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rbeutel committed Mar 14, 2023
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23 changes: 14 additions & 9 deletions ariane.rst
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Expand Up @@ -205,7 +205,8 @@ This mode can be used to make estimates of transport through cross-sections by r
The namelist for quantitative mode is very similar to qualitative mode, note the frequency of calculation is now set in the ``QUANTITATIVE`` section.
Here is an example of a quantitative namelist.

.. code-block:: text
.. code-block:: fortran
&ARIANE
key_alltracers =.FALSE.,
key_sequential =.FALSE.,
Expand Down Expand Up @@ -366,8 +367,6 @@ Land points are :kbd:`#` and ocean points are :kbd:`-`.

* Run :kbd:`mkseg`

.. code-block:: bash
mkseg
* This will print out whether you succeeded or not and let you know the extent of the sections you defined. If something went wrong in editing :file:`segrid` the message will let you know how, this usually entails accidentally deleting a land point, not closing your boundaries, or forgetting to place the :kbd:`@` symbol somewhere!
* Once you have that without errors, section definitions will be copied automatically into a file called :file:`sections.txt`. The section definitions should look something like this::

Expand Down Expand Up @@ -435,7 +434,8 @@ Time Considerations

Particles initialized later in the simulation do not have as much time to cross one of the sections so it could be beneficial to impose a maximum age of each particle. This can be achieved by modifying :file:`mod_criter1.f90` in :kbd:`src/ariane` as follows:

.. code-block:: text
.. code-block:: fortran
!----------------------------------------!
!- ADD AT THE END OF EACH LINE "!!ctr1" -!
!----------------------------------------!
Expand All @@ -456,7 +456,8 @@ Defining and tracking water masses
You can also impose a density and/or salinity and/or temperature criteria on the initial particles in order to track different water masses. You can achieve this by editing :file:`mod_criter0.f90`.


.. code-block:: text
.. code-block:: fortran
!criter0=.TRUE. !!ctr0
!
!------------!
Expand Down Expand Up @@ -485,7 +486,8 @@ The following items must be changed or added to the namelist file:
Temperature
^^^^^^^^^^^

.. code-block:: text
.. code-block:: fortran
&TEMPERAT
c_dir_te ='/ocean/nsoontie/MEOPAR/SalishSea/results/storm-surges/final/dec2006/all_forcing/30min/',
c_prefix_te ='SalishSea_30m_20061214_20061215_grid_T.nc',
Expand All @@ -501,7 +503,8 @@ Temperature
Salinity
^^^^^^^^

.. code-block:: text
.. code-block:: fortran
&SALINITY
c_dir_sa ='/ocean/nsoontie/MEOPAR/SalishSea/results/storm-surges/final/dec2006/all_forcing/30min/',
c_prefix_sa ='SalishSea_30m_20061214_20061215_grid_T.nc',
Expand Down Expand Up @@ -585,7 +588,8 @@ Now that we have formatted the filenames as *prefix_number_suffix*, :kbd:`c_pref

For example, the **ZONALCRT** section would look like the following for input files **SalishSea_01_grid_U.nc** and **SalishSea_02_grid_U.nc** :

.. code-block:: text
.. code-block:: fortran
&ZONALCRT
c_dir_zo ='/ocean/imachuca/MEOPAR/Ariane/results/drifter_compare/sequential/',
c_prefix_zo ='SalishSea_',
Expand Down Expand Up @@ -614,7 +618,8 @@ Add a **SEQUENTIAL** section in namelist. This section has one parameter, :kbd:`
Sequential
^^^^^^^^^^

.. code-block:: text
.. code-block:: fortran
&SEQUENTIAL
maxcycles =1,
/
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