RAMSES with RADMC3D
by Lamberts, Astrid
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/... ).
Has this issue been fixed somewhere?
How can we get this to work?
Thanks,
Astrid
Astrid Lamberts
Postdoctoral Researcher
TAPIR Group, Caltech
1 year
Re: yt-users Digest, Vol 120, Issue 10
by Kazem Ardaneh
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:
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> 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
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> >>
> >> _______________________________________________
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> >>
> >
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>
> --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>
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> target=3D"_=
> blank">yt-users(a)python.org</a><br>
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> " target=3D"_blank">yt-users-leave(a)python.org</a><br>
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> " target=3D"_blank">yt-users-leave(a)python.org</a><br>
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> </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"
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> blank">yt-users(a)python.org</a><br>
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> 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
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>
> ------------------------------
>
> End of yt-users Digest, Vol 120, Issue 10
> *****************************************
>
1 year, 1 month
Loading a large gadget snapshot
by Jared Coughlin
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
1 year, 1 month
Re: Error while running yt with MPI
by Nick Gnedin
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 year, 1 month
Error while running yt with MPI
by Nick Gnedin
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
1 year, 1 month
set ticks and label for AxesGrid colorbar
by Kazem Ardaneh
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
1 year, 1 month
Axis in streamline plotting
by Sushilkumar
Dear yt:
Is there a way to have normalized axis units for streamline plotting?
I want my x axis (xmin, xmax) to be in the units of (xmin/30, xmax/30).
Similarly, for y axis.
Thank you in advance
SCRIPT:
import yt
import numpy as np
import os
import matplotlib.pyplot as plt
import matplotlib
ms = 24000000
vector_max=ms-(ms/3)
ms1=ms-vector_max
dims = (200,200,200)
x =
np.genfromtxt("/work/jbi157/MODEL7/UPDATE_B/yo_n_t105.mtx",skip_header=2,usecols=1,
dtype="f8")
x = x.reshape((8000000, 3), order="F")
field1 = x[:,2].reshape(dims, order="F")
field2 = x[:,1].reshape(dims, order="F")
field3 = x[:,0].reshape(dims, order="F")
data = dict(velocity_x = field1,
velocity_y = field2,
velocity_z = field3)
bbox = np.array([[-100, 99], [-100, 99], [-100, 99]])
ds = yt.load_uniform_grid(data, dims, 'km', bbox=bbox, nprocs=1)
L = [0, 1, 0]
north_vector = [0.87, 0, 0.5]
slc = yt.OffAxisSlicePlot(ds, L, 'cutting_plane_velocity_x',
center=[0,0,0], width=(180,'km'), north_vector=north_vector)
vel = slc._frb['velocity_magnitude']
U = slc._frb['cutting_plane_velocity_y']
V = slc._frb['cutting_plane_velocity_x']
extentx = [slc.xlim[i].in_units('km') for i in (0, 1)]
extenty = [slc.ylim[i].in_units('km') for i in (0, 1)]
extent = extentx + extenty
x = np.linspace(extentx[0], extentx[1], vel.shape[0])
y = np.linspace(extenty[1], extenty[0], vel.shape[1])
X, Y = np.meshgrid(x, y)
normalize = False # Turn off normalize if you use streamplot
if normalize is True:
N = np.sqrt(U**2+V**2)
U /= N
V /= N
else:
U = U.d
V = V.d
factor = 40
#norm = matplotlib.colors.Normalize(vmin=vel.min(), vmax=vel.max(),
clip=True)
#norm = matplotlib.colors.LogNorm(vmin=vel.min(), vmax=vel.max(),
clip=True)
#norm = matplotlib.colors.NoNorm(vmin=vel.min(), vmax=vel.max(), clip=True)
#norm = matplotlib.colors.PowerNorm(gamma=0.5,vmin=vel.min(),
vmax=vel.max(), clip=True)
norm = matplotlib.colors.SymLogNorm(linthresh=0.01,vmin=vel.min(),
vmax=vel.max(), clip=True)
plt.streamplot(np.array(X),np.array(Y),np.array(U),np.array(V),
density=2,color='blue') # Here density adjusts the density of streamlines
#plt.imshow(vel.d, extent=extent, norm=norm)
#plt.imshow(vel.d, extent=extent, norm=norm, cmap='seismic')
plt.imshow(vel.d, extent=extent, norm=norm, cmap=plt.cm.coolwarm)
circle=plt.Circle((0,0),9,color='gray')
fig = plt.gcf()
fig.gca().add_artist(circle)
plt.colorbar()
#plt.title("Angle = 45$^{\circ}$, Grid size = 200\n Power Normalize, Gamma
= 0.5")
#plt.title("Angle = 45$^{\circ}$, Grid size = 200\n Linear Normalize")
plt.title("Angle = 60$^{\circ}$, x-z plane")
plt.axis([-72, 72, -72, 72])
plt.axis('off')
#plt.savefig('stream_plot_Norm.png')
#plt.savefig('stream_plot_LogNorm.png')
#plt.savefig('stream_plot_NoNorm.png')
#plt.savefig('stream_plot_PowerNorm.png')
plt.savefig('stream_plot_t0105.png')
--
*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.**"*
1 year, 1 month
volume rendering with streamlines?
by astroodie＠gmail.com
Hello,
I knew that I could use annotate_magnetic_field(), annotate_streamlines(), annotate_line_integral_convolution(), or annotate_cquiver() for 2D plots,
and yt.visualization.api, Streamlines for 3D stream lines (with Axes3D, ugly).
Is it possible to plot streamlines/vectors (magnetic field or velocity field) together with a volume rendering plot (not Isocontours)?
Many thanks,
Kuo-Chuan
1 year, 1 month
ANN: yt 3.4.1 releaed
by Nathan Goldbaum
yt 3.4.1 release notes
The yt community is proud to announce the release of yt 3.4.1. This is a
patch release and includes a number of improvements and bugfixes. Note that
one of the bugs fixed in this release silently produced invalid results for
the values of certain yt fields. See the release notes below for more
details.
yt (https://yt-project.org) is an open source, community developed toolkit
for the analysis and visualization of volumetric data. Development is
hosted on GitHub (https://github.com/yt-project/yt).
This release includes contributions from 20 contributors, five of whom
contributed for the first time:
- *Christoph Behrens*
- *Josh Borrow*
- Corentin Cadiou
- Yi-Hao Chen
- Bili Dong
- Nathan Goldbaum
- Philipp Grete
- *Stephanie Ho*
- Cameron Hummels
- Suoqing Ji
- Max Katz
- Kacper Kowalik
- Andrew Myers
- Hugo Pfister
- Justin Schive
- Britton Smith
- *Josh Soref*
- Matthew Turk
- *Daniel Wilcox*
- John ZuHone
The bolded names indicate first-time contributors. We extend our sincere
gratitude to everyone who has contributed!
See the changelog below for a summary of new features, changes, and
bugfixes.
For more information, including installation instructions, links to
community resources, and information on contributing to yt’s development,
please see the yt homepage at http://yt-project.org and the documentation
for yt 3.4.1 at http://yt-project.org/docs/3.4.1.
Binaries for yt 3.4.1 are available via pip and conda. If you installed via
the install script or use conda to manage your python installation, you can
update yt via:
$ conda update -c conda-forge yt
And via pip if you manage your python installation with pip:
$ pip install -U yt
As always, if you have any questions, concerns, or run into any trouble
updating please don’t hesitate to send a message to the mailing list or
stop by our Slack or IRC channel.
yt is the product of a large community of developers and users and we are
extraordinarily grateful for and proud of their contributions. Please
forward this announcement on to any interested parties.
Best,
The yt development team
<https://hackmd.io/CYMwhgjGYBzAtAUwGwQEbwCwFYQbIgMabwAMYAnMmoYQOywgDMQA?bo...>Critical
Bugfixes
- The data returned by fields corresponding to the theta or phi
component of a vector field in spherical coordinates or the theta component
in cylindrical coordinates, including velocity_spherical_theta,
velocity_spherical_phi, and velocity_cylindrical_theta as well as the
corresponding magnetic field components have been silently returning
incorrect results. If you are doing analysis using those fields we strongly
encourage you to update to this latest release to get fixed versions of
these fields. See PR 1687 <https://github.com/yt-project/yt/pull/1687>.
- Define the code_specific_energy unit and ds.specific_energy_unit
attribute. This allows user control over the value of the specific energy
unit independent of the velocity unit and fixes an inconsistency in the
units of the Gadget internal energy and temperature fields. See PR 1611
<https://github.com/yt-project/yt/pull/1611> and PR 1675
<https://github.com/yt-project/yt/pull/1675>.
- Numpy 1.14.0 introduced changes to array printing which caused
recursion errors when printing a YTArray instance. This will be fixed
upstream in 1.14.1 but we have also restored support for NumPy 1.14.0 in yt
by avoiding triggering the error. See PR 1661
<https://github.com/yt-project/yt/pull/1661>.
<https://hackmd.io/CYMwhgjGYBzAtAUwGwQEbwCwFYQbIgMabwAMYAnMmoYQOywgDMQA?bo...>Minor
Improvements and Bugfixes
- Halo finders can now run in parallel on Python 3. See PR 1538
<https://github.com/yt-project/yt/pull/1538> and pPR 1690](
https://github.com/yt-project/yt/pull/1690).
- The QT5 backend can now be used to display yt plots interactively. See PR
1540 <https://github.com/yt-project/yt/pull/1540>.
- A number of misspellings across the codebase and documentation have
been corrected. See PR 1542 <https://github.com/yt-project/yt/pull/1542>
and PR 1575 <https://github.com/yt-project/yt/pull/1575>.
- An off-by-one error in the particle_filter_sfr.py cookbook recipe has
been fixed. See PR 1547 <https://github.com/yt-project/yt/pull/1547>.
- The tipsy frontend will ignore invalid auxiliary files instead of
raising an exception. See PR 1549
<https://github.com/yt-project/yt/pull/1549>.
- Fixed a typo in the Gadget header specification. See PR 1550
<https://github.com/yt-project/yt/pull/1550>.
- Parse units more gracefully in the FITS frontend. See PR 1553
<https://github.com/yt-project/yt/pull/1553>.
- Handle units more gracefully when calculating quantities in the halo
catalog. See PR 1558 <https://github.com/yt-project/yt/pull/1558>.
- Ensure the PPVCube functionality works when a temperature field is not
present. See PR 1562 <https://github.com/yt-project/yt/pull/1562>.
- Avoid an error when saving spatial fields for a clump data object. See PR
1567 <https://github.com/yt-project/yt/pull/1567>.
- ProfilePlot.set_unit and PhasePlot.set_unit will now handle tuple
field names correctly. See PR 1568
<https://github.com/yt-project/yt/pull/1568>.
- Properly set attributes when reloading ytdata datasets generated from
an arbitrary_grid data object. See PR 1569
<https://github.com/yt-project/yt/pull/1569>.
- Fix units in light cone projection. See PR 1574
<https://github.com/yt-project/yt/pull/1574>.
- Allow loading Gadget datasets when some cosmology parameters are not
present in the header. See PR 1578
<https://github.com/yt-project/yt/pull/1578>.
- Correct typo in WarpX field definitions. See PR 1583
<https://github.com/yt-project/yt/pull/1583>.
- Fix corner case in parsing Enzo parameter files. See PR 1586
<https://github.com/yt-project/yt/pull/1586>.
- Ensure clump parents ids are updated correctly when child clumps are
pruned. See PR 1587 <https://github.com/yt-project/yt/pull/1587>.
- Ensure the bulk_magnetic_field field parameter is always set to a null
default value if it is not otherwise explicitly set. See PR 1588
<https://github.com/yt-project/yt/pull/1588>.
- Prevent NaNs from polluting profile calculations when the profile
weight field has values equal to zero. See PR 1590
<https://github.com/yt-project/yt/pull/1590>.
- Ensure _switch_ds() works with ParticleProjectionPlot. See PR 1594
<https://github.com/yt-project/yt/pull/1594>.
- Fix the colors of the axes triad generated by the volume rendering
annotate_axes helper function. See PR 1596
<https://github.com/yt-project/yt/pull/1596>.
- Fix zooming of slices and projections of data with a 2D cylindrical
geometry. See PR 1597 <https://github.com/yt-project/yt/pull/1597>.
- Ensure field accesses on 2D grid data objects return data with a dummy
dimension. See PR 1603 <https://github.com/yt-project/yt/pull/1603>.
- Fix broken links in the documentation. See PR 1615
<https://github.com/yt-project/yt/pull/1615> and PR 1627
<https://github.com/yt-project/yt/pull/1627>.
- Avoid errors when parsing boolean parameters in the Boxlib frontend.
See PR 1619 <https://github.com/yt-project/yt/pull/1619>.
- Populate the _particle_type_counts dictionary for AMReX datasets. This
means that ds.particle_type_counts will function correctly. See PR 1621
<https://github.com/yt-project/yt/pull/1621>.
- Ensure the "rad" (an alias to the "radian" unit defined for
compatibility with Astropy) has the correct dimensions of angle instead of
solid angle. See PR 1628 <https://github.com/yt-project/yt/pull/1628>.
- Fix unit conversion issue in the annotate_quiver plot callback. See PR
1633 <https://github.com/yt-project/yt/pull/1633>.
- Fix unit conversion error in deposited particle velocity and age
fields. See PR 1638 <https://github.com/yt-project/yt/pull/1638>.
- Added deprecation warnings for the LightRay and AbsorptionSpectrum
functionality. Development of this functionality has moved to the Trident
package. See PR 1644 <https://github.com/yt-project/yt/pull/1644>.
- Support new AMReX particle data files with 5 digit IDs. See PR 1653
<https://github.com/yt-project/yt/pull/1653>.
- Handle reloading pickle files with very early YTArray data. See PR 1656
<https://github.com/yt-project/yt/pull/1656>.
- Fix initializing species charge and mass fields in the AMReX frontend.
See PR 1658 <https://github.com/yt-project/yt/pull/1658>.
- Keep units for domain edges when saving ytdata datasets from a
FixedResolutionBuffer object. See PR 1659
<https://github.com/yt-project/yt/pull/1659>.
- Use the correct matplotlib keyword argument name when specifying
contour colors. See PR 1664 <https://github.com/yt-project/yt/pull/1664>.
- Support Enzo active particle fields that map to arrays. See PR 1665
<https://github.com/yt-project/yt/pull/1665>.
- Use a smarter algorithm for clipping particle positions to the domain
boundaries in the rockstar halo finder. See PR 1679
<https://github.com/yt-project/yt/pull/1679>.
- Make the annotate_clumps plot callback work correctly with reloaded
ytdata clump datasets. See PR 1683
<https://github.com/yt-project/yt/pull/1683>.
- Calculate velocity vector components without using the
velocity_magnitude field. This avoids inconsistencies when the
bulk_velocity field parameter is set to a nonzero value. See PR 1688
<https://github.com/yt-project/yt/pull/1688>.
- Avoid truncating Gadget particle IDs by casting from uint32 to float32.
See PR 1692 <https://github.com/yt-project/yt/pull/1692>.
1 year, 1 month
Attached velocity arrows to particles
by John Regan
Hi Guys,
Just wondering if anyone knows how to attach velocity magnitude arrows to
particles (e.g. star particles)? There are the annotate callbacks to place
particles on top of gas fields but can I then somehow also view the
particle velocity magnitudes.
Any tips much appreciated.
Cheers,
John
1 year, 1 month
