[yt-users] fields in ghost zones

[David Collins]

Hi, JC--


Would it be easier to skip YT all together, and just have your problem
generator read the HDF5 file produced by the 1d run directly?  This would
streamline your processes, and you wouldn't have the noise incurred by both the
ASCII file format and the two units conversions.

I would probably approach your task by looping over only the active
zones in enzo, and incrementing an extra counter.

int counter = 0;
for(int field=0;field<NumberOfBaryonFields;field++)
for(int k=GridStartIndex[2];k<=GridEndIndex[2]; k++)
  for(int j=GridStartIndex[1];j<=GridEndIndex[1]; j++)
    for(int i=GridStartIndex[0];i<=GridEndIndex[0]; i++){
      index = i + GridDimension[0]*(j + GridDimension[1]*k);
      BaryonField[ DensNum ][ i ] = DensityFromFile[ counter ];
      counter++
    }



This code snippit came from the wiki page on Baryon access, for future
reference:
http://lca.ucsd.edu/projects/enzo/wiki/Tutorials/BaryonFieldAccess

Does that help?
d.


On Wed, Jun 2, 2010 at 12:07 PM, Jean-Claude Passy <jcpassy at gmail.com> wrote:
> Hi Matt,
>
> I will try to explain what my goal is.
> I have a 1D profile of a star that is physically at the equilibrium.
> Regarding the problem initialization, I set up the density and the total
> specific energy fields according to the model, velocities equal 0. However,
> the star is not numerically stable so I have to relax it. Therefore, I
> divide the velocity by 2 at each timestep, and I let Enzo run for a few
> dynamical times. Then, I read the last data dump and create an
> relaxed_model.dat:
>
> ##########################################################
> region = pf.h.region([0.5, 0.5, 0.5], [0.0, 0.0, 0.0], [1.0, 1.0, 1.0])
> output = 'relaxed_model.dat' f = open(output,'w') print >>f, '# Grid Index
> rho pressure' density = region["Density"] pressure = region["Pressure"] size
> = NP.size(density)
> for i in range(0,size,1):             dtmp = density[i]             ptmp =
> pressure[i]             print >>f, "0", i, '%06e' % dtmp, '%06e' % ptmp
> ##########################################################
>
> so I end up with a file like this:
>
> ########################################################## # Restart file
> for only one grid
> # Grid Index rho pressure 0 0 5.099011e-10 2.568020e+05 0 1 5.099011e-10
> 2.568020e+05 0 2 5.099011e-10 2.568020e+05
> ...
> ##########################################################
> Finally, I read index, density, pressure from that previous file and do:
>
> ##########################################################  for (k = 0; k <
> GridDimension[2]; k++)       for (j = 0; j < GridDimension[1]; j++)
> for (i = 0; i < GridDimension[0]; i++) {
>           index = i + GridDimension[0]*(j + GridDimension[1]*k);
> density  /= DensityUnits;           pressure /= PressureUnits;
> BaryonField[0][index] = density;           BaryonField[1][index] = pressure
> / ((Gamma - 1.0) * density);
> ##########################################################
> The problem is GridDimensions contain the ghost zones so the variable index
> does not match with the actual index read in the file relaxed_model.dat.
> That is why I wanted to have that file values for the ghost zones as well.
>
> Does it make sense ? Do you have any suggestion ?
>
> Thanks for your help,
>
>
> JC
>
> Matthew Turk a écrit :
>
> Hi Jean-Claude,
>
> There are a couple aspects to this.  The first is that Enzo doesn't
> output the ghost zones -- so any ghost zones handled inside yt are
> generated by yt.  Were Enzo to output the ghost zones, we would
> probably be able to handle this, but it does not.
>
> Derived fields can depend on the generation of ghost zones, but keep
> in mind that these are ghost zones generated by yt.  These ghost zones
> are constructed in a similar manner to how Enzo generates them, but
> there may be minor differences.  You can manually inspect ghost zones
> on a *grid* by calling retrieve_ghost_zones on that grid.
>
> If you could tell us a bit more about your goal, maybe we could help
> out a bit more?
>
> -Matt
>
> On Wed, Jun 2, 2010 at 9:32 AM, Jean-Claude Passy <jcpassy at gmail.com> wrote:
>
>
> Dear all,
>
> in order to set up my simulation, I need to access the values of certain
> fields in the ghost zones.
> If I do something like:
>
> pf = load(data) region = pf.h.region(...) x = region[field]
>
> x contains the values of field for the physical grid only. Is there a way I
> can get the same 1D-array but with the ghost zones included as well ?
>
> Thanks for your help,
>
> Jean-Claude
>
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