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Merge pull request #716 from ImperialCollegeLondon/715-extend-path-re…
…solution-in-configuration-files Update config file path resolution
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,278 +1,278 @@ | ||
| [core.data_output_options] | ||
| save_initial_state = true | ||
| out_continuous_file_name = "all_continuous_data.nc" | ||
| out_final_file_name = "final_state.nc" | ||
| out_initial_file_name = "initial_state.nc" | ||
| out_merge_file_name = "vr_full_model_configuration.toml" | ||
| out_path = "/tmp/ve_example/out" | ||
| save_continuous_data = true | ||
| save_final_state = true | ||
| save_initial_state = true | ||
| save_merged_config = true | ||
| out_initial_file_name = "initial_state.nc" | ||
| out_continuous_file_name = "all_continuous_data.nc" | ||
| out_final_file_name = "final_state.nc" | ||
| out_merge_file_name = "vr_full_model_configuration.toml" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_climate_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_climate_data.nc" | ||
| var_name = "air_temperature_ref" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_climate_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_climate_data.nc" | ||
| var_name = "relative_humidity_ref" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_climate_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_climate_data.nc" | ||
| var_name = "atmospheric_pressure_ref" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_climate_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_climate_data.nc" | ||
| var_name = "precipitation" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_climate_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_climate_data.nc" | ||
| var_name = "atmospheric_co2_ref" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_climate_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_climate_data.nc" | ||
| var_name = "mean_annual_temperature" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_climate_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_climate_data.nc" | ||
| var_name = "wind_speed_ref" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_elevation_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_elevation_data.nc" | ||
| var_name = "elevation" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_surface_runoff_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_surface_runoff_data.nc" | ||
| var_name = "surface_runoff" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| var_name = "pH" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| var_name = "bulk_density" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| var_name = "clay_fraction" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| var_name = "soil_c_pool_lmwc" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| var_name = "soil_c_pool_maom" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| var_name = "soil_c_pool_microbe" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| var_name = "soil_c_pool_pom" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| var_name = "soil_c_pool_necromass" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| var_name = "soil_enzyme_pom" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_soil_data.nc" | ||
| var_name = "soil_enzyme_maom" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_litter_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_litter_data.nc" | ||
| var_name = "litter_pool_above_metabolic" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_litter_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_litter_data.nc" | ||
| var_name = "litter_pool_above_structural" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_litter_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_litter_data.nc" | ||
| var_name = "litter_pool_woody" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_litter_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_litter_data.nc" | ||
| var_name = "litter_pool_below_metabolic" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_litter_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_litter_data.nc" | ||
| var_name = "litter_pool_below_structural" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_litter_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_litter_data.nc" | ||
| var_name = "lignin_above_structural" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_litter_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_litter_data.nc" | ||
| var_name = "lignin_woody" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_litter_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_litter_data.nc" | ||
| var_name = "lignin_below_structural" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_plant_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_plant_data.nc" | ||
| var_name = "plant_cohorts_n" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_plant_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_plant_data.nc" | ||
| var_name = "plant_cohorts_pft" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_plant_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_plant_data.nc" | ||
| var_name = "plant_cohorts_cell_id" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_plant_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_plant_data.nc" | ||
| var_name = "plant_cohorts_dbh" | ||
|
|
||
| [[core.data.variable]] | ||
| file = "/private/tmp/ve_example/data/example_plant_data.nc" | ||
| file_path = "/private/tmp/ve_example/data/example_plant_data.nc" | ||
| var_name = "photosynthetic_photon_flux_density" | ||
|
|
||
| [core.grid] | ||
| grid_type = "square" | ||
| cell_area = 8100 | ||
| cell_nx = 9 | ||
| cell_ny = 9 | ||
| grid_type = "square" | ||
| xoff = -45.0 | ||
| yoff = -45.0 | ||
|
|
||
| [core.timing] | ||
| run_length = "2 years" | ||
| start_date = "2013-01-01" | ||
| update_interval = "1 month" | ||
| run_length = "2 years" | ||
|
|
||
| [core.layers] | ||
| above_canopy_height_offset = 2.0 | ||
| canopy_layers = 10 | ||
| soil_layers = [ | ||
| -0.25, | ||
| -1.0, | ||
| -0.25, | ||
| -1.0, | ||
| ] | ||
| canopy_layers = 10 | ||
| above_canopy_height_offset = 2.0 | ||
| surface_layer_height = 0.1 | ||
| subcanopy_layer_height = 1.5 | ||
| surface_layer_height = 0.1 | ||
|
|
||
| [hydrology] | ||
| initial_soil_moisture = 0.5 | ||
| initial_groundwater_saturation = 0.9 | ||
| initial_soil_moisture = 0.5 | ||
|
|
||
| [abiotic_simple] | ||
|
|
||
| [[animal.functional_groups]] | ||
| name = "carnivorous_bird" | ||
| taxa = "bird" | ||
| adult_mass = 1.0 | ||
| birth_mass = 0.1 | ||
| development_status = "adult" | ||
| development_type = "direct" | ||
| diet = "carnivore" | ||
| excretion_type = "uricotelic" | ||
| metabolic_type = "endothermic" | ||
| reproductive_type = "iteroparous" | ||
| development_type = "direct" | ||
| development_status = "adult" | ||
| name = "carnivorous_bird" | ||
| offspring_functional_group = "carnivorous_bird" | ||
| excretion_type = "uricotelic" | ||
| birth_mass = 0.1 | ||
| adult_mass = 1.0 | ||
| reproductive_type = "iteroparous" | ||
| taxa = "bird" | ||
|
|
||
| [[animal.functional_groups]] | ||
| name = "herbivorous_bird" | ||
| taxa = "bird" | ||
| adult_mass = 0.5 | ||
| birth_mass = 0.05 | ||
| development_status = "adult" | ||
| development_type = "direct" | ||
| diet = "herbivore" | ||
| excretion_type = "uricotelic" | ||
| metabolic_type = "endothermic" | ||
| reproductive_type = "iteroparous" | ||
| development_type = "direct" | ||
| development_status = "adult" | ||
| name = "herbivorous_bird" | ||
| offspring_functional_group = "herbivorous_bird" | ||
| excretion_type = "uricotelic" | ||
| birth_mass = 0.05 | ||
| adult_mass = 0.5 | ||
| reproductive_type = "iteroparous" | ||
| taxa = "bird" | ||
|
|
||
| [[animal.functional_groups]] | ||
| name = "carnivorous_mammal" | ||
| taxa = "mammal" | ||
| adult_mass = 40.0 | ||
| birth_mass = 4.0 | ||
| development_status = "adult" | ||
| development_type = "direct" | ||
| diet = "carnivore" | ||
| excretion_type = "ureotelic" | ||
| metabolic_type = "endothermic" | ||
| reproductive_type = "iteroparous" | ||
| development_type = "direct" | ||
| development_status = "adult" | ||
| name = "carnivorous_mammal" | ||
| offspring_functional_group = "carnivorous_mammal" | ||
| excretion_type = "ureotelic" | ||
| birth_mass = 4.0 | ||
| adult_mass = 40.0 | ||
| reproductive_type = "iteroparous" | ||
| taxa = "mammal" | ||
|
|
||
| [[animal.functional_groups]] | ||
| name = "herbivorous_mammal" | ||
| taxa = "mammal" | ||
| adult_mass = 10.0 | ||
| birth_mass = 1.0 | ||
| development_status = "adult" | ||
| development_type = "direct" | ||
| diet = "herbivore" | ||
| excretion_type = "ureotelic" | ||
| metabolic_type = "endothermic" | ||
| reproductive_type = "iteroparous" | ||
| development_type = "direct" | ||
| development_status = "adult" | ||
| name = "herbivorous_mammal" | ||
| offspring_functional_group = "herbivorous_mammal" | ||
| excretion_type = "ureotelic" | ||
| birth_mass = 1.0 | ||
| adult_mass = 10.0 | ||
| reproductive_type = "iteroparous" | ||
| taxa = "mammal" | ||
|
|
||
| [[animal.functional_groups]] | ||
| name = "carnivorous_insect" | ||
| taxa = "insect" | ||
| adult_mass = 0.01 | ||
| birth_mass = 0.001 | ||
| development_status = "adult" | ||
| development_type = "direct" | ||
| diet = "carnivore" | ||
| excretion_type = "uricotelic" | ||
| metabolic_type = "ectothermic" | ||
| reproductive_type = "iteroparous" | ||
| development_type = "direct" | ||
| development_status = "adult" | ||
| name = "carnivorous_insect" | ||
| offspring_functional_group = "carnivorous_insect" | ||
| excretion_type = "uricotelic" | ||
| birth_mass = 0.001 | ||
| adult_mass = 0.01 | ||
| reproductive_type = "iteroparous" | ||
| taxa = "insect" | ||
|
|
||
| [[animal.functional_groups]] | ||
| name = "herbivorous_insect" | ||
| taxa = "insect" | ||
| adult_mass = 0.005 | ||
| birth_mass = 0.0005 | ||
| development_status = "adult" | ||
| development_type = "direct" | ||
| diet = "herbivore" | ||
| excretion_type = "uricotelic" | ||
| metabolic_type = "ectothermic" | ||
| reproductive_type = "semelparous" | ||
| development_type = "direct" | ||
| development_status = "adult" | ||
| name = "herbivorous_insect" | ||
| offspring_functional_group = "herbivorous_insect" | ||
| excretion_type = "uricotelic" | ||
| birth_mass = 0.0005 | ||
| adult_mass = 0.005 | ||
| reproductive_type = "semelparous" | ||
| taxa = "insect" | ||
|
|
||
| [[animal.functional_groups]] | ||
| name = "butterfly" | ||
| taxa = "insect" | ||
| adult_mass = 0.005 | ||
| birth_mass = 0.0005 | ||
| development_status = "adult" | ||
| development_type = "indirect" | ||
| diet = "herbivore" | ||
| excretion_type = "uricotelic" | ||
| metabolic_type = "ectothermic" | ||
| reproductive_type = "semelparous" | ||
| development_type = "indirect" | ||
| development_status = "adult" | ||
| name = "butterfly" | ||
| offspring_functional_group = "caterpillar" | ||
| excretion_type = "uricotelic" | ||
| birth_mass = 0.0005 | ||
| adult_mass = 0.005 | ||
| reproductive_type = "semelparous" | ||
| taxa = "insect" | ||
|
|
||
| [[animal.functional_groups]] | ||
| name = "caterpillar" | ||
| taxa = "insect" | ||
| adult_mass = 0.005 | ||
| birth_mass = 0.0005 | ||
| development_status = "larval" | ||
| development_type = "indirect" | ||
| diet = "herbivore" | ||
| excretion_type = "uricotelic" | ||
| metabolic_type = "ectothermic" | ||
| reproductive_type = "nonreproductive" | ||
| development_type = "indirect" | ||
| development_status = "larval" | ||
| name = "caterpillar" | ||
| offspring_functional_group = "butterfly" | ||
| excretion_type = "uricotelic" | ||
| birth_mass = 0.0005 | ||
| adult_mass = 0.005 | ||
| reproductive_type = "nonreproductive" | ||
| taxa = "insect" | ||
|
|
||
| [plants] | ||
| a_plant_integer = 12 | ||
| ftypes = [ | ||
| { pft_name = "shrub", max_height = 1.0 }, | ||
| { pft_name = "broadleaf", max_height = 50.0 }, | ||
| ] | ||
| {pft_name = "shrub", max_height = 1.0}, | ||
| {pft_name = "broadleaf", max_height = 50.0}, | ||
| ] |
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