #install(TARGETS XGEMS_STATIC DESTINATION "lib" COMPONENT libraries)
+endif()
 
 # Create a library using the collected source files
 add_library(ThermoFun ${HEADER_FILES} ${SOURCE_FILES})
-
 # Add aliases for ThermoFun shared and static libraries
 add_library(ThermoFun::ThermoFun ALIAS ThermoFun)
 

ThermoFun/Common/ThermoScalar.hpp

@@ -64,7 +64,7 @@ class ThermoScalarBase
     /// Construct a custom ThermoScalarBase instance with given value only.
     /// @param val The value of the thermodynamic property
     explicit ThermoScalarBase(double val)
-        : ThermoScalarBase(val, 0.0, 0.0, 0.0, {Status::initialized, ""}) {}
+        : ThermoScalarBase(val, 0.0, 0.0, 0.0, {Status::notdefined, ""}) {}
 
     /// Construct a custom ThermoScalarBase instance with given value and derivatives.
     /// @param val The value of the thermodynamic property

ThermoFun/Database.cpp

@@ -68,23 +68,23 @@ struct Database::Impl
 
     auto addElement(const Element& element) -> void
     {
-        checkIfSymbolExists(elements_map, "element", element.symbol());
         elements_map.insert({element.symbol(), element});
     }
 
     auto setElement(const Element& element) -> void
     {
+        checkIfSymbolExists(elements_map, "element", element.symbol());
         elements_map[element.symbol()] = element;
     }
 
     auto addSubstance(const Substance& substance) -> void
     {
-        checkIfSymbolExists(substances_map, "substance", substance.symbol());
         substances_map.insert({substance.symbol(), substance});
     }
 
     auto setSubstance(const Substance& substance) -> void
     {
+        checkIfSymbolExists(substances_map, "substance", substance.symbol());
         substances_map[substance.symbol()] = substance;
     }
 
@@ -100,12 +100,12 @@ struct Database::Impl
 
     auto addReaction(const Reaction& reaction) -> void
     {
-        checkIfSymbolExists(reactions_map, "reaction", reaction.symbol());
         reactions_map.insert({reaction.symbol(), reaction});
     }
 
     auto setReaction(const Reaction& reaction) -> void
     {
+        checkIfSymbolExists(reactions_map, "reaction", reaction.symbol());
         reactions_map[reaction.symbol()] = reaction;
     }
 
@@ -210,16 +210,16 @@ struct Database::Impl
 
     auto addRecord(json j, std::string _label) -> void
     {
-        auto properties = j;
+        auto props= j;
 
         if (j.contains("properties"))
             if (!j["properties"].is_null())
-                properties = j["properties"];
+                props = j["properties"];
         if (j.contains("_label"))
             if (!j["_label"].is_null())
                 _label = j["_label"].get<std::string>();
 
-        auto props = properties.dump();
+        props = props.dump();
 
         if (_label == "substance")
         {
@@ -343,12 +343,18 @@ auto Database::operator=(Database other) -> Database&
 
 auto Database::appendData(std::string filename) -> void
 {
+    auto elements_number = pimpl->mapElements().size();
     pimpl->fromFile(filename);
+    if (elements_number != pimpl->mapElements().size())
+        ChemicalFormula::setDBElements(pimpl->mapElements());
 }
 
 auto Database::appendData(vector<string> jsonRecords, std::string _label = "unknown label") -> void
 {
+    auto elements_number = pimpl->mapElements().size();
     pimpl->fromJSONs(jsonRecords, _label);
+    if (elements_number != pimpl->mapElements().size())
+        ChemicalFormula::setDBElements(pimpl->mapElements());
 }
 
 auto Database::addElement(const Element& element) -> void

ThermoFun/GlobalVariables.h

@@ -155,6 +155,7 @@ const std::map<const SubstanceTPMethodType, const std::vector<std::string>> meth
 /// Indexes for species-dependent EoS subroutines used in thrift DOM and ThermoFun class
 typedef struct {
   enum type {
+    CTPM_CON = 99, // constant properties from ref T-P
     CTPM_CPT = 100,
     CTPM_HKF = 101,
     CTPM_REA = 102,
@@ -573,10 +574,17 @@ typedef struct {
 typedef struct {
   enum type {
     DCOMP = 0,            ///< Dependent component, properties calculated using a PT model for the substance
-    REACDC = 1            ///< Reaction dependent component, proeprties claculated from the reaction properties
+    REACDC = 1            ///< Reaction dependent component, properties calculated from the reaction properties
   };
 } SubstanceThermoCalculationType;
 
+typedef struct {
+  enum type {
+    REACTION = 0,            ///< Reaction, properties calculated using a PT model for the reaction
+    REACTANTS = 1            ///< Properties calculated from reactants
+  };
+} RectionThermoCalculationType;
+
 
 /// Key for reading substance / reaction data from input files
 static const char * label                   = "_label";

ThermoFun/Reaction.cpp

@@ -40,6 +40,10 @@ struct Reaction::Impl
     /// Method of pressure correction of thermodynamic properties
     MethodCorrP_Thrift::type  method_P;
 
+    /// Type of calculation used for determining the reaction properties
+    /// using a defined PT correction model or from reactants
+    RectionThermoCalculationType::type thermo_calculation_type = RectionThermoCalculationType::type::REACTANTS;
+
     /// Reference temperature (in K)
     double reference_T = 298.15;
 

ThermoFun/Reactions/RyzhenkoBryzgalyn.cpp

@@ -71,7 +71,7 @@ auto thermoPropertiesRyzhenkoBryzgalin(Reaktoro_::Temperature TK, Reaktoro_::Pre
     tpr.reaction_entropy           = dSr;
     tpr.reaction_enthalpy          = dHr;
     tpr.reaction_heat_capacity_cp  = dCPr;
-    tpr.reaction_volume            = dVr;
+    tpr.reaction_volume            = dVr*1e5; // to J/bar
     tpr.reaction_helmholtz_energy  = dAr;
     tpr.reaction_internal_energy   = dUr;
 

ThermoFun/ThermoEngine.cpp

@@ -213,6 +213,14 @@ struct ThermoEngine::Impl
 
         if (pref.isHydrogen)
         {
+            tps.volume = 0.0;
+            tps.entropy = 0.0;
+            tps.enthalpy = 0.0;
+            tps.gibbs_energy = 0.0;
+            tps.internal_energy = 0.0;
+            tps.heat_capacity_cp = 0.0;
+            tps.heat_capacity_cv = 0.0;
+            tps.helmholtz_energy = 0.0;
             return tps;
         }
 
@@ -223,6 +231,11 @@ struct ThermoEngine::Impl
                 // metohd EOS
                 switch (pref.method_genEOS)
                 {
+                case MethodGenEoS_Thrift::type::CTPM_CON:
+                {
+                    tps = substance.thermoReferenceProperties();
+                    break;
+                }
                 case MethodGenEoS_Thrift::type::CTPM_CPT:
                 {
                     tps = EmpiricalCpIntegration(pref.workSubstance).thermoProperties(T, P);
@@ -574,9 +587,16 @@ struct ThermoEngine::Impl
         {
             switch (pref.method_genEOS)
             {
+            case MethodGenEoS_Thrift::type::CTPM_CON:
+            {
+                tpr = reaction.thermoReferenceProperties();
+                break;
+            }
             case MethodGenEoS_Thrift::type::CTPM_REA:
+            {
                 pref.method_T = MethodCorrT_Thrift::type::CTM_LGK;
-
+                break;
+            }
             }
 
             switch (pref.method_T)
@@ -660,7 +680,7 @@ struct ThermoEngine::Impl
         else
             tpr = thermoPropertiesReactionFromReactants(T, P, reaction);
 
-        return tpr;
+        return tpr; 
     }
 
     auto thermoPropertiesReactionFromReactants(double T, double &P, std::string symbol) const -> ThermoPropertiesReaction

ci/appveyor/install.bat

@@ -1,6 +1,6 @@
-conda config --set always_yes yes --set changeps1 no
-conda config --add channels conda-forge
-conda install conda-devenv
+conda config --system --set always_yes yes --set changeps1 no
+conda config --system --append channels conda-forge
+conda install -n base conda-devenv
 conda update -q conda
 conda info -a
 conda devenv