remove prints, and changed how planet_radius is set

photochem/cython/EvoAtmosphere.pyx

@@ -385,18 +385,6 @@ cdef class EvoAtmosphere:
     if len(err.strip()) > 0:
       raise PhotoException(err.decode("utf-8").strip())
 
-  def update_planet_mass_radius(self, double planet_mass, double planet_radius):
-    """Updates planet mass and radius. The routine recomputes gravity vs. altitude.
-
-    Parameters
-    ----------
-    planet_mass : float
-        In grams
-    planet_radius : float
-        In cm
-    """
-    ea_pxd.evoatmosphere_update_planet_mass_radius_wrapper(&self._ptr, &planet_mass, &planet_radius)
-
   def regrid_prep_atmosphere(self, ndarray[double, ndim=2] usol, double top_atmos):
     """This subroutine calculates re-grids the model so that the top of the model domain 
     is at `top_atmos` the computes reaction rates, photolysis rates, etc.

photochem/cython/EvoAtmosphere_pxd.pxd

@@ -32,7 +32,6 @@ cdef extern void evoatmosphere_set_press_temp_edd_wrapper(void *ptr, int *P_dim1
                                                       bool *hydro_pressure, bool *hydro_pressure_present, char *err)
 cdef extern void evoatmosphere_update_vertical_grid_wrapper(void *ptr, double *toa_alt, bool *toa_alt_present,
                                                          double *toa_pressure, bool *toa_pressure_present, char *err)
-cdef extern void evoatmosphere_update_planet_mass_radius_wrapper(void *ptr, double *planet_mass, double *planet_radius)
 cdef extern void evoatmosphere_regrid_prep_atmosphere_wrapper(void *ptr, int *nq, int *nz, double *usol, double *top_atmos, char *err)
 
 cdef extern void evoatmosphere_evolve_wrapper(void *ptr, char *filename, 

photochem/cython/PhotochemData.pyx

@@ -82,6 +82,8 @@ cdef class PhotochemData:
       cdef double val
       dat_pxd.photochemdata_planet_radius_get(&self._ptr, &val)
       return val
+    def __set__(self, double val):
+      dat_pxd.photochemdata_planet_radius_set(&self._ptr, &val)
 
   property species_names:
     """List, shape (nsp+2). A list of the species in the model (particles and gases). 

photochem/cython/PhotochemData_pxd.pxd

@@ -16,6 +16,7 @@ cdef extern void photochemdata_nw_get(void *ptr, int *nq)
 cdef extern void photochemdata_planet_mass_get(void *ptr, double *val)
 
 cdef extern void photochemdata_planet_radius_get(void *ptr, double *val)
+cdef extern void photochemdata_planet_radius_set(void *ptr, double *val)
 
 cdef extern void photochemdata_species_names_get_size(void *ptr, int *dim1)
 cdef extern void photochemdata_species_names_get(void *ptr, int *dim1, char* species_names)

photochem/fortran/EvoAtmosphere_wrapper.f90

@@ -334,16 +334,6 @@ subroutine evoatmosphere_update_vertical_grid_wrapper(ptr, TOA_alt, TOA_alt_pres
 
   end subroutine
 
-  subroutine evoatmosphere_update_planet_mass_radius_wrapper(ptr, planet_mass, planet_radius) bind(c)
-    type(c_ptr), intent(in) :: ptr
-    real(c_double), intent(in) :: planet_mass, planet_radius
-    type(EvoAtmosphere), pointer :: pc
-
-    call c_f_pointer(ptr, pc)
-    call pc%update_planet_mass_radius(planet_mass, planet_radius)
-
-  end subroutine
-
   subroutine evoatmosphere_regrid_prep_atmosphere_wrapper(ptr, nq, nz, usol, top_atmos, err) bind(c)
     type(c_ptr), intent(in) :: ptr
     integer(c_int), intent(in) :: nq, nz

photochem/fortran/PhotochemData_wrapper.f90

@@ -92,6 +92,14 @@ subroutine photochemdata_planet_radius_get(ptr, val) bind(c)
     call c_f_pointer(ptr, dat)
     val = dat%planet_radius
   end subroutine
+
+  subroutine photochemdata_planet_radius_set(ptr, val) bind(c)
+    type(c_ptr), intent(in) :: ptr
+    real(c_double), intent(in) :: val
+    type(PhotochemData), pointer :: dat
+    call c_f_pointer(ptr, dat)
+    dat%planet_radius = val
+  end subroutine
 
   subroutine photochemdata_species_names_get_size(ptr, dim1) bind(c)
     type(c_ptr), intent(in) :: ptr

src/evoatmosphere/photochem_evoatmosphere.f90

@@ -64,7 +64,6 @@ function temp_dependent_albedo_fcn(T_surf) result(albedo)
     procedure :: set_temperature
     procedure :: set_press_temp_edd
     procedure :: update_vertical_grid
-    procedure :: update_planet_mass_radius
     procedure :: rebin_update_vertical_grid
     procedure :: regrid_prep_atmosphere
 
@@ -315,12 +314,6 @@ module subroutine update_vertical_grid(self, TOA_alt, TOA_pressure, err)
       character(:), allocatable, intent(out) :: err
     end subroutine
 
-    !> Updates planet mass and radius. The routine recomputes gravity vs. altitude.
-    module subroutine update_planet_mass_radius(self, planet_mass, planet_radius)
-      class(EvoAtmosphere), target, intent(inout) :: self
-      real(dp), intent(in) :: planet_mass, planet_radius
-    end subroutine
-
     ! Both below are needed only for `evolve` routine and probably should not be used most of the time.
 
     module subroutine rebin_update_vertical_grid(self, usol_old, top_atmos, usol_new, err)

src/evoatmosphere/photochem_evoatmosphere_utils.f90

@@ -793,16 +793,6 @@ module subroutine update_vertical_grid(self, TOA_alt, TOA_pressure, err)
 
   end subroutine
 
-  module subroutine update_planet_mass_radius(self, planet_mass, planet_radius)
-    use photochem_eqns, only: gravity
-    class(EvoAtmosphere), target, intent(inout) :: self
-    real(dp), intent(in) :: planet_mass, planet_radius
-    self%dat%planet_mass = planet_mass
-    self%dat%planet_radius = planet_radius
-    call gravity(self%dat%planet_radius, self%dat%planet_mass, &
-                 self%var%nz, self%var%z, self%var%grav)
-  end subroutine
-
   ! Below is mostly stuff needed in `evolve` routine
 
   module subroutine rebin_update_vertical_grid(self, usol_old, top_atmos, usol_new, err)

src/input/photochem_input_after_read.f90

@@ -109,14 +109,6 @@ subroutine interp2atmosfile(dat, var, err)
       var%particle_radius = 10.0_dp**var%particle_radius
     endif
 
-    if (var%z(1) < dat%z_file(1)) then
-      print*,'Warning: vertical grid is being extrapolated below where there is input data.'
-    endif
-
-    if (var%z(var%nz) > dat%z_file(dat%nzf)) then
-      print*,'Warning: vertical grid is being extrapolated above where there is input data.'
-    endif
-
   end subroutine
 
   subroutine interp2atmosfile_mixconserving(dat, var, err)

src/input/photochem_input_read.f90

@@ -2558,14 +2558,12 @@ subroutine read_atmosphere_file(atmosphere_txt, dat, var, err)
     character(:), allocatable, intent(out) :: err
 
     character(len=10000) :: line
-    character(len=:), allocatable :: message
     character(len=s_str_len) :: arr1(1000)
     character(len=s_str_len) :: arr11(1000)
     character(len=s_str_len),allocatable, dimension(:) :: labels
     integer :: ind(1)
     real(dp), allocatable :: temp(:,:)
     integer :: io, i, n, nn, ii
-    logical :: missing
 
     open(4, file=trim(atmosphere_txt),status='old',iostat=io)
     if (io /= 0) then
@@ -2632,24 +2630,14 @@ subroutine read_atmosphere_file(atmosphere_txt, dat, var, err)
     close(4)
 
     ! reads in mixing ratios
-    missing = .false.
     do i=1,dat%nq
       ind = findloc(labels,dat%species_names(i))
       if (ind(1) /= 0) then
         dat%mix_file(i,:) = temp(ind(1),:)
-      else
-        missing = .true.
       endif
     enddo
 
-    if (missing) then
-      message = 'Warning: Did not find initial data for some species in '// &
-                trim(atmosphere_txt)//' . The program will assume initial mixing ratios of 1.0e-40'
-      print*,message
-    endif
-
     if (dat%there_are_particles) then
-      missing = .false.
       do i=1,dat%npq
         ind = findloc(labels,trim(dat%species_names(i))//"_r")
         if (ind(1) /= 0) then
@@ -2658,14 +2646,8 @@ subroutine read_atmosphere_file(atmosphere_txt, dat, var, err)
           ! did not find the data
           ! will set to 0.1 micron
           dat%particle_radius_file(i,:) = 1.0e-5_dp
-          missing = .true.
         endif
       enddo
-
-      if (missing) then
-        print*,'Warning: Did not find particle radii for some species in '//&
-                trim(atmosphere_txt)//' . The program will assume 0.1 micron raddii.'
-      endif
     endif
 
     ! reads in temperature