Add option to run a series of time-steps with varying input parameters that preserve the previous state

Author: langmm

.gitignore

@@ -1,3 +1,5 @@
+*.DS_Store
+
 # Prerequisites
 *.d
 

bin/ePhotosynthesis.cpp

@@ -93,6 +93,7 @@ void param2ygg(const std::map<std::string, T>& v,
 #define varSearchD(x) varSearch(x, convD)
 #define varSearchI(x) varSearch(x, convI)
 #define varSearchS(x) varSearch(x, convS)
+#define varSearchB(x) varSearch(x, convB)
 #define varSet(xcli, xfile) (result.count(#xcli) || inputs.count(#xfile))
 #define fileProvided(xcli, xfile) varSet(xcli, xfile)
 
@@ -118,10 +119,12 @@ int main(int argc, const char* argv[]) {
     try {
         bool record = false;
         bool useC3 = false;
+        bool iterationsPreserveState = false;
         cxxopts::Options options("ePhoto", "Command line interface to C++ implementation of the matlab original");
         options.show_positional_help();
         std::string evn, atpcost, optionsFile, enzymeFile, grnFile,
-	  outputFile, outputVars, outputParamVars, outputParamBase;
+	  outputFile, outputVars, outputParamVars, outputParamBase,
+          iterationsFile;
         double stoptime, begintime, stepsize;
         double abstol, reltol;
         double Tp;
@@ -137,6 +140,10 @@ int main(int argc, const char* argv[]) {
                 ("n,enzyme", "The file (including path) containing enzyme activities like InputEnzyme.txt", cxxopts::value<std::string>(enzymeFile)->default_value(""))
                 ("g,grn", "The file (including path) containing protein ratios for relevant genes like InputGRNC.txt",
 		 cxxopts::value<std::string>(grnFile)->default_value(""))
+                ("iterations", "The file (including path) times and variables that should be updated at those times",
+                 cxxopts::value<std::string>(iterationsFile)->default_value(""))
+                ("iterationsPreserveState", "Preserve the internal state when iterations are performed (including for yggdrasil iterations)",
+                 cxxopts::value<bool>(iterationsPreserveState)->default_value("false"))
                 ("b,begintime", "The starting time for the calculations.", cxxopts::value<double>(begintime)->default_value("0.0"))
                 ("s,stoptime", "The time to stop calculations.", cxxopts::value<double>(stoptime)->default_value("5000.0"))
                 ("z,stepsize", "The step size to use in the calculations.", cxxopts::value<double>(stepsize)->default_value("1.0"))
@@ -253,6 +260,7 @@ int main(int argc, const char* argv[]) {
             varSearchS(enzymeFile);
             varSearchS(grnFile);
             varSearchS(outputFile);
+            varSearchS(iterationsFile);
             varSearchD(begintime);
             varSearchD(stoptime);
             varSearchD(stepsize);
@@ -266,6 +274,7 @@ int main(int argc, const char* argv[]) {
             varSearchI(outputParam);
             varSearchS(outputParamBase);
             varSearchS(outputParamVars);
+            varSearchB(iterationsPreserveState);
         }
         driverChoice = static_cast<DriverType>(driver);
 	// TODO: Do yggdrasil initial input before this point so driver
@@ -312,6 +321,7 @@ int main(int argc, const char* argv[]) {
         if (!fileProvided(atpcost, atpcost)) atpcost = "";
         if (!fileProvided(enzyme, enzymeFile)) enzymeFile = "";
         if (!fileProvided(grn, grnFile)) grnFile = "";
+        if (!fileProvided(iterations, iterationsFile)) iterationsFile = "";
 
         std::vector<std::string> outputVarsV;
         if (!outputVars.empty())
@@ -323,10 +333,11 @@ int main(int argc, const char* argv[]) {
                        begintime, stoptime, stepsize, maxSubSteps,
                        abstol, reltol, inputs, useC3,
                        evn, atpcost, enzymeFile, grnFile,
+                       iterationsFile,
                        outputFile, outputVarsV, outputParam,
                        outputParamBase, outputParamVarsV,
                        dbglvl, debugDelta, debugInternal, record,
-                       theVars);
+                       iterationsPreserveState, theVars);
         return (EXIT_SUCCESS);
     } catch (std::exception& e) {
         std::cout << "An error occurred: " << e.what() << std:: endl;

include/ValueSet.hpp

@@ -1058,9 +1058,11 @@ namespace ePhotosynthesis {
       }
       std::map<std::string, std::string>::const_iterator it_alias = key_aliases.find(iname);
       if (!utils::contains(skip_keys, iname)) {
-        out << space << std::setw(pad + tab_size) << std::left;
         if (it_alias != key_aliases.end())
           iname = it_alias->second;
+        if (iname.length() > pad)
+          pad = iname.length();
+        out << space << std::setw(pad + tab_size) << std::left;
         out << iname;
         print_value(val, out, show_pointers);
         out << std::endl;
@@ -1110,7 +1112,7 @@ namespace ePhotosynthesis {
     }
     /**
        Display the values in a value map.
-       \tparam V Type of value in value map.
+       \tparam V Value map value type.
        \param vals Value map to display.
        \param out Output stream.
        \param tab Number of tabs to prefix each line in the output with.
@@ -1146,6 +1148,44 @@ namespace ePhotosynthesis {
       }
       return out;
     }
+    /**
+       Display the values in a value map.
+       \tparam V Value map value type.
+       \param vals Value map to display.
+       \param out Output stream.
+       \param tab Number of tabs to prefix each line in the output with.
+       \param pad Number of characters that key names should be padded
+         to fill.
+       \param includePrefixes If true, the module & parameter type
+         prefixes will be added to the member names.
+       \param includeSkipped If true, skipped keys will be output.
+       \param skip_keys Key strings to skip in output.
+       \param key_aliases String aliases to use for keys.
+       \param show_pointers If true, the pointers will be displayed
+         instead of the values.
+       \returns Output stream.
+     */
+    template<typename V>
+    static std::ostream& print_value_map(const std::map<std::string, V>& vals,
+					 std::ostream &out,
+					 const uint tab=0,
+					 std::size_t pad=0,
+					 bool includePrefixes=false,
+					 bool includeSkipped=false,
+					 const std::vector<std::string>& skip_keys={},
+					 const std::map<std::string, std::string>& key_aliases={},
+					 bool show_pointers=false) {
+      check_value_map(vals, "print_value_map: ");
+      if (pad == 0)
+        pad = field_width_value_map(vals, includePrefixes);
+      for (typename std::map<std::string, V>::const_iterator it = vals.begin();
+           it != vals.end(); it++) {
+        print_value(it->first, it->second,
+                    out, tab, pad, includePrefixes, includeSkipped,
+                    skip_keys, key_aliases, show_pointers, it->first);
+      }
+      return out;
+    }
     template<typename V>
     static std::string to_string_with_precision(V const a_value,
 						const int n = COMPARE_PRECISION) {
@@ -1248,12 +1288,13 @@ namespace ePhotosynthesis {
 			      const std::string& context = "");
     /**
        Throw an error if a map is empty;
-       \tparam V Value map type.
+       \tparam K Value map key type.
+       \tparam V Value map value type.
        \param vals Value map to check.
        \param context String to prefix the error message with.
      */
-    template<typename V>
-    static void check_value_map(const std::map<EnumType, V>& vals,
+    template<typename K, typename V>
+    static void check_value_map(const std::map<K, V>& vals,
 				const std::string& context = "") {
       if (vals.empty() && !defaults.empty()) {
         ERROR_VALUE_SET(context, "Value map empty");

include/Variables.hpp

@@ -149,12 +149,17 @@ class Variables : public VALUE_SET_PARENT(Variables, Variables, MODULE_ALL, PARA
 
  protected:
     static void _initStaticMembers();
-    
+
+    /**
+       Copy non-member attributes.
+       \param[in] other Variables instance to copy.
+     */
+    void __copyNonMembers(const Variables& other);
     /**
        Copy additional members.
          Some variables are not included in the default copy (e.g. alfa, 
 	 fc, lightParam, CO2A, RedoxReg_MP, module *_Param values, & 
-	 rates). To include these, use deepcopy.
+	 rates). To include these, use deepcopy (or __copyNonMembers).
        \param[in] other Variables instance to copy.
      */
     void __copyMembers(const Variables& other) override;
@@ -166,16 +171,37 @@ class Variables : public VALUE_SET_PARENT(Variables, Variables, MODULE_ALL, PARA
 		      bool noChildren = false) const override;
  public:
 
+    /**
+       Check if a variable was 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;
+    /**
+       Throw an error if the named variable was updated.
+     */
+    EPHOTO_API void assertCalcNotUpdated(const std::string& name) const;
     /**
        Finalize variables read from input including any unit changes.
+       \param[in] dontReset If true, don't set the inputsFinalized flag
+         to true or clear inputsUpdated.
      */
-    EPHOTO_API void finalizeInputs();
+    EPHOTO_API void finalizeInputs(const bool dontReset=false);
     /**
        Create a deep copy of this instance including variables excluded
          from a default copy.
        \returns New instance with all parameters copied.
      */
     EPHOTO_API Variables* deepcopy() const;
+    /**
+       Copy another instance including variables excluded from a default
+         copy.
+       \param[in] Instance to copy.
+     */
+    EPHOTO_API void deepcopy(const Variables& rhs);
     /** \copydoc ValueSet::equals */
     bool equals(const ValueSet_t& b,
 		const bool noChildren = false) const override;
@@ -211,6 +237,7 @@ class Variables : public VALUE_SET_PARENT(Variables, Variables, MODULE_ALL, PARA
        \param[in] conditions Map of conditions for composite modules that
          are not stored on Variables instances.
        \param[in] subset Subset of parameters to output.
+       \param[in] additionalVars Map of additional names & values to dump.
      */
     void dump(const std::string& filename,
               const bool includeSkipped = false,
@@ -219,7 +246,8 @@ class Variables : public VALUE_SET_PARENT(Variables, Variables, MODULE_ALL, PARA
               const std::vector<std::string>& skip_keys={},
               const std::map<std::string, std::string>& key_aliases={},
               const std::map<MODULE, const ValueSet_t*>& conditions={},
-              const std::vector<std::string>& subset={}) const;
+              const std::vector<std::string>& subset={},
+              const std::map<std::string, double>& additionalVars={}) const;
     /**
        Serialize all parameters attached to this instance to an output
          stream.
@@ -234,6 +262,7 @@ class Variables : public VALUE_SET_PARENT(Variables, Variables, MODULE_ALL, PARA
        \param[in] conditions Map of conditions for composite modules that
          are not stored on Variables instances.
        \param[in] subset Subset of parameters to output.
+       \param[in] additionalVars Map of additional names & values to dump.
        \returns Updated output stream.
      */
     std::ostream& dump(std::ostream& out,
@@ -243,7 +272,8 @@ class Variables : public VALUE_SET_PARENT(Variables, Variables, MODULE_ALL, PARA
                        const std::vector<std::string>& skip_keys={},
                        const std::map<std::string, std::string>& key_aliases={},
                        const std::map<MODULE, const ValueSet_t*>& conditions={},
-                       const std::vector<std::string>& subset={}) const;
+                       const std::vector<std::string>& subset={},
+                       const std::map<std::string, double>& additionalVars={}) const;
     /**
        Serialize parameters for a single value set to an output stream.
        \param[in] module ID for module that should be serialized.
@@ -810,6 +840,7 @@ class Variables : public VALUE_SET_PARENT(Variables, Variables, MODULE_ALL, PARA
     EPHOTO_API void readGRN(const std::string& fname);
 
     bool inputsFinalized = false;
+    std::map<std::string, bool> inputsUpdated; /**< Name of variables that were updated after inputs were finalized. */
     bool record = false;
     int GP = 0;
     int GRNC = 0; /**< Control parameter; if 1, VfactorCp values will be used to scale enzyme activities in the PS, PR, & SUCS modules when CO2 > 0 */

include/drivers/CM_Driver.hpp

@@ -46,16 +46,6 @@ class CMDriver : public DriverBase<CMDriver, MODULE_CM> {
 	     const std::size_t para = 0, const double ratio = 0,
              const bool showWarn = false,
 	     const std::vector<std::string>& outVars = {});
-
-    /**
-      \copydoc drivers::Driver::setup
-      */
-    void setup() override;
-
-    /**
-      \copydoc drivers::Driver::getResults
-      */
-    void getResults() override;
 
 };
 

include/drivers/DynaPS_Driver.hpp

@@ -49,16 +49,6 @@ class DynaPSDriver : public DriverBase<DynaPSDriver, MODULE_DynaPS> {
 		 const bool showWarn = false,
 		 const std::vector<std::string>& outVars = {});
 
-    /**
-      \copydoc drivers::Driver::setup
-      */
-    void setup() override;
-
-    /**
-      \copydoc drivers::Driver::getResults
-      */
-    void getResults() override;
-
 };
 
 }  // namespace drivers

include/drivers/EPS_Driver.hpp

@@ -47,20 +47,10 @@ class EPSDriver : public DriverBase<EPSDriver, MODULE_EPS> {
               const bool showWarn = false,
 	      const std::vector<std::string>& outVars = {});
 
-    /**
-      \copydoc drivers::Driver::setup
-      */
-    void setup() override;
-
-    /**
-      \copydoc drivers::Driver::getResults
-      */
-    void getResults() override;
-
 private:
 
     //double Ca;
-    //double Li;
+    double Li;
     double AtpCost;
 };