Hi,
I have written some new fields in yt/yt/fileds file named as XXX.py, but I have no idea how to make it work correctly like kinetic-energy, thermal-energy etc which can be projected and sliced.
Please help me to work it out!!!
Hi yt-users!
I have been fiddling some more with yt's clump finder and have another
question. I want to use density to find clumps, but want my maximum
threshold value to be below the fiducial setting--instead of above the
maximum possible density in the code I just want the finder to stop
searching at, say 3.2e-24.
The code was working but running out of memory until I set the max
threshold, and I now get this error:
....lots of pleasant looking output messages....
Updating joins ... : 0%| | 0/7 [00:00<?, ?it/s]
Updating joins ... : 100%|██████████| 7/7 [00:00<00:00, 48933.55it/s]
yt : [INFO ] 2018-09-07 14:08:55,007 Investigating 2 children.
yt : [INFO ] 2018-09-07 14:08:55,007 Finding clumps: min: 3.200000e-24,
max: 3.200000e-24, step: 2.000000
yt : [INFO ] 2018-09-07 14:08:55,041 Finding clumps: min: 3.200000e-24,
max: 3.200000e-24, step: 2.000000
yt : [INFO ] 2018-09-07 14:08:55,042 Eliminating invalid, childless
clump with 2 cells.
yt : [INFO ] 2018-09-07 14:08:55,042 1 of 2 children survived, linking
its children to parent.
Traceback (most recent call last):
File "yt_clump_fingert.py", line 59, in <module>
find_clumps(master_clump, c_min, c_max, step)
File
"/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py",
line 444, in find_clumps
find_clumps(child, min_val*d_clump, max_val, d_clump)
File
"/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py",
line 438, in find_clumps
find_clumps(clump, min_val*d_clump, max_val, d_clump)
File
"/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py",
line 438, in find_clumps
find_clumps(clump, min_val*d_clump, max_val, d_clump)
File
"/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py",
line 438, in find_clumps
find_clumps(clump, min_val*d_clump, max_val, d_clump)
File
"/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py",
line 461, in find_clumps
for child in clump.children:
TypeError: 'NoneType' object is not iterable
I tried to circumvent this error by changing my max to 2e-24 (not a
multiple of 2 of 1e-25), and got the same error when the min was 3.2e-24
and the max was 2e-24 (!).
Is there any way I can get around this error and have the clumpfinder stop
looking once it has clump edges at my maximum density?
Thanks!
Stephanie
--
Dr. Stephanie Tonnesen
Associate Research Scientist
CCA, Flatiron Institute
New York, NY
stonnes(a)gmail.com
Hello all,
I’d like to extend my congratulations to Ashley Kelly and Corentin Cadiou
for winning the innaugural NumFOCUS new contributor award!
https://numfocus.org/blog/inaugural-numfocus-awards-and-new-contributor-r...
This is a new award that honors new contributors to NumFOCUS projects. The
yt executive committee nominated Ashley and Corentin and they were both
recognized at the awards dinner on Sunday night after the sustainability
summit.
Let’s all give a warm round of emoji applause!
👏👏👏👏👏👏👏👏
Nathan
Ashley Kelly
Ashley Kelly participated in Google Summer of Code this year with yt via
the NumFOCUS umbrella org. rom the outset, Ashley proposed a very ambitious
plan. Privately I felt that the plan was probably overambitious but with
the expectation that we would likely descope the plan, we decided to press
ahead wit the project. Not only did we not need to descope, In my opinion
Ashley exceeded his original plans. We are now in a much better position to
ship major new features next year thanks to Ashley’s efforts.
Corentin Cadiou
Corentin Cadiou began contributing to yt completely unprompted by any of
the core developers, working from Europe without in-person contact from the
bulk of the yt contributor base in the United States. Corentin has
substantially improved support for simulation data produced by the RAMSES
code, and has contributed a number of other bugfixes, performance
improvements, and nice new features. Corentin has doggedly made sure that
his code gets merged and regularly helps out new users on Slack and the
mailing list. Thanks to his efforts future RAMSES users and users of octree
AMR codes will have a much nicer experience with yt than when he began
contributing.
Hi,
I recently tried to re-install yt on my home directory of a local cluster.
I used the all in one script. After installation I added the yt path to the
PATH environment variable.
The installation looks ok, and the command "yt --help" works. However,
when I try to load data, which worked with a previous installation, I get
this error:
Python 3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 09:53:17)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import yt
>>> yt.load("disk_mhdhdf5_chk_0020")
python:
/home/conda/feedstock_root/build_artifacts/libnetcdf_1535659474245/work/libsrc4/nc4var.c:431:
nc4_vararray_add: Assertion `var->varid == grp->vars.nelems' failed.
Aborted (core dumped)
Does anyone know what this means? I must have missed something in the
setup. I haven't used conda before.
Thanks!
Paco
Dear yt users,
We are currently testing the revived nightly builds of yt. It would be
enormously helpful to have some real-world testing before making it
official. And we need your help!
We have set up the system so that the latest development version of yt
could be installed from our custom anaconda channel using the command:
>>> conda install -c yt-project/label/dev yt
If you have a few minutes time, you could help testing doing the following:
1. Install yt using the command above in a fresh conda environment.
2. Try some simple yt scripts, like loading a dataset.
3. Report back here whether it is a success and whatever issues you have
encountered. Also include the system information (Linux, macOS, Windows)
and Python version (2.7, 3.5, 3.6, 3.7).
For people more developer-minded, we welcome your comments in the pull
request: yt-project/yt#2030 <https://github.com/yt-project/yt/pull/2030>.
Thanks in advance for your invaluable feedback!
Best regards,
Bili
hi all
i am trying to install rockstar, but make gives a lot of warning then it does work. this is the outcome of make lib in rockstar directory
https://justpaste.it/7d4x7
your input is highly appreciated!
thanks
cynthia
Cynthia Saad
Hi,
I write some new fields in yt/yt/fields named as XXX.py, but I have no idea about how to make it work correctly like yt's density, temperature etc which can be projected or sliced plots.
Hello Mat,
Ok. I will report it on the github site.
Cheers,
El jue., 13 sept. 2018 a las 11:01, <yt-users-request(a)python.org> escribió:
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> than "Re: Contents of yt-users digest..."
>
> Today's Topics:
>
> 1. Point function not working for negative coordinates
> (Guido granda muñoz)
> 2. Re: Point function not working for negative coordinates
> (Matthew Turk)
>
>
> ----------------------------------------------------------------------
>
> Date: Wed, 12 Sep 2018 17:47:31 -0500
> From: Guido granda muñoz <guidogranda(a)gmail.com>
> Subject: [yt-users] Point function not working for negative
> coordinates
> To: yt-users(a)python.org
> Message-ID:
> <
> CALOHZ_28Yh_4gVR53jZhdNUzCCM9C4PsU2-5UineUcyQdexGQA(a)mail.gmail.com>
> Content-Type: multipart/alternative;
> boundary="000000000000e2ae280575b46045"
>
> --000000000000e2ae280575b46045
> Content-Type: text/plain; charset="UTF-8"
>
> Hello yt users,
>
> I have been trying to obtain density values at different points using point
> data object. The problem is that this function does not work for negative
> coordinates regardless the fact that the computational domain contains
> those coordinates.
>
> This is the error I got:
>
> Entering folder ./lr_teq_p_3_nk4
> Using rho_0: 6.372606e-24
> Using 5.0 snapshots
> yt : [INFO ] 2018-09-12 17:34:34,371 Parameters: current_time
> = 0.0
> yt : [INFO ] 2018-09-12 17:34:34,371 Parameters: domain_dimensions
> = [256 256 256]
> yt : [INFO ] 2018-09-12 17:34:34,372 Parameters: domain_left_edge
> = [ -1.54283920e+19 -1.54283920e+19 -1.54283920e+19]
> yt : [INFO ] 2018-09-12 17:34:34,372 Parameters: domain_right_edge
> = [ 1.54283920e+19 1.54283920e+19 1.54283920e+19]
> yt : [INFO ] 2018-09-12 17:34:34,372 Parameters:
> cosmological_simulation = 0.0
> domain: [ 10.00000265 10.00000265 10.00000265] pc
> YTPoint (lr_hdf5_plt_cnt_0000): , p=[ 1. 1. -0.001] cm
> [] g/cm**3
> ---------------------------------------------------------------------------
> ValueError Traceback (most recent call last)
> /share/Part1/guido/w_profile2.py in <module>()
> 84 print(point)
> 85 print(point['gas','density'])
> ---> 86
> dens_array[snap_order,ipoint]=point['gas','density']
> 87 ipoint=ipoint+1
> 88 print("time :",time)
>
> ValueError: setting an array element with a sequence.
>
> As you can see, the point p=[ 1. 1. -0.001] cm belongs to the
> computational domain. When I only use positive coordinates the code runs
> well. Correct me if I am wrong, but I think this is a bug. Do you guys know
> another way to get values of any field at a fixed point?
>
> Cheers,
> --
> Guido
>
> --000000000000e2ae280575b46045
> Content-Type: text/html; charset="UTF-8"
> Content-Transfer-Encoding: quoted-printable
>
> <div dir=3D"ltr"><div dir=3D"ltr">Hello yt users,<div><br></div><div>I
> have=
> been trying to obtain density values at different points using point data
> =
> object. The problem is that this function does not work for negative
> coordi=
> nates regardless the fact that the computational domain contains those
> coor=
> dinates.</div><div><br></div><div>This is the error I
> got:</div><div><br></=
> div><div><div>Entering folder ./lr_teq_p_3_nk4</div><div>Using rho_0:
> 6.372=
> 606e-24=C2=A0</div><div>Using 5.0 snapshots</div><div>yt : [INFO=C2=A0 =C2=
> =A0 =C2=A0] 2018-09-12 17:34:34,371 Parameters: current_time=C2=A0 =C2=A0 =
> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =3D 0.0</div><div>yt : [INFO=C2=A0 =C2=
> =A0 =C2=A0] 2018-09-12 17:34:34,371 Parameters: domain_dimensions=C2=A0
> =C2=
> =A0 =C2=A0 =C2=A0 =C2=A0=3D [256 256 256]</div><div>yt : [INFO=C2=A0
> =C2=A0=
> =C2=A0] 2018-09-12 17:34:34,372 Parameters: domain_left_edge=C2=A0 =C2=A0
> =
> =C2=A0 =C2=A0 =C2=A0 =3D [ -1.54283920e+19=C2=A0 -1.54283920e+19=C2=A0
> -1.5=
> 4283920e+19]</div><div>yt : [INFO=C2=A0 =C2=A0 =C2=A0] 2018-09-12
> 17:34:34,=
> 372 Parameters: domain_right_edge=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=3D
> [=C2=
> =A0 1.54283920e+19=C2=A0 =C2=A01.54283920e+19=C2=A0
> =C2=A01.54283920e+19]</=
> div><div>yt : [INFO=C2=A0 =C2=A0 =C2=A0] 2018-09-12 17:34:34,372
> Parameters=
> : cosmological_simulation=C2=A0 =C2=A0=3D 0.0</div><div>domain: [
> 10.000002=
> 65=C2=A0 10.00000265=C2=A0 10.00000265] pc</div><div>YTPoint
> (lr_hdf5_plt_c=
> nt_0000): , p=3D[ 1.=C2=A0 =C2=A0 =C2=A01.=C2=A0 =C2=A0 -0.001]
> cm</div><di=
> v>[]
> g/cm**3</div><div>----------------------------------------------------=
> -----------------------</div><div>ValueError=C2=A0 =C2=A0 =C2=A0 =C2=A0
> =C2=
> =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =
> =C2=A0 Traceback (most recent call
> last)</div><div>/share/Part1/guido/w_pro=
> file2.py in <module>()</div><div>=C2=A0 =C2=A0 =C2=A084=C2=A0 =C2=A0
> =
> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
> =A0 print(point)</div><div>=C2=A0 =C2=A0 =C2=A085=C2=A0 =C2=A0 =C2=A0 =C2=
> =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
> print(po=
> int['gas','density'])</div><div>---> 86=C2=A0 =C2=A0
> =C2=
> =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
> d=
>
> ens_array[snap_order,ipoint]=3Dpoint['gas','density']</div>=
> <div>=C2=A0 =C2=A0 =C2=A087=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
> =C2=A0=
> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ipoint=3Dipoint+1</div><div>=C2=
> =A0 =C2=A0 =C2=A088=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0print("time
> :&quo=
> t;,time)</div><div><br></div><div>ValueError: setting an array element
> with=
> a sequence.</div><div><br></div><div>As you can see, the point p=3D[
> 1.=C2=
> =A0 =C2=A0 =C2=A01.=C2=A0 =C2=A0 -0.001] cm belongs to the computational
> do=
> main. When I only use positive coordinates the code runs well. Correct me
> i=
> f I am wrong, but I think this is a bug. Do you guys know another way to
> ge=
> t values of any field at a fixed
> point?</div><div><br></div><div>Cheers,</d=
> iv>-- <br><div dir=3D"ltr"
> class=3D"gmail_signature">Guido</div></div></div=
> ></div>
>
> --000000000000e2ae280575b46045--
>
> ------------------------------
>
> Date: Thu, 13 Sep 2018 10:53:29 -0500
> From: Matthew Turk <matthewturk(a)gmail.com>
> Subject: [yt-users] Re: Point function not working for negative
> coordinates
> To: Discussion of the yt analysis package <yt-users(a)python.org>
> Message-ID:
> <CALO3=5E21MrkThu+MQPK4EFsoBLBEybUNzF35bHRnDG=
> Y9f5gQ(a)mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Guido,
>
> This looks like a bug to me! Can you file an issue and we'll discuss
> there? I think I have an idea how to fix it, but having the issue to
> discuss would be great.
>
> https://github.com/yt-project/yt/issues/new
>
> -Matt
> On Wed, Sep 12, 2018 at 5:49 PM Guido granda muñoz
> <guidogranda(a)gmail.com> wrote:
> >
> > Hello yt users,
> >
> > I have been trying to obtain density values at different points using
> point data object. The problem is that this function does not work for
> negative coordinates regardless the fact that the computational domain
> contains those coordinates.
> >
> > This is the error I got:
> >
> > Entering folder ./lr_teq_p_3_nk4
> > Using rho_0: 6.372606e-24
> > Using 5.0 snapshots
> > yt : [INFO ] 2018-09-12 17:34:34,371 Parameters: current_time
> = 0.0
> > yt : [INFO ] 2018-09-12 17:34:34,371 Parameters: domain_dimensions
> = [256 256 256]
> > yt : [INFO ] 2018-09-12 17:34:34,372 Parameters: domain_left_edge
> = [ -1.54283920e+19 -1.54283920e+19 -1.54283920e+19]
> > yt : [INFO ] 2018-09-12 17:34:34,372 Parameters: domain_right_edge
> = [ 1.54283920e+19 1.54283920e+19 1.54283920e+19]
> > yt : [INFO ] 2018-09-12 17:34:34,372 Parameters:
> cosmological_simulation = 0.0
> > domain: [ 10.00000265 10.00000265 10.00000265] pc
> > YTPoint (lr_hdf5_plt_cnt_0000): , p=[ 1. 1. -0.001] cm
> > [] g/cm**3
> >
> ---------------------------------------------------------------------------
> > ValueError Traceback (most recent call
> last)
> > /share/Part1/guido/w_profile2.py in <module>()
> > 84 print(point)
> > 85 print(point['gas','density'])
> > ---> 86
> dens_array[snap_order,ipoint]=point['gas','density']
> > 87 ipoint=ipoint+1
> > 88 print("time :",time)
> >
> > ValueError: setting an array element with a sequence.
> >
> > As you can see, the point p=[ 1. 1. -0.001] cm belongs to the
> computational domain. When I only use positive coordinates the code runs
> well. Correct me if I am wrong, but I think this is a bug. Do you guys know
> another way to get values of any field at a fixed point?
> >
> > Cheers,
> > --
> > Guido
> > _______________________________________________
> > yt-users mailing list -- yt-users(a)python.org
> > To unsubscribe send an email to yt-users-leave(a)python.org
>
> ------------------------------
>
> 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 127, Issue 6
> ****************************************
>
--
Guido
Hello yt users,
I have been trying to obtain density values at different points using point
data object. The problem is that this function does not work for negative
coordinates regardless the fact that the computational domain contains
those coordinates.
This is the error I got:
Entering folder ./lr_teq_p_3_nk4
Using rho_0: 6.372606e-24
Using 5.0 snapshots
yt : [INFO ] 2018-09-12 17:34:34,371 Parameters: current_time
= 0.0
yt : [INFO ] 2018-09-12 17:34:34,371 Parameters: domain_dimensions
= [256 256 256]
yt : [INFO ] 2018-09-12 17:34:34,372 Parameters: domain_left_edge
= [ -1.54283920e+19 -1.54283920e+19 -1.54283920e+19]
yt : [INFO ] 2018-09-12 17:34:34,372 Parameters: domain_right_edge
= [ 1.54283920e+19 1.54283920e+19 1.54283920e+19]
yt : [INFO ] 2018-09-12 17:34:34,372 Parameters:
cosmological_simulation = 0.0
domain: [ 10.00000265 10.00000265 10.00000265] pc
YTPoint (lr_hdf5_plt_cnt_0000): , p=[ 1. 1. -0.001] cm
[] g/cm**3
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
/share/Part1/guido/w_profile2.py in <module>()
84 print(point)
85 print(point['gas','density'])
---> 86
dens_array[snap_order,ipoint]=point['gas','density']
87 ipoint=ipoint+1
88 print("time :",time)
ValueError: setting an array element with a sequence.
As you can see, the point p=[ 1. 1. -0.001] cm belongs to the
computational domain. When I only use positive coordinates the code runs
well. Correct me if I am wrong, but I think this is a bug. Do you guys know
another way to get values of any field at a fixed point?
Cheers,
--
Guido
