add output documentation

book/_toc.yml

@@ -10,7 +10,7 @@ parts:
   - caption: Running your first case in DALES
     chapters:
       - file: running/testcase.ipynb
-      - file: running/output.ipynb
+      - file: running/output.md
   - caption: Setting up your own case
     chapters:
       - file: running/basic_namoptions.ipynb

book/running/output.md

@@ -0,0 +1,68 @@
+# DALES Output
+
+## Enabling output
+
+To save cross sections or 3D fields the following settings are needed in the namelist file for Dales. Output is saved in netCDF format by default.
+
+```
+&NAMCROSSSECTION
+lcross      = .true.
+crossheight = 20,40,80
+dtav        = 60
+/
+```
+crossheights is a list of z-levels for which to save horizontal cross sections.
+
+```
+&NAMFIELDDUMP
+lfielddump  = .true.
+dtav        = 60
+/
+```
+
+
+## Output with one directory per MPI row
+When running with many cores the amount of output files in the run directory becomes annoying (and some supercomputer file systems don't like more than a few thousand files per directory).
+With the option `loutdirs` set to true, the output from each row of MPI processes is placed in its own directory: 000, 001, 002, ... .
+```
+&RUN
+loutdirs = .true.
+/
+```
+
+## Merging netCDF tiles
+
+For 2D and 3D output, each DALES process saves it's own  
+The command `cdo` can be used to merge netCDF tiles.
+Use cdo version >= 2.0.6.
+
+```
+cdo -O collgrid crossxy.0001.*.nc  crossxy.0001.nc
+```
+
+`-O` is for overwriting the target file if it exists.
+
+### Selecting variables
+
+```
+cdo -O collgrid,vxy crossxy.0001.*.nc  crossxy.0001.nc
+```
+To include only selected variables in the output, add a comma-separated list after collgrid (no spaces).
+
+### Compression
+Optionally add flags to enable compressed netCDF4 output:
+```
+cdo -f nc4 -z zip_6 -O collgrid crossxy.0001.*.nc  crossxy.0001.nc
+```
+
+### NetCDF time units
+
+If both `xyear` and `xday` are present in the DOMAIN namelist,
+DALES outputs proper time units in the netCDF: `seconds since 2020-01-02T00:00:00.` Otherwise the unit is just `s`, meaning seconds since the start of the simulation.
+
+### Handling large cases
+
+If cdo runs out of memory, it may help to do the merging in two steps:
+first merge each row of tiles into a stripe, then merge the stripes.
+To save time, do not enable compression for the intermediate files.
+