Plotfiles

Controlling PlotFile Generation

“Plotfiles” can be written very efficiently in parallel in a native AMReX format or NetCDF (via PnetCDF).

The following options in the inputs file control the generation of plotfiles.

List of Parameters

Parameter	Definition	Acceptable Values	Default
remora.plotfile_type	AMReX or NETCDF plotfiles	amrex or netcdf	amrex
remora.file_min_digits	Minimum number of digits in iteration number appended to plotfile, checkpoint, or chunked history files	Integer >= 0	5
remora.write_history_file	do we write netcdf files at each timestep or one file for all timesteps?	false or true	true
remora.chunk_history_file	do we divide netcdf history files so that each file contains only a certain number of time steps?	false or true	false
remora.steps_per_history_file	Maximum number of steps per netcdf history file. If <=0, calculate automatically such that each file is less than 2GB	integer	-1
remora.plot_file	prefix for plotfiles	String	“plt”
remora.plot_int	how often (by level-0 time steps) to write plot files	Integer \(> 0\)	-1
remora.plot_int_time	how often (in simulation time seconds) to write plot files	Real \(> 0\)	-1.0
remora.plot_vars_3d	name of 3D variables to include in plotfiles. Not used for netCDF	list of names (see table below)	None
remora.plot_vars_2d	name of 2D variables to include in plotfiles. Not used for netCDF	list of names (see table below)	None
remora.plot_staggered_vels	whether to output velocities on cell faces. They will be in the UFace/VFace/WFace multifab. Not used for netCDF	false or true	false
remora.expand_plotvars_to_unif_rr	whether to expand a multilevel plotfile to have a uniform refinement ratio on levels > 0. This is necessary for amrvis.	false or true	false

Notes

• The NetCDF option is only available if REMORA has been built with USE_PNETCDF enabled.

• The write_history_file option is only available if plotfile_type = netcdf

• Depending on your PnetCDF build, the code may be unable to write files larger than 2 GB. If the code crashes when writing a NetCDF history file (or a single time step, if you have a particularly large grid), consider building with MPICH v4.2.2 or instead outputting a native AMReX plotfile instead.

• Velocity components are defined on faces within the REMORA code, but are averaged onto cell centers when written in amrex/native plotfiles. They are not averaged when writing NetCDF files.

• File prefixes can include directories.

• If both remora.plot_int and remora.plot_int_time have been set, plotfile output will occur

plot_int steps or plot_int_time simulation seconds after the last plotfile, whichever happens first.

3D Plotfile Field Options

Field	Definition
salt	salinity
temp	temperature
scalar	passive scalar
x_velocity	velocity in x-direction
y_velocity	velocity in y-direction
z_velocity	velocity in z-direction
vorticity	vorticity

2D Plotfile Field Options

Field	Definition
zeta
h
ubar
sustr
bustr
vbar
svstr
bvstr

Examples of Usage

• remora.plotfile_type = amrex

• remora.plot_file = out/plt_run

• remora.plot_int = 10

  means that native plot files (actually directories) starting with the prefix “plt_run” will be generated every 10 level-0 time steps in the directory out. If using amrex format, that directory names will be plt_run00000, plt_run00010, plt_run00020, etc. If using NetCDF format, the names will have “.nc” appended.

  AMReX plotfiles will contain data at all of the refinement levels. NetCDF files will not be output if there is more than one level.