[yt-users] yt-users Digest, Vol 78, Issue 39
Professor Maller
amaller at citytech.cuny.edu
Fri Aug 15 07:54:20 PDT 2014
Hi Matt,
ds.field_info.create_cooling_fields("") done directly after loading gives
an error no field_info. I do a
ds.field_list first to so that ds.field_info exists, then
ds.field_info.create_cooling_fields("") gives no error, but also no changes
that I can see. That is nothing is added to ds.derived_field_lists and
doing dd=ds.all_data()
HI=dd[('gas','HI')]
gives could not find field '('gas','HI')'
For others, I'm trying to get the ionization state information from the
cooling??.dat files, this run has no ionization information in the hydro
output files.
Thanks,
Ari
On Fri, Aug 15, 2014 at 4:21 AM, <yt-users-request at lists.spacepope.org>
wrote:
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> Today's Topics:
>
> 1. Re: yt-users Digest, Vol 78, Issue 38 (Professor Maller)
> 2. Re: yt-users Digest, Vol 78, Issue 38 (Matthew Turk)
> 3. " cannot import name YTDomainOverflow" after hg update to an
> earlier version (Hao Wang)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 14 Aug 2014 14:56:22 -0400
> From: Professor Maller <amaller at citytech.cuny.edu>
> To: yt-users at lists.spacepope.org
> Subject: Re: [yt-users] yt-users Digest, Vol 78, Issue 38
> Message-ID:
> <CACCSjdMFbhvsBhpH3ybzvW=
> dEGSkMRYBetsJG-deSEjyiqztHg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Matt,
>
> Those fields are not in my derived field list. That is
> ds.derived_field_list. Do I have to add them in some way? Or is there a way
> to check if yt didn't find the cooling??.dat files?
>
> Thanks,
>
> Ari
>
>
> On Thu, Aug 14, 2014 at 1:54 PM, <yt-users-request at lists.spacepope.org>
> wrote:
>
> > Send yt-users mailing list submissions to
> > yt-users at lists.spacepope.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
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> > or, via email, send a message with subject or body 'help' to
> > yt-users-request at lists.spacepope.org
> >
> > You can reach the person managing the list at
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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. ionization states in ramses data sets (Professor Maller)
> > 2. Re: ionization states in ramses data sets (Geoffrey So)
> > 3. Re: ionization states in ramses data sets (Matthew Turk)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 14 Aug 2014 13:12:11 -0400
> > From: Professor Maller <amaller at citytech.cuny.edu>
> > To: yt-users at lists.spacepope.org
> > Subject: [yt-users] ionization states in ramses data sets
> > Message-ID:
> > <
> > CACCSjdOxDp+Mmgae1XLYJJvC7vJn52Xu59ppUA+p0mq7Fggz8A at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi,
> >
> > Does anyone have code to create derived fields of ionization states, e.g.
> > HI, for ramses data sets? If that's a no, does anyone have an example
> of a
> > derived field where you have to read in a table and interpolate the field
> > values.
> >
> > Thanks,
> >
> > Ari
> > -------------- next part --------------
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> > >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Thu, 14 Aug 2014 10:19:49 -0700
> > From: Geoffrey So <gsiisg at gmail.com>
> > To: Discussion of the yt analysis package
> > <yt-users at lists.spacepope.org>
> > Subject: Re: [yt-users] ionization states in ramses data sets
> > Message-ID:
> > <
> > CAM-dO+DM+ygbGg3GG9vrxjSn+JM9mGGgHDXA1UEJu1KYpnJJqw at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi,
> >
> > according to
> > http://yt-project.org/docs/2.6/analyzing/creating_derived_fields.html?
> >
> > what worked for me for enzo data is the following
> >
> > def _HINeutralFraction(field, data):
> > return data['HI_Density']/(data['HI_Density']+data['HII_Density'])
> >
> > add_field('HINeutralFraction',function=_HINeutralFraction,
> > units=r"\rho_\mathrm{HI}/\rho_\mathrm{H}")
> >
> > unless there's something strange with ramses dataset, the above should
> > work.
> >
> > From
> > G.S.
> >
> >
> > On Thu, Aug 14, 2014 at 10:12 AM, Professor Maller <
> > amaller at citytech.cuny.edu> wrote:
> >
> > > Hi,
> > >
> > > Does anyone have code to create derived fields of ionization states,
> e.g.
> > > HI, for ramses data sets? If that's a no, does anyone have an example
> > of a
> > > derived field where you have to read in a table and interpolate the
> field
> > > values.
> > >
> > > Thanks,
> > >
> > > Ari
> > >
> > > _______________________________________________
> > > yt-users mailing list
> > > yt-users at lists.spacepope.org
> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> > >
> > >
> > -------------- next part --------------
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> > >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Thu, 14 Aug 2014 12:22:16 -0500
> > From: Matthew Turk <matthewturk at gmail.com>
> > To: Discussion of the yt analysis package
> > <yt-users at lists.spacepope.org>
> > Subject: Re: [yt-users] ionization states in ramses data sets
> > Message-ID:
> > <CALO3=
> > 5HE+5eFNfXaWqJ_ApFCZeE_Sy73EEj+O5y7CuqMiVQ9sQ at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi Ari,
> >
> > My reading of yt/frontends/ramses/fields.py is that this should be
> > implemented already, using the cooling_%05i.dat files. If it's able
> > to find those files, it will create the appropriate derived fields
> > from them -- specifically, I think it can do Electron, HI, HII, HeI,
> > HeII, and HeIII. Is it not creating those?
> >
> > On Thu, Aug 14, 2014 at 12:12 PM, Professor Maller
> > <amaller at citytech.cuny.edu> wrote:
> > > Hi,
> > >
> > > Does anyone have code to create derived fields of ionization states,
> e.g.
> > > HI, for ramses data sets? If that's a no, does anyone have an example
> > of a
> > > derived field where you have to read in a table and interpolate the
> field
> > > values.
> > >
> > > Thanks,
> > >
> > > Ari
> > >
> > > _______________________________________________
> > > yt-users mailing list
> > > yt-users at lists.spacepope.org
> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> > >
> >
> >
> > ------------------------------
> >
> > Subject: Digest Footer
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
> >
> > ------------------------------
> >
> > End of yt-users Digest, Vol 78, Issue 38
> > ****************************************
> >
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>
> ------------------------------
>
> Message: 2
> Date: Thu, 14 Aug 2014 14:05:04 -0500
> From: Matthew Turk <matthewturk at gmail.com>
> To: Discussion of the yt analysis package
> <yt-users at lists.spacepope.org>
> Subject: Re: [yt-users] yt-users Digest, Vol 78, Issue 38
> Message-ID:
> <CALO3=
> 5EBSnthcHi+SzWTvWvmTbj7751MjPQ_+tVK4+GDes2OHA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Ari,
>
> Looks to me like it may actually not be enabled by default for some
> reason. Can you try calling:
>
> ds.field_info.create_cooling_fields("")
>
> and seeing if that adds the correct fields? If so, I'll update the
> code to do this automatically.
>
> -Matt
>
> On Thu, Aug 14, 2014 at 1:56 PM, Professor Maller
> <amaller at citytech.cuny.edu> wrote:
> > Hi Matt,
> >
> > Those fields are not in my derived field list. That is
> > ds.derived_field_list. Do I have to add them in some way? Or is there a
> way
> > to check if yt didn't find the cooling??.dat files?
> >
> > Thanks,
> >
> > Ari
> >
> >
> > On Thu, Aug 14, 2014 at 1:54 PM, <yt-users-request at lists.spacepope.org>
> > wrote:
> >>
> >> Send yt-users mailing list submissions to
> >> yt-users at 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 at lists.spacepope.org
> >>
> >> You can reach the person managing the list at
> >> yt-users-owner at 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. ionization states in ramses data sets (Professor Maller)
> >> 2. Re: ionization states in ramses data sets (Geoffrey So)
> >> 3. Re: ionization states in ramses data sets (Matthew Turk)
> >>
> >>
> >> ----------------------------------------------------------------------
> >>
> >> Message: 1
> >> Date: Thu, 14 Aug 2014 13:12:11 -0400
> >> From: Professor Maller <amaller at citytech.cuny.edu>
> >> To: yt-users at lists.spacepope.org
> >> Subject: [yt-users] ionization states in ramses data sets
> >> Message-ID:
> >>
> >> <CACCSjdOxDp+Mmgae1XLYJJvC7vJn52Xu59ppUA+p0mq7Fggz8A at mail.gmail.com>
> >> Content-Type: text/plain; charset="utf-8"
> >>
> >> Hi,
> >>
> >> Does anyone have code to create derived fields of ionization states,
> e.g.
> >> HI, for ramses data sets? If that's a no, does anyone have an example
> of
> >> a
> >> derived field where you have to read in a table and interpolate the
> field
> >> values.
> >>
> >> Thanks,
> >>
> >> Ari
> >> -------------- next part --------------
> >> An HTML attachment was scrubbed...
> >> URL:
> >> <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20140814/6c53560d/attachment.html
> >
> >>
> >> ------------------------------
> >>
> >> Message: 2
> >> Date: Thu, 14 Aug 2014 10:19:49 -0700
> >> From: Geoffrey So <gsiisg at gmail.com>
> >> To: Discussion of the yt analysis package
> >> <yt-users at lists.spacepope.org>
> >> Subject: Re: [yt-users] ionization states in ramses data sets
> >> Message-ID:
> >>
> >> <CAM-dO+DM+ygbGg3GG9vrxjSn+JM9mGGgHDXA1UEJu1KYpnJJqw at mail.gmail.com>
> >> Content-Type: text/plain; charset="utf-8"
> >>
> >> Hi,
> >>
> >> according to
> >> http://yt-project.org/docs/2.6/analyzing/creating_derived_fields.html?
> >>
> >> what worked for me for enzo data is the following
> >>
> >> def _HINeutralFraction(field, data):
> >> return data['HI_Density']/(data['HI_Density']+data['HII_Density'])
> >>
> >> add_field('HINeutralFraction',function=_HINeutralFraction,
> >> units=r"\rho_\mathrm{HI}/\rho_\mathrm{H}")
> >>
> >> unless there's something strange with ramses dataset, the above should
> >> work.
> >>
> >> From
> >> G.S.
> >>
> >>
> >> On Thu, Aug 14, 2014 at 10:12 AM, Professor Maller <
> >> amaller at citytech.cuny.edu> wrote:
> >>
> >> > Hi,
> >> >
> >> > Does anyone have code to create derived fields of ionization states,
> >> > e.g.
> >> > HI, for ramses data sets? If that's a no, does anyone have an example
> >> > of a
> >> > derived field where you have to read in a table and interpolate the
> >> > field
> >> > values.
> >> >
> >> > Thanks,
> >> >
> >> > Ari
> >> >
> >> > _______________________________________________
> >> > yt-users mailing list
> >> > yt-users at 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/20140814/14caf322/attachment-0001.htm
> >
> >>
> >> ------------------------------
> >>
> >> Message: 3
> >> Date: Thu, 14 Aug 2014 12:22:16 -0500
> >> From: Matthew Turk <matthewturk at gmail.com>
> >> To: Discussion of the yt analysis package
> >> <yt-users at lists.spacepope.org>
> >> Subject: Re: [yt-users] ionization states in ramses data sets
> >> Message-ID:
> >>
> >> <CALO3=5HE+5eFNfXaWqJ_ApFCZeE_Sy73EEj+O5y7CuqMiVQ9sQ at mail.gmail.com>
> >> Content-Type: text/plain; charset=UTF-8
> >>
> >> Hi Ari,
> >>
> >> My reading of yt/frontends/ramses/fields.py is that this should be
> >> implemented already, using the cooling_%05i.dat files. If it's able
> >> to find those files, it will create the appropriate derived fields
> >> from them -- specifically, I think it can do Electron, HI, HII, HeI,
> >> HeII, and HeIII. Is it not creating those?
> >>
> >> On Thu, Aug 14, 2014 at 12:12 PM, Professor Maller
> >> <amaller at citytech.cuny.edu> wrote:
> >> > Hi,
> >> >
> >> > Does anyone have code to create derived fields of ionization states,
> >> > e.g.
> >> > HI, for ramses data sets? If that's a no, does anyone have an example
> >> > of a
> >> > derived field where you have to read in a table and interpolate the
> >> > field
> >> > values.
> >> >
> >> > Thanks,
> >> >
> >> > Ari
> >> >
> >> > _______________________________________________
> >> > yt-users mailing list
> >> > yt-users at lists.spacepope.org
> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >
> >>
> >>
> >> ------------------------------
> >>
> >> Subject: Digest Footer
> >>
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users at lists.spacepope.org
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>
> >>
> >> ------------------------------
> >>
> >> End of yt-users Digest, Vol 78, Issue 38
> >> ****************************************
> >
> >
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 15 Aug 2014 16:21:05 +0800
> From: Hao Wang <hwang.phy at gmail.com>
> To: yt-users at lists.spacepope.org
> Subject: [yt-users] " cannot import name YTDomainOverflow" after hg
> update to an earlier version
> Message-ID:
> <CAD_YEuC99LOH2p8n8zfdrLEZ7=
> 7__QNjSeEis3nyz2mEio5SSQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all,
>
> I was using YT when some error messages appeared; since this happened
> immediately after I updated yt, I tried to "hg update 13651" to an earlier
> version.
>
> It turned out to be a big mistake -- suddenly every command I tried (yt; yt
> update; hg update; and yt notebook) gave the following error:
> =======================================
> Traceback (most recent call last):
> File "/home/hao/projects/yt/bin/yt", line 9, in <module>
> load_entry_point('yt==3.0dev', 'console_scripts', 'yt')()
> File
>
> "/home/hao/projects/yt/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py",
> line 337, in load_entry_point
> return get_distribution(dist).load_entry_point(group, name)
> File
>
> "/home/hao/projects/yt/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py",
> line 2311, in load_entry_point
> return ep.load()
> File
>
> "/home/hao/projects/yt/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py",
> line 2017, in load
> entry = __import__(self.module_name, globals(),globals(), ['__name__'])
> File "/home/hao/projects/yt/src/yt-hg/yt/utilities/command_line.py", line
> 19, in <module>
> from yt.mods import *
> File "/home/hao/projects/yt/src/yt-hg/yt/mods.py", line 50, in <module>
> from yt.data_objects.api import \
> File "/home/hao/projects/yt/src/yt-hg/yt/data_objects/api.py", line 13,
> in <module>
> from grid_patch import \
> File "/home/hao/projects/yt/src/yt-hg/yt/data_objects/grid_patch.py",
> line 25, in <module>
> from yt.data_objects.data_containers import YTFieldData
> File
> "/home/hao/projects/yt/src/yt-hg/yt/data_objects/data_containers.py", line
> 31, in <module>
> from yt.data_objects.derived_quantities import GridChildMaskWrapper
> File
> "/home/hao/projects/yt/src/yt-hg/yt/data_objects/derived_quantities.py",
> line 26, in <module>
> from yt.utilities.parallel_tools.parallel_analysis_interface import \
> File
>
> "/home/hao/projects/yt/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
> line 29, in <module>
> from yt.utilities.lib import \
> File "/home/hao/projects/yt/src/yt-hg/yt/utilities/lib/__init__.py", line
> 21, in <module>
> from .geometry_utils import *
> File "geometry_utils.pyx", line 22, in init
> yt.utilities.lib.geometry_utils (yt/utilities/lib/geometry_utils.c:10907)
> ImportError: cannot import name YTDomainOverflow
> ========================================
> Anything to do to fix the damage besides a reinstallation?
>
> Thanks!
>
> Hao
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>
> Subject: Digest Footer
>
> _______________________________________________
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>
> ------------------------------
>
> End of yt-users Digest, Vol 78, Issue 39
> ****************************************
>
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