diff --git a/makie_post_processing/makie_post_processing/src/setup_defaults.jl b/makie_post_processing/makie_post_processing/src/setup_defaults.jl
index 286cdd4fc..4b34d0bce 100644
--- a/makie_post_processing/makie_post_processing/src/setup_defaults.jl
+++ b/makie_post_processing/makie_post_processing/src/setup_defaults.jl
@@ -100,6 +100,9 @@ end
 function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
                               new_input_dict::AbstractDict{String,Any}, run_info,
                               dfns::Bool)
+    # Error on unexpected options, so that the user can fix them.
+    warn_unexpected = false
+
     # Remove all existing entries from this_input_dict
     clear_Dict!(this_input_dict)
 
@@ -172,7 +175,7 @@ function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
     only_global_options = ("itime_min", "itime_max", "itime_skip", "itime_min_dfns",
                            "itime_max_dfns", "itime_skip_dfns", "handle_errors")
 
-    set_defaults_and_check_top_level!(this_input_dict;
+    set_defaults_and_check_top_level!(this_input_dict, warn_unexpected;
        # Options that only apply at the global level (not per-variable)
        ################################################################
        # Options that provide the defaults for per-variable settings
@@ -231,7 +234,7 @@ function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
                                       !(k ∈ only_global_options))
     for variable_name ∈ tuple(all_moment_variables..., timestep_diagnostic_variables...)
         set_defaults_and_check_section!(
-            this_input_dict, variable_name;
+            this_input_dict, variable_name, warn_unexpected;
             OrderedDict(Symbol(k)=>v for (k,v) ∈ section_defaults)...)
     end
 
@@ -245,7 +248,7 @@ function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
     animate_log_options_2d = Tuple(Symbol(:animate_log_vs_, d2, :_, d1) for (d1, d2) ∈ two_dimension_combinations_no_t)
     for variable_name ∈ all_dfn_variables
         set_defaults_and_check_section!(
-            this_input_dict, variable_name;
+            this_input_dict, variable_name, warn_unexpected;
             check_moments=false,
             (o=>false for o ∈ plot_options_1d if String(o) ∉ keys(section_defaults))...,
             (o=>false for o ∈ plot_log_options_1d if String(o) ∉ keys(section_defaults))...,
@@ -277,7 +280,7 @@ function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
     end
 
     set_defaults_and_check_section!(
-        this_input_dict, "wall_pdf";
+        this_input_dict, "wall_pdf", warn_unexpected;
         plot=false,
         animate=false,
         advection_velocity=false,
@@ -287,7 +290,7 @@ function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
        )
 
     set_defaults_and_check_section!(
-        this_input_dict, "wall_pdf_electron";
+        this_input_dict, "wall_pdf_electron", warn_unexpected;
         plot=false,
         animate=false,
         advection_velocity=false,
@@ -297,7 +300,7 @@ function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
        )
 
     set_defaults_and_check_section!(
-        this_input_dict, "wall_pdf_neutral";
+        this_input_dict, "wall_pdf_neutral", warn_unexpected;
         plot=false,
         animate=false,
         advection_velocity=false,
@@ -307,7 +310,7 @@ function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
        )
 
     set_defaults_and_check_section!(
-        this_input_dict, "constraints";
+        this_input_dict, "constraints", warn_unexpected;
         plot=false,
         animate=false,
         it0=this_input_dict["it0"],
@@ -323,7 +326,7 @@ function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
        )
 
     set_defaults_and_check_section!(
-        this_input_dict, "Chodura_condition";
+        this_input_dict, "Chodura_condition", warn_unexpected;
         plot_vs_t=false,
         plot_vs_r=false,
         plot_vs_r_t=false,
@@ -335,7 +338,7 @@ function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
        )
 
     set_defaults_and_check_section!(
-        this_input_dict, "instability2D";
+        this_input_dict, "instability2D", warn_unexpected;
         plot_1d=false,
         plot_2d=false,
         animate_perturbations=false,
@@ -344,7 +347,7 @@ function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
        )
 
     set_defaults_and_check_section!(
-        this_input_dict, "sound_wave_fit";
+        this_input_dict, "sound_wave_fit", warn_unexpected;
         calculate_frequency=false,
         plot=false,
         ir0=this_input_dict["ir0"],
@@ -352,7 +355,7 @@ function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
        )
 
     set_defaults_and_check_section!(
-        this_input_dict, "manufactured_solns";
+        this_input_dict, "manufactured_solns", warn_unexpected;
         calculate_error_norms=true,
         wall_plots=false,
         (o=>false for o ∈ plot_options_1d)...,
@@ -371,7 +374,7 @@ function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
     sort!(this_input_dict["manufactured_solns"])
 
     set_defaults_and_check_section!(
-        this_input_dict, "timestep_diagnostics";
+        this_input_dict, "timestep_diagnostics", warn_unexpected;
         plot=true,
         animate_CFL=false,
         plot_timestep_residual=false,
@@ -383,7 +386,7 @@ function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
        )
     
     set_defaults_and_check_section!(
-        this_input_dict, "collisionality_plots";
+        this_input_dict, "collisionality_plots", warn_unexpected;
         plot=true,
         plot_dT_dz_vs_z=false,
         animate_dT_dz_vs_z=false,
@@ -405,7 +408,7 @@ function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
        )
        
     set_defaults_and_check_section!(
-        this_input_dict, "timing_data";
+        this_input_dict, "timing_data", warn_unexpected;
         plot=false,
         threshold=1.0e-2,
         include_patterns=String[],
diff --git a/moment_kinetics/src/coordinates.jl b/moment_kinetics/src/coordinates.jl
index 7f71fd12a..e4611fa01 100644
--- a/moment_kinetics/src/coordinates.jl
+++ b/moment_kinetics/src/coordinates.jl
@@ -148,11 +148,13 @@ struct coordinate{T <: AbstractVector{mk_float}, Ti <: AbstractVector{mk_int}, T
 end
 
 """
-    get_coordinate_input(input_dict, name)
+    get_coordinate_input(input_dict, name; ignore_MPI=false,
+                         warn_unexpected::Bool=false)
 
 Read the input for coordinate `name` from `input_dict`, setting defaults, etc.
 """
-function get_coordinate_input(input_dict, name; ignore_MPI=false)
+function get_coordinate_input(input_dict, name; ignore_MPI=false,
+                              warn_unexpected::Bool=false)
     if name == "z"
         default_bc = "wall"
     elseif name == "r"
@@ -163,7 +165,7 @@ function get_coordinate_input(input_dict, name; ignore_MPI=false)
         default_bc = "zero"
     end
     coord_input_dict = set_defaults_and_check_section!(
-        input_dict, name;
+        input_dict, name, warn_unexpected;
         # ngrid is number of grid points per element
         ngrid=1,
         # nelement is the number of elements in total
@@ -223,7 +225,7 @@ function get_coordinate_input(input_dict, name; ignore_MPI=false)
             boundary_parameters_defaults[:epsz] = 0.0
         end
         boundary_parameters_input = set_defaults_and_check_section!(
-            input_dict, "$(name)_boundary_condition_parameters";
+            input_dict, "$(name)_boundary_condition_parameters", warn_unexpected;
             boundary_parameters_defaults...
            )
         boundary_parameters = Dict_to_NamedTuple(boundary_parameters_input)
@@ -256,9 +258,9 @@ When `coord_input` is passed, it should be a `NamedTuple` as generated by
 """
 function define_coordinate end
 
-function define_coordinate(input_dict, name; kwargs...)
+function define_coordinate(input_dict, name, warn_unexpected::Bool=false; kwargs...)
 
-    coord_input = get_coordinate_input(input_dict, name)
+    coord_input = get_coordinate_input(input_dict, name, warn_unexpected=warn_unexpected)
 
     return define_coordinate(coord_input; kwargs...)
 end
diff --git a/moment_kinetics/src/external_sources.jl b/moment_kinetics/src/external_sources.jl
index 00ea31958..a35fc86c3 100644
--- a/moment_kinetics/src/external_sources.jl
+++ b/moment_kinetics/src/external_sources.jl
@@ -46,10 +46,11 @@ and z-coordinates.
 Returns a NamedTuple `(ion=ion_source_settings, neutral=neutral_source_settings)`
 containing two NamedTuples of settings.
 """
-function setup_external_sources!(input_dict, r, z, electron_physics; ignore_MPI=false)
+function setup_external_sources!(input_dict, r, z, electron_physics,
+                                 warn_unexpected::Bool; ignore_MPI=false)
     function get_settings_ions(source_index, active_flag)
         input = set_defaults_and_check_section!(
-                     input_dict, "ion_source_$source_index";
+                     input_dict, "ion_source_$source_index", warn_unexpected;
                      active=active_flag,
                      source_strength=1.0,
                      source_n=1.0,
@@ -229,7 +230,7 @@ function setup_external_sources!(input_dict, r, z, electron_physics; ignore_MPI=
 
     function get_settings_neutrals(source_index, active_flag)
         input = set_defaults_and_check_section!(
-                     input_dict, "neutral_source_$source_index";
+                     input_dict, "neutral_source_$source_index", warn_unexpected;
                      active=active_flag,
                      source_strength=1.0,
                      source_n=1.0,
@@ -393,7 +394,7 @@ function setup_external_sources!(input_dict, r, z, electron_physics; ignore_MPI=
         # electrons. `source_T` can be set independently, and when using
         # `source_type="energy"`, the `source_strength` could also be set.
         input = set_defaults_and_check_section!(
-                     input_dict, "electron_source_$i";
+                     input_dict, "electron_source_$i", warn_unexpected;
                      source_strength=ion_settings.source_strength,
                      source_T=ion_settings.source_T,
                     )
diff --git a/moment_kinetics/src/file_io.jl b/moment_kinetics/src/file_io.jl
index a2d8eaddf..e1ac98012 100644
--- a/moment_kinetics/src/file_io.jl
+++ b/moment_kinetics/src/file_io.jl
@@ -347,9 +347,10 @@ end
 """
 Read the settings for I/O
 """
-function setup_io_input(input_dict, timestepping_section; ignore_MPI=false)
+function setup_io_input(input_dict, timestepping_section, warn_unexpected::Bool;
+                        ignore_MPI=false)
     io_settings = set_defaults_and_check_section!(
-        input_dict, "output";
+        input_dict, "output", warn_unexpected;
         run_name="",
         base_directory="runs",
         ascii_output=false,
diff --git a/moment_kinetics/src/fokker_planck.jl b/moment_kinetics/src/fokker_planck.jl
index e6e717bf5..2507be3c5 100644
--- a/moment_kinetics/src/fokker_planck.jl
+++ b/moment_kinetics/src/fokker_planck.jl
@@ -84,26 +84,27 @@ Structure the namelist as follows.
     nuii = 1.0
     frequency_option = "manual"
 """
-function setup_fkpl_collisions_input(toml_input::AbstractDict)
-    reference_params = setup_reference_parameters(toml_input)
+function setup_fkpl_collisions_input(toml_input::AbstractDict, warn_unexpected::Bool)
+    reference_params = setup_reference_parameters(toml_input, warn_unexpected)
     # get reference collision frequency (note factor of 1/2 due to definition choices)
     nuii_fkpl_default = 0.5*get_reference_collision_frequency_ii(reference_params)
     # read the input toml and specify a sensible default
-    input_section = set_defaults_and_check_section!(toml_input, "fokker_planck_collisions",
-       # begin default inputs (as kwargs)
-       use_fokker_planck = false,
-       nuii = -1.0,
-       frequency_option = "reference_parameters",
-       self_collisions = true,
-       use_conserving_corrections = true,
-       boundary_data_option = direct_integration,
-       slowing_down_test = false,
-       sd_density = 1.0,
-       sd_temp = 0.01,
-       sd_q = 1.0,
-       sd_mi = 0.25,
-       sd_me = 0.25/1836.0,
-       Zi = 1.0)
+    input_section = set_defaults_and_check_section!(
+        toml_input, "fokker_planck_collisions", warn_unexpected;
+        # begin default inputs (as kwargs)
+        use_fokker_planck = false,
+        nuii = -1.0,
+        frequency_option = "reference_parameters",
+        self_collisions = true,
+        use_conserving_corrections = true,
+        boundary_data_option = direct_integration,
+        slowing_down_test = false,
+        sd_density = 1.0,
+        sd_temp = 0.01,
+        sd_q = 1.0,
+        sd_mi = 0.25,
+        sd_me = 0.25/1836.0,
+        Zi = 1.0)
     # ensure that the collision frequency is consistent with the input option
     frequency_option = input_section["frequency_option"]
     if frequency_option == "reference_parameters"
diff --git a/moment_kinetics/src/geo.jl b/moment_kinetics/src/geo.jl
index 933598a65..64a122c6d 100644
--- a/moment_kinetics/src/geo.jl
+++ b/moment_kinetics/src/geo.jl
@@ -83,12 +83,13 @@ DeltaB = 0.0
 option = ""
 
 """
-function setup_geometry_input(toml_input::AbstractDict)
+function setup_geometry_input(toml_input::AbstractDict, warn_unexpected::Bool)
 
-    reference_params = setup_reference_parameters(toml_input)
+    reference_params = setup_reference_parameters(toml_input, warn_unexpected)
     reference_rhostar = get_default_rhostar(reference_params)
     # read the input toml and specify a sensible default
-    input_section = set_defaults_and_check_section!(toml_input, "geometry",
+    input_section = set_defaults_and_check_section!(
+        toml_input, "geometry", warn_unexpected;
         # begin default inputs (as kwargs)
         # rhostar ion (ref)
         rhostar = reference_rhostar, #used to premultiply ExB drift terms
diff --git a/moment_kinetics/src/input_structs.jl b/moment_kinetics/src/input_structs.jl
index 84707eb0f..1fc5317c8 100644
--- a/moment_kinetics/src/input_structs.jl
+++ b/moment_kinetics/src/input_structs.jl
@@ -796,7 +796,8 @@ are not already present.
 
 Ignores any sections, as these will be checked separately.
 """
-function set_defaults_and_check_top_level!(options::OptionsDict; kwargs...)
+function set_defaults_and_check_top_level!(options::OptionsDict, warn_unexpected::Bool;
+                                           kwargs...)
     # Check for any unexpected values in the options - all options that are set should be
     # present in the kwargs of this function call
     options_keys_symbols = keys(kwargs)
@@ -804,7 +805,12 @@ function set_defaults_and_check_top_level!(options::OptionsDict; kwargs...)
     for (key, value) in options
         # Ignore any ssections when checking
         if !(isa(value, AbstractDict) || key ∈ options_keys)
-            error("Unexpected option '$key=$value' in top-level options")
+            if warn_unexpected
+                println("Unexpected option '$key=$value' in top-level options")
+                pop!(options, key)
+            else
+                error("Unexpected option '$key=$value' in top-level options")
+            end
         end
     end
 
@@ -821,7 +827,7 @@ function set_defaults_and_check_top_level!(options::OptionsDict; kwargs...)
 end
 
 function _get_section_and_check_option_names(options::OptionsDict, section_name,
-                                             section_keys)
+                                             section_keys, warn_unexpected::Bool)
 
     if !(section_name ∈ keys(options))
         # If section is not present, create it
@@ -844,7 +850,14 @@ function _get_section_and_check_option_names(options::OptionsDict, section_name,
         end
     end
     if length(unexpected_options) > 0
-        error("Unexpected options $(join(("$k=$(section[k])" for k ∈ unexpected_options), ", ", ", and ")) in section '$section_name'")
+        if warn_unexpected
+            println("Unexpected options $(join(("$k=$(section[k])" for k ∈ unexpected_options), ", ", ", and ")) in section '$section_name'")
+            for key ∈ unexpected_options
+                pop!(section, key)
+            end
+        else
+            error("Unexpected options $(join(("$k=$(section[k])" for k ∈ unexpected_options), ", ", ", and ")) in section '$section_name'")
+        end
     end
 
     return section
@@ -880,11 +893,13 @@ options (i.e. options that have no default).
 Modifies the options[section_name]::OptionsDict by adding defaults for any values that
 are not already present.
 """
-function set_defaults_and_check_section!(options::OptionsDict, section_name; kwargs...)
+function set_defaults_and_check_section!(options::OptionsDict, section_name::String,
+                                         warn_unexpected::Bool; kwargs...)
 
     section_keys_symbols = keys(kwargs)
     section_keys = (String(k) for k ∈ section_keys_symbols)
-    section = _get_section_and_check_option_names(options, section_name, section_keys)
+    section = _get_section_and_check_option_names(options, section_name, section_keys,
+                                                  warn_unexpected)
 
     # Set default values if a key was not set explicitly
     for (key_sym, default_value) ∈ kwargs
@@ -920,13 +935,15 @@ The name of the section in the options that will be read defaults to the name of
 Returns an instance of `struct_type`.
 """
 function set_defaults_and_check_section!(options::OptionsDict, struct_type::Type,
+                                         warn_unexpected::Bool,
                                          section_name::Union{String,Nothing}=nothing)
 
     if section_name === nothing
         section_name = String(nameof(struct_type))
     end
     section_keys = (String(key) for key ∈ fieldnames(struct_type))
-    section = _get_section_and_check_option_names(options, section_name, section_keys)
+    section = _get_section_and_check_option_names(options, section_name, section_keys,
+                                                  warn_unexpected)
 
     # Pass the settings in `section` as kwargs to the constructor for `struct_type`.
     # `struct_type` is an `@kwdef` struct, so this constructor takes care of the default
diff --git a/moment_kinetics/src/krook_collisions.jl b/moment_kinetics/src/krook_collisions.jl
index 14e209a89..31a5c1c88 100644
--- a/moment_kinetics/src/krook_collisions.jl
+++ b/moment_kinetics/src/krook_collisions.jl
@@ -22,20 +22,21 @@ use_krook = true
 nuii0 = 1.0
 frequency_option = "manual"
 """
-function setup_krook_collisions_input(toml_input::AbstractDict)
-    reference_params = setup_reference_parameters(toml_input)
+function setup_krook_collisions_input(toml_input::AbstractDict, warn_unexpected::Bool)
+    reference_params = setup_reference_parameters(toml_input, warn_unexpected)
     # get reference collision frequency
     nuii_krook_default = get_reference_collision_frequency_ii(reference_params)
     nuee_krook_default = get_reference_collision_frequency_ee(reference_params)
     nuei_krook_default = get_reference_collision_frequency_ei(reference_params)
     # read the input toml and specify a sensible default    
-    input_section = input_section = set_defaults_and_check_section!(toml_input, "krook_collisions",
-       # begin default inputs (as kwargs)
-       use_krook = false,
-       nuii0 = -1.0,
-       nuee0 = -1.0,
-       nuei0 = -1.0,
-       frequency_option = "reference_parameters")
+    input_section = input_section = set_defaults_and_check_section!(
+        toml_input, "krook_collisions", warn_unexpected;
+        # begin default inputs (as kwargs)
+        use_krook = false,
+        nuii0 = -1.0,
+        nuee0 = -1.0,
+        nuei0 = -1.0,
+        frequency_option = "reference_parameters")
        
     # ensure that the collision frequency is consistent with the input option
     frequency_option = input_section["frequency_option"]
diff --git a/moment_kinetics/src/load_data.jl b/moment_kinetics/src/load_data.jl
index 15de297ab..c17844424 100644
--- a/moment_kinetics/src/load_data.jl
+++ b/moment_kinetics/src/load_data.jl
@@ -3522,7 +3522,7 @@ function get_run_info_no_setup(run_dir::Union{AbstractString,Tuple{AbstractStrin
     # and check input to catch errors
     io_input, evolve_moments, t_input, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
         composition, species, collisions, geometry, drive_input, external_source_settings,
-        num_diss_params, manufactured_solns_input = mk_input(input)
+        num_diss_params, manufactured_solns_input = mk_input(input; warn_unexpected=true)
 
     n_ion_species, n_neutral_species = load_species_data(file_final_restart)
     evolve_density, evolve_upar, evolve_ppar = load_mk_options(file_final_restart)
diff --git a/moment_kinetics/src/manufactured_solns.jl b/moment_kinetics/src/manufactured_solns.jl
index 06768c22b..ad5f3b51f 100644
--- a/moment_kinetics/src/manufactured_solns.jl
+++ b/moment_kinetics/src/manufactured_solns.jl
@@ -29,11 +29,11 @@ function __init__()
     end
 end
 
-function setup_manufactured_solutions(input_dict)
+function setup_manufactured_solutions(input_dict, warn_unexpected::Bool)
     use_for_init_is_default = !(("manufactured_solns" ∈ keys(input_dict)) &&
                                 ("use_for_init" ∈ keys(input_dict["manufactured_solns"])))
     manufactured_solns_section = set_defaults_and_check_section!(
-        input_dict, "manufactured_solns";
+        input_dict, "manufactured_solns", warn_unexpected;
         use_for_advance=false,
         use_for_init=false,
         # constant to be used to control Ez divergence in MMS tests
diff --git a/moment_kinetics/src/maxwell_diffusion.jl b/moment_kinetics/src/maxwell_diffusion.jl
index 85d2d4639..a1ce6f393 100644
--- a/moment_kinetics/src/maxwell_diffusion.jl
+++ b/moment_kinetics/src/maxwell_diffusion.jl
@@ -32,20 +32,21 @@ use_maxwell_diffusion = true
 D_ii = 1.0
 diffusion_coefficient_option = "manual"
 """
-function setup_mxwl_diff_collisions_input(toml_input::AbstractDict)
-    reference_params = setup_reference_parameters(toml_input)
+function setup_mxwl_diff_collisions_input(toml_input::AbstractDict, warn_unexpected::Bool)
+    reference_params = setup_reference_parameters(toml_input, warn_unexpected)
     # get reference diffusion coefficient, made up of collision frequency and 
     # thermal speed for now. NOTE THAT THIS CONSTANT PRODUCES ERRORS. DO NOT USE
     D_ii_mxwl_diff_default = get_reference_collision_frequency_ii(reference_params)# *
                              #2 * reference_params.Tref/reference_params.mref
     D_nn_mxwl_diff_default = D_ii_mxwl_diff_default
     # read the input toml and specify a sensible default    
-    input_section = set_defaults_and_check_section!(toml_input, "maxwell_diffusion_collisions",
-       # begin default inputs (as kwargs)
-       use_maxwell_diffusion = false,
-       D_ii = -1.0,
-       D_nn = -1.0,
-       diffusion_coefficient_option = "reference_parameters")
+    input_section = set_defaults_and_check_section!(
+        toml_input, "maxwell_diffusion_collisions", warn_unexpected;
+        # begin default inputs (as kwargs)
+        use_maxwell_diffusion = false,
+        D_ii = -1.0,
+        D_nn = -1.0,
+        diffusion_coefficient_option = "reference_parameters")
        
     # ensure that the diffusion coefficient is consistent with the input option
     diffusion_coefficient_option = input_section["diffusion_coefficient_option"]
diff --git a/moment_kinetics/src/moment_kinetics_input.jl b/moment_kinetics/src/moment_kinetics_input.jl
index cb5c29c01..9f0928df0 100644
--- a/moment_kinetics/src/moment_kinetics_input.jl
+++ b/moment_kinetics/src/moment_kinetics_input.jl
@@ -53,7 +53,8 @@ false for other situations (e.g. when post-processing).
 `ignore_MPI` should be false when actually running a simulation, but defaults to true for
 other situations (e.g. when post-processing).
 """
-function mk_input(input_dict=OptionsDict(); save_inputs_to_txt=false, ignore_MPI=true)
+function mk_input(input_dict=OptionsDict(); save_inputs_to_txt=false, ignore_MPI=true,
+                  warn_unexpected=false)
 
     # Check for input options that used to exist, but do not any more. If these are
     # present, the user probably needs to update their input file.
@@ -90,14 +91,14 @@ function mk_input(input_dict=OptionsDict(); save_inputs_to_txt=false, ignore_MPI
     end
     
     # read composition and species data
-    composition = get_species_input(input_dict)
+    composition = get_species_input(input_dict, warn_unexpected)
     n_ion_species = composition.n_ion_species
     n_neutral_species = composition.n_neutral_species
     
     # if evolve_moments.density = true, evolve density via continuity eqn
     # and g = f/n via modified drift kinetic equation
     evolve_moments_settings = set_defaults_and_check_section!(
-        input_dict, "evolve_moments";
+        input_dict, "evolve_moments", warn_unexpected;
         density=false,
         parallel_flow=false,
         parallel_pressure=false,
@@ -107,40 +108,40 @@ function mk_input(input_dict=OptionsDict(); save_inputs_to_txt=false, ignore_MPI
 
     # Reference parameters that define the conversion between physical quantities and
     # normalised values used in the code.
-    reference_params = setup_reference_parameters(input_dict)
+    reference_params = setup_reference_parameters(input_dict, warn_unexpected)
     
     ## set geometry_input
-    geometry_in = setup_geometry_input(input_dict)
+    geometry_in = setup_geometry_input(input_dict, warn_unexpected)
     
     em_input = set_defaults_and_check_section!(
-        input_dict, em_fields_input, "em_fields"
+        input_dict, em_fields_input, warn_unexpected, "em_fields"
        )
 
-    manufactured_solns_input = setup_manufactured_solutions(input_dict)
+    manufactured_solns_input = setup_manufactured_solutions(input_dict, warn_unexpected)
 
     reactions_input = set_defaults_and_check_section!(
-        input_dict, reactions
+        input_dict, reactions, warn_unexpected
        )
     electron_fluid_collisions_input = set_defaults_and_check_section!(
-        input_dict, electron_fluid_collisions
+        input_dict, electron_fluid_collisions, warn_unexpected
        )
     # set up krook collision inputs
-    krook_input = setup_krook_collisions_input(input_dict)
+    krook_input = setup_krook_collisions_input(input_dict, warn_unexpected)
     # set up Fokker-Planck collision inputs
-    fkpl_input = setup_fkpl_collisions_input(input_dict)
+    fkpl_input = setup_fkpl_collisions_input(input_dict, warn_unexpected)
     # set up maxwell diffusion collision inputs
-    mxwl_diff_input = setup_mxwl_diff_collisions_input(input_dict)
+    mxwl_diff_input = setup_mxwl_diff_collisions_input(input_dict, warn_unexpected)
     # write total collision struct using the structs above, as each setup function 
     # for the collisions outputs itself a struct of the type of collision, which
     # is a substruct of the overall collisions_input struct.
     collisions = collisions_input(reactions_input, electron_fluid_collisions_input,
                                   krook_input, fkpl_input, mxwl_diff_input)
 
-    num_diss_params = setup_numerical_dissipation(input_dict)
+    num_diss_params = setup_numerical_dissipation(input_dict, warn_unexpected)
 
     # parameters related to the time stepping
     timestepping_section = set_defaults_and_check_section!(
-        input_dict, "timestepping";
+        input_dict, "timestepping", warn_unexpected;
         nstep=5,
         dt=0.00025/sqrt(composition.ion[1].initial_temperature),
         CFL_prefactor=-1.0,
@@ -186,7 +187,7 @@ function mk_input(input_dict=OptionsDict(); save_inputs_to_txt=false, ignore_MPI
 
     # parameters related to electron time stepping
     electron_timestepping_section = set_defaults_and_check_section!(
-        input_dict, "electron_timestepping";
+        input_dict, "electron_timestepping", warn_unexpected;
         nstep=50000,
         dt=timestepping_section["dt"] * sqrt(composition.me_over_mi),
         CFL_prefactor=timestepping_section["CFL_prefactor"],
@@ -314,8 +315,10 @@ function mk_input(input_dict=OptionsDict(); save_inputs_to_txt=false, ignore_MPI
     # set up distributed-memory MPI information for z and r coords
     # need grid and MPI information to determine these values 
     # MRH just put dummy values now 
-    r_coord_input = get_coordinate_input(input_dict, "r"; ignore_MPI=ignore_MPI)
-    z_coord_input = get_coordinate_input(input_dict, "z"; ignore_MPI=ignore_MPI)
+    r_coord_input = get_coordinate_input(input_dict, "r"; ignore_MPI=ignore_MPI,
+                                         warn_unexpected=warn_unexpected)
+    z_coord_input = get_coordinate_input(input_dict, "z"; ignore_MPI=ignore_MPI,
+                                         warn_unexpected=warn_unexpected)
     if ignore_MPI
         irank_z = irank_r = 0
         nrank_z = nrank_r = 1
@@ -328,7 +331,8 @@ function mk_input(input_dict=OptionsDict(); save_inputs_to_txt=false, ignore_MPI
                                          r_coord_input.nelement_local)
     end
 
-    io_immutable = setup_io_input(input_dict, timestepping_section; ignore_MPI=ignore_MPI)
+    io_immutable = setup_io_input(input_dict, timestepping_section, warn_unexpected;
+                                  ignore_MPI=ignore_MPI)
 
     # this is the directory where the simulation data will be stored
     timestepping_section["stopfile_name"] = joinpath(io_immutable.output_dir, "stop")
@@ -348,38 +352,40 @@ function mk_input(input_dict=OptionsDict(); save_inputs_to_txt=false, ignore_MPI
                                       run_directory=run_directory, ignore_MPI=ignore_MPI,
                                       irank=irank_r, nrank=nrank_r, comm=comm_sub_r)
     # initialize vpa grid and write grid point locations to file
-    vpa, vpa_spectral = define_coordinate(input_dict, "vpa";
+    vpa, vpa_spectral = define_coordinate(input_dict, "vpa", warn_unexpected;
                                           parallel_io=io_immutable.parallel_io,
                                           run_directory=run_directory,
                                           ignore_MPI=ignore_MPI)
     # initialize vperp grid and write grid point locations to file
-    vperp, vperp_spectral = define_coordinate(input_dict, "vperp";
+    vperp, vperp_spectral = define_coordinate(input_dict, "vperp", warn_unexpected;
                                               parallel_io=io_immutable.parallel_io,
                                               run_directory=run_directory,
                                               ignore_MPI=ignore_MPI)
     # initialize gyrophase grid and write grid point locations to file
-    gyrophase, gyrophase_spectral = define_coordinate(input_dict, "gyrophase";
+    gyrophase, gyrophase_spectral = define_coordinate(input_dict, "gyrophase",
+                                                      warn_unexpected;
                                                       parallel_io=io_immutable.parallel_io,
                                                       run_directory=run_directory,
                                                       ignore_MPI=ignore_MPI)
     # initialize vz grid and write grid point locations to file
-    vz, vz_spectral = define_coordinate(input_dict, "vz";
+    vz, vz_spectral = define_coordinate(input_dict, "vz", warn_unexpected;
                                         parallel_io=io_immutable.parallel_io,
                                         run_directory=run_directory,
                                         ignore_MPI=ignore_MPI)
     # initialize vr grid and write grid point locations to file
-    vr, vr_spectral = define_coordinate(input_dict, "vr";
+    vr, vr_spectral = define_coordinate(input_dict, "vr", warn_unexpected;
                                         parallel_io=io_immutable.parallel_io,
                                         run_directory=run_directory,
                                         ignore_MPI=ignore_MPI)
     # initialize vr grid and write grid point locations to file
-    vzeta, vzeta_spectral = define_coordinate(input_dict, "vzeta";
+    vzeta, vzeta_spectral = define_coordinate(input_dict, "vzeta", warn_unexpected;
                                               parallel_io=io_immutable.parallel_io,
                                               run_directory=run_directory,
                                               ignore_MPI=ignore_MPI)
 
     external_source_settings = setup_external_sources!(input_dict, r, z,
-                                                       composition.electron_physics;
+                                                       composition.electron_physics,
+                                                       warn_unexpected;
                                                        ignore_MPI=ignore_MPI)
 
     geometry = init_magnetic_geometry(geometry_in,z,r)
diff --git a/moment_kinetics/src/nonlinear_solvers.jl b/moment_kinetics/src/nonlinear_solvers.jl
index 361547970..21cf86145 100644
--- a/moment_kinetics/src/nonlinear_solvers.jl
+++ b/moment_kinetics/src/nonlinear_solvers.jl
@@ -88,9 +88,10 @@ for example a preconditioner object for each point in that outer loop.
 """
 function setup_nonlinear_solve(active, input_dict, coords, outer_coords=(); default_rtol=1.0e-5,
                                default_atol=1.0e-12, serial_solve=false,
-                               electron_ppar_pdf_solve=false, preconditioner_type=Val(:none))
+                               electron_ppar_pdf_solve=false,
+                               preconditioner_type=Val(:none), warn_unexpected=false)
     nl_solver_section = set_defaults_and_check_section!(
-        input_dict, "nonlinear_solver";
+        input_dict, "nonlinear_solver", warn_unexpected;
         rtol=default_rtol,
         atol=default_atol,
         nonlinear_max_iterations=20,
diff --git a/moment_kinetics/src/numerical_dissipation.jl b/moment_kinetics/src/numerical_dissipation.jl
index cfa355d42..35c0a40bf 100644
--- a/moment_kinetics/src/numerical_dissipation.jl
+++ b/moment_kinetics/src/numerical_dissipation.jl
@@ -79,15 +79,17 @@ vz_dissipation_coefficient
 
 There will still be the -1.0 default parameters.
 """
-function setup_numerical_dissipation(input_dict)
+function setup_numerical_dissipation(input_dict, warn_unexpected::Bool)
     ion_params = set_defaults_and_check_section!(
-        input_dict, ion_num_diss_params, "ion_numerical_dissipation"
+        input_dict, ion_num_diss_params, warn_unexpected, "ion_numerical_dissipation"
        )
     electron_params = set_defaults_and_check_section!(
-        input_dict, electron_num_diss_params, "electron_numerical_dissipation"
+        input_dict, electron_num_diss_params, warn_unexpected,
+        "electron_numerical_dissipation"
        )
     neutral_params = set_defaults_and_check_section!(
-        input_dict, neutral_num_diss_params, "neutral_numerical_dissipation"
+        input_dict, neutral_num_diss_params, warn_unexpected,
+        "neutral_numerical_dissipation"
        )
 
     return numerical_dissipation_parameters(ion_params, electron_params, neutral_params)
diff --git a/moment_kinetics/src/reference_parameters.jl b/moment_kinetics/src/reference_parameters.jl
index 97b771228..8fc4509cf 100644
--- a/moment_kinetics/src/reference_parameters.jl
+++ b/moment_kinetics/src/reference_parameters.jl
@@ -16,10 +16,10 @@ using ..input_structs
 
 """
 """
-function setup_reference_parameters(input_dict)
+function setup_reference_parameters(input_dict, warn_unexpected::Bool)
     # Get reference parameters for normalizations
     reference_parameter_section = copy(set_defaults_and_check_section!(
-        input_dict, "reference_params";
+        input_dict, "reference_params", warn_unexpected;
         Bref=1.0,
         Lref=10.0,
         Nref=1.0e19,
diff --git a/moment_kinetics/src/species_input.jl b/moment_kinetics/src/species_input.jl
index dae8137ab..1d7df3aa6 100644
--- a/moment_kinetics/src/species_input.jl
+++ b/moment_kinetics/src/species_input.jl
@@ -16,12 +16,13 @@ using ..reference_parameters: setup_reference_parameters
 
 using OrderedCollections: OrderedDict
 
-function get_species_input(toml_input)
+function get_species_input(toml_input, warn_unexpected::Bool)
     
-    reference_params = setup_reference_parameters(toml_input)
+    reference_params = setup_reference_parameters(toml_input, warn_unexpected)
     
     # read general composition parameters
-    composition_section = set_defaults_and_check_section!(toml_input, "composition",
+    composition_section = set_defaults_and_check_section!(
+        toml_input, "composition", warn_unexpected;
         # n_ion_species is the number of evolved ion species
         n_ion_species = 1,
         # n_neutral_species is the number of evolved neutral species
@@ -65,7 +66,8 @@ function get_species_input(toml_input)
     ion_spec_params_list = Array{ion_species_parameters,1}(undef,nspec_ion)
     neutral_spec_params_list = Array{neutral_species_parameters,1}(undef,nspec_neutral)
     for is in 1:nspec_ion
-        spec_section = set_defaults_and_check_section!(toml_input, "ion_species_$is",
+        spec_section = set_defaults_and_check_section!(
+            toml_input, "ion_species_$is", warn_unexpected;
             # [ion_species_1], [ion_species_2], etc 
             # mass of ion species
             mass = 1.0,
@@ -78,14 +80,15 @@ function get_species_input(toml_input)
         
         z_IC = set_defaults_and_check_section!(toml_input,
                                                spatial_initial_condition_input,
-                                               "z_IC_ion_species_$is")
+                                               warn_unexpected, "z_IC_ion_species_$is")
         
         r_IC = set_defaults_and_check_section!(toml_input,
                                                spatial_initial_condition_input,
-                                               "r_IC_ion_species_$is")
+                                               warn_unexpected, "r_IC_ion_species_$is")
         
         vpa_IC = set_defaults_and_check_section!(toml_input,
                                                  velocity_initial_condition_input,
+                                                 warn_unexpected,
                                                  "vpa_IC_ion_species_$is")
         
         spec_input = OrderedDict(Symbol(k)=>v for (k,v) in spec_section)
@@ -94,7 +97,8 @@ function get_species_input(toml_input)
                                                             spec_input...)
     end
     for isn in 1:nspec_neutral
-        spec_section = set_defaults_and_check_section!(toml_input, "neutral_species_$isn",
+        spec_section = set_defaults_and_check_section!(
+            toml_input, "neutral_species_$isn", warn_unexpected;
             # [neutral_species_1], [neutral_species_2], etc
             # mass of neutral species
             mass = 1.0,
@@ -105,14 +109,17 @@ function get_species_input(toml_input)
         
         z_IC = set_defaults_and_check_section!(toml_input,
                                                spatial_initial_condition_input,
+                                               warn_unexpected,
                                                "z_IC_neutral_species_$isn")
         
         r_IC = set_defaults_and_check_section!(toml_input,
                                                spatial_initial_condition_input,
+                                               warn_unexpected,
                                                "r_IC_neutral_species_$isn")
         
         vz_IC = set_defaults_and_check_section!(toml_input,
                                                 velocity_initial_condition_input,
+                                                warn_unexpected,
                                                 "vz_IC_neutral_species_$isn")
         
         spec_input = OrderedDict(Symbol(k)=>v for (k,v) in spec_section)
diff --git a/moment_kinetics/test/gyroaverage_tests.jl b/moment_kinetics/test/gyroaverage_tests.jl
index 4f89f46d8..799ce0ad1 100644
--- a/moment_kinetics/test/gyroaverage_tests.jl
+++ b/moment_kinetics/test/gyroaverage_tests.jl
@@ -167,7 +167,7 @@ function gyroaverage_test(absolute_error; rhostar=0.1, pitch=0.5, ngrid=5, kr=2,
         # create test geometry
         option = "constant-helical"
         inputdict = OptionsDict("geometry" => OptionsDict("option" => option, "rhostar" => rhostar, "pitch" => pitch))
-        geometry_in = setup_geometry_input(inputdict)
+        geometry_in = setup_geometry_input(inputdict, true)
         geometry = init_magnetic_geometry(geometry_in,z,r)
         
         # create test composition