Output files¶

uDALES writes its outputs as NetCDF files. Simulations run on more than one CPU write one file per CPU for most output types; files that are already reduced across the whole domain (e.g. the y-, xy- and xy-time-averaged statistics, the TKE budget and the facet energy balance files) are written once, by rank 0. Per-CPU files use the naming pattern <name>.<px>.<py>.<expnr>.nc, where <px> and <py> are the three-digit x- and y-pencil ranks; reduced files use <name>.<expnr>.nc. Use gather_outputs.sh (or its HPC/ARCHER2 wrappers) to merge the per-CPU files into single files per experiment — see Post-processing.

All switches and frequency parameters below live in the &OUTPUT, &TREES, &WALLS and &ENERGYBALANCE namelists of namoptions; see the Configuration page for their defaults and constraints.

Output files¶

File	Enabled by	Frequency	Contents
Statistics (time- and/or space-averaged)
`tdump.<px>.<py>.<expnr>.nc`	`ltdump`	`tstatsdump`	Time-averaged 3D statistics per CPU: mean velocity, temperature, moisture, pressure and scalar fields; PSS defect; turbulent momentum/heat/scalar fluxes; variances and TKE; SGS scalar fluxes.
`mintdump.<px>.<py>.<expnr>.nc`	`lmintdump`	`tstatsdump`	Reduced time-averaged 3D statistics per CPU: mean u, v, w, temperature and moisture, and pressure only (lighter-weight alternative to `tdump`).
`xytdump.<expnr>.nc`	`lxytdump`	`tstatsdump`	x-, y- and time-averaged 1D (height) statistics: mean velocity/temperature/moisture/pressure profiles, turbulent/kinematic/SGS fluxes, temperature and momentum variances, TKE.
`xydump.<expnr>.nc`	`lxydump`	`tsample`	x- and y-averaged instantaneous 1D (height) profiles: velocity, temperature, moisture, pressure, turbulent/SGS momentum and heat fluxes, advective fluxes.
`ytdump.<expnr>.nc`	`lytdump`	`tstatsdump`	y- and time-averaged 2D (x, height) statistics: mean velocity/temperature/moisture/scalar profiles, turbulent/kinematic/SGS fluxes, variances. Only functional if the x-direction is not parallelised.
`ydump.<expnr>.nc`	`lydump`	`tsample`	y-averaged instantaneous 2D (x, height) profiles: velocity, temperature, moisture, scalars, turbulent/SGS momentum and heat fluxes, advective fluxes. Only functional if the x-direction is not parallelised.
`tkedump.<expnr>.nc`	`ltkedump`	`tstatsdump`	xy-averaged TKE budget terms vs. height: buoyancy production, total transport, advection, turbulent transport, SGS transport, shear production, viscous and SGS dissipation. Disabled. The budget terms are never accumulated, so the file would contain nothing but zeros; setting `ltkedump = .true.` now aborts the run with an error instead. Tracked in issue #352.
`treedump.<px>.<py>.<expnr>.nc`	`ltreedump` (`&TREES`)	`tstatsdump`	Time-averaged 3D vegetation/tree terms per CPU: drag in x, y, z; temperature and moisture source/sink terms; scalar source/sink terms; decoupling factor.
Instantaneous fields
`fielddump.<px>.<py>.<expnr>.nc`	`lfielddump`	`tfielddump`	Instantaneous 3D snapshots of the variables listed in `fieldvars` (e.g. velocity components, temperature, moisture, pressure, scalars, wall stresses, heat flux, IBM masks, divergence), per CPU.
Slices
`kslicedump.<px>.<py>.<expnr>.nc`	`lkslicedump`	`tsample`	Instantaneous horizontal (x, y) slice at `k = kslice` of u, v, w, temperature and moisture, per CPU.
`islicedump.<px>.<py>.<expnr>.nc`	`lislicedump`	`tsample`	Instantaneous vertical (y, z) slice at `i = islice` of u, v, w, temperature and moisture; written only by the CPU(s) owning that i-index.
`jslicedump.<px>.<py>.<expnr>.nc`	`ljslicedump`	`tsample`	Instantaneous vertical (x, z) slice at `j = jslice` of u, v, w, temperature and moisture; written only by the CPU(s) owning that j-index.
Facets
`fac.<expnr>.nc`	`lwritefac` (`&WALLS`)	`dtfac`	Facet momentum and heat-transfer data per facet, averaged over the `dtfac` window: surface shear stresses `tau_x`, `tau_y`, `tau_z`, pressure and pressure fluctuation, heat transfer coefficients.
`facT.<expnr>.nc`	`lwriteEBfiles` (requires `lEB`)	`dtEB`	Facet layer temperature (`T`) and temperature gradient (`dTdz`) per facet and facet layer.
`facEB.<expnr>.nc`	`lwriteEBfiles` (requires `lEB`)	`dtEB`	Facet surface energy-balance terms per facet: net shortwave, incoming longwave, outgoing longwave, sensible heat flux, latent heat flux, soil water content.

Statistics that are sampled every tsample and only dumped every tstatsdump (tdump, mintdump, xytdump, ytdump, treedump, tkedump) report the average over the preceding tstatsdump window; the switches whose frequency is tsample (xydump, ydump, the slice dumps) instead write an instantaneous sample every tsample. Sampling/averaging only starts once the simulation time passes tstatstart.

Subgrid-scale (SGS) flux variables¶

The statistics files listed above contain SGS counterparts of the resolved fluxes, named usgs*, vsgs*, wsgs*, thlsgs*, qtsgs* and sv1sgs–sv4sgs (sca1sgs*–sca3sgs* in the y-averaged files).

Sign convention¶

These are fluxes, and they carry the same sign as the resolved fluxes written alongside them in the same file with the same units. Explicitly, with K_m the eddy viscosity (ekm) and K_h the eddy diffusivity (ekh):

Variable	Definition
`usgs`	`<u'w'>_sgs = -K_m (du/dz + dw/dx)`, at the uw corner
`vsgs`	`<v'w'>_sgs = -K_m (dv/dz + dw/dy)`, at the vw corner
`wsgs`	`tau_33 = -2 K_m dw/dz`, at the cell centre
`thlsgs`	`<w'thl'>_sgs = -K_h dthl/dz`, at the w-level
`qtsgs`	`<w'qt'>_sgs = -K_h dqt/dz`, at the w-level
`sv1sgs`–`sv4sgs`	`<w'sv_n'>_sgs = -K_h dsv_n/dz`, at the w-level

The total flux is therefore the sum of the resolved and SGS parts, for example uwxyt + upwpxyt + usgsxyt for the total vertical flux of streamwise momentum.

Breaking change

Before the fix of issue #306 (PR #358, November 2026) these variables were stored without the leading minus sign, i.e. as +K dphi/dn, and were therefore opposite in sign to the resolved fluxes in the same file. Any analysis that compensated for that (by negating the SGS term, or by subtracting rather than adding it) must be updated. Note also that wsgs was previously not a flux at all but the vertical part of the w-diffusion tendency, in m/s^2 rather than m^2/s^2, and located at the w-level rather than the cell centre.

No surface contribution¶

The SGS statistics are computed from the interior eddy-diffusivity formulas only. The fluxes that the wall model and the immersed-boundary method actually impose at surfaces (momfluxb/tfluxb, the facet stresses tau_x, tau_y, tau_z, and thl_flux) are not accumulated into them. Consequences:

The total-stress profile does not close at the wall: near solid surfaces the resolved plus SGS flux is smaller in magnitude than the true total flux by the missing surface contribution.
Levels that the masks exclude — in particular the bottom level kb of the w-located profiles, which the IBM masks out entirely — are reported as -999. rather than as a number.
In the 3-D tdump output, sv1sgs–sv4sgs are likewise set to -999. at solid and wall-adjacent faces, where the interior formula does not describe what the solver applied.

Adding the surface contribution is tracked in issue #353.

Restart files¶

If trestart is smaller than runtime, uDALES periodically writes unformatted (non-NetCDF) restart files per CPU: initd<ntrun>_<px>_<py>.<expnr> holds the flow fields (mindist, wall, u0, v0, w0, pres0, thl0, e120, ekm, qt0, ql0, ql0h, plus the current time and timestep), and, if nsv > 0, a companion inits<ntrun>_<px>_<py>.<expnr> holds the scalar fields sv0. ntrun is an 8-digit run counter embedded in the filename. These are written by writerestartfiles in modsave.f90, at the interval set by trestart, and additionally whenever an exit_now.<expnr> file is detected or (for driver simulations) when the inlet file store is exhausted.

A third restart file, initf<ntrun>.<expnr>, holds the facet state. It is written whenever nfcts > 0 and at least one of lEB, iwalltemp = 2, iwallmom = 2 or iwallmoist = 2 is active. Unlike the flow fields, the facet arrays are global rather than domain-decomposed, so this file is written by rank 0 only and carries no _<px>_<py> rank fields in its name. It is self-describing: record 1 is an integer header (format version, nfcts, nfaclyrs), followed by the wall temperature profile facT (nfcts facets by nfaclyrs + 1 layer interfaces), the soil moisture facwsoil (only when lEB), the saturation humidity facqsat, the relative humidity fachurel, the green-roof resistance factors facf, and the current time. When lEB is active the file continues with the state of the energy-balance interval in progress: the time of the last and of the next energy-balance update (tEB, tnextEB) and the facet heat and moisture fluxes accumulated since the last update (fachfi, facefi). On a warm start these let the interval continue where the checkpoint interrupted it. The file is the only source of the facet state on a warm start: with lreadfacT = .true. (the default) Tfacinit.inp.<expnr> is not read, and a missing, truncated or differently versioned file aborts the run.

To resume from a restart file, set lwarmstart = .true. (or lstratstart = .true.) and point startfile at the initd... filename of the desired restart point (the trailing digits of startfile must match the experiment's iexpnr); the matching inits... files (when nsv > 0) and the initf... file are read automatically. If initf... is missing, or its format version, nfcts or nfaclyrs do not match the current build and namoptions, the run aborts with an explicit message. Set lreadfacT = .false. to deliberately re-seed the facet temperatures from Tfacinit.inp.<expnr> (or Tfacinit_layers.inp.<expnr> with lfacTlyrs) on a warm start; that is the only case in which those files are read on a warm start. See the RUN and SCALARS namelists on the Configuration page for the exact parameter definitions.