Mailman 3 December 2015 - yt-users

help: yt Halo finder for Nyx data
by Dr. Surajit Paul 24 Dec '15

24 Dec '15

Hi, I was just trying to compute the halos from a Nyx data. While running the halo finder it stops saying ........ yt.data_objects.field_info_container.NeedsDataField: (['particle_mass']) Below is the code, results and the list of fields available. In the list I have "particle_mass_density" instead of "particle_mass". Please suggest me how I can make it running. Thanks, surajit from yt.mods import * import fields # Load the dataset. pf = load("/gfs1/work/nipiagws/MUSIC/102-26468_512zoom2a_amr2_sgs2_si_600_05_flat/plt02593_z01") halos = HaloFinder(pf) halos.write_out("%s_halos.txt") Traceback (most recent call last): File "halos.py", line 14, in <module> halos = HaloFinder(pf) File "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/halo_objects.py", line 2484, in __init__ self.comm.mpi_allreduce((self._data_source["ParticleMassMsun"][select]).sum(dtype='float64'), op='sum') File "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 318, in __getitem__ self.get_data(key) File "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 2619, in get_data if self._generate_field(field): File "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 345, in _generate_field self._generate_field_in_grids(field, ngt_exception.ghost_zones) File "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 355, in _generate_field_in_grids grid[field] = self.__touch_grid_field(grid, field) File "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 81, in save_state tr = func(self, grid, field, *args, **kwargs) File "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 359, in __touch_grid_field return grid[field] File "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 147, in __getitem__ self.get_data(key) File "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 190, in get_data self._generate_field(field) File "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 122, in _generate_field self.pf.field_info[field].check_available(self) File "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 356, in check_available validator(data) File "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 450, in __call__ raise NeedsDataField(doesnt_have) yt.data_objects.field_info_container.NeedsDataField: (['particle_mass']) filed_list AveMomX AveMomY AveMomZ ErrCovarX ErrCovarY ErrCovarZ Ne Temp density diss_sgs divu grav_x grav_y grav_z magvort particle_mass_density phi_grav prod_sgs rho_E rho_H rho_He rho_K rho_e support_sgs support_therm support_turb turb_src xmom ymom zmom _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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yt update to 3.0
by Sushilkumar 24 Dec '15

24 Dec '15

Hi yt: I am currently running yt version 2.6.1 and want to update to version 3 (to read text files). Could you provide me link to so? I tried it from yt update --all as per the link http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-v… . But it wont update to 3.0 and still shows as 2.6.1 Kindly help Thanks in advance sushilkumar On Mon, Dec 21, 2015 at 12:33 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. help: yt Halo finder for Nyx data (Dr. Surajit Paul) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 21 Dec 2015 20:55:19 +0530 > From: "Dr. Surajit Paul" <surajit(a)physics.unipune.ac.in> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] help: yt Halo finder for Nyx data > Message-ID: > < > ef2adab2876566c33b22a1695592c3d6.squirrel(a)physics.unipune.ernet.in> > Content-Type: text/plain;charset=iso-8859-1 > > Hi, > I was just trying to compute the halos from a Nyx data. While running > the halo finder it stops saying > ........ > yt.data_objects.field_info_container.NeedsDataField: (['particle_mass']) > > Below is the code, results and the list of fields available. In the > list I have "particle_mass_density" instead of > "particle_mass". Please suggest me how I can make it running. > > Thanks, > surajit > > from yt.mods import * > import fields > > # Load the dataset. > pf = > load("/gfs1/work/nipiagws/MUSIC/102-26468_512zoom2a_amr2_sgs2_si_600_05_flat/plt02593_z01") > halos = HaloFinder(pf) > > halos.write_out("%s_halos.txt") > > > > Traceback (most recent call last): > File "halos.py", line 14, in <module> > halos = HaloFinder(pf) > File > "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/halo_objects.py", > line 2484, in __init__ > > self.comm.mpi_allreduce((self._data_source["ParticleMassMsun"][select]).sum(dtype='float64'), > op='sum') > File > "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", > line 318, in __getitem__ > self.get_data(key) > File > "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", > line 2619, in get_data > if self._generate_field(field): > File > "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", > line 345, in _generate_field > self._generate_field_in_grids(field, ngt_exception.ghost_zones) > File > "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", > line 355, in _generate_field_in_grids > grid[field] = self.__touch_grid_field(grid, field) > File > "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", > line 81, in save_state > tr = func(self, grid, field, *args, **kwargs) > File > "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", > line 359, in __touch_grid_field > return grid[field] > File > "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line > 147, in __getitem__ > self.get_data(key) > File > "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line > 190, in get_data > self._generate_field(field) > File > "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line > 122, in _generate_field > self.pf.field_info[field].check_available(self) > File > "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", > line 356, in check_available > validator(data) > File > "/home/h/nipiagws/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", > line 450, in __call__ > raise NeedsDataField(doesnt_have) > yt.data_objects.field_info_container.NeedsDataField: (['particle_mass']) > > > filed_list > > AveMomX > AveMomY > AveMomZ > ErrCovarX > ErrCovarY > ErrCovarZ > Ne > Temp > density > diss_sgs > divu > grav_x > grav_y > grav_z > magvort > particle_mass_density > phi_grav > prod_sgs > rho_E > rho_H > rho_He > rho_K > rho_e > support_sgs > support_therm > support_turb > turb_src > xmom > ymom > zmom > > > > > > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 94, Issue 17 > **************************************** > -- *SK2* *"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"* _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Error installing using Installation script
by Jasmine Grosso 24 Dec '15

24 Dec '15

I've tried to install yt using the all-in-one installation script, but always come across this error. FAILURE REPORT: ******************************************** from /System/Library/Frameworks/CoreGraphics.framework/Headers/CGBitmapContext.h:9, from /System/Library/Frameworks/CoreGraphics.framework/Headers/CoreGraphics.h:11, from /System/Library/Frameworks/ApplicationServices.framework/Headers/ApplicationServices.h:35, from /System/Library/Frameworks/Carbon.framework/Headers/Carbon.h:24, from Include/pymactoolbox.h:10, from Python/mactoolboxglue.c:27: /System/Library/Frameworks/CoreGraphics.framework/Headers/CGFont.h:53:1: error: initializer element is not constant static const CGFontIndex kCGGlyphMax = kCGFontIndexMax; ^ make: *** [Python/mactoolboxglue.o] Error 1 ******************************************** ******************************************** Failure. Check /Users/jasminegrosso/Dropbox/Project/enzo/yt-x86_64/yt_install.log. The last 10 lines are above. I'm running bash install_script.sh on El capitan, and am struglling finding info to help with this. Thanks! _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Quiver plot query
by Sushilkumar 19 Dec '15

19 Dec '15

Hi: Does yt support 3D quiver plot equivalent to matplotlib? If so could you direct me to an example of the same? Thank you in advance On Fri, Dec 18, 2015 at 12:52 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. PhasePlot losing negative values (Alex Hill) > 2. Re: PhasePlot losing negative values (Nathan Goldbaum) > 3. Re: PhasePlot losing negative values (Alex Hill) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Dec 2015 15:55:15 -0500 > From: Alex Hill <ashill(a)haverford.edu> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: [yt-users] PhasePlot losing negative values > Message-ID: <AE0250F8-7C84-4468-AFEE-3479E5A0499E(a)haverford.edu> > Content-Type: text/plain; charset=utf-8 > > Hi, > > I?m trying to create a PhasePlot of one component of velocity (which can > be negative) as a function of temperature. > > f = yt.PhasePlot(box, ?temperature?, ?velocity_z?,[?cell_mass?], > weight_field=None,fractional=True) > f.set_log(?velocity_z?, False) > f.show() > > This works as expected for cells with positive velocity. However, cells > with negative velocities get completely dropped; everything with velocity_z > <= 0 is blank. > > I assume that PhasePlot took the logarithm of velocity_z at some point in > producing the plot and lost negative data. Is there an option I?m missing > to tell PhasePlot not to do this? > > Running yt 3.2.2 and python 2.7 on a Mac. > > Cheers, > Alex > > --------- > Alex Hill > Senior Postdoctoral Research Associate > Office: KINSC Link L106 > Department of Astronomy, Haverford College > 370 Lancaster Ave, Haverford, PA 19041 USA > phone: +1 484 297 2136 > email/iMessage: ashill(a)haverford.edu > > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Dec 2015 15:13:29 -0600 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] PhasePlot losing negative values > Message-ID: > <CAJXewOnmcLgLVgRaKKuZfW+ymmF=3o3xruBfE= > V97SnFuwD7vg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Alex, > > So I think what's happening is that the call to set_log() doesn't cause the > plot limits for the velocity_z axis to be rescaled, cutting off the > negative values in the plot. This can be fixed by calling set_ylim() after > set_log(): > > *https://gist.github.com/anonymous/4ec4fdfd66b0eee2015a > <https://gist.github.com/anonymous/4ec4fdfd66b0eee2015a>* > > I think a good enhancement would be to somehow invalidate the plot limits > after calling set_log() so the y-axis limits are automatically > re-determined. I think this would be a reasonably straightforward fix and a > good first yt contribution if you're up for it. If you're not interested in > working on that yourself, can you go ahead and open an issue so we don't > lose this in the shuffle: > > https://bitbucket.org/yt_analysis/yt/issues/new > > Thanks! > > -Nathan > > On Thu, Dec 17, 2015 at 2:55 PM, Alex Hill <ashill(a)haverford.edu> wrote: > > > Hi, > > > > I?m trying to create a PhasePlot of one component of velocity (which can > > be negative) as a function of temperature. > > > > f = yt.PhasePlot(box, ?temperature?, ?velocity_z?,[?cell_mass?], > > weight_field=None,fractional=True) > > f.set_log(?velocity_z?, False) > > f.show() > > > > This works as expected for cells with positive velocity. However, cells > > with negative velocities get completely dropped; everything with > velocity_z > > <= 0 is blank. > > > > I assume that PhasePlot took the logarithm of velocity_z at some point in > > producing the plot and lost negative data. Is there an option I?m missing > > to tell PhasePlot not to do this? > > > > Running yt 3.2.2 and python 2.7 on a Mac. > > > > Cheers, > > Alex > > > > --------- > > Alex Hill > > Senior Postdoctoral Research Associate > > Office: KINSC Link L106 > > Department of Astronomy, Haverford College > > 370 Lancaster Ave, Haverford, PA 19041 USA > > phone: +1 484 297 2136 > > email/iMessage: ashill(a)haverford.edu > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 3 > Date: Fri, 18 Dec 2015 11:02:14 -0500 > From: Alex Hill <ashill(a)haverford.edu> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] PhasePlot losing negative values > Message-ID: <EB53655E-A427-44B4-8D64-3872026C76CB(a)haverford.edu> > Content-Type: text/plain; charset=utf-8 > > Thanks, Nathan. > > I was doing something similar to that but omitted it from what I included > in my first email: > > f = yt.PhasePlot(box, ?temperature?, ?velocity_z?,[?cell_mass?], > weight_field=None,fractional=True) > f.set_log(?velocity_z?, False) > ax = f.plots[?cell_mass?].axes > ax.set_ylim(-5e7,5e7) > f.show() > > It turns out that I was running yt 3.1 (though I thought I was running > 3.2.2). In 3.1, the whole range was shown after the ax.set_ylim step, but > everything at velocity_z <= 0 was white. I see that improved handling of > f.set_ylim in this case was noted in the 3.2 release notes. After > successfully updating to 3.2.2, with the f.set_ylim step, this works as > expected. > > I?ll look into implementing the fix you suggest in a bit (or open an issue > if I don?t get to it soon). > > Cheers, > Alex > > > On Dec 17, 2015, at 16:13, Nathan Goldbaum <nathan12343(a)gmail.com> > wrote: > > > > Hi Alex, > > > > So I think what's happening is that the call to set_log() doesn't cause > the plot limits for the velocity_z axis to be rescaled, cutting off the > negative values in the plot. This can be fixed by calling set_ylim() after > set_log(): > > > > https://gist.github.com/anonymous/4ec4fdfd66b0eee2015a > > > > I think a good enhancement would be to somehow invalidate the plot > limits after calling set_log() so the y-axis limits are automatically > re-determined. I think this would be a reasonably straightforward fix and a > good first yt contribution if you're up for it. If you're not interested in > working on that yourself, can you go ahead and open an issue so we don't > lose this in the shuffle: > > > > https://bitbucket.org/yt_analysis/yt/issues/new > > > > Thanks! > > > > -Nathan > > > > On Thu, Dec 17, 2015 at 2:55 PM, Alex Hill <ashill(a)haverford.edu> wrote: > > Hi, > > > > I?m trying to create a PhasePlot of one component of velocity (which can > be negative) as a function of temperature. > > > > f = yt.PhasePlot(box, ?temperature?, ?velocity_z?,[?cell_mass?], > weight_field=None,fractional=True) > > f.set_log(?velocity_z?, False) > > f.show() > > > > This works as expected for cells with positive velocity. However, cells > with negative velocities get completely dropped; everything with velocity_z > <= 0 is blank. > > > > I assume that PhasePlot took the logarithm of velocity_z at some point > in producing the plot and lost negative data. Is there an option I?m > missing to tell PhasePlot not to do this? > > > > Running yt 3.2.2 and python 2.7 on a Mac. > > > > Cheers, > > Alex > > > > --------- > > Alex Hill > > Senior Postdoctoral Research Associate > > Office: KINSC Link L106 > > Department of Astronomy, Haverford College > > 370 Lancaster Ave, Haverford, PA 19041 USA > > phone: +1 484 297 2136 > > email/iMessage: ashill(a)haverford.edu > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 94, Issue 15 > **************************************** > -- *SK2* *"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*

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Re: [yt-users] yt-users Digest, Vol 94, Issue 15
by Sushilkumar 19 Dec '15

19 Dec '15

Hi: Does yt support 3D quiver plot equivalent to matplotlib? If so could you direct me to an example of the same? Thank you in advance On Fri, Dec 18, 2015 at 12:52 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. PhasePlot losing negative values (Alex Hill) > 2. Re: PhasePlot losing negative values (Nathan Goldbaum) > 3. Re: PhasePlot losing negative values (Alex Hill) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Dec 2015 15:55:15 -0500 > From: Alex Hill <ashill(a)haverford.edu> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: [yt-users] PhasePlot losing negative values > Message-ID: <AE0250F8-7C84-4468-AFEE-3479E5A0499E(a)haverford.edu> > Content-Type: text/plain; charset=utf-8 > > Hi, > > I?m trying to create a PhasePlot of one component of velocity (which can > be negative) as a function of temperature. > > f = yt.PhasePlot(box, ?temperature?, ?velocity_z?,[?cell_mass?], > weight_field=None,fractional=True) > f.set_log(?velocity_z?, False) > f.show() > > This works as expected for cells with positive velocity. However, cells > with negative velocities get completely dropped; everything with velocity_z > <= 0 is blank. > > I assume that PhasePlot took the logarithm of velocity_z at some point in > producing the plot and lost negative data. Is there an option I?m missing > to tell PhasePlot not to do this? > > Running yt 3.2.2 and python 2.7 on a Mac. > > Cheers, > Alex > > --------- > Alex Hill > Senior Postdoctoral Research Associate > Office: KINSC Link L106 > Department of Astronomy, Haverford College > 370 Lancaster Ave, Haverford, PA 19041 USA > phone: +1 484 297 2136 > email/iMessage: ashill(a)haverford.edu > > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Dec 2015 15:13:29 -0600 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] PhasePlot losing negative values > Message-ID: > <CAJXewOnmcLgLVgRaKKuZfW+ymmF=3o3xruBfE= > V97SnFuwD7vg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Alex, > > So I think what's happening is that the call to set_log() doesn't cause the > plot limits for the velocity_z axis to be rescaled, cutting off the > negative values in the plot. This can be fixed by calling set_ylim() after > set_log(): > > *https://gist.github.com/anonymous/4ec4fdfd66b0eee2015a > <https://gist.github.com/anonymous/4ec4fdfd66b0eee2015a>* > > I think a good enhancement would be to somehow invalidate the plot limits > after calling set_log() so the y-axis limits are automatically > re-determined. I think this would be a reasonably straightforward fix and a > good first yt contribution if you're up for it. If you're not interested in > working on that yourself, can you go ahead and open an issue so we don't > lose this in the shuffle: > > https://bitbucket.org/yt_analysis/yt/issues/new > > Thanks! > > -Nathan > > On Thu, Dec 17, 2015 at 2:55 PM, Alex Hill <ashill(a)haverford.edu> wrote: > > > Hi, > > > > I?m trying to create a PhasePlot of one component of velocity (which can > > be negative) as a function of temperature. > > > > f = yt.PhasePlot(box, ?temperature?, ?velocity_z?,[?cell_mass?], > > weight_field=None,fractional=True) > > f.set_log(?velocity_z?, False) > > f.show() > > > > This works as expected for cells with positive velocity. However, cells > > with negative velocities get completely dropped; everything with > velocity_z > > <= 0 is blank. > > > > I assume that PhasePlot took the logarithm of velocity_z at some point in > > producing the plot and lost negative data. Is there an option I?m missing > > to tell PhasePlot not to do this? > > > > Running yt 3.2.2 and python 2.7 on a Mac. > > > > Cheers, > > Alex > > > > --------- > > Alex Hill > > Senior Postdoctoral Research Associate > > Office: KINSC Link L106 > > Department of Astronomy, Haverford College > > 370 Lancaster Ave, Haverford, PA 19041 USA > > phone: +1 484 297 2136 > > email/iMessage: ashill(a)haverford.edu > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 3 > Date: Fri, 18 Dec 2015 11:02:14 -0500 > From: Alex Hill <ashill(a)haverford.edu> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] PhasePlot losing negative values > Message-ID: <EB53655E-A427-44B4-8D64-3872026C76CB(a)haverford.edu> > Content-Type: text/plain; charset=utf-8 > > Thanks, Nathan. > > I was doing something similar to that but omitted it from what I included > in my first email: > > f = yt.PhasePlot(box, ?temperature?, ?velocity_z?,[?cell_mass?], > weight_field=None,fractional=True) > f.set_log(?velocity_z?, False) > ax = f.plots[?cell_mass?].axes > ax.set_ylim(-5e7,5e7) > f.show() > > It turns out that I was running yt 3.1 (though I thought I was running > 3.2.2). In 3.1, the whole range was shown after the ax.set_ylim step, but > everything at velocity_z <= 0 was white. I see that improved handling of > f.set_ylim in this case was noted in the 3.2 release notes. After > successfully updating to 3.2.2, with the f.set_ylim step, this works as > expected. > > I?ll look into implementing the fix you suggest in a bit (or open an issue > if I don?t get to it soon). > > Cheers, > Alex > > > On Dec 17, 2015, at 16:13, Nathan Goldbaum <nathan12343(a)gmail.com> > wrote: > > > > Hi Alex, > > > > So I think what's happening is that the call to set_log() doesn't cause > the plot limits for the velocity_z axis to be rescaled, cutting off the > negative values in the plot. This can be fixed by calling set_ylim() after > set_log(): > > > > https://gist.github.com/anonymous/4ec4fdfd66b0eee2015a > > > > I think a good enhancement would be to somehow invalidate the plot > limits after calling set_log() so the y-axis limits are automatically > re-determined. I think this would be a reasonably straightforward fix and a > good first yt contribution if you're up for it. If you're not interested in > working on that yourself, can you go ahead and open an issue so we don't > lose this in the shuffle: > > > > https://bitbucket.org/yt_analysis/yt/issues/new > > > > Thanks! > > > > -Nathan > > > > On Thu, Dec 17, 2015 at 2:55 PM, Alex Hill <ashill(a)haverford.edu> wrote: > > Hi, > > > > I?m trying to create a PhasePlot of one component of velocity (which can > be negative) as a function of temperature. > > > > f = yt.PhasePlot(box, ?temperature?, ?velocity_z?,[?cell_mass?], > weight_field=None,fractional=True) > > f.set_log(?velocity_z?, False) > > f.show() > > > > This works as expected for cells with positive velocity. However, cells > with negative velocities get completely dropped; everything with velocity_z > <= 0 is blank. > > > > I assume that PhasePlot took the logarithm of velocity_z at some point > in producing the plot and lost negative data. Is there an option I?m > missing to tell PhasePlot not to do this? > > > > Running yt 3.2.2 and python 2.7 on a Mac. > > > > Cheers, > > Alex > > > > --------- > > Alex Hill > > Senior Postdoctoral Research Associate > > Office: KINSC Link L106 > > Department of Astronomy, Haverford College > > 370 Lancaster Ave, Haverford, PA 19041 USA > > phone: +1 484 297 2136 > > email/iMessage: ashill(a)haverford.edu > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 94, Issue 15 > **************************************** > -- *SK2* *"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*

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PhasePlot losing negative values
by Alex Hill 18 Dec '15

18 Dec '15

Hi, I’m trying to create a PhasePlot of one component of velocity (which can be negative) as a function of temperature. f = yt.PhasePlot(box, ‘temperature’, ‘velocity_z’,[‘cell_mass’], weight_field=None,fractional=True) f.set_log(‘velocity_z’, False) f.show() This works as expected for cells with positive velocity. However, cells with negative velocities get completely dropped; everything with velocity_z <= 0 is blank. I assume that PhasePlot took the logarithm of velocity_z at some point in producing the plot and lost negative data. Is there an option I’m missing to tell PhasePlot not to do this? Running yt 3.2.2 and python 2.7 on a Mac. Cheers, Alex --------- Alex Hill Senior Postdoctoral Research Associate Office: KINSC Link L106 Department of Astronomy, Haverford College 370 Lancaster Ave, Haverford, PA 19041 USA phone: +1 484 297 2136 email/iMessage: ashill(a)haverford.edu

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TIPSY to regular grid
by Bruno Villasenor 16 Dec '15

16 Dec '15

Hello yt-users, I'm trying to get data from a TIPSY file to a fixed resolution array, The simplest version of my code is below: ##################################################### ds = yt.load( dataDir + dataFile, parameter_file= dataDir + paramFile ) ad = ds.all_data() left = ad.left_edge level = 1 data = ds.covering_grid(level=level, left_edge=left, dims=ds.domain_dimensions * 2**level) dmDens = data[('deposit','DarkMatter_density')] #################################################### I'm getting this error: ValueError: operands could not be broadcast together with shapes (2,2,2,8) (2,2,2,0) (2,2,2,8) Any ideas? YT_version: 3.1-dev Thanks in advance. Bruno

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Radial-averaged Profile error
by Junhwan Choi (최준환) 15 Dec '15

15 Dec '15

Dear yt users and developers, I get an error while I try to make a radial-averaged profile using yt. In order to compute the profile I wrote the following script: =================================== import matplotlib as matplotlib matplotlib.use('Agg') import yt import yt.units as units import numpy as np import matplotlib.pyplot as plt def _radiuspc(field, data): return data[('radius')].in_units('pc') yt.add_field('radiuspc', function=_radiuspc, units="pc") rmax = 1000 Nbin = 50 ds = yt.load("../DD0099/DD0099") ds.index ad= ds.all_data() center = ds.find_max("density")[1] my_sphere = ds.sphere("center", (rmax, "pc")) rmin = max([0.1,2.0*ds.index.get_smallest_dx().in_units('pc')]) profile = yt.BinnedProfile1D(my_sphere, Nbin, 'radius', rmin, rmax*units.pc, log_space=True, end_collect=False) profile.add_fields(('gas','density'), weight='cell_volume') plt.plot(na.log10(profile['radius']), na.log10(profile['density'])) plt.savefig('ProfGasDensity') =================================== And, I get an following error to compute the density profile ……. yt : [INFO ] 2015-12-14 17:54:21,484 Max Value is 5.46111e-09 at 0.5093630427891190 0.4991425970893048 0.5065899804849306 Traceback (most recent call last): File "test_prof.py", line 26, in <module> profile.add_fields(('gas','density'), weight='cell_volume') File "/home/jhchoi/common-anaconda/src/yt/yt/data_objects/profiles.py", line 117, in add_fields self["%s_std" % field] = np.sqrt(std_data[field]) TypeError: not all arguments converted during string formatting Could anyone inform me how to resolve this error? Thank you in advance, Junhwan

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Halo dataset not loading into yt properly
by Storey-Fisher, Kate 15 Dec '15

15 Dec '15

Hello, I am trying to run Rockstar on a ramses particle dataset outside of yt. I wrote a Rockstar config file and a high res dark matter particle data file, and successfully output a correct ascii halo data file. However, when I load the binary halo data file into yt, it doesn't have any of the field info and thus I can't create a halo catalog or use this data. When I run Rockstar in yt, this works fine - both ascii and binary halo files successfully write. How can I run Rockstar outside of yt so that the binary data file is written correctly, with the field info? Thank you! Best, Kate Storey-Fisher -- Kate Storey-Fisher Physics Sc.B. Candidate Brown University 2016

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Loading files query
by Sushilkumar 10 Dec '15

10 Dec '15

Dear yt: Thank you for your reply . Now, my code generates a file which is in matrix market format. I would like to plot this file using yt. Is there a way that yt can read this type of file format? Thanks in advance On Wed, Dec 9, 2015 at 12:50 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. yt query (Sushilkumar) > 2. Re: yt query (Nathan Goldbaum) > 3. Re: code support for ZEUS-MP 2 (Andrea Negri) > 4. Re: code support for ZEUS-MP 2 (Matthew Turk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 8 Dec 2015 12:56:03 -0600 > From: Sushilkumar <sushil.sush19us(a)gmail.com> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] yt query > Message-ID: > <CAKARaKXB9FxdXv=_= > q2iW7+eCfofsjW0oKsXTYiPh-vMtH6MBA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear yt: > > I would like to plot magnetic field lines in 3D using either streamline or > 3D quiver plots. Could you suggest me ways for the doing the same? > > Thanks in advance > > > > -- > *SK2* > > *"**Claiming that something can move faster than light is a good > conversation-stopper in physics. People edge away from you in cocktail > parties; friends never return phone calls. You just don?t mess with Albert > Einstein.**"* > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 2 > Date: Tue, 8 Dec 2015 13:52:17 -0600 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] yt query > Message-ID: > <CAJXewOnxB9hbTKWwiiJrX+Q7un0fQrqHw99J55P6c= > D4bG4vew(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > If you have data that's loadable by yt, you should be able to create the > streamlines following this document: > > http://yt-project.org/doc/visualizing/streamlines.html > > yt doesn't natively visualize streamlines, but you can use matplotlib or > mayavi to visualize the streamlines in 3d: > > * http://docs.enthought.com/mayavi/mayavi/mlab.html > * http://matplotlib.org/mpl_toolkits/mplot3d/tutorial.html > > Hope that helps, > > Nathan > > On Tue, Dec 8, 2015 at 12:56 PM, Sushilkumar <sushil.sush19us(a)gmail.com> > wrote: > > > Dear yt: > > > > I would like to plot magnetic field lines in 3D using either streamline > or > > 3D quiver plots. Could you suggest me ways for the doing the same? > > > > Thanks in advance > > > > > > > > -- > > *SK2* > > > > *"**Claiming that something can move faster than light is a good > > conversation-stopper in physics. People edge away from you in cocktail > > parties; friends never return phone calls. You just don?t mess with > Albert > > Einstein.**"* > > > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 3 > Date: Wed, 9 Dec 2015 10:38:43 +0100 > From: Andrea Negri <negri.andre(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] code support for ZEUS-MP 2 > Message-ID: > <CAPUxaiQnwSY=FT_e+a0AQi= > uu8mx42K9pO3pj6kRwBnTvtJGNg(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Matthew, > sorry for the late reply. > > I forgot to say that the spacing of the (spherical) radial grid is not > constant with the radius, but it is logarithmically sampled. Is it a > problem? > > > Andrea > > On 2 December 2015 at 18:13, Matthew Turk <matthewturk(a)gmail.com> wrote: > > Hi Andrea, > > > > It should be straightforward to do this. You can load it in to yt > > using the yt.load_uniform_grid function, and then specify the geometry > > as spherical. In the docs we have some examples: > > > > > http://yt-project.org/docs/3.2/examining/loading_data.html#generic-array-da… > > > > Specifying geometry="spherical" works here, and if your data is not in > > r,theta,phi, you can specify the axis ordering with > > geometry=("spherical", ("theta", "phi", "r")) (or whatever). > > > > -Matt > > > > On Wed, Dec 2, 2015 at 10:43 AM, Andrea Negri <negri(a)iap.fr> wrote: > >> Hello, > >> > >> I'm a ZEUS-MP 2 user, and I was wondering if is it possible to add the > >> support to ZEUS-MP 2 data, which are stored in HDF5 files. > >> > >> The data are nothing special or fancy, forget about particles or > multiple > >> levels of refinement. The code has a fixed grid in spherical > coordinates, > >> and all my simulations are axially symmetric, i.e. all the variables > depends > >> only on the spherical radius and co-latitude. > >> > >> It would be great to benefits of all the yt features! > >> > >> Thanks in advance, > >> Andrea Negri > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > Message: 4 > Date: Wed, 9 Dec 2015 05:56:05 -0600 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] code support for ZEUS-MP 2 > Message-ID: > <CALO3=5HPm=HoxuXwJnSXjuU= > NX26pDHNGqCC+Ry-aLVwETfXEw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Andrea, > > For that, you can use the load_hexahedral_mesh function. There's an example > in the docs as well. > > Matt > On Dec 9, 2015 3:39 AM, "Andrea Negri" <negri.andre(a)gmail.com> wrote: > > > Hi Matthew, > > sorry for the late reply. > > > > I forgot to say that the spacing of the (spherical) radial grid is not > > constant with the radius, but it is logarithmically sampled. Is it a > > problem? > > > > > > Andrea > > > > On 2 December 2015 at 18:13, Matthew Turk <matthewturk(a)gmail.com> wrote: > > > Hi Andrea, > > > > > > It should be straightforward to do this. You can load it in to yt > > > using the yt.load_uniform_grid function, and then specify the geometry > > > as spherical. In the docs we have some examples: > > > > > > > > > http://yt-project.org/docs/3.2/examining/loading_data.html#generic-array-da… > > > > > > Specifying geometry="spherical" works here, and if your data is not in > > > r,theta,phi, you can specify the axis ordering with > > > geometry=("spherical", ("theta", "phi", "r")) (or whatever). > > > > > > -Matt > > > > > > On Wed, Dec 2, 2015 at 10:43 AM, Andrea Negri <negri(a)iap.fr> wrote: > > >> Hello, > > >> > > >> I'm a ZEUS-MP 2 user, and I was wondering if is it possible to add the > > >> support to ZEUS-MP 2 data, which are stored in HDF5 files. > > >> > > >> The data are nothing special or fancy, forget about particles or > > multiple > > >> levels of refinement. The code has a fixed grid in spherical > > coordinates, > > >> and all my simulations are axially symmetric, i.e. all the variables > > depends > > >> only on the spherical radius and co-latitude. > > >> > > >> It would be great to benefits of all the yt features! > > >> > > >> Thanks in advance, > > >> Andrea Negri > > >> _______________________________________________ > > >> yt-users mailing list > > >> yt-users(a)lists.spacepope.org > > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > _______________________________________________ > > > yt-users mailing list > > > yt-users(a)lists.spacepope.org > > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 94, Issue 5 > *************************************** > -- *SK2* *"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*

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