The frame you choose doesn't really matter. We included the renormalization to center on where the galaxy would be at the later time just as a convenience, but as you noticed, it just shifts things over, and it doesn't change anything. Good luck with your new refinement simulations. Cameron On Wed, Oct 29, 2014 at 11:21 AM, Chen Jingjing <chenjj235@gmail.com> wrote:
Hi Cameron, It seems that box containing the particles is too big for our afterwards simulation. The box contains ~500x mass of the halo mass, which means that we will be doing refined simulation on a lot of particles that we don't concern if we use that box. So we think that instead of finding the box, we will find the distribution of all the particles that forms the halo.
What I am not sure about is, should I use the original frame or the periodic frame for each particle's position? Your comment in the code said that "it depends on which one gives a smaller extent in their frame. " However now that I am not considering a box, which means there is no extent, what is the criteria for choosing the frame?
Thanks, Jingjing
2014-10-29 9:49 GMT-04:00 Cameron Hummels <chummels@gmail.com>:
Yes, that's right, and the halo should be found at the new normalized
position of 0.5, 0.5, 0.5. Good luck!
Cameron
On Tue, Oct 28, 2014 at 7:50 PM, Chen Jingjing <chenjj235@gmail.com> wrote:
Thanks! I think I got it. But just to make sure that I really understand it: so if I am tracing the box that contains all the particles which forms a halo at later stage, I will be using the bounding box whose values are the normalized position of the bottom left and top right corner of the box. Right?
Jingjing
2014-10-28 16:17 GMT-04:00 Cameron Hummels <chummels@gmail.com>:
It looks like there is substantial drift in your halos from the start
output to the final output. As I mentioned previously, the first bounding box is in the coordinate system of the earliest output. When it goes above 1, it's just referring to a periodic boundary. The center of mass is of the final halo in the later output file, and it doesn't have to be in the bounding box if there is substantial drift of the halo from the early output to the final output, as it appears there is in these simulations. Are you choosing dwarf galaxies, which tend to be more susceptible to drift in cosmological runs like this?
The final output is the same as the first bounding box, but it has been shifted over in space, so that the COM of the 2nd step sits at 0.5, 0.5, 0.5. This makes a lot more sense if you choose a halo which has no drift, so its center of mass remains inside of the bounding box of the earliest output.
I'd suggest picking a galaxy which doesn't have so much drift for re-simulation. Let me know if you have any other questions!
Cameron
On Tue, Oct 28, 2014 at 12:58 PM, Cameron Hummels <chummels@gmail.com> wrote:
Oops. I just saw that you did include the outputs. Let me look into this and get back to you in a moment.
Cameron
On Tue, Oct 28, 2014 at 12:56 PM, Cameron Hummels <chummels@gmail.com> wrote:
Hi Jingjing,
I'm sorry that you're running into some problems with yt.lagrangian_region. Let me see if I can help you.
The output of the code should return a box in code units containing all of the DM particles in the selected halo. I've only tested this with enzo outputs (and I believe that is what you're using it on too), so those code units will go from 0 to 1 in x, y, z. In addition to this output, the code also will recenter these coordinates so that the final halo coordinates will sit at 0.5, 0.5, 0.5 at the center of the box. It provides the original box shifted over in coordinates to accomodate this recentering. Lastly, you are correct that some of the coordinates will go above 1 in cases when the particles shift over the periodic boundary condition.
Do your results make more sense given this information? If you're still confused, can you send us the text of your outputs, so that we can try to figure them out?
I'm actually working on a newer version of this which will work with yt 3.0 as part of a larger effort to make efficient zoom simulations, but I've not yet finished working on it. I'll make sure to announce it here when this is complete and ready.
Cameron
On Tue, Oct 28, 2014 at 12:00 PM, Chen Jingjing <chenjj235@gmail.com> wrote:
> Hi, > I am using the code yt.lagrangian_volume to trace the box that > contains the dark matter particles at an early stage(higher redshift). But > I was quite confused about the output. I am attaching the output file > below. > (1) I don't know what the values for the box in the new frame mean, > i.e. what is the unit of these values? It seems to be the normalized scale > because the values are about 1. But it does not seem to be normalized too > because there are some values that are larger than 1. Is that due to the > periodicity of the box? > (2) The bounding box and box in the new frame seems to have the same > size. The difference between the two box is just translation. But I was > expecting that the box should be expanding/collapsing. > (3) The COM (center of mass) in the output is within neither of the > box. > > Does anyone know how to explain the box values in the output file? > > Thanks, > Jingjing > > -- > > Jingjing Chen [ chenjj235@gmail.com ] > Department of Astronomy > Columbia University > 550 West 120th Street > New York, New York 10027 > Cell Phone: +1(347)5746709 > > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >
-- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org
-- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org
-- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
--
Jingjing Chen [ chenjj235@gmail.com ] Department of Astronomy Columbia University 550 West 120th Street New York, New York 10027 Cell Phone: +1(347)5746709
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
--
Jingjing Chen [ chenjj235@gmail.com ] Department of Astronomy Columbia University 550 West 120th Street New York, New York 10027 Cell Phone: +1(347)5746709
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org