Ramses star- dark matter particle filter
by Vadlamani Samhitha
Hi, I would like to know if it’s possible to have a particle filter based
on the mass resolutions of the particles. I am using RAMSES data where I
can distinguish stars and dark matter only from their mass resolutions (no
particle_type). Any help is highly appreciated.
2 months, 2 weeks
ERROR IN PARTICLE FILTER
by Vadlamani Samhitha
Hi,
I am trying to make a particle filter for just the old stars for which my
simulation requires pruning with two fields "particle_mass" and
"particle_age".
def old(pfilter, data):
>
> age = data["all", "particle_age"]
>
> old_only = data["all", "particle_mass"]
>
> filter = np.logical_and(age.in_units('Myr') = 0,
> old_only.in_units('Msun') < 4e6)
>
> return filter
>
>
>
But I encounter an error:
File "new-old-stars.py", line 14
> filter = np.logical_and(age.in_units('Myr') = 0,
> old_only.in_units('Msun') < 4e6)
> ^
> SyntaxError: keyword can't be an expression
Could someone please point out what the issue here could be? Can I not use
a filter with two different fields?
2 months, 2 weeks
Re: Merger trees
by Nick Gnedin
Britton,
Thank you very much for the instructions, Rockstar seems to work well
with a time series dataset.
Could you briefly tell me what the difference is between the two methods
for building merger trees: (1) using consistent-trees and (2) using
ytree directrly with ytree.load("out_0.list")? What would ytree use for
making a merger tree?
n
On 11/25/18 12:02 PM, Britton Smith wrote:
> Hi Nick,
>
> Sorry for the long delay. Lots of travel this past week.
>
> After reading through this discussion, I have two comments that might help.
>
> First, to get rockstar to run on multiple datasets, you need to create a
> time series object and pass that directly to the RockstarHaloFinder. For
> example,
>
> import yt
> yt.enable_parallelism()
> from yt.extensions.astro_analysis.halo_finding.rockstar.api import \
> RockstarHaloFinder
> ts = yt.DatasetSeries(LIST_OF_FILES)
> rh = RockstarHaloFinder(ts, num_readers=1, num_writers=1)
> rh.run()
>
> Note, I'm using the yt_astro_analysis
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_yt-2Dproj...> package,
> where all these tools have now moved for future development. I think the
> installation docs are also a bit clearer there. The halo finding part of
> the documentation definitely needs improvement. I'll try to do this
> within yt_astro_analysis docs
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysi...>.
>
> Second, if you've now got all of the rockstar catalogs and don't want to
> use consistent-trees, what you'll need are the out_*.list files that get
> made. There will be one for each snapshot. You should find these within
> the rockstar_halos directory. If you have those, you can feed the first
> one, usually out_0.list, straight to ytree and it will assemble the
> merger trees.
> import ytree
> a = ytree.load("out_0.list")
>
> Britton
>
> On Wed, Nov 21, 2018 at 11:43 AM Nick Gnedin <gnedin(a)fnal.gov
> <mailto:gnedin@fnal.gov>> wrote:
>
>
> Britton,
>
> I am still confused about making merger trees with yt. I ran
> rockstar on
> my snapshots, but the ytree doc page says it is only able to make trees
> from Gadget FoF/Subfind halo finders.
>
> I could use Consistent Trees, but it needs halo catalogs in rockstar
> native format, not in h5 format that is produced by yt.
>
> Nick
>
>
> On 10/5/2018 12:06 PM, Britton Smith wrote:
> > HI Nick,
> >
> > Sadly, yt's FoF and HOP finders don't output member particle
> information
> > for the halos, so it might not be possible to use those catalogs
> to make
> > merger trees. ytree's merger-tree creation works with FoF catalogs
> > generated by the inline Gadget halo finder, for which yt supports
> > extracting member particle information. If you're looking to make
> > merger-trees, the best route currently is probably
> > Rockstar/consistent-trees, the outputs of which can be loaded by
> ytree.
> >
> > It is probably a week's worth of work to fix up yt's HOP/FoF
> finders to
> > output particle information and then to add support for loading that
> > into yt.
> >
> > Britton
> >
> > On Fri, Oct 5, 2018 at 6:07 AM Nick Gnedin <gnedin(a)fnal.gov
> <mailto:gnedin@fnal.gov>
> > <mailto:gnedin@fnal.gov <mailto:gnedin@fnal.gov>>> wrote:
> >
> >
> > Folks,
> >
> > I am confused about how to compute merger trees with yt.
> Documentation
> >
> (https://yt-project.org/doc/analyzing/analysis_modules/halo_merger_tree.ht... <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dproject.org_doc...>
> >
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dproject.org_doc...>)
> >
> > refers to ytree package, but that package documentation seems to
> > indicate that only FoF or Subfind halo catalogs can be
> converted into a
> > merger tree, while the halo finder in yt is HOP.
> >
> > I have run HOP for several snapshots from a simulation. What
> would you
> > recommend to use to make a merger tree from such a data set?
> >
> > Thank you,
> >
> > Nick Gnedin
> >
> > _______________________________________________
> > yt-users mailing list -- yt-users(a)python.org
> <mailto:yt-users@python.org>
> > <mailto:yt-users@python.org <mailto:yt-users@python.org>>
> > To unsubscribe send an email to yt-users-leave(a)python.org
> <mailto:yt-users-leave@python.org>
> > <mailto:yt-users-leave@python.org
> <mailto:yt-users-leave@python.org>>
> >
> >
> >
> <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_c...
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>
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>
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>
> >
> >
> > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
2 months, 2 weeks
How can I set a value with its units to derived_field?
by lianxiaoli87＠sjtu.edu.cn
Hi, all:
I need an initial value of CMB magnetic to derive a new field in plugins python file. How can I set the unit of "gauss " to this value?
For I can not carry on my calculation between CMB magnetic strength (dimensionless) and the outputs of Enzo (in units of gauss).
2 months, 3 weeks
Re: Merger trees
by Nick Gnedin
Britton,
I am still confused about making merger trees with yt. I ran rockstar on
my snapshots, but the ytree doc page says it is only able to make trees
from Gadget FoF/Subfind halo finders.
I could use Consistent Trees, but it needs halo catalogs in rockstar
native format, not in h5 format that is produced by yt.
Nick
On 10/5/2018 12:06 PM, Britton Smith wrote:
> HI Nick,
>
> Sadly, yt's FoF and HOP finders don't output member particle information
> for the halos, so it might not be possible to use those catalogs to make
> merger trees. ytree's merger-tree creation works with FoF catalogs
> generated by the inline Gadget halo finder, for which yt supports
> extracting member particle information. If you're looking to make
> merger-trees, the best route currently is probably
> Rockstar/consistent-trees, the outputs of which can be loaded by ytree.
>
> It is probably a week's worth of work to fix up yt's HOP/FoF finders to
> output particle information and then to add support for loading that
> into yt.
>
> Britton
>
> On Fri, Oct 5, 2018 at 6:07 AM Nick Gnedin <gnedin(a)fnal.gov
> <mailto:gnedin@fnal.gov>> wrote:
>
>
> Folks,
>
> I am confused about how to compute merger trees with yt. Documentation
> (https://yt-project.org/doc/analyzing/analysis_modules/halo_merger_tree.ht...
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dproject.org_doc...>)
>
> refers to ytree package, but that package documentation seems to
> indicate that only FoF or Subfind halo catalogs can be converted into a
> merger tree, while the halo finder in yt is HOP.
>
> I have run HOP for several snapshots from a simulation. What would you
> recommend to use to make a merger tree from such a data set?
>
> Thank you,
>
> Nick Gnedin
>
> _______________________________________________
> yt-users mailing list -- yt-users(a)python.org
> <mailto:yt-users@python.org>
> To unsubscribe send an email to yt-users-leave(a)python.org
> <mailto:yt-users-leave@python.org>
>
>
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>
>
> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
2 months, 3 weeks
Re: Merger trees
by Nick Gnedin
Nathan,
I added rockstar to my yt installation, and it works, but only one
snapshot at a time. I.e, when I try running the halo finder in the loop:
for set in sets:
d = yt.load(set)
hc =
HaloCatalog(data_ds=d,finder_method='rockstar',finder_kwargs={'dm_only':True,'particle_type':'N-BODY'})
hc.create()
if(yt.is_root()): print('Memory: ',yt.funcs.get_memory_usage())
it runs once, but at the second loop iteration gives the following
error. I checked the memory use, it is very small for this small
simulation, so the segfault is most likely the result of the network
failure.
This was run with 1 reader and 1 writer on a single node:
mpirun -n 3 python3 hfc-rs.py
but I also tried more ranks, the error occurs independently of the
number of ranks used.
This is not critical, since I can run the script for each snapshot
separately, but it would be nice to be able to run all of them at once.
Perhaps, some network connections are not properly cleaned - I heard
that rockstar does something weird with networking.
Nick
------------- error messages ------------------------------
...
P001 yt : [WARNING ] 2018-11-21 10:54:13,109 Total Particle Count:
1.342e+08
[ 0s] Accepting connections...
[ 0s] Accepted all reader / writer connections.
[Warning] Network IO Failure (PID 146476): Connection reset by peer
[Warning] Network IO Failure (PID 146476): Success
[Network] Packet receive retry count at: 1
[Warning] Connection attempt 1 to nanna.uchicago.edu:59013 failed: :
Connection refused
[Warning] Network IO Failure (PID 146477): Connection reset by peer
[Warning] Network IO Failure (PID 146477): Success
[Network] Packet receive retry count at: 1
[Warning] Connection attempt 1 to nanna.uchicago.edu:59013 failed: :
Connection refused
=====================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 139
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
=====================================================================================
APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
On 11/19/18 4:12 PM, Nathan Goldbaum wrote:
> Hi Nick,
>
> See the installation docs here, in particular the section titled
> “installing support for the rockstar halo finder”:
>
> http://yt-project.org/doc/installing.html
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__yt-2Dproject.org_doc_...>
>
> Nathan
>
> On Mon, Nov 19, 2018 at 2:47 PM Nick Gnedin <gnedin(a)fnal.gov
> <mailto:gnedin@fnal.gov>> wrote:
>
>
> Britton,
>
> How would I install Rockstar for yt to use? Your webpage mentions
> install-script.sh, but my from-source installation lacks it:
>
> ~/ART/yt >ls
> appveyor.yml CONTRIBUTING.rst MANIFEST.in setup.cfg yt.egg-info
> benchmarks COPYING.txt nose.cfg setupext.py
> build CREDITS __pycache__ setup.py
> CITATION doc README.md tests
> clean.sh docker scripts yt
>
> I downloaded it as the help recommends, but then the script tries to
> download and install yet another yt installation.
>
> I need to use my clone, since I made some changes to it that I haven't
> yet submitted in a pull request.
>
>
>
>
>
> On 10/5/2018 12:23 PM, Britton Smith wrote:
> > Hi Nick,
> >
> > Ok, good luck. It should be noted that the version of Rockstar
> that runs
> > with yt is not the latest version of Rockstar, known as
> > Rockstar-Galaxies. yt's Rockstar does not support multi-mass
> > simulations. You may also find different i/o performance between
> the two
> > versions, so it's worth experimenting, if both options are available.
> >
> > Britton
> >
> > On Fri, Oct 5, 2018 at 10:10 AM Nick Gnedin <gnedin(a)fnal.gov
> <mailto:gnedin@fnal.gov>
> > <mailto:gnedin@fnal.gov <mailto:gnedin@fnal.gov>>> wrote:
> >
> >
> > Britton,
> >
> > Thank you very much, I will try Rockstar first.
> >
> > n
> >
> >
> > On 10/5/2018 7:06 PM, Britton Smith wrote:
> > > HI Nick,
> > >
> > > Sadly, yt's FoF and HOP finders don't output member particle
> > information
> > > for the halos, so it might not be possible to use those
> catalogs
> > to make
> > > merger trees. ytree's merger-tree creation works with FoF
> catalogs
> > > generated by the inline Gadget halo finder, for which yt
> supports
> > > extracting member particle information. If you're looking
> to make
> > > merger-trees, the best route currently is probably
> > > Rockstar/consistent-trees, the outputs of which can be
> loaded by
> > ytree.
> > >
> > > It is probably a week's worth of work to fix up yt's HOP/FoF
> > finders to
> > > output particle information and then to add support for
> loading that
> > > into yt.
> > >
> > > Britton
> > >
> > > On Fri, Oct 5, 2018 at 6:07 AM Nick Gnedin
> <gnedin(a)fnal.gov <mailto:gnedin@fnal.gov>
> > <mailto:gnedin@fnal.gov <mailto:gnedin@fnal.gov>>
> > > <mailto:gnedin@fnal.gov <mailto:gnedin@fnal.gov>
> <mailto:gnedin@fnal.gov <mailto:gnedin@fnal.gov>>>> wrote:
> > >
> > >
> > > Folks,
> > >
> > > I am confused about how to compute merger trees with yt.
> > Documentation
> > >
> >
> (https://yt-project.org/doc/analyzing/analysis_modules/halo_merger_tree.ht... <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dproject.org_doc...> <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dproject.org_doc...>
> > >
> >
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dproject.org_doc...>)
> > >
> > > refers to ytree package, but that package
> documentation seems to
> > > indicate that only FoF or Subfind halo catalogs can be
> > converted into a
> > > merger tree, while the halo finder in yt is HOP.
> > >
> > > I have run HOP for several snapshots from a
> simulation. What
> > would you
> > > recommend to use to make a merger tree from such a
> data set?
> > >
> > > Thank you,
> > >
> > > Nick Gnedin
> > >
> > > _______________________________________________
> > > yt-users mailing list -- yt-users(a)python.org
> <mailto:yt-users@python.org>
> > <mailto:yt-users@python.org <mailto:yt-users@python.org>>
> > > <mailto:yt-users@python.org
> <mailto:yt-users@python.org> <mailto:yt-users@python.org
> <mailto:yt-users@python.org>>>
> > > To unsubscribe send an email to
> yt-users-leave(a)python.org <mailto:yt-users-leave@python.org>
> > <mailto:yt-users-leave@python.org
> <mailto:yt-users-leave@python.org>>
> > > <mailto:yt-users-leave@python.org
> <mailto:yt-users-leave@python.org>
> > <mailto:yt-users-leave@python.org
> <mailto:yt-users-leave@python.org>>>
> > >
> > >
> > >
> >
> <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_c... <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.avg.com_email-2Ds...>
> >
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> >
> > > Virus-free. www.avg.com
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> >
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> >
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> >
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> > >
> > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> >
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>
2 months, 3 weeks
Re: Merger trees
by Nick Gnedin
Britton,
How would I install Rockstar for yt to use? Your webpage mentions
install-script.sh, but my from-source installation lacks it:
~/ART/yt >ls
appveyor.yml CONTRIBUTING.rst MANIFEST.in setup.cfg yt.egg-info
benchmarks COPYING.txt nose.cfg setupext.py
build CREDITS __pycache__ setup.py
CITATION doc README.md tests
clean.sh docker scripts yt
I downloaded it as the help recommends, but then the script tries to
download and install yet another yt installation.
I need to use my clone, since I made some changes to it that I haven't
yet submitted in a pull request.
On 10/5/2018 12:23 PM, Britton Smith wrote:
> Hi Nick,
>
> Ok, good luck. It should be noted that the version of Rockstar that runs
> with yt is not the latest version of Rockstar, known as
> Rockstar-Galaxies. yt's Rockstar does not support multi-mass
> simulations. You may also find different i/o performance between the two
> versions, so it's worth experimenting, if both options are available.
>
> Britton
>
> On Fri, Oct 5, 2018 at 10:10 AM Nick Gnedin <gnedin(a)fnal.gov
> <mailto:gnedin@fnal.gov>> wrote:
>
>
> Britton,
>
> Thank you very much, I will try Rockstar first.
>
> n
>
>
> On 10/5/2018 7:06 PM, Britton Smith wrote:
> > HI Nick,
> >
> > Sadly, yt's FoF and HOP finders don't output member particle
> information
> > for the halos, so it might not be possible to use those catalogs
> to make
> > merger trees. ytree's merger-tree creation works with FoF catalogs
> > generated by the inline Gadget halo finder, for which yt supports
> > extracting member particle information. If you're looking to make
> > merger-trees, the best route currently is probably
> > Rockstar/consistent-trees, the outputs of which can be loaded by
> ytree.
> >
> > It is probably a week's worth of work to fix up yt's HOP/FoF
> finders to
> > output particle information and then to add support for loading that
> > into yt.
> >
> > Britton
> >
> > On Fri, Oct 5, 2018 at 6:07 AM Nick Gnedin <gnedin(a)fnal.gov
> <mailto:gnedin@fnal.gov>
> > <mailto:gnedin@fnal.gov <mailto:gnedin@fnal.gov>>> wrote:
> >
> >
> > Folks,
> >
> > I am confused about how to compute merger trees with yt.
> Documentation
> >
> (https://yt-project.org/doc/analyzing/analysis_modules/halo_merger_tree.ht... <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dproject.org_doc...>
> >
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dproject.org_doc...>)
> >
> > refers to ytree package, but that package documentation seems to
> > indicate that only FoF or Subfind halo catalogs can be
> converted into a
> > merger tree, while the halo finder in yt is HOP.
> >
> > I have run HOP for several snapshots from a simulation. What
> would you
> > recommend to use to make a merger tree from such a data set?
> >
> > Thank you,
> >
> > Nick Gnedin
> >
> > _______________________________________________
> > yt-users mailing list -- yt-users(a)python.org
> <mailto:yt-users@python.org>
> > <mailto:yt-users@python.org <mailto:yt-users@python.org>>
> > To unsubscribe send an email to yt-users-leave(a)python.org
> <mailto:yt-users-leave@python.org>
> > <mailto:yt-users-leave@python.org
> <mailto:yt-users-leave@python.org>>
> >
> >
> >
> <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_c...
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>
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>
> >
> >
> > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
2 months, 4 weeks
AREA UNDER PROFILE PLOTS
by Vadlamani Samhitha
Hi,
Is there a way to obtain area under the curves for 1D profile plots in yt?
2 months, 4 weeks
Re: writing PPV cubes with fields other than density
by Nathan Goldbaum
Yes, it should be just using the gas mass. Apologies for the confusion and
thanks for filing an issue, hopefully future users will be less confused :)
On Fri, Nov 16, 2018 at 3:46 PM Samantha M Benincasa <
smbenincasa(a)ucdavis.edu> wrote:
> Hi John,
>
> You're right, using only "cell_mass" instead of ("gas","cell_mass") does
> the trick! Does this still use only the gas mass though?
>
> Either way, I've also submitted the issue as suggested.
>
> Cheers,
> Sam
>
> On Wed, 14 Nov 2018 at 11:56, John Zuhone <jzuhone(a)gmail.com> wrote:
>
>> Hi Sam,
>>
>> I believe this is a bug now, but can you try setting the field name as
>> “cell_mass” instead of the tuple in the call to PPVCube as a workaround?
>>
>> Can you file this as an issue at
>> http://github.com/yt-project/yt_astro_analysis/issues with the code and
>> traceback?
>>
>> Thanks,
>>
>> John
>>
>> On Nov 14, 2018, at 2:46 PM, Samantha M Benincasa <
>> smbenincasa(a)ucdavis.edu> wrote:
>>
>> Hi John,
>>
>> I believe it does. It shows up in the derived field list and the command
>> for cube creation runs and produces reasonable output.
>>
>> Cheers,
>> Sam
>>
>> On Wed, Nov 14, 2018, 11:14 AM John Zuhone <jzuhone(a)gmail.com wrote:
>>
>>> Hi Sam,
>>>
>>> I think the issue here is that the Gizmo simulation you are using
>>> doesn’t have a “cell_mass” field (someone should correct me if I am missing
>>> something but I am pretty sure this is the case). This is only true for
>>> grid-based datasets.
>>>
>>> You could try using (“deposit”, “PartType0_mass") instead, which will
>>> give you the deposited gas mass on the ochre.
>>>
>>> We plan to make these things less confusing in yt 4.0.
>>>
>>> Best,
>>>
>>> John Z
>>>
>>> On Nov 14, 2018, at 1:52 PM, Samantha M Benincasa <
>>> smbenincasa(a)ucdavis.edu> wrote:
>>>
>>> Hi everyone,
>>>
>>> I'm currently using the PPVcube function to make FITS files of a gizmo
>>> simulation. I would like the field used to make the cubes to be mass rather
>>> than density. The cube is created however, when I try to write the cube, I
>>> get the error copied below. I included the code directly before it.
>>>
>>> Is it not possible to write FITS cubes with other fields?
>>>
>>> Cheers,
>>> Sam
>>>
>>> cubeL = PPVCube(ds, L, ("gas","cell_mass"), (-150.,150.,6,"km/s"), dim s
>>> =100, method="sum", center=c,width=(0.01, "Mpc"), data_source=sp)
>>>
>>> cubeL.write_fits("mass.fits",length_unit="kpc", clobber='True')
>>> --------------------------------------------------------------------
>>>
>>> -------
>>> KeyError Traceback (most recent cal
>>> l last)
>>>
>>> <ipython-input-9-4e7ff69a0d0f> in <module>()----> 1 cubeL.write_fits("mass.fits",length_unit="kpc", clobber='Tru
>>> e')
>>>
>>> /anaconda2/lib/python2.7/site-packages/yt/utilities/parallel_tools/p
>>> arallel_analysis_interface.pyc in root_only(*args, **kwargs)
>>>
>>> 317
>>>
>>> 318
>>>
>>> --> 319
>>>
>>> 320 321
>>>
>>> def root_only(*args, **kwargs): if not parallel_capable:
>>>
>>> return func(*args, **kwargs) comm = _get_comm(args) rv = None
>>>
>>> /anaconda2/lib/python2.7/site-packages/yt/analysis_modules/ppv_cube/
>>> ppv_cube.pyc in write_fits(self, filename, overwrite, length_unit, s
>>> ky_scale, sky_center, **kwargs)
>>>
>>> 313
>>>
>>> 314
>>>
>>> --> 315
>>>
>>> 317 fib.update_all_headers("btype", self.field)
>>>
>>> /anaconda2/lib/python2.7/site-packages/yt/visualization/fits_image.p
>>> yc in __init__(self, data, fields, units, width, wcs)
>>>
>>> w.wcs.ctype = ["LINEAR","LINEAR",vtype]
>>>
>>> fib = FITSImageData(self.data.transpose(), fields=se
>>>
>>> fib.update_all_headers("bunit", re.sub('()', '', str(self.proj_units)))
>>>
>>> lf.field, wcs=w)316
>>>
>>> 158
>>>
>>> 159
>>>
>>> --> 160
>>>
>>> 161
>>>
>>> eld].units)162
>>>
>>> KeyError: 'cell_mass'
>>>
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>>>
>>>
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3 months
