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fix quoting in extended_modflow.tex
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mjreno committed Dec 10, 2024
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\subsection{NetCDF Export Files}

The extended build of \mf can optionally create model NetCDF export files. \mf supports two types of NetCDF exports, referred to here as ''structured'' and ''mesh''.
The extended build of \mf can optionally create model NetCDF export files. \mf supports two types of NetCDF exports, referred to here as ``structured'' and ``mesh''.

\mf NetCDF exports by default contain model dependent variable timeseries data, e.g. head. In addition, \mf package griddata input arrays can be configured to be written to the export file. Creating export files containing only one or the other of these these types of data form two distinct uses for the exports. Generating exports of these two types will described below.

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\mf structured NetCDF exports define x and y geometric coordinate variables and are not based on the UGRID specification. \mf structured exports can be generated with a DIS based GWF, GWT, or GWE model.

\subsubsection{Dependent variable exports}
A typical use case creates an export that capture timeseries output for the model dependent variable. This export can be optioned simply by adding the ''EXPORT\_NETCDF'' keyword to a GWF, GWT, or GWE model name file. This keyword takes an argument for the NetCDF export type, either ''STRUCTURED'' or ''MESH'' (or alternatively, ''UGRID''). Configured in this way, the export will contain only the mesh or x and y coordinate variables and the dependent variable(s). Additional configuration options are possible when a NetCDF configuration package (UTL-NCF) is created, such as per-variable compression, chunking options, and options meant to support visualization in post-processing tools like QGIS. This package is described below.
A typical use case creates an export that capture timeseries output for the model dependent variable. This export can be optioned simply by adding the ``EXPORT\_NETCDF'' keyword to a GWF, GWT, or GWE model name file. This keyword takes an argument for the NetCDF export type, either ``STRUCTURED'' or ``MESH'' (or alternatively, ``UGRID''). Configured in this way, the export will contain only the mesh or x and y coordinate variables and the dependent variable(s). Additional configuration options are possible when a NetCDF configuration package (UTL-NCF) is created, such as per-variable compression, chunking options, and options meant to support visualization in post-processing tools like QGIS. This package is described below.

\subsubsection{Exporting array input}
Packages that support exporting griddata input arrays to model NetCDF files support the ''EXPORT\_ARRAY\_NETCDF'' keyword. Using this keyword, when model NetCDF export also is active, has the effect of writing all package griddata arrays to the NetCDF export. Writing candidate arrays to a NetCDF file offers an alternative to storing them in an ascii or binary input file.
Packages that support exporting griddata input arrays to model NetCDF files support the ``EXPORT\_ARRAY\_NETCDF'' keyword. Using this keyword, when model NetCDF export also is active, has the effect of writing all package griddata arrays to the NetCDF export. Writing candidate arrays to a NetCDF file offers an alternative to storing them in an ascii or binary input file.

One approach to converting existing ascii or binary inputs to NetCDF inputs is described next. \mf supports a validate mode option intended to support error checking. In this mode no matrix equations are assembled or solved and no solution based outputs are created. Input, however, is still read in validate mode and thus can be written to NetCDF exports when configured. Specific IDP supported packages can be configured to export griddata array input by using the 'EXPORT\_ARRAY\_NETCDF'' package option when running the simulation in validate mode. When configured in this way, \mf will generate a NetCDF export file, absent a dependent or time coordinate variable, that can serve as a separate input file for model gridded package data.
One approach to converting existing ascii or binary inputs to NetCDF inputs is described next. \mf supports a validate mode option intended to support error checking. In this mode no matrix equations are assembled or solved and no solution based outputs are created. Input, however, is still read in validate mode and thus can be written to NetCDF exports when configured. Specific IDP supported packages can be configured to export griddata array input by using the ``EXPORT\_ARRAY\_NETCDF'' package option when running the simulation in validate mode. When configured in this way, \mf will generate a NetCDF export file, absent a dependent or time coordinate variable, that can serve as a separate input file for model gridded package data.

\subsection{NetCDF as simulation input}
\mf can read NetCDF files as model inputs containing package griddata array input. Files generated using the validate method described in the previous section are suitable as inputs- note that \mf expects specific annotations for NetCDF input variables and that these are written by default into \mf NetCDF exports. An example follows showing a model name file that configures a NetCDF input and IC and NPF input files that specify specific griddata parameters should be read from the model NetCDF input:
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