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Merge pull request #324 from hklion/plotfile_docs
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Plotfile docs
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hklion authored Dec 27, 2024
2 parents 329a16b + ca9da09 commit ae87d7d
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30 changes: 17 additions & 13 deletions Docs/sphinx_doc/Checkpoint.rst
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Expand Up @@ -22,19 +22,23 @@ Writing the Checkpoint "Files"
List of Parameters
------------------

+----------------------------------+----------------+----------------+----------------+
| Parameter | Definition | Acceptable | Default |
| | | Values | |
+==================================+================+================+================+
| **remora.check_file** | prefix for | String | “*chk*” |
| | restart files | | |
+----------------------------------+----------------+----------------+----------------+
| **remora.check_int** | how often (by | Integer | -1 |
| | level-0 time | :math:`> 0` | |
| | steps) to | | |
| | write restart | | |
| | files | | |
+----------------------------------+----------------+----------------+----------------+
+----------------------------------+-----------------------------------+----------------+----------------+
| Parameter | Definition | Acceptable | Default |
| | | Values | |
+==================================+===================================+================+================+
| **remora.check_file** | prefix for | String | “*chk*” |
| | restart files | | |
+----------------------------------+-----------------------------------+----------------+----------------+
| **remora.check_int** | how often (by | Integer | -1 |
| | level-0 time | :math:`> 0` | |
| | steps) to | | |
| | write restart | | |
| | files | | |
+----------------------------------+-----------------------------------+----------------+----------------+
| **remora.file_min_digits** | Minimum number of digits | Integer >= 0 | 5 |
| | in iteration number appended to | | |
| | plotfile and checkpoint files | | |
+----------------------------------+-----------------------------------+----------------+----------------+

Restarting
==========
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23 changes: 9 additions & 14 deletions Docs/sphinx_doc/Inputs.rst
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Expand Up @@ -70,9 +70,16 @@ Instructions for how to specify domain boundary conditions, with usage examples
Imposing Boundary and Initial Conditions from NetCDF File
=========================================================

Grid, initial, and time-dependent boundary data can be specified using NetCDF files, as in ROMS. REMORA expects files in the same format as ROMS, in NetCDF classic format (32- or 64-bit).
Currently, if one of these are specified in a file, they all must be. Boundary condition options with NetCDF boundary data are equivalent to ROMS clamped, Chapman-Flather, and Orlanski + Nudging boundary conditions. Options and examples can be found in the section on :ref:`Domain Boundary Conditions`<sec:domainBCs>`.
Grid, initial, and time-dependent boundary data can be specified using NetCDF files, as in ROMS. REMORA expects files in the same format as ROMS, in NetCDF classic format (32- or 64-bit). Other versions of NetCDF files can be converted to 64-bit NetCDF classic by running the command:

.. code:: shell
ncks -5 old_file.nc converted_file.nc
The utility ``ncks`` is part of the `NCO <https://nco.sourceforge.net>`_ suite.

Currently, if one of these are speci fied in a file, they all must be. Boundary condition options with NetCDF boundary data are equivalent to ROMS clamped, Chapman-Flather, and Orlanski + Nudging boundary conditions. Options and examples can be found in the section on :ref:`Domain Boundary Conditions`<sec:domainBCs>`.
--
List of Parameters
------------------

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**remora.init_shrink** :math:`\neq 1` then the first time step will in
fact be **remora.init_shrink** \* **remora.fixed_dt**.
File Output
===========

+-------------------------------+-----------------------------------+----------------+----------------------------+
| Parameter | Definition | Acceptable | Default |
| | | Values | |
+===============================+===================================+================+============================+
| **remora.file_min_digits** | Minimum number of digits | Integer >= 0 | 5 |
| | in iteration number appended to | | |
| | plotfile and checkpoint files | | |
+-------------------------------+-----------------------------------+----------------+----------------------------+

Restart Capability
==================

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58 changes: 31 additions & 27 deletions Docs/sphinx_doc/Plotfiles.rst
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Expand Up @@ -21,33 +21,37 @@ The following options in the inputs file control the generation of plotfiles.
List of Parameters
------------------

+--------------------------------+------------------+-----------------------+------------+
| Parameter | Definition | Acceptable | Default |
| | | Values | |
+================================+==================+=======================+============+
| **remora.plotfile_type** | AMReX or NETCDF | "amrex" or | "amrex" |
| | | "netcdf / "NetCDF" | |
+--------------------------------+------------------+-----------------------+------------+
| **remora.write_history_file** | do we write | false or true | true |
| | netcdf files at | | |
| | each timestep | | |
| | or one file for | | |
| | all timesteps? | | |
+--------------------------------+------------------+-----------------------+------------+
| **remora.plot_file** | prefix for | String | “plt” |
| | plotfiles | | |
+--------------------------------+------------------+-----------------------+------------+
| **remora.plot_int** | how often (by | Integer | -1 |
| | level-0 time | :math:`> 0` | |
| | steps) to write | | |
| | plot files | | |
+--------------------------------+------------------+-----------------------+------------+
| **remora.plot_vars** | name of | list of names | None |
| | variables to | (see table below) | |
| | include in | | |
| | plotfiles. Not | | |
| | used for netCDF | | |
+--------------------------------+------------------+-----------------------+------------+
+--------------------------------+-----------------------------------+-----------------------+------------+
| Parameter | Definition | Acceptable | Default |
| | | Values | |
+================================+===================================+=======================+============+
| **remora.plotfile_type** | AMReX or NETCDF plotfiles | "amrex" or | "amrex" |
| | | "netcdf / "NetCDF" | |
+--------------------------------+-----------------------------------+-----------------------+------------+
| **remora.file_min_digits** | Minimum number of digits | Integer >= 0 | 5 |
| | in iteration number appended to | | |
| | plotfile and checkpoint files | | |
+--------------------------------+-----------------------------------+-----------------------+------------+
| **remora.write_history_file** | do we write | false or true | true |
| | netcdf files at | | |
| | each timestep | | |
| | or one file for | | |
| | all timesteps? | | |
+--------------------------------+-----------------------------------+-----------------------+------------+
| **remora.plot_file** | prefix for | String | “plt” |
| | plotfiles | | |
+--------------------------------+-----------------------------------+-----------------------+------------+
| **remora.plot_int** | how often (by | Integer | -1 |
| | level-0 time | :math:`> 0` | |
| | steps) to write | | |
| | plot files | | |
+--------------------------------+-----------------------------------+-----------------------+------------+
| **remora.plot_vars** | name of | list of names | None |
| | variables to | (see table below) | |
| | include in | | |
| | plotfiles. Not | | |
| | used for netCDF | | |
+--------------------------------+-----------------------------------+-----------------------+------------+

.. _notes-5:

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