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Hi David,<br>
<br>
thanks for you help. I think this is a good strategy !<br>
I will let you know how it goes.<br>
<br>
Thanks again,<br>
<br>
JC<br>
<br>
David Collins a écrit :
<blockquote
cite="mid:AANLkTimRKTO0Y9aZPwlY35ZG5G-BPVk4q_1BbguZLtBx@mail.gmail.com"
type="cite">
<pre wrap="">Hi, Jean-Claude--
(I copied this to the list, so all may enjoy my wisdom.)
HDF5 brings some extra work over straight ascii files, but it's 1000%
worth it in the long run. It's your call if you think it's right for
this problem. I'm the kind of person who will go far out of my way to
be lazy later, so this is what I'd do. (Even if it's not right for
this problem, HDF5 is worth knowing. I hate all datasets that aren't
in HDF5, now that I've gotten comfortable with it.)
The HDF5 website is here:
<a class="moz-txt-link-freetext" href="http://www.hdfgroup.org/HDF5/">http://www.hdfgroup.org/HDF5/</a>
I've been told that the HDF5 Lite interface is pretty good:
<a class="moz-txt-link-freetext" href="http://www.hdfgroup.org/HDF5/Tutor/h5lite.html">http://www.hdfgroup.org/HDF5/Tutor/h5lite.html</a>
though I haven't used it myself, the syntax is supposed to be simpler.
It's worth going through a few examples on the website to get used to
it.
I would do it using a similar syntax that's in Grid_Group_ReadGrid.C,
though this file has a bunch of enzo baggage in it, so it's kind of
difficult to read. One thing to note is that HDF5 is a C library, but
Enzo arrays are stored in Fortran ordering. So be careful that the
array will have the X and Z indices swapped if you go to 3d. Another
thing is to watch out for data types.
The short version: HDF5 files have a directory structure like a unix
directory tree. Enzo output files have a format like
File/Grid Group/ Dataset
Each processor does it's own output, so there should be one cpu????
file for each MPI task. So you need to do the following in your
code:
1.) Open the file (data0000.cpu0001)
2.) Open the "Group", in this case the grid ID, which will be
something like Grid00001. h5ls will show you the contents of the file
3.) Open the dataset ('Density', 'x-velocity', etc)
4.) Read the dataset
5.) Close the dataset, group, file
Syntax and details can be found on the hdf5 websites or in the Enzo
Grid_Group_ReadGrid.C files.
Hope that helps!
d.
On Wed, Jun 2, 2010 at 2:06 PM, Jean-Claude Passy <a class="moz-txt-link-rfc2396E" href="mailto:jcpassy@gmail.com"><jcpassy@gmail.com></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi David,
it looks like a good idea, thanks.
Could you just be more specific and explain briefly how to read the HDF5
file, especially in a C++ program ? I am sorry but I am also not familiar
with the h5ls command.
Thanks a lot,
Jean-Claude
David Collins a écrit :
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:
<a class="moz-txt-link-freetext" href="http://lca.ucsd.edu/projects/enzo/wiki/Tutorials/BaryonFieldAccess">http://lca.ucsd.edu/projects/enzo/wiki/Tutorials/BaryonFieldAccess</a>
Does that help?
d.
On Wed, Jun 2, 2010 at 12:07 PM, Jean-Claude Passy <a class="moz-txt-link-rfc2396E" href="mailto:jcpassy@gmail.com"><jcpassy@gmail.com></a>
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 <a class="moz-txt-link-rfc2396E" href="mailto:jcpassy@gmail.com"><jcpassy@gmail.com></a> 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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