[yt-dev] [continued] RAMSES units bug in yt-3.0

Wed May 21 09:51:25 PDT 2014

It should be the tip of the yt-3.0 branch of the yt repo. I'll 
double-check that I haven't somehow messed up my install of yt or 
something. If you don't find a similar issue it's probably on my end...

On 21/05/14 18:47, Matthew Turk wrote:
> Hi Sam,
>
> What's teh changeset hash? All of my tests have been against the "tip"
> of the yt-3.0 branch.  Note that the repository yt_analysis/yt-3.0 is
> no longer in use.
>
> On Wed, May 21, 2014 at 12:19 PM, Sam Geen <samgeen at astro.ox.ac.uk> wrote:
>> Hi again,
>>
>> I've downloaded the latest version of yt-3.0, and am finding total mass
>> values of 0.002 g for a simulation of a cloud of mass 10^5 Msun. I'm also
>> finding that the temperature values are way too high (a max of 10^9K or so,
>> when the max should be more like 10^5K). Finally, the pressure units are
>> listed as code_mass/(code_length*code_time**2) rather than cgs (I have no
>> idea if this represents a problem, but it could be related to the
>> temperature bug).
>>
>> Out of interest, is there a recommended version of yt-3.0 to use before the
>> units were added to compare against? (I believe the old units system gave
>> the correct values for RAMSES data).
>>
>> Thanks,
>>
>> Sam
>>
>>
>> On 14/05/14 16:38, Sam Geen wrote:
>>> Hi Matt,
>>>
>>> Sorry for the confusion - I've cross-checked against another dataset and
>>> the cell mass should be more like 2.5e8Msun, as you find; I thought the
>>> density values seemed very low (as well as the mass fraction of gas to dark
>>> matter) and hence added a factor of boxlen**3, which seemed more reasonable,
>>> but checking against another run it seems that the other run just has very
>>> low densities, and so the density unit doesn't need converting by boxlen**3
>>> after all, so the only thing to be careful of is to make sure that
>>> cell-based spatial units are multiplied by boxlen while particle-based
>>> spatial units aren't; this way both the lengths and masses should be
>>> consistent. The particle mass should still be 1.8e10Msun.
>>>
>>> Thanks for your work on this!
>>>
>>> Sam
>>>
>>> On 14/05/14 14:22, Matthew Turk wrote:
>>>> Hi all,
>>>>
>>>> I've got Sam's dataset here.  As a quick note, with current yt-3.0
>>>> tip, all results are correct for cosmology.
>>>>
>>>> With the outstanding pull request, here are the results:
>>>>
>>>> Cell Mass: 2.474e+08 Msun (5.300e+13 desired, 4.669e-06 ratio)
>>>> Part Mass: 3.865e+15 Msun (1.800e+10 desired, 2.147e+05 ratio)
>>>>
>>>> Without it:
>>>>
>>>> Cell Mass: 1.146e+03 Msun (5.300e+13 desired, 2.161e-11 ratio)
>>>> Part Mass: 1.789e+10 Msun (1.800e+10 desired, 9.941e-01 ratio)
>>>>
>>>> So the particle mass is correct in current yt-3.0 tip, and the cell
>>>> mass isn't right in either the tip or the pull request.  Now, if I use
>>>> yt-3.0 tip and compare cell_mass*boxlen**6 against the known, I get
>>>> the right answer.
>>>>
>>>> To solve this asymmetry between the particles and the cell density,
>>>> I've added a "code_density" unit and updated the pull request. I now
>>>> get correct results for non-cosmo and cosmo runs.  This is in
>>>> changeset 8847f04588b1:
>>>>
>>>>
>>>> https://bitbucket.org/yt_analysis/yt/pull-request/895/fixing-ramses-density-and-mass-units
>>>>
>>>> -Matt
>>>>
>>>> On Tue, May 13, 2014 at 8:59 AM, Sam Geen <samgeen at astro.ox.ac.uk> wrote:
>>>>> I'll try to hunt down and upload a sample dataset shortly.
>>>>>
>>>>>
>>>>> On 13/05/2014 14:52, Matthew Turk wrote:
>>>>>> On Tue, May 13, 2014 at 8:48 AM, Sam Geen <samgeen at astro.ox.ac.uk>
>>>>>> wrote:
>>>>>>> Ah, very good, thanks for the link to that old PR! I was worried I was
>>>>>>> going
>>>>>>> crazy... in any case, whichever is the easiest way to make the
>>>>>>> position/length units consistent.
>>>>>> I change the particle positions in the ingestion phase, so at no point
>>>>>> should they appear incorrect.  I'd really like to figure out the
>>>>>> boxlen != 1.0 ...
>>>>>>
>>>>>>> By the way, I took a quick look at reading the grav_ files recently,
>>>>>>> although the output seems kind of strange, so I haven't issued a PR
>>>>>>> yet
>>>>>>> until I understand what it's doing (plus I still don't 100% understand
>>>>>>> the
>>>>>>> units). I suspect it might be reading in the wrong order or something.
>>>>>>> It
>>>>>>> also complicates the code, so it might be worth refactoring a bit to
>>>>>>> make
>>>>>>> a
>>>>>>> universal "AMR-like" data_structures/io interface for the files called
>>>>>>> hydro_, grav_, rt_, etc, rather than what I did which was to scatter a
>>>>>>> bunch
>>>>>>> of conditionals into the existing functions.
>>>>>> That could be -- I think there was some discussion that they might
>>>>>> also include ghost zones?
>>>>>>
>>>>>> I've also run some checks on cosmology runs.  Here's what I've found.
>>>>>> With no changes to the current tip of yt-3.0, I have run this script:
>>>>>>
>>>>>> --
>>>>>> ds = yt.load("output_00010/info_00010.txt")
>>>>>> dd = ds.all_data()
>>>>>>
>>>>>> # Let's find the total mass
>>>>>> pmass = dd["particle_mass"].sum().in_units("Msun")
>>>>>> cmass = dd["cell_mass"].sum().in_units("Msun")
>>>>>> rho = ds.cosmology.critical_density(ds.current_redshift)
>>>>>> crit_mass = (rho * dd["cell_volume"]).sum().in_units("Msun")
>>>>>> print pmass
>>>>>> print cmass
>>>>>> print pmass / (pmass + cmass)
>>>>>> print ((pmass + cmass) / crit_mass)
>>>>>> --
>>>>>>
>>>>>> The results are good.  I get roughly 0.84 for pmass / (pmass + cmass),
>>>>>> and I get 0.998 for the final check, which seems within the parameters
>>>>>> of the simulation.  So the cosmological units should be correct, and
>>>>>> more to the point, they match up with what I'm expecting having read
>>>>>> over the code carefully.
>>>>>>
>>>>>> So it looks to me like there is in fact a boxlen missing, but that as
>>>>>> it stands, the particle and density units are correct for boxlen =
>>>>>> 1.0.  Nick's message is worrisome because the factor isn't exactly 1e3
>>>>>> between his max density.  I have a boxlen != 1.0 dataset, but I have
>>>>>> no reference values to compare it again.  Any chance there's one with
>>>>>> *reference* results for total mass in particles, total mass in gas,
>>>>>> etc?
>>>>>>
>>>>>> -Matt
>>>>>>
>>>>>>> On 13/05/2014 14:21, Matthew Turk wrote:
>>>>>>>> Hi Sam,
>>>>>>>>
>>>>>>>> So, here's an old pull request I found:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> http://hg.yt-project.org/yt-3.0/pull-request/62/adding-boxlen-to-ramses-units-for-mass-and
>>>>>>>>
>>>>>>>> and then there's the units.f90 from RAMSES itself:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> https://bitbucket.org/rteyssie/ramses/src/81ab29b8a405e7ccf6bf30fd67582b4edacddd6e/trunk/ramses/amr/units.f90?at=master
>>>>>>>>
>>>>>>>> I'm going to take care of this, update the PR, and ping you both.
>>>>>>>> (And maybe we should move to yt-dev? :)
>>>>>>>>
>>>>>>>> -Matt
>>>>>>>>
>>>>>>>> On Tue, May 13, 2014 at 8:17 AM, Sam Geen <samgeen at astro.ox.ac.uk>
>>>>>>>> wrote:
>>>>>>>>> Huh, that difference in the max density is very strange. I can't
>>>>>>>>> think
>>>>>>>>> why
>>>>>>>>> you'd have that difference; it's not an obvious multiple.
>>>>>>>>>
>>>>>>>>> Actually, I'm looking at the code and it's possible that the
>>>>>>>>> particle
>>>>>>>>> positions are scaled from 0 to boxlen and the grid positions from 0
>>>>>>>>> to
>>>>>>>>> 1,
>>>>>>>>> though I'd need to open up the raw values in a RAMSES file to
>>>>>>>>> confirm
>>>>>>>>> this.
>>>>>>>>> If this is true, I suppose one "fix" could be to hard-multiply the
>>>>>>>>> cell
>>>>>>>>> sizes by pf["boxlen"] when you load them so that the length units
>>>>>>>>> are
>>>>>>>>> consistent for all data. I *think* that the older version of yt-3.0
>>>>>>>>> gave
>>>>>>>>> correct answers, though, so that should at least be a way to
>>>>>>>>> calibrate
>>>>>>>>> the
>>>>>>>>> new version.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 13/05/2014 14:01, nick moeckel wrote:
>>>>>>>>>
>>>>>>>>> I had a chance to test out an older and a newer version of yt-3 on a
>>>>>>>>> small
>>>>>>>>> dataset that has boxlen=10. This seems to confirm a boxlen**3 factor
>>>>>>>>> somewhere, although there's a further difference in the max density.
>>>>>>>>>
>>>>>>>>> more recent version (hg id -i gives f4838a2165c0):
>>>>>>>>>
>>>>>>>>> after dd = ds.all_data():
>>>>>>>>>
>>>>>>>>> In [11]: dd.quantities.extrema('density')
>>>>>>>>>
>>>>>>>>> Out[11]: (2.00739832795e-28 g/cm**3, 4.54771338163e-24 g/cm**3)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> older version (hg id -i gives 3e8b733c9ee9):
>>>>>>>>>
>>>>>>>>> after dd = ds.h.all_data():
>>>>>>>>>
>>>>>>>>> In [10]: dd.quantities.extrema('Density')
>>>>>>>>>
>>>>>>>>> Out[10]: [(2.0073983279492632e-25, 4.0079147772594363e-21)]
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Fri, May 9, 2014 at 5:50 PM, Sam Geen <samgeen at astro.ox.ac.uk>
>>>>>>>>> wrote:
>>>>>>>>>> Yep, that looks like it should work. I'll try to run it on some
>>>>>>>>>> particle
>>>>>>>>>> data when I get the time, but like I said I'm 99% sure the mass
>>>>>>>>>> units
>>>>>>>>>> should
>>>>>>>>>> be identical for both grid hydro and particle data.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 09/05/14 17:46, Matthew Turk wrote:
>>>>>>>>>>> Hi Sam,
>>>>>>>>>>>
>>>>>>>>>>> Okay, I've looked over a bit, and I think the correct change would
>>>>>>>>>>> be:
>>>>>>>>>>>
>>>>>>>>>>> mass_unit = rho_u * length_unit**3.
>>>>>>>>>>>
>>>>>>>>>>> That should include the correct length unit, and I think will
>>>>>>>>>>> reduce
>>>>>>>>>>> "density" back to the "unit_d" that's in the parameter file.  If
>>>>>>>>>>> this
>>>>>>>>>>> looks okay to you, I will push it, but I really do want to make
>>>>>>>>>>> sure
>>>>>>>>>>> the particle masses are correct.  Can Nick or Romain provide a bit
>>>>>>>>>>> of
>>>>>>>>>>> guidance here?
>>>>>>>>>>>
>>>>>>>>>>> -Matt
>>>>>>>>>>>
>>>>>>>>>>> On Fri, May 9, 2014 at 11:25 AM, Sam Geen <samgeen at astro.ox.ac.uk>
>>>>>>>>>>> wrote:
>>>>>>>>>>>> OK, interesting. In theory RAMSES should have identical units for
>>>>>>>>>>>> both
>>>>>>>>>>>> particles and gas. I can hunt down a run with particles to test
>>>>>>>>>>>> if
>>>>>>>>>>>> you
>>>>>>>>>>>> like.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks!
>>>>>>>>>>>> Sam
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On 09/05/14 17:22, Matthew Turk wrote:
>>>>>>>>>>>>> Hi Sam,
>>>>>>>>>>>>>
>>>>>>>>>>>>> On reflection, I think this might be related to getting the
>>>>>>>>>>>>> *particle*
>>>>>>>>>>>>> masses correct.  I will take a look at it as soon as I can.
>>>>>>>>>>>>>
>>>>>>>>>>>>> -Matt
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Fri, May 9, 2014 at 11:00 AM, Sam Geen
>>>>>>>>>>>>> <samgeen at astro.ox.ac.uk>
>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>> Hmm, that looks like it should be "mass_unit = rho_u *
>>>>>>>>>>>>>> length_unit**3"
>>>>>>>>>>>>>> in
>>>>>>>>>>>>>> line 492. You're right that it mentions the boxlength issue,
>>>>>>>>>>>>>> though.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On 09/05/14 16:50, Matthew Turk wrote:
>>>>>>>>>>>>>>> Hi Sam,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Okay, sounds good.  Looking at how code unit attributes are
>>>>>>>>>>>>>>> set
>>>>>>>>>>>>>>> up:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> https://bitbucket.org/yt_analysis/yt/src/a14a150c7c81850df81346162bdaff271e77eb50/yt/frontends/ramses/data_structures.py?at=yt-3.0#cl-482
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> suggests to me that length_unit takes into account boxlen, and
>>>>>>>>>>>>>>> mass_unit does not.  The comments have some indication why
>>>>>>>>>>>>>>> this
>>>>>>>>>>>>>>> might
>>>>>>>>>>>>>>> be.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> -Matt
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Fri, May 9, 2014 at 10:46 AM, Sam Geen
>>>>>>>>>>>>>>> <samgeen at astro.ox.ac.uk>
>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>> Yep; both this and dd["density"] give cgs values that are too
>>>>>>>>>>>>>>>> small
>>>>>>>>>>>>>>>> by
>>>>>>>>>>>>>>>> roughly a factor of boxlen**3.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> One other thing I need to try is to make sure I'm using the
>>>>>>>>>>>>>>>> very
>>>>>>>>>>>>>>>> latest
>>>>>>>>>>>>>>>> version of YT; I've been playing around with the Ramses
>>>>>>>>>>>>>>>> frontend
>>>>>>>>>>>>>>>> so
>>>>>>>>>>>>>>>> it's
>>>>>>>>>>>>>>>> possible my version is somehow out of sync. Will let you know
>>>>>>>>>>>>>>>> if
>>>>>>>>>>>>>>>> this
>>>>>>>>>>>>>>>> fixes
>>>>>>>>>>>>>>>> things.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On 09/05/14 16:42, Matthew Turk wrote:
>>>>>>>>>>>>>>>>> Hi Sam,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Can you verify the units are in fact incorrect in *cgs*?
>>>>>>>>>>>>>>>>> Something
>>>>>>>>>>>>>>>>> like this would work:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> ds = load(...)
>>>>>>>>>>>>>>>>> dd = ds.all_data()
>>>>>>>>>>>>>>>>> print dd.quantities.total_quantitiy("cell_mass").in_cgs()
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Your second message makes me wonder if there's just a slipup
>>>>>>>>>>>>>>>>> in
>>>>>>>>>>>>>>>>> how
>>>>>>>>>>>>>>>>> the units are returned.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> -Matt
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Fri, May 9, 2014 at 10:37 AM, Sam Geen
>>>>>>>>>>>>>>>>> <samgeen at astro.ox.ac.uk>
>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>> Sorry for the spam; a second bug I've seen is that the
>>>>>>>>>>>>>>>>>> density
>>>>>>>>>>>>>>>>>> and
>>>>>>>>>>>>>>>>>> pressure
>>>>>>>>>>>>>>>>>> unit labels on figures appears to be broken; it seems to
>>>>>>>>>>>>>>>>>> print
>>>>>>>>>>>>>>>>>> a
>>>>>>>>>>>>>>>>>> latex-mangled code names for the units rather than the cgs
>>>>>>>>>>>>>>>>>> name
>>>>>>>>>>>>>>>>>> of
>>>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>>>> units; see attached example. Temperature is fine.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On 09/05/14 16:28, Sam Geen wrote:
>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Just to say that in the latest version of yt-3.0 (i.e.
>>>>>>>>>>>>>>>>>>> since
>>>>>>>>>>>>>>>>>>> various
>>>>>>>>>>>>>>>>>>> fields were renamed or re-implemented), I've found a bug
>>>>>>>>>>>>>>>>>>> in
>>>>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>>>>> implementation of "cell_mass", which is giving results
>>>>>>>>>>>>>>>>>>> that
>>>>>>>>>>>>>>>>>>> are
>>>>>>>>>>>>>>>>>>> too
>>>>>>>>>>>>>>>>>>> low
>>>>>>>>>>>>>>>>>>> in
>>>>>>>>>>>>>>>>>>> my runs; I believe the issue is that it's missing a factor
>>>>>>>>>>>>>>>>>>> of
>>>>>>>>>>>>>>>>>>> pf["boxlen"]**3 (which is of course only a problem if
>>>>>>>>>>>>>>>>>>> boxlen
>>>>>>>>>>>>>>>>>>> is
>>>>>>>>>>>>>>>>>>> not
>>>>>>>>>>>>>>>>>>> 1).
>>>>>>>>>>>>>>>>>>> The
>>>>>>>>>>>>>>>>>>> previous "CellMass_Msun" worked fine. If I get time I
>>>>>>>>>>>>>>>>>>> might
>>>>>>>>>>>>>>>>>>> take
>>>>>>>>>>>>>>>>>>> a
>>>>>>>>>>>>>>>>>>> look
>>>>>>>>>>>>>>>>>>> and
>>>>>>>>>>>>>>>>>>> issue a pull request, but otherwise I'm just flagging this
>>>>>>>>>>>>>>>>>>> in
>>>>>>>>>>>>>>>>>>> case
>>>>>>>>>>>>>>>>>>> someone
>>>>>>>>>>>>>>>>>>> else runs into problems; you can just manually multiply
>>>>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>>>>> result
>>>>>>>>>>>>>>>>>>> by
>>>>>>>>>>>>>>>>>>> pf["boxlen"]**3 until it's fixed.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>>>>>> _______________________________________________
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