The Gerris Flow Solver

Hi Ben,

 > To get the code to run i have to displace the all the sides slightly. I 
 > can understand this for the bottom of the cube as it is at the same 
 > height as the floor, but why the other sides?

This can happen whenever faces of the solid surface coincide with, not
only the boundaries of the simulation domain but also with the
boundaries of any discretisation cells. Basically, it can happen
whenever the code needs to do boolean operations in discretisation
cells cut by the solid boundaries.

Two notes on that:
1) Most of the time these warnings are harmless and can be ignored.
2) the new version of the GTS library should solve most of these problems.

 > I'm sure this has been asked and is specified somewhere, but i can't 
 > find a full description of the output.  What are all the numbers in the 
 > output file?

Good question. I should add a header describing the output at the top
of the file. For the moment the only way to know is to look into the
source code... In your case (version 0.2.0) this should be

TIME X Y Z P U V W C CH

where C and CH are the tracer concentrations at the full and half
timestep respectively.

 > I would like a time averaged wind speed profile above the cube.  Would 
 > I have to specify a number of monitoring points at different heights,  
 > or is there a method to time average over a line through the solution 
 > domain?

There is no method to do line averaging at the moment, however there
is a method which averages (or more exactly stores the sum) of a given
variable in time over the whole domain. You can do it like that:
 
  GfsEventSum { start = 1 istep = 1 } U SUx
  GfsEventSum { start = 1 istep = 1 } V SUy
  GfsEventSum { start = 1 istep = 1 } W SUz
  GfsEventSum2 { start = 1 istep = 1 } U SU2x
  GfsEventSum2 { start = 1 istep = 1 } V SU2y
  GfsEventSum2 { start = 1 istep = 1 } W SU2z
  GfsOutputSimulation { start = end } simulation-sum { 
    variables = SUx,SUy,SUz,SU2x,SU2y,SU2z
  }

which would add U to SUx at every timestep (istep = 1) starting from
time 1 (start = 1) etc... and U^2 to SU2x at every timestep
etc.... The resultings sums are then written at the end of the
simulation in the file "simulation-sum". This file can then be
post-processed (using gfs2oogl for example) to obtain averages,
standard deviations etc... (along any curves you want of course).

Hope this helps,

Stephane