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

15 Aug 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, 
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 
To: yt-users@lists.spacepope.org
Subject: Re: [yt-users] yt-users Digest, Vol 78, Issue 38
Message-ID:

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, 
wrote:
...
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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 
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
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Message: 2
Date: Thu, 14 Aug 2014 10:19:49 -0700
From: Geoffrey So 
To: Discussion of the yt analysis package

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
_______________________________________________
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http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Message: 3
Date: Thu, 14 Aug 2014 12:22:16 -0500
From: Matthew Turk 
To: Discussion of the yt analysis package

Subject: Re: [yt-users] ionization states in ramses data sets
Message-ID:

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
 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
_______________________________________________
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http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Message: 2
Date: Thu, 14 Aug 2014 14:05:04 -0500
From: Matthew Turk 
To: Discussion of the yt analysis package

Subject: Re: [yt-users] yt-users Digest, Vol 78, Issue 38
Message-ID:

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
 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, 
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 
To: yt-users@lists.spacepope.org
Subject: [yt-users] ionization states in ramses data sets
Message-ID:

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
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Message: 2
Date: Thu, 14 Aug 2014 10:19:49 -0700
From: Geoffrey So 
To: Discussion of the yt analysis package

Subject: Re: [yt-users] ionization states in ramses data sets
Message-ID:

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
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Message: 3
Date: Thu, 14 Aug 2014 12:22:16 -0500
From: Matthew Turk 
To: Discussion of the yt analysis package

Subject: Re: [yt-users] ionization states in ramses data sets
Message-ID:

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
 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
------------------------------
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Message: 3
Date: Fri, 15 Aug 2014 16:21:05 +0800
From: Hao Wang 
To: yt-users@lists.spacepope.org
Subject: [yt-users] " cannot import name YTDomainOverflow" after hg
        update  to an earlier version
Message-ID:

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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