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<p>Hi Konrad,</p>
<p>All of the hdf5 2d outputs (e.g. admbase::lapse) include the grid
data as well at each iteration. For these quick things, I tend to
use Visit from LLNL to plot the lapse and the mesh overtop so I
can see the position of the grid as the system evolves. You could
likely do the same plot with something like KuiBit, but I haven't
messed with plotting the grid with that yet. <br>
</p>
<p>Also, in the output you just sent, it looks like you are using
your grhydro par file, however, in the grhydro par you sent
before, quite a lot of the puncture tracker settings are commented
out including track puncture. <br>
</p>
<p>Finally, the warnings of "the refined region #" is inactive for a
specific surface is also likely a contributor. I'm sure Erik et
al are more knowledgeable on resolving this, but usually this was
an issue I had based on my refinement level and spherical surface
setup.<br>
</p>
<p>Cheers,</p>
<p>Samuel<br>
</p>
<div class="moz-cite-prefix">On 8/23/21 7:54 PM, Konrad Topolski
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAEx5SMFdHy2v6GEdMCEoD=Tc8hNrnN8EmzmG2mZeaBFW3VOWeQ@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">
<div>Hi</div>
<div><br>
</div>
<div>I cannot set up the tracker correctly in either of these
parameter files. <br>
</div>
<div>The "pt_loc_" timeseries all display the (0,0,0) position
at all times.<br>
</div>
<div>The 'NaNMask' data is probably corrupted by simulation
shutting down, as I cannot open it.<br>
</div>
<div><br>
</div>
<div>What are the "mesh grid variables" exactly that I should
use in this diagnostics and in which thorns should I look for
them?</div>
<div><br>
</div>
<div>Here's part of the log (common for both simulations in the
PunctureTracker part):</div>
<div><span dir="ltr"
style="font-family:sans-serif;margin-top:0px;margin-bottom:0px">mesh
grid variables" that</span></div>
<div>[...]<br>
INFO (GRHydro): Setting up the atmosphere mask: all points are
not_atmosphere<br>
INFO (PunctureTracker): Tracking punctures...<br>
INFO (PunctureTracker): Puncture #0 is at
(17.3774,-0.0975486,0)<br>
INFO (PunctureTracker): Shift at puncture #0 is at (0,0,0)<br>
INFO (AHFinderDirect): proc 0: searching for horizon 1/1<br>
INFO (PunctureTracker): Setting spherical surface 0 centroid
from puncture #0 to (17.3774,-0.0975486,0)<br>
1 0.022 | 6.0400998 | -nan -nan
| -nan -nan | 2516 3089 | 0
0<br>
INFO (CarpetTracker): Setting position of refined region #1
from surface #0 to (17.3774,-0.0975486,0)<br>
INFO (CarpetTracker): Refined region #2 (depending on surface
#1) is inactive<br>
INFO (PunctureTracker): Tracking punctures...<br>
INFO (PunctureTracker): Puncture #0 is at
(17.3774,-0.0975486,0)<br>
INFO (PunctureTracker): Shift at puncture #0 is at
(-nan,-nan,-nan)<br>
ERROR from host nid00681 process 0<br>
while executing schedule bin CCTK_EVOL, routine
PunctureTracker::PunctureTracker_Track<br>
in thorn PunctureTracker, file
/lustre/tetyda/home/topolski/Cactus/arrangements/EinsteinAnalysis/PunctureTracker/src/puncture_tracker.cc:204:<br>
-> Shift at puncture #0 is (-nan,-nan,-nan). This likely
indicates an error in the simulation.</div>
<div><br>
</div>
<div><br>
</div>
<div>I'm also sending the initial data to confirm the initial
guess for the puncture.</div>
<div><br>
</div>
<div>Best <br>
</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">niedz., 22 sie 2021 o
08:59 Samuel Tootle <<a
href="mailto:tootle@itp.uni-frankfurt.de" target="_blank"
moz-do-not-send="true">tootle@itp.uni-frankfurt.de</a>>
napisał(a):<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div> <span dir="ltr"
style="font-family:sans-serif;margin-top:0px;margin-bottom:0px">Hi
Konrad,</span> <br>
<br>
<span dir="ltr"
style="font-family:sans-serif;margin-top:0px;margin-bottom:0px">The
matter looks reasonable in all the iterations until the
end, so that's good. Have you looked at the mesh grid to
see if both objects are being tracked properly? You asked
about this being a possibility in your first note, but
didn't mention if you looked at the grid or not.</span> <br>
<br>
<span dir="ltr"
style="font-family:sans-serif;margin-top:0px;margin-bottom:0px">Cheers,</span>
<br>
<span dir="ltr"
style="font-family:sans-serif;margin-top:0px;margin-bottom:0px">Samuel</span>
<br>
<div> <br>
<div>
<p><strong>From: </strong>Konrad Topolski <<a
href="mailto:k.topolski2@student.uw.edu.pl"
target="_blank" moz-do-not-send="true">k.topolski2@student.uw.edu.pl</a>><br>
<strong>To: </strong>Samuel Tootle <<a
href="mailto:tootle@itp.uni-frankfurt.de"
target="_blank" moz-do-not-send="true">tootle@itp.uni-frankfurt.de</a>>;
Einstein Toolkit Users <<a
href="mailto:users@einsteintoolkit.org"
target="_blank" moz-do-not-send="true">users@einsteintoolkit.org</a>><br>
<strong>Date: </strong>Aug 21, 2021 23:20:30<br>
<strong>Subject: </strong>Re: [Users] BHNS simulation
issues - Hamiltonian constraint violations and general
problems<br>
</p>
</div>
<blockquote style="border-left:3px solid
rgb(204,204,204);padding-left:3px">
<div dir="ltr">
<div> Hi Sam </div>
<div> <br>
</div>
<div> I am sending the pictures of the density in a
few iterations. </div>
<div> Something indeed goes <b>very </b>bad (and
possibly in the wrong direction pretty soon from the
start). </div>
<div> <br>
</div>
<div> But before a chunk of the NS turns into
atmosphere it doesn't look like it would end up like
that. </div>
<div> <br>
</div>
<div> This is rho.maximum: <br>
</div>
<div> <br>
</div>
<div> 0 0 0.00181508688452629 <br>
16 0.4 0.00181562065714772 <br>
32 0.8 0.00181716349263237 <br>
48 1.2 0.00181971188439579 <br>
64 1.6 0.00182322915996771 <br>
80 2 0.00182773078378139 <br>
<br>
And this is rho.average: <br>
</div>
<div> <br>
</div>
<div> 0 0 1.23447090415481e-07 <br>
16 0.4 1.2346439769246e-07 <br>
32 0.8 1.23490260581956e-07 <br>
48 1.2 1.23521771090518e-07 <br>
64 1.6 1.23554773904041e-07 <br>
80 2 1.23584518348538e-07 <br>
</div>
<div> <br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr"> sob., 21 sie 2021 o
23:03 Samuel Tootle <<a
href="mailto:tootle@itp.uni-frankfurt.de"
target="_blank" moz-do-not-send="true">tootle@itp.uni-frankfurt.de</a>>
napisał(a): <br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px
0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div> <span dir="ltr"
style="font-family:sans-serif;margin-top:0px;margin-bottom:0px">Hi
Konrad,</span> <br>
<br>
<span dir="ltr"
style="font-family:sans-serif;margin-top:0px;margin-bottom:0px">Have
you checked the import of the ID from the hydro
point of view (i.e. plot rho in for the first
iterations). If you see drastic changes in the
NS density in the initial iterations, it usually
means the EOS manager isn't configured correctly
which routinely results in the NS "vanishing"
thereby destroying the solution and the
evolution. </span> <br>
<br>
<span dir="ltr"
style="font-family:sans-serif;margin-top:0px;margin-bottom:0px">Cheers,</span>
<br>
<span dir="ltr"
style="font-family:sans-serif;margin-top:0px;margin-bottom:0px">Samuel</span>
<br>
<div> <br>
<div>
<p><strong>From: </strong>Konrad Topolski
<<a
href="mailto:k.topolski2@student.uw.edu.pl"
target="_blank" moz-do-not-send="true">k.topolski2@student.uw.edu.pl</a>><br>
<strong>To: </strong>Einstein Toolkit Users
<<a
href="mailto:users@einsteintoolkit.org"
target="_blank" moz-do-not-send="true">users@einsteintoolkit.org</a>><br>
<strong>Date: </strong>Aug 21, 2021
22:30:57<br>
<strong>Subject: </strong>[Users] BHNS
simulation issues - Hamiltonian constraint
violations and general problems<br>
</p>
</div>
<blockquote style="border-left:3px solid
rgb(204,204,204);padding-left:3px">
<div dir="ltr">
<div> Hi all </div>
<div> <br>
</div>
<div> I am trying to run a BH-NS simulation
using at least one of some (and sometimes
more) unofficial thors. </div>
<div> That would be Kadath for the initial
data and possibly THC for hydro evolution.
</div>
<div> I'm trying to run the simulation
either with GRHydro or with THC. <br>
</div>
<div> <br>
</div>
<div> In both cases I believe that the
initial data gets imported correctly - I
have looked at some simple visuals which
I'm attaching to this mail. </div>
<div> <br>
</div>
<div> However, as the simulation proceeds,
huge hamiltonian constraint violations
occur and e.x. the lapse gets driven to 0
globally. This can also be seen. </div>
<div> <br>
</div>
<div> How can I help this? Is it because the
puncture is not tracked correctly? Trying
to set up a PunctureTracker at the
location of the black hole yields a
failure very soon, as the shift at
puncture is said to be (nan, nan, nan). </div>
<div> <br>
</div>
<div> I'm sending the .par files, outputs
(.out), errors (.err) and visualization
(.png). <br>
</div>
<div> <br>
</div>
<div> Best regards </div>
<font color="#888888">
<div> Konrad </div>
</font> </div>
<div>
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</blockquote>
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