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	Time steps per netcdf history file. Must be > 0 when chunking.	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. Also used to select optional 3D tracer/derived fields in NetCDF plotfiles.	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.plot_nodal_data	whether to output nodal data (3D coordinates at nodes). Includes amrexvec_nu_x, amrexvec_nu_y, amrexvec_nu_z. Not used for netCDF	false or true	true
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
remora.plotfile_fill_value	fill value to use in AMReX plotfiles to mask values when using land/sea mask	Real	0.0
remora.netcdf_fill_value	fill value to use in NetCDF output to mask values when using land/sea mask	Real	1.0e37

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
REMORA writes CDF-5 files, which have no practical size limit. Some MPI builds still fail on writes larger than 2 GB — a limit of the MPI-IO layer, not the file format. If a large write crashes, see the MPICH note in the NetCDF build instructions, or use a native AMReX plotfile.
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. This combination is not allowed when writing a NetCDF history file, as noted above.
When Fennel biology is enabled, fennel in remora.plot_vars_3d expands to all active biology tracers. Active biology tracers can also be requested by name. See Fennel Biology for tracer names and component options.
Passive dye is opt-in: tracer is only available when remora.nscalar is at least 1 (see Inputs). Naming a field the run does not carry is not fatal – REMORA warns that the variable is not available and writes the plotfile without it – so a missing dye shows up as a missing column rather than a failed run.

3D Plotfile Field Options

Field	Definition
salt	salinity
temp	temperature
tracer	passive dye; also `tracer_1`, `tracer_2`, … for additional dyes
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
f	Coriolis parameter
visc2	horizontal viscosity
diff2_temp	horizontal diffusivity for temperature
diff2_salt	horizontal diffusivity for salinity
diff2_tracer	horizontal diffusivity for passive tracer
ubar
sustr
bustr
vbar
svstr
bvstr
stflux_{scalar}	surface tracer flux for for scalar = temp, salt, etc
srflux	shortwave radiation flux [W/m2]
lrflux	longwave radiation flux [W/m2]
lhflux	latent heat flux [W/m2]
shflux	sensible heat flux [W/m2]
mask_rho	rho-point mask (sea = 1, land = 0)
mask_u	u-point mask (sea = 1, land = 0)
mask_v	v-point mask (sea = 1, land = 0)

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.
remora.plot_nodal_data = false

To reduce plotfile size by excluding nodal coordinate data (amrexvec_nu_x, amrexvec_nu_y, amrexvec_nu_z), set this parameter to false. By default, nodal data is included (true).
remora.plot_staggered_vels = true

To include velocity components on cell faces (UFace, VFace, WFace multifabs) in the plotfile, set this parameter to true. By default, velocities are not included on faces (false).