Additional enum instrumentation

cropsinsilico · Sep 5, 2024 · 2dc327c · 2dc327c
1 parent 34f88ae
commit 2dc327c
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Showing 10 changed files with 222 additions and 29 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -174,6 +174,7 @@ foreach(suffix rate_constants conditions)
     "${ENUM_SRC_REGEX}" --src-regex --dst-type=c --dst=${ENUM_DST}
     --dst-maps=${ENUM_MAP} --dst-maps-header=${ENUM_MAP_H}
     --dst-global=${ENUM_GLOBAL}
+    --enum-name-global=MODULE
     --root-include-dir=${CMAKE_CURRENT_SOURCE_DIR}/include
     --include-file-maps=${ENUM_UTILS}
     --prefix-by-split=${suffix} --overwrite  # --verbose

diff --git a/cmake/FindSUNDIALS.cmake b/cmake/FindSUNDIALS.cmake
@@ -153,7 +153,7 @@ if (SUNDIALS_INCLUDE_DIR)
 	    CVODE_DIRECT_INCLUDE_DIR
 	    NVECTOR_INCLUDE_DIR
 	    KINSOL_INCLUDE_DIR)
-      if(NOT ${${x}} STREQUAL "NOTFOUND")
+      if(NOT ${${x}} STREQUAL "${x}-NOTFOUND")
         list(APPEND SUNDIALS_INCLUDE_DIRS ${${x}})
       endif()
     endforeach()

diff --git a/include/enums/enums.hpp b/include/enums/enums.hpp
@@ -1,4 +1,19 @@
 #pragma once
+
 #include "enums/enums_conditions.hpp"
 #include "enums/enums_rate_constants.hpp"
 
+enum EMPTY_ENUM {};
+enum MODULE {
+  MODULE_NONE     ,
+  MODULE_PR       ,
+  MODULE_PS       ,
+  MODULE_RedoxReg ,
+  MODULE_FI       ,
+  MODULE_RuACT    ,
+  MODULE_XanCycle ,
+  MODULE_SUCS     ,
+  MODULE_BF       ,
+  MODULE_RROEA    ,
+  MODULE_MAX      ,
+};
diff --git a/include/enums/enums_conditions.hpp b/include/enums/enums_conditions.hpp
@@ -1,6 +1,7 @@
 #pragma once
 
 enum PR_conditions {
+  PR_conditions_NONE     ,
   PR_GCEA      ,  //!< Glycerate in chloroplast; derived based on V113
   PR_GCA       ,  //!< Derived from radioactive labelling experiment; assume equal concenatration inside and outshide chloroplast
   PR_PGCA      ,  //!< Phosphoglycolate in chloroplast derived based on the Km112; orignal value is : 0.0029;
@@ -11,9 +12,11 @@ enum PR_conditions {
   PR_HPRc      ,  //!< HydroxylPyruvate; derived from equation 123;
   PR_GCEAc     ,  //!< Glycerate in cytosol; assume at equilibrium with GCEA initially.
   PR_RuBP      ,  //!< RuBP concentration
+  PR_conditions_MAX     ,
 };
 
 enum PS_conditions {
+  PS_conditions_NONE     ,
   PS_RuBP     ,
   PS_PGA      ,
   PS_DPGA     ,
@@ -26,17 +29,21 @@ enum PS_conditions {
   PS_ATP      ,
   PS_HexP     ,
   PS_PenP     ,
+  PS_conditions_MAX     ,
 };
 
 enum RedoxReg_conditions {
+  RedoxReg_conditions_NONE     ,
   RedoxReg_ThioRatio     ,
   RedoxReg_FBPase        ,
   RedoxReg_SBPase        ,
   RedoxReg_PRK           ,
   RedoxReg_ATPase        ,
+  RedoxReg_conditions_MAX     ,
 };
 
 enum FI_conditions {
+  FI_conditions_NONE     ,
   FI_A              ,  //!< The concentration of excitons in the peripheral antenna
   FI_U              ,  //!< The concentration fo excitons in the core antenna
   FI_P680ePheo      ,  //!< The concentration of the P680Pheo
@@ -59,23 +66,29 @@ enum FI_conditions {
   FI_QAQB2n         ,  //!< The concentration of [QAQB2-]
   FI_QAnQB2n        ,  //!< The concentration of [QA-QB2-]
   FI_PQn            ,  //!< The concentration of reduced PQ, i.e. PQH2;
+  FI_conditions_MAX     ,
 };
 
 enum RuACT_conditions {
+  RuACT_conditions_NONE     ,
   RuACT_ER       ,  //!< The concentration of inactive ER
   RuACT_Eaf      ,  //!< The total concentration of E, EC, AND ECM
   RuACT_ECMR     ,  //!< The concentration of ECMR
   RuACT_RuBP     ,  //!< The concentration of ECMR
+  RuACT_conditions_MAX     ,
 };
 
 enum XanCycle_conditions {
+  XanCycle_conditions_NONE     ,
   XanCycle_Vx      ,  //!< * 0.37
   XanCycle_Ax      ,  //!< * 0.37
   XanCycle_Zx      ,  //!< * 0.37
   XanCycle_ABA     ,
+  XanCycle_conditions_MAX     ,
 };
 
 enum SUCS_conditions {
+  SUCS_conditions_NONE     ,
   SUCS_T3Pc       ,
   SUCS_FBPc       ,
   SUCS_HexPc      ,
@@ -84,9 +97,11 @@ enum SUCS_conditions {
   SUCS_SUCP       ,
   SUCS_SUC        ,
   SUCS_PGAc       ,
+  SUCS_conditions_MAX     ,
 };
 
 enum BF_conditions {
+  BF_conditions_NONE     ,
   BF_ISPHr       ,  //!< The reduced ion sulfer protein (ISPH)
   BF_cytc1       ,  //!< The oxidized state of cytc1
   BF_ISPo        ,  //!< The oxidized ion sulfer protein (ISP)
@@ -116,12 +131,15 @@ enum BF_conditions {
   BF_PHs         ,  //!< The PH value of the stroma
   BF_PHl         ,  //!< The PH value of the lumen
   BF_NADPH       ,  //!< The NADPH concentration in stroma, Unit: mmol l-1;
+  BF_conditions_MAX     ,
 };
 
 enum RROEA_conditions {
+  RROEA_conditions_NONE     ,
   RROEA_MDH       ,  //!< The initial concentration of actove MDH
   RROEA_Thio      ,  //!< The initial concentration of reduced thioredoxin
   RROEA_Fd        ,  //!< The initial concentration of reduced ferrodoxin
   RROEA_RuACT     ,  //!< The initial concentration of active Rubisco activase
+  RROEA_conditions_MAX     ,
 };
 
diff --git a/include/enums/enums_rate_constants.hpp b/include/enums/enums_rate_constants.hpp
@@ -1,6 +1,7 @@
 #pragma once
 
 enum RuACT_rate_constants {
+  RuACT_rate_constants_NONE     ,
   RuACT_k1      ,  //!< The rate constant of the activation of the Rubisco bound with RuBP. This step is associated with the ARubisco theVars->activase content or activity;
   RuACT_kn1     ,  //!< The rate constant of E inactivation by binding of RuBP;
   RuACT_km1     ,  //!< The michaelis menton constant for RuBP with E.
@@ -15,16 +16,20 @@ enum RuACT_rate_constants {
   RuACT_C       ,  //!< mM
   RuACT_O       ,  //!< mM
   RuACT_M       ,
+  RuACT_rate_constants_MAX     ,
 };
 
 enum RedoxReg_rate_constants {
+  RedoxReg_rate_constants_NONE     ,
   RedoxReg_Fd_Thio_ET         ,
   RedoxReg_ThioT              ,
   RedoxReg_Thio_Oxidation     ,
   RedoxReg_Thion0             ,  //!< This is a wild guess
+  RedoxReg_rate_constants_MAX     ,
 };
 
 enum PR_rate_constants {
+  PR_rate_constants_NONE     ,
   PR_V111           ,  //!< Reaction 111: RUBP+O2<-->PGlycolate + PGA
   PR_V112           ,  //!< Reaction 112: PGlycolate-->Pi+Glycolate;
   PR_V113           ,  //!< Reaction 113: Gcea+ATP<-->ADP + PGA
@@ -82,9 +87,11 @@ enum PR_rate_constants {
   PR_Vf_T121        ,  //!< VfactorT used with GRNT & Tp > 25
   PR_Vf_T122        ,  //!< VfactorT used with GRNT & Tp > 25
   PR_Vf_T112        ,  //!< VfactorT used with GRNT & Tp > 25
+  PR_rate_constants_MAX     ,
 };
 
 enum BF_rate_constants {
+  BF_rate_constants_NONE     ,
   BF_K1           ,  //!< The rate constant for formation of ISP.QH2 complex; unit:  per second
   BF_K2           ,  //!< The rate constant for ISP.QH2-->QH(semi) + ISPH(red) ; unit:  per second
   BF_K3           ,  //!< The rate constant for QH. + cytbL --> Q + cytbL- + H+ Unit: s-1
@@ -132,9 +139,11 @@ enum BF_rate_constants {
   BF_k12          ,  //!< The total concentration of buffer in lumen; unit: mmol per liter
   BF_k23          ,  //!< The total number of P700; unit: micromole m-2 leaf area
   BF_k30          ,  //!< The total concentration of NADPH in stroma; 1 is an guessed value;
+  BF_rate_constants_MAX     ,
 };
 
 enum RROEA_rate_constants {
+  RROEA_rate_constants_NONE     ,
   RROEA_ke2GAPDH        ,  //!< The rate constant of electron transfer to GAPDH. From literature.
   RROEA_ke2MDH          ,  //!< The rate constant of electront transfer to MDH, this rate is totally ASSUMED.
   RROEA_ke2FBPase       ,  //!< The rate constant of electron transfer from thioredoxin to FBPase.
@@ -171,9 +180,11 @@ enum RROEA_rate_constants {
   RROEA_FdT             ,  //!< Not used with RROEA_EPS
   RROEA_ThioT           ,
   RROEA_RuACTT          ,
+  RROEA_rate_constants_MAX     ,
 };
 
 enum SUCS_rate_constants {
+  SUCS_rate_constants_NONE     ,
   SUCS_V51          ,  //!< DHAP+GAP --FBP; default 0.5
   SUCS_V52          ,  //!< FBP --F6P + Pi
   SUCS_V55          ,  //!< G1P+UTP --OPOP+UDPG
@@ -225,16 +236,20 @@ enum SUCS_rate_constants {
   SUCS_KE59         ,
   SUCS_KE61         ,
   SUCS_Km621        ,
+  SUCS_rate_constants_MAX     ,
 };
 
 enum XanCycle_rate_constants {
+  XanCycle_rate_constants_NONE     ,
   XanCycle_kva     ,  //!< Ruth Frommolt et a; 2001; Planta
   XanCycle_kaz     ,  //!< Ruth Frommolt et a; 2001; Planta
   XanCycle_kza     ,  //!< Ruth Frommolt et a; 2001; Planta
   XanCycle_kav     ,  //!< Ruth Frommolt et a; 2001; Planta. This is not given in the paper. Therefore, teh value is really an educated guess.
+  XanCycle_rate_constants_MAX     ,
 };
 
 enum FI_rate_constants {
+  FI_rate_constants_NONE     ,
   FI_kA_d         ,  //!< The rate constant of heat dissipation from peripheral antenna Lazar (1999), 0.25~1 *10^(9)
   FI_kA_f         ,  //!< The rate constant of fluorescence emission from peripheral antenna Lazar 1999, with a lifetime of 5 ns at closed reaction center
   FI_kA_U         ,  //!< The rate constant of exciton transfer from periphral antenna to core antenna Reference needed, a guess
@@ -258,9 +273,11 @@ enum FI_rate_constants {
   FI_k_pq_oxy     ,  //!< The rate constant of the PQH2 oxidation Lazar (1999),50~500
   FI_QBt          ,  //!< The total concentration of Qb site;
   FI_PQT          ,  //!< The total concentration of PQ;
+  FI_rate_constants_MAX     ,
 };
 
 enum PS_rate_constants {
+  PS_rate_constants_NONE     ,
   PS_CP            ,  //!< Global constant for the total phosphate
   PS_CA            ,  //!< Global constant for the total adenylates
   PS_CN            ,  //!< Global constant for the cytosolic Phosphate concentration;
@@ -373,5 +390,6 @@ enum PS_rate_constants {
   PS_Vf_T9         ,  //!< VfactorT used with GRNT & Tp > 25
   PS_Vf_T13        ,  //!< VfactorT used with GRNT & Tp > 25
   PS_Vf_T23        ,  //!< VfactorT used with GRNT & Tp > 25
+  PS_rate_constants_MAX     ,
 };
 
diff --git a/include/enums/enums_utils.hpp b/include/enums/enums_utils.hpp
@@ -18,6 +18,11 @@ const std::map<const T, const std::string>& get_enum_map() {
   return out;
 }
 
+template<typename T>
+MODULE get_enum_module() {
+  return MODULE_NONE;
+}
+
 namespace ePhotosynthesis {
   namespace utils {
 
@@ -44,8 +49,8 @@ namespace ePhotosynthesis {
     }
 
     template<typename Tenum, typename Tval>
-    void readEnumFile(const std::string &filename,
-		      std::map<Tenum, Tval> &map) {
+    std::map<Tenum, Tval> readEnumFile(const std::string &filename) {
+      std::map<Tenum, Tval> map;
       std::vector<std::string> tempVec;
       std::string comment = "#";
       std::string input;
@@ -67,7 +72,7 @@ namespace ePhotosynthesis {
         count++;
         map.insert(std::pair<Tenum, Tval>(key, val));
       }
-
+      return map;
     }
 
     template<typename T1>

diff --git a/src/enums/enums_conditions_map.cpp b/src/enums/enums_conditions_map.cpp
@@ -21,6 +21,9 @@ const std::map<const PR_conditions, const std::string>& PR_conditions_map() {
 template<> const std::map<const PR_conditions, const std::string>& get_enum_map<enum PR_conditions>() {
   return PR_conditions_map();
 };
+template<> MODULE get_enum_module<enum PR_conditions>() {
+  return MODULE_PR;
+}
 
 const std::map<const PS_conditions, const std::string>& PS_conditions_map() {
   static const std::map<const PS_conditions, const std::string> map {
@@ -42,6 +45,9 @@ const std::map<const PS_conditions, const std::string>& PS_conditions_map() {
 template<> const std::map<const PS_conditions, const std::string>& get_enum_map<enum PS_conditions>() {
   return PS_conditions_map();
 };
+template<> MODULE get_enum_module<enum PS_conditions>() {
+  return MODULE_PS;
+}
 
 const std::map<const RedoxReg_conditions, const std::string>& RedoxReg_conditions_map() {
   static const std::map<const RedoxReg_conditions, const std::string> map {
@@ -56,6 +62,9 @@ const std::map<const RedoxReg_conditions, const std::string>& RedoxReg_condition
 template<> const std::map<const RedoxReg_conditions, const std::string>& get_enum_map<enum RedoxReg_conditions>() {
   return RedoxReg_conditions_map();
 };
+template<> MODULE get_enum_module<enum RedoxReg_conditions>() {
+  return MODULE_RedoxReg;
+}
 
 const std::map<const FI_conditions, const std::string>& FI_conditions_map() {
   static const std::map<const FI_conditions, const std::string> map {
@@ -87,6 +96,9 @@ const std::map<const FI_conditions, const std::string>& FI_conditions_map() {
 template<> const std::map<const FI_conditions, const std::string>& get_enum_map<enum FI_conditions>() {
   return FI_conditions_map();
 };
+template<> MODULE get_enum_module<enum FI_conditions>() {
+  return MODULE_FI;
+}
 
 const std::map<const RuACT_conditions, const std::string>& RuACT_conditions_map() {
   static const std::map<const RuACT_conditions, const std::string> map {
@@ -100,6 +112,9 @@ const std::map<const RuACT_conditions, const std::string>& RuACT_conditions_map(
 template<> const std::map<const RuACT_conditions, const std::string>& get_enum_map<enum RuACT_conditions>() {
   return RuACT_conditions_map();
 };
+template<> MODULE get_enum_module<enum RuACT_conditions>() {
+  return MODULE_RuACT;
+}
 
 const std::map<const XanCycle_conditions, const std::string>& XanCycle_conditions_map() {
   static const std::map<const XanCycle_conditions, const std::string> map {
@@ -113,6 +128,9 @@ const std::map<const XanCycle_conditions, const std::string>& XanCycle_condition
 template<> const std::map<const XanCycle_conditions, const std::string>& get_enum_map<enum XanCycle_conditions>() {
   return XanCycle_conditions_map();
 };
+template<> MODULE get_enum_module<enum XanCycle_conditions>() {
+  return MODULE_XanCycle;
+}
 
 const std::map<const SUCS_conditions, const std::string>& SUCS_conditions_map() {
   static const std::map<const SUCS_conditions, const std::string> map {
@@ -130,6 +148,9 @@ const std::map<const SUCS_conditions, const std::string>& SUCS_conditions_map()
 template<> const std::map<const SUCS_conditions, const std::string>& get_enum_map<enum SUCS_conditions>() {
   return SUCS_conditions_map();
 };
+template<> MODULE get_enum_module<enum SUCS_conditions>() {
+  return MODULE_SUCS;
+}
 
 const std::map<const BF_conditions, const std::string>& BF_conditions_map() {
   static const std::map<const BF_conditions, const std::string> map {
@@ -168,6 +189,9 @@ const std::map<const BF_conditions, const std::string>& BF_conditions_map() {
 template<> const std::map<const BF_conditions, const std::string>& get_enum_map<enum BF_conditions>() {
   return BF_conditions_map();
 };
+template<> MODULE get_enum_module<enum BF_conditions>() {
+  return MODULE_BF;
+}
 
 const std::map<const RROEA_conditions, const std::string>& RROEA_conditions_map() {
   static const std::map<const RROEA_conditions, const std::string> map {
@@ -181,4 +205,7 @@ const std::map<const RROEA_conditions, const std::string>& RROEA_conditions_map(
 template<> const std::map<const RROEA_conditions, const std::string>& get_enum_map<enum RROEA_conditions>() {
   return RROEA_conditions_map();
 };
+template<> MODULE get_enum_module<enum RROEA_conditions>() {
+  return MODULE_RROEA;
+}