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Update usage.rst #252

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Mar 2, 2021
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Update usage.rst #252

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b178062
Update usage.rst
rabernat Jan 13, 2021
cb0a691
Update usage.rst
rabernat Jan 13, 2021
0e870ac
address atmospheric configurations
rabernat Jan 13, 2021
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18 changes: 14 additions & 4 deletions doc/usage.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -152,9 +152,9 @@ standard names have been assigned according to `CF Conventions`_.
+----------------------+---------------------------------------+
| YG | latitude_at_f_location |
+----------------------+---------------------------------------+
| Zl | depth_at_upper_w_location |
| Zl | depth_at_lower_w_location |
+----------------------+---------------------------------------+
| Zu | depth_at_lower_w_location |
| Zu | depth_at_upper_w_location |
+----------------------+---------------------------------------+
| Z | depth |
+----------------------+---------------------------------------+
Expand Down Expand Up @@ -206,9 +206,9 @@ conventions. These logical spatial dimensions are
+------+----------------------------------+------+-------------------+
| k | z_grid_index | Z | |
+------+----------------------------------+------+-------------------+
| k_u | z_grid_index_at_lower_w_location | Z | -0.5 |
| k_l | z_grid_index_at_lower_w_location | Z | -0.5 |
+------+----------------------------------+------+-------------------+
| k_l | z_grid_index_at_upper_w_location | Z | 0.5 |
| k_u | z_grid_index_at_upper_w_location | Z | 0.5 |
+------+----------------------------------+------+-------------------+
| k_p1 | z_grid_index_at_w_location | Z | (-0.5, 0.5) |
+------+----------------------------------+------+-------------------+
Expand All @@ -233,6 +233,16 @@ xarray_ distinguishes between "coordinates" and "data_vars". By default,
this behavior and treat grid variables as data_vars, use
``grid_vars_to_coords=False``.

.. warning::
For vertical coordinates (``Zl``, ``k_l``, etc.) the notion of "lower" and
"upper" always refers to the *logical* grid position, NOT the *physical* grid position.
This can be a major point of confusion. In array index space, the point ``k_l``
is indeed lower than ``k_u``; however, for typical MITgcm ocean model configurations,
in physical space the point ``k_l`` is physically *above* ``k_u``. This is because,
the Z axis starts from the ocean surface and increases downward.
In contrast, for atmospheric configurations which start from the ground and increase upwards,
the logical and physical positions are self-consistent.

Time
----

Expand Down