Statistics user flow

[MartinKarp]

Daniele started writing a small guide on how to use the stats and post-process them. I share them here with you, they are done with srun, but it translates to mpirun and such too.

Notes on the statistics calculation in Neko

Daniele Massaro, Martin Karp (KTH)

1. Run your simulations and collect mean_field* and stats* files.

2. For each RUN_i, you get a set of mean_field* and stats* files. You can average them for each single RUN_i, or average all of them only once (after re-ordering them properly). If you follow the second approach, go to step 4.
   Here, for each RUN_i, we compute the averaged means with "average_fields_in_time":
   --mean
   srun --unbuffered /your/location/neko/bin/average_fields_in_time meanXX.fld T0 mean_p.fld
   where T0 is the initial time. To get some hints on the input for the script one can simply run ./average_fields_in_time without any arguments. For RUN_1 the time T0 can be taken from the log of the first simulation, or from the header of the first mean_field* file; in this way you discard that file. For RUN_i, with i>1, it can be taken from header of the last file mean_field* of the previous simulation RUN_{i-1}.
   In the command line, for the name "meanXX.fld", XX indicates the number of the nek5000 file. In mean_fieldXX.nek5000 you set the number of the first mean0* file to read and the number of steps corresponding to the number of files. In this way, the code generates a mean_p0.f00000 and mean_post0.nek5000. It is suggested to rename mean_p0.f00000 as mean_p0.f0000i and move it to a separate folder where you take the average with all the others.
   --stats
   srun --unbuffered /your/location/neko/bin/average_fields_in_time statXX.fld T0 stat_p.fld
   T0 is the same as before. In stat0.nek5000 you set the number of the first stat0* file to read and the number of steps corresponds to the number of files. It is suggested to rename stat_p0.f00000 as stat_p0.f0000i and move it to a separate folder where you take the average with all the others.
   Repeat this for each RUN_i folder. Eventually, given n RUN_i folders, you will get n mean_p* and stat_p* files.

3. Take the average of the averaged runs. Now, the time average over all the n simulations is taken. The procedure is similar, but changing the output name is recommended to avoid over-writing.
   -- mean
   srun --unbuffered /your/location/neko/bin/average_fields mean_p0.fld T0 mean_post.fld
   where T0 is the initial time which has been used to compute mean_p* for RUN_1.
   -- stats
   srun --unbuffered /your/location/neko/bin/average_fields stat_p0.fld T0 stat_post.fld
   where T0 is the initial time which has been used to compute mean_p* for RUN_1.

4. Compute Reynolds stress tensors and other statistical moments (see the list).
   srun --unbuffered /your/location/neko/bin/postprocess_fluid_stats mesh_file.nmsh mean_post0.fld stat_post0.fld

5. We also provide a tool to average the resulting field in a homogenous direction in bin/average_field_in_space. The required arguments are shown if one runs the program without any input. Currently it requires the number of elements in the homogenous direction as an input argument, e.g.
   ./average_field_in_space mesh.nmsh field.fld x 18 outfield.fld
   if we want to average a field in the x direction on a mesh with 18 elements in x and output the averaged field in outfield0.nek5000.

[njansson]

Great, how about adding this as a page in the doxygen documentation?