Add doc page with input parameters and descriptions

Docs/sphinx_documentation/source/InputParameters.rst

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+..
+  COMMENT: This page uses the built-in python syntax highlighting to get things to
+  highlight correctly in the final output.
+
+.. _input_parameters:
+
+Input Parameters
+================
+
+This page contains a list of AMReX input parameters. These values can be accessed by
+either including them in an inputs file, or specifying them at the command line.
+For more information see :ref:`sec:basics:parmparse`.
+
+Plotfile Parameters
+-------------------
+
+The parameters below affect plotfile operations:
+
+amr prefix
+~~~~~~~~~~
+
+.. py:data:: amr.plot_vars
+   :type: string
+
+   Specify list of variables to be included in plot.
+   E.g. ``var1 var2 var3``. Use ``ALL`` to plot all variables, and
+   ``NONE`` to clear all plot variables.
+
+.. py:data:: amr.derive_plot_vars
+   :type: string
+
+   Specify list of derived variables to be included in plot.
+   E.g. ``var1 var2 var3``. Use ``ALL`` to plot all variables, and
+   ``NONE`` to clear all plot variables.
+
+.. py:data:: amr.small_plot_vars
+   :type: string
+
+   Specify list of variables to be included in small plot.
+   E.g. ``var1 var2 var3``. Use ``ALL`` to plot all variables, and
+   ``NONE`` to clear all plot variables.
+
+.. py:data:: amr.small_derive_plot_vars
+   :type: string
+
+   Specify list of derived variables to be included in small plot.
+   E.g. ``var1 var2 var3``. Use ``ALL`` to plot all variables, and
+   ``NONE`` to clear all plot variables.
+
+.. py:data:: amr.plotfile_on_restart
+   :type: bool
+
+   Write plotfile when we restart ( only used if ``plot_int > 0``)
+
+.. py:data:: amr.file_name_digits
+   :type: int
+
+   Specify how many zeros to use when padding the filename. E.g. ``amr.file_name_digits=5``
+   with the 37th plot will have suffix, ``00037``.
+
+.. py:data:: amr.plot_files_output
+   :type: bool
+
+   To enable or disable plotting.
+
+.. py:data:: amr.plot_nfiles
+   :type: int
+
+   Number of processes to use/number of plotfiles to write simultaneously.
+
+.. py:data:: amr.plot_file
+   :type: string
+   :value: "plt" (default)
+
+   Plotfile root filename. E.g. ``amr.plot_file="plot"`` would give ``plot00000``.
+
+.. py:data:: amr.plot_int
+   :type: int
+
+   Frequency of plotfile output.
+
+.. py:data:: amr.plot_per
+   :type: amrex::Real
+
+   How often to plot in units of time. Set to negative value to disable.
+
+.. py:data:: amr.plot_log_per
+   :type: amrex::Real
+
+   How often to plot in units of :math:`\log_{10}{}` time.
+   Set to a negative value to disable.
+
+.. py:data:: amr.small_plot_file
+   :type: string
+   :value: "smallplt" (default)
+
+   Small plotfile root filename. E.g. ``amr.plot_file="plot"`` would give ``plot00000``.
+
+.. py:data:: amr.small_plot_int
+   :type: int
+
+   Frequency of small plotfile output.
+
+.. py:data:: amr.small_plot_per
+   :type: amrex::Real
+
+   How often to plot the small plotfile in units of time. Set to a negative
+   value to disable.
+
+.. py:data:: amr.small_plot_log_per
+   :type: amrex::Real
+
+   How often to plot the small plotfile in units of :math:`\log_{10}{}` time.
+   Set to a negative value to disable.
+
+.. py:data:: amr.write_plotfile_with_checkpoint
+   :type: int
+
+   Set to 1 to write a plotfile whenever a checkpoint is written.
+
+.. py:data:: amr.stream_max_tries
+   :type: int
+   :value: 4 (default)
+
+   Set maximum number of attempts to write plotfile. Does not apply to AsyncOut.
+
+.. py:data:: amr.abort_on_stream_retry_failure
+   :type: bool
+   :value: False (default)
+
+   If true, will AMReX will abort when a file cannot be written after exceeding
+   the number of attempts specified.
+
+.. py:data:: amr.precreateDirectories
+   :type: bool
+   :value: True (default)
+
+   Write all directories at once.
+
+.. py:data:: amr.prereadFAHeaders
+   :type: bool
+   :value: True (default)
+
+   Preread and broadcast all FabArray headers.
+
+.. py:data:: amr.plot_headerversion
+   :type: int
+   :value: 1 (default)
+
+   Specify a version of the FabArray Header code. If the version does not match default,
+   the specified version is used.
+
+------
+
+
+vismf prefix
+~~~~~~~~~~~~
+
+.. py:data:: vismf.v
+   :type: int
+
+   Set to 1 for verbose output of VisMF operations.
+
+.. py:data:: vismf.headerversion
+   :type: int
+
+   Specify a version for the output file  header. If the version does not match default,
+   the specified version is used.
+
+.. py:data:: vismf.groupsets
+   :type: bool
+   :value: False (default)
+
+   Wait to receive each group of processes, rather than each individual process.
+
+..
+  HACK: Needs verification
+
+.. py:data:: vismf.setbuf
+   :type: bool
+   :value: True (default)
+
+   Resize the butter to ``GetIOBufferSize``.
+
+.. py:data:: vismf.usesingleread
+   :type: bool
+   :value: False (default)
+
+   Read all FabArrays at one time.
+
+.. py:data:: vismf.usesinglewrite
+   :type: bool
+   :value: False (default)
+
+   Write all FabArrays at one time.
+
+.. py:data:: vismf.checkfilepositions
+   :type: bool
+   :value: False (default)
+
+   Verify that the bytes written match string stream.
+
+.. py:data:: vismf.usepersistentifstreams
+   :type: bool
+   :value: False (default)
+
+   *Description Needed.*
+
+.. py:data:: vismf.usesyhchronousreads
+   :type: bool
+   :value: False (default)
+
+   *Description Needed.*
+
+.. py:data:: vismf.usedynamicsetselection
+   :type: bool
+   :value: True (default)
+
+   Dynamically decide which proc writes to file.
+
+.. py:data:: vismf.iobuffersize
+   :type: Long
+   :value: 262144*8 (default)
+
+   Set the I/O buffer size.
+
+.. py:data:: vismf.allowsparsewrites
+   :type: Long
+   :value: True (default)
+
+   Allow writing when the MultiFab is determined to contain sparse data.
+