Mailman 3 November 2018 - yt-users

Re: Merger trees
by Nick Gnedin Nov. 21, 2018

Nov. 21, 2018

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_in…> > > 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.html… <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dproject.org_doc_a…> <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dproject.org_doc_a…> > > > > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dproject.org_doc_a…>) > > > > > > 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_cam… <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.avg.com_email-2Dsig…> > > > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.avg.com_email-2Dsig…>> > > > > > Virus-free. www.avg.com > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.avg.com&d=DwMFaQ&c=…> > > > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.avg.com&d=DwMFaQ&c=…> > > > > > > > > <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam… <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.avg.com_email-2Dsig…> > > > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.avg.com_email-2Dsig…>> > > > > > > > > > > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > > _______________________________________________ > 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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Re: Merger trees
by Nick Gnedin Nov. 19, 2018

Nov. 19, 2018

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.html… <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dproject.org_doc_a…> > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dproject.org_doc_a…>) > > > > 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_cam… > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.avg.com_email-2Dsig…>> > > > Virus-free. www.avg.com > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.avg.com&d=DwMFaQ&c=…> > > > > <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam… > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.avg.com_email-2Dsig…>> > > > > > > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >

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AREA UNDER PROFILE PLOTS
by Vadlamani Samhitha Nov. 19, 2018

Nov. 19, 2018

Hi, Is there a way to obtain area under the curves for 1D profile plots in yt?

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Re: writing PPV cubes with fields other than density
by Nathan Goldbaum Nov. 17, 2018

Nov. 17, 2018

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' >>> >>> _______________________________________________ >>> yt-users mailing list -- yt-users(a)python.org >>> To unsubscribe send an email to yt-users-leave(a)python.org >>> >>> >>> _______________________________________________ >>> yt-users mailing list -- yt-users(a)python.org >>> To unsubscribe send an email to yt-users-leave(a)python.org >>> >> _______________________________________________ >> yt-users mailing list -- yt-users(a)python.org >> To unsubscribe send an email to yt-users-leave(a)python.org >> >> >> _______________________________________________ >> yt-users mailing list -- yt-users(a)python.org >> To unsubscribe send an email to yt-users-leave(a)python.org >> > _______________________________________________ > yt-users mailing list -- yt-users(a)python.org > To unsubscribe send an email to yt-users-leave(a)python.org >

1 0

Re: writing PPV cubes with fields other than density
by John Zuhone Nov. 16, 2018

Nov. 16, 2018

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 <mailto:jzuhone@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 <mailto:smbenincasa@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' >> >> _______________________________________________ >> 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> > > _______________________________________________ > 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> > _______________________________________________ > yt-users mailing list -- yt-users(a)python.org > To unsubscribe send an email to yt-users-leave(a)python.org

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Why the key word "weight_field" in project_light_core must be set None?
by lianxiaoli87＠sjtu.edu.cn Nov. 15, 2018

Nov. 15, 2018

Dear all: I need use the "project_light_core" in my work. If the key word "weight_field " = None, I can obtain my results. But I should set a weighted field, when I set weight_filed = 'density', I received a error like: I found that the 'density' can not be set to weight_field, I have no ideal about this. Traceback (most recent call last): File "./light_core_projection.py", line 37, in <module> njobs=1) File "/mnt/ddnfs/data_users/xllian/software/yt/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py", line 343, in project_light_cone frb["weight_field"]), File "/mnt/ddnfs/data_users/xllian/software/yt/yt/visualization/fixed_resolution.py", line 134, in __getitem__ int(self.antialias)) File "/mnt/ddnfs/data_users/xllian/software/yt/yt/geometry/coordinates/cartesian_coordinates.py", line 158, in pixelize antialias, dimension, periodic) File "/mnt/ddnfs/data_users/xllian/software/yt/yt/geometry/coordinates/cartesian_coordinates.py", line 225, in _ortho_pixelize finfo = self.ds._get_field_info(field) File "/mnt/ddnfs/data_users/xllian/software/yt/yt/data_objects/static_output.py", line 773, in _get_field_info raise YTFieldNotFound((ftype, fname), self) yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all', 'weight_field')' in RD0033. Thanks all

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Re: writing PPV cubes with fields other than density
by John Zuhone Nov. 14, 2018

Nov. 14, 2018

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' > > _______________________________________________ > yt-users mailing list -- yt-users(a)python.org > To unsubscribe send an email to yt-users-leave(a)python.org

2 1

writing PPV cubes with fields other than density
by Samantha M Benincasa Nov. 14, 2018

Nov. 14, 2018

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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Plotting H2 mass fraction
by Andrew Cook Nov. 12, 2018

Nov. 12, 2018

Hello, I'm currently working on an Enzo 2.5 simulation using yt 3.5 in python 3. Is there a fieldname for plotting the H2 mass fraction of a gas cloud? Many thanks Andrew Cook

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Request to join community group
by Andrew Cook Nov. 6, 2018

Nov. 6, 2018

Hello My name is Andrew and I'm currently working in Python 3 to visualise enzo 2.5 data with your yt 3.5 package. I need some assistance with a specific field i'm trying to find to plot molecular H2 and have been told the community group would be a good place to get some help from. Many thanks Andrew

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