yt-users February 2018

yt-users@python.org

13 participants
20 discussions

Porting .ply files to Blender with colors?
by Jill P. Naiman 14 Aug '22

14 Aug '22

Hi All, I was curious if anyone has had any luck porting .ply files generated with yt into Blender with colors? It seems to port in the surfaces just fine, but they are a uniform color. From what I can gather, Blender imports .ply files with face color instead of vertex so I tried the surf.export_ply routine with "face" instead of "vertex" for sample_type, but no luck ("vertex" doesn't work either). Let me know if I can provide any more useful info. Thanks for any help, -J

3 2

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

8 14

Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

6 8

3-D Mass power spectra
by 梁家豪 03 Jun '19

03 Jun '19

Dear yt Can current yt calculate 3-D Mass power spectra? I checked the website but I didn't find any information. I think calculating 3-D Mass power spectra is a very useful for cosmological simulations. So I guess maybe yt supports this function now....? Thanks in advance

4 7

RAMSES with RADMC3D
by Lamberts, Astrid 27 Feb '18

27 Feb '18

Hi all, We are trying to obtain inputs for RADMC3D from RAMSES data using the method from : http://yt-project.org/doc/analyzing/analysis_modules/radmc3d_export.html I get the following error message In [5]: writer = RadMC3DWriter(ds) --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-5-e2ea2893623c> in <module>() ----> 1 writer = RadMC3DWriter(ds) /Users/astrid/miniconda2/lib/python2.7/site-packages/yt/analysis_modules/radmc3d_export/RadMC3DInterface.pyc in __init__(self, ds, max_level) 146 self.cell_count += np.product(ds.domain_dimensions) 147 --> 148 sorted_grids = sorted(ds.index.grids, key=lambda x: x.Level) 149 for grid in sorted_grids: 150 if grid.Level <= self.max_level: AttributeError: 'RAMSESIndex' object has no attribute 'grids' which apparently has already popped up in the past (http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2015-October/00… ). Has this issue been fixed somewhere? How can we get this to work? Thanks, Astrid Astrid Lamberts Postdoctoral Researcher TAPIR Group, Caltech

2 1

Re: yt-users Digest, Vol 120, Issue 10
by Kazem Ardaneh 22 Feb '18

22 Feb '18

Hi Nathan My script is as bellow: fns = [ "../DD0072/DD0072","../DD0102/DD0102","../DD0422/DD0422", "../DD1117/DD1117", "../DD1676/DD1676","../DD1902/DD1902","../DD1992/DD1992", "../DD2054/DD2054", "../DD3275/DD3275","../DD3601/DD3601","../DD3963/DD3963", "../DD6300/DD6300" ] fig = plt.figure() grid = AxesGrid(fig, (0.02,0.02,0.84,0.84), nrows_ncols = (3, 4), axes_pad = 0.05, label_mode = "L", share_all = True, cbar_location="right", cbar_mode="single", cbar_size="4%", cbar_pad="1%”) field = ['logD'] for i, fn in enumerate(fns): ds = yt.load(fn) p = yt.SlicePlot(ds, 'y', field) p.set_zlim('logD', -12, np.log10(5e-7)) p.hide_axes() p.set_cmap('logD','jet') plot = p.plots['logD'] plot.figure = fig plot.axes = grid[i].axes plot.cax = grid.cbar_axes[i] p._setup_plots() I want to set ticks as [-12,-11,-10,-9,-8,-7], with similar labels. What I do is as bellow: cbar=plot.cb cbar.set_ylabel(r'$\mathbf{log\ \rho\ [g\ cm^{-3}]}$') cbar.ticklabels(['{:.0f}'.format(x) for x in np.arange(-12, np.log10(5e-7), 1)]) as is discussed here: http://yt-project.org/doc/cookbook/custom_colorbar_tickmarks.html But it seems it does not work for this plot. Kazem On Thu, Feb 22, 2018 at 2:00 AM, <yt-users-request(a)python.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)python.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.python.org/mm3/mailman3/lists/yt-users.python.org/ > or, via email, send a message with subject or body 'help' to > yt-users-request(a)python.org > > You can reach the person managing the list at > yt-users-owner(a)python.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > Today's Topics: > > 1. Re: Loading a large gadget snapshot (Nathan Goldbaum) > 2. Re: set ticks and label for AxesGrid colorbar (Nathan Goldbaum) > > > ---------------------------------------------------------------------- > > Date: Tue, 20 Feb 2018 19:57:25 -0600 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > Subject: [yt-users] Re: Loading a large gadget snapshot > To: Desika Narayanan <desika.narayanan(a)gmail.com>, Discussion of > the yt analysis package <yt-users(a)python.org> > Message-ID: > <CAJXewOnftkyL3GvXC-bafgCWcn0nPaEN7ktNKv6eYx1vEJcU > Xg(a)mail.gmail.com> > Content-Type: multipart/alternative; > boundary="94eb2c05f198e4c8590565af4076" > > --94eb2c05f198e4c8590565af4076 > Content-Type: text/plain; charset="UTF-8" > > Yes, apologies, I got that backwards. A larger n_ref means there needs be > more particles per octree leaf zone to trigger refinement on that zone, so > the you end up with fewer octree leaf nodes over all and you need less > memory. > > -Nathan > > On Tue, Feb 20, 2018 at 7:53 PM, Desika Narayanan < > desika.narayanan(a)gmail.com> wrote: > > > quick note -- set n_ref=64 or 128 (or bigger than 32) to reduce RAM > > footprint (instead of 16). > > > > -d > > > > On Tue, Feb 20, 2018 at 8:37 PM, Nathan Goldbaum <nathan12343(a)gmail.com> > > wrote: > > > >> Hi Jared, > >> > >> Just a comment that for these really big particle simulations the way yt > >> currently supports particle data doesn't scale terribly well, so you > might > >> run into either issues with operations taking a very long time or using > too > >> much RAM. > >> > >> You may find it useful to only load in data in a subset of the > simulation > >> domain to restrict the number of particles yt is dealing with at any one > >> time. This can be controlled at a coarse level via the "bounding_box" > >> keyword argument to the load() function, in particular by supplying a > >> bounding box that only covers a portion of the domain. It might also > help > >> with RAM usage to supply n_ref=16 instead of the default (32). There's > more > >> detail about what these parameters do in the docs: > >> > >> http://yt-project.org/docs/3.4.1/examining/loading_data. > html#gadget-data > >> > >> If you'd like you could also try the "sph-viz" branch on my fork of yt > at > >> https://github.com/ngoldbaum/yt. This branch contains an implementation > >> of the next-generation support for particle data in yt that is still > under > >> development. This version will scale much better for a dataset as big as > >> yours. > >> > >> Best, > >> > >> Nathan > >> > >> On Tue, Feb 20, 2018 at 7:22 PM, Matthew Turk <matthewturk(a)gmail.com> > >> wrote: > >> > >>> Hi Jared, > >>> > >>> I know you can make the particle IDs work by specifying the dtype, but > >>> my reading of the _validate_header code is the same as yours. I think > >>> it would be a pretty straightforward change to conditionally make the > >>> 'I' read into the struct into a 64-bit variable, but it's not there > >>> now. > >>> > >>> -Matt > >>> > >>> On Tue, Feb 20, 2018 at 7:16 PM, Jared Coughlin > >>> <Jared.W.Coughlin.29(a)nd.edu> wrote: > >>> > Hello! I have a gadget snapshot file with 1024^3 particles. When I > >>> tried to > >>> > load it with yt, yt fails by saying that it cannot identify the file > >>> type. I > >>> > did some digging and found that the way yt validates a gadget > snapshot > >>> is by > >>> > reading the number of particles from the header and then comparing > that > >>> > number to the number derived from the size of the position block. > This > >>> size > >>> > is 1024^3 *3*4 (the number of particles times 3 positions times 4 > >>> bytes per > >>> > position). However, as I just discovered, this number is larger than > >>> the max > >>> > value of an int in c, and so gadget writes a value of 0 due to the > >>> overflow. > >>> > As such, I need to use gadget's unsigned long long int for the > >>> padding, but > >>> > this is 8 bytes, not 4. I was just wondering if yt had some ability > to > >>> > detect the need to use something larger than an int? If not, I can > add > >>> it. > >>> > Thanks! > >>> > -Jared > >>> > > >>> > _______________________________________________ > >>> > 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 > >> > >> _______________________________________________ > >> 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 > > > > > > --94eb2c05f198e4c8590565af4076 > Content-Type: text/html; charset="UTF-8" > Content-Transfer-Encoding: quoted-printable > > <div dir=3D"ltr"><div>Yes, apologies, I got that backwards. A larger n_ref > = > means there needs be more particles per octree leaf zone to trigger > refinem= > ent on that zone, so the you end up with fewer octree leaf nodes over all > a= > nd you need less memory.<br><br></div>-Nathan<br></div><div > class=3D"gmail_= > extra"><br><div class=3D"gmail_quote">On Tue, Feb 20, 2018 at 7:53 PM, > Desi= > ka Narayanan <span dir=3D"ltr"><<a href=3D"mailto:desika. > narayanan@gmail= > .com" target=3D"_blank">desika.narayanan(a)gmail.com</a>></span> > wrote:<br= > ><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 > .8ex;border-left:1= > px #ccc solid;padding-left:1ex"><div dir=3D"ltr">quick note -- > set=C2=A0<sp= > an style=3D"color:rgb(34,34,34);font-family:arial,sans-serif; > font-size:12.8= > px;font-style:normal;font-variant-ligatures:normal;font- > variant-caps:normal= > ;font-weight:400;letter-spacing:normal;text-align: > start;text-indent:0px;tex= > t-transform:none;white-space:normal;word-spacing:0px; > background-color:rgb(2= > 55,255,255);text-decoration-style:initial;text-decoration- > color:initial;flo= > at:none;display:inline">n_ref=3D64 or 128 (or bigger than 32) to reduce > RAM= > footprint (instead of 16).=C2=A0 =C2=A0</span><span > class=3D"HOEnZb"><font= > color=3D"#888888"><div><span style=3D"color:rgb(34,34,34); > font-family:aria= > l,sans-serif;font-size:12.8px;font-style:normal;font- > variant-ligatures:norm= > al;font-variant-caps:normal;font-weight:400;letter- > spacing:normal;text-alig= > n:start;text-indent:0px;text-transform:none;white-space: > normal;word-spacing= > :0px;background-color:rgb(255,255,255);text-decoration- > style:initial;text-d= > ecoration-color:initial;float:none;display:inline"><br></ > span></div><div><s= > pan style=3D"color:rgb(34,34,34);font-family:arial,sans-serif; > font-size:12.= > 8px;font-style:normal;font-variant-ligatures:normal;font- > variant-caps:norma= > l;font-weight:400;letter-spacing:normal;text-align: > start;text-indent:0px;te= > xt-transform:none;white-space:normal;word-spacing:0px; > background-color:rgb(= > 255,255,255);text-decoration-style:initial;text-decoration- > color:initial;fl= > oat:none;display:inline">-d</span></div></font></span><div><div > class=3D"h5= > "><div class=3D"gmail_extra"><br><div class=3D"gmail_quote">On Tue, Feb > 20,= > 2018 at 8:37 PM, Nathan Goldbaum <span dir=3D"ltr"><<a href=3D"mailto: > n= > athan12343(a)gmail.com" target=3D"_blank">nathan12343(a)gmail.com > </a>></span= > > wrote:<br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 > .8ex;bo= > rder-left:1px #ccc solid;padding-left:1ex"><div dir=3D"ltr"><div><div>Hi > Ja= > red,<br><br></div>Just a comment that for these really big particle > simulat= > ions the way yt currently supports particle data doesn't scale > terribly= > well, so you might run into either issues with operations taking a very > lo= > ng time or using too much RAM.<br><br></div><div>You may find it useful to > = > only load in data in a subset of the simulation domain to restrict the > numb= > er of particles yt is dealing with at any one time. This can be controlled > = > at a coarse level via the "bounding_box" keyword argument to the > = > load() function, in particular by supplying a bounding box that only > covers= > a portion of the domain. It might also help with RAM usage to supply > n_ref= > =3D16 instead of the default (32). There's more detail about what > these= > parameters do in the docs:<br><br><a href=3D"http://yt-project.org/ > docs/3.= > 4.1/examining/loading_data.html#gadget-data" target=3D"_blank"> > http://yt-pr= > oject.org/docs/3.4<wbr>.1/examining/loading_data.html< > wbr>#gadget-data</a><= > br><br></div><div>If you'd like you could also try the > "sph-viz&qu= > ot; branch on my fork of yt at <a href=3D"https://github.com/ngoldbaum/yt" > = > target=3D"_blank">https://github.com/ngoldbaum/y<wbr>t</a>. This branch > con= > tains an implementation of the next-generation support for particle data > in= > yt that is still under development. This version will scale much better > fo= > r a dataset as big as yours.<br><br></div><div>Best, > <br><br></div><div>Nath= > an<br></div></div><div class=3D"m_6788941403835052387m_- > 5788644225450873479= > HOEnZb"><div class=3D"m_6788941403835052387m_-5788644225450873479h5"><div > c= > lass=3D"gmail_extra"><br><div class=3D"gmail_quote">On Tue, Feb 20, 2018 > at= > 7:22 PM, Matthew Turk <span dir=3D"ltr"><<a href=3D"mailto: > matthewturk@= > gmail.com" target=3D"_blank">matthewturk(a)gmail.com</a>></span> > wrote:<br= > ><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 > .8ex;border-left:1= > px #ccc solid;padding-left:1ex">Hi Jared,<br> > <br> > I know you can make the particle IDs work by specifying the dtype, but<br> > my reading of the _validate_header code is the same as yours.=C2=A0 I > think= > <br> > it would be a pretty straightforward change to conditionally make the<br> > 'I' read into the struct into a 64-bit variable, but it's not > t= > here<br> > now.<br> > <br> > -Matt<br> > <div><div class=3D"m_6788941403835052387m_-5788644225450873479m_ > 23635419532= > 30957494h5"><br> > On Tue, Feb 20, 2018 at 7:16 PM, Jared Coughlin<br> > <<a href=3D"mailto:Jared.W.Coughlin.29@nd.edu" > target=3D"_blank">Jared.W= > .Coughlin.29(a)nd.edu</a>> wrote:<br> > > Hello! I have a gadget snapshot file with 1024^3 particles. When I > tri= > ed to<br> > > load it with yt, yt fails by saying that it cannot identify the file > t= > ype. I<br> > > did some digging and found that the way yt validates a gadget > snapshot= > is by<br> > > reading the number of particles from the header and then comparing > tha= > t<br> > > number to the number derived from the size of the position block. > This= > size<br> > > is 1024^3 *3*4 (the number of particles times 3 positions times 4 > byte= > s per<br> > > position). However, as I just discovered, this number is larger than > t= > he max<br> > > value of an int in c, and so gadget writes a value of 0 due to the > ove= > rflow.<br> > > As such, I need to use gadget's unsigned long long int for the > pad= > ding, but<br> > > this is 8 bytes, not 4. I was just wondering if yt had some ability > to= > <br> > > detect the need to use something larger than an int? If not, I can > add= > it.<br> > > Thanks!<br> > > -Jared<br> > ><br> > </div></div>> ______________________________<wbr>_________________<br> > > yt-users mailing list -- <a href=3D"mailto:yt-users@python.org" > target= > =3D"_blank">yt-users(a)python.org</a><br> > > To unsubscribe send an email to <a href=3D"mailto:yt-users-leave@ > pytho= > n.org" target=3D"_blank">yt-users-leave(a)python.org</a><br> > ><br> > > ______________________________<wbr>_________________<br> > > yt-users mailing list -- <a href=3D"mailto:yt-users@python.org" > target= > =3D"_blank">yt-users(a)python.org</a><br> > > To unsubscribe send an email to <a href=3D"mailto:yt-users-leave@ > pytho= > n.org" target=3D"_blank">yt-users-leave(a)python.org</a><br> > ><br> > ______________________________<wbr>_________________<br> > yt-users mailing list -- <a href=3D"mailto:yt-users@python.org" > target=3D"_= > blank">yt-users(a)python.org</a><br> > To unsubscribe send an email to <a href=3D"mailto:yt-users-leave@ > python.org= > " target=3D"_blank">yt-users-leave(a)python.org</a><br> > ______________________________<wbr>_________________<br> > yt-users mailing list -- <a href=3D"mailto:yt-users@python.org" > target=3D"_= > blank">yt-users(a)python.org</a><br> > To unsubscribe send an email to <a href=3D"mailto:yt-users-leave@ > python.org= > " target=3D"_blank">yt-users-leave(a)python.org</a><br> > </blockquote></div><br></div> > </div></div><br>______________________________<wbr>_________________<br> > yt-users mailing list -- <a href=3D"mailto:yt-users@python.org" > target=3D"_= > blank">yt-users(a)python.org</a><br> > To unsubscribe send an email to <a href=3D"mailto:yt-users-leave@ > python.org= > " target=3D"_blank">yt-users-leave(a)python.org</a><br> > <br>______________________________<wbr>_________________<br> > yt-users mailing list -- <a href=3D"mailto:yt-users@python.org" > target=3D"_= > blank">yt-users(a)python.org</a><br> > To unsubscribe send an email to <a href=3D"mailto:yt-users-leave@ > python.org= > " target=3D"_blank">yt-users-leave(a)python.org</a><br> > <br></blockquote></div><br></div></div></div></div> > <br>______________________________<wbr>_________________<br> > yt-users mailing list -- <a href=3D"mailto:yt-users@python.org > ">yt-users@py= > thon.org</a><br> > To unsubscribe send an email to <a href=3D"mailto:yt-users-leave@ > python.org= > ">yt-users-leave(a)python.org</a><br> > <br>______________________________<wbr>_________________<br> > yt-users mailing list -- <a href=3D"mailto:yt-users@python.org > ">yt-users@py= > thon.org</a><br> > To unsubscribe send an email to <a href=3D"mailto:yt-users-leave@ > python.org= > ">yt-users-leave(a)python.org</a><br> > <br></blockquote></div><br></div> > > --94eb2c05f198e4c8590565af4076-- > > ------------------------------ > > Date: Wed, 21 Feb 2018 08:45:41 -0600 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > Subject: [yt-users] Re: set ticks and label for AxesGrid colorbar > To: Discussion of the yt analysis package <yt-users(a)python.org> > Message-ID: > <CAJXewOmPkcsv6F+G74zwLEOEn-Qq294gMiyRVYPQoG1PqeT5nw@mail. > gmail.com> > Content-Type: multipart/alternative; > boundary="94eb2c1935b46c17a80565b9fc54" > > --94eb2c1935b46c17a80565b9fc54 > Content-Type: text/plain; charset="UTF-8" > Content-Transfer-Encoding: quoted-printable > > Is there any chance you can make a self-contained runnable example that > demonstrates the issue you are having? That will make it easier to > reproduce the issue and allow us to suggest a concrete modification. > > -Nathan > > On Tue, Feb 20, 2018 at 7:47 PM, Kazem Ardaneh <kazem.arrdaneh(a)gmail.com> > wrote: > > > Dear All, > > > > I have a question about costume ticks and ticks label in YT when we use > > AxesGrid. > > I have a plot > > =E2=80=8Bof =E2=80=8B > > density and velocity vectors as over plotted. I want to use a custom > > colorbar ticks and tickslablel. After setup the plots, I have used > > colorbar.set_ticks, and colorbar.set_ticklabels, where > colorbar=3Dplot.cb= > . > > However, they are not changed. Does anyone has a suggestion? > > > > > > > > Kazem > > > > _______________________________________________ > > 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 > > > > > > --94eb2c1935b46c17a80565b9fc54 > Content-Type: text/html; charset="UTF-8" > Content-Transfer-Encoding: quoted-printable > > <div dir=3D"ltr"><div>Is there any chance you can make a self-contained > run= > nable example that demonstrates the issue you are having? That will make > it= > easier to reproduce the issue and allow us to suggest a concrete > modificat= > ion.<br></div><div><br></div>-Nathan<br></div><div > class=3D"gmail_extra"><b= > r><div class=3D"gmail_quote">On Tue, Feb 20, 2018 at 7:47 PM, Kazem > Ardaneh= > <span dir=3D"ltr"><<a href=3D"mailto:kazem.arrdaneh@gmail.com" target= > =3D"_blank">kazem.arrdaneh(a)gmail.com</a>></span> wrote:<br><blockquote > c= > lass=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc > solid;= > padding-left:1ex"><div dir=3D"ltr">Dear All, <br><br>I have a question > abou= > t costume ticks and ticks label in YT when we use AxesGrid.<br>I have a > plo= > t <div class=3D"gmail_default" style=3D"font-size:small; > display:inline">=E2= > =80=8Bof =E2=80=8B</div>density and velocity vectors as over plotted. I > wan= > t to use a custom colorbar ticks and tickslablel. After setup the plots, I > = > have used colorbar.set_ticks, and colorbar.set_ticklabels, where colorbar= > =3Dplot.cb. However, they are not changed. Does anyone has a suggestion? > <s= > pan class=3D"HOEnZb"><font color=3D"#888888"><div class=3D"gmail_default" > s= > tyle=3D"font-size:small"><p style=3D"margin:0px;font- > stretch:normal;font-si= > ze:14px;line-height:normal;font-family:Menlo;color:rgb(205,121,35)"><span > s= > tyle=3D"font-variant-ligatures:no-common-ligatures; > color:rgb(0,0,0)"><br></= > span></p></div><div><div class=3D"m_6492320114560421087gmail-m_ > 626533431233= > 1061960gmail_signature"><div dir=3D"ltr"><div><div dir=3D"ltr"><div><div > di= > r=3D"ltr"><br>Kazem </div></div></div></div></div></div></div> > </font></span></div> > <br>______________________________<wbr>_________________<br> > yt-users mailing list -- <a href=3D"mailto:yt-users@python.org > ">yt-users@py= > thon.org</a><br> > To unsubscribe send an email to <a href=3D"mailto:yt-users-leave@ > python.org= > ">yt-users-leave(a)python.org</a><br> > <br>______________________________<wbr>_________________<br> > yt-users mailing list -- <a href=3D"mailto:yt-users@python.org > ">yt-users@py= > thon.org</a><br> > To unsubscribe send an email to <a href=3D"mailto:yt-users-leave@ > python.org= > ">yt-users-leave(a)python.org</a><br> > <br></blockquote></div><br></div> > > --94eb2c1935b46c17a80565b9fc54-- > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list -- yt-users(a)python.org > To unsubscribe send an email to yt-users-leave(a)python.org > > > ------------------------------ > > End of yt-users Digest, Vol 120, Issue 10 > ***************************************** >

1 0

Loading a large gadget snapshot
by Jared Coughlin 21 Feb '18

21 Feb '18

Hello! I have a gadget snapshot file with 1024^3 particles. When I tried to load it with yt, yt fails by saying that it cannot identify the file type. I did some digging and found that the way yt validates a gadget snapshot is by reading the number of particles from the header and then comparing that number to the number derived from the size of the position block. This size is 1024^3 *3*4 (the number of particles times 3 positions times 4 bytes per position). However, as I just discovered, this number is larger than the max value of an int in c, and so gadget writes a value of 0 due to the overflow. As such, I need to use gadget's unsigned long long int for the padding, but this is 8 bytes, not 4. I was just wondering if yt had some ability to detect the need to use something larger than an int? If not, I can add it. Thanks! -Jared

4 6

Re: Error while running yt with MPI
by Nick Gnedin 21 Feb '18

21 Feb '18

It works now, thank you. On 2/21/2018 11:40 AM, Nathan Goldbaum wrote: > Hi Nick, > > Are you running yt 3.4.1? I'm pretty sure you're running into the bug > that was fixed by this pull request: > > https://github.com/yt-project/yt/pull/1538 > > We just released yt 3.4.1 last Friday and it should be available to > install via conda-forge: > > $ conda update -c conda-forge yt > > Hope that helps, > > Nathan > > On Wed, Feb 21, 2018 at 11:29 AM, Nick Gnedin <ngnedin(a)gmail.com > <mailto:ngnedin@gmail.com>> wrote: > > > Folks, > > I am trying to run yt halo finder with MPI, and I am encounter the > following error. Could you perhaps give me a hint how to debug it > further? > > Here is a simple script: > > ---- SCRIPT ------- > import yt > from yt.analysis_modules.halo_analysis.api import HaloCatalog > yt.enable_parallelism() > path = "." > aexp = "0.0802" > d = yt.load(path+"/rei10_a"+aexp +"/rei10_a"+aexp+".art") > hc = > HaloCatalog(data_ds=d,finder_method='hop',output_dir=path+"/a="+aexp+"/hop2",finder_kwargs={"dm_only":False,"ptype":"N-BODY"}) > hc.create() > ------------------- > > It runs just fine in a serial mode (with yt.enable_parallelism() > call commented out), but with MPI it gives a type error deep inside yt: > > ---- SERIAL OUTPUT ------- > /data/gnedin/REI/TMP >p hf.py > yt : [WARNING ] 2018-02-21 11:02:26,502 DeltaDC != 0, which implies > auni != abox. Be sure you understand which expansion parameter is > appropriate for your use! (Gnedin, Kravtsov, & Rudd 2011) > yt : [INFO ] 2018-02-21 11:02:26,520 Parameters: current_time > = 392162249.38323104 yr > yt : [INFO ] 2018-02-21 11:02:26,520 Parameters: > domain_dimensions = [64 64 64] > yt : [INFO ] 2018-02-21 11:02:26,521 Parameters: > domain_left_edge = [ 0. 0. 0.] > yt : [INFO ] 2018-02-21 11:02:26,521 Parameters: > domain_right_edge = [ 64. 64. 64.] > yt : [INFO ] 2018-02-21 11:02:26,522 Parameters: > cosmological_simulation = True > yt : [INFO ] 2018-02-21 11:02:26,522 Parameters: > current_redshift = 11.470684242933336 > yt : [INFO ] 2018-02-21 11:02:26,522 Parameters: omega_lambda > = 0.6964000165462494 > yt : [INFO ] 2018-02-21 11:02:26,522 Parameters: omega_matter > = 0.3035999834537506 > yt : [INFO ] 2018-02-21 11:02:26,522 Parameters: > hubble_constant = 0.6814000010490417 > yt : [INFO ] 2018-02-21 11:02:34,808 Created 256 chunks for ARTIO > yt : [INFO ] 2018-02-21 11:02:38,656 Initializing HOP > yt : [INFO ] 2018-02-21 11:02:38,658 Created 256 chunks for ARTIO > Copying arrays for 16777216 particles > Calling hop... 16777216 1.600e+02 > nSmooth = 65 kd->nActive = 16777216 > Building Tree... > Finding Densities... > Finding Densest Neighbors... > Grouping... > Merging Groups... > Writing Output... > All Done!Calling regroup... > No minimum group size specified. Assuming 10 particles. > ngroups = 51045 > yt : [INFO ] 2018-02-21 11:07:11,099 Parsing outputs > yt : [INFO ] 2018-02-21 11:07:38,770 Parameters: current_time > = 0.0 > yt : [INFO ] 2018-02-21 11:07:38,770 Parameters: > domain_dimensions = [2 2 2] > yt : [INFO ] 2018-02-21 11:07:38,770 Parameters: > domain_left_edge = [ 0. 0. 0.] > yt : [INFO ] 2018-02-21 11:07:38,771 Parameters: > domain_right_edge = [ 3.56553853e+24 3.56553853e+24 > 3.56553853e+24] > yt : [INFO ] 2018-02-21 11:07:38,771 Parameters: > cosmological_simulation = 0.0 > yt : [INFO ] 2018-02-21 11:07:38,789 Allocating for 3.240e+02 > particles (index particle type 'all') > yt : [INFO ] 2018-02-21 11:07:38,790 Identified 1.700e+01 octs > /data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/units/yt_array.py:990: > RuntimeWarning: divide by zero encountered in true_divide > return super(YTArray, self).__truediv__(ro) > yt : [INFO ] 2018-02-21 11:07:39,223 Saving halo catalog (324 > halos) to ./a=0.0802/hop/hop. > --------------------------- > > ------ MPI OUTPUT --------- > /data/gnedin/REI/TMP >/data/gnedin/soft/anaconda3/bin/mpirun -n 2 > /data/gnedin/soft/anaconda3/bin/python3 hf.py > yt : [INFO ] 2018-02-21 11:20:47,675 Global parallel computation > enabled: 0 / 2 > yt : [INFO ] 2018-02-21 11:20:47,676 Global parallel computation > enabled: 1 / 2 > P000 yt : [WARNING ] 2018-02-21 11:20:47,681 DeltaDC != 0, which > implies auni != abox. Be sure you understand which expansion > parameter is appropriate for your use! (Gnedin, Kravtsov, & Rudd 2011) > P001 yt : [WARNING ] 2018-02-21 11:20:47,687 DeltaDC != 0, which > implies auni != abox. Be sure you understand which expansion > parameter is appropriate for your use! (Gnedin, Kravtsov, & Rudd 2011) > P000 yt : [INFO ] 2018-02-21 11:20:47,691 Parameters: > current_time = 392162249.38323104 yr > P000 yt : [INFO ] 2018-02-21 11:20:47,691 Parameters: > domain_dimensions = [64 64 64] > P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: > domain_left_edge = [ 0. 0. 0.] > P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: > domain_right_edge = [ 64. 64. 64.] > P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: > cosmological_simulation = True > P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: > current_redshift = 11.470684242933336 > P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: > omega_lambda = 0.6964000165462494 > P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: > omega_matter = 0.3035999834537506 > P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: > hubble_constant = 0.6814000010490417 > File "hf.py", line 15, in <module> > hc.create() > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_catalog.py", > line 334, in create > self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", > line 306, in barrierize > retval = func(*args, **kwargs) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_catalog.py", > line 403, in _run > self.halos_ds = self.finder_method(self.data_ds) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_finding_methods.py", > line 44, in __call__ > return self.function(ds, *self.args, **self.kwargs) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_finding_methods.py", > line 51, in _hop_method > halo_list = HOPHaloFinder(ds, **finder_kwargs) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_finding/halo_objects.py", > line 1483, in __init__ > padding=self.padding) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", > line 1191, in partition_index_3d > cx, cy, cz = np.unravel_index(mi, cc) > File "hf.py", line 15, in <module> > hc.create() > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_catalog.py", > line 334, in create > self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", > line 306, in barrierize > retval = func(*args, **kwargs) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_catalog.py", > line 403, in _run > self.halos_ds = self.finder_method(self.data_ds) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_finding_methods.py", > line 44, in __call__ > return self.function(ds, *self.args, **self.kwargs) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_finding_methods.py", > line 51, in _hop_method > halo_list = HOPHaloFinder(ds, **finder_kwargs) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_finding/halo_objects.py", > line 1483, in __init__ > padding=self.padding) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", > line 1191, in partition_index_3d > cx, cy, cz = np.unravel_index(mi, cc) > P000 yt : [ERROR ] 2018-02-21 11:20:48,807 TypeError: Iterator > operand 0 dtype could not be cast from dtype('float64') to > dtype('int64') according to the rule 'same_kind' > P000 yt : [ERROR ] 2018-02-21 11:20:48,807 Error occured on rank 0. > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 > P001 yt : [ERROR ] 2018-02-21 11:20:48,807 TypeError: Iterator > operand 0 dtype could not be cast from dtype('float64') to > dtype('int64') according to the rule 'same_kind' > P001 yt : [ERROR ] 2018-02-21 11:20:48,807 Error occured on rank 1. > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1 > ------------------------------------- > > > Any suggestion would be highly appreciated. > > 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> > _______________________________________________ > 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> > >

1 0

Error while running yt with MPI
by Nick Gnedin 21 Feb '18

21 Feb '18

Folks, I am trying to run yt halo finder with MPI, and I am encounter the following error. Could you perhaps give me a hint how to debug it further? Here is a simple script: ---- SCRIPT ------- import yt from yt.analysis_modules.halo_analysis.api import HaloCatalog yt.enable_parallelism() path = "." aexp = "0.0802" d = yt.load(path+"/rei10_a"+aexp +"/rei10_a"+aexp+".art") hc = HaloCatalog(data_ds=d,finder_method='hop',output_dir=path+"/a="+aexp+"/hop2",finder_kwargs={"dm_only":False,"ptype":"N-BODY"}) hc.create() ------------------- It runs just fine in a serial mode (with yt.enable_parallelism() call commented out), but with MPI it gives a type error deep inside yt: ---- SERIAL OUTPUT ------- /data/gnedin/REI/TMP >p hf.py yt : [WARNING ] 2018-02-21 11:02:26,502 DeltaDC != 0, which implies auni != abox. Be sure you understand which expansion parameter is appropriate for your use! (Gnedin, Kravtsov, & Rudd 2011) yt : [INFO ] 2018-02-21 11:02:26,520 Parameters: current_time = 392162249.38323104 yr yt : [INFO ] 2018-02-21 11:02:26,520 Parameters: domain_dimensions = [64 64 64] yt : [INFO ] 2018-02-21 11:02:26,521 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2018-02-21 11:02:26,521 Parameters: domain_right_edge = [ 64. 64. 64.] yt : [INFO ] 2018-02-21 11:02:26,522 Parameters: cosmological_simulation = True yt : [INFO ] 2018-02-21 11:02:26,522 Parameters: current_redshift = 11.470684242933336 yt : [INFO ] 2018-02-21 11:02:26,522 Parameters: omega_lambda = 0.6964000165462494 yt : [INFO ] 2018-02-21 11:02:26,522 Parameters: omega_matter = 0.3035999834537506 yt : [INFO ] 2018-02-21 11:02:26,522 Parameters: hubble_constant = 0.6814000010490417 yt : [INFO ] 2018-02-21 11:02:34,808 Created 256 chunks for ARTIO yt : [INFO ] 2018-02-21 11:02:38,656 Initializing HOP yt : [INFO ] 2018-02-21 11:02:38,658 Created 256 chunks for ARTIO Copying arrays for 16777216 particles Calling hop... 16777216 1.600e+02 nSmooth = 65 kd->nActive = 16777216 Building Tree... Finding Densities... Finding Densest Neighbors... Grouping... Merging Groups... Writing Output... All Done!Calling regroup... No minimum group size specified. Assuming 10 particles. ngroups = 51045 yt : [INFO ] 2018-02-21 11:07:11,099 Parsing outputs yt : [INFO ] 2018-02-21 11:07:38,770 Parameters: current_time = 0.0 yt : [INFO ] 2018-02-21 11:07:38,770 Parameters: domain_dimensions = [2 2 2] yt : [INFO ] 2018-02-21 11:07:38,770 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2018-02-21 11:07:38,771 Parameters: domain_right_edge = [ 3.56553853e+24 3.56553853e+24 3.56553853e+24] yt : [INFO ] 2018-02-21 11:07:38,771 Parameters: cosmological_simulation = 0.0 yt : [INFO ] 2018-02-21 11:07:38,789 Allocating for 3.240e+02 particles (index particle type 'all') yt : [INFO ] 2018-02-21 11:07:38,790 Identified 1.700e+01 octs /data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/units/yt_array.py:990: RuntimeWarning: divide by zero encountered in true_divide return super(YTArray, self).__truediv__(ro) yt : [INFO ] 2018-02-21 11:07:39,223 Saving halo catalog (324 halos) to ./a=0.0802/hop/hop. --------------------------- ------ MPI OUTPUT --------- /data/gnedin/REI/TMP >/data/gnedin/soft/anaconda3/bin/mpirun -n 2 /data/gnedin/soft/anaconda3/bin/python3 hf.py yt : [INFO ] 2018-02-21 11:20:47,675 Global parallel computation enabled: 0 / 2 yt : [INFO ] 2018-02-21 11:20:47,676 Global parallel computation enabled: 1 / 2 P000 yt : [WARNING ] 2018-02-21 11:20:47,681 DeltaDC != 0, which implies auni != abox. Be sure you understand which expansion parameter is appropriate for your use! (Gnedin, Kravtsov, & Rudd 2011) P001 yt : [WARNING ] 2018-02-21 11:20:47,687 DeltaDC != 0, which implies auni != abox. Be sure you understand which expansion parameter is appropriate for your use! (Gnedin, Kravtsov, & Rudd 2011) P000 yt : [INFO ] 2018-02-21 11:20:47,691 Parameters: current_time = 392162249.38323104 yr P000 yt : [INFO ] 2018-02-21 11:20:47,691 Parameters: domain_dimensions = [64 64 64] P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: domain_left_edge = [ 0. 0. 0.] P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: domain_right_edge = [ 64. 64. 64.] P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: cosmological_simulation = True P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: current_redshift = 11.470684242933336 P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: omega_lambda = 0.6964000165462494 P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: omega_matter = 0.3035999834537506 P000 yt : [INFO ] 2018-02-21 11:20:47,692 Parameters: hubble_constant = 0.6814000010490417 File "hf.py", line 15, in <module> hc.create() File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_catalog.py", line 334, in create self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 306, in barrierize retval = func(*args, **kwargs) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_catalog.py", line 403, in _run self.halos_ds = self.finder_method(self.data_ds) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_finding_methods.py", line 44, in __call__ return self.function(ds, *self.args, **self.kwargs) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_finding_methods.py", line 51, in _hop_method halo_list = HOPHaloFinder(ds, **finder_kwargs) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_finding/halo_objects.py", line 1483, in __init__ padding=self.padding) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 1191, in partition_index_3d cx, cy, cz = np.unravel_index(mi, cc) File "hf.py", line 15, in <module> hc.create() File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_catalog.py", line 334, in create self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 306, in barrierize retval = func(*args, **kwargs) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_catalog.py", line 403, in _run self.halos_ds = self.finder_method(self.data_ds) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_finding_methods.py", line 44, in __call__ return self.function(ds, *self.args, **self.kwargs) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_finding_methods.py", line 51, in _hop_method halo_list = HOPHaloFinder(ds, **finder_kwargs) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_finding/halo_objects.py", line 1483, in __init__ padding=self.padding) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 1191, in partition_index_3d cx, cy, cz = np.unravel_index(mi, cc) P000 yt : [ERROR ] 2018-02-21 11:20:48,807 TypeError: Iterator operand 0 dtype could not be cast from dtype('float64') to dtype('int64') according to the rule 'same_kind' P000 yt : [ERROR ] 2018-02-21 11:20:48,807 Error occured on rank 0. application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 P001 yt : [ERROR ] 2018-02-21 11:20:48,807 TypeError: Iterator operand 0 dtype could not be cast from dtype('float64') to dtype('int64') according to the rule 'same_kind' P001 yt : [ERROR ] 2018-02-21 11:20:48,807 Error occured on rank 1. application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1 ------------------------------------- Any suggestion would be highly appreciated. Nick Gnedin

2 1

set ticks and label for AxesGrid colorbar
by Kazem Ardaneh 21 Feb '18

21 Feb '18

Dear All, I have a question about costume ticks and ticks label in YT when we use AxesGrid. I have a plot of density and velocity vectors as over plotted. I want to use a custom colorbar ticks and tickslablel. After setup the plots, I have used colorbar.set_ticks, and colorbar.set_ticklabels, where colorbar=plot.cb. However, they are not changed. Does anyone has a suggestion? Kazem

2 1

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