[Users] problem with first example simulation with ETK
Ian Hinder
ian.hinder at aei.mpg.de
Tue Jan 17 07:18:36 CST 2012
On 17 Jan 2012, at 13:37, Jose Fiestas Iquira wrote:
> The Einstein Analysis guide is very useful. I found here
> http://einsteintoolkit.org/documentation/ThornGuide/ThornGuidech142.html#x159-2520000P8.4
> the units used in 'Hydrobase'.
>
> If I assume these are the units for all thorns, I obtain from data in
> BH_diagnostics.ah1.gp a unit of distance of about 1 Km. To estimate
> the time I am using a mass of ~0.5 M_sun for both BHs (m_irreducible
> ?) , and I read a final time (cctk_time) ~ 1microsec. Are these
> quantities in the usual range?
The length unit is G M / c^2 and the time unit is G M / c^3. For M = M_sun, I get the length unit as 1.5 km and the time unit as 4.9 us. The final time in the simulation is 100 M (i.e. 100 G M / c^3), which would be 0.5 ms.
>
> Jose
>
>
> On Tue, Jan 17, 2012 at 4:04 AM, Jose Fiestas Iquira <jafiestas at lbl.gov> wrote:
>> I sent the wrong file, here is the right one.
>>
>> $ hg tip
>> gives me:
>> -----------------------------------------------------
>> changeset: 3421:dff4df2b3687
>> tag: tip
>> user: Erik Schnetter <schnetter at cct.lsu.edu>
>> date: Thu Jan 12 14:11:27 2012 -0500
>> summary: CarpetLib: Allocate space for dstbox before
>> restricting/prolongating
>>
>> [40514 refs]
>> -----------------------------------------------------
>>
>> I copied this version from:
>>
>> ./GetComponents -a
>> http://svn.einsteintoolkit.org/manifest/trunk/einsteintoolkit.th
>>
>> Thanks,
>> Jose
>>
>>
>>
>>
>> On Tue, Jan 17, 2012 at 1:13 AM, Ian Hinder <ian.hinder at aei.mpg.de> wrote:
>>>
>>> On 16 Jan 2012, at 23:21, Jose Fiestas Iquira wrote:
>>>
>>> Thanks, I am attaching the output file.
>>>
>>>
>>> The output file looks fine - I can't see any problem with the simulation.
>>> According to the output file, it reached t = 100 M, and in the parameter
>>> file that is listed as cctk_final_time, so all looks well!
>>>
>>> I did copy the development version. As I can see, it was already
>>> fixed, so I should not get this warning, since I copied the
>>> development version.
>>>
>>>
>>> Yes, if you are using the current development version, then I don't know why
>>> you get the warning. Can you check which version of Carpet you have by
>>> doing
>>>
>>> cd repos/carpet
>>> hg tip
>>>
>>> to be sure you are using the development version?
>>>
>>> Is the puncture tracker not a better way to plot BH trajectories.
>>>
>>>
>>> It's cheaper to use the puncture tracker, because computing the horizon
>>> centroid is more expensive, but it has to be done every iteration, whereas
>>> the horizon can be found less frequently. For comparison with
>>> point-particle results, I don't think it makes much difference; the results
>>> are gauge dependent anyway so differences on the order of the horizon size
>>> cannot be interpreted physically. Since the parameter file already has
>>> horizon-finding built in, it is easier for you to use that.
>>>
>>> If you want to figure out how to add the puncture tracker to the simulation,
>>> you can start with these parameters:
>>>
>>> ActiveThorns = "PunctureTracker"
>>>
>>> PunctureTracker::track [0] = yes
>>> PunctureTracker::initial_x [0] = $xp
>>> PunctureTracker::which_surface_to_store_info[0] = 0
>>> PunctureTracker::track [1] = yes
>>> PunctureTracker::initial_x [1] = $xm
>>> PunctureTracker::which_surface_to_store_info[1] = 1
>>>
>>> IOASCII::out0D_vars = "PunctureTracker::pt_loc"
>>>
>>> Replace $xp and $xm with the initial x coordinates of the +x and -x
>>> punctures (this will be \pm TwoPunctures::par_b). You then need to choose
>>> two spherical surfaces
>>> (https://docs.einsteintoolkit.org/et-docs/Einstein_Toolkit_standards) which
>>> are not being used currently to store the puncture locations in. If there
>>> is already 0D output, just add the puncturetracker variable separated with a
>>> space.
>>>
>>> I
>>> did some plots, what are really the combinations xx, xy, xz, yy, zz ?
>>> Are they related to the trajectories of one BH (projections)? What
>>> about the second BH?
>>>
>>>
>>> You should have BH_diagnostics.ah1.gp and BH_diagnostics.ah2.gp. These
>>> correspond to the first and second BHs. If you look at the top of these
>>> files, you will see an explanation of the columns. More information about
>>> each column is available in the AHFinderDirect documentation
>>> (http://einsteintoolkit.org/documentation/ThornGuide/ThornGuidech128.html#x144-2264000O4).
>>> Specifically, information about the BH_diagnostics output files is
>>> at http://einsteintoolkit.org/documentation/ThornGuide/ThornGuidech128.html#x144-2274000O4.5.5
>>>
>>> To plot the trajectory of one of the BHs, you want to plot column 3 and
>>> column 4 in a parametric plot.
>>>
>>>
>>> Cheers,
>>> Jose
>>>
>>> On Mon, Jan 16, 2012 at 4:39 AM, Ian Hinder <ian.hinder at aei.mpg.de> wrote:
>>>
>>>
>>> On 14 Jan 2012, at 00:41, Jose Fiestas Iquira wrote:
>>>
>>>
>>> Hi Ian,
>>>
>>> I did the changes but it started and finished early. I am attaching
>>>
>>> the qc0-mclachlan.err file. At the end there is a warning in one of
>>>
>>> the Carpet files (mask_test.c)
>>>
>>>
>>>
>>> The warning you see,
>>>
>>>
>>> WARNING level 1 in thorn CarpetReduce processor 0 host qb517
>>>
>>> (line 120 of
>>>
>>> /home/ettest24/Cactus/arrangements/Carpet/CarpetReduce/src/mask_test.c):
>>>
>>> -> Simulation domain volume and reduction weight sum differ
>>>
>>>
>>> is a known issue (https://trac.einsteintoolkit.org/ticket/434) which was
>>>
>>> fixed after the last release and the fix is only available in the
>>>
>>> development version. I believe that the warning is not fatal, and it should
>>>
>>> not have terminated the simulation. Can you also post the qc0-mclachlan.out
>>>
>>> file?
>>>
>>>
>>> Where can I find the puncture tracker?
>>>
>>>
>>>
>>> The PunctureTracker thorn is part of the Einstein Toolkit thornlist, so you
>>>
>>> should have it already. However, I think the best thing for you to do
>>>
>>> initially would be to look at the BH_diagnostics files for the apparent
>>>
>>> horizon centroid locations for tracking the locations of the BHs.
>>>
>>>
>>>
>>>
>>>
>>> Thanks,
>>>
>>> Jose
>>>
>>>
>>> On Fri, Jan 13, 2012 at 4:38 AM, Ian Hinder <ian.hinder at aei.mpg.de> wrote:
>>>
>>>
>>>
>>> On 13 Jan 2012, at 12:32, Jose Fiestas Iquira wrote:
>>>
>>>
>>>
>>> Yes, trajectories and wave forms would be enough for now. Which are
>>>
>>>
>>> the names of this files? Many of the .asc files have data like kxx,
>>>
>>>
>>> kxy, kxz, etc. Is there any description of them?
>>>
>>>
>>>
>>> Not that I am aware of. Files with extension .x.asc are 1D ascii output of
>>>
>>> grid functions from CarpetIOASCII. kxy is the variable name for the x,y
>>>
>>> component of the extrinsic curvature tensor K. The waveform file should be
>>>
>>> in mp_psi4_l2_m2_r*.asc where * corresponds to the radius of the extraction
>>>
>>> sphere. However, looking at the qc0-mclachlan.par file, I see that there is
>>>
>>> no wave extraction switched on. You should be able to enable wave
>>>
>>> extraction by adding something like the following to the parameter file:
>>>
>>>
>>>
>>> ActiveThorns = "WeylScal4 CarpetInterp AEILocalInterp Multipole"
>>>
>>>
>>>
>>> Multipole::nradii = 3
>>>
>>>
>>> Multipole::radius[0] = 30
>>>
>>>
>>> Multipole::radius[1] = 40
>>>
>>>
>>> Multipole::radius[2] = 50
>>>
>>>
>>> Multipole::variables = "WeylScal4::Psi4r{sw=-2 cmplx=’WeylScal4::Psi4i’}"
>>>
>>>
>>> Multipole::l_max = 4
>>>
>>>
>>> WeylScal4::fdOrder = 4
>>>
>>>
>>>
>>> (I haven't tested this, so let me know if it doesn't work)
>>>
>>>
>>>
>>> I've just found that the usual PunctureTracker thorn is not enabled in this
>>>
>>> example parameter file. So to look at trajectories you will have to use the
>>>
>>> apparent horizon centroids. These are in the files BH_diagnostics.ah*.gp.
>>>
>>> The meanings of the columns are at the top of the files. You want the
>>>
>>> centroid x and y columns to plot in GnuPlot.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Thanks,
>>>
>>>
>>> Jose
>>>
>>>
>>>
>>> On Fri, Jan 13, 2012 at 12:41 AM, Ian Hinder <ian.hinder at aei.mpg.de> wrote:
>>>
>>>
>>>
>>> On 12 Jan 2012, at 23:46, Jose Fiestas Iquira wrote:
>>>
>>>
>>>
>>> Dear all,
>>>
>>>
>>>
>>> I run the tutorial and found other interesting examples like the
>>>
>>>
>>> McLachlan tool for Binary Black Holes.
>>>
>>>
>>>
>>> Regarding the McLachlan tool,
>>>
>>>
>>> Could somebody help me finding a description of the output? Is all
>>>
>>>
>>> contained in the .asc files? I would like to visualize it.
>>>
>>>
>>>
>>>
>>> Hi Jose,
>>>
>>>
>>>
>>> What sort of output do you want to visualise? Cactus thorns typically
>>>
>>>
>>> output "lightweight" information such as BH trajectories and waveforms as
>>>
>>>
>>> ASCII, and more heavyweight data -- like gridfunctions -- as HDF5. For the
>>>
>>>
>>> trajectories (from thorn Puncture Tracker) and waveforms (from Multipole)
>>>
>>>
>>> you can use gnuplot or anything that can read standard ASCII output to
>>>
>>>
>>> visualise them. For gridfunctions in HDF5 format, I think the easiest way
>>>
>>>
>>> to get started is to use VisIt, for which there is a Carpet plugin (though
>>>
>>>
>>> installing VisIt is sometimes not so easy!).
>>>
>>>
>>>
>>> Does anyone know if the Carpet plugin is distributed with VisIt yet? I
>>>
>>>
>>> believe that was the intention.
>>>
>>>
>>>
>>>
>>>
>>> Cheers,
>>>
>>>
>>> Jose
>>>
>>>
>>>
>>>
>>> On Wed, Jan 11, 2012 at 7:06 PM, Jose Fiestas Iquira <jafiestas at lbl.gov>
>>>
>>>
>>> wrote:
>>>
>>>
>>>
>>> Thanks to Erik for advise. ETK example simulation run successfully.
>>>
>>>
>>>
>>>
>>>
>>> On Wed, Jan 11, 2012 at 11:49 AM, Jose Fiestas Iquira <jafiestas at lbl.gov>
>>>
>>>
>>> wrote:
>>>
>>>
>>>
>>> Right, it looks good now:
>>>
>>>
>>>
>>>
>>> ./simfactory/bin/sim list-simulations
>>>
>>>
>>>
>>> static_tov [ACTIVE (RUNNING), restart 0000, job id 595490]
>>>
>>>
>>>
>>>
>>> Let see how it looks when it finishes. The example was set to 8 hours.
>>>
>>>
>>>
>>>
>>> Thanks,
>>>
>>>
>>>
>>> Jose
>>>
>>>
>>>
>>>
>>>
>>> On Wed, Jan 11, 2012 at 11:45 AM, Erik Schnetter <schnetter at cct.lsu.edu>
>>>
>>>
>>> wrote:
>>>
>>>
>>>
>>> On Wed, Jan 11, 2012 at 2:42 PM, Jose Fiestas Iquira <jafiestas at lbl.gov>
>>>
>>>
>>> wrote:
>>>
>>>
>>>
>>>
>>> The only thing is that now
>>>
>>>
>>>
>>> $ ./simfactory/bin/sim list-simulations
>>>
>>>
>>>
>>> returns
>>>
>>>
>>>
>>>
>>> Error: unknown command list-simulation
>>>
>>>
>>>
>>> Aborting Simfactory.
>>>
>>>
>>>
>>>
>>> Did you really type "list-simulations", and the error message says
>>>
>>>
>>>
>>> "list-simulation" (without the final "s")?
>>>
>>>
>>>
>>>
>>> -erik
>>>
>>>
>>>
>>>
>>> --
>>>
>>>
>>>
>>> Erik Schnetter <schnetter at cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/
>>>
>>>
>>>
>>> _______________________________________________
>>>
>>>
>>>
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>>>
>>>
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>>>
>>>
>>> http://lists.einsteintoolkit.org/mailman/listinfo/users
>>>
>>>
>>>
>>>
>>> --
>>>
>>>
>>> Ian Hinder
>>>
>>>
>>> http://numrel.aei.mpg.de/people/hinder
>>>
>>>
>>>
>>>
>>> --
>>>
>>>
>>> Ian Hinder
>>>
>>>
>>> http://numrel.aei.mpg.de/people/hinder
>>>
>>>
>>>
>>> <qc0-mclachlan.err>
>>>
>>>
>>>
>>> --
>>>
>>> Ian Hinder
>>>
>>> http://numrel.aei.mpg.de/people/hinder
>>>
>>>
>>> <qc0-mclachlan.out>
>>>
>>>
>>> --
>>> Ian Hinder
>>> http://numrel.aei.mpg.de/people/hinder
>>>
--
Ian Hinder
http://numrel.aei.mpg.de/people/hinder
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