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xylar committed Apr 21, 2021
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206 changes: 123 additions & 83 deletions docs/ocean/design_docs/min_level_cell.rst
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Expand Up @@ -130,13 +130,13 @@ several other derivative fields are initialized based on ``maxLevelCell``.
We will rename this function ``ocn_init_routines_compute_min_max_level()``
and will initialized the following new variables:

* ``minLevelEdgeTop``
* ``minLevelEdgeTop`` - the minimum of ``minLevelCell`` on adjacent cells

* ``minLevelEdgeBot``
* ``minLevelEdgeBot`` - the maximum of ``minLevelCell`` on adjacent cells

* ``minLevelVertexTop``
* ``minLevelVertexTop`` - the minimum of ``minLevelCell`` on adjacent cells

* ``minLevelVertexBot``
* ``minLevelVertexBot`` - the maximum of ``minLevelCell`` on adjacent cells

The definitions of the following variables currently in this routine will be
updated to include ``minLevelCell``:
Expand Down Expand Up @@ -220,51 +220,51 @@ Forward:
* [ ] ``ocn_meshDestroy()``

* [ ] ``ocn_tendency``:

* [ ] ``ocn_tend_tracer``

* [ ] ``ocn_forcing``:

* [ ] ``ocn_forcing_build_fraction_absorbed_array``

* [ ] ``ocn_thick_hadv``:

* [ ] ``ocn_hadv_thick_tend``

* [ ] ``ocn_thick_vadv``:

* [ ] ``ocn_vadv_thick_tend``

* [ ] ``ocn_thick_surface_flux``:

* [ ] ``ocn_thick_surface_flux_tend``

* [ ] ``ocn_tracer_advection``:

* [ ] ``ocn_tracer_advection_tend``

* [ ] ``ocn_tracer_advection_mono``:

* [ ] ``ocn_tracer_advection_mono_tend``

* [ ] ``ocn_vel_forcing_surface_stress``:

* [ ] ``ocn_vel_forcing_surface_stress_tend``

* [ ] ``ocn_vel_hmix_del2``:

* [ ] ``ocn_vel_hmix_del2_tend``

* [ ] ``ocn_vel_hadv_coriolis``:

* [ ] ``ocn_vel_hadv_coriolis_tend``

* [ ] ``ocn_vel_vadv``:

* [ ] ``ocn_vel_vadv_tend``

* [ ] ``ocn_vmix_cvmix``:

* [ ] ``ocn_vmix_coefs_cvmix_build``

* [ ] ``ocn_diagnostics``:
Expand Down Expand Up @@ -298,15 +298,15 @@ Forward:
* [ ] ``ocn_ALE_thickness``

* [ ] ``ocn_vel_pressure_grad``:

* [ ] ``ocn_vel_pressure_grad_tend``

* [ ] ``ocn_vmix``:

* [ ] ``ocn_vmix_implicit``

* [ ] ``ocn_vel_vmix_tend_implicit``

* [ ] ``ocn_tracer_vmix_tend_implicit``

...
Expand All @@ -322,12 +322,12 @@ Forward:

.. note::

``ocn_forcing_build_fraction_absorbed_array`` is currently only called once
``ocn_forcing_build_fraction_absorbed_array`` is currently only called once
by ``ocn_init_routines`` and would need to be called multiple times to correctly
distribute surface fluxes unless we use an alternative approach where the vertical
index of transmissionCoeff is number of cells from minLevelCell rather than k-levels


Here is a (by no means complete) checklist of routines not used by
``sub_ice_shelf_2D`` test cases that are a lower priority to update:

Expand Down Expand Up @@ -374,25 +374,25 @@ Forward:
* [ ] ``ocn_GM_compute_Bolus_velocity()``

* [ ] ``ocn_tendency``:

* [ ] ``ocn_tend_freq_filtered_thickness``

* [ ] ``ocn_tidal_forcing``:

* [ ] ``ocn_tidal_forcing_build_array``

* [ ] ``ocn_tidal_forcing_layer_thickness``

* [ ] ``ocn_vel_tidal_potential``:

* [ ] ``ocn_vel_tidal_potential_tend``

* [ ] ``ocn_tracer_advection_std``:

* [ ] ``ocn_tracer_advection_std_tend``

* [ ] ``ocn_wetting_drying``:

* [ ] ``ocn_wetting_drying_verify``

* [ ] ``ocn_prevent_drying_rk4``
Expand All @@ -402,69 +402,69 @@ Forward:
* [ ] ``ocn_vmix``:

* [ ] ``ocn_vel_vmix_tend_implicit_spatially_variable``

* [ ] ``ocn_vel_vmix_tend_implicit_spatially_variable_mannings``

* [ ] ``ocn_vel_vmix_tend_implicit_rayleigh``

* [ ] ``ocn_compute_kpp_rhs``

* [ ] ``ocn_tracer_exponential_decay``:

* [ ] ``ocn_tracer_exponential_decay_compute``

* [ ] ``ocn_tracer_DMS``:

* [ ] ``ocn_tracer_DMS_compute``

* [ ] ``ocn_tracer_DMS_surface_flux_compute``: iLevelSurface

* [ ] ``ocn_tracer_ecosys``:

* [ ] ``ocn_tracer_ecosys_compute``

* [ ] ``ocn_tracer_ecosys_surface_flux_compute``: iLevelSurface

* [ ] ``ocn_compute_tidal_potential_forcing``

* [ ] ``ocn_frazil_forcing``:

* [ ] ``ocn_frazil_forcing_layer_thickness``

* [ ] ``ocn_frazil_forcing_active_tracers``

* [ ] ``ocn_frazil_forcing_build_arrays``

* [ ] ``ocn_sea_ice``:

* [ ] ``ocn_sea_ice_formation``

* [ ] ``ocn_sea_ice_init``

* [ ] ``ocn_tracer_hmix_del2``:

* [ ] ``ocn_tracer_hmix_del2_tend``

* [ ] ``ocn_tracer_hmix_del4``:

* [ ] ``ocn_tracer_hmix_del4_tend``

* [ ] ``ocn_tracer_hmix_Redi``:

* [ ] ``ocn_tracer_hmix_Redi_tend``

* [ ] ``ocn_high_freq_thickness_hmix_del2``:

* [ ] ``ocn_high_freq_thickness_hmix_del2_tend``

* [ ] ``ocn_vel_hmix_del4``:

* [ ] ``ocn_vel_hmix_del4_tend``

* [ ] ``ocn_vel_hmix_leith``:

* [ ] ``ocn_vel_hmix_leith_tend``

* [ ] ``ocn_tracer_ideal_age``:

* [ ] ``ocn_tracer_ideal_age_compute``
Expand Down Expand Up @@ -492,15 +492,15 @@ Forward:
* [ ] ``ocn_tracer_surface_flux_tend``

* [ ] ``ocn_tracer_interior_restoring``:

* [ ] ``ocn_tracer_interior_restoring_compute``

...

.. note::

May need to reconsider nVertLevels argument to ``ocn_sea_ice_init``


Implementation: Surface fields and fluxes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Expand Down Expand Up @@ -639,31 +639,63 @@ Testing: Inactive top cells

Date last modified: 2021/02/11

Contributors: Xylar Asay-Davis
Contributors: Xylar Asay-Davis, Mark Petersen

We will ensure that all 3D, prognostic variables have been initialized to the
NetCDF fill value in inactive cells at the top of the water column. We will
attempt to do the same for 3D diagnostic variables. This should expose any
computations involving these invalid cells.

We will modify the ``sub_ice_shelf_2D`` configuration in legacy COMPASS to
We have modified the ``sub_ice_shelf_2D`` configuration in legacy COMPASS to
support a z-level initial coordinate in the ice-shelf cavity (including writing
out ``minLevelCell`` in the initial condition). Then, we will run the
following test cases in this configuration with the new coordinate:

* ``default``

* ``restart_test``

* ``iterative_init``

We will run on multiple machines (Ubuntu laptop, Anvil, Grizzly, Compy) with a
mix of Gnu and Intel compilers. We will plot the resulting T, S and KE fields
to make sure they look comparable to the results with the current
out ``minLevelCell`` in the initial condition). The implementation is in a
`add_z_level_sub_ice_shelf_2D COMPASS branch <https://github.com/xylar/compass/tree/add_z_level_sub_ice_shelf_2D>`_
and a corresponding `add_z_level_sub_ice_shelf_2D MPAS-Model branch <https://github.com/xylar/MPAS-Model/tree/ocean/add_z_level_sub_ice_shelf_2D>`_.


To begin wth, these tests also have melt fluxes disabled along with all
tendency terms.

The test cases include "partial top cells", analogous to "partial bottom
cells". When constructing your initial domain with variable ``minLevelCell``,
we have generalized the namelist options for partial bottom cells to refer to
both bottom and top cells, so that we can specify either full or partial
(bottom and top) cells. The eventual goal is always partial top cells, to model
the ice draft more realistically. But it is useful to have a full cell option
in your standard test suite.

When initialize with constant T and S horizontally and no surface forcing, a
zero initial velocity should remain exactly zero with full top and bottom
cells. Pressure gradient errors with partial top/bottom cells will mean that
the velocity will be nonzero but should remain small. This is similar to the
sea mount test, where the velocity is a measure of the error.

We will progress through the following 3 test cases:
These define 3 new test cases:

1. ``z_level_full_cells_const_S`` - T and S are uniform in 3D. Full top and
bottom cells. Verify min and max T and S remain exactly constant, velocity
remains exactly zero.

2. ``z_level_full_cells`` - S is horizontally uniform (T remains uniform in
3D), stably stratified in vertical. Disable vertical tracer mixing. Full top
and bottom cells. Verify T and S remain unchanged, velocity remains exactly
zero.

3. ``z_level`` - Same as 2. but partial top and bottom cells. Maximum velocity
is a measure of the error and should grow slowly at top and bottom(e.g.
1e-6m/s after a day).

To begin with, these tests also have melt fluxes disabled along with all
tendency terms. As part of debugging, we will gradually turn on tendencies
and check the behavior.

We will run on multiple machines (Ubuntu laptop, Anvil, Grizzly, Cori, Compy)
with a mix of Gnu and Intel compilers. We will plot the resulting T, S and KE
fields to make sure they look comparable to the results with the current
terrain-following coordinate.

We will test with both the linear (I believe the default) and JM equations of
state.
We will test with JM and Wright equations of state.

Testing: Surface fields and fluxes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Expand All @@ -680,12 +712,14 @@ and other parameterizations that are not part of this configuration by default.
Testing: Correct boundary conditions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Date last modified: 2021/02/11

Contributors: ???
Date last modified: 2021/02/25

<<<Need to think about this...>>>
Contributors: Mark Petersen and Xylar Asay-Davis

The 3 z-level versions of ``sub_ice_shelf_2D`` described above should provide
sufficient testing of the boundary conditions related to tendency terms (e.g.
higher-order tracer reconstruction). More sophisticated parameterizations
(KPP and GM) will be addressed in the second phase of this work.

Testing: Inactivate cells during simulation
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Expand Down Expand Up @@ -713,9 +747,15 @@ and Intel compilers to make sure nothing has changed when we run with

We will also run the following E3SM tests before and after the changes:

* ``SMS.T62_oQU120_ais20.MPAS_LISIO_TEST.anvil_intel``
* ``<<help>>``
* ``SMS.T62_oQU120_ais20.MPAS_LISIO_TEST.<<machine>>_intel``
* ``SMS.T62_oQU120_ais20.MPAS_LISIO_TEST.<<machine>>_gnu``

We will run the following E3SM tests after changes:
* ``PET_Ln9.T62_oQU240.GMPAS-IAF.<<machine>>_intel``
* ``PEM_Ln9.T62_oQU240.GMPAS-IAF.<<machine>>_gnu``
* ``PET_Ln3.T62_oEC60to30v3wLI.GMPAS-DIB-IAF-ISMF.<<machine>>_intel``
* ``PET_Ln9_P1024.ne30_oECv3_ICG.A_WCYCL1850S.<<machine>>_gnu``
* ``PEM_Ln9_P1024.ne30_oECv3_ICG.A_WCYCL1850S.<<machine>>_intel``

Testing: No significant loss of performance
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Expand Down

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