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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">
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        <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>
            -&gt; 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 &lt;<a
            href="mailto:tootle@itp.uni-frankfurt.de" target="_blank"
            moz-do-not-send="true">tootle@itp.uni-frankfurt.de</a>&gt;
          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 &lt;<a
                    href="mailto:k.topolski2@student.uw.edu.pl"
                    target="_blank" moz-do-not-send="true">k.topolski2@student.uw.edu.pl</a>&gt;<br>
                  <strong>To: </strong>Samuel Tootle &lt;<a
                    href="mailto:tootle@itp.uni-frankfurt.de"
                    target="_blank" moz-do-not-send="true">tootle@itp.uni-frankfurt.de</a>&gt;;
                  Einstein Toolkit Users &lt;<a
                    href="mailto:users@einsteintoolkit.org"
                    target="_blank" moz-do-not-send="true">users@einsteintoolkit.org</a>&gt;<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 &lt;<a
                      href="mailto:tootle@itp.uni-frankfurt.de"
                      target="_blank" moz-do-not-send="true">tootle@itp.uni-frankfurt.de</a>&gt;
                    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
                            &lt;<a
                              href="mailto:k.topolski2@student.uw.edu.pl"
                              target="_blank" moz-do-not-send="true">k.topolski2@student.uw.edu.pl</a>&gt;<br>
                            <strong>To: </strong>Einstein Toolkit Users
                            &lt;<a
                              href="mailto:users@einsteintoolkit.org"
                              target="_blank" moz-do-not-send="true">users@einsteintoolkit.org</a>&gt;<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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