adding parameters.rst to docs

docs/index.rst

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    equations
    flowchart
    tests/index
+   parameters
    api
    bibliography
 

docs/parameters.rst

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+.. Runtime parameters
+
+Runtime parameters
+==========================
+
+This document lists all of the runtime parameters in Quokka.
+Using the AMReX ParmParse object, these parameters are read in the `readParameters()` function in `simulation.hpp` from an input file or from command line arguments.
+
+.. list-table:: Table of runtime parameters.
+   :widths: 25 25 50
+   :header-rows: 1
+
+   * - Parameter Name
+     - Type
+     - Description
+   * - max_timesteps
+     - Integer
+     - The maximum number of time steps for the simulation.
+   * - cfl
+     - Float
+     - Sets the CFL number for the simulation.
+   * - amr_interpolation_method
+     - Integer
+     - Selects the method (piecewise constant or piecewise linear with limiters) used to interpolate from coarse to fine AMR levels. Except for debugging, this should not be changed.
+   * - stop_time
+     - Float
+     - The simulation time at which to stop evolving the simulation.
+   * - ascent_interval
+     - Integer
+     - The number of coarse timesteps between Ascent outputs.
+   * - plotfile_interval
+     - Integer
+     - The number of coarse timesteps between plotfile outputs.
+   * - plottime_interval
+     - Float
+     - The time interval (in simulated time) between plotfile outputs.
+   * - projection_interval
+     - Integer
+     - The number of coarse timesteps between 2D projection outputs.
+   * - statistics_interval
+     - Integer
+     - The number of coarse timesteps between statistics outputs.
+   * - checkpoint_interval
+     - Float
+     - The number of coarse timesteps between checkpoint outputs.
+   * - checkpointtime_interval
+     - Float
+     - The time interval (in simulated time) between checkpoint outputs.
+   * - do_reflux
+     - Integer
+     - this turns on refluxing at coarse-fine boundaries (1) or turns it off (0). Except for debugging, this should always be on when AMR is used.
+   * - suppress_output
+     - Integer
+     - If set to 1, this disables output to stdout while the simulation is running.
+   * - derived_vars
+     - String
+     - A list of the names of derived variables that should be included in the plotfile and Ascent outputs.
+   * - regrid_interval
+     - Integer
+     - The number of timesteps between AMR regridding.
+   * - density_floor
+     - Float
+     - The minimum density value allowed in the simulation. Enforced through EnforceLimits.
+   * - temperature_ceiling
+     - Float
+     - The ceiling on temperature values in the simulation. Enforced through EnforceLimits.
+   * - speed_ceiling
+     - Float
+     - The ceiling on the absolute value of the fluid velocity in the simulation. Enforced through EnforceLimits.
+   * - max_walltime
+     - String
+     - The maximum walltime for the simulation in the format DD:HH:SS (days/hours/seconds). After 90% of this walltime elapses, the simulation will automatically stop and exit.