Mailman 3 June 2017 - yt-users

yt with gadget
by Aaron 16 Jun '17

16 Jun '17

Hi everyone, I’m pretty new to this package and primarily use it to load Gadget snapshots, I’m wondering if it can in turn generate snapshots (used as initial conditions) , given all the initial conditions.

3 2

Getting colored multi-surfaces 3D models in sketchfab
by Yuanze Luo 16 Jun '17

16 Jun '17

Dear Ms.Jill Naiman, I'm one of the yt users and I'm referring to your script on this webpage <http://yt-project.org/doc/visualizing/sketchfab.html> in order to get a multi-surfaces 3D model of galaxies like the one you made <https://skfb.ly/y96Y>. However, when I zipped my .obj and .mtl file and uploaded to sketchfab, my model was just plain white, no other colors. Attached is a screenshot of the code that I was using and I wish to know what's wrong with it and how to get a model like yours. Hope you can find a time to look at it and tell me my problems. Sorry about any trouble this might bring and thank you in advance for your time and patience. Sincerely, Yuanze Luo luo35(a)illinois.edu

2 1

find_point function with EnzoDataset
by Carla Bernhardt 16 Jun '17

16 Jun '17

Hi yt-users, I am trying to use the find_point() function as described as a low-level data inspection example here <http://yt-project.org/doc/examining/low_level_inspection.html#finding-data-…>. However, when I try the given example, I get this error: >>> gs,gi=ds.find_point((0.5, 0.5, 0.5)) Traceback (most recent call last): File "<stdin>", line 1, in <module> AttributeError: 'EnzoDataset' object has no attribute 'find_point' If this function doesn't work with an EnzoDataset, what does it work with? I am ultimately trying to find the highest AMR level at a given point. Cheers, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg

2 2

yt for analyzing Millennium simulation data
by Ankit Singh 14 Jun '17

14 Jun '17

Hi all, For some work, I had to use Millenium Simulation data. I have a catalog of halos with their positions, and I wanted to get the halos in voids. Can yt be of any use for such an analysis? The thing that makes it difficult is periodic boundary conditions it doesn't allow you to use KDtree straight away. Please help, Thanks, With Regards, Ankit

2 1

Workaround for creating OffAxisProjectionPlots with a data_source
by Setton, David Jonathan - (davidsetton) 13 Jun '17

13 Jun '17

Hi all, I'm trying to make some plots of a simulation with a temperature cut projected along the viewing frame from the earth, which is not one of the natural xyz coordinates in the simulation. I have been doing this using the cut_region() function on my full data set. I can create projections along x, y, and z using yt.ProjectionPlot with a data_source keyword, but the feature does not appear to be implemented for Off Axis projections. Has anyone developed a workaround for this? Best, David Setton

2 1

Physical constants list
by Sam Patrick 13 Jun '17

13 Jun '17

Hi, I'm relatively new to yt and was wondering if there was any resource outlining the names of all physical constants programed into yt and how to access them i.e: Newton's constant: G Boltzmann constant; kboltz Speed of light: c etc. specifically I need the name for the mass of hydrogen used within the program but I can foresee such a list being very useful in the future. many thanks, Sam P

3 2

Normalized axis
by Sushilkumar 09 Jun '17

09 Jun '17

On Fri, Jun 9, 2017 at 9:11 AM, <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. Normalized axis (Sushilkumar) > 2. Re: Normalized axis (Nathan Goldbaum) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 9 Jun 2017 09:08:36 -0500 > From: Sushilkumar <sushil.sush19us(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: [yt-users] Normalized axis > Message-ID: > <CAKARaKWnE99yKGhb8yQTQY7zYkwe+oBNbqJtPRUHcZ2KT=f=dQ@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear yt > > How do I label the axis of a plot in normalized values? > > On my plot I want to label my x and y axis in terms of the vertical line. > > Do I use convert_to_plot under streamlines? > > Link to the plot and script is below > > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc > > Thanks in advance > > > > On Thu, Jun 8, 2017 at 1:01 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: selecting data by refinement level (Klaus Weide) > > 2. Re: selecting data by refinement level (Matthew Turk) > > 3. Re: selecting data by refinement level (Nathan Goldbaum) > > 4. Re: selecting data by refinement level (Klaus Weide) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Wed, 7 Jun 2017 13:53:49 -0500 (CDT) > > From: Klaus Weide <klaus(a)flash.uchicago.edu> > > To: Discussion of the yt analysis package > > <yt-users(a)lists.spacepope.org> > > Subject: Re: [yt-users] selecting data by refinement level > > Message-ID: <Pine.LNX.4.64.1706071350010.1322(a)flash.uchicago.edu> > > Content-Type: TEXT/PLAIN; charset=US-ASCII > > > > On Wed, 7 Jun 2017, Matthew Turk wrote: > > > > > Hi Klaus, > > > > > > Whoops, I said "grid_collection" but I meant "data_collection". > > > > Thanks Matt. I have not tried the 'collection of grids' approach yet, but > > the following does what I want: > > > > ds = yt.load(dump_path) > > > > ad = ds.all_data() > > if fine_only: > > maxreflevel = ad.index.grid_levels.max() > > print '*** Filtering data so that only FLASH refinement level > > {} cells are used'.format(maxreflevel+1) > > ad.min_level = maxreflevel > > ad.max_level = maxreflevel > > print 'These cover a volume of %s' % ad['cell_volume'].sum() > > # ..... > > data = {} > > data['dens'] = ad['dens'].to_ndarray() > > # ..... > > > > > > Klaus > > > > > > ------------------------------ > > > > Message: 2 > > Date: Wed, 7 Jun 2017 13:56:51 -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] selecting data by refinement level > > Message-ID: > > <CALO3=5HbBWfPj8hf5KEwMq1CiU932Q_u+=hHcBzYirQzGYCm3A@mail. > > gmail.com> > > Content-Type: text/plain; charset="UTF-8" > > > > Great! As a quick note, you can use `.d` as shorthand for > > `to_ndarray()`. The YTArray it returns is a subclass of ndarray, so > > should in general be usable in both ways; as you probably figured out, > > if you do any manipulation of individual elements it adds overhead and > > (often frustrating, but hopefully ultimately helpful), restrictions on > > combining incorrect units unless you look at it as a strict ndarray. > > > > On Wed, Jun 7, 2017 at 1:53 PM, Klaus Weide <klaus(a)flash.uchicago.edu> > > wrote: > > > On Wed, 7 Jun 2017, Matthew Turk wrote: > > > > > >> Hi Klaus, > > >> > > >> Whoops, I said "grid_collection" but I meant "data_collection". > > > > > > Thanks Matt. I have not tried the 'collection of grids' approach yet, > but > > > the following does what I want: > > > > > > ds = yt.load(dump_path) > > > > > > ad = ds.all_data() > > > if fine_only: > > > maxreflevel = ad.index.grid_levels.max() > > > print '*** Filtering data so that only FLASH refinement > > level {} cells are used'.format(maxreflevel+1) > > > ad.min_level = maxreflevel > > > ad.max_level = maxreflevel > > > print 'These cover a volume of %s' % > ad['cell_volume'].sum() > > > # ..... > > > data = {} > > > data['dens'] = ad['dens'].to_ndarray() > > > # ..... > > > > > > > > > Klaus > > > _______________________________________________ > > > yt-users mailing list > > > yt-users(a)lists.spacepope.org > > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > > ------------------------------ > > > > Message: 3 > > Date: Wed, 7 Jun 2017 12:00:44 -0700 > > From: Nathan Goldbaum <nathan12343(a)gmail.com> > > To: Discussion of the yt analysis package > > <yt-users(a)lists.spacepope.org> > > Subject: Re: [yt-users] selecting data by refinement level > > Message-ID: > > <CAJXewO=gk4Fqrh_fKxmgKVu9vgu53TVQd0P0-Ra5wBBSPm-_Gg@mail. > > gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > On Wed, Jun 7, 2017 at 11:56 AM, Matthew Turk <matthewturk(a)gmail.com> > > wrote: > > > > > Great! As a quick note, you can use `.d` as shorthand for > > > `to_ndarray()`. The YTArray it returns is a subclass of ndarray, so > > > should in general be usable in both ways; as you probably figured out, > > > if you do any manipulation of individual elements it adds overhead and > > > (often frustrating, but hopefully ultimately helpful), restrictions on > > > combining incorrect units unless you look at it as a strict ndarray. > > > > > > > One tiny note: > > > > YTArray.d is short for YTArray.ndarray_view(), which returns a view onto > > the array. This doesn't copy the underlying data. > > > > YTArray.to_ndarray() is equivalend to YTArray.value or YTArray.v, whcih > > returns an ndarray containing a copy of the underlying array data. > Getting > > a copy sometimes adds overhead. > > > > Choosing whether or now you want a copy comes down to what exactly you > are > > doing, since copying adds overhead, but it also prevents silently > > overwriting data in an unexpected, nonlocal fashion. > > > > > > > > > > On Wed, Jun 7, 2017 at 1:53 PM, Klaus Weide <klaus(a)flash.uchicago.edu> > > > wrote: > > > > On Wed, 7 Jun 2017, Matthew Turk wrote: > > > > > > > >> Hi Klaus, > > > >> > > > >> Whoops, I said "grid_collection" but I meant "data_collection". > > > > > > > > Thanks Matt. I have not tried the 'collection of grids' approach yet, > > but > > > > the following does what I want: > > > > > > > > ds = yt.load(dump_path) > > > > > > > > ad = ds.all_data() > > > > if fine_only: > > > > maxreflevel = ad.index.grid_levels.max() > > > > print '*** Filtering data so that only FLASH refinement > > > level {} cells are used'.format(maxreflevel+1) > > > > ad.min_level = maxreflevel > > > > ad.max_level = maxreflevel > > > > print 'These cover a volume of %s' % > > ad['cell_volume'].sum() > > > > # ..... > > > > data = {} > > > > data['dens'] = ad['dens'].to_ndarray() > > > > # ..... > > > > > > > > > > > > Klaus > > > > _______________________________________________ > > > > 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/20170607/6450bc9f/attachment.html> > > > > ------------------------------ > > > > Message: 4 > > Date: Wed, 7 Jun 2017 14:45:52 -0500 (CDT) > > From: Klaus Weide <klaus(a)flash.uchicago.edu> > > To: Discussion of the yt analysis package > > <yt-users(a)lists.spacepope.org> > > Subject: Re: [yt-users] selecting data by refinement level > > Message-ID: <Pine.LNX.4.64.1706071443510.1322(a)flash.uchicago.edu> > > Content-Type: TEXT/PLAIN; charset=US-ASCII > > > > On Wed, 7 Jun 2017, Nathan Goldbaum wrote: > > > On Wed, Jun 7, 2017 at 11:56 AM, Matthew Turk <matthewturk(a)gmail.com> > > wrote: > > > > > > > Great! As a quick note, you can use `.d` as shorthand for > > > > `to_ndarray()`. > > > > > One tiny note: > > > > > > YTArray.d is short for YTArray.ndarray_view(), which returns a view > onto > > > the array. This doesn't copy the underlying data. > > > > Matt and Nathan, > > > > Thanks for the additional info, I think it's very useful to know. > > > > Klaus > > > > > > ------------------------------ > > > > 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 112, Issue 5 > > **************************************** > > > > > > -- > *SK2* > > *"**Claiming that something can move faster than light is a good > conversation-stopper in physics. People edge away from you in cocktail > parties; friends never return phone calls. You just don?t mess with Albert > Einstein.**"* > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope. > org/attachments/20170609/f3381db8/attachment-0001.htm> > > ------------------------------ > > Message: 2 > Date: Fri, 09 Jun 2017 14:10:49 +0000 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Normalized axis > Message-ID: > <CAJXewOk5YFHL90v0dRwJZL5M5OzQypAh6iNabrUm-W7EJ0BaMg@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Try to use plot.set_axes_unit("unitary"). > On Fri, Jun 9, 2017 at 9:08 AM Sushilkumar <sushil.sush19us(a)gmail.com> > wrote: > > > Dear yt > > > > How do I label the axis of a plot in normalized values? > > > > On my plot I want to label my x and y axis in terms of the vertical line. > > > > Do I use convert_to_plot under streamlines? > > > > Link to the plot and script is below > > > > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc > > > > Thanks in advance > > > > > > > > On Thu, Jun 8, 2017 at 1:01 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: selecting data by refinement level (Klaus Weide) > >> 2. Re: selecting data by refinement level (Matthew Turk) > >> 3. Re: selecting data by refinement level (Nathan Goldbaum) > >> 4. Re: selecting data by refinement level (Klaus Weide) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Wed, 7 Jun 2017 13:53:49 -0500 (CDT) > >> From: Klaus Weide <klaus(a)flash.uchicago.edu> > >> To: Discussion of the yt analysis package > >> <yt-users(a)lists.spacepope.org> > >> Subject: Re: [yt-users] selecting data by refinement level > >> Message-ID: <Pine.LNX.4.64.1706071350010.1322(a)flash.uchicago.edu> > >> Content-Type: TEXT/PLAIN; charset=US-ASCII > >> > >> On Wed, 7 Jun 2017, Matthew Turk wrote: > >> > >> > Hi Klaus, > >> > > >> > Whoops, I said "grid_collection" but I meant "data_collection". > >> > >> Thanks Matt. I have not tried the 'collection of grids' approach yet, > but > >> the following does what I want: > >> > >> ds = yt.load(dump_path) > >> > >> ad = ds.all_data() > >> if fine_only: > >> maxreflevel = ad.index.grid_levels.max() > >> print '*** Filtering data so that only FLASH refinement > level > >> {} cells are used'.format(maxreflevel+1) > >> ad.min_level = maxreflevel > >> ad.max_level = maxreflevel > >> print 'These cover a volume of %s' % ad['cell_volume'].sum() > >> # ..... > >> data = {} > >> data['dens'] = ad['dens'].to_ndarray() > >> # ..... > >> > >> > >> Klaus > >> > >> > >> ------------------------------ > >> > >> Message: 2 > >> Date: Wed, 7 Jun 2017 13:56:51 -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] selecting data by refinement level > >> Message-ID: > >> <CALO3=5HbBWfPj8hf5KEwMq1CiU932Q_u+= > >> hHcBzYirQzGYCm3A(a)mail.gmail.com> > >> Content-Type: text/plain; charset="UTF-8" > >> > >> Great! As a quick note, you can use `.d` as shorthand for > >> `to_ndarray()`. The YTArray it returns is a subclass of ndarray, so > >> should in general be usable in both ways; as you probably figured out, > >> if you do any manipulation of individual elements it adds overhead and > >> (often frustrating, but hopefully ultimately helpful), restrictions on > >> combining incorrect units unless you look at it as a strict ndarray. > >> > >> On Wed, Jun 7, 2017 at 1:53 PM, Klaus Weide <klaus(a)flash.uchicago.edu> > >> wrote: > >> > On Wed, 7 Jun 2017, Matthew Turk wrote: > >> > > >> >> Hi Klaus, > >> >> > >> >> Whoops, I said "grid_collection" but I meant "data_collection". > >> > > >> > Thanks Matt. I have not tried the 'collection of grids' approach yet, > >> but > >> > the following does what I want: > >> > > >> > ds = yt.load(dump_path) > >> > > >> > ad = ds.all_data() > >> > if fine_only: > >> > maxreflevel = ad.index.grid_levels.max() > >> > print '*** Filtering data so that only FLASH refinement > >> level {} cells are used'.format(maxreflevel+1) > >> > ad.min_level = maxreflevel > >> > ad.max_level = maxreflevel > >> > print 'These cover a volume of %s' % > ad['cell_volume'].sum() > >> > # ..... > >> > data = {} > >> > data['dens'] = ad['dens'].to_ndarray() > >> > # ..... > >> > > >> > > >> > Klaus > >> > _______________________________________________ > >> > yt-users mailing list > >> > yt-users(a)lists.spacepope.org > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > >> ------------------------------ > >> > >> Message: 3 > >> Date: Wed, 7 Jun 2017 12:00:44 -0700 > >> From: Nathan Goldbaum <nathan12343(a)gmail.com> > >> To: Discussion of the yt analysis package > >> <yt-users(a)lists.spacepope.org> > >> Subject: Re: [yt-users] selecting data by refinement level > >> Message-ID: > >> <CAJXewO= > >> gk4Fqrh_fKxmgKVu9vgu53TVQd0P0-Ra5wBBSPm-_Gg(a)mail.gmail.com> > >> Content-Type: text/plain; charset="utf-8" > >> > >> On Wed, Jun 7, 2017 at 11:56 AM, Matthew Turk <matthewturk(a)gmail.com> > >> wrote: > >> > >> > Great! As a quick note, you can use `.d` as shorthand for > >> > `to_ndarray()`. The YTArray it returns is a subclass of ndarray, so > >> > should in general be usable in both ways; as you probably figured out, > >> > if you do any manipulation of individual elements it adds overhead and > >> > (often frustrating, but hopefully ultimately helpful), restrictions on > >> > combining incorrect units unless you look at it as a strict ndarray. > >> > > >> > >> One tiny note: > >> > >> YTArray.d is short for YTArray.ndarray_view(), which returns a view onto > >> the array. This doesn't copy the underlying data. > >> > >> YTArray.to_ndarray() is equivalend to YTArray.value or YTArray.v, whcih > >> returns an ndarray containing a copy of the underlying array data. > Getting > >> a copy sometimes adds overhead. > >> > >> Choosing whether or now you want a copy comes down to what exactly you > are > >> doing, since copying adds overhead, but it also prevents silently > >> overwriting data in an unexpected, nonlocal fashion. > >> > >> > >> > > >> > On Wed, Jun 7, 2017 at 1:53 PM, Klaus Weide <klaus(a)flash.uchicago.edu > > > >> > wrote: > >> > > On Wed, 7 Jun 2017, Matthew Turk wrote: > >> > > > >> > >> Hi Klaus, > >> > >> > >> > >> Whoops, I said "grid_collection" but I meant "data_collection". > >> > > > >> > > Thanks Matt. I have not tried the 'collection of grids' approach > yet, > >> but > >> > > the following does what I want: > >> > > > >> > > ds = yt.load(dump_path) > >> > > > >> > > ad = ds.all_data() > >> > > if fine_only: > >> > > maxreflevel = ad.index.grid_levels.max() > >> > > print '*** Filtering data so that only FLASH refinement > >> > level {} cells are used'.format(maxreflevel+1) > >> > > ad.min_level = maxreflevel > >> > > ad.max_level = maxreflevel > >> > > print 'These cover a volume of %s' % > >> ad['cell_volume'].sum() > >> > > # ..... > >> > > data = {} > >> > > data['dens'] = ad['dens'].to_ndarray() > >> > > # ..... > >> > > > >> > > > >> > > Klaus > >> > > _______________________________________________ > >> > > 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/20170607/6450bc9f/attachment.html > >> > > >> > >> ------------------------------ > >> > >> Message: 4 > >> Date: Wed, 7 Jun 2017 14:45:52 -0500 (CDT) > >> From: Klaus Weide <klaus(a)flash.uchicago.edu> > >> To: Discussion of the yt analysis package > >> <yt-users(a)lists.spacepope.org> > >> Subject: Re: [yt-users] selecting data by refinement level > >> Message-ID: <Pine.LNX.4.64.1706071443510.1322(a)flash.uchicago.edu> > >> Content-Type: TEXT/PLAIN; charset=US-ASCII > >> > >> On Wed, 7 Jun 2017, Nathan Goldbaum wrote: > >> > On Wed, Jun 7, 2017 at 11:56 AM, Matthew Turk <matthewturk(a)gmail.com> > >> wrote: > >> > > >> > > Great! As a quick note, you can use `.d` as shorthand for > >> > > `to_ndarray()`. > >> > >> > One tiny note: > >> > > >> > YTArray.d is short for YTArray.ndarray_view(), which returns a view > onto > >> > the array. This doesn't copy the underlying data. > >> > >> Matt and Nathan, > >> > >> Thanks for the additional info, I think it's very useful to know. > >> > >> Klaus > >> > >> > >> ------------------------------ > >> > >> 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 112, Issue 5 > >> **************************************** > >> > > > > > > > > -- > > *SK2* > > > > *"**Claiming that something can move faster than light is a good > > conversation-stopper in physics. People edge away from you in cocktail > > parties; friends never return phone calls. You just don?t mess with > Albert > > Einstein.**"* > > > > _______________________________________________ > > 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/20170609/f3281531/attachment.htm> > > ------------------------------ > > 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 112, Issue 6 > **************************************** > -- *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 2

Normalized axis
by Sushilkumar 09 Jun '17

09 Jun '17

Dear yt How do I label the axis of a plot in normalized values? On my plot I want to label my x and y axis in terms of the vertical line. Do I use convert_to_plot under streamlines? Link to the plot and script is below https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc Thanks in advance On Thu, Jun 8, 2017 at 1:01 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: selecting data by refinement level (Klaus Weide) > 2. Re: selecting data by refinement level (Matthew Turk) > 3. Re: selecting data by refinement level (Nathan Goldbaum) > 4. Re: selecting data by refinement level (Klaus Weide) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 7 Jun 2017 13:53:49 -0500 (CDT) > From: Klaus Weide <klaus(a)flash.uchicago.edu> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] selecting data by refinement level > Message-ID: <Pine.LNX.4.64.1706071350010.1322(a)flash.uchicago.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > On Wed, 7 Jun 2017, Matthew Turk wrote: > > > Hi Klaus, > > > > Whoops, I said "grid_collection" but I meant "data_collection". > > Thanks Matt. I have not tried the 'collection of grids' approach yet, but > the following does what I want: > > ds = yt.load(dump_path) > > ad = ds.all_data() > if fine_only: > maxreflevel = ad.index.grid_levels.max() > print '*** Filtering data so that only FLASH refinement level > {} cells are used'.format(maxreflevel+1) > ad.min_level = maxreflevel > ad.max_level = maxreflevel > print 'These cover a volume of %s' % ad['cell_volume'].sum() > # ..... > data = {} > data['dens'] = ad['dens'].to_ndarray() > # ..... > > > Klaus > > > ------------------------------ > > Message: 2 > Date: Wed, 7 Jun 2017 13:56:51 -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] selecting data by refinement level > Message-ID: > <CALO3=5HbBWfPj8hf5KEwMq1CiU932Q_u+=hHcBzYirQzGYCm3A@mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Great! As a quick note, you can use `.d` as shorthand for > `to_ndarray()`. The YTArray it returns is a subclass of ndarray, so > should in general be usable in both ways; as you probably figured out, > if you do any manipulation of individual elements it adds overhead and > (often frustrating, but hopefully ultimately helpful), restrictions on > combining incorrect units unless you look at it as a strict ndarray. > > On Wed, Jun 7, 2017 at 1:53 PM, Klaus Weide <klaus(a)flash.uchicago.edu> > wrote: > > On Wed, 7 Jun 2017, Matthew Turk wrote: > > > >> Hi Klaus, > >> > >> Whoops, I said "grid_collection" but I meant "data_collection". > > > > Thanks Matt. I have not tried the 'collection of grids' approach yet, but > > the following does what I want: > > > > ds = yt.load(dump_path) > > > > ad = ds.all_data() > > if fine_only: > > maxreflevel = ad.index.grid_levels.max() > > print '*** Filtering data so that only FLASH refinement > level {} cells are used'.format(maxreflevel+1) > > ad.min_level = maxreflevel > > ad.max_level = maxreflevel > > print 'These cover a volume of %s' % ad['cell_volume'].sum() > > # ..... > > data = {} > > data['dens'] = ad['dens'].to_ndarray() > > # ..... > > > > > > Klaus > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > Message: 3 > Date: Wed, 7 Jun 2017 12:00:44 -0700 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] selecting data by refinement level > Message-ID: > <CAJXewO=gk4Fqrh_fKxmgKVu9vgu53TVQd0P0-Ra5wBBSPm-_Gg@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > On Wed, Jun 7, 2017 at 11:56 AM, Matthew Turk <matthewturk(a)gmail.com> > wrote: > > > Great! As a quick note, you can use `.d` as shorthand for > > `to_ndarray()`. The YTArray it returns is a subclass of ndarray, so > > should in general be usable in both ways; as you probably figured out, > > if you do any manipulation of individual elements it adds overhead and > > (often frustrating, but hopefully ultimately helpful), restrictions on > > combining incorrect units unless you look at it as a strict ndarray. > > > > One tiny note: > > YTArray.d is short for YTArray.ndarray_view(), which returns a view onto > the array. This doesn't copy the underlying data. > > YTArray.to_ndarray() is equivalend to YTArray.value or YTArray.v, whcih > returns an ndarray containing a copy of the underlying array data. Getting > a copy sometimes adds overhead. > > Choosing whether or now you want a copy comes down to what exactly you are > doing, since copying adds overhead, but it also prevents silently > overwriting data in an unexpected, nonlocal fashion. > > > > > > On Wed, Jun 7, 2017 at 1:53 PM, Klaus Weide <klaus(a)flash.uchicago.edu> > > wrote: > > > On Wed, 7 Jun 2017, Matthew Turk wrote: > > > > > >> Hi Klaus, > > >> > > >> Whoops, I said "grid_collection" but I meant "data_collection". > > > > > > Thanks Matt. I have not tried the 'collection of grids' approach yet, > but > > > the following does what I want: > > > > > > ds = yt.load(dump_path) > > > > > > ad = ds.all_data() > > > if fine_only: > > > maxreflevel = ad.index.grid_levels.max() > > > print '*** Filtering data so that only FLASH refinement > > level {} cells are used'.format(maxreflevel+1) > > > ad.min_level = maxreflevel > > > ad.max_level = maxreflevel > > > print 'These cover a volume of %s' % > ad['cell_volume'].sum() > > > # ..... > > > data = {} > > > data['dens'] = ad['dens'].to_ndarray() > > > # ..... > > > > > > > > > Klaus > > > _______________________________________________ > > > 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/20170607/6450bc9f/attachment.html> > > ------------------------------ > > Message: 4 > Date: Wed, 7 Jun 2017 14:45:52 -0500 (CDT) > From: Klaus Weide <klaus(a)flash.uchicago.edu> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] selecting data by refinement level > Message-ID: <Pine.LNX.4.64.1706071443510.1322(a)flash.uchicago.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > On Wed, 7 Jun 2017, Nathan Goldbaum wrote: > > On Wed, Jun 7, 2017 at 11:56 AM, Matthew Turk <matthewturk(a)gmail.com> > wrote: > > > > > Great! As a quick note, you can use `.d` as shorthand for > > > `to_ndarray()`. > > > One tiny note: > > > > YTArray.d is short for YTArray.ndarray_view(), which returns a view onto > > the array. This doesn't copy the underlying data. > > Matt and Nathan, > > Thanks for the additional info, I think it's very useful to know. > > Klaus > > > ------------------------------ > > 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 112, Issue 5 > **************************************** > -- *SK2* *"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*

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selecting data by refinement level
by Klaus Weide 07 Jun '17

07 Jun '17

Hi all, I have recently started using yt to for processing some FLASH results. Here is something that I think should be easy, but I haven't found an obvious and simple way in the documentation. I would like to analyze only cells (blocks) that are at a specific refinement level (let's say the highest) and discard all other cells (blocks). Is there an interface for defining a region by refinement level(s), immediately after loading an AMR file? I know I have access to cell properties like 'dx', 'dy' and could select cells based on that, but hopefully there is a more direct (and perhaps more efficient) way. Klaus

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Re: [yt-users] reading the fields correctly (ramses-rt)
by sacielo 05 Jun '17

05 Jun '17

Hi Nathan, thanks for your reply. I had no idea this issue existed already, but perhaps I can think of some simple solution. I have been checking with some true ramses-rt expert, and we are quite confident we can do this. News will (hopefully) follow soon. Best, On Wed, May 31, 2017 at 11:39 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. reading the fields correctly (ramses-rt) (sacielo) > 2. Re: reading the fields correctly (ramses-rt) (Nathan Goldbaum) > 3. Covering GIZMO data to uniform grid (???) > 4. Re: Covering GIZMO data to uniform grid (Nathan Goldbaum) > 5. Re: Covering GIZMO data to uniform grid (???) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 31 May 2017 21:01:17 +0200 > From: sacielo <sacielo(a)gmail.com> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] reading the fields correctly (ramses-rt) > Message-ID: > <CALAgqdLMTbUv1L+BPW=n-D4K3jo-bNZi01pKm9rkyirKkMZ99A@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I'm experiencing a little trouble in reading some RAMSES files which > include radiative transfer. > In this (broadly used) implementation some of the fields do not follow the > order they have classical RAMSES files; e.g. the pressure field is later in > the fields list. Indeed when I read the files those fields do not have the > correct content. > > Can someone please suggest a possible workaround? For instance a plugin for > this kind of files, if it exists, or suggest how I could swap the fields, > or rename them with the correct name? > I do not want simply to create new fields, without correcting the default > ones, as all derived fields (and possibly other valuable yt features) would > not work properly. > > Thank you very much! > > Best, > > Salvatore > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope. > org/attachments/20170531/ada41771/attachment-0001.htm> > > ------------------------------ > > Message: 2 > Date: Wed, 31 May 2017 14:13:07 -0500 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] reading the fields correctly (ramses-rt) > Message-ID: > <CAJXewOkKBdcXp00fXYBxSs2cBGFiVUJeb8g5Op1NoL1OSQkzpA@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Salvatore, > > I think we'll need to add support for these data formats to yt itself. > > Before we moved to github there were some attempts to add support for more > ramses fields in these pull requests: > > https://bitbucket.org/yt_analysis/yt/pull-requests/1464 > https://bitbucket.org/yt_analysis/yt/pull-requests/2139 > https://bitbucket.org/yt_analysis/yt/pull-requests/2499 > https://bitbucket.org/yt_analysis/yt/pull-requests/2500 > > Unfortunately none of those efforts proceeded to the point where we could > merge the code in. > > If you'd be interested in working on this, I think it would be a great > initial contribution to yt. > > If you're not interested in adding support for this, then we could at least > open an issue to track this feature request: > > https://github.com/yt-project/yt/issues/new > > It would also be nice if you could include some sample datasets that > someone who is interested in working on this but does not have access to > ramses-rt could use to debug with while working on this feature. > > In the end yt's support for data formats is limited by what sorts of data > the developers who have worked on any given part of the codebase have had > access to. Unfortunately given the culture of astronomical simulation > codes, that sometimes means we do not support all possible versions of a > given data format simply because we were not aware of that subset of the > data format when we initially added support. > > Hope that helps, > > Nathan > > On Wed, May 31, 2017 at 2:01 PM, sacielo <sacielo(a)gmail.com> wrote: > > > Hi all, > > > > I'm experiencing a little trouble in reading some RAMSES files which > > include radiative transfer. > > In this (broadly used) implementation some of the fields do not follow > the > > order they have classical RAMSES files; e.g. the pressure field is later > in > > the fields list. Indeed when I read the files those fields do not have > the > > correct content. > > > > Can someone please suggest a possible workaround? For instance a plugin > > for this kind of files, if it exists, or suggest how I could swap the > > fields, or rename them with the correct name? > > I do not want simply to create new fields, without correcting the default > > ones, as all derived fields (and possibly other valuable yt features) > would > > not work properly. > > > > Thank you very much! > > > > Best, > > > > Salvatore > > > > _______________________________________________ > > 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/20170531/8f143504/attachment-0001.htm> > > ------------------------------ > > Message: 3 > Date: Thu, 1 Jun 2017 05:11:28 +0800 > From: ??? <setsuna(a)phys.tw> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] Covering GIZMO data to uniform grid > Message-ID: > <CAEtGJOwBwxmcUxb4QTG_gwXbxQrmwiEx-8enFVn8L7ZC- > sMrtw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello yt-commuinty, > > I was trying to use yt to analyse GIZMO data. > Is there a function which can translate GIZMO gas data,particle0, to > uniform grid with neutral hydrogen,velocity,temperature.etc? > I know the "deposit " field and covering_grid in yt, but "deposit" isn't > uniform and covering_grid is designed for grid-like data.. > > Thank you! > Edward > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope. > org/attachments/20170601/c99f249c/attachment-0001.htm> > > ------------------------------ > > Message: 4 > Date: Wed, 31 May 2017 21:14:03 +0000 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Covering GIZMO data to uniform grid > Message-ID: > <CAJXewOkYxpiOixKJbbDGPJYXPhtgfkudN0zjptQS2V5QX9nCLA@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > The covering grid should work with deposit fields. > > You could also look at the arbitrary_grid, which is a little bit less > restrictive than covering_grid about the resolution and left and right > edge. > > > On Wed, May 31, 2017 at 4:11 PM ??? <setsuna(a)phys.tw> wrote: > > > Hello yt-commuinty, > > > > I was trying to use yt to analyse GIZMO data. > > Is there a function which can translate GIZMO gas data,particle0, to > > uniform grid with neutral hydrogen,velocity,temperature.etc? > > I know the "deposit " field and covering_grid in yt, but "deposit" isn't > > uniform and covering_grid is designed for grid-like data.. > > > > Thank you! > > Edward > > _______________________________________________ > > 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/20170531/105b3190/attachment-0001.htm> > > ------------------------------ > > Message: 5 > Date: Thu, 1 Jun 2017 05:39:43 +0800 > From: ??? <setsuna(a)phys.tw> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Covering GIZMO data to uniform grid > Message-ID: > <CAEtGJOzMpv7HVmHU=nRnLt7nbcjeNaRKFh+bEDreM_4-n95v3w@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Nathan! > > Do you mean that I should put deposit fields instead of GIZMO data into > covering grid/ arbitrary_grid? > > 2017-06-01 5:14 GMT+08:00 Nathan Goldbaum <nathan12343(a)gmail.com>: > > > The covering grid should work with deposit fields. > > > > You could also look at the arbitrary_grid, which is a little bit less > > restrictive than covering_grid about the resolution and left and right > edge. > > > > > > On Wed, May 31, 2017 at 4:11 PM ??? <setsuna(a)phys.tw> wrote: > > > >> Hello yt-commuinty, > >> > >> I was trying to use yt to analyse GIZMO data. > >> Is there a function which can translate GIZMO gas data,particle0, to > >> uniform grid with neutral hydrogen,velocity,temperature.etc? > >> I know the "deposit " field and covering_grid in yt, but "deposit" > isn't > >> uniform and covering_grid is designed for grid-like data.. > >> > >> Thank you! > >> Edward > >> _______________________________________________ > >> 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/20170601/f6cd25ef/attachment.htm> > > ------------------------------ > > 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 111, Issue 51 > ***************************************** > -- Salvatore

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