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Merge pull request #77 from nextsimdg/docs
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‎docs/Doxyfile‎

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GENERATE_MAN = NO
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GENERATE_RTF = NO
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CASE_SENSE_NAMES = NO
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GENERATE_HTML = YES
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GENERATE_XML = YES
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RECURSIVE = YES
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QUIET = YES
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GENERATE_TREEVIEW = YES
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SOURCE_BROWSER = YES
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# WARN_IF_UNDOCUMENTED = YES
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#---------------------------------------------------------------------------
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# Configuration options related to the dot tool
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#---------------------------------------------------------------------------
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CLASS_DIAGRAMS = YES
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MSCGEN_PATH =
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DIA_PATH =
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HIDE_UNDOC_RELATIONS = YES
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HAVE_DOT = YES
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DOT_NUM_THREADS = 0
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DOT_FONTNAME = Helvetica
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DOT_FONTSIZE = 10
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DOT_FONTPATH =
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CLASS_GRAPH = YES
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COLLABORATION_GRAPH = YES
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GROUP_GRAPHS = YES
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UML_LOOK = YES
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UML_LIMIT_NUM_FIELDS = 50
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TEMPLATE_RELATIONS = YES
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INCLUDE_GRAPH = YES
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INCLUDED_BY_GRAPH = YES
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CALL_GRAPH = YES
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CALLER_GRAPH = YES
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GRAPHICAL_HIERARCHY = YES
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DIRECTORY_GRAPH = YES
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DOT_IMAGE_FORMAT = png
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INTERACTIVE_SVG = NO
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DOT_PATH =
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DOTFILE_DIRS =
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MSCFILE_DIRS =
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DIAFILE_DIRS =
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PLANTUML_JAR_PATH =
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PLANTUML_INCLUDE_PATH =
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DOT_GRAPH_MAX_NODES = 100
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MAX_DOT_GRAPH_DEPTH = 0
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DOT_TRANSPARENT = YES
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DOT_MULTI_TARGETS = NO
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GENERATE_LEGEND = YES
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DOT_CLEANUP = YES
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#---------------------------------------------------------------------------
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# Configuration options related to the dot tool

‎docs/api/class.rst‎

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.. Copyright (c) 2021, Nansen Environmental and Remote Sensing Center
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Classes
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-------
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.. doxygenclass:: nextsim::model
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:project: nextsimdg
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:members:

‎docs/api/counttimercpp.rst‎

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.. Copyright (c) 2021, Nansen Environmental and Remote Sensing Center
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CountTimer.cpp
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--------------
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.. doxygenfile:: CountTimer.cpp
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:project: nextsimdg
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:members:

‎docs/api/function.rst‎

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.. Copyright (c) 2021, Nansen Environmental and Remote Sensing Center
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Functions
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---------
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.. doxygenfunction::

‎docs/api/index.rst‎

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.. Copyright (c) 2021, Nansen Environmental and Remote Sensing Center
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Index
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-----
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.. doxygenindex::
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:project: nextsimdg
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:outline:
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:no-link:

‎docs/api/num.rst‎

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.. Copyright (c) 2021, Nansen Environmental and Remote Sensing Center
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Enumerator
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----------
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.. doxygenenum::

‎docs/api/structure.rst‎

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.. Copyright (c) 2021, Nansen Environmental and Remote Sensing Center
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Structure
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---------
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.. doxygenstruct::

‎docs/api/typedef.rst‎

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.. Copyright (c) 2021, Nansen Environmental and Remote Sensing Center
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Typedef
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-------
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.. doxygentypedef::

‎docs/getting_started.rst‎

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.. Copyright (c) 2021, Nansen Environmental and Remote Sensing Center
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.. raw:: html
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Getting Started
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===============
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This short guide explains how to get started with nextsimdg once you have installed it with one of the methods described in the installation section.
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Simple Example
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--------------
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Control of nextsimdg is done using configuration files. One or more of these can be specified on the command line using the `--config-file` (for a single file) or `--config-files` (for several files) options. These files specify the configuration of the model, including the initial restart file (`model.init_file`) and the start (`model.start`), stop (`model.stop`) and time step (`model.time_step`) values, formatted as simple integers. The configuration of parts of the model can also be changed, but this is beyond the scope of a simple example.
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As part of the 0.1.0 release, the model operates on a simple fixed 10x10 grid of data. The restart file can be generated using the Python script `dev_res.py`. This generates an initial restart file of the correct format, which is a netCDF file of the correct structure. The desired data can be provided by editing the python script.
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With the value of the `model.init_file` variable set to the name of the correct initialization file, add the name of the configuration file as a `config-file` argument to the command line and execute. The model will produce a restart file named `restart.nc`. The results of applying the model physics to the initial data over the specified number of time steps will be found here.
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An example config file (`dev1.cfg`) and shell script (`dev1.sh`) to run the model can be found in the `run` directory.
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First Example
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-------------
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In this first example, we are going to ...

‎docs/index.rst‎

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.. toctree::
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:caption: API REFERENCE
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:caption: API Documentation
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:maxdepth: 2
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html/index.html
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api/library_root
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api/index
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All `Doxygen documentation`_
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.. _Doxygen documentation : https://nextsimdg.github.io/nextsimdg/index.html

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