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Add GEOS-MLT upper atmosphere dynamics - #130
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Andrew-won-Lee wants to merge 30 commits into
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added 26 commits
April 30, 2026 13:55
…flux from outside the model as a default
… friction based, roll back the centeralized MSIS startegy because in that case we reencountered gz issue in geopk.
Update hydrostatic layer thickness from the newly diagnosed geopotential during FV3 dynamics (n_split) and after Lagrangian-to-Eulerian remapping. This ensures that MSIS altitude calculations use the evolving hydrostatic geometry rather than a frozen DZ field inherited from the restart. The nonhydrostatic update_dz_d pathway is unchanged.
Allow hydrostatic altitude reconstruction to continue over below-sea-level surfaces in both dyn_core and fv_mapz. Clamp negative layer-midpoint altitudes to 0 km only for the MSIS input while preserving the actual interface heights for upward geometric integration. This prevents valid low elevation columns, such as the Caspian Sea region!!, from switching the entire column to the pressure-based altitude fallback.
Initialize the dynamics-side MSIS wrapper during FV3 setup and pass the correct UT seconds since midnight from the ESMF clock. Cache F10.7, F10.7A, and Ap once per model hour to avoid repeatedly searching the space-weather table at every grid point and level. Continue evaluating MSIS independently at each requested location and altitude. Require exact hourly index records and stop when the forcing table is unavailable or does not cover the current model time.
Correct two grid-staggering inconsistencies affecting the GEOS-MLT upper-atmosphere calculations. First, interpolate the hydrostatic top-interface pk from the A grid to the B grid in one_grad_p. Standard FV3 skips this interpolation because the top value is horizontally constant. In GEOS-MLT, however, the local Kappa_MLT field makes the top-interface pk horizontally variable, so the standard assumption is no longer valid. Start the interpolation at k=1 for hydrostatic GEOS-MLT config, while preserving the existing k=2 behavior for all other configurations. Second, preserve the final A-grid interface geopotential before the pressure-gradient routines convert the working gz array to the B grid in place. Molecular momentum diffusion and thermal conduction are A-grid vertical column operators called after the acoustic split loop. Pass the preserved A-grid geopotential to these operators instead of the B-grid-converted working array.
Recomputes geopotential after pt is adjusted to the MLT-aware pkz Replaces the explicit vertical conduction tendency with a column-wise frozen-coefficient backward-Euler tridiagonal solve.
Replace the explicit GEOS-MLT molecular momentum diffusion calculation with a backward-Euler implicit vertical solver. The new implementation solves tridiagonal systems for the future A-grid zonal and meridional winds and returns the implicit increments through the existing FV3 tendency interface. Main changes: - Add the dynamics timestep to the molecular momentum diffusion routine. - Solve vertical molecular diffusion implicitly for both wind components. - Reuse one factored tridiagonal matrix for the zonal and meridional winds. - Apply the pressure taper to interface dynamic viscosity. - Retain zero-flux upper and lower boundary conditions. - Calculate dynamic viscosity directly as Pr * lambda / cp. - Use double precision for the tridiagonal solver workspace. - Diagnose optional KE-loss heating from the implicitly solved wind gradients. - Set the default thermal-conduction tendency limit to false. Remove redundant molecular momentum diffusion controls: - geos_mlt_momdiff_diag - geos_mlt_momdiff_kmax - geos_mlt_momdiff_print_stride - geos_mlt_momdiff_nu_scale - geos_mlt_momdiff_rmax - geos_mlt_momdiff_nu_max The remaining runtime controls are: - geos_mlt_momdiff_enable - geos_mlt_momdiff_heat - geos_mlt_momdiff_pr - geos_mlt_momdiff_pmax_pa
Replace the fixed upper-column thermal-conduction level limit with a pressure-based active mask. Previously, NRLMSIS sampling for thermal conduction was restricted to the top 40 model levels. Although this worked reasonably for the current L190 configuration, the cutoff depended on vertical level index rather than a physical pressure threshold. As a result, changing the vertical grid could move the effective thermal-conduction lower boundary to a different pressure and altitude. This update defines the thermal-conduction domain using the existing GEOS-MLT pressure cutoff of 1 Pa (0.01 hPa) and passes the same conduction-active mask through the thermal-conduction driver. Main changes: * Remove the fixed `GEOS_MLT_MSIS_LOOKUP_KMAX = 40` limit. * Remove the separate 70-km minimum-altitude criterion for MSIS sampling. * Define thermal-conduction activity from layer-center pressure. * Pass the pressure-based active mask from `dyn_core` to `cond_driver_apply`. * Restrict MSIS composition sampling to active thermal-conduction layers. * Use the same active mask when applying the resulting temperature tendency. * Keep MSIS altitude validity checks as numerical safety guards. * Add consistency checks for the active-mask dimensions. This makes the thermal-conduction implementation independent of the number and spacing of vertical levels and ensures that the domain used to calculate the conduction tendency is consistent with the domain where the tendency is applied. The lower boundary remains approximately 1 Pa, below which molecular thermal conduction is assumed to be small enough to neglect in the current GEOS-MLT configuration.
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Use composition dependent Cp and kappa in the GEOS-MLT subgrid mixing energy calculation. Reuse the final remap MLT thermodynamic state in fv_sg without additional MSIS calls. Require valid model time inputs for GEOS-MLT MSIS calculations and accumulate GEOS-MLT tendency diagnostics consistently across k_split. Require molecular diffusion heating to be used with momentum diffusion. Restrict GEOS-MLT to remap_option=0 and consv_te=0 until the alternative formulations are made composition aware and validated. Reduce unnecessary GEOS-MLT work-array allocation and remove unused thermodynamic fields. Print the GEOS-MLT thermal conduction and molecular diffusion configuration once per model execution instead of once per dynamics call
Expose MSIS F10.7 forcing for GEOS-MLT ion drag
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Summary
This PR merges the GEOS-MLT upper-atmosphere updates into the
GEOS-11_7_2-MLT-0_0_1integration branch.The changes extend the FV3/GFDL atmospheric dynamics needed for the GEOS-MLT.
Changes
The GEOS-MLT specific behavior is enabled through the GEOS-MLT configuration so that standard GEOS configurations retain their existing path.
Related work
This PR is intended to be used with the corresponding GEOS-MLT updates in
FVdycoreCubed_GridComp,GEOSgcm_GridComp,GEOSradiation_GridComp, andGEOSgcm_App.The target integration branch is based on the GFDL atmospheric component (geos/v2.9.1) used by GEOSgcm v11.7.2.