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fixing the list in tracer section #321

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fixing the list in tracer section #321

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64 changes: 32 additions & 32 deletions doc/source/developer_guide/dg_other.rst
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Expand Up @@ -160,57 +160,57 @@ Additional information about tracers can be found in the
To add a tracer, follow these steps using one of the existing tracers as
a pattern.

#. **icepack\_tracers.F90** and **icepack\_[tracer].F90**: declare tracers,
add flags and indices, and create physics routines as described in the
`Icepack documentation <https://cice-consortium-icepack.readthedocs.io/en/master/developer_guide/dg_adding_tracers.html>`_
1) **icepack\_tracers.F90** and **icepack\_[tracer].F90**: declare tracers,
add flags and indices, and create physics routines as described in the
`Icepack documentation <https://cice-consortium-icepack.readthedocs.io/en/master/developer_guide/dg_adding_tracers.html>`_

#. **ice_arrays_column.F90**: declare arrays
2) **ice_arrays_column.F90**: declare arrays

#. **ice_init_column.F90**: initialize arrays
3) **ice_init_column.F90**: initialize arrays

#. **ice\_init.F90**: (some of this may be done in **icepack\_[tracer].F90**
instead)
4) **ice\_init.F90**: (some of this may be done in **icepack\_[tracer].F90**
instead)

- declare ``tr_[tracer]`` and ``nt_[tracer]`` as needed
- declare ``tr_[tracer]`` and ``nt_[tracer]`` as needed

- add logical namelist variables ``tr_[tracer]``, ``restart_[tracer]``
- add logical namelist variables ``tr_[tracer]``, ``restart_[tracer]``

- initialize and broadcast namelist variables
- initialize and broadcast namelist variables

- check for potential conflicts, aborting if any occur
- check for potential conflicts, aborting if any occur

- print namelist variables to diagnostic output file
- print namelist variables to diagnostic output file

- initialize tracer flags etc in icepack (call *icepack_init_tracer_flags* etc)
- initialize tracer flags etc in icepack (call *icepack_init_tracer_flags* etc)

- increment number of tracers in use based on namelist input (``ntrcr``)
- increment number of tracers in use based on namelist input (``ntrcr``)

- define tracer dependencies
- define tracer dependencies

#. **CICE\_InitMod.F90**: initialize tracer (includes reading restart file)
5) **CICE\_InitMod.F90**: initialize tracer (includes reading restart file)

#. **CICE\_RunMod.F90**, **ice\_step\_mod.F90** (and elsewhere as needed):
6) **CICE\_RunMod.F90**, **ice\_step\_mod.F90** (and elsewhere as needed):

- call routine to write tracer restart data
- call routine to write tracer restart data

- call Icepack or other routines to update tracer value
(often called from **ice\_step\_mod.F90**)
- call Icepack or other routines to update tracer value
(often called from **ice\_step\_mod.F90**)

#. **ice\_restart.F90**: define restart variables (for binary, netCDF and PIO)
7) **ice\_restart.F90**: define restart variables (for binary, netCDF and PIO)

#. **ice\_restart\_column.F90**: create routines to read, write tracer restart data
8) **ice\_restart\_column.F90**: create routines to read, write tracer restart data

#. **ice\_fileunits.F90**: add new dump and restart file units
9) **ice\_fileunits.F90**: add new dump and restart file units

#. **ice\_history\_[tracer].F90**: add history variables
(Section :ref:`addhist`)
10) **ice\_history\_[tracer].F90**: add history variables
(Section :ref:`addhist`)

#. **ice\_in**: add namelist variables to *tracer\_nml* and
*icefields\_nml*. Best practice is to set the namelist values so that the
new capability is turned off, and create an option file with your preferred
configuration in **configuration/scripts/options**.
11) **ice\_in**: add namelist variables to *tracer\_nml* and
*icefields\_nml*. Best practice is to set the namelist values so that the
new capability is turned off, and create an option file with your preferred
configuration in **configuration/scripts/options**.

#. If strict conservation is necessary, add diagnostics as noted for
topo ponds in the `Icepack documentation <https://cice-consortium-icepack.readthedocs.io/en/master/science_guide/index.html>`_.
12) If strict conservation is necessary, add diagnostics as noted for
topo ponds in the `Icepack documentation <https://cice-consortium-icepack.readthedocs.io/en/master/science_guide/index.html>`_.

#. Update documentation, including **cice_index.rst** and **ug_case_settings.rst**
13) Update documentation, including **cice_index.rst** and **ug_case_settings.rst**