python wrapper for autodiff and version

CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION "3.14")
 cmake_policy(SET CMP0148 OLD)
-project(Photochem LANGUAGES Fortran C VERSION "0.4.7")
+project(Photochem LANGUAGES Fortran C VERSION "0.5.0")
 
 include(FortranCInterface)
 FortranCInterface_VERIFY()

photochem/cython/PhotochemVars.pyx

@@ -205,7 +205,9 @@ cdef class PhotochemVars:
       var_pxd.photochemvars_rtol_set(&self._ptr, &val)
 
   property atol:
-    "double. Integration absolute tolerance."
+    """double. Integration absolute tolerance. If autodiff == .true., then the model
+    works better when atol is smaller (e.g., atol = ~1.0e-18).
+    """
     def __get__(self):
       cdef double val
       var_pxd.photochemvars_atol_get(&self._ptr, &val)
@@ -252,7 +254,9 @@ cdef class PhotochemVars:
       var_pxd.photochemvars_conv_min_mix_set(&self._ptr, &val)
 
   property conv_longdy:
-    "double. Threshold normalized change in mixing ratios for converchecking check."
+    """double. Threshold normalized change in mixing ratios for converchecking check.
+    A reasonable value is ~1.0e-2.
+    """
     def __get__(self):
       cdef double val
       var_pxd.photochemvars_conv_longdy_get(&self._ptr, &val)
@@ -271,7 +275,19 @@ cdef class PhotochemVars:
     def __set__(self, double val):
       var_pxd.photochemvars_conv_longdydt_set(&self._ptr, &val)
 
+  property autodiff:
+    """bool. If True, then the chemistry terms of the Jacobian are computed uses 
+    foward mode automatic differentiation.
+    """
+    def __get__(self):
+      cdef bool val
+      var_pxd.photochemvars_autodiff_get(&self._ptr, &val)
+      return val
+    def __set__(self, bool val):
+      var_pxd.photochemvars_autodiff_set(&self._ptr, &val)
+
   property epsj:
+    "double. Perturbation for finite difference Jacobian calculation, when autodiff == .false."
     def __get__(self):
       cdef double val
       var_pxd.photochemvars_epsj_get(&self._ptr, &val)

photochem/cython/PhotochemVars_pxd.pxd

@@ -77,6 +77,9 @@ cdef extern void photochemvars_conv_longdy_set(void *ptr, double *val)
 cdef extern void photochemvars_conv_longdydt_get(void *ptr, double *val)
 cdef extern void photochemvars_conv_longdydt_set(void *ptr, double *val)
 
+cdef extern void photochemvars_autodiff_get(void *ptr, bool *val)
+cdef extern void photochemvars_autodiff_set(void *ptr, bool *val)
+
 cdef extern void photochemvars_epsj_get(void *ptr, double *val)
 cdef extern void photochemvars_epsj_set(void *ptr, double *val)
 

photochem/fortran/PhotochemVars_wrapper.f90

@@ -385,6 +385,22 @@ subroutine photochemvars_conv_longdydt_set(ptr, val) bind(c)
     var%conv_longdydt = val
   end subroutine
 
+  subroutine photochemvars_autodiff_get(ptr, val) bind(c)
+    type(c_ptr), intent(in) :: ptr
+    logical(c_bool), intent(out) :: val
+    type(PhotochemVars), pointer :: var
+    call c_f_pointer(ptr, var)
+    val = var%autodiff
+  end subroutine
+
+  subroutine photochemvars_autodiff_set(ptr, val) bind(c)
+    type(c_ptr), intent(in) :: ptr
+    logical(c_bool), intent(in) :: val
+    type(PhotochemVars), pointer :: var
+    call c_f_pointer(ptr, var)
+    var%autodiff = val
+  end subroutine
+
   subroutine photochemvars_epsj_get(ptr, val) bind(c)
     type(c_ptr), intent(in) :: ptr
     real(c_double), intent(out) :: val