Merge pull request #54 from jimmielin/misc_cleanup

Remove Vdotout functionality

CHANGELOG.md

@@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
-- C-lanugage updates
+- C-language updates
   - Restored driver programs `general.c` and `general_adj.c`
   - Updated rate-law functions in `util/UserRateLaws.c`
   - Added C-I tests for C-language integrators (using the
@@ -41,6 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Removed
 - bibtex.json (no longer needed w/ Sphinx 3.5.4)
+- Fun() no longer uses Vdotout since it can be retrieved from `Vdot`
 
 ## [2.6.0]
 
@@ -74,6 +75,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - Make sure to inline parameter "sp" into the _Global.F90 file
     when the "#DOUBLE off" option is used.
 
+
 ### Changed
 - Code updates
    - Rewrote code to remove compiler warnings

docs/source/using_kpp/05_output_from_kpp.rst

@@ -334,7 +334,7 @@ first the vector :code:`A` of reaction rates and then the vector
 species, fixed species, and the rate coefficients,
 respectively. :code:`A` and :code:`Vdot` may be returned to the
 calling program (for diagnostic purposes) with optional ouptut
-arguments :code:`Aout` and :code:`Vdotout`. Below is the Fortran90
+argument :code:`Aout`. Below is the Fortran90
 code generated by KPP for the ODE function of our
 :program:`small_strato` example.
 
@@ -352,8 +352,6 @@ code generated by KPP for the ODE function of our
      REAL(kind=dp) :: Vdot(NVAR)
    ! Aout - Optional argument to return equation rate constants
      REAL(kind=dp), OPTIONAL :: Aout(NREACT)
-   ! Vdotout - Optional argument to return time derivative of variable species
-     REAL(kind=dp), OPTIONAL :: Vdotout(NVAR)
 
 
    ! Computation of equation rates
@@ -380,9 +378,6 @@ code generated by KPP for the ODE function of our
      Vdot(4) = -A(8)+A(9)+A(10)
      Vdot(5) = A(8)-A(9)-A(10)
 
-     !### Use Vdotout to return time deriv. of variable species
-     IF ( PRESENT( Vdotout ) ) Vdotout = V
-
    END SUBROUTINE Fun
 
 .. _Jacobian-and-JacobianSP:

src/gen.c

@@ -52,7 +52,7 @@ int DC;
 int ARP, JVRP, NJVRP, CROW_JVRP, IROW_JVRP, ICOL_JVRP;
 int V, F, VAR, FIX;
 int RCONST, RCT;
-int Vdot, P_VAR, D_VAR, Aout, Vdotout;
+int Vdot, P_VAR, D_VAR, Aout;
 int StoichNum;
 int KR, A, BV, BR, IV, RR;
 int JV, UV, JUV, JTUV, JVS;
@@ -302,9 +302,6 @@ int i,j;
   Aout = DefvElmO( "Aout", real, -NREACT,
                    "Optional argument to return equation rate constants" );
 
-  Vdotout = DefvElmO( "Vdotout", real, -NVAR,
-       "Optional argument to return time derivative of variable species" );
-
   /* Elements of Stochastic simulation*/
   NMLCV = DefvElm( "NmlcV", INT, -NVAR, "No. molecules of variable species" );
   NMLCF = DefvElm( "NmlcF", INT, -NFIX, "No. molecules of fixed species" );
@@ -662,7 +659,10 @@ int F_VAR, FSPLIT_VAR;
   if (useLang != MATLAB_LANG)  /* Matlab generates an additional file per function */
        UseFile( functionFile );
 
-  F_VAR = DefFnc( "Fun", 6,
+  // Note: When changing the FunctionBegin declarations below,
+  // the number of arguments minus one must be changed in DefFnc here
+  // as well. (hplin, 7/6/22)
+  F_VAR = DefFnc( "Fun", 5,
                   "time derivatives of variables - Aggregate form");
 
   FSPLIT_VAR = DefFnc( "Fun_SPLIT", 7,
@@ -673,8 +673,10 @@ int F_VAR, FSPLIT_VAR;
   // time derivative of variable species from Fun via optional arguments
   // Aout and VdotOut (when z_useAggregate=1)
   //   -- Bob Yantosca (03 May 2022)
+  //
+  // Vdotout functionality can be accomplished using Vdot (hplin, 7/6/22)
   if( z_useAggregate ) {
-    FunctionBegin( F_VAR, V, F, RCT, Vdot, Aout, Vdotout );
+    FunctionBegin( F_VAR, V, F, RCT, Vdot, Aout );
   }
   else {
     FunctionBegin( FSPLIT_VAR, V, F, RCT, Vdot, P_VAR, D_VAR, Aout );
@@ -745,14 +747,6 @@ int F_VAR, FSPLIT_VAR;
       Assign( Elm( Vdot, i ), sum );
     }
 
-    // Add code to return time derivative of variable species (Vdotout)
-    //   -- Bob Yantosca (03 May 2022)
-    NewLines(1);
-    if ( useLang == F90_LANG ) {
-      fprintf(functionFile, "  !### Use Vdotout to return time deriv. of variable species\n");
-      fprintf(functionFile, "  IF ( PRESENT( Vdotout ) ) Vdotout = Vdot\n");
-    }
-
   } else {
 
     NewLines(1);
@@ -801,9 +795,7 @@ int F_VAR, FSPLIT_VAR;
     }
   }
 
-  if( z_useAggregate )
-    MATLAB_Inline("\n   Vdotout = Vdot(:);\n");
-  else
+  if( !z_useAggregate )
     MATLAB_Inline("\n   P_VAR = P_VAR(:);\n   D_VAR = D_VAR(:);\n");
 
   if( z_useAggregate )