During post-processing, only warn when unexpected options found

Options may sometimes be removed, so old output files may include
options that are 'unexpected' by the current version of the code. For
post-processing it is unlikely that this matters, so just print a
warning and then ignore the value of the old option.

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,
@@ -344,15 +347,15 @@ 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"],
         iz0=this_input_dict["iz0"],
        )
 
     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[],

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

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,
                     )

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,

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"

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

moment_kinetics/src/input_structs.jl

@@ -796,15 +796,21 @@ 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)
     options_keys = (String(k) for k ∈ options_keys_symbols)
     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