removed manifest. removed photolysis-grid

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "photochem/data"]
-	path = photochem/data
-	url = https://github.com/Nicholaswogan/photochem_clima_data

examples/ModernEarth/settings.yaml

@@ -4,12 +4,6 @@ atmosphere-grid:
   top: 1.0e7 # cm
   number-of-layers: 100
 
-photolysis-grid:
-  regular-grid: true
-  lower-wavelength: 92.5 # nm
-  upper-wavelength: 855.0 # nm
-  number-of-bins: 200
-
 planet:
   planet-mass: 5.972e27 # grams
   planet-radius: 6.371e8 # cm. Radius to bottom of atmosphere-grid
@@ -58,7 +52,7 @@ boundary-conditions:
   lower-boundary: {type: press, press: 360.0}
   upper-boundary: {type: veff, veff: 0.0}
 - name: CH4
-  lower-boundary: {type: flux, flux: 5.0e10}
+  lower-boundary: {type: flux, flux: 1.0e11}
   upper-boundary: {type: veff, veff: 0.0}
 - name: CO
   lower-boundary: {type: press, press: 0.11}

examples/ModernEarth/settings_Atmosphere.yaml

@@ -4,12 +4,6 @@ atmosphere-grid:
   top: 1.0e7 # cm
   number-of-layers: 100
 
-photolysis-grid:
-  regular-grid: true
-  lower-wavelength: 92.5 # nm
-  upper-wavelength: 855.0 # nm
-  number-of-bins: 200
-
 planet:
   background-gas: N2
   surface-pressure: 1.01325
@@ -57,7 +51,7 @@ boundary-conditions:
   lower-boundary: {type: mix, mix: 3.606975e-04}
   upper-boundary: {type: veff, veff: 0.0}
 - name: CH4
-  lower-boundary: {type: flux, flux: 5.0e10}
+  lower-boundary: {type: flux, flux: 9.0e10}
   upper-boundary: {type: veff, veff: 0.0}
 - name: CO
   lower-boundary: {type: mix, mix: 1.102131e-07}

setup.py

@@ -25,7 +25,6 @@
     long_description=long_description,
     long_description_content_type='text/markdown',
     url = "https://github.com/Nicholaswogan/Photochem",
-    include_package_data=True,
     cmake_args=['-DBUILD_PYTHON_PHOTOCHEM=ON',\
                 '-DBUILD_EXECUTABLES=OFF',\
                 '-DBUILD_WITH_OPENMP=ON']

src/input/photochem_input_read.f90

@@ -619,19 +619,6 @@ subroutine unpack_settings(infile, s, dat, var, err)
     endif
     var%nz = s%nz
 
-    !!!!!!!!!!!!!!!!!!!!!!!
-    !!! photolysis-grid !!!
-    !!!!!!!!!!!!!!!!!!!!!!!
-    dat%regular_grid = s%regular_grid
-
-    if (dat%regular_grid) then
-      dat%lower_wavelength = s%lower_wv
-      dat%upper_wavelength = s%upper_wv
-      dat%nw = s%nw
-    else
-      dat%grid_file = s%grid_file
-    endif
-
     !!!!!!!!!!!!!!
     !!! planet !!!
     !!!!!!!!!!!!!!

src/photochem_types.f90

@@ -54,13 +54,6 @@ module photochem_types ! make a giant IO object
     character(:), allocatable :: top
     integer :: nz
 
-    ! photolysis-grid
-    logical :: regular_grid
-    real(dp) :: lower_wv
-    real(dp) :: upper_wv
-    integer :: nw
-    character(:), allocatable :: grid_file
-
     ! planet
     character(:), allocatable :: back_gas_name
     real(dp), allocatable :: P_surf
@@ -366,10 +359,6 @@ subroutine time_dependent_rate_fcn(tn, nz, rate)
     real(dp), allocatable :: particle_radius_file(:,:) !! (np,nzf) cm
 
     ! settings
-    logical :: regular_grid !! True of wavelength grid is evenly spaced
-    real(dp) :: lower_wavelength !! nm
-    real(dp) :: upper_wavelength !! nm
-    character(:), allocatable :: grid_file !! filename of grid file. Only if regular_grid == False
     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

src/photochem_types_create.f90

@@ -74,42 +74,6 @@ function unpack_PhotoSettings(root, filename, err) result(s)
       return
     endif
 
-    !!!!!!!!!!!!!!!!!!!!!!!
-    !!! photolysis-grid !!!
-    !!!!!!!!!!!!!!!!!!!!!!!
-    dict => root%get_dictionary('photolysis-grid',.true.,error = io_err)
-    if (allocated(io_err)) then; err = trim(filename)//trim(io_err%message); return; endif
-    s%regular_grid = dict%get_logical('regular-grid',error = io_err)
-    if (allocated(io_err)) then; err = trim(filename)//trim(io_err%message); return; endif
-
-    if (s%regular_grid) then
-      s%lower_wv = dict%get_real('lower-wavelength',error = io_err)
-      if (allocated(io_err)) then; err = trim(filename)//trim(io_err%message); return; endif
-      s%upper_wv = dict%get_real('upper-wavelength',error = io_err)
-      if (allocated(io_err)) then; err = trim(filename)//trim(io_err%message); return; endif
-      s%nw = dict%get_integer('number-of-bins',error = io_err)
-      if (allocated(io_err)) then; err = trim(filename)//trim(io_err%message); return; endif
-      if (s%nw < 1) then 
-        err = 'Number of photolysis bins must be >= 1 in '//trim(filename)
-        return
-      endif
-      if (s%lower_wv > s%upper_wv) then
-        err = 'lower-wavelength must be smaller than upper-wavelength in '//trim(filename)
-        return
-      endif
-    else
-      s%grid_file = dict%get_string('input-file',error = io_err)
-      if (allocated(io_err)) then; err = trim(filename)//trim(io_err%message); return; endif
-    endif
-    ! make sure photon-scale-factor is not in the photolysis-grid dictionary
-    scalar => dict%get_scalar('photon-scale-factor',required=.false.,error = io_err)
-    if (allocated(io_err)) then; err = trim(filename)//trim(io_err%message); return; endif
-    if (associated(scalar)) then
-      err = '"photon-scale-factor" is no longer specified in the "photolysis-grid" dictionary. '// &
-            'Instead, specify "photon-scale-factor" in the "planet" dictionary.'
-      return
-    endif
-
     !!!!!!!!!!!!!!
     !!! planet !!!
     !!!!!!!!!!!!!!

tests/test_settings1.yaml

@@ -4,12 +4,6 @@ atmosphere-grid:
   top: 1.0e7 # cm
   number-of-layers: 80
 
-photolysis-grid:
-  regular-grid: true
-  lower-wavelength: 92.5 # nm
-  upper-wavelength: 855.0 # nm
-  number-of-bins: 200
-
 planet:
   planet-mass: 5.972e27 # grams
   planet-radius: 6.371e8 # cm. Radius to bottom of atmosphere-grid