diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml
index 59a4c7c7cd..13f667fc5b 100644
--- a/.buildkite/pipeline.yml
+++ b/.buildkite/pipeline.yml
@@ -188,6 +188,14 @@ steps:
 
       # AMIP EXPERIMENTS
 
+      # Test default behavior with no config file or job ID provided
+      - label: "AMIP: default"
+        key: "amip_default"
+        command: "julia --color=yes --project=experiments/ClimaEarth/ experiments/ClimaEarth/run_amip.jl"
+        artifact_paths: "experiments/ClimaEarth/output/amip_default/artifacts/*"
+        agents:
+          slurm_mem: 20GB
+
       - label: "AMIP target: albedo from function"
         key: "target_amip_albedo_function"
         command: "julia --color=yes --project=experiments/ClimaEarth/ experiments/ClimaEarth/run_amip.jl --config_file $CONFIG_PATH/amip_albedo_function.yml --job_id target_amip_albedo_function"
diff --git a/config/amip_configs/amip.yml b/config/amip_configs/amip.yml
index 3bfbf92d7e..2648ea5d43 100644
--- a/config/amip_configs/amip.yml
+++ b/config/amip_configs/amip.yml
@@ -3,7 +3,7 @@ albedo_model: "CouplerAlbedo"
 atmos_config_file: "config/longrun_configs/amip_target_diagedmf.yml"
 coupler_toml_file: "toml/amip.toml"
 dt: "120secs"
-dt_cpl: 120
+dt_cpl: "120secs"
 dt_save_state_to_disk: "30days"
 dt_save_to_sol: "30days"
 dz_bottom: 30.0
diff --git a/config/benchmark_configs/amip_diagedmf.yml b/config/benchmark_configs/amip_diagedmf.yml
index e9aff1243d..13535b9b22 100644
--- a/config/benchmark_configs/amip_diagedmf.yml
+++ b/config/benchmark_configs/amip_diagedmf.yml
@@ -2,7 +2,7 @@ FLOAT_TYPE: "Float32"
 atmos_config_file: "config/benchmark_configs/climaatmos_diagedmf.yml"
 atmos_config_repo: "ClimaCoupler"
 dt: "120secs"
-dt_cpl: 120
+dt_cpl: "120secs"
 dt_save_state_to_disk: "Inf"
 dt_save_to_sol: "Inf"
 energy_check: false
diff --git a/config/benchmark_configs/amip_diagedmf_io.yml b/config/benchmark_configs/amip_diagedmf_io.yml
index b776fdaa8a..61040582d0 100644
--- a/config/benchmark_configs/amip_diagedmf_io.yml
+++ b/config/benchmark_configs/amip_diagedmf_io.yml
@@ -2,7 +2,7 @@ FLOAT_TYPE: "Float32"
 atmos_config_file: "config/benchmark_configs/climaatmos_diagedmf_io.yml"
 atmos_config_repo: "ClimaCoupler"
 dt: "120secs"
-dt_cpl: 120
+dt_cpl: "120secs"
 dt_save_state_to_disk: "12hours"
 dt_save_to_sol: "12hours"
 energy_check: false
diff --git a/config/benchmark_configs/climaatmos_diagedmf_io.yml b/config/benchmark_configs/climaatmos_diagedmf_io.yml
index 506cafec76..a9a5cc8a3c 100644
--- a/config/benchmark_configs/climaatmos_diagedmf_io.yml
+++ b/config/benchmark_configs/climaatmos_diagedmf_io.yml
@@ -32,6 +32,6 @@ output_default_diagnostics: false
 prescribe_ozone: true
 aerosol_radiation: true
 prescribed_aerosols: ["CB1", "CB2", "DST01", "OC1", "OC2", "SO4", "SSLT01"]
-diagnostics:
+extra_atmos_diagnostics:
   - short_name: [pfull, rsut, rlut, pr, hus, rv]
     period: 10hours
diff --git a/config/ci_configs/amip_albedo_function.yml b/config/ci_configs/amip_albedo_function.yml
index 8fb7219f7e..bf32083c70 100644
--- a/config/ci_configs/amip_albedo_function.yml
+++ b/config/ci_configs/amip_albedo_function.yml
@@ -1,6 +1,6 @@
 apply_limiter: false
 dt: "150secs"
-dt_cpl: 150
+dt_cpl: "150secs"
 dt_rad: "1hours"
 dt_save_to_sol: "1days"
 dz_bottom: 30
diff --git a/config/ci_configs/amip_albedo_temporal_map.yml b/config/ci_configs/amip_albedo_temporal_map.yml
index 928acb1933..f481bc7763 100644
--- a/config/ci_configs/amip_albedo_temporal_map.yml
+++ b/config/ci_configs/amip_albedo_temporal_map.yml
@@ -1,6 +1,6 @@
 apply_limiter: false
 dt: "150secs"
-dt_cpl: 150
+dt_cpl: "150secs"
 dt_rad: "1hours"
 dt_save_to_sol: "1days"
 dz_bottom: 30
diff --git a/config/ci_configs/amip_albedo_temporal_map_1M.yml b/config/ci_configs/amip_albedo_temporal_map_1M.yml
index 5353a753b9..fc424f4287 100644
--- a/config/ci_configs/amip_albedo_temporal_map_1M.yml
+++ b/config/ci_configs/amip_albedo_temporal_map_1M.yml
@@ -1,6 +1,6 @@
 apply_limiter: false
 dt: "150secs"
-dt_cpl: 150
+dt_cpl: "150secs"
 dt_rad: "1hours"
 dt_save_to_sol: "1days"
 dz_bottom: 30
diff --git a/config/ci_configs/amip_coarse_ft32.yml b/config/ci_configs/amip_coarse_ft32.yml
index b7fa9d1120..283fdd80ea 100644
--- a/config/ci_configs/amip_coarse_ft32.yml
+++ b/config/ci_configs/amip_coarse_ft32.yml
@@ -1,7 +1,5 @@
 FLOAT_TYPE: "Float32"
 apply_limiter: false
-dt: "400secs"
-dt_cpl: 400
 dt_save_to_sol: "100days"
 energy_check: false
 h_elem: 6
diff --git a/config/ci_configs/amip_coarse_ft64_hourly_checkpoints.yml b/config/ci_configs/amip_coarse_ft64_hourly_checkpoints.yml
index 26e1ab41ee..e1f5cd8c6a 100644
--- a/config/ci_configs/amip_coarse_ft64_hourly_checkpoints.yml
+++ b/config/ci_configs/amip_coarse_ft64_hourly_checkpoints.yml
@@ -1,6 +1,4 @@
 apply_limiter: false
-dt: "400secs"
-dt_cpl: 400
 dt_save_to_sol: "1days"
 energy_check: false
 h_elem: 6
diff --git a/config/ci_configs/amip_coarse_ft64_hourly_checkpoints_restart.yml b/config/ci_configs/amip_coarse_ft64_hourly_checkpoints_restart.yml
index 0fc0a6b844..03367c0b21 100644
--- a/config/ci_configs/amip_coarse_ft64_hourly_checkpoints_restart.yml
+++ b/config/ci_configs/amip_coarse_ft64_hourly_checkpoints_restart.yml
@@ -1,6 +1,4 @@
 apply_limiter: false
-dt: "400secs"
-dt_cpl: 400
 dt_save_restart: "10days"
 dt_save_to_sol: "1days"
 energy_check: false
diff --git a/config/ci_configs/amip_coarse_mpi.yml b/config/ci_configs/amip_coarse_mpi.yml
index c5fea07a2e..5894fc1fe4 100644
--- a/config/ci_configs/amip_coarse_mpi.yml
+++ b/config/ci_configs/amip_coarse_mpi.yml
@@ -1,6 +1,4 @@
 apply_limiter: false
-dt: "400secs"
-dt_cpl: 400
 dt_save_to_sol: "1days"
 energy_check: false
 h_elem: 6
diff --git a/config/ci_configs/amip_component_dts.yml b/config/ci_configs/amip_component_dts.yml
index 01725c31bd..ea0c3d5052 100644
--- a/config/ci_configs/amip_component_dts.yml
+++ b/config/ci_configs/amip_component_dts.yml
@@ -3,7 +3,7 @@ dt_atmos: "150secs"
 dt_land: "50secs"
 dt_ocean: "30secs"
 dt_seaice: "75secs"
-dt_cpl: 150
+dt_cpl: "150secs"
 dt_rad: "1hours"
 dt_save_to_sol: "1days"
 dz_bottom: 30
diff --git a/config/ci_configs/amip_default.yml b/config/ci_configs/amip_default.yml
index f88629ea37..9369e9e02a 100644
--- a/config/ci_configs/amip_default.yml
+++ b/config/ci_configs/amip_default.yml
@@ -1,6 +1,6 @@
 apply_limiter: false
 dt: "150secs"
-dt_cpl: 150
+dt_cpl: "150secs"
 dt_rad: "1hours"
 dt_save_to_sol: "1days"
 dz_bottom: 30
diff --git a/config/ci_configs/amip_n1_shortrun.yml b/config/ci_configs/amip_n1_shortrun.yml
index 6595005e04..dc09486662 100644
--- a/config/ci_configs/amip_n1_shortrun.yml
+++ b/config/ci_configs/amip_n1_shortrun.yml
@@ -1,6 +1,6 @@
 apply_limiter: false
 dt: "150secs"
-dt_cpl: 150
+dt_cpl: "150secs"
 dt_rad: "1hours"
 dt_save_to_sol: "1days"
 dz_bottom: 30
diff --git a/config/ci_configs/amip_target_topo_diagedmf_shortrun.yml b/config/ci_configs/amip_target_topo_diagedmf_shortrun.yml
index d01d2025c0..e73477831f 100644
--- a/config/ci_configs/amip_target_topo_diagedmf_shortrun.yml
+++ b/config/ci_configs/amip_target_topo_diagedmf_shortrun.yml
@@ -3,7 +3,7 @@ apply_limiter: false
 atmos_config_file: "config/longrun_configs/longrun_aquaplanet_allsky_diagedmf_0M.yml"
 dt: "100secs"
 dt_cloud_fraction: "1hours"
-dt_cpl: 100
+dt_cpl: "100secs"
 dt_rad: "1hours"
 dt_save_state_to_disk: "1days"
 dt_save_to_sol: "1days"
diff --git a/config/ci_configs/interactive_debug.yml b/config/ci_configs/interactive_debug.yml
deleted file mode 100644
index 70abc041f9..0000000000
--- a/config/ci_configs/interactive_debug.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-apply_limiter: false
-coupler_output_dir: "experiments/ClimaEarth/output"
-dt: "200secs"
-dt_cpl: 200
-dt_save_to_sol: "10days"
-energy_check: true
-evolving_ocean: true
-h_elem: 4
-land_albedo_type: "function"
-mode_name: "slabplanet"
-moist: "equil"
-mono_surface: true
-precip_model: "0M"
-rad: "gray"
-start_date: "20100101"
-surface_setup: "PrescribedSurface"
-t_end: "20days"
-turb_flux_partition: "CombinedStateFluxesMOST"
-vert_diff: "true"
diff --git a/config/ci_configs/slabplanet_albedo_function.yml b/config/ci_configs/slabplanet_albedo_function.yml
index 7b499e1002..8a4c096653 100644
--- a/config/ci_configs/slabplanet_albedo_function.yml
+++ b/config/ci_configs/slabplanet_albedo_function.yml
@@ -1,6 +1,6 @@
 apply_limiter: false
 dt: "200secs"
-dt_cpl: 200
+dt_cpl: "200secs"
 dt_save_to_sol: "3600secs"
 energy_check: true
 h_elem: 4
diff --git a/config/ci_configs/slabplanet_albedo_temporal_map.yml b/config/ci_configs/slabplanet_albedo_temporal_map.yml
index 96ea2d5c43..f7fe507e86 100644
--- a/config/ci_configs/slabplanet_albedo_temporal_map.yml
+++ b/config/ci_configs/slabplanet_albedo_temporal_map.yml
@@ -1,6 +1,6 @@
 apply_limiter: false
 dt: "200secs"
-dt_cpl: 200
+dt_cpl: "200secs"
 dt_save_to_sol: "3600secs"
 energy_check: true
 h_elem: 4
diff --git a/config/ci_configs/slabplanet_atmos_diags.yml b/config/ci_configs/slabplanet_atmos_diags.yml
index 2a6e83e3b9..ecb0efbfac 100644
--- a/config/ci_configs/slabplanet_atmos_diags.yml
+++ b/config/ci_configs/slabplanet_atmos_diags.yml
@@ -1,7 +1,7 @@
 apply_limiter: false
-ci_plots: true
+plot_diagnostics: true
 dt: "200secs"
-dt_cpl: 200
+dt_cpl: "200secs"
 dt_save_to_sol: "9days"
 energy_check: true
 h_elem: 4
@@ -12,7 +12,7 @@ precip_model: "0M"
 rad: "gray"
 t_end: "10days"
 vert_diff: "true"
-diagnostics:
+extra_atmos_diagnostics:
   - short_name: [mse, lr, edt, evu, ts, mass_strf, stab, vt, egr, toa_fluxes_net]
     reduction_time: average
     period: 1days
diff --git a/config/ci_configs/slabplanet_default.yml b/config/ci_configs/slabplanet_default.yml
index 19aea4a20f..3dd0d678c6 100644
--- a/config/ci_configs/slabplanet_default.yml
+++ b/config/ci_configs/slabplanet_default.yml
@@ -1,6 +1,6 @@
 apply_limiter: false
 dt: "200secs"
-dt_cpl: 200
+dt_cpl: "200secs"
 dt_save_to_sol: "9days"
 energy_check: true
 h_elem: 4
@@ -12,6 +12,6 @@ rad: "gray"
 t_end: "10days"
 vert_diff: "true"
 output_default_diagnostics: false
-diagnostics:
+extra_atmos_diagnostics:
  - short_name: [mse, lr, edt, evu, hfes, evspsbl, ts]
    period: 1days
diff --git a/config/ci_configs/slabplanet_dry_norad.yml b/config/ci_configs/slabplanet_dry_norad.yml
index 63ab9b298a..7658748e2f 100644
--- a/config/ci_configs/slabplanet_dry_norad.yml
+++ b/config/ci_configs/slabplanet_dry_norad.yml
@@ -1,7 +1,7 @@
 apply_limiter: false
 conservation_softfail: true
 dt: "200secs"
-dt_cpl: 200
+dt_cpl: "200secs"
 dt_save_to_sol: "9days"
 energy_check: true
 h_elem: 4
diff --git a/config/ci_configs/slabplanet_eisenman.yml b/config/ci_configs/slabplanet_eisenman.yml
index 049a455d20..c277beed05 100644
--- a/config/ci_configs/slabplanet_eisenman.yml
+++ b/config/ci_configs/slabplanet_eisenman.yml
@@ -1,7 +1,7 @@
 apply_limiter: false
 conservation_softfail: true
 dt: "200secs"
-dt_cpl: 200
+dt_cpl: "200secs"
 dt_save_to_sol: "9days"
 energy_check: true
 h_elem: 6
diff --git a/config/ci_configs/slabplanet_ft32.yml b/config/ci_configs/slabplanet_ft32.yml
index 264c95c506..810c70fde7 100644
--- a/config/ci_configs/slabplanet_ft32.yml
+++ b/config/ci_configs/slabplanet_ft32.yml
@@ -1,7 +1,7 @@
 FLOAT_TYPE: "Float32"
 apply_limiter: false
 dt: "200secs"
-dt_cpl: 200
+dt_cpl: "200secs"
 dt_save_to_sol: "9days"
 energy_check: true
 h_elem: 4
diff --git a/config/ci_configs/slabplanet_nonmono.yml b/config/ci_configs/slabplanet_nonmono.yml
index 8cbb9b2a5b..56f522126f 100644
--- a/config/ci_configs/slabplanet_nonmono.yml
+++ b/config/ci_configs/slabplanet_nonmono.yml
@@ -1,6 +1,6 @@
 apply_limiter: false
 dt: "200secs"
-dt_cpl: 200
+dt_cpl: "200secs"
 dt_save_to_sol: "9days"
 energy_check: true
 h_elem: 4
diff --git a/config/ci_configs/slabplanet_partitioned_fluxes.yml b/config/ci_configs/slabplanet_partitioned_fluxes.yml
index 4978872107..c6e8b9cd06 100644
--- a/config/ci_configs/slabplanet_partitioned_fluxes.yml
+++ b/config/ci_configs/slabplanet_partitioned_fluxes.yml
@@ -1,6 +1,6 @@
 apply_limiter: false
 dt: "200secs"
-dt_cpl: 200
+dt_cpl: "200secs"
 dt_save_to_sol: "9days"
 energy_check: true
 h_elem: 4
diff --git a/config/ci_configs/slabplanet_realinsol_rayleigh.yml b/config/ci_configs/slabplanet_realinsol_rayleigh.yml
index 836dca4296..72eb630c54 100644
--- a/config/ci_configs/slabplanet_realinsol_rayleigh.yml
+++ b/config/ci_configs/slabplanet_realinsol_rayleigh.yml
@@ -1,7 +1,7 @@
 apply_limiter: false
 conservation_softfail: true
 dt: "200secs"
-dt_cpl: 3600
+dt_cpl: "3600secs"
 dt_rad: "6hours"
 dt_save_to_sol: "3600secs"
 energy_check: true
diff --git a/config/longrun_configs/amip_target.yml b/config/longrun_configs/amip_target.yml
index 898a0e44e8..2c22691535 100644
--- a/config/longrun_configs/amip_target.yml
+++ b/config/longrun_configs/amip_target.yml
@@ -2,7 +2,7 @@ FLOAT_TYPE: "Float32"
 atmos_config_file: "config/longrun_configs/longrun_aquaplanet_allsky_0M.yml"
 dt: "120secs"
 dt_cloud_fraction: "1hours"
-dt_cpl: 120
+dt_cpl: "120secs"
 dt_rad: "1hours"
 dt_save_state_to_disk: "20days"
 energy_check: false
diff --git a/config/longrun_configs/amip_target_topo.yml b/config/longrun_configs/amip_target_topo.yml
index 5e01bc6632..1081e82788 100644
--- a/config/longrun_configs/amip_target_topo.yml
+++ b/config/longrun_configs/amip_target_topo.yml
@@ -3,7 +3,7 @@ albedo_model: "CouplerAlbedo"
 atmos_config_file: "config/longrun_configs/longrun_aquaplanet_allsky_0M_earth.yml"
 dt: "120secs"
 dt_cloud_fraction: "1hours"
-dt_cpl: 120
+dt_cpl: "120secs"
 dt_rad: "1hours"
 dt_save_state_to_disk: "20days"
 energy_check: false
diff --git a/config/longrun_configs/amip_target_topo_diagedmf_cpu.yml b/config/longrun_configs/amip_target_topo_diagedmf_cpu.yml
index f8c827515a..bca89d6cfa 100644
--- a/config/longrun_configs/amip_target_topo_diagedmf_cpu.yml
+++ b/config/longrun_configs/amip_target_topo_diagedmf_cpu.yml
@@ -3,7 +3,7 @@ albedo_model: "CouplerAlbedo"
 atmos_config_file: "config/longrun_configs/longrun_aquaplanet_allsky_diagedmf_0M.yml"
 dt: "120secs"
 dt_cloud_fraction: "1hours"
-dt_cpl: 120
+dt_cpl: "120secs"
 dt_rad: "1hours"
 dt_save_state_to_disk: "20days"
 energy_check: false
diff --git a/config/longrun_configs/amip_target_topo_diagedmf_gpu.yml b/config/longrun_configs/amip_target_topo_diagedmf_gpu.yml
index cdf0b8f8c8..439fe0ebbc 100644
--- a/config/longrun_configs/amip_target_topo_diagedmf_gpu.yml
+++ b/config/longrun_configs/amip_target_topo_diagedmf_gpu.yml
@@ -3,7 +3,7 @@ albedo_model: "CouplerAlbedo"
 atmos_config_file: "config/longrun_configs/longrun_aquaplanet_allsky_diagedmf_0M.yml"
 dt: "120secs"
 dt_cloud_fraction: "1hours"
-dt_cpl: 120
+dt_cpl: "120secs"
 dt_rad: "1hours"
 dt_save_state_to_disk: "20days"
 energy_check: false
diff --git a/config/longrun_configs/longrun_amip_dyamond.yml b/config/longrun_configs/longrun_amip_dyamond.yml
index b23c0f2216..68cd8e940e 100644
--- a/config/longrun_configs/longrun_amip_dyamond.yml
+++ b/config/longrun_configs/longrun_amip_dyamond.yml
@@ -1,6 +1,6 @@
 atmos_config_file: "config/longrun_configs/longrun_aquaplanet_dyamond.yml"
 dt: "30secs"
-dt_cpl: 30
+dt_cpl: "30secs"
 dt_save_state_to_disk: "0.5days"
 dt_save_to_sol: "0.5days"
 energy_check: false
diff --git a/config/longrun_configs/slabplanet_aqua_atmos_sf_couple.yml b/config/longrun_configs/slabplanet_aqua_atmos_sf_couple.yml
index 31d0f5d9cb..7493bbd6db 100644
--- a/config/longrun_configs/slabplanet_aqua_atmos_sf_couple.yml
+++ b/config/longrun_configs/slabplanet_aqua_atmos_sf_couple.yml
@@ -1,6 +1,6 @@
 conservation_softfail: true
 dt: "200secs"
-dt_cpl: 200
+dt_cpl: "200secs"
 dt_save_to_sol: "10days"
 energy_check: true
 evolving_ocean: false
diff --git a/config/longrun_configs/slabplanet_aqua_atmos_sf_nocouple.yml b/config/longrun_configs/slabplanet_aqua_atmos_sf_nocouple.yml
index 4bec7a7b2a..764274d669 100644
--- a/config/longrun_configs/slabplanet_aqua_atmos_sf_nocouple.yml
+++ b/config/longrun_configs/slabplanet_aqua_atmos_sf_nocouple.yml
@@ -1,6 +1,6 @@
 conservation_softfail: true
 dt: "200secs"
-dt_cpl: 1728000
+dt_cpl: "1728000secs"
 dt_save_to_sol: "10days"
 energy_check: true
 evolving_ocean: false
diff --git a/config/longrun_configs/slabplanet_aqua_coupler_sf.yml b/config/longrun_configs/slabplanet_aqua_coupler_sf.yml
index 2ce52bb35f..ae5bcf64cf 100644
--- a/config/longrun_configs/slabplanet_aqua_coupler_sf.yml
+++ b/config/longrun_configs/slabplanet_aqua_coupler_sf.yml
@@ -1,6 +1,6 @@
 conservation_softfail: true
 dt: "200secs"
-dt_cpl: 200
+dt_cpl: "200secs"
 dt_save_to_sol: "10days"
 energy_check: true
 evolving_ocean: false
diff --git a/config/longrun_configs/slabplanet_aqua_coupler_sf_evolve_ocn.yml b/config/longrun_configs/slabplanet_aqua_coupler_sf_evolve_ocn.yml
index a94fd257ba..4aca82c82f 100644
--- a/config/longrun_configs/slabplanet_aqua_coupler_sf_evolve_ocn.yml
+++ b/config/longrun_configs/slabplanet_aqua_coupler_sf_evolve_ocn.yml
@@ -1,5 +1,5 @@
 dt: "200secs"
-dt_cpl: 200
+dt_cpl: "200secs"
 dt_save_to_sol: "10days"
 energy_check: true
 evolving_ocean: true
diff --git a/config/longrun_configs/slabplanet_aqua_target.yml b/config/longrun_configs/slabplanet_aqua_target.yml
index 3598204e93..59eb173088 100644
--- a/config/longrun_configs/slabplanet_aqua_target.yml
+++ b/config/longrun_configs/slabplanet_aqua_target.yml
@@ -1,7 +1,7 @@
 atmos_config_file: "config/longrun_configs/longrun_aquaplanet_allsky_0M.yml"
 dt: "120secs"
 dt_cloud_fraction: "1hours"
-dt_cpl: 120
+dt_cpl: "120secs"
 dt_rad: "1hours"
 dt_save_state_to_disk: "20days"
 dt_save_to_sol: "10days"
diff --git a/config/longrun_configs/slabplanet_aqua_target_evolve_ocn.yml b/config/longrun_configs/slabplanet_aqua_target_evolve_ocn.yml
index 2e7394dfb0..62a9bbcee4 100644
--- a/config/longrun_configs/slabplanet_aqua_target_evolve_ocn.yml
+++ b/config/longrun_configs/slabplanet_aqua_target_evolve_ocn.yml
@@ -1,7 +1,7 @@
 atmos_config_file: "config/longrun_configs/longrun_aquaplanet_allsky_0M.yml"
 dt: "120secs"
 dt_cloud_fraction: "1hours"
-dt_cpl: 120
+dt_cpl: "120secs"
 dt_rad: "1hours"
 dt_save_state_to_disk: "20days"
 dt_save_to_sol: "10days"
diff --git a/config/longrun_configs/slabplanet_aqua_target_nocouple.yml b/config/longrun_configs/slabplanet_aqua_target_nocouple.yml
index 46e658604f..4caa587aca 100644
--- a/config/longrun_configs/slabplanet_aqua_target_nocouple.yml
+++ b/config/longrun_configs/slabplanet_aqua_target_nocouple.yml
@@ -1,7 +1,7 @@
 atmos_config_file: "config/longrun_configs/longrun_aquaplanet_allsky_0M.yml"
 dt: "120secs"
 dt_cloud_fraction: "1hours"
-dt_cpl: 10368000
+dt_cpl: "10368000secs"
 dt_rad: "1hours"
 dt_save_state_to_disk: "20days"
 dt_save_to_sol: "10days"
diff --git a/config/longrun_configs/slabplanet_coupler_sf_evolve_ocn.yml b/config/longrun_configs/slabplanet_coupler_sf_evolve_ocn.yml
index 501b5071a9..a8aafa2cec 100644
--- a/config/longrun_configs/slabplanet_coupler_sf_evolve_ocn.yml
+++ b/config/longrun_configs/slabplanet_coupler_sf_evolve_ocn.yml
@@ -1,5 +1,5 @@
 dt: "200secs"
-dt_cpl: 200
+dt_cpl: "200secs"
 dt_save_to_sol: "10days"
 energy_check: true
 evolving_ocean: true
diff --git a/config/longrun_configs/slabplanet_target.yml b/config/longrun_configs/slabplanet_target.yml
index fb428e0fed..dee938f45d 100644
--- a/config/longrun_configs/slabplanet_target.yml
+++ b/config/longrun_configs/slabplanet_target.yml
@@ -1,7 +1,7 @@
 atmos_config_file: "config/longrun_configs/longrun_aquaplanet_allsky_0M.yml"
 dt: "120secs"
 dt_cloud_fraction: "1hours"
-dt_cpl: 120
+dt_cpl: "120secs"
 dt_rad: "1hours"
 dt_save_state_to_disk: "20days"
 dt_save_to_sol: "10days"
diff --git a/config/longrun_configs/slabplanet_target_evolve_ocn.yml b/config/longrun_configs/slabplanet_target_evolve_ocn.yml
index bcf8f4cf3e..bdb88b729e 100644
--- a/config/longrun_configs/slabplanet_target_evolve_ocn.yml
+++ b/config/longrun_configs/slabplanet_target_evolve_ocn.yml
@@ -1,7 +1,7 @@
 atmos_config_file: "config/longrun_configs/longrun_aquaplanet_allsky_0M.yml"
 dt: "120secs"
 dt_cloud_fraction: "1hours"
-dt_cpl: 120
+dt_cpl: "120secs"
 dt_rad: "1hours"
 dt_save_state_to_disk: "20days"
 dt_save_to_sol: "10days"
diff --git a/config/longrun_configs/slabplanet_terra.yml b/config/longrun_configs/slabplanet_terra.yml
index 49036dd264..9db3573a9b 100644
--- a/config/longrun_configs/slabplanet_terra.yml
+++ b/config/longrun_configs/slabplanet_terra.yml
@@ -1,6 +1,6 @@
 conservation_softfail: true
 dt: "200secs"
-dt_cpl: 200
+dt_cpl: "200secs"
 dt_save_to_sol: "10days"
 energy_check: true
 h_elem: 4
diff --git a/config/nightly_configs/amip_coarse.yml b/config/nightly_configs/amip_coarse.yml
index 8dd3910a0c..e15d9e24ae 100644
--- a/config/nightly_configs/amip_coarse.yml
+++ b/config/nightly_configs/amip_coarse.yml
@@ -3,7 +3,7 @@ albedo_model: "CouplerAlbedo"
 atmos_config_file: "config/longrun_configs/amip_target_diagedmf.yml"
 coupler_toml_file: "toml/amip.toml"
 dt: "240secs"
-dt_cpl: 240
+dt_cpl: "240secs"
 dt_save_state_to_disk: "30days"
 dt_save_to_sol: "30days"
 dz_bottom: 100.0
diff --git a/config/nightly_configs/amip_coarse_random.yml b/config/nightly_configs/amip_coarse_random.yml
index 5259572ea3..2a7f772d27 100644
--- a/config/nightly_configs/amip_coarse_random.yml
+++ b/config/nightly_configs/amip_coarse_random.yml
@@ -3,7 +3,7 @@ albedo_model: "CouplerAlbedo"
 atmos_config_file: "config/longrun_configs/amip_target_diagedmf.yml"
 coupler_toml_file: "toml/amip.toml"
 dt: "240secs"
-dt_cpl: 240
+dt_cpl: "240secs"
 dt_save_state_to_disk: "30days"
 dt_save_to_sol: "30days"
 dz_bottom: 100.0
diff --git a/experiments/ClimaEarth/cli_options.jl b/experiments/ClimaEarth/cli_options.jl
index ed0e63cc75..1c3f0e6647 100644
--- a/experiments/ClimaEarth/cli_options.jl
+++ b/experiments/ClimaEarth/cli_options.jl
@@ -2,107 +2,138 @@ import ArgParse
 function argparse_settings()
     s = ArgParse.ArgParseSettings()
     ArgParse.@add_arg_table! s begin
-        # ClimaCoupler flags
-        "--dt_cpl"
-        help = " Coupling time step in seconds"
-        arg_type = Int
-        default = 400
-        "--dt_atmos"
-        help = " Atmos simulation time step"
-        arg_type = String
-        "--dt_land"
-        help = " Land simulation time step"
-        arg_type = String
-        "--dt_ocean"
-        help = " Ocean simulation time step"
+        ### ClimaCoupler flags
+        # Simulation-identifying information
+        "--config_file"
+        help = "A yaml file used to set the configuration of the coupled model [\"config/ci_configs/amip_default.yml\" (default)]"
         arg_type = String
-        "--dt_seaice"
-        help = " Sea Ice simulation time step"
+        default = "config/ci_configs/amip_default.yml"
+        "--job_id"
+        help = "A unique identifier for this run, defaults to the config file name"
         arg_type = String
-        "--energy_check"
-        help = "Boolean flag indicating whether to check energy conservation"
-        arg_type = Bool
-        default = false
-        "--ci_plots"
-        help = "Boolean flag indicating whether to make CI plots"
-        arg_type = Bool
-        default = false
-        "--conservation_softfail"
-        help = "Boolean flag indicating whether to soft fail on conservation errors"
+        default = nothing
+        "--print_config_dict"
+        help = "Boolean flag indicating whether to print the final configuration dictionary [`true` (default), `false`]"
         arg_type = Bool
-        default = false
+        default = true
         "--mode_name"
         help = "Mode of coupled simulation. [`amip` (default), `slabplanet`, `slabplanet_aqua`, `slabplanet_terra`, `slabplanet_eisenman`]"
         arg_type = String
         default = "amip"
-        "--mono_surface"
-        help = "Boolean flag indicating whether (1st order) monotone and conservative remapping is applied."
+        "--coupler_toml_file"
+        help = "An optional toml file used to overwrite the default model parameters."
+        default = nothing
+        # Computational simulation setup information
+        "--unique_seed"
+        help = "Boolean flag indicating whether to set the random number seed to a unique value [`false` (default), `true`]"
         arg_type = Bool
         default = false
-        "--turb_flux_partition"
-        help = "Method to partition turbulent fluxes. [`PartitionedStateFluxes`, `CombinedStateFluxesMOST` (default)]"
+        "--FLOAT_TYPE"
+        help = "Floating point precision  [`Float64` (default), `Float32`]"
         arg_type = String
-        default = "CombinedStateFluxesMOST"
+        default = "Float64"
+        "--device"
+        help = "Device type to use [\"auto\" (default), \"CPUSingleThreaded\", \"CPUMultiThreaded\", \"CUDADevice\"]"
+        arg_type = String
+        default = "auto"
+        # Time information
+        "--t_end"
+        help = "End time of the simulation [\"800secs\"; allowed formats: \"Nsecs\", \"Nmins\", \"Nhours\", \"Ndays\", \"Inf\"]"
+        arg_type = String
+        default = "800secs"
+        "--t_start"
+        help = "Start time of the simulation [\"0secs\" (default); allowed formats: \"Nsecs\", \"Nmins\", \"Nhours\", \"Ndays\", \"Inf\"]"
+        arg_type = String
+        default = "0secs"
+        "--start_date"
+        help = "Start date of the simulation, in format \"YYYYMMDD\" [\"20100101\" (default)]"
+        arg_type = String
+        default = "20000101"
+        "--dt_cpl"
+        help = "Coupling time step in seconds [400 (default); allowed formats: \"Nsecs\", \"Nmins\", \"Nhours\", \"Ndays\", \"Inf\"]"
+        arg_type = String
+        default = "400secs"
+        "--dt"
+        help = "Component model time step [allowed formats: \"Nsecs\", \"Nmins\", \"Nhours\", \"Ndays\", \"Inf\"]"
+        arg_type = String
+        default = "400secs"
+        "--dt_atmos"
+        help = "Atmos simulation time step (alternative to `dt`; no default) [allowed formats: \"Nsecs\", \"Nmins\", \"Nhours\", \"Ndays\", \"Inf\"]"
+        arg_type = String
+        "--dt_land"
+        help = "Land simulation time step (alternative to `dt`; no default) [allowed formats: \"Nsecs\", \"Nmins\", \"Nhours\", \"Ndays\", \"Inf\"]"
+        arg_type = String
+        "--dt_ocean"
+        help = "Ocean simulation time step (alternative to `dt`; no default) [allowed formats: \"Nsecs\", \"Nmins\", \"Nhours\", \"Ndays\", \"Inf\"]"
+        arg_type = String
+        "--dt_seaice"
+        help = "Sea ice simulation time step (alternative to `dt`; no default) [allowed formats: \"Nsecs\", \"Nmins\", \"Nhours\", \"Ndays\", \"Inf\"]"
+        arg_type = String
+        "--dt_save_to_sol"
+        help = "Time interval for saving output [\"10days\" (default); allowed formats: \"Nsecs\", \"Nmins\", \"Nhours\", \"Ndays\", \"Inf\"]"
+        arg_type = String
+        default = "10days"
+        # Checkpointing information
         "--hourly_checkpoint"
-        help = "Boolean flag indicating whether to checkpoint at intervals of 1 hour or multiple hours"
+        help = "Boolean flag indicating whether to checkpoint at multiple-hourly intervals [false (default), true]"
         arg_type = Bool
         default = false
         "--hourly_checkpoint_dt"
-        help = "Time interval for hourly checkpointing in hours (20 days by default)"
+        help = "Time interval for hourly checkpointing in hours [480 (default)]"
         arg_type = Int
         default = 480
-        "--coupler_output_dir"
-        help = "Directory to save output files. Note that TempestRemap fails if interactive and paths are too long."
-        arg_type = String
-        default = "experiments/ClimaEarth/output"
+        # Restart information
         "--restart_dir"
         help = "Directory containing restart files"
         arg_type = String
-        default = "unspecified"
+        default = nothing
         "--restart_t"
-        help = "Restart time"
+        help = "Integer time to use at `t_start` for restarted simulation [0 (default)]"
         arg_type = Int
         default = 0
-        "--config_file"
-        help = "A yaml file used to set the configuration of the coupled model"
-        arg_type = String
-        "--job_id"
-        help = "A unique identifier for this run"
-        arg_type = String
-        default = nothing
-        "--print_config_dict"
-        help = "Boolean flag indicating whether to print the final configuration dictionary"
+        # Diagnostics information
+        "--use_coupler_diagnostics"
+        help = "Boolean flag indicating whether to compute and output coupler diagnostics [`true` (default), `false`]"
         arg_type = Bool
         default = true
-        "--FLOAT_TYPE"
-        help = "Floating point precision  [`Float64` (default), `Float32`]"
-        arg_type = String
-        default = "Float64"
-        "--coupler_toml_file"
-        help = "A toml file used to overwrite the model parameters. If nothing is specified, the default parameters are used."
+        # Physical simulation information
         "--evolving_ocean"
-        help = "Boolean flag indicating whether to use a dynamic slab ocean model or constant surface temperatures"
+        help = "Boolean flag indicating whether to use a dynamic slab ocean model, as opposed to constant surface temperatures [`true` (default), `false`]"
         arg_type = Bool
         default = true
-        "--device"
-        help = "Device type to use [`auto` (default) `CPUSingleThreaded`, `CPUMultiThreaded`, `CUDADevice`]"
+        "--mono_surface"
+        help = "Boolean flag indicating whether (1st order) monotone and conservative remapping is applied. [`false` (default), `true`]"
+        arg_type = Bool
+        default = false
+        "--turb_flux_partition"
+        help = "Method to partition turbulent fluxes. [`PartitionedStateFluxes`, `CombinedStateFluxesMOST` (default)]"
         arg_type = String
-        default = "auto"
-        "--use_coupler_diagnostics"
-        help = "Boolean flag indicating whether to compute and output coupler diagnostics [`true` (default), `false`]"
+        default = "CombinedStateFluxesMOST"
+        # Conservation information
+        "--energy_check"
+        help = "Boolean flag indicating whether to check energy conservation [`false` (default), `true`]"
         arg_type = Bool
-        default = true
-        "--unique_seed"
-        help = "Boolean flag indicating whether to set the random number seed to a unique value [`false` (default), `true`]"
+        default = false
+        "--conservation_softfail"
+        help = "Boolean flag indicating whether to soft fail on conservation errors [`false` (default), `true`]"
+        arg_type = Bool
+        default = false
+        # Output information
+        "--coupler_output_dir"
+        help = "Directory to save output files. Note that TempestRemap fails if interactive and paths are too long. [\"experiments/ClimaEarth/output\" (default)]"
+        arg_type = String
+        default = "experiments/ClimaEarth/output"
+        "--plot_diagnostics"
+        help = "Boolean flag indicating whether to make plot diagnostics [`false` (default), `true`]"
         arg_type = Bool
         default = false
         # ClimaAtmos specific
         "--surface_setup"
-        help = "Triggers ClimaAtmos into the coupled mode [`PrescribedSurface` (default)]" # retained here for standalone Atmos benchmarks
+        help = "Triggers ClimaAtmos into the coupled mode [`PrescribedSurface` (default), `DefaultMoninObukhov`]" # retained here for standalone Atmos benchmarks
         arg_type = String
         default = "PrescribedSurface"
         "--atmos_config_file"
-        help = "A yaml file used to set the atmospheric model configuration. If nothing is specified, the default configuration is used."
+        help = "An optional YAML file used to overwrite the default model parameters."
         "--albedo_model"
         help = "Type of albedo model. [`ConstantAlbedo`, `RegressionFunctionAlbedo`, `CouplerAlbedo` (default)]"
         arg_type = String
@@ -111,15 +142,19 @@ function argparse_settings()
         help = "The repository containing the ClimaAtmos configuration file to use [`ClimaAtmos` (default), `ClimaCoupler`]"
         arg_type = String
         default = "ClimaAtmos"
-        # ClimaLand specific
-        "--land_albedo_type"
-        help = "Access land surface albedo information from data file. [`map_static` (default), `function`, `map_temporal`]"
-        arg_type = String
-        default = "map_static" # to be replaced by land config file, when available
+        "--extra_atmos_diagnostics"
+        help = "List of dictionaries containing information about additional atmosphere diagnostics to output [nothing (default)]"
+        arg_type = Vector{Dict{Any, Any}}
+        default = []
+        ### ClimaLand specific
         "--land_domain_type"
         help = "Type of land domain. [`sphere` (default), `single_column`]"
         arg_type = String
         default = "sphere"
+        "--land_albedo_type"
+        help = "Access land surface albedo information from data file. [`map_static` (default), `function`, `map_temporal`]"
+        arg_type = String
+        default = "map_static" # to be replaced by land config file, when available
         "--land_temperature_anomaly"
         help = "Type of temperature anomaly for bucket model. [`amip`, `aquaplanet` (default)]"
         arg_type = String
diff --git a/experiments/ClimaEarth/components/atmosphere/climaatmos.jl b/experiments/ClimaEarth/components/atmosphere/climaatmos.jl
index 6e60e90daf..cad9f7ec4c 100644
--- a/experiments/ClimaEarth/components/atmosphere/climaatmos.jl
+++ b/experiments/ClimaEarth/components/atmosphere/climaatmos.jl
@@ -296,10 +296,22 @@ FluxCalculator.get_surface_params(sim::ClimaAtmosSimulation) = CAP.surface_fluxe
     get_atmos_config_dict(coupler_dict::Dict, job_id::String)
 
 Returns the specified atmospheric configuration (`atmos_config`) overwitten by arguments
-in the coupler dictionary (`config_dict`). The returned `atmos_config` dictionary will then be passed to CA.AtmosConfig().
-The `atmos_config_repo` flag allows us to
-use a configuration specified within the ClimaCoupler repo, which is useful for direct
+in the coupler dictionary (`config_dict`).
+The returned `atmos_config` dictionary will then be used to set up the atmosphere simulation.
+
+The `atmos_config_repo` flag allows us to use a configuration specified within
+either the ClimaCoupler or ClimaAtmos repos, which is useful for direct
 coupled/atmos-only comparisons.
+
+In this function, parameters are overwritten in a specific order, from lowest to highest priority:
+    1. Default atmos config
+    2. Provided atmos config file (if any)
+    3. TOML parameter file
+    5. Output directory and timestep are set explicitly based on the coupler config
+
+The TOML parameter file to use is chosen using the following priority:
+If a coupler TOML file is provided, it is used. Otherwise we use an atmos TOML
+file if it's provided. If neither is provided, we use a default coupler TOML file.
 """
 function get_atmos_config_dict(coupler_dict::Dict, job_id::String)
     atmos_config_file = coupler_dict["atmos_config_file"]
@@ -344,23 +356,24 @@ function get_atmos_config_dict(coupler_dict::Dict, job_id::String)
         atmos_config = merge(atmos_config, Dict("toml" => [toml_file]))
     end
 
-    # specify atmos output directory to be inside the coupler output directory
+    # Specify atmos output directory to be inside the coupler output directory
     atmos_output_dir = joinpath(coupler_dict["coupler_output_dir"], job_id, "clima_atmos")
+    atmos_config["output_dir"] = atmos_output_dir
+
+    # Access extra atmosphere diagnostics from coupler so we can rename for atmos code
+    atmos_config["diagnostics"] = coupler_dict["extra_atmos_diagnostics"]
 
-    # merge configs
-    # (if there are common keys, the last dictionary in the `merge` arguments takes precedence)
     # The Atmos `get_simulation` function expects the atmos config to contains its timestep size
     # in the `dt` field. If there is a `dt_atmos` field in coupler_dict, we add it to the atmos config as `dt`
     dt_atmos = haskey(coupler_dict, "dt_atmos") ? coupler_dict["dt_atmos"] : coupler_dict["dt"]
-    atmos_config = merge(atmos_config, Dict("output_dir" => atmos_output_dir, "dt" => dt_atmos))
-    coupler_config = merge(atmos_config, coupler_dict)
+    atmos_config["dt"] = dt_atmos
 
     # set restart file to the initial file saved in this location if it is not nothing
     # TODO this is hardcoded and should be fixed once we have a better restart system
     if !isnothing(atmos_config["restart_file"])
         atmos_config["restart_file"] = replace(atmos_config["restart_file"], "active" => "0000")
     end
-    return atmos_config, coupler_config
+    return atmos_config
 end
 
 
diff --git a/experiments/ClimaEarth/run_amip.jl b/experiments/ClimaEarth/run_amip.jl
index 0265ea0a0d..eb9b6f4a16 100644
--- a/experiments/ClimaEarth/run_amip.jl
+++ b/experiments/ClimaEarth/run_amip.jl
@@ -38,7 +38,6 @@ We then specify the input data file names. If these are not already downloaded,
 
 ## standard packages
 import Dates
-import YAML
 import DelimitedFiles
 
 # ## ClimaESM packages
@@ -86,133 +85,58 @@ dictionary and the simulation-specific configuration dictionary, which allows th
 We can additionally pass the configuration dictionary to the component model initializers, which will then override the default settings of the component models.
 =#
 
-## coupler simulation default configuration
 include("cli_options.jl")
-parsed_args = parse_commandline(argparse_settings())
-
-## modify parsed args for fast testing from REPL #hide
-if isinteractive()
-    parsed_args["config_file"] =
-        isnothing(parsed_args["config_file"]) ? joinpath(pkg_dir, "config/ci_configs/interactive_debug.yml") :
-        parsed_args["config_file"]
-    parsed_args["job_id"] = "interactive_debug"
-end
-
-## the unique job id should be passed in via the command line
-job_id = parsed_args["job_id"]
-@assert !isnothing(job_id) "job_id must be passed in via the command line"
-
-## read in config dictionary from file, overriding the coupler defaults in `parsed_args`
-config_dict = YAML.load_file(parsed_args["config_file"])
-config_dict = merge(parsed_args, config_dict)
+include("user_io/arg_parsing.jl")
+config_dict = get_coupler_config()
+
+# Select the correct timestep for each component model based on which are available
+parse_component_dts!(config_dict)
+# Add extra diagnostics if specified
+add_extra_diagnostics!(config_dict)
+
+(;
+    job_id,
+    mode_name,
+    random_seed,
+    FT,
+    comms_ctx,
+    t_end,
+    t_start,
+    date0,
+    date,
+    Δt_cpl,
+    component_dt_dict,
+    saveat,
+    hourly_checkpoint,
+    hourly_checkpoint_dt,
+    restart_dir,
+    restart_t,
+    use_coupler_diagnostics,
+    use_land_diagnostics,
+    calendar_dt,
+    evolving_ocean,
+    mono_surface,
+    turb_flux_partition,
+    land_domain_type,
+    land_albedo_type,
+    land_temperature_anomaly,
+    energy_check,
+    conservation_softfail,
+    output_dir_root,
+    plot_diagnostics,
+) = get_coupler_args(config_dict)
 
-comms_ctx = Utilities.get_comms_context(config_dict)
+## get component model dictionaries (if applicable)
+## Note this step must come after parsing the coupler config dictionary, since
+##  some parameters are passed from the coupler config to the component model configs
+atmos_config_dict = get_atmos_config_dict(config_dict, job_id)
+(; dt_rad, output_default_diagnostics) = get_atmos_args(atmos_config_dict)
 
 ## set unique random seed if desired, otherwise use default
-random_seed = config_dict["unique_seed"] ? time_ns() : 1234
 Random.seed!(random_seed)
 @info "Random seed set to $(random_seed)"
 
-## set up diagnostics before retrieving atmos config
-mode_name = config_dict["mode_name"]
-use_coupler_diagnostics = config_dict["use_coupler_diagnostics"]
-t_end = Float64(Utilities.time_to_seconds(config_dict["t_end"]))
-t_start = 0.0
-
-function get_period(t_start, t_end)
-    sim_duration = t_end - t_start
-    secs_per_day = 86400
-    if sim_duration >= 90 * secs_per_day
-        # if duration >= 90 days, take monthly means
-        period = "1months"
-        calendar_dt = Dates.Month(1)
-    elseif sim_duration >= 30 * secs_per_day
-        # if duration >= 30 days, take means over 10 days
-        period = "10days"
-        calendar_dt = Dates.Day(10)
-    elseif sim_duration >= secs_per_day
-        # if duration >= 1 day, take daily means
-        period = "1days"
-        calendar_dt = Dates.Day(1)
-    else
-        # if duration < 1 day, take hourly means
-        period = "1hours"
-        calendar_dt = Dates.Hour(1)
-    end
-    return (period, calendar_dt)
-end
-
-if mode_name == "amip" && use_coupler_diagnostics
-    @info "Using default AMIP diagnostics"
-    (period, calendar_dt) = get_period(t_start, t_end)
-
-    !haskey(config_dict, "diagnostics") && (config_dict["diagnostics"] = Vector{Dict{Any, Any}}())
-    push!(
-        config_dict["diagnostics"],
-        Dict("short_name" => ["toa_fluxes_net"], "reduction_time" => "average", "period" => period),
-    )
-end
-
-
-## read in some parsed command line arguments, required by this script
-energy_check = config_dict["energy_check"]
-const FT = config_dict["FLOAT_TYPE"] == "Float64" ? Float64 : Float32
-land_sim_name = "bucket"
-t_end = Float64(Utilities.time_to_seconds(config_dict["t_end"]))
-t_start = 0.0
 tspan = (t_start, t_end)
-Δt_cpl = Float64(config_dict["dt_cpl"])
-component_dt_names = ["dt_atmos", "dt_land", "dt_ocean", "dt_seaice"]
-component_dt_dict = Dict{String, Float64}()
-# check if all component dt's are specified
-if all(key -> !isnothing(config_dict[key]), component_dt_names)
-    # when all component dt's are specified, ignore the dt field
-    if haskey(config_dict, "dt")
-        @warn "Removing dt in favor of individual component dt's"
-        delete!(config_dict, "dt")
-    end
-    for key in component_dt_names
-        component_dt = Float64(Utilities.time_to_seconds(config_dict[key]))
-        @assert Δt_cpl % component_dt == 0.0 "Coupler dt must be divisible by all component dt's\n dt_cpl = $Δt_cpl\n $key = $component_dt"
-        component_dt_dict[key] = component_dt
-    end
-else
-    # when not all component dt's are specified, use the dt field
-    @assert haskey(config_dict, "dt") "dt or (dt_atmos, dt_land, dt_ocean, and dt_seaice) must be specified"
-    for key in component_dt_names
-        if !isnothing(config_dict[key])
-            @warn "Removing $key from config in favor of dt because not all component dt's are specified"
-        end
-        delete!(config_dict, key)
-        component_dt_dict[key] = Float64(Utilities.time_to_seconds(config_dict["dt"]))
-    end
-end
-## get component model dictionaries (if applicable)
-atmos_config_dict, config_dict = get_atmos_config_dict(config_dict, job_id)
-atmos_config_object = CA.AtmosConfig(atmos_config_dict)
-
-saveat = Float64(Utilities.time_to_seconds(config_dict["dt_save_to_sol"]))
-date0 = date = Dates.DateTime(config_dict["start_date"], Dates.dateformat"yyyymmdd")
-mono_surface = config_dict["mono_surface"]
-hourly_checkpoint = config_dict["hourly_checkpoint"]
-hourly_checkpoint_dt = config_dict["hourly_checkpoint_dt"]
-restart_dir = config_dict["restart_dir"]
-restart_t = Int(config_dict["restart_t"])
-evolving_ocean = config_dict["evolving_ocean"]
-dt_rad = config_dict["dt_rad"]
-use_land_diagnostics = config_dict["use_land_diagnostics"]
-
-#=
-## Setup Communication Context
-We set up communication context for CPU single thread/CPU with MPI/GPU. If no device is passed to `ClimaComms.context()`
-then `ClimaComms` automatically selects the device from which this code is called.
-=#
-
-
-## make sure we don't use animations for GPU runs
-if comms_ctx.device isa ClimaComms.CUDADevice
-    config_dict["anim"] = false
-end
 
 #=
 ### I/O Directory Setup
@@ -221,14 +145,11 @@ the plots (from postprocessing and the conservation checks) of the simulation wi
 temporary files will be saved.
 =#
 
-COUPLER_OUTPUT_DIR = joinpath(config_dict["coupler_output_dir"], job_id)
+COUPLER_OUTPUT_DIR = joinpath(output_dir_root, job_id)
 dir_paths = Utilities.setup_output_dirs(output_dir = COUPLER_OUTPUT_DIR, comms_ctx = comms_ctx)
 @info "Coupler output directory $(dir_paths.output)"
 @info "Coupler artifacts directory $(dir_paths.artifacts)"
 
-@info(dir_paths.output)
-config_dict["print_config_dict"] && @info(config_dict)
-
 #=
 ## Data File Paths
 =#
@@ -264,7 +185,7 @@ This uses the `ClimaAtmos.jl` model, with parameterization options specified in
 Utilities.show_memory_usage()
 
 ## init atmos model component
-atmos_sim = atmos_init(atmos_config_object);
+atmos_sim = atmos_init(CA.AtmosConfig(atmos_config_dict));
 # Get surface elevation from `atmos` coordinate field
 surface_elevation = CC.Fields.level(CC.Fields.coordinate_field(atmos_sim.integrator.u.f).z, CC.Utilities.half)
 Utilities.show_memory_usage()
@@ -329,9 +250,9 @@ if mode_name == "amip"
     land_sim = bucket_init(
         FT,
         tspan,
-        config_dict["land_domain_type"],
-        config_dict["land_albedo_type"],
-        config_dict["land_temperature_anomaly"],
+        land_domain_type,
+        land_albedo_type,
+        land_temperature_anomaly,
         dir_paths;
         dt = component_dt_dict["dt_land"],
         space = boundary_space,
@@ -427,9 +348,9 @@ elseif mode_name in ("slabplanet", "slabplanet_aqua", "slabplanet_terra")
     land_sim = bucket_init(
         FT,
         tspan,
-        config_dict["land_domain_type"],
-        config_dict["land_albedo_type"],
-        config_dict["land_temperature_anomaly"],
+        land_domain_type,
+        land_albedo_type,
+        land_temperature_anomaly,
         dir_paths;
         dt = component_dt_dict["dt_land"],
         space = boundary_space,
@@ -477,9 +398,9 @@ elseif mode_name == "slabplanet_eisenman"
     land_sim = bucket_init(
         FT,
         tspan,
-        config_dict["land_domain_type"],
-        config_dict["land_albedo_type"],
-        config_dict["land_temperature_anomaly"],
+        land_domain_type,
+        land_albedo_type,
+        land_temperature_anomaly,
         dir_paths;
         dt = component_dt_dict["dt_land"],
         space = boundary_space,
@@ -622,9 +543,9 @@ callbacks =
 Decide on the type of turbulent flux partition, partitioned or combined (see `FluxCalculator` documentation for more details).
 =#
 turbulent_fluxes = nothing
-if config_dict["turb_flux_partition"] == "PartitionedStateFluxes"
+if turb_flux_partition == "PartitionedStateFluxes"
     turbulent_fluxes = FluxCalculator.PartitionedStateFluxes()
-elseif config_dict["turb_flux_partition"] == "CombinedStateFluxesMOST"
+elseif turb_flux_partition == "CombinedStateFluxesMOST"
     turbulent_fluxes = FluxCalculator.CombinedStateFluxesMOST()
 else
     error("turb_flux_partition must be either PartitionedStateFluxes or CombinedStateFluxesMOST")
@@ -673,7 +594,7 @@ If a restart directory is specified and contains output files from the `checkpoi
 is specified in the `config_dict` dictionary. The `restart_t` field specifies the time step at which the restart is performed.
 =#
 
-if restart_dir !== "unspecified"
+if !isnothing(restart_dir)
     for sim in cs.model_sims
         if Checkpointer.get_model_prog_state(sim) !== nothing
             Checkpointer.restart_model_state!(sim, comms_ctx, restart_t; input_dir = restart_dir)
@@ -891,7 +812,7 @@ end
 #=
 ## Postprocessing
 All postprocessing is performed using the root process only, if applicable.
-Our postprocessing consists of outputting a number of plots and animations to visualize the model output.
+Our postprocessing consists of outputting a number of plots to visualize the model output.
 
 The postprocessing includes:
 - Energy and water conservation checks (if running SlabPlanet with checks enabled)
@@ -910,14 +831,14 @@ if ClimaComms.iamroot(comms_ctx)
         plot_global_conservation(
             cs.conservation_checks.energy,
             cs,
-            config_dict["conservation_softfail"],
+            conservation_softfail,
             figname1 = joinpath(dir_paths.artifacts, "total_energy_bucket.png"),
             figname2 = joinpath(dir_paths.artifacts, "total_energy_log_bucket.png"),
         )
         plot_global_conservation(
             cs.conservation_checks.water,
             cs,
-            config_dict["conservation_softfail"],
+            conservation_softfail,
             figname1 = joinpath(dir_paths.artifacts, "total_water_bucket.png"),
             figname2 = joinpath(dir_paths.artifacts, "total_water_log_bucket.png"),
         )
@@ -930,7 +851,7 @@ if ClimaComms.iamroot(comms_ctx)
             @info "AMIP plots"
 
             ## ClimaESM
-            include("user_io/ci_plots.jl")
+            include("user_io/diagnostics_plots.jl")
 
             # define variable names and output directories for each diagnostic
             amip_short_names_atmos = ["ta", "ua", "hus", "clw", "pr", "ts", "toa_fluxes_net"]
@@ -939,13 +860,13 @@ if ClimaComms.iamroot(comms_ctx)
             output_dir_coupler = dir_paths.output
 
             # Check if all output variables are available in the specified directories
-            make_ci_plots(
+            make_diagnostics_plots(
                 output_dir_atmos,
                 dir_paths.artifacts,
                 short_names = amip_short_names_atmos,
                 output_prefix = "atmos_",
             )
-            make_ci_plots(
+            make_diagnostics_plots(
                 output_dir_coupler,
                 dir_paths.artifacts,
                 short_names = amip_short_names_coupler,
@@ -954,7 +875,7 @@ if ClimaComms.iamroot(comms_ctx)
         end
 
         # Check this because we only want monthly data for making plots
-        if t_end > 84600 * 31 * 3 && config_dict["output_default_diagnostics"]
+        if t_end > 84600 * 31 * 3 && output_default_diagnostics
             include("leaderboard/leaderboard.jl")
             diagnostics_folder_path = atmos_sim.integrator.p.output_dir
             leaderboard_base_path = dir_paths.artifacts
@@ -962,10 +883,10 @@ if ClimaComms.iamroot(comms_ctx)
         end
     end
     ## plot extra atmosphere diagnostics if specified
-    if config_dict["ci_plots"]
-        @info "Generating CI plots"
-        include("user_io/ci_plots.jl")
-        make_ci_plots(atmos_sim.integrator.p.output_dir, dir_paths.artifacts)
+    if plot_diagnostics
+        @info "Plotting diagnostics"
+        include("user_io/diagnostics_plots.jl")
+        make_diagnostics_plots(atmos_sim.integrator.p.output_dir, dir_paths.artifacts)
     end
 
     ## plot all model states and coupler fields (useful for debugging)
diff --git a/experiments/ClimaEarth/run_cloudless_aquaplanet.jl b/experiments/ClimaEarth/run_cloudless_aquaplanet.jl
index eaa37e206d..b70ca50305 100644
--- a/experiments/ClimaEarth/run_cloudless_aquaplanet.jl
+++ b/experiments/ClimaEarth/run_cloudless_aquaplanet.jl
@@ -15,7 +15,6 @@ redirect_stderr(IOContext(stderr, :stacktrace_types_limited => Ref(false)))
 
 ## standard packages
 import Dates
-import YAML
 
 # ## ClimaESM packages
 import ClimaAtmos as CA
@@ -45,7 +44,7 @@ include("components/ocean/slab_ocean.jl")
 job_id = "cloudless_aquaplanet"
 coupler_output_dir = "$job_id"
 const FT = Float64
-restart_dir = "unspecified"
+restart_dir = nothing
 restart_t = Int(0)
 
 ## coupler simulation specific configuration
@@ -90,7 +89,7 @@ config_dict = Dict(
     "surface_setup" => "PrescribedSurface",
     # diagnostic (nested with period and short_name)
     "output_default_diagnostics" => false,
-    "diagnostics" => [
+    "extra_atmos_diagnostics" => [
         Dict(
             "short_name" =>
                 ["mse", "lr", "mass_strf", "stab", "vt", "egr", "ua", "va", "wa", "ta", "rhoa", "pfull"],
@@ -110,7 +109,7 @@ config_dict = Dict(
 )
 
 ## merge dictionaries of command line arguments, coupler dictionary and component model dictionaries
-atmos_config_dict, config_dict = get_atmos_config_dict(config_dict, job_id)
+atmos_config_dict = get_atmos_config_dict(config_dict, job_id)
 atmos_config_object = CA.AtmosConfig(atmos_config_dict)
 
 #=
@@ -262,7 +261,7 @@ cs = Interfacer.CoupledSimulation{FT}(
 ## Restart component model states if specified in the config_dict
 =#
 
-if restart_dir !== "unspecified"
+if !isnothing(restart_dir)
     for sim in cs.model_sims
         if Checkpointer.get_model_prog_state(sim) !== nothing
             Checkpointer.restart_model_state!(sim, comms_ctx, restart_t; input_dir = restart_dir)
diff --git a/experiments/ClimaEarth/run_cloudy_aquaplanet.jl b/experiments/ClimaEarth/run_cloudy_aquaplanet.jl
index f01cb7a9d8..49d363d496 100644
--- a/experiments/ClimaEarth/run_cloudy_aquaplanet.jl
+++ b/experiments/ClimaEarth/run_cloudy_aquaplanet.jl
@@ -14,7 +14,6 @@ redirect_stderr(IOContext(stderr, :stacktrace_types_limited => Ref(false)))
 
 ## standard packages
 import Dates
-import YAML
 
 # ## ClimaESM packages
 import ClimaComms
@@ -45,7 +44,7 @@ include("components/ocean/slab_ocean.jl")
 job_id = "cloudy_aquaplanet"
 coupler_output_dir = "$job_id"
 const FT = Float64
-restart_dir = "unspecified"
+restart_dir = nothing
 restart_t = Int(0)
 
 ## coupler simulation specific configuration
@@ -90,7 +89,7 @@ config_dict = Dict(
     "surface_setup" => "PrescribedSurface",
     # diagnostic (nested with period and short_name)
     "output_default_diagnostics" => false,
-    "diagnostics" => [
+    "extra_atmos_diagnostics" => [
         Dict(
             "short_name" =>
                 ["mse", "lr", "mass_strf", "stab", "vt", "egr", "ua", "va", "wa", "ta", "rhoa", "pfull"],
@@ -123,7 +122,7 @@ config_dict = Dict(
 )
 
 ## merge dictionaries of command line arguments, coupler dictionary and component model dictionaries
-atmos_config_dict, config_dict = get_atmos_config_dict(config_dict, job_id)
+atmos_config_dict = get_atmos_config_dict(config_dict, job_id)
 atmos_config_object = CA.AtmosConfig(atmos_config_dict)
 
 ## override default toml parameters
@@ -277,7 +276,7 @@ cs = Interfacer.CoupledSimulation{FT}(
 ## Restart component model states if specified in the config_dict
 =#
 
-if restart_dir !== "unspecified"
+if !isnothing(restart_dir)
     for sim in cs.model_sims
         if Checkpointer.get_model_prog_state(sim) !== nothing
             Checkpointer.restart_model_state!(sim, comms_ctx, restart_t; input_dir = restart_dir)
diff --git a/experiments/ClimaEarth/run_cloudy_slabplanet.jl b/experiments/ClimaEarth/run_cloudy_slabplanet.jl
index ab3951c26b..1128407b3e 100644
--- a/experiments/ClimaEarth/run_cloudy_slabplanet.jl
+++ b/experiments/ClimaEarth/run_cloudy_slabplanet.jl
@@ -14,7 +14,6 @@ redirect_stderr(IOContext(stderr, :stacktrace_types_limited => Ref(false)))
 
 ## standard packages
 import Dates
-import YAML
 
 # ## ClimaESM packages
 import ClimaComms
@@ -50,7 +49,7 @@ include("components/land/climaland_bucket.jl")
 job_id = "cloudy_slabplanet"
 coupler_output_dir = "$job_id"
 const FT = Float64
-restart_dir = "unspecified"
+restart_dir = nothing
 restart_t = Int(0)
 
 ## coupler simulation specific configuration
@@ -96,7 +95,7 @@ config_dict = Dict(
     "surface_setup" => "PrescribedSurface",
     # diagnostic (nested with period and short_name)
     "output_default_diagnostics" => false,
-    "diagnostics" => [
+    "extra_atmos_diagnostics" => [
         Dict(
             "short_name" =>
                 ["mse", "lr", "mass_strf", "stab", "vt", "egr", "ua", "va", "wa", "ta", "rhoa", "pfull"],
@@ -127,7 +126,7 @@ config_dict = Dict(
 )
 
 ## merge dictionaries of command line arguments, coupler dictionary and component model dictionaries
-atmos_config_dict, config_dict = get_atmos_config_dict(config_dict, job_id)
+atmos_config_dict = get_atmos_config_dict(config_dict, job_id)
 atmos_config_object = CA.AtmosConfig(atmos_config_dict)
 
 # override default toml parameters
@@ -328,7 +327,7 @@ cs = Interfacer.CoupledSimulation{FT}(
 ## Restart component model states if specified in the config_dict
 =#
 
-if restart_dir !== "unspecified"
+if !isnothing(restart_dir)
     for sim in cs.model_sims
         if Checkpointer.get_model_prog_state(sim) !== nothing
             Checkpointer.restart_model_state!(sim, comms_ctx, restart_t; input_dir = restart_dir)
diff --git a/experiments/ClimaEarth/run_dry_held_suarez.jl b/experiments/ClimaEarth/run_dry_held_suarez.jl
index fcb4080f95..b76b615484 100644
--- a/experiments/ClimaEarth/run_dry_held_suarez.jl
+++ b/experiments/ClimaEarth/run_dry_held_suarez.jl
@@ -16,7 +16,6 @@ redirect_stderr(IOContext(stderr, :stacktrace_types_limited => Ref(false)))
 
 ## standard packages
 using Dates
-import YAML
 
 ## ClimaESM packages
 using ClimaComms
@@ -46,7 +45,7 @@ Here we follow ClimaCore's dry Held-Suarez `held_suarez_rhoe` example.
 job_id = "dry_held_suarez"
 coupler_output_dir = "$job_id"
 const FT = Float64
-restart_dir = "unspecified"
+restart_dir = nothing
 restart_t = Int(0)
 
 ## coupler simulation specific configuration
@@ -89,7 +88,7 @@ config_dict = Dict(
     "surface_setup" => "PrescribedSurface",
     # diagnostic (nested with period and short_name)
     "output_default_diagnostics" => false,
-    "diagnostics" => [
+    "extra_atmos_diagnostics" => [
         Dict(
             "short_name" =>
                 ["mse", "lr", "mass_strf", "stab", "vt", "egr", "ua", "va", "wa", "ta", "rhoa", "pfull"],
@@ -102,7 +101,7 @@ config_dict = Dict(
 )
 
 ## merge dictionaries of command line arguments, coupler dictionary and component model dictionaries
-atmos_config_dict, config_dict = get_atmos_config_dict(config_dict, job_id)
+atmos_config_dict = get_atmos_config_dict(config_dict, job_id)
 atmos_config_object = CA.AtmosConfig(atmos_config_dict)
 
 #=
@@ -207,7 +206,7 @@ cs = Interfacer.CoupledSimulation{FT}(
 ## Restart component model states if specified in the config_dict
 =#
 
-if restart_dir !== "unspecified"
+if !isnothing(restart_dir)
     for sim in cs.model_sims
         if get_model_prog_state(sim) !== nothing
             Checkpointer.restart_model_state!(sim, comms_ctx, restart_t; input_dir = restart_dir)
diff --git a/experiments/ClimaEarth/run_moist_held_suarez.jl b/experiments/ClimaEarth/run_moist_held_suarez.jl
index 98cc9094b1..7fefba21f8 100644
--- a/experiments/ClimaEarth/run_moist_held_suarez.jl
+++ b/experiments/ClimaEarth/run_moist_held_suarez.jl
@@ -17,7 +17,6 @@ redirect_stderr(IOContext(stderr, :stacktrace_types_limited => Ref(false)))
 
 ## standard packages
 import Dates
-import YAML
 
 # ## ClimaESM packages
 import ClimaComms
@@ -48,7 +47,7 @@ Here we follow Thatcher and Jablonowski (2016).
 job_id = "moist_held_suarez"
 coupler_output_dir = "$job_id"
 const FT = Float64
-restart_dir = "unspecified"
+restart_dir = nothing
 restart_t = Int(0)
 
 ## coupler simulation specific configuration
@@ -92,7 +91,7 @@ config_dict = Dict(
     "surface_setup" => "PrescribedSurface",
     # diagnostic (nested with period and short_name)
     "output_default_diagnostics" => false,
-    "diagnostics" => [
+    "extra_atmos_diagnostics" => [
         Dict(
             "short_name" =>
                 ["mse", "lr", "mass_strf", "stab", "vt", "egr", "ua", "va", "wa", "ta", "rhoa", "pfull"],
@@ -110,7 +109,7 @@ config_dict = Dict(
 # TODO: may need to switch to Bulk fluxes
 
 ## merge dictionaries of command line arguments, coupler dictionary and component model dictionaries
-atmos_config_dict, config_dict = get_atmos_config_dict(config_dict, job_id)
+atmos_config_dict = get_atmos_config_dict(config_dict, job_id)
 atmos_config_object = CA.AtmosConfig(atmos_config_dict)
 
 #=
@@ -258,7 +257,7 @@ cs = Interfacer.CoupledSimulation{FT}(
 ## Restart component model states if specified in the config_dict
 =#
 
-if restart_dir !== "unspecified"
+if !isnothing(restart_dir)
     for sim in cs.model_sims
         if Checkpointer.get_model_prog_state(sim) !== nothing
             Checkpointer.restart_model_state!(sim, comms_ctx, restart_t; input_dir = restart_dir)
diff --git a/experiments/ClimaEarth/test/amip_test.yml b/experiments/ClimaEarth/test/amip_test.yml
index 101a17368d..71dbbc265e 100644
--- a/experiments/ClimaEarth/test/amip_test.yml
+++ b/experiments/ClimaEarth/test/amip_test.yml
@@ -3,7 +3,7 @@ albedo_model: "CouplerAlbedo"
 atmos_config_file: "config/longrun_configs/amip_target_diagedmf.yml"
 coupler_toml_file: "toml/amip.toml"
 dt: "180secs"
-dt_cpl: 180
+dt_cpl: "180secs"
 dt_save_state_to_disk: "30days"
 dt_save_to_sol: "30days"
 dz_bottom: 100.0
diff --git a/experiments/ClimaEarth/user_io/arg_parsing.jl b/experiments/ClimaEarth/user_io/arg_parsing.jl
new file mode 100644
index 0000000000..26af20034a
--- /dev/null
+++ b/experiments/ClimaEarth/user_io/arg_parsing.jl
@@ -0,0 +1,272 @@
+import YAML
+
+"""
+    get_coupler_config()
+
+Read in the configuration file and job ID from the command line.
+A dictionary is constructed from the input configuration file and returned.
+
+# Returns
+- `config_dict`: A dictionary mapping configuration keys to the specified settings
+"""
+function get_coupler_config()
+    # Read in command line arguments
+    parsed_args = parse_commandline(argparse_settings())
+
+    # Extract the configuration file and job ID
+    config_file = parsed_args["config_file"]
+    job_id = parsed_args["job_id"]
+    # Get the job ID from the config file string if not provided
+    job_id = isnothing(job_id) ? string(split(split(config_file, '/')[end], '.')[1]) : job_id
+
+    # Read in config dictionary from file, overriding the defaults in `parsed_args`
+    config_dict = merge(parsed_args, YAML.load_file(parsed_args["config_file"]))
+    config_dict["job_id"] = job_id
+    return config_dict
+end
+
+"""
+    get_coupler_args(config_dict)
+
+Extract the necessary arguments from the coupled configuration dictionary.
+This function may modify the input dictionary to remove unnecessary keys.
+
+# Arguments
+- `config_dict`: A dictionary mapping configuration keys to the specified settings
+
+# Returns
+- All arguments needed for the coupled simulation
+"""
+function get_coupler_args(config_dict::Dict)
+    # Simulation-identifying information; Print `config_dict` if requested
+    config_dict["print_config_dict"] && @info(config_dict)
+    job_id = config_dict["job_id"]
+    mode_name = config_dict["mode_name"]
+
+    # Computational simulation setup information
+    random_seed = config_dict["unique_seed"] ? time_ns() : 1234
+    FT = config_dict["FLOAT_TYPE"] == "Float64" ? Float64 : Float32
+    comms_ctx = Utilities.get_comms_context(config_dict)
+
+    # Time information
+    t_end = Float64(Utilities.time_to_seconds(config_dict["t_end"]))
+    t_start = Float64(Utilities.time_to_seconds(config_dict["t_start"]))
+    date0 = date = Dates.DateTime(config_dict["start_date"], Dates.dateformat"yyyymmdd")
+    Δt_cpl = Float64(Utilities.time_to_seconds(config_dict["dt_cpl"]))
+    saveat = Float64(Utilities.time_to_seconds(config_dict["dt_save_to_sol"]))
+    component_dt_dict = config_dict["component_dt_dict"]
+
+    # Checkpointing information
+    hourly_checkpoint = config_dict["hourly_checkpoint"]
+    hourly_checkpoint_dt = config_dict["hourly_checkpoint_dt"]
+
+    # Restart information
+    restart_dir = config_dict["restart_dir"]
+    restart_t = Int(config_dict["restart_t"])
+
+    # Diagnostics information
+    use_coupler_diagnostics = config_dict["use_coupler_diagnostics"]
+    use_land_diagnostics = config_dict["use_land_diagnostics"]
+    calendar_dt = config_dict["calendar_dt"]
+
+    # Physical simulation information
+    evolving_ocean = config_dict["evolving_ocean"]
+    mono_surface = config_dict["mono_surface"]
+    turb_flux_partition = config_dict["turb_flux_partition"]
+
+    # Conservation information
+    energy_check = config_dict["energy_check"]
+    conservation_softfail = config_dict["conservation_softfail"]
+
+    # Output information
+    output_dir_root = config_dict["coupler_output_dir"]
+    plot_diagnostics = config_dict["plot_diagnostics"]
+
+    # ClimaLand-specific information
+    land_domain_type = config_dict["land_domain_type"]
+    land_albedo_type = config_dict["land_albedo_type"]
+    land_temperature_anomaly = config_dict["land_temperature_anomaly"]
+    use_land_diagnostics = config_dict["use_land_diagnostics"]
+
+    return (;
+        job_id,
+        mode_name,
+        random_seed,
+        FT,
+        comms_ctx,
+        t_end,
+        t_start,
+        date0,
+        date,
+        Δt_cpl,
+        component_dt_dict,
+        saveat,
+        hourly_checkpoint,
+        hourly_checkpoint_dt,
+        restart_dir,
+        restart_t,
+        use_coupler_diagnostics,
+        calendar_dt,
+        evolving_ocean,
+        mono_surface,
+        turb_flux_partition,
+        energy_check,
+        conservation_softfail,
+        output_dir_root,
+        plot_diagnostics,
+        land_domain_type,
+        land_albedo_type,
+        land_temperature_anomaly,
+        use_land_diagnostics,
+    )
+end
+
+"""
+    get_atmos_args(atmos_config_dict)
+
+Extract the necessary arguments from the atmosphere configuration dictionary.
+
+# Arguments
+- `atmos_config_dict`: A dictionary mapping atmosphere configuration keys to the specified settings
+
+# Returns
+- All arguments needed for the atmosphere simulation
+"""
+function get_atmos_args(atmos_config_dict)
+    dt_rad = atmos_config_dict["dt_rad"]
+    output_default_diagnostics = atmos_config_dict["output_default_diagnostics"]
+
+    return (; dt_rad, output_default_diagnostics)
+end
+
+
+### Helper functions used in argument parsing ###
+
+"""
+    get_diag_period()
+
+Determine the frequency at which to average and output diagnostics based on the
+simulation start and end times.
+
+The default periods are:
+- 1 month for simulations longer than 90 days
+- 10 days for simulations longer than 30 days
+- 1 day for simulations longer than 1 day
+- 1 hour for simulations shorter than 1 day
+
+# Arguments
+- `t_start`: The start time of the simulation
+- `t_end`: The end time of the simulation
+
+# Returns
+- `period`: A String of how often to average and output diagnostics
+- `calendar_dt`: A DateTime interval representing the period
+"""
+function get_diag_period(t_start, t_end)
+    sim_duration = t_end - t_start
+    secs_per_day = 86400
+    if sim_duration >= 90 * secs_per_day
+        # if duration >= 90 days, take monthly means
+        period = "1months"
+        calendar_dt = Dates.Month(1)
+    elseif sim_duration >= 30 * secs_per_day
+        # if duration >= 30 days, take means over 10 days
+        period = "10days"
+        calendar_dt = Dates.Day(10)
+    elseif sim_duration >= secs_per_day
+        # if duration >= 1 day, take daily means
+        period = "1days"
+        calendar_dt = Dates.Day(1)
+    else
+        # if duration < 1 day, take hourly means
+        period = "1hours"
+        calendar_dt = Dates.Hour(1)
+    end
+    return (period, calendar_dt)
+end
+
+"""
+    parse_component_dts!(config_dict)
+
+Check which timesteps are specified in the config file, and use them to choose
+the correct timestep for each component model.
+If all component timesteps `dt_\$component` are specified in the config file, use those
+and remove `dt` if it was provided.
+Otherwise, use the generic component timestep `dt` specified in the config file.
+If some (but not all) component timesteps and the generic timestep `dt` are specified,
+use the generic timestep and remove the others from the config dict.
+
+The timestep for each component model is stored in the `component_dt_dict` field of the config dict.
+
+# Arguments
+- `config_dict`: A dictionary mapping configuration keys to the specified settings
+"""
+function parse_component_dts!(config_dict)
+    # Retrieve coupling timestep
+    Δt_cpl = Float64(Utilities.time_to_seconds(config_dict["dt_cpl"]))
+
+    # Specify component model names
+    component_dt_names = ["dt_atmos", "dt_land", "dt_ocean", "dt_seaice"]
+    component_dt_dict = Dict{String, Float64}()
+    # check if all component dt's are specified
+    if all(key -> !isnothing(config_dict[key]), component_dt_names)
+        # when all component dt's are specified, ignore the dt field
+        if haskey(config_dict, "dt")
+            @warn "Removing dt in favor of individual component dt's"
+            delete!(config_dict, "dt")
+        end
+        for key in component_dt_names
+            component_dt = Float64(Utilities.time_to_seconds(config_dict[key]))
+            @assert isapprox(Δt_cpl % component_dt, 0.0) "Coupler dt must be divisible by all component dt's\n dt_cpl = $Δt_cpl\n $key = $component_dt"
+            component_dt_dict[key] = component_dt
+        end
+    else
+        # when not all component dt's are specified, use the dt field
+        @assert haskey(config_dict, "dt") "dt or (dt_atmos, dt_land, dt_ocean, and dt_seaice) must be specified"
+        for key in component_dt_names
+            if !isnothing(config_dict[key])
+                @warn "Removing $key from config in favor of dt because not all component dt's are specified"
+            end
+            delete!(config_dict, key)
+            component_dt_dict[key] = Float64(Utilities.time_to_seconds(config_dict["dt"]))
+        end
+    end
+    config_dict["component_dt_dict"] = component_dt_dict
+end
+
+"""
+    add_extra_diagnostics!(config_dict)
+
+Conditionally add extra diagnostics to the config dictionary based on the
+simulation type and flag to use diagnostics. Currently, the only extra
+diagnostic is the atmosphere TOA net flux for AMIP simulations, but more diagnostics
+can be added for any component by following the structure in `climaatmos_extra_diags.jl`.
+
+The added atmosphere diagnostics are added to the `extra_atmos_diagnostics` field
+of the config dict. The `calendar_dt` field is also added to the config dict to
+coordinate the output frequency of the diagnostics.
+
+# Arguments
+- `config_dict`: A dictionary mapping configuration keys to the specified settings
+"""
+function add_extra_diagnostics!(config_dict)
+    # Diagnostics information
+    mode_name = config_dict["mode_name"]
+    use_coupler_diagnostics = config_dict["use_coupler_diagnostics"]
+    t_end = Float64(Utilities.time_to_seconds(config_dict["t_end"]))
+    t_start = Float64(Utilities.time_to_seconds(config_dict["t_start"]))
+    calendar_dt = nothing
+    if mode_name == "amip" && use_coupler_diagnostics
+        @info "Using default AMIP diagnostics"
+        (period, calendar_dt) = get_diag_period(t_start, t_end)
+
+        # Additional atmosphere diagnostics
+        !haskey(config_dict, "extra_atmos_diagnostics") &&
+            (config_dict["extra_atmos_diagnostics"] = Vector{Dict{Any, Any}}())
+        push!(
+            config_dict["extra_atmos_diagnostics"],
+            Dict("short_name" => ["toa_fluxes_net"], "reduction_time" => "average", "period" => period),
+        )
+    end
+    config_dict["calendar_dt"] = calendar_dt
+end
diff --git a/experiments/ClimaEarth/user_io/ci_plots.jl b/experiments/ClimaEarth/user_io/diagnostics_plots.jl
similarity index 96%
rename from experiments/ClimaEarth/user_io/ci_plots.jl
rename to experiments/ClimaEarth/user_io/diagnostics_plots.jl
index 944c49f28a..e0b2ba355b 100644
--- a/experiments/ClimaEarth/user_io/ci_plots.jl
+++ b/experiments/ClimaEarth/user_io/diagnostics_plots.jl
@@ -144,19 +144,19 @@ function map_comparison(func, simdirs, args)
 end
 
 """
-    make_ci_plots(
+    make_diagnostics_plots(
         output_path::AbstractString,
         plot_path::AbstractString;
         short_names::Vector{<:AbstractString} = ["mse", "lr", "edt", "ts"],
         reduction::String = "average",
         output_prefix = "",
     )
-Create plots for the general CI diagnostics. The plots are saved to `plot_path`.
-This is the default plotting function for the CI diagnostics and it can be extended
+Create plots for diagnostics. The plots are saved to `plot_path`.
+This is the default plotting function for diagnostics and it can be extended
 to include additional diagnostics.
 The `reduction` keyword argument should be consistent with the reduction used to save the diagnostics.
 """
-function make_ci_plots(
+function make_diagnostics_plots(
     output_path::AbstractString,
     plot_path::AbstractString;
     short_names::Vector{<:AbstractString} = ["mse", "lr", "edt", "ts"],
diff --git a/src/Utilities.jl b/src/Utilities.jl
index 13c71a96bf..79c0166ee8 100644
--- a/src/Utilities.jl
+++ b/src/Utilities.jl
@@ -51,7 +51,14 @@ end
 """
     get_comms_context(config_dict)
 
-Sets up the appropriate ClimaComms context for the device the model is to be run on
+Sets up the appropriate ClimaComms context for the device the model is to be run on,
+choosing from the following options:
+    - CPU single threaded
+    - CPU with MPI
+    - GPU
+
+If no device is passed to `ClimaComms.context()` then `ClimaComms` automatically
+selects the device from which this code is called.
 
 # Arguments
 `config_dict`: dictionary containing a "device" flag whcih decides which device context is needed