Add other calculated variables & move from drivers to Variables

Reconcile alternate inputs (e.g. CO2, O2, Light)
Disambiguate light by setting PAR to have W/s units & PPFD to have umol/m2/s
Updated condition to actual use input O2 concentration
Add tables from Zhu2012 as csv
Add explicit parameters for constants defined in source code & Zhu2021 tables

Author: langmm

TODO.txt

@@ -22,3 +22,5 @@
 - Standardize setVar for control parameters on Variables
 - Update variables from yggdrasil document
 - Only export select members of value set
+- Include yaml file in installation (e.g. share)
+- Fix variable names in BF_Pool

include/Variables.hpp

@@ -172,14 +172,11 @@ class Variables : public VALUE_SET_PARENT(Variables, Variables, MODULE_ALL, PARA
  public:
 
     /**
-       Check if a variable was updated since the last time the input
-       was finalized.
+       Check if a variable was explicitly updated since the last time
+         the input was finalized.
        \param[in] name Variable name.
-       \param[in] ignoreClassFlag If true, only return true if the
-         specific variable was updated.
      */
-    EPHOTO_API bool inputUpdated(const std::string& name,
-                                 const bool ignoreClassFlag=false) const;
+    EPHOTO_API bool inputUpdated(const std::string& name) const;
     /**
        Throw an error if the named variable was updated.
      */
@@ -238,6 +235,8 @@ class Variables : public VALUE_SET_PARENT(Variables, Variables, MODULE_ALL, PARA
          are not stored on Variables instances.
        \param[in] subset Subset of parameters to output.
        \param[in] additionalVars Map of additional names & values to dump.
+       \param[in] skip_calculated If true, don't output the calculated
+         variables.
      */
     void dump(const std::string& filename,
               const bool includeSkipped = false,
@@ -247,7 +246,8 @@ class Variables : public VALUE_SET_PARENT(Variables, Variables, MODULE_ALL, PARA
               const std::map<std::string, std::string>& key_aliases={},
               const std::map<MODULE, const ValueSet_t*>& conditions={},
               const std::vector<std::string>& subset={},
-              const std::map<std::string, double>& additionalVars={}) const;
+              const std::map<std::string, double>& additionalVars={},
+              const bool skip_calculated=false) const;
     /**
        Serialize all parameters attached to this instance to an output
          stream.
@@ -263,6 +263,8 @@ class Variables : public VALUE_SET_PARENT(Variables, Variables, MODULE_ALL, PARA
          are not stored on Variables instances.
        \param[in] subset Subset of parameters to output.
        \param[in] additionalVars Map of additional names & values to dump.
+       \param[in] skip_calculated If true, don't output the calculated
+         variables.
        \returns Updated output stream.
      */
     std::ostream& dump(std::ostream& out,
@@ -273,7 +275,8 @@ class Variables : public VALUE_SET_PARENT(Variables, Variables, MODULE_ALL, PARA
                        const std::map<std::string, std::string>& key_aliases={},
                        const std::map<MODULE, const ValueSet_t*>& conditions={},
                        const std::vector<std::string>& subset={},
-                       const std::map<std::string, double>& additionalVars={}) const;
+                       const std::map<std::string, double>& additionalVars={},
+                       const bool skip_calculated=false) const;
     /**
        Serialize parameters for a single value set to an output stream.
        \param[in] module ID for module that should be serialized.
@@ -649,31 +652,75 @@ class Variables : public VALUE_SET_PARENT(Variables, Variables, MODULE_ALL, PARA
        \param[in] name String identifying the variable.
        \param[in] isGlymaID If true, name will be treated as a GlymaID.
          If false, name will be treated as the variable name.
+       \param[in] conditions Map of conditions for composite modules that
+         are not stored on Variables instances.
        \returns Variable value.
      */
     EPHOTO_API double getVar(const MODULE& mod, const PARAM_TYPE& pt,
                              const std::string& name,
-                             const bool& isGlymaID = false) const;
+                             const bool& isGlymaID = false,
+                             const std::map<MODULE, const ValueSet_t*>& conditions={}) const;
     /**
        Get the value of a variable in a value set.
        \param[in] mod Module associated with the value set that the
          variable is part of.
        \param[in] pt Parameter type associated with the value set that the
          variable is part of.
        \param[in] key Key identifying the variable.
+       \param[in] conditions Map of conditions for composite modules that
+         are not stored on Variables instances.
        \returns Variable value.
      */
     EPHOTO_API double getVar(const MODULE& mod, const PARAM_TYPE& pt,
-                             const int& key) const;
+                             const int& key,
+                             const std::map<MODULE, const ValueSet_t*>& conditions={}) const;
     /**
        Get the value of a variable in a value set.
        \param[in] k String identifying the variable.
        \param[in] isGlymaID If true, name will be treated as a GlymaID.
          If false, name will be treated as the variable name.
+       \param[in] conditions Map of conditions for composite modules that
+         are not stored on Variables instances.
        \returns Variable value.
      */
     EPHOTO_API double getVar(const std::string& k,
-                             const bool& isGlymaID = false) const;
+                             const bool& isGlymaID = false,
+                             const std::map<MODULE, const ValueSet_t*>& conditions={}) const;
+    /**
+       Get the value of a calculated quantity using variables from the
+         current value sets.
+       \param[in] name String identifying the variable.
+       \param[in] conditions Map of conditions for composite modules that
+         are not stored on Variables instances.
+       \returns Variable value.
+     */
+    EPHOTO_API double getVarCalculated(const std::string& name,
+                                       const std::map<MODULE, const ValueSet_t*>& conditions={}) const;
+    
+    /**
+       Get information about the modules required to calculate variables.
+       These variables can be retrieved via the Variables::getVar,
+       Variables::getVarCalculated or Variables::getCalculatedVars
+       methods.
+     */
+    EPHOTO_API static const std::map<std::string, std::vector<MODULE> >&
+      getCalculatedVariableRegistry();
+    /**
+       Get the set of variable names that can be calculated. These
+       variables can be retrieved via the Variables::getVar,
+       Variables::getVarCalculated or Variables::getCalculatedVars
+       methods.
+     */
+    EPHOTO_API const std::vector<std::string>&
+      getCalculatedVarNames() const;
+    /**
+       Populate a map with calculated variables.
+       \param[out] dest Map that should be populated.
+       \param[in] conditions Map of conditions for composite modules that
+         are not stored on Variables instances.
+     */
+    EPHOTO_API void getCalculatedVars(std::map<std::string, double>& dest,
+                                      const std::map<MODULE, const ValueSet_t*>& conditions) const;
     /**
        Get the documentation string for a variable in a value set.
        \param[in] mod Module associated with the value set that the

include/conditions/FIBFCondition.hpp

@@ -34,7 +34,7 @@
 #define PARENT_FIBF EPS
 #define NRATIO_FIBF 0
 #define CHILDREN_FIBF BF, FI
-#define PARAM_TYPES_FIBF COND, POOL
+#define PARAM_TYPES_FIBF COND, POOL, RC
 
 namespace ePhotosynthesis {
 

include/conditions/RedoxRegCondition.hpp

@@ -31,7 +31,7 @@
 #define PARENT_RedoxReg RedoxReg
 #define NRATIO_RedoxReg 0
 #define CHILDREN_RedoxReg RA
-#define PARAM_TYPES_RedoxReg COND, VEL
+#define PARAM_TYPES_RedoxReg COND, VEL, RC
 #define CONNECT_RedoxReg
 #define COUNT_RedoxReg
 #define CONTROL_RedoxReg

include/drivers/driver.hpp

@@ -250,9 +250,11 @@ class Driver : public DriverParam {
 
     /**
        Get output variables.
-       \param theVars Structure containing current variables.
+       \param[in] theVars Structure containing current variables.
+       \param[in] con Pointer to current conditions.
      */
-    void getOutputVars(Variables* theVars);
+    void getOutputVars(const Variables* theVars=nullptr,
+                       const ValueSet_t* con=nullptr);
 
     /**
        Set the output variables.
@@ -268,24 +270,22 @@ class Driver : public DriverParam {
 
     /**
        Get a variable given the current state defined by theVars.
-       \param[in] theVars Current variable state.
        \param[in] k Name of variable to return.
-     */
-    double getVar(const Variables* theVars, const std::string& k) const;
-  
-    /**
-       Populate a map with calculated variables.
        \param[in] theVars Current variable state.
-       \param[out] dest Map that should be populated.
+       \param[in] con Pointer to current conditions.
      */
-    void getCalculatedVars(const Variables* theVars,
-                           std::map<std::string, double>& dest) const;
+    double getVar(const std::string& k, const Variables* theVars=nullptr,
+                  const ValueSet_t* con=nullptr) const;
+  
     /**
-       Get a map containing calculated variables.
+       Get a variable given the current state defined by theVars.
+       \param[in] k Name of variable to return.
        \param[in] theVars Current variable state.
-       \returns Calculated variables.
+       \param[in] conditions Map of conditions for composite modules that
+         are not stored on Variables instances.
      */
-    std::map<std::string, double> getCalculatedVars(const Variables* theVars) const;
+    double getVar(const std::string& k, const Variables* theVars,
+                  const std::map<MODULE, const ValueSet_t*>& conditions) const ;
 
     /**
       Runs the solver one more time on the intermediate results to get the solution at the end time
@@ -301,7 +301,7 @@ class Driver : public DriverParam {
          should be created from.
        \returns Conditions value set.
      */
-    virtual ValueSet_t* currentConditions(realtype *x = nullptr) {
+    virtual ValueSet_t* currentConditions(realtype *x = nullptr) const {
 	UNUSED(x);
 	return nullptr;
     }
@@ -416,13 +416,6 @@ class Driver : public DriverParam {
       \param user_data Any user supplied data.
       */
     static int calculate(realtype t, N_Vector u, N_Vector u_dot, void *user_data);
-    /**
-       Get the set of variable names that the driver can calculate. These
-       variables can be retrieved via the Driver::getVar method or
-       getCalculatedVars.
-     */
-    static const std::vector<std::string>&
-    getCalculatedVarNames();
 
 
 #ifdef SUNDIALS_CONTEXT_REQUIRED
@@ -552,7 +545,7 @@ const MODULE DriverBase<T, M>::module = M;
   /** \copydoc drivers::DriverBase::enableC3 */				\
   static void enableC3(const bool x = true);				\
   /** \copydoc drivers::Driver::currentConditions */			\
-  ValueSet_t* currentConditions(realtype *x = nullptr) override;	\
+  ValueSet_t* currentConditions(realtype *x = nullptr) const override;	\
   /** \copydoc drivers::Driver::setup_connections */                    \
   void setup_connections(Variables* theVars) override;                  \
   /** \copydoc drivers::Driver::setup_variables */                      \
@@ -589,7 +582,7 @@ private:								\
   void name ## Driver::enableC3(const bool x) {                         \
     return VARS_CLASS_CALL(enableC3, (x), name, MOD);			\
   }									\
-  ValueSet_t* name ## Driver::currentConditions(realtype *x) {		\
+  ValueSet_t* name ## Driver::currentConditions(realtype *x) const {    \
       if (x) {								\
 	return new VARS_CLASS_VAR(name, COND)(x);			\
       }									\

include/enums/enums_helpers.hpp

@@ -958,6 +958,7 @@ namespace ePhotosynthesis {
       EPS_ATP_Rate     ,		\
       _Pi              ,		\
       PMODTEM          ,		\
+      F                ,		\
       RT               ,		\
       DeltaGo          ,		\
       MAX
@@ -1318,6 +1319,7 @@ namespace ePhotosynthesis {
       Q10_10        ,		\
       Q10_13        ,		\
       Q10_23        ,		\
+      F             ,		\
       R             ,		\
       c_c           ,		\
       dHa_c         ,		\
@@ -1634,7 +1636,9 @@ namespace ePhotosynthesis {
 }
 namespace ePhotosynthesis {
   #define MEMBERS_FIBFRC		\
-      NONE   ,		\
+      NONE     ,		\
+      RC0      ,		\
+      RC       ,		\
       MAX
   #ifdef EPHOTO_USE_SCOPED_ENUM
   enum class ENUM_FIBF_RC : int {
@@ -1916,11 +1920,17 @@ namespace ePhotosynthesis {
 }
 namespace ePhotosynthesis {
   #define MEMBERS_RedoxRegRC		\
-      NONE               ,		\
-      Fd_Thio_ET         ,		\
-      ThioT              ,		\
-      Thio_Oxidation     ,		\
-      Thion0             ,		\
+      NONE          ,		\
+      Thiom0        ,		\
+      FBPase0       ,		\
+      SBPase0       ,		\
+      PRK0          ,		\
+      ATPase0       ,		\
+      Em_Thiom      ,		\
+      Em_FBPase     ,		\
+      Em_SBPase     ,		\
+      Em_PRK        ,		\
+      Em_ATPase     ,		\
       MAX
   #ifdef EPHOTO_USE_SCOPED_ENUM
   enum class ENUM_RedoxReg_RC : int {
@@ -1947,6 +1957,8 @@ namespace ePhotosynthesis {
       ko       ,		\
       k7       ,		\
       kr       ,		\
+      kn7      ,		\
+      RCA      ,		\
       MAX
   #ifdef EPHOTO_USE_SCOPED_ENUM
   enum class ENUM_RuACT_RC : int {

include/rc/FIBFRC.hpp

@@ -0,0 +1,64 @@
+#pragma once
+
+/**********************************************************************************************************************************************
+ *   Copyright   Xin-Guang Zhu, Yu Wang, Donald R. ORT and Stephen P. LONG
+ *
+ * CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai,200031
+ * China Institute of Genomic Biology and Department of Plant Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai,200031
+ * University of Illinois at Urbana Champaign
+ * Global Change and Photosynthesis Research Unit, USDA/ARS, 1406 Institute of Genomic Biology, Urbana, IL 61801, USA.
+ *
+ * Converted from Matlab to C++ by Douglas N. Friedel, National Center for Supercomputing Applications (2020)
+ *
+ *   This file is part of e-photosynthesis.
+ *
+ *    e-photosynthesis is free software; you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation;
+ *
+ *    e-photosynthesis is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License (GPL)
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ **********************************************************************************************************************************************/
+
+#include "../definitions.hpp"
+#include "RCBase.hpp"
+
+namespace ePhotosynthesis {
+namespace RC {
+
+// class for holding FIBFRC data
+class FIBFRC : public RCBase<FIBFRC, MODULE_FIBF> {
+public:
+    DECLARE_VALUE_SET(FIBFRC, RCBase<FIBFRC, MODULE_FIBF>)
+    FIBFRC() : RCBase<FIBFRC, MODULE_FIBF>() {
+        initMembers();
+    }
+
+    /**
+      Copy constructor that makes a deep copy of the given object
+
+      @param other The FIBFRC object to copy
+      */
+    FIBFRC(const FIBFRC &other) : RCBase<FIBFRC, MODULE_FIBF>(other) {
+      initMembers();
+      *this = other;
+    }
+    FIBFRC& operator=(const FIBFRC &other) {
+      RC0 = other.RC0; // The maximal relaxation constant for heat dissipation, which is one term borrowed from Laisk et al., 1997;
+      RC = other.RC;
+      copyMembers(other);
+      return *this;
+    }
+
+};
+
+  DEFINE_VALUE_SET_HEADER(FIBFRC);
+
+}  // namespace RC
+}  // namespace ePhotosynthesis

include/rc/RCAll.hpp

@@ -29,5 +29,7 @@
 #include "RCBase.hpp"
 #include "BFRC.hpp"
 #include "FIRC.hpp"
+#include "FIBFRC.hpp"
 #include "RROEARC.hpp"
 #include "RuACTRC.hpp"
+#include "RedoxRegRC.hpp"

include/rc/RCBase.hpp

@@ -28,6 +28,6 @@
 
 #include "../ValueSet.hpp"
 
-#define MEMBERS_RC BF, FI, RROEA, RuACT
+#define MEMBERS_RC BF, FI, FIBF, RROEA, RuACT, RedoxReg
 
 DECLARE_PARAM_BASE(RC)