got rid of function for time dependent photons

photochem/cython/Atmosphere.pyx

@@ -450,34 +450,6 @@ cdef class Atmosphere:
     if len(err.strip()) > 0:
       raise PhotoException(err.decode("utf-8").strip())
 
-  def set_photon_flux_fcn(self, object fcn):
-    """Sets a function describing a time-dependent photon flux. 
-    This is useful for modeling flares.
-
-    Parameters
-    ----------
-    fcn : function
-        A Numba cfunc that describes the time-dependent photon flux
-    """
-    cdef uintptr_t fcn_l
-    cdef a_pxd.time_dependent_flux_fcn fcn_c
-
-    if fcn is None:
-      fcn_l = 0
-      fcn_c = NULL
-    else:
-      argtypes = (ct.c_double, ct.c_int32, ct.POINTER(ct.c_double))
-      restype = None
-      if not fcn.ctypes.argtypes == argtypes:
-        raise PhotoException("The callback function has the wrong argument types.")
-      if not fcn.ctypes.restype == restype:
-        raise PhotoException("The callback function has the wrong return type.")
-
-      fcn_l = fcn.address
-      fcn_c = <a_pxd.time_dependent_flux_fcn> fcn_l
-
-    a_pxd.atmosphere_set_photon_flux_fcn_wrapper(&self._ptr, fcn_c)
-
   def set_rate_fcn(self, str species, object fcn):
     """Sets a function describing a custom rate for a species.
     This could be useful for modeling external processes not in the

photochem/cython/Atmosphere_pxd.pxd

@@ -3,7 +3,6 @@ cdef extern from "<stdbool.h>":
   pass
 
 # callback signatures
-ctypedef void (*time_dependent_flux_fcn)(double tn, int nw, double *photon_flux)
 ctypedef void (*time_dependent_rate_fcn)(double tn, int nz, double *rate)
 
 # allocate and destroy
@@ -45,6 +44,4 @@ cdef extern void atmosphere_evolve_wrapper(void *ptr, char *filename,
 cdef extern void atmosphere_set_temperature_wrapper(void *ptr, int *nz, double *temperature, 
                                                     double *trop_alt, bool *trop_alt_present, char *err)
 
-cdef extern void atmosphere_set_photon_flux_fcn_wrapper(void *ptr, time_dependent_flux_fcn fcn)
-
 cdef extern void atmosphere_set_rate_fcn_wrapper(void *ptr, char *species_c, time_dependent_rate_fcn fcn, char *err)

photochem/cython/PhotochemVars.pyx

@@ -61,7 +61,27 @@ cdef class PhotochemVars:
       cdef ndarray arr = np.empty(dim1, np.double)
       var_pxd.photochemvars_z_get(&self._ptr, &dim1, <double *>arr.data)
       return arr
-
+
+  property photon_flux_fcn:
+    "A function for altering the photon flux over time"
+    def __set__(self, object fcn):
+      cdef uintptr_t fcn_l
+      cdef var_pxd.time_dependent_flux_fcn fcn_c
+      if fcn is None:
+        fcn_l = 0
+        fcn_c = NULL
+      else:
+        argtypes = (ct.c_double, ct.c_int32, ct.POINTER(ct.c_double))
+        restype = None
+        if not fcn.ctypes.argtypes == argtypes:
+          raise PhotoException("The callback function has the wrong argument types.")
+        if not fcn.ctypes.restype == restype:
+          raise PhotoException("The callback function has the wrong return type.")
+        fcn_l = fcn.address
+        fcn_c = <var_pxd.time_dependent_flux_fcn> fcn_l
+
+      var_pxd.photochemvars_photon_flux_fcn_set(&self._ptr, fcn_c)
+
   property temperature:
     "ndarray[double,dim=1], shape (nz). The temperature of each atmospheric layer (K)"
     def __get__(self):

photochem/cython/PhotochemVars_pxd.pxd

@@ -2,6 +2,9 @@ from libcpp cimport bool
 cdef extern from "<stdbool.h>":
   pass
 
+# callback signatures
+ctypedef void (*time_dependent_flux_fcn)(double tn, int nw, double *photon_flux)
+
 cdef extern void allocate_photochemvars(void *ptr)
 cdef extern void deallocate_photochemvars(void *ptr)
 
@@ -16,6 +19,8 @@ cdef extern void photochemvars_at_photo_equilibrium_get(void *ptr, bool *at_phot
 cdef extern void photochemvars_usol_init_get_size(void *ptr, int *dim1, int *dim2)
 cdef extern void photochemvars_usol_init_get(void *ptr, int *dim1, int *dim2, double *usol_init)
 
+cdef extern void photochemvars_photon_flux_fcn_set(void *ptr, time_dependent_flux_fcn fcn)
+
 cdef extern void photochemvars_temperature_get_size(void *ptr, int *dim1)
 cdef extern void photochemvars_temperature_get(void *ptr, int *dim1, double *temperature)
 

photochem/fortran/Atmosphere_wrapper.f90

@@ -441,21 +441,6 @@ subroutine atmosphere_set_temperature_wrapper(ptr, nz, temperature, &
 
   end subroutine
 
-  subroutine atmosphere_set_photon_flux_fcn_wrapper(ptr, photon_flux_fcn_c) bind(c)
-    use photochem_types, only: time_dependent_flux_fcn
-    type(c_ptr), intent(in) :: ptr
-    type(c_funptr), value, intent(in) :: photon_flux_fcn_c
-
-    procedure(time_dependent_flux_fcn), pointer :: photon_flux_fcn_f
-
-    type(Atmosphere), pointer :: pc
-
-    call c_f_pointer(ptr, pc)
-    call c_f_procpointer(photon_flux_fcn_c, photon_flux_fcn_f)
-    call pc%set_photon_flux_fcn(photon_flux_fcn_f)
-
-  end subroutine
-
   subroutine atmosphere_set_rate_fcn_wrapper(ptr, species_c, fcn_c, err) bind(c)
     use photochem_types, only: time_dependent_rate_fcn
     type(c_ptr), intent(in) :: ptr

photochem/fortran/PhotochemVars_wrapper.f90

@@ -70,6 +70,20 @@ subroutine photochemvars_usol_init_get(ptr, dim1, dim2, usol_init) bind(c)
     call c_f_pointer(ptr, var)
     usol_init = var%usol_init
   end subroutine
+
+  subroutine photochemvars_photon_flux_fcn_set(ptr, photon_flux_fcn_c) bind(c)
+    use photochem_types, only: time_dependent_flux_fcn
+    type(c_ptr), intent(in) :: ptr
+    type(c_funptr), value, intent(in) :: photon_flux_fcn_c
+
+    procedure(time_dependent_flux_fcn), pointer :: photon_flux_fcn_f
+    type(PhotochemVars), pointer :: var
+
+    call c_f_pointer(ptr, var)
+    call c_f_procpointer(photon_flux_fcn_c, photon_flux_fcn_f)
+    var%photon_flux_fcn => photon_flux_fcn_f
+
+  end subroutine
 
   subroutine photochemvars_temperature_get_size(ptr, dim1) bind(c)
     type(c_ptr), intent(in) :: ptr

src/atmosphere/photochem_atmosphere.f90

@@ -40,7 +40,6 @@ module photochem_atmosphere
     procedure :: set_lower_bc
     procedure :: set_upper_bc
     procedure :: set_temperature
-    procedure :: set_photon_flux_fcn
     procedure :: set_rate_fcn
   end type
   interface Atmosphere
@@ -271,14 +270,6 @@ module subroutine set_temperature(self, temperature, trop_alt, err)
       character(:), allocatable, intent(out) :: err
     end subroutine
 
-    !> Sets a function describing a time-dependent photon flux. 
-    !> This is useful for modeling flares.
-    module subroutine set_photon_flux_fcn(self, photon_flux_fcn)
-      use photochem_types, only: time_dependent_flux_fcn
-      class(Atmosphere), target, intent(inout) :: self
-      procedure(time_dependent_flux_fcn), pointer :: photon_flux_fcn
-    end subroutine
-
     !> Sets a function describing a custom rate for a species.
     !> This could be useful for modeling external processes not in the
     !> model.

src/atmosphere/photochem_atmosphere_utils.f90

@@ -605,13 +605,6 @@ module subroutine set_temperature(self, temperature, trop_alt, err)
 
   end subroutine
 
-  module subroutine set_photon_flux_fcn(self, photon_flux_fcn)
-    use photochem_types, only: time_dependent_flux_fcn
-    class(Atmosphere), target, intent(inout) :: self
-    procedure(time_dependent_flux_fcn), pointer :: photon_flux_fcn
-    self%var%photon_flux_fcn => photon_flux_fcn
-  end subroutine
-
   module subroutine set_rate_fcn(self, species, fcn, err)
     use photochem_types, only: time_dependent_rate_fcn
     class(Atmosphere), target, intent(inout) :: self

tests/test.py

@@ -8,34 +8,8 @@ def main():
                     "../templates/ModernEarth/atmosphere_ModernEarth.txt")
 
     pc.initialize_stepper(pc.wrk.usol)
-    tn = 0
-    while tn < 1e17:
-        tn = pc.step()
+    tn = pc.step()
     pc.destroy_stepper()
 
-    con = pc.redox_conservation()
-    print('redox conservation = '+'%.2e'%con)
-    assert con < 1e-4
-
-    con = pc.atom_conservation('C').factor
-    print('C conservation = '+'%.2e'%con)
-    assert con < 1e-6
-
-    con = pc.atom_conservation('S').factor
-    print('S conservation = '+'%.2e'%con)
-    assert con < 1e-6
-
-    con = pc.atom_conservation('H').factor
-    print('H conservation = '+'%.2e'%con)
-    assert con < 1e-6
-
-    con = pc.atom_conservation('O').factor
-    print('O conservation = '+'%.2e'%con)
-    assert con < 1e-6
-
-    con = pc.atom_conservation('Cl').factor
-    print('Cl conservation = '+'%.2e'%con)
-    assert con < 1e-6
-
 if __name__ == "__main__":
     main()