Re: [yt-users] yt-users Digest, Vol 78, Issue 39

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@lists.spacepope.org> wrote:
Send yt-users mailing list submissions to yt-users@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@lists.spacepope.org
You can reach the person managing the list at yt-users-owner@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: 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@citytech.cuny.edu> To: yt-users@lists.spacepope.org Subject: Re: [yt-users] yt-users Digest, Vol 78, Issue 38 Message-ID: <CACCSjdMFbhvsBhpH3ybzvW= dEGSkMRYBetsJG-deSEjyiqztHg@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@lists.spacepope.org> wrote:
Send yt-users mailing list submissions to yt-users@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@lists.spacepope.org
You can reach the person managing the list at yt-users-owner@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@citytech.cuny.edu> To: yt-users@lists.spacepope.org Subject: [yt-users] ionization states in ramses data sets Message-ID: < CACCSjdOxDp+Mmgae1XLYJJvC7vJn52Xu59ppUA+p0mq7Fggz8A@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/2014...
------------------------------
Message: 2 Date: Thu, 14 Aug 2014 10:19:49 -0700 From: Geoffrey So <gsiisg@gmail.com> To: Discussion of the yt analysis package <yt-users@lists.spacepope.org> Subject: Re: [yt-users] ionization states in ramses data sets Message-ID: < CAM-dO+DM+ygbGg3GG9vrxjSn+JM9mGGgHDXA1UEJu1KYpnJJqw@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@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@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/2014...
------------------------------
Message: 3 Date: Thu, 14 Aug 2014 12:22:16 -0500 From: Matthew Turk <matthewturk@gmail.com> To: Discussion of the yt analysis package <yt-users@lists.spacepope.org> Subject: Re: [yt-users] ionization states in ramses data sets Message-ID: <CALO3= 5HE+5eFNfXaWqJ_ApFCZeE_Sy73EEj+O5y7CuqMiVQ9sQ@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@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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
------------------------------
Subject: Digest Footer
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
------------------------------
End of yt-users Digest, Vol 78, Issue 38 ****************************************
-------------- next part -------------- An HTML attachment was scrubbed... URL: < http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2014...
------------------------------
Message: 2 Date: Thu, 14 Aug 2014 14:05:04 -0500 From: Matthew Turk <matthewturk@gmail.com> To: Discussion of the yt analysis package <yt-users@lists.spacepope.org> Subject: Re: [yt-users] yt-users Digest, Vol 78, Issue 38 Message-ID: <CALO3= 5EBSnthcHi+SzWTvWvmTbj7751MjPQ_+tVK4+GDes2OHA@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@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@lists.spacepope.org> wrote:
Send yt-users mailing list submissions to yt-users@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@lists.spacepope.org
You can reach the person managing the list at yt-users-owner@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@citytech.cuny.edu> To: yt-users@lists.spacepope.org Subject: [yt-users] ionization states in ramses data sets Message-ID:
<CACCSjdOxDp+Mmgae1XLYJJvC7vJn52Xu59ppUA+p0mq7Fggz8A@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/2014...
------------------------------
Message: 2 Date: Thu, 14 Aug 2014 10:19:49 -0700 From: Geoffrey So <gsiisg@gmail.com> To: Discussion of the yt analysis package <yt-users@lists.spacepope.org> Subject: Re: [yt-users] ionization states in ramses data sets Message-ID:
<CAM-dO+DM+ygbGg3GG9vrxjSn+JM9mGGgHDXA1UEJu1KYpnJJqw@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@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@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/2014...
------------------------------
Message: 3 Date: Thu, 14 Aug 2014 12:22:16 -0500 From: Matthew Turk <matthewturk@gmail.com> To: Discussion of the yt analysis package <yt-users@lists.spacepope.org> Subject: Re: [yt-users] ionization states in ramses data sets Message-ID:
<CALO3=5HE+5eFNfXaWqJ_ApFCZeE_Sy73EEj+O5y7CuqMiVQ9sQ@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@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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
------------------------------
Subject: Digest Footer
_______________________________________________ yt-users mailing list yt-users@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@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@gmail.com> To: yt-users@lists.spacepope.org Subject: [yt-users] " cannot import name YTDomainOverflow" after hg update to an earlier version Message-ID: <CAD_YEuC99LOH2p8n8zfdrLEZ7= 7__QNjSeEis3nyz2mEio5SSQ@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 -------------- next part -------------- An HTML attachment was scrubbed... URL: < http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2014...
------------------------------
Subject: Digest Footer
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
------------------------------
End of yt-users Digest, Vol 78, Issue 39 ****************************************
participants (1)
-
Professor Maller