Fixed bug when reading initial conditions from parameters (set defaults rather than read into output concentrations)

Updated BF::RC::KBs & BF::RC::KBl values & code to actually use them to match Zhu 2012. The constants were not used and had different values defined, the original values are still in the parameter file, but commented out
Added option for running with Zhu 2012 parameters
Set initial values for calculated variables in parameter files to allow for comparison
Fix some typos identified in initCalc methods
Use BF::RC::KBl in FIBF

Author: langmm

include/ValueSet.hpp

@@ -3108,7 +3108,7 @@ namespace ePhotosynthesis {
     EVAL(FOR_EACH_GENERIC(MOD2PT_PAIRS_DEFERED,				\
 			  CALL_WITH_SUFFIX_ARGS_DEFER,			\
 			  SEP_COMMA, (MOD2PT_COND),			\
-			  EXPAND VARS_INST_MODULES)),			\
+			  EXPAND VARS_INST_MODULES, FIBF)),             \
     EVAL(FOR_EACH_GENERIC(MOD2PT_PAIRS_DEFERED,				\
 			  CALL_WITH_SUFFIX_ARGS_DEFER,			\
 			  SEP_COMMA, (MOD2PT_NO_COND),			\

include/Variables.hpp

@@ -711,7 +711,7 @@ class Variables : public VALUE_SET_PARENT(Variables, Variables, MODULE_ALL, PARA
        Variables::getVarCalculated or Variables::getCalculatedVars
        methods.
      */
-    EPHOTO_API const std::vector<std::string>&
+    EPHOTO_API std::vector<std::string>
       getCalculatedVarNames() const;
     /**
        Populate a map with calculated variables.
@@ -837,16 +837,20 @@ class Variables : public VALUE_SET_PARENT(Variables, Variables, MODULE_ALL, PARA
     static void _readParam(const std::string& fname,
                            std::map<std::string, std::string>& inputs,
                            Variables* theVars = nullptr,
+                           const bool init = false,
                            const std::string& context="_readParam");
  public:
     /**
        Update the default parameters from a map.
        \param[in, out] inputs Map of parameters that should be added.
        \param[in] theVars Variable instance that should be updated.
+       \param[in] init If true, condition parameters will be used to set
+         defaults.
        \param[in] context String providing context for errors.
      */
     EPHOTO_API static void updateParam(std::map<std::string, std::string>& inputs,
                                        Variables* theVars = nullptr,
+                                       const bool init = false,
                                        const std::string& context="updateParam");
 
     /**
@@ -865,16 +869,22 @@ class Variables : public VALUE_SET_PARENT(Variables, Variables, MODULE_ALL, PARA
     /**
        Read parameters from a file.
        \param[in] fname File to read.
+       \param[in] init If true, condition parameters will be used to set
+         defaults.
      */
-    EPHOTO_API void readParam(const std::string& fname);
+    EPHOTO_API void readParam(const std::string& fname,
+                              const bool init = false);
     /**
        Read parameters from a file, checking for duplicates
        \param[in] fname File to read.
        \param[in, out] inputs Map that read variables should be checked
          against for duplicates and copied into.
+       \param[in] init If true, condition parameters will be used to set
+         defaults.
      */
     EPHOTO_API void readParam(const std::string& fname,
-                              std::map<std::string, std::string>& inputs);
+                              std::map<std::string, std::string>& inputs,
+                              const bool init = false);
     /**
        Read Enzyme activities from a file.
        \param[in] File to read.

include/enums/enums_helpers.hpp

@@ -1639,6 +1639,7 @@ namespace ePhotosynthesis {
       NONE     ,		\
       RC0      ,		\
       RC       ,		\
+      kdm0     ,		\
       MAX
   #ifdef EPHOTO_USE_SCOPED_ENUM
   enum class ENUM_FIBF_RC : int {
@@ -1946,19 +1947,20 @@ namespace ePhotosynthesis {
 }
 namespace ePhotosynthesis {
   #define MEMBERS_RuACTRC		\
-      NONE     ,		\
-      k1       ,		\
-      kn1      ,		\
-      km1      ,		\
-      Ke2      ,		\
-      Ke3      ,		\
-      k6       ,		\
-      kc       ,		\
-      ko       ,		\
-      k7       ,		\
-      kr       ,		\
-      kn7      ,		\
-      RCA      ,		\
+      NONE          ,		\
+      k1            ,		\
+      kn1           ,		\
+      km1           ,		\
+      Ke2           ,		\
+      Ke3           ,		\
+      k6            ,		\
+      kc            ,		\
+      ko            ,		\
+      k7            ,		\
+      kr            ,		\
+      factor_n7     ,		\
+      kn7           ,		\
+      RCA           ,		\
       MAX
   #ifdef EPHOTO_USE_SCOPED_ENUM
   enum class ENUM_RuACT_RC : int {

param/BF_RC.txt

@@ -18,17 +18,19 @@ Kau		1.0e10		# The rate constant for exciton transfer from perpheral antenna to
 Kua		1.0e10		# The rate constant for exciton transfer from core antenna to peripheral antenna, SEE FI Unit: s-1
 Kf		6.3e6		# The rate constant for fluorescence emission, see the note in FI Unit: s-1
 Kd		2.0e8		# The rate constant for heat dissipation; see the note for FI Unit: s-1
-KE8		0.0		# [CALC] ISPHr + cytc1 --> ISPHox + cytc1-; Calculated from Em_IPS, Em_Cytf & Em_PG; Unit: s-1
-KE9		0.0		# [CALC] cytc1- + cytc2 --> cytc1 + cytc2-; Calculated from Em_IPS, Em_Cytf & Em_PG; Unit: s-1
+KE8		0.21		# [CALC] ISPHr + cytc1 --> ISPHox + cytc1-; Calculated from Em_IPS, Em_Cytf & Em_PG; Unit: s-1
+KE9		22.55		# [CALC] cytc1- + cytc2 --> cytc1 + cytc2-; Calculated from Em_IPS, Em_Cytf & Em_PG; Unit: s-1
 K15		1.0e10		# The rate constant for primary charge separation in PSI Unit: s-1
 K16		1.0e5		# The rate constant for electron tranfer from electron acceptor of PSI to Fd Unit: s-1
 Em_IPS		0.31		# [CONST] ISPHr + cytc1 --> ISPHox + cytc1-
 Em_Cytf		0.27		# [CONST] ISPHr + cytc1 --> ISPHox + cytc1-
 Em_PG		0.35		# [CONST] cytc1- + cytc2 --> cytc1 + cytc2-
 MemCap		0.6e-6		# The membrane capacity
 RVA		8.0e-10		# The ratio of lumen volume to thylakoid membrane area
-KBs		1.1e-8 		# The buffer equilibrium constant in stroma
-KBl		5.1e-6		# The buffer equilibrium constant in lumen
+KBs             0.015           # The buffer equilibrium constant in stroma; mol l-1 (pH unit)-1
+KBl             0.015           # The buffer equilibrium constant in lumen; mol l-1 (pH unit)-1
+# KBs		1.1e-8 		# The buffer equilibrium constant in stroma (this is the value that was stated, but the variable was never used and a hard coded value was used instead)
+# KBl		5.1e-6		# The buffer equilibrium constant in lumen
 KM1ATP		0.12		# The michaelis menton constant for ATP for ATP synthesis
 KM1ADP		0.014		# The michaelis menton constant for ATP for ADP synthesis
 KM1PI		0.3		# The michaelis menton constant for ATP for PI synthesis

param/FIBF_RC.txt

@@ -1,3 +1,4 @@
 # Name		Value	C3Value	Docs
 RC0             0.1             # Maximal relaxation constant for changes in the ‘rate constant’ of heat dissipation, which is one term borrowed from Laisk et al., 1997;
 RC              0.1             # Maximal relaxation constant for changes in ‘rate constant’ of heat dissipation under a particular Xstate,Laisk et al. (1997)
+kdm0            5.0e8           # Maximum heat dissipation ‘rate constant’

param/RuACT_COND.txt

@@ -2,4 +2,4 @@
 ER		0.20		# The concentration of inactive ER
 Eaf		0.20		# The total concentration of E, EC, AND ECM
 ECMR		0.8		# The concentration of ECMR
-RuBP		2.0		# The concentration of ECMR
+RuBP		2.0		# The concentration of RuBP

param/RuACT_RC.txt

@@ -9,5 +9,6 @@ kc		0.016		# Michaelis menton constant for CO2
 ko		0.448		# Michaelis menton constant for O2
 k7		10.0		# The rate constant for ecm to ecmr
 kr		20.0e-3		# The apparaent michaelis menton constant for RuBP
-kn7             1.0             # Rate constants for RuBP dissociation from ECMR
+factor_n7       1.0             # Scale factor for kn7
+kn7             0.5             # Rate constant for RuBP dissociation from ECMR
 RCA             0.0000768403258029814  # 1 / (60. * 216.9); The rate constant of the activation reaction which will be scaled by the concentration of Rubisco activase

param/SUCS_MOD.txt

@@ -55,6 +55,8 @@ Km602		0.0		1.66		# Nucleoside Diphosphate Kinase 2.7.4.6 60 NI Km602 ATP 1.66 R
 Km603		0.0		0.28		# Nucleoside Diphosphate Kinase 2.7.4.6 60 NI Km603 UDP 0.28 Saccharomyces cerevisiae {Jong, 1991 #2518}; Skipped w/o C3
 Km604		0.0		16.		# Nucleoside Diphosphate Kinase 2.7.4.6 60 NI Km604 UTP 16 Rattus norvegicus {Fukuchi, 1994 #2519}; Skipped w/o C3
 KE60		0.0		16.		# Nucleoside Diphosphate Kinase 2.7.4.6 60 NI KE60  16 1.04 {Lynn, 1978 #2520}; Skipped w/o C3
+# The version below seems to have been a typo where 10**7 was interpreted as 107
+# KE61		1.2e7		1.2e7		# Pyrophosphate hydrolysis    KE61  1.2*107  {Flodgaard, 1974 #2521}; SUCSRatio 58
 KE61		128.4		128.4		# Pyrophosphate hydrolysis    KE61  1.2*107  {Flodgaard, 1974 #2521}; SUCSRatio 58
 Km621		5.0		5.0		# Vsink   Notice: pH dependent Km621 Sucrose 5  {Weschke, 2000 #2522}
 ATPc		0.4		0.35
@@ -79,7 +81,7 @@ SUCSV58		0.0     	0.0     	# Set by calculation for C3
 # Variables only set during calculations
 SUCS2PS_Pic	0.0		0.0		# [INIT_ONCE]
 KE5Ratio	0.0		0.0		# Calculated from KE541 & KE531
-ADPc		0.0		0.0		# Calculated from ATc & ATPc
+ADPc		0.6		0.65		# Calculated from ATc & ATPc
 Vmatpf		0.25		0.25		# [CONST] Previously stored as constant
 Q10_51		2.0				# [CONST] DHAP+GAP --FBP; unused w/o C3
 Q10_52		1.6				# [CONST] FBP --F6P + Pi; unused w/o C3