Problem when run yt dev in parallel on Blue Waters
by Pengfei Chen
Hi all,
I have trouble running yt in parallel on Blue Waters. I installed yt using
miniconda, the version of yt is
~/miniconda/lib $yt version
yt module located at:
/u/sciteam/madcpf/miniconda/lib/python2.7/site-packages/yt-3.3.dev0-py2.7-linux-x86_64.egg
The current version and changeset for the code is:
---
Version = 3.3-dev
Changeset = 90f900be7a36+ yt
Then with miniconda/bin in PATH I installed mpi4py-2.0.0. But when I tried
to make the following simple output in parallel, I get:
import yt
yt.enable_parallelism()
from yt.utilities.parallel_tools.parallel_analysis_interface import\
parallel_objects, communication_system
comm = communication_system.communicators[-1]
print comm.rank, comm.size
0 1
0 1
0 1
0 1
0 1
0 1
0 1
0 1
...
When I run a similar code but with yt-2.x also on Blue Waters, I get what I
expect:
7 16
15 16
6 16
9 16
11 16
8 16
0 16
4 16
...
I'm confused about it. Could anyone give me some suggestions please?
Thanks,
Pengfei
2 years, 7 months
rockstar question
by Robert Thompson
Hi yt users! I had two quick questions regarding yt’s Rockstar implementation. Within the data returned from the return_halos() method:
1) how would one determine parent/child relationship?
2) how would one determine which particles belong to which halo? The returned data has “num_p" and “p_start” variables, but I’m not sure if those indexes line up with the ordering in which I passed the particles in to the make_rockstar_fof() function.
Thanks!
-Robert Thompson
2 years, 11 months
load spherical polar coordinate data with mesh refinement in HDF5
by Jiang, Yanfei
Hi,
I have some data from a new version of Athena simulations. It is
in spherical polar coordinate with mesh refinement written in HDF5. The
data structure is similar to flash data but not the same. Does anyone have
suggestions to load such data to yt directly?
Thank you.
--
Yan-Fei Jiang
Einstein Fellow
Harvard-Smithsonian Center for Astrophysics
60 Garden Street, Cambridge MA USA 02138
2 years, 11 months
Covering Grid Dimensions: multiple refinement levels
by Carla Bernhardt
Dear YT Users,
To better understand covering_grid (or smoothed_covering_grid), can someone
explain what dimensions I should use when I have multiple levels of
refinement? If I have 1 level of refinement from AMR data, the dimensions
should be the same, I believe, but what if I have 2 or 3 levels of
refinement? Should the fixed resolution region then have dimensions of
dims*2^2 and dims*3^2 respectively?
Here is one example from a tutorial
<http://yt-project.org/doc/examining/low_level_inspection.html#examining-g...>
if that helps isolate my question:
all_data_level_2 = ds.covering_grid(level=2, left_edge=[0,0.0,0.0],
dims=ds.domain_dimensions * 2**2)
Thanks in advance,
Carla
2 years, 11 months
Inclination problem
by Sushilkumar
Dear Matt:
Pleas correct me if I am wrong but "off axis slices" takes slices of the
plot that is already plotted.
However, I would like to plot my data in a new coordinate frame (x`,y`,z`)
which is inclined at an angle of say alpha from the default (x,y,z) frame.
Or I would like to plot my data in a rotated frame (x`,y`,z`), which is
rotated at an angle of alpha from (x,y,z).
On Wed, Mar 30, 2016 at 5:01 PM, <yt-users-request(a)lists.spacepope.org>
wrote:
> Send yt-users mailing list submissions to
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>
> Today's Topics:
>
> 1. Re: load spherical polar coordinate data with mesh refinement
> in HDF5 (Jiang, Yanfei)
> 2. Re: load spherical polar coordinate data with mesh refinement
> in HDF5 (Matthew Turk)
> 3. Re: Inclination problem (Matthew Turk)
> 4. Re: load spherical polar coordinate data with mesh refinement
> in HDF5 (Jonah Miller)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 30 Mar 2016 15:49:26 -0400
> From: "Jiang, Yanfei" <yanfei.jiang(a)cfa.harvard.edu>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] load spherical polar coordinate data with mesh
> refinement in HDF5
> Message-ID:
> <
> CANixPav-VmbXfhNvmA5wb5gj19mF+-Ryq5YD-LrYrByDe3Ne7A(a)mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Jonah,
>
> I am able to load the data to yt now using load_amr_grids(). I notice
> that it can also set geometry to spherical. This is great. But to make life
> more complicate. Is it possible to let yt know that the grid is
> logarithmic? Currently, load_amr_grids() just take left and right edges of
> each block. I guess yt assumes the grid is uniform between left and right
> edges. Is it possible to provide arrays of coordinate values for each cell
> in each block?
>
> Thanks.
>
> On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller <
> jonah.maxwell.miller(a)gmail.com> wrote:
>
> > Hi Yan-Feng,
> >
> > I haven't tried it, but I think there is functionality for this. You can
> > use the load_amr_grids() function which can load amr data in Cartesian,
> > spherical, or polar coordinates. Here's the documentation:
> >
> >
> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy...
> >
> >
> >
> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.dat...
> >
> > Best,
> > Jonah
> >
> > On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
> yanfei.jiang(a)cfa.harvard.edu>
> > wrote:
> >
> >> Hi,
> >> I have some data from a new version of Athena simulations. It
> is
> >> in spherical polar coordinate with mesh refinement written in HDF5. The
> >> data structure is similar to flash data but not the same. Does anyone
> have
> >> suggestions to load such data to yt directly?
> >>
> >> Thank you.
> >> --
> >> Yan-Fei Jiang
> >>
> >> Einstein Fellow
> >> Harvard-Smithsonian Center for Astrophysics
> >> 60 Garden Street, Cambridge MA USA 02138
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users(a)lists.spacepope.org
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users(a)lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
> >
>
>
> --
> Yan-Fei Jiang
>
> Einstein Fellow
> Harvard-Smithsonian Center for Astrophysics
> 60 Garden Street, Cambridge MA USA 02138
> -------------- next part --------------
> An HTML attachment was scrubbed...
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> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2...
> >
>
> ------------------------------
>
> Message: 2
> Date: Wed, 30 Mar 2016 16:15:30 -0500
> From: Matthew Turk <matthewturk(a)gmail.com>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] load spherical polar coordinate data with mesh
> refinement in HDF5
> Message-ID:
> <CALO3=
> 5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA(a)mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Yanfei,
>
> This is possible -- but it will also slow some things down. You can
> use the load_hexahedral_mesh function, and there're examples of this.
> This takes away some of the optimizations that regular grids can do,
> but we're hoping to add them back in shortly. Like the other
> functions it too takes a geometry argument.
>
> -Matt
>
> On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei
> <yanfei.jiang(a)cfa.harvard.edu> wrote:
> > Hi Jonah,
> >
> > I am able to load the data to yt now using load_amr_grids(). I notice
> > that it can also set geometry to spherical. This is great. But to make
> life
> > more complicate. Is it possible to let yt know that the grid is
> logarithmic?
> > Currently, load_amr_grids() just take left and right edges of each
> block. I
> > guess yt assumes the grid is uniform between left and right edges. Is it
> > possible to provide arrays of coordinate values for each cell in each
> block?
> >
> > Thanks.
> >
> > On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller
> > <jonah.maxwell.miller(a)gmail.com> wrote:
> >>
> >> Hi Yan-Feng,
> >>
> >> I haven't tried it, but I think there is functionality for this. You can
> >> use the load_amr_grids() function which can load amr data in Cartesian,
> >> spherical, or polar coordinates. Here's the documentation:
> >>
> >>
> >>
> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy...
> >>
> >>
> >>
> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.dat...
> >>
> >> Best,
> >> Jonah
> >>
> >> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
> yanfei.jiang(a)cfa.harvard.edu>
> >> wrote:
> >>>
> >>> Hi,
> >>> I have some data from a new version of Athena simulations. It
> is
> >>> in spherical polar coordinate with mesh refinement written in HDF5.
> The data
> >>> structure is similar to flash data but not the same. Does anyone have
> >>> suggestions to load such data to yt directly?
> >>>
> >>> Thank you.
> >>> --
> >>> Yan-Fei Jiang
> >>>
> >>> Einstein Fellow
> >>> Harvard-Smithsonian Center for Astrophysics
> >>> 60 Garden Street, Cambridge MA USA 02138
> >>> _______________________________________________
> >>> yt-users mailing list
> >>> yt-users(a)lists.spacepope.org
> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>
> >>
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users(a)lists.spacepope.org
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>
> >
> >
> >
> > --
> > Yan-Fei Jiang
> >
> > Einstein Fellow
> > Harvard-Smithsonian Center for Astrophysics
> > 60 Garden Street, Cambridge MA USA 02138
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users(a)lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 30 Mar 2016 16:16:22 -0500
> From: Matthew Turk <matthewturk(a)gmail.com>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] Inclination problem
> Message-ID:
> <CALO3=5HMB=
> joejr6BBh+zdxkwGzJS2NPrkK9tvMJnbch5-7BgQ(a)mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi SK,
>
> I'm not sure I totally understand, but if you have an inclination
> angle you can use this directly in yt in the off axis slices and so
> on. They typically take a vector, but you should be able to convert
> one to the other.
>
> -Matt
>
> On Tue, Mar 29, 2016 at 1:37 PM, Sushilkumar <sushil.sush19us(a)gmail.com>
> wrote:
> > Dear yt:
> >
> > I am trying to numerically solve the region around a pulsar. Now since
> > pulsar is an inclined rotator with inclination angle between rotation
> axis
> > and dipole axis I would like to include in my yt script.
> >
> > My original code written in FORTRAN incorporated this inclination but how
> > would I incorporate it into my visualization using yt without changing my
> > data.
> >
> > Could you suggest ways for the same?
> >
> > The google drive link to my script (streamline.py) and streamline plot
> > (streamline_t000.png) is included
> >
> > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc
> >
> > Thanks in advance
> >
> > On Tue, Mar 29, 2016 at 12:54 PM, <yt-users-request(a)lists.spacepope.org>
> > wrote:
> >>
> >> Send yt-users mailing list submissions to
> >> yt-users(a)lists.spacepope.org
> >>
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> or, via email, send a message with subject or body 'help' to
> >> yt-users-request(a)lists.spacepope.org
> >>
> >> You can reach the person managing the list at
> >> yt-users-owner(a)lists.spacepope.org
> >>
> >> When replying, please edit your Subject line so it is more specific
> >> than "Re: Contents of yt-users digest..."
> >>
> >>
> >> Today's Topics:
> >>
> >> 1. Re: gadget onto unigrid (Carla Bernhardt)
> >> 2. Re: gadget onto unigrid (Matthew Turk)
> >>
> >>
> >> ----------------------------------------------------------------------
> >>
> >> Message: 1
> >> Date: Tue, 29 Mar 2016 15:55:27 +0200
> >> From: Carla Bernhardt <carla.j.bernhardt(a)gmail.com>
> >> To: Discussion of the yt analysis package
> >> <yt-users(a)lists.spacepope.org>
> >> Subject: Re: [yt-users] gadget onto unigrid
> >> Message-ID:
> >>
> >> <CAFK0O=2vH24ViqeZ5QS3DY3uido0kEaF=UhyGS_beuiUMbw7Ag(a)mail.gmail.com>
> >> Content-Type: text/plain; charset="utf-8"
> >>
> >> Hi All,
> >>
> >> A follow-up question: In using arbitrary_grid (but with enzo data), how
> >> does one then extract a field of an arbitrary_grid? I tried
> >> arbgrid["density"] as I have done with a smoothed_covering_grid object,
> >> but
> >> it does not work (here is the traceback <http://pastebin.com/afgcgpp0>
> I
> >> got).
> >>
> >> Thanks,
> >> Carla
> >>
> >> 2016-02-23 17:21 GMT+01:00 Matthew Turk <matthewturk(a)gmail.com>:
> >>
> >> > Hi Desika,
> >> >
> >> > Yup, this can be done reasonably easily using either the
> >> > .arbitrary_grid object (which was designed for this) or the interface
> >> > to the arbitrary grid that's in the development version, which is
> >> > ds.r[ ... ] where the ... is some combination of bounds and steps.
> >> >
> >> > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid
> >> >
> >> >
> >> >
> http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-...
> >> >
> >> > On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan
> >> > <desika.narayanan(a)gmail.com> wrote:
> >> > > Hi All,
> >> > >
> >> > > Is it possible to deposit the particles from a gadget data set onto
> a
> >> > > uniform grid in yt? Or, could it be possible to trick the octree
> >> > deposition
> >> > > into doing it by forcing no refinements, but some sort of native
> grid
> >> > > resolution?
> >> > >
> >> > > thanks,
> >> > > desika
> >> > >
> >> > >
> >> > > _______________________________________________
> >> > > yt-users mailing list
> >> > > yt-users(a)lists.spacepope.org
> >> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> > >
> >> > _______________________________________________
> >> > yt-users mailing list
> >> > yt-users(a)lists.spacepope.org
> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >
> >> -------------- next part --------------
> >> An HTML attachment was scrubbed...
> >> URL:
> >> <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2...
> >
> >>
> >> ------------------------------
> >>
> >> Message: 2
> >> Date: Tue, 29 Mar 2016 08:57:08 -0500
> >> From: Matthew Turk <matthewturk(a)gmail.com>
> >> To: Discussion of the yt analysis package
> >> <yt-users(a)lists.spacepope.org>
> >> Subject: Re: [yt-users] gadget onto unigrid
> >> Message-ID:
> >>
> >> <CALO3=5HR=zLHujWKgLpqwei_98vBOjpYvQ4m8nnUFR=P098utA(a)mail.gmail.com>
> >> Content-Type: text/plain; charset=UTF-8
> >>
> >> Hi Carla,
> >>
> >> This functionality was recently implemented and is in the development
> >> version, but not yet in the stable. We're hoping for a release very
> >> shortly, but you can also try the dev version if you'd like!
> >>
> >> -Matt
> >>
> >> On Tue, Mar 29, 2016 at 8:55 AM, Carla Bernhardt
> >> <carla.j.bernhardt(a)gmail.com> wrote:
> >> > Hi All,
> >> >
> >> > A follow-up question: In using arbitrary_grid (but with enzo data),
> how
> >> > does
> >> > one then extract a field of an arbitrary_grid? I tried
> >> > arbgrid["density"] as
> >> > I have done with a smoothed_covering_grid object, but it does not work
> >> > (here
> >> > is the traceback I got).
> >> >
> >> > Thanks,
> >> > Carla
> >> >
> >> > 2016-02-23 17:21 GMT+01:00 Matthew Turk <matthewturk(a)gmail.com>:
> >> >>
> >> >> Hi Desika,
> >> >>
> >> >> Yup, this can be done reasonably easily using either the
> >> >> .arbitrary_grid object (which was designed for this) or the interface
> >> >> to the arbitrary grid that's in the development version, which is
> >> >> ds.r[ ... ] where the ... is some combination of bounds and steps.
> >> >>
> >> >> http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid
> >> >>
> >> >>
> >> >>
> http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-...
> >> >>
> >> >> On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan
> >> >> <desika.narayanan(a)gmail.com> wrote:
> >> >> > Hi All,
> >> >> >
> >> >> > Is it possible to deposit the particles from a gadget data set
> onto a
> >> >> > uniform grid in yt? Or, could it be possible to trick the octree
> >> >> > deposition
> >> >> > into doing it by forcing no refinements, but some sort of native
> grid
> >> >> > resolution?
> >> >> >
> >> >> > thanks,
> >> >> > desika
> >> >> >
> >> >> >
> >> >> > _______________________________________________
> >> >> > yt-users mailing list
> >> >> > yt-users(a)lists.spacepope.org
> >> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >> >
> >> >> _______________________________________________
> >> >> yt-users mailing list
> >> >> yt-users(a)lists.spacepope.org
> >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > yt-users mailing list
> >> > yt-users(a)lists.spacepope.org
> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >
> >>
> >>
> >> ------------------------------
> >>
> >> Subject: Digest Footer
> >>
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users(a)lists.spacepope.org
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>
> >>
> >> ------------------------------
> >>
> >> End of yt-users Digest, Vol 97, Issue 34
> >> ****************************************
> >
> >
> >
> >
> > --
> > SK2
> >
> > "Claiming that something can move faster than light is a good
> > conversation-stopper in physics. People edge away from you in cocktail
> > parties; friends never return phone calls. You just don?t mess with
> Albert
> > Einstein."
> >
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users(a)lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 30 Mar 2016 18:01:04 -0400
> From: Jonah Miller <jonah.maxwell.miller(a)gmail.com>
> To: yt-users(a)lists.spacepope.org
> Subject: Re: [yt-users] load spherical polar coordinate data with mesh
> refinement in HDF5
> Message-ID: <56FC4CA0.4030403(a)gmail.com>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Hi Yanfei,
>
> To add to Matt's comment. Here is the documentation for using
> load_hexahedral_mesh.
>
> http://yt-project.org/doc/examining/loading_data.html#semi-structured-gri...
>
> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.dat...
>
> Best,
> Jonah
>
> On 16-03-30 05:15 PM, Matthew Turk wrote:
> > Hi Yanfei,
> >
> > This is possible -- but it will also slow some things down. You can
> > use the load_hexahedral_mesh function, and there're examples of this.
> > This takes away some of the optimizations that regular grids can do,
> > but we're hoping to add them back in shortly. Like the other
> > functions it too takes a geometry argument.
> >
> > -Matt
> >
> > On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei
> > <yanfei.jiang(a)cfa.harvard.edu> wrote:
> >> Hi Jonah,
> >>
> >> I am able to load the data to yt now using load_amr_grids(). I
> notice
> >> that it can also set geometry to spherical. This is great. But to make
> life
> >> more complicate. Is it possible to let yt know that the grid is
> logarithmic?
> >> Currently, load_amr_grids() just take left and right edges of each
> block. I
> >> guess yt assumes the grid is uniform between left and right edges. Is it
> >> possible to provide arrays of coordinate values for each cell in each
> block?
> >>
> >> Thanks.
> >>
> >> On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller
> >> <jonah.maxwell.miller(a)gmail.com> wrote:
> >>> Hi Yan-Feng,
> >>>
> >>> I haven't tried it, but I think there is functionality for this. You
> can
> >>> use the load_amr_grids() function which can load amr data in Cartesian,
> >>> spherical, or polar coordinates. Here's the documentation:
> >>>
> >>>
> >>>
> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy...
> >>>
> >>>
> >>>
> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.dat...
> >>>
> >>> Best,
> >>> Jonah
> >>>
> >>> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
> yanfei.jiang(a)cfa.harvard.edu>
> >>> wrote:
> >>>> Hi,
> >>>> I have some data from a new version of Athena simulations.
> It is
> >>>> in spherical polar coordinate with mesh refinement written in HDF5.
> The data
> >>>> structure is similar to flash data but not the same. Does anyone have
> >>>> suggestions to load such data to yt directly?
> >>>>
> >>>> Thank you.
> >>>> --
> >>>> Yan-Fei Jiang
> >>>>
> >>>> Einstein Fellow
> >>>> Harvard-Smithsonian Center for Astrophysics
> >>>> 60 Garden Street, Cambridge MA USA 02138
> >>>> _______________________________________________
> >>>> yt-users mailing list
> >>>> yt-users(a)lists.spacepope.org
> >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>
> >>> _______________________________________________
> >>> yt-users mailing list
> >>> yt-users(a)lists.spacepope.org
> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>
> >>
> >>
> >> --
> >> Yan-Fei Jiang
> >>
> >> Einstein Fellow
> >> Harvard-Smithsonian Center for Astrophysics
> >> 60 Garden Street, Cambridge MA USA 02138
> >>
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users(a)lists.spacepope.org
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>
> > _______________________________________________
> > yt-users mailing list
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>
--
*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.**"*
2 years, 12 months
Inclination problem
by Sushilkumar
Dear yt:
I am trying to numerically solve the region around a pulsar. Now since
pulsar is an inclined rotator with inclination angle between rotation axis
and dipole axis I would like to include in my yt script.
My original code written in FORTRAN incorporated this inclination but how
would I incorporate it into my visualization using yt without changing my
data.
Could you suggest ways for the same?
The google drive link to my script (streamline.py) and streamline plot
(streamline_t000.png) is included
https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc
Thanks in advance
On Tue, Mar 29, 2016 at 12:54 PM, <yt-users-request(a)lists.spacepope.org>
wrote:
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> Today's Topics:
>
> 1. Re: gadget onto unigrid (Carla Bernhardt)
> 2. Re: gadget onto unigrid (Matthew Turk)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 29 Mar 2016 15:55:27 +0200
> From: Carla Bernhardt <carla.j.bernhardt(a)gmail.com>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] gadget onto unigrid
> Message-ID:
> <CAFK0O=2vH24ViqeZ5QS3DY3uido0kEaF=
> UhyGS_beuiUMbw7Ag(a)mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi All,
>
> A follow-up question: In using arbitrary_grid (but with enzo data), how
> does one then extract a field of an arbitrary_grid? I tried
> arbgrid["density"] as I have done with a smoothed_covering_grid object, but
> it does not work (here is the traceback <http://pastebin.com/afgcgpp0> I
> got).
>
> Thanks,
> Carla
>
> 2016-02-23 17:21 GMT+01:00 Matthew Turk <matthewturk(a)gmail.com>:
>
> > Hi Desika,
> >
> > Yup, this can be done reasonably easily using either the
> > .arbitrary_grid object (which was designed for this) or the interface
> > to the arbitrary grid that's in the development version, which is
> > ds.r[ ... ] where the ... is some combination of bounds and steps.
> >
> > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid
> >
> >
> http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-...
> >
> > On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan
> > <desika.narayanan(a)gmail.com> wrote:
> > > Hi All,
> > >
> > > Is it possible to deposit the particles from a gadget data set onto a
> > > uniform grid in yt? Or, could it be possible to trick the octree
> > deposition
> > > into doing it by forcing no refinements, but some sort of native grid
> > > resolution?
> > >
> > > thanks,
> > > desika
> > >
> > >
> > > _______________________________________________
> > > yt-users mailing list
> > > yt-users(a)lists.spacepope.org
> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> > >
> > _______________________________________________
> > yt-users mailing list
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> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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> ------------------------------
>
> Message: 2
> Date: Tue, 29 Mar 2016 08:57:08 -0500
> From: Matthew Turk <matthewturk(a)gmail.com>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] gadget onto unigrid
> Message-ID:
> <CALO3=5HR=zLHujWKgLpqwei_98vBOjpYvQ4m8nnUFR=
> P098utA(a)mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Carla,
>
> This functionality was recently implemented and is in the development
> version, but not yet in the stable. We're hoping for a release very
> shortly, but you can also try the dev version if you'd like!
>
> -Matt
>
> On Tue, Mar 29, 2016 at 8:55 AM, Carla Bernhardt
> <carla.j.bernhardt(a)gmail.com> wrote:
> > Hi All,
> >
> > A follow-up question: In using arbitrary_grid (but with enzo data), how
> does
> > one then extract a field of an arbitrary_grid? I tried
> arbgrid["density"] as
> > I have done with a smoothed_covering_grid object, but it does not work
> (here
> > is the traceback I got).
> >
> > Thanks,
> > Carla
> >
> > 2016-02-23 17:21 GMT+01:00 Matthew Turk <matthewturk(a)gmail.com>:
> >>
> >> Hi Desika,
> >>
> >> Yup, this can be done reasonably easily using either the
> >> .arbitrary_grid object (which was designed for this) or the interface
> >> to the arbitrary grid that's in the development version, which is
> >> ds.r[ ... ] where the ... is some combination of bounds and steps.
> >>
> >> http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid
> >>
> >>
> http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-...
> >>
> >> On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan
> >> <desika.narayanan(a)gmail.com> wrote:
> >> > Hi All,
> >> >
> >> > Is it possible to deposit the particles from a gadget data set onto a
> >> > uniform grid in yt? Or, could it be possible to trick the octree
> >> > deposition
> >> > into doing it by forcing no refinements, but some sort of native grid
> >> > resolution?
> >> >
> >> > thanks,
> >> > desika
> >> >
> >> >
> >> > _______________________________________________
> >> > yt-users mailing list
> >> > yt-users(a)lists.spacepope.org
> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users(a)lists.spacepope.org
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
> >
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users(a)lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
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>
> ------------------------------
>
> End of yt-users Digest, Vol 97, Issue 34
> ****************************************
>
--
*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.**"*
2 years, 12 months
gadget onto unigrid
by Desika Narayanan
Hi All,
Is it possible to deposit the particles from a gadget data set onto a
uniform grid in yt? Or, could it be possible to trick the octree
deposition into doing it by forcing no refinements, but some sort of native
grid resolution?
thanks,
desika
2 years, 12 months
Inclined rotator
by Sushilkumar
Dear yt:
I am trying to numerically solve the region around a pulsar. Now since
pulsar is an inclined rotator with inclination angle between rotation axis
and dipole axis I would like to include in my yt script.
My original code written in FORTRAN incorporated this inclination but how
would I incorporate it into my visualization using yt without changing my
data.
Could you suggest ways for the same?
The google drive link to my script (streamline.py) and streamline plot
(streamline_t000.png) is included
https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc
Thanks in advance
On Sun, Mar 27, 2016 at 1:07 PM, <yt-users-request(a)lists.spacepope.org>
wrote:
> Send yt-users mailing list submissions to
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> or, via email, send a message with subject or body 'help' to
> yt-users-request(a)lists.spacepope.org
>
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of yt-users digest..."
>
>
> Today's Topics:
>
> 1. Re: Plotting mesh cells (cell edges) (Matthew Turk)
> 2. Re: Plotting mesh cells (cell edges) (Matthew Turk)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 27 Mar 2016 09:42:44 -0500
> From: Matthew Turk <matthewturk(a)gmail.com>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] Plotting mesh cells (cell edges)
> Message-ID:
> <CALO3=
> 5Hpndt85jra405LCQ4KP1ugYyX_GkAv-6dWXn865u2HPw(a)mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Xinsheng,
>
> Right now this isn't possible -- it tends not to be something that comes up
> too often. But, I think it should be relatively straightforward. I've
> added an issue for it, and I'm going to try to take a look at it tomorrow.
>
>
> https://bitbucket.org/yt_analysis/yt/issues/1198/add-ability-to-plot-cell...
>
> I've marked it a blocker for our next release.
>
> -Matt
>
> On Sun, Mar 27, 2016 at 1:00 AM, Shawn Qin <xsqin(a)uw.edu> wrote:
>
> > Hello,
> >
> > Does anybody know if yt can plot mesh cells (cell edges) besides edges of
> > patches in a 2D slice plot (with AMR grid data), like the one below (only
> > cell edges in some patches were plotted)? I was able to plot edges of
> > different AMR grid patches with the *annotate_grids* method of
> > *OffAxisSlicePlot* object. I checked all annotate_* methods but didn't
> > find any method that seems to do this job?
> >
> >
> > I am using yt 3.2.3.
> >
> > Any suggestions and discussion will be appreciated.
> >
> > Thank you!
> >
> > Best,
> >
> > --
> > ~~~~~~~~~~~~~~~~~
> >
> > Xinsheng Qin
> > Ph.D. candidate
> > Department of Civil and Environmental Engineering
> > University of Washingtonxsqin(a)uw.edu
> >
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users(a)lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
> >
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> ------------------------------
>
> Message: 2
> Date: Sun, 27 Mar 2016 10:36:52 -0500
> From: Matthew Turk <matthewturk(a)gmail.com>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] Plotting mesh cells (cell edges)
> Message-ID:
> <CALO3=5HO7gQEF=71Y+6ObG=
> uCwd2KzjnDivLdO6QpbLi4ALAQw(a)mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> I've found a few minutes and issued a pull request:
>
>
> https://bitbucket.org/yt_analysis/yt/pull-requests/2088/adding-annotate_c...
>
>
> On Sun, Mar 27, 2016 at 9:42 AM, Matthew Turk <matthewturk(a)gmail.com>
> wrote:
>
> > Hi Xinsheng,
> >
> > Right now this isn't possible -- it tends not to be something that comes
> > up too often. But, I think it should be relatively straightforward.
> I've
> > added an issue for it, and I'm going to try to take a look at it
> tomorrow.
> >
> >
> >
> https://bitbucket.org/yt_analysis/yt/issues/1198/add-ability-to-plot-cell...
> >
> > I've marked it a blocker for our next release.
> >
> > -Matt
> >
> > On Sun, Mar 27, 2016 at 1:00 AM, Shawn Qin <xsqin(a)uw.edu> wrote:
> >
> >> Hello,
> >>
> >> Does anybody know if yt can plot mesh cells (cell edges) besides edges
> of
> >> patches in a 2D slice plot (with AMR grid data), like the one below
> (only
> >> cell edges in some patches were plotted)? I was able to plot edges of
> >> different AMR grid patches with the *annotate_grids* method of
> >> *OffAxisSlicePlot* object. I checked all annotate_* methods but didn't
> >> find any method that seems to do this job?
> >>
> >>
> >> I am using yt 3.2.3.
> >>
> >> Any suggestions and discussion will be appreciated.
> >>
> >> Thank you!
> >>
> >> Best,
> >>
> >> --
> >> ~~~~~~~~~~~~~~~~~
> >>
> >> Xinsheng Qin
> >> Ph.D. candidate
> >> Department of Civil and Environmental Engineering
> >> University of Washingtonxsqin(a)uw.edu
> >>
> >>
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users(a)lists.spacepope.org
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>
> >>
> >
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> Subject: Digest Footer
>
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>
> ------------------------------
>
> End of yt-users Digest, Vol 97, Issue 32
> ****************************************
>
--
*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.**"*
2 years, 12 months
Plotting mesh cells (cell edges)
by Shawn Qin
Hello,
Does anybody know if yt can plot mesh cells (cell edges) besides edges
of patches in a 2D slice plot (with AMR grid data), like the one below
(only cell edges in some patches were plotted)? I was able to plot
edges of different AMR grid patches with the *annotate_grids* method of
*OffAxisSlicePlot* object. I checked all annotate_* methods but didn't
find any method that seems to do this job?
I am using yt 3.2.3.
Any suggestions and discussion will be appreciated.
Thank you!
Best,
--
~~~~~~~~~~~~~~~~~
Xinsheng Qin
Ph.D. candidate
Department of Civil and Environmental Engineering
University of Washington
xsqin(a)uw.edu
�PNG
2 years, 12 months
non-uniform Cartesian grid volume rendering
by Samuel Jones
Dear yt-users,
I have had generally a very smooth ride in the past using yt for volume
rendering of data on a uniform Cartesian grid. Now, however, I am trying
to do similar things with data on a non-uniform Cartesian grid, having
loaded it in with load_hexahedral_mesh.
I managed to get embree, pyembree built together with yt version
3.3-dev. I can create the hexahedral dataset with no problem (at least
no errors), but when I try to create a scene in which to do some volume
rendering I get the error copied below. I think I must doing something
wrong but I don't know what!
Thanks and Best Wishes,
Sam
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-11-e24c1c1430d9> in <module>()
----> 1 sc = yt.create_scene(ds,'lset')
/home/swj/softs/yt/yt/visualization/volume_rendering/volume_rendering.pyc in
create_scene(data_source, field, lens_type)
72
73 if hasattr(data_source.ds.index, "meshes"):
---> 74 source = MeshSource(data_source, field=field)
75 else:
76 source = VolumeSource(data_source, field=field)
/home/swj/softs/yt/yt/visualization/volume_rendering/render_source.pyc
in __init__(self, data_source, field)
369
370 self.scene = mesh_traversal.YTEmbreeScene()
--> 371 self.build_mesh()
372
373 def cmap():
/home/swj/softs/yt/yt/visualization/volume_rendering/render_source.pyc
in build_mesh(self)
421 """
422 ftype, fname = self.field
--> 423 mesh_id = int(ftype[-1]) - 1
424 index = self.data_source.ds.index
425 offset = index.meshes[mesh_id]._index_offset
ValueError: invalid literal for int() with base 10: 'm'
*****************************************
some debug:
>
/home/swj/softs/yt/yt/visualization/volume_rendering/render_source.py(423)build_mesh()
422 ftype, fname = self.field
--> 423 mesh_id = int(ftype[-1]) - 1
424 index = self.data_source.ds.index
ipdb> print ftype
stream
ipdb> self.field
('stream', 'lset')
ipdb> exit
--
Samuel Jones
Physik stellarer Objekte | Physics of Stellar Objects
Heidelberger Institut für Theoretische Studien | Heidelberg Institute
for Theoretical Studies
samuel.jones(a)h-its.org
3 years
