deleted not needed background gas vars

src/evoatmosphere/photochem_evoatmosphere_init.f90

@@ -37,8 +37,7 @@ module function create_EvoAtmosphere(mechanism_file, settings_file, flux_file, a
     allocate(self%wrk)
 
     self%var%data_dir = data_dir
-    call setup(mechanism_file, s, flux_file, atmosphere_txt, .false., &
-               self%dat, self%var, err)
+    call setup(mechanism_file, s, flux_file, atmosphere_txt, self%dat, self%var, err)
     if (allocated(err)) return 
 
     call self%wrk%init(self%dat%nsp, self%dat%np, self%dat%nq, &

src/evoatmosphere/photochem_evoatmosphere_utils.f90

@@ -250,7 +250,7 @@ module subroutine set_rate_fcn(self, species, fcn, err)
     ind = findloc(self%dat%species_names(1:self%dat%nq), species, 1)
     if (ind == 0) then
       err = 'Species "'//species//'" is not in the list of species, '// &
-            'or is a background or short-lived species.'
+            'or is a short-lived species.'
       return
     endif
 
@@ -607,7 +607,7 @@ subroutine properties_for_new_TOA(self, usol, top_atmos_new, &
                               particle_radius_new, pressure_new, err)
     use photochem_enum, only: DensityBC, PressureBC
     use futils, only: interp
-    use photochem_eqns, only: vertical_grid, molar_weight, press_and_den, gravity
+    use photochem_eqns, only: vertical_grid, press_and_den, gravity
     use photochem_const, only: small_real, k_boltz
     class(EvoAtmosphere), target, intent(inout) :: self
     real(dp), intent(in) :: usol(:,:)

src/input/photochem_input.f90

@@ -24,13 +24,11 @@ module subroutine after_read_setup(dat, var, err)
       character(:), allocatable, intent(out) :: err
     end subroutine
 
-    module subroutine read_all_files(mechanism_file, s, flux_file, atmosphere_txt, back_gas, &
-                              dat, var, err)
+    module subroutine read_all_files(mechanism_file, s, flux_file, atmosphere_txt, dat, var, err)
       character(len=*), intent(in) :: mechanism_file
       type(PhotoSettings), intent(in) :: s
       character(len=*), intent(in) :: flux_file
       character(len=*), intent(in) :: atmosphere_txt
-      logical, intent(in) :: back_gas
       type(PhotochemData), intent(inout) :: dat
       type(PhotochemVars), intent(inout) :: var
       character(:), allocatable, intent(out) :: err
@@ -59,20 +57,17 @@ module subroutine interp2particlexsdata(dat, var, err)
 
 contains
 
-  subroutine setup(mechanism_file, s, flux_file, atmosphere_txt, back_gas, &
-                   dat, var, err)
+  subroutine setup(mechanism_file, s, flux_file, atmosphere_txt, dat, var, err)
 
     character(len=*), intent(in) :: mechanism_file
     type(PhotoSettings), intent(in) :: s
     character(len=*), intent(in) :: flux_file
     character(len=*), intent(in) :: atmosphere_txt
-    logical, intent(in) :: back_gas
     type(PhotochemData), intent(inout) :: dat
     type(PhotochemVars), intent(inout) :: var
     character(:), allocatable, intent(out) :: err
 
-    call read_all_files(mechanism_file, s, flux_file, atmosphere_txt, back_gas, &
-                        dat, var, err)
+    call read_all_files(mechanism_file, s, flux_file, atmosphere_txt, dat, var, err)
     if (allocated(err)) return     
 
     call after_read_setup(dat, var, err)

src/input/photochem_input_after_read.f90

@@ -74,27 +74,12 @@ subroutine interp2atmosfile(dat, var, err)
     endif
     var%edd = 10.0_dp**var%edd
 
-    if (dat%back_gas) then
-      do i = 1,dat%nq
-        call interp(var%nz, dat%nzf, var%z, dat%z_file,&
-                    log10(abs(dat%mix_file(i,:))), var%usol_init(i,:), ierr)
-        if (ierr /= 0) then
-          err = 'Subroutine interp returned an error.'
-          return
-        endif
-      enddo
-      var%usol_init = 10.0_dp**var%usol_init
-
+    if (dat%conserving_init) then
+      call interp2atmosfile_mixconserving(dat, var, err)
+      if (allocated(err)) return
     else
-
-      if (dat%conserving_init) then
-        call interp2atmosfile_mixconserving(dat, var, err)
-        if (allocated(err)) return
-      else
-        call interp2atmosfile_mix(dat, var, err)
-        if (allocated(err)) return
-      endif
-
+      call interp2atmosfile_mix(dat, var, err)
+      if (allocated(err)) return
     endif
 
     if (dat%there_are_particles) then

src/input/photochem_input_read.f90

@@ -3,27 +3,16 @@
 
 contains
 
-  module subroutine read_all_files(mechanism_file, s, flux_file, atmosphere_txt, back_gas, &
-                                   dat, var, err)
+  module subroutine read_all_files(mechanism_file, s, flux_file, atmosphere_txt, dat, var, err)
     character(len=*), intent(in) :: mechanism_file
     type(PhotoSettings), intent(in) :: s
     character(len=*), intent(in) :: flux_file
     character(len=*), intent(in) :: atmosphere_txt
-    logical, intent(in) :: back_gas
     type(PhotochemData), intent(inout) :: dat
     type(PhotochemVars), intent(inout) :: var
     character(:), allocatable, intent(out) :: err
 
     ! stuff dat needs before entering get_photomech
-    dat%back_gas = back_gas
-    if (dat%back_gas) then
-      if (allocated(s%back_gas_name)) then
-        dat%back_gas_name = s%back_gas_name
-      else
-        err = 'A background gas is required but not specified in '//trim(s%filename)
-        return
-      endif
-    endif
     dat%nsl = s%nsl
     dat%SL_names = s%SL_names
 
@@ -97,7 +86,7 @@ subroutine get_rxmechanism(mapping, infile, dat, var, err)
     ! temporary work variables
     character(len=str_len) :: tmpchar
     character(len=str_len) :: tmp
-    character(len=:), allocatable :: rxstring, back_gas_name_tmp
+    character(len=:), allocatable :: rxstring
     integer :: i, ii, j, k, kk, l, ind(1)
     logical :: reverse
     ! all_species causes a small memory leak. Not sure how to free the memory properly
@@ -266,13 +255,7 @@ subroutine get_rxmechanism(mapping, infile, dat, var, err)
       dat%ng = dat%ng + 1
     enddo
 
-    if (dat%back_gas) then
-      dat%nll = dat%ng - dat%nsl - 1 ! minus 1 for background
-      back_gas_name_tmp = dat%back_gas_name
-    else
-      dat%nll = dat%ng - dat%nsl
-      back_gas_name_tmp = "Not a => gas!"
-    endif
+    dat%nll = dat%ng - dat%nsl
 
     dat%ng_1 = dat%npq + 1 ! the long lived gas index
     ! dat%nq is the last ll gas index
@@ -326,8 +309,6 @@ subroutine get_rxmechanism(mapping, infile, dat, var, err)
           if (ind(1) /= 0) then ! short lived species
             j = dat%nq + l 
             l = l + 1
-          elseif (tmpchar == back_gas_name_tmp) then ! background gas
-            j = dat%nsp
           else ! long lived species
             j = kk
             kk = kk + 1
@@ -372,13 +353,6 @@ subroutine get_rxmechanism(mapping, infile, dat, var, err)
       err = 'IOError: One of the short lived species is not in the file '//trim(infile)
       return
     endif
-    if (dat%back_gas) then
-      ind = findloc(dat%species_names,dat%back_gas_name)
-      if (ind(1) == 0) then
-        err = 'IOError: The specified background gas is not in '//trim(infile)
-        return
-      endif
-    endif
     i = check_for_duplicates(dat%species_names)
     if (i /= 0) then
       err = 'Species "'//trim(dat%species_names(i))//'" is a duplicate in '//trim(infile)
@@ -405,7 +379,7 @@ subroutine get_rxmechanism(mapping, infile, dat, var, err)
             err = "Particle "//trim(dat%particle_names(i))// &
                   " can not be made from "//trim(dat%particle_gas_phase(i))// &
                   " because "//trim(dat%particle_gas_phase(i))//" is"// &
-                  " is a particle, short-lived species, or background gas."
+                  " is a particle or is short-lived species."
             return
           else
             dat%particle_gas_phase_ind(i) = ind(1)
@@ -586,7 +560,7 @@ subroutine get_rxmechanism(mapping, infile, dat, var, err)
 
   subroutine unpack_settings(infile, s, dat, var, err)
     use photochem_enum, only: CondensingParticle
-    use photochem_enum, only: VelocityBC, DensityBC, MixingRatioBC, PressureBC
+    use photochem_enum, only: VelocityBC, DensityBC, PressureBC
     use photochem_enum, only: DiffusionLimHydrogenEscape, ZahnleHydrogenEscape, NoHydrogenEscape
     use photochem_types, only: PhotoSettings
     character(len=*), intent(in) :: infile
@@ -622,16 +596,6 @@ subroutine unpack_settings(infile, s, dat, var, err)
     !!!!!!!!!!!!!!
     !!! planet !!!
     !!!!!!!!!!!!!!
-    ! dat%back_gas
-    ! dat%back_gas_name
-    ! already set earlier
-    if (dat%back_gas) then
-      if (.not. allocated(s%P_surf)) then
-        err = 'The settings file does not contain a "surface-pressure"'
-        return
-      endif
-      var%surface_pressure = s%P_surf
-    endif
     dat%planet_mass = s%planet_mass
     dat%planet_radius = s%planet_radius
     var%surface_albedo = s%surface_albedo
@@ -672,13 +636,6 @@ subroutine unpack_settings(infile, s, dat, var, err)
         allocate(dat%H_escape_coeff)
         dat%H_escape_coeff = zahnle_Hescape_coeff(s%H_escape_S1)
 
-        if (dat%back_gas) then
-          if (dat%back_gas_name == "H2") then
-            err = "zahnle hydrogen escape does not work when the background gas is H2."
-            return
-          endif
-        endif
-
       endblock; endif
 
     endif
@@ -770,23 +727,12 @@ subroutine unpack_settings(infile, s, dat, var, err)
     !!!!!!!!!!!!!!!!!!!!!!!!!!!
     !!! boundary-conditions !!!
     !!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-    if (dat%back_gas) then
-      ind = findloc(dat%species_names,trim(dat%back_gas_name))
-      dat%back_gas_ind = ind(1)
-      dat%back_gas_mu = dat%species_mass(ind(1))
-    endif
-
     allocate(var%lowerboundcond(dat%nq))
     allocate(var%lower_vdep(dat%nq))
     allocate(var%lower_flux(dat%nq))
     allocate(var%lower_dist_height(dat%nq))
-    if (dat%back_gas) then
-      allocate(var%lower_fix_mr(dat%nq))
-    else
-      allocate(var%lower_fix_den(dat%nq))
-      allocate(var%lower_fix_press(dat%nq))
-    endif
+    allocate(var%lower_fix_den(dat%nq))
+    allocate(var%lower_fix_press(dat%nq))
     allocate(var%upperboundcond(dat%nq))
     allocate(var%upper_veff(dat%nq))
     allocate(var%upper_flux(dat%nq))
@@ -815,26 +761,15 @@ subroutine unpack_settings(infile, s, dat, var, err)
         ' in settings file is not in the reaction mechanism file.'
         return 
       endif
-      if (dat%back_gas) then
-        if (ind(1) == dat%back_gas_ind) then ! can't be background gas
-          err = "IOError: Species "//trim(s%sp_names(j))// &
-          ' in settings file is the background gas, and can not have boundary conditions.'
-          return
-        endif
-      endif
 
       if (s%sp_types(j) == 'long lived') then
 
         var%lowerboundcond(ind(1)) = s%lbcs(j)%bc_type
         var%lower_vdep(ind(1)) = s%lbcs(j)%vel
         var%lower_flux(ind(1)) = s%lbcs(j)%flux
         var%lower_dist_height(ind(1)) = s%lbcs(j)%height
-        if (dat%back_gas) then
-          var%lower_fix_mr(ind(1)) = s%lbcs(j)%mix
-        else
-          var%lower_fix_den(ind(1)) = s%lbcs(j)%den
-          var%lower_fix_press(ind(1)) = s%lbcs(j)%press
-        endif
+        var%lower_fix_den(ind(1)) = s%lbcs(j)%den
+        var%lower_fix_press(ind(1)) = s%lbcs(j)%press
 
         var%upperboundcond(ind(1)) = s%ubcs(j)%bc_type
         var%upper_veff(ind(1)) = s%ubcs(j)%vel
@@ -849,20 +784,10 @@ subroutine unpack_settings(infile, s, dat, var, err)
     ! Make sure that upper boundary condition for H and H2 are
     ! effusion velocities, if diffusion limited escape
     if (dat%H_escape_type == DiffusionLimHydrogenEscape) then
-      if (dat%back_gas) then
-        if (dat%back_gas_name /= "H2") then
-          if (var%upperboundcond(dat%LH2) /= VelocityBC) then
-            err = "IOError: H2 must have a have a effusion velocity upper boundary"// &
-                  " for diffusion limited hydrogen escape"
-            return
-          endif
-        endif
-      else
-        if (var%upperboundcond(dat%LH2) /= VelocityBC) then
-          err = "IOError: H2 must have a have a effusion velocity upper boundary"// &
-                " for diffusion limited hydrogen escape"
-          return
-        endif
+      if (var%upperboundcond(dat%LH2) /= VelocityBC) then
+        err = "IOError: H2 must have a have a effusion velocity upper boundary"// &
+              " for diffusion limited hydrogen escape"
+        return
       endif
       if (var%upperboundcond(dat%LH) /= VelocityBC) then
         err = "IOError: H must have a have a effusion velocity upper boundary"// &
@@ -883,23 +808,6 @@ subroutine unpack_settings(infile, s, dat, var, err)
       enddo
     endif
 
-    ! make sure bc work for the model
-    if (dat%back_gas) then
-      if (any(var%lowerboundcond == DensityBC)) then
-        err = 'Fixed density boundary conditions are not allowed for class "Atmosphere".'
-        return
-      endif
-      if (any(var%lowerboundcond == PressureBC)) then
-        err = 'Fixed pressure boundary conditions are not allowed for class "Atmosphere".'
-        return
-      endif
-    else
-      if (any(var%lowerboundcond == MixingRatioBC)) then
-        err = 'Fixed mixing ratio boundary conditions are not allowed for class "EvoAtmosphere".'
-        return
-      endif
-    endif
-
     ! check for SL nonlinearities
     call check_sl(dat, err)
     if (allocated(err)) return

src/photochem_enum.f90

@@ -32,7 +32,6 @@ module photochem_enum
   enumerator :: &
     MosesBC = -1, &
     VelocityBC = 0, &
-    MixingRatioBC = 1, &
     FluxBC = 2, &
     VelocityDistributedFluxBC = 3, &
     DensityBC = 4, &

src/photochem_eqns.f90

@@ -221,26 +221,6 @@ pure subroutine press_and_den(nz, T, grav, Psurf, dz, &
 
   end subroutine
 
-  pure subroutine molar_weight(nll, usol_layer, sum_usol_layer, masses, background_mu, mubar_layer)
-    implicit none
-    integer, intent(in) :: nll
-    real(dp), intent(in) :: usol_layer(nll)
-    real(dp), intent(in) :: sum_usol_layer
-    real(dp), intent(in) :: masses(nll)
-    real(dp), intent(in) :: background_mu
-    real(dp), intent(out) :: mubar_layer
-    integer :: j
-    real(dp) :: f_background
-
-    mubar_layer = 0.0_dp
-    do j = 1, nll
-      mubar_layer = mubar_layer + usol_layer(j) * masses(j)
-    enddo
-    f_background = 1.0_dp - sum_usol_layer
-    mubar_layer = mubar_layer + f_background * background_mu
-
-  end subroutine
-
   pure function dynamic_viscosity_air(T) result(eta)
       real(dp), intent(in) :: T
       real(dp) :: eta ! dynamic viscosity [dynes s/cm^2]

src/photochem_types.f90

@@ -55,8 +55,6 @@ module photochem_types ! make a giant IO object
     integer :: nz
 
     ! planet
-    character(:), allocatable :: back_gas_name
-    real(dp), allocatable :: P_surf
     real(dp) :: planet_mass
     real(dp) :: planet_radius
     real(dp) :: surface_albedo
@@ -266,12 +264,12 @@ subroutine time_dependent_rate_fcn(tn, nz, rate)
 
     ! species
     ! Organization is as follows
-    ! [       nsp       ]
-    ! [   nq   + nsl + 1]
-    ! [np + ng + nsl + 1]
+    ! [     nsp     ]
+    ! [   nq   + nsl]
+    ! [np + ng + nsl]
     ! |_______|
     !     |
-    ! Only np + ng = nq evolve through time. nsl are assumed to be in equilibrium. +1 is background gas.
+    ! Only np + ng = nq evolve through time. nsl are assumed to be in equilibrium.
     integer :: nq !! number of gases + particles which evolve over time from integration
     integer :: ng_1 !! index of first gas
     integer :: nll !! number of long-lived gas molecules
@@ -346,10 +344,6 @@ subroutine time_dependent_rate_fcn(tn, nz, rate)
     real(dp), allocatable :: particle_radius_file(:,:) !! (np,nzf) cm
 
     ! settings
-    logical :: back_gas !! True if background gas is used
-    character(:), allocatable :: back_gas_name !! Normally N2, but can be most any gas.
-    real(dp), allocatable :: back_gas_mu !! g/mol
-    integer, allocatable :: back_gas_ind !! index of the background gas
     real(dp) :: planet_mass !! grams
     real(dp) :: planet_radius !! cm
     logical :: fix_water_in_trop !! True if fixing water in troposphere