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

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
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]

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).