Re: [yt-users] Problem in simple volume rendering (yt-users Digest, Vol 36, Issue 18)
by Kuo-Chuan Pan
Dear Matt,
Thank you very much for your quick reply.
1. The balck_center I found is
back_center = [-0.28306926 -0.1132277 -0.39629696]
2. The physical size I used is from -8.2605e11 cm to 8.2605e11 cm (same for x,y,z directions)
The domain is correctly printing when running my yt script
yt INFO 2011-02-24 13:08:20,186 Parameters: domain_left_edge = [ -8.26050000e+11 -8.26050000e+11 -8.26050000e+11]
yt INFO 2011-02-24 13:08:20,186 Parameters: domain_right_edge = [ 8.26050000e+11 8.26050000e+11 8.26050000e+11]
3. I set the width = 1 as used in the example code.
(all value are the same as the example code, except center, c=[0.,0.,0.] and the datafile is the Flash output file)
Thank you very much for your kindly assistance.
Best,
Kuo-Chuan
I have got some warning from yt, but I think that may not relate to my problem.
The whole output are listed as bellow:
[kpan2@taranaki yt-scripts]$ ./ShowPlots.py
yt WARNING 2011-02-24 13:21:00,791 Setting 1.0 in code units to be 1.0 cm
yt WARNING 2011-02-24 13:21:00,793 No time units. Setting 1.0 = 1 second.
yt INFO 2011-02-24 13:21:00,794 Parameters: current_time = 5635.73778789
yt ERROR 2011-02-24 13:21:00,794 Missing domain_dimensions in parameter file definition!
yt INFO 2011-02-24 13:21:00,794 Parameters: domain_left_edge = [ -8.26050000e+11 -8.26050000e+11 -8.26050000e+11]
yt INFO 2011-02-24 13:21:00,794 Parameters: domain_right_edge = [ 8.26050000e+11 8.26050000e+11 8.26050000e+11]
yt INFO 2011-02-24 13:21:00,795 Parameters: cosmological_simulation = 0.0
yt WARNING 2011-02-24 13:21:00,795 Setting 1.0 in code units to be 1.0 cm
yt WARNING 2011-02-24 13:21:00,795 No time units. Setting 1.0 = 1 second.
Warning: invalid value encountered in sqrt
Warning: invalid value encountered in sqrt
Adding gaussian at -5.8560788466 with width 0.02 and colors (0.2867691866508944, 0.015686274509803921, 0.031372549019607843, 0.01)
Adding gaussian at -4.32198464433 with width 0.02 and colors (0.23702881439314105, 0.20784313725490194, 0.41568627450980389, 0.025118864315095794)
Adding gaussian at -2.78789044206 with width 0.02 and colors (0.40392156862745099, 0.40392156862745099, 0.80784313725490198, 0.063095734448019331)
Adding gaussian at -1.25379623979 with width 0.02 and colors (0.59607843137254901, 0.59607843137254901, 0.59115561118064242, 0.15848931924611143)
Adding gaussian at 0.280297962486 with width 0.02 and colors (0.792156862745098, 0.792156862745098, 0.21568627450980413, 0.39810717055349731)
Adding gaussian at 1.81439216476 with width 0.02 and colors (0.98431372549019602, 0.98431372549019602, 0.94080651128375881, 1.0)
THIS MANY GRIDS! 0| | ETA: --:--:--
Partitioning 100% |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00
KC>>> back_center = [ 0.21693074 0.3867723 0.10370304]
KC>>> bricks = []
KC>>> LE = []
Traceback (most recent call last):
File "./ShowPlots.py", line 161, in <module>
test.plotVR()
File "./ShowPlots.py", line 126, in plotVR
vp.ray_cast()
File "/home/kpan2/softwares/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/software_sampler.py", line 111, in ray_cast
LE = na.array(LE) - self.back_center
ValueError: shape mismatch: objects cannot be broadcast to a single shape
Exception AttributeError: "'NoneType' object has no attribute 'chdir'" in <bound method ShowPlots.__del__ of <__main__.ShowPlots instance at 0x17bb3200>> ignored
PS. (the lines with "KC>>>" are my debug outputs )
On Feb 24, 2011, at 1:11 PM, yt-users-request(a)lists.spacepope.org wrote:
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> Today's Topics:
>
> 1. Problem in simple volume rendering (Kuo-Chuan Pan)
> 2. Re: Problem in simple volume rendering (Matthew Turk)
> 3. Forthon and yt installation problems. (Andrew Davis)
> 4. Re: Forthon and yt installation problems. (Matthew Turk)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 24 Feb 2011 04:12:18 -0600
> From: Kuo-Chuan Pan <kpan2(a)astro.illinois.edu>
> To: yt-users(a)lists.spacepope.org
> Subject: [yt-users] Problem in simple volume rendering
> Message-ID: <7301A4B8-2601-4AFB-960D-D6CAC55F6D29(a)astro.illinois.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Sir/Madam,
>
> I am new in yt and trying to visualize my FLASH simulation data (3D) with volume rendering.
> I followed the cookbook in:
>
> http://hg.enzotools.org/cookbook/raw-file/tip/recipes/simple_volume_rende...
>
> However I got an error message:
>
> File "/home/kpan2/softwares/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/software_sampler.py", line 110, in ray_cast
> LE = na.array(LE) - self.back_center
> ValueError: shape mismatch: objects cannot be broadcast to a single shape
>
> I looked the software_sampler.py file and found all LE, RE, self.bricks are empty lists ( = []), but self.back_center is not and correct.
> I guess there are some problems when setting self.bricks.
>
> If anyone has any suggestions, I would be very happy to hear.
> Thank you.
>
> Best regards,
> Kuo-Chuan
>
> ------------------------------
>
> Message: 2
> Date: Thu, 24 Feb 2011 07:49:45 -0500
> From: Matthew Turk <matthewturk(a)gmail.com>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Cc: Kuo-Chuan Pan <kpan2(a)astro.illinois.edu>
> Subject: Re: [yt-users] Problem in simple volume rendering
> Message-ID:
> <AANLkTi=MeytZo=-7ENNgHs7KTeGmemtrT32CYUGYpep1(a)mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Kuo-Chuan,
>
> Sorry to hear it didn't work for you! Do you think you could help us
> out with a bit more information, and then we'll see if we can get it
> working for you?
>
> * What is the exact value of back_center that you find?
> * What is the physical size of your domain?
> * What is the width you supplied to the volume_rendering object?
>
> It might also be easier if you could try it with the "Camera"
> interface as described here:
>
> http://yt.enzotools.org/doc/visualizing/volume_rendering.html#volume-rend...
>
> That should allow for a bit more flexibility in describing the scene,
> and may help us narrow down the error.
>
> Best wishes,
>
> Matt
>
> On Thu, Feb 24, 2011 at 5:12 AM, Kuo-Chuan Pan <kpan2(a)astro.illinois.edu> wrote:
>> Dear Sir/Madam,
>>
>> I am new in yt and trying to visualize my FLASH simulation data (3D) with volume rendering.
>> I followed the cookbook in:
>>
>> ? ?http://hg.enzotools.org/cookbook/raw-file/tip/recipes/simple_volume_rendering.py
>>
>> However I got an error message:
>>
>> ?File "/home/kpan2/softwares/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/software_sampler.py", line 110, in ray_cast
>> ? ?LE = na.array(LE) - self.back_center
>> ValueError: shape mismatch: objects cannot be broadcast to a single shape
>>
>> I looked the software_sampler.py file and found all LE, RE, self.bricks are empty lists ( = []), but self.back_center is not and correct.
>> I guess there are some problems when setting self.bricks.
>>
>> If anyone has any suggestions, I would be very happy to hear.
>> Thank you.
>>
>> Best regards,
>> Kuo-Chuan
>> _______________________________________________
>> yt-users mailing list
>> yt-users(a)lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 24 Feb 2011 11:44:37 -0500
> From: Andrew Davis <andrew.davis(a)yale.edu>
> To: yt-users(a)lists.spacepope.org
> Subject: [yt-users] Forthon and yt installation problems.
> Message-ID: <20110224114437.djff25pj404cc8sg(a)www.mail.yale.edu>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi folks,
>
> I'm updating my yt to the latest version, and so I'm just starting from scratch
> in installing everything on a local cluster. I am running into errors, however
> with the install script (line 479). When running the script, I get the
> following output regarding Forthon:
>
> Installing Forthon-0.8.4 (arguments: 'Forthon-0.8.4')
> Doing yt update, wiping local changes and updating to branch stable
> Installing yt
> install_script.sh: line 479: cd: yt/utilities/kdtree: No such file or directory
> Failure. Check /home/ajd53/YT_NEW/yt-x86_64/yt_install.log.
>
> I haven't been able to find any directory called yt/utilities, which is probably
> why it can't find it.
> At the end of the yt_install.log file, I see the following error, which doesn't
> seem to be related to the install error at first glance:
>
> abort: data/doc/install_script.sh.i@908327e16660: no match found!
> /home/ajd53/YT_NEW/yt-x86_64/bin/python2.6: can't open file 'setup.py': [Errno
> 2] No such file or directory
>
> Any thoughts?
>
> Thanks,
> andrew
>
>
> *************************************************************
> ** Andrew J. Davis andrew.davis(a)yale.edu **
> ** Dept. of Astronomy 203-432-5119 **
> ** Yale University www.astro.yale.edu/adavis **
> *************************************************************
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 24 Feb 2011 11:51:38 -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] Forthon and yt installation problems.
> Message-ID:
> <AANLkTinvoEfjmRD1n80kk4=Ppmab9M3rGWdViwY_ta3z(a)mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Andrew,
>
> Sorry about the problem -- this looks like an issue with our hg
> server; I don't believe it's directly with Forthon. There's something
> up with the webserver, so you should be able to do this:
>
> cd /home/ajd53/YT_NEW/yt-x86_64/src
> rm -rf yt-hg
> /home/ajd53/YT_NEW/yt-x86_64/bin/hg clone --pull --uncompressed
> http://hg.enzotools.org/yt ./yt-hg
>
> and that *should* get you the full set of yt, and then re-run the
> install script with no modifications. Please let me know if that
> doesn't work.
>
> -Matt
>
> PS The webserver for serving hg has been an issue for a while now, and
> I'm embarrassed by the problem. I had hoped to move us to a different
> host several weeks ago, but we've been trying to get the username
> "yt." I think I need to give up that particular goal and settle for
> something different. I'll have an update on this soon.
>
> On Thu, Feb 24, 2011 at 11:44 AM, Andrew Davis <andrew.davis(a)yale.edu> wrote:
>> Hi folks,
>>
>> I'm updating my yt to the latest version, and so I'm just starting from scratch
>> in installing everything on a local cluster. ?I am running into errors, however
>> with the install script (line 479). ?When running the script, I get the
>> following output regarding Forthon:
>>
>> Installing Forthon-0.8.4 (arguments: 'Forthon-0.8.4')
>> Doing yt update, wiping local changes and updating to branch stable
>> Installing yt
>> install_script.sh: line 479: cd: yt/utilities/kdtree: No such file or directory
>> Failure. ?Check /home/ajd53/YT_NEW/yt-x86_64/yt_install.log.
>>
>> I haven't been able to find any directory called yt/utilities, which is probably
>> why it can't find it.
>> At the end of the yt_install.log file, I see the following error, which doesn't
>> seem to be related to the install error at first glance:
>>
>> abort: data/doc/install_script.sh.i@908327e16660: no match found!
>> /home/ajd53/YT_NEW/yt-x86_64/bin/python2.6: can't open file 'setup.py': [Errno
>> 2] No such file or directory
>>
>> Any thoughts?
>>
>> Thanks,
>> andrew
>>
>>
>> *************************************************************
>> ** ?Andrew J. Davis ? ? ? ? ? ? andrew.davis(a)yale.edu ? ? ?**
>> ** ?Dept. of Astronomy ? ? ? ? ?203-432-5119 ? ? ? ? ? ? ? **
>> ** ?Yale University ? ? ? ? ? ? www.astro.yale.edu/adavis ?**
>> *************************************************************
>>
>>
>>
>> _______________________________________________
>> 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
>
>
> End of yt-users Digest, Vol 36, Issue 18
> ****************************************
8 years
log scale issues when zero.....
by Elizabeth Harper-Clark
Hi guys,
one more thing. I want to calculate the radiation pressure force, and when
there is some then plot it with a log scale. However if I set:
def _ConvertAccel(data):
return data.convert("Length") / (data.convert("Time"))**2.0
def _RadiationAccelerationMagnitude(field, data):
return ( (data["RadAccel1"])**2.0 + \
(data["RadAccel2"])**2.0 + \
(data["RadAccel3"])**2.0 )**(1.0/2.0)
add_field("RadiationAccelerationMagnitude",
function=_RadiationAccelerationMagnitude,
*take_log=True*,convert_function=_ConvertAccel,
units=r"\rm{cm}/\rm{s}^{2}")
def _RadiationForceMagnitude(field, data):
return ( data["RadiationAccelerationMagnitude"] * data["Density"] *
data["CellVolume"])
add_field("RadiationForceMagnitude", function=_RadiationForceMagnitude, *
take_log=True*, units=r"\rm{dynes}")
before the stars switch on when the radiation acceleration baryon fields are
all 0.0 everywhere I get the following error:
Traceback (most recent call last):
File "MultiPlotProj.py", line 65, in <module>
s = pc.add_projection("RadiationForceMagnitude", ax,
weight_field="Density", figure=fig, axes=axes[0][3], use_colorbar=False)
File "/home/h-clark/YT/src/yt-hg/yt/visualization/plot_collection.py",
line 742, in add_projection
size=fig_size, periodic=periodic))
File "/home/h-clark/YT/src/yt-hg/yt/visualization/plot_types.py", line
310, in __init__
self.__init_temp_image(use_colorbar)
File "/home/h-clark/YT/src/yt-hg/yt/visualization/plot_types.py", line
347, in __init_temp_image
self.set_width(1,'unitary')
File "/home/h-clark/YT/src/yt-hg/yt/visualization/plot_types.py", line
436, in set_width
self._refresh_display_width()
File "/home/h-clark/YT/src/yt-hg/yt/visualization/plot_types.py", line
454, in _refresh_display_width
self._redraw_image()
File "/home/h-clark/YT/src/yt-hg/yt/visualization/plot_types.py", line
384, in _redraw_image
newmin = na.nanmin(buff[bI])
File
"/home/h-clark/YT/lib/python2.6/site-packages/numpy/lib/function_base.py",
line 1494, in nanmin
return _nanop(np.min, np.inf, a, axis)
File
"/home/h-clark/YT/lib/python2.6/site-packages/numpy/lib/function_base.py",
line 1355, in _nanop
res = op(y, axis=axis)
File
"/home/h-clark/YT/lib/python2.6/site-packages/numpy/core/fromnumeric.py",
line 1829, in amin
return amin(axis, out)
ValueError: zero-size array to ufunc.reduce without identity
Is there a way to set it so I get a log scale when plotting projections that
does not break when the fields are all zero?
Many thanks,
Libby
--
Elizabeth Harper-Clark MA MSci
PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT
Sciences and Engineering Coordinator, Teaching Assistants' Training Program,
UofT
www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark>
h-clark(a)cita.utoronto.ca
Astronomy office phone: +1-416-978-5759
8 years
Multiplot - 2x2 and 4 different color bars
by Elizabeth Harper-Clark
Hi guys,
I want a 2x2 multiplot showing 4 different things (density, temperature, HII
fraction and radiation force). How do i get 4 different colorbars on a 2x2
image? currently it will only give me two.
Thanks,
Libby
my scripts as it stands:
from yt.mods import * # set up our namespace
import matplotlib.colorbar as cb
import os
orient = 'horizontal'
frame_template = "aaSN/%s/Multiplotproj_%02ipc_%01i_%04i.eps"
ss = float(sys.argv[2])
rho_min = 1.e-25
rho_max = 1.e-20
temp_min = 1
temp_max = 10000
HII_min = 1.e-5
HII_max = 1.0
rp_min = 1e24
rp_max = 1e26
name = sys.argv[1]
firststar = 0
def _ConvertAccel(data):
return data.convert("Length") / (data.convert("Time"))**2.0
def _RadiationAccelerationMagnitude(field, data):
return ( (data["RadAccel1"])**2.0 + \
(data["RadAccel2"])**2.0 + \
(data["RadAccel3"])**2.0 )**(1.0/2.0)
add_field("RadiationAccelerationMagnitude",
function=_RadiationAccelerationMagnitude,
take_log=False,convert_function=_ConvertAccel, units=r"\rm{cm}/\rm{s}^{2}")
def _RadiationForceMagnitude(field, data):
return ( data["RadiationAccelerationMagnitude"] * data["Density"] *
data["CellVolume"])
add_field("RadiationForceMagnitude", function=_RadiationForceMagnitude,
take_log=False, units=r"\rm{dynes}")
for n in range(50,100,10):
pf = load("SciNet/%s/DD%04i/data%04i" % (name,n, n)) # load data
if pf is None: continue
for ax in range (0,1):
if os.path.exists(frame_template % (name,ss,ax,n)) is True:
print "file exists"
continue
xc = 0.5
yc = 0.5
zc = 0.5
print "Dump:", n, "axis:", ax
fig, axes, colorbars = get_multi_plot( 2, 2, colorbar=orient, bw =
6)
pc = PlotCollection(pf, center=(xc, yc, zc))
p = pc.add_projection("Density", ax, weight_field="Density", figure
= fig, axes = axes[0][0], use_colorbar=False)
p.set_cmap("bds_highcontrast")
p.set_zlim(rho_min, rho_max)
q = pc.add_projection("Temperature", ax, weight_field="Density",
figure=fig, axes=axes[0][1], use_colorbar=False)
q.set_cmap("hot")
q.set_zlim(temp_min, temp_max)
r = pc.add_projection("HII_Fraction", ax, weight_field="Density",
figure=fig, axes=axes[1][0], use_colorbar=False)
r.set_cmap("jet")
r.set_zlim(HII_min, HII_max)
s = pc.add_projection("RadiationForceMagnitude", ax,
weight_field="Density", figure=fig, axes=axes[1][1], use_colorbar=False)
s.set_cmap("Greys")
s.set_zlim(rp_min, rp_max)
pc.set_width(ss, 'pc')
sp = pf.h.all_data()
if na.any(pf.h.grid_particle_count):
p.modify["particles"](2.0, p_size=1.0, col='k', minimum_mass=
6.e0)
q.modify["particles"](2.0, p_size=1.0, col='k', minimum_mass=
6.e0)
r.modify["particles"](2.0, p_size=1.0, col='k', minimum_mass=
6.e0)
s.modify["particles"](2.0, p_size=1.0, col='k', minimum_mass=
6.e0)
print " XXXXX Particles present XXXXX"
Timemyr = pf["InitialTime"]*pf["years"]/1.e6 - firststar*.1
p.modify["text"]((0.051,0.949),"Time = %5.1f Myr" % (Timemyr),
text_args = {'color':'k'})
p.modify["text"]((0.05,0.95),"Time = %5.1f Myr" % (Timemyr),
text_args = {'color':'w'})
for p, cax in zip(pc.plots, colorbars):
p._redraw_image()
cbar = cb.Colorbar(cax, p.image, orientation=orient)
p.colorbar = cbar
p._autoset_label()
fig.savefig(frame_template % (name,ss,ax,n), format="eps")
--
Elizabeth Harper-Clark MA MSci
PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT
Sciences and Engineering Coordinator, Teaching Assistants' Training Program,
UofT
www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark>
h-clark(a)cita.utoronto.ca
Astronomy office phone: +1-416-978-5759
8 years
psf convolution
by Charles Hansen
Does anyone know a way to convolve a yt image (preferably
pc.add_projection) with a telescope psf? This would be useful for
simulated observations. At the moment, the best I can do is make an
image in yt and then convolve that image in pixel space, but this ends
up blurring out things I do not want blurred (like particle markers, or
velocity arrows). The psf does not need to be fancy, I just want a 2D
gaussian with an adjustable width.
Ideally, there would be a call
pc.add_projection("Density", 0, psf_width = 1.5e13)
#create a projection with a psf width of 1 AU at the observed distance
Charles
8 years
Re: [yt-users] error in creating plot collection
by Stephen Skory
Christine,
> /share/home/01112/tg803911/yt_new/yt/yt/frontends/enzo/data_structures.pyc in
> _parse_binary_hierarchy(self)
> 288 except h5py.h5.H5Error:
> 289 return False
> --> 290 self.grid_dimensions[:] = f["/ActiveDimensions"][:]
> 291 self.grid_left_edge[:] = f["/LeftEdges"][:]
> 292 self.grid_right_edge[:] = f["/RightEdges"][:]
>
> ValueError: shape mismatch: objects cannot be broadcast to a single
> shape
This error appears to be coming from the binary hierarchy in that particular data dump. The file may be corrupted. You can try deleting the "*.harrays" file, and yt should rebuild it.
Good luck!
Stephen Skory
stephenskory(a)yahoo.com
http://stephenskory.com/
510.621.3687 (google voice)
8 years
error in creating plot collection
by Christine Simpson
Hi all,
I'm getting an error in trying to do some very simple analysis on one
output of an enzo simulation I have. I don't have this issue with any
other output of the simulation. Basically I can load the data and
that's it; every other routine I try on it crashes. I have a feeling
this may be an issue with my data, not yt, but I was wondering if you yt
folks could give some insight as to what is crashing yt. Any help would
be appreciated. Here is a sample error where I try to create a plot
collection:
In [12]: pf = load("DD0008/output_0008")
yt INFO 2011-02-25 17:03:41,236 Parameters: current_time
= 40.8164738158
yt INFO 2011-02-25 17:03:41,236 Parameters:
domain_dimensions = [128, 128, 128]
yt INFO 2011-02-25 17:03:41,236 Parameters:
domain_left_edge = [ 0. 0. 0.]
yt INFO 2011-02-25 17:03:41,237 Parameters:
domain_right_edge = [ 1. 1. 1.]
yt INFO 2011-02-25 17:03:41,238 Parameters:
cosmological_simulation = 1
yt INFO 2011-02-25 17:03:41,238 Parameters:
current_redshift = 6.36375016055
yt INFO 2011-02-25 17:03:41,238 Parameters: omega_lambda
= 0.726
yt INFO 2011-02-25 17:03:41,238 Parameters: omega_matter
= 0.274
yt INFO 2011-02-25 17:03:41,238 Parameters:
hubble_constant = 0.705
In [13]: pc = PlotCollectionInteractive(pf)
yt INFO 2011-02-25 17:03:44,967 Getting the binary
hierarchy
ERROR: An unexpected error occurred while tokenizing input
The following traceback may be corrupted or invalid
The error message is: ('EOF in multi-line statement', (92, 0))
---------------------------------------------------------------------------
ValueError Traceback (most recent call
last)
/share/home/01112/tg803911/yt_new/yt/scripts/iyt in <module>()
----> 1
2
3
4
5
/share/home/01112/tg803911/yt_new/yt/yt/visualization/plot_collection.pyc in __init__(self, *args, **kwargs)
1602 import pylab
1603 self.pylab = pylab
-> 1604 super(PlotCollectionInteractive, self).__init__(*args,
**kwargs)
1605
1606 def redraw(self):
/share/home/01112/tg803911/yt_new/yt/yt/visualization/plot_collection.pyc in __init__(self, pf, center)
101 self.pf = pf
102 if center == None:
--> 103 v,self.c = pf.h.find_max("Density") # @todo: ensure
no caching
104 elif center == "center" or center == "c":
105 self.c = (pf.domain_right_edge +
pf.domain_left_edge)/2.0
/share/home/01112/tg803911/yt_new/yt/yt/data_objects/static_output.pyc
in _get_hierarchy(self)
157 if self._hierarchy_class == None:
158 raise RuntimeError("You should not instantiate
StaticOutput.")
--> 159 self.__hierarchy = self._hierarchy_class(self,
data_style=self.data_style)
160 return self.__hierarchy
161
/share/home/01112/tg803911/yt_new/yt/yt/frontends/enzo/data_structures.pyc in __init__(self, pf, data_style)
155 self.float_type = 'float64'
156
--> 157 AMRHierarchy.__init__(self, pf, data_style)
158 # sync it back
159 self.parameter_file.data_style = self.data_style
/share/home/01112/tg803911/yt_new/yt/yt/data_objects/hierarchy.pyc in
__init__(self, pf, data_style)
68
69 mylog.debug("Parsing hierarchy.")
---> 70 self._parse_hierarchy()
71
72 mylog.debug("Constructing grid objects.")
/share/home/01112/tg803911/yt_new/yt/yt/frontends/enzo/data_structures.pyc in _parse_hierarchy(self)
217 return line.split()[2:]
218 if os.path.exists(self.hierarchy_filename[:-9] +
"harrays"):
--> 219 if self._parse_binary_hierarchy(): return
220 t1 = time.time()
221 pattern = r"Pointer: Grid\[(\d*)\]->NextGrid(Next|
This)Level = (\d*)\s+$"
/share/home/01112/tg803911/yt_new/yt/yt/frontends/enzo/data_structures.pyc in _parse_binary_hierarchy(self)
288 except h5py.h5.H5Error:
289 return False
--> 290 self.grid_dimensions[:] = f["/ActiveDimensions"][:]
291 self.grid_left_edge[:] = f["/LeftEdges"][:]
292 self.grid_right_edge[:] = f["/RightEdges"][:]
ValueError: shape mismatch: objects cannot be broadcast to a single
shape
8 years
yt's moving!
by Matthew Turk
Hi all,
I'm writing to let you know that we have outgrown our homegrown
mercurial serving (as some of you may have noticed with the
installation errors) and we have moved the yt source code to
BitBucket. Here are the three takeaways:
* You should not have to make any changes for "yt instinfo -u" to
continue working.
* This should fix all outstanding issues with the install script
timing out when downloading yt.
* You can now much more easily contribute changes!
The new source code location is the same as the old source code
location: http://hg.enzotools.org/ . The username on BitBucket is
"yt_analysis". The DNS might take a few hours to get circulated
around, so if it doesn't work just now, it will by tonight or
tomorrow.
To contribute changes you can go here: http://hg.enzotools.org/yt/fork
to get your own version of the yt repository, where you can make
changes and commit, and even notify the main repo when your changes
are ready to push back upstream. We're very excited that this will
enable much greater participation, and I hope that this will lower the
barrier to entry for developing yt! I'm rewriting the developer guide
now, but the short answer to how to make changes has gotten a lot
shorter: just fork the repository and issue a "pull request" when
you're ready to contribute back upstream.
Let us know if this causes any unforeseen problems, and please feel
encouraged to fork and contribute!
Best,
Matt
8 years
Forthon and yt installation problems.
by Andrew Davis
Hi folks,
I'm updating my yt to the latest version, and so I'm just starting from scratch
in installing everything on a local cluster. I am running into errors, however
with the install script (line 479). When running the script, I get the
following output regarding Forthon:
Installing Forthon-0.8.4 (arguments: 'Forthon-0.8.4')
Doing yt update, wiping local changes and updating to branch stable
Installing yt
install_script.sh: line 479: cd: yt/utilities/kdtree: No such file or directory
Failure. Check /home/ajd53/YT_NEW/yt-x86_64/yt_install.log.
I haven't been able to find any directory called yt/utilities, which is probably
why it can't find it.
At the end of the yt_install.log file, I see the following error, which doesn't
seem to be related to the install error at first glance:
abort: data/doc/install_script.sh.i@908327e16660: no match found!
/home/ajd53/YT_NEW/yt-x86_64/bin/python2.6: can't open file 'setup.py': [Errno
2] No such file or directory
Any thoughts?
Thanks,
andrew
*************************************************************
** Andrew J. Davis andrew.davis(a)yale.edu **
** Dept. of Astronomy 203-432-5119 **
** Yale University www.astro.yale.edu/adavis **
*************************************************************
8 years, 1 month
Problem in simple volume rendering
by Kuo-Chuan Pan
Dear Sir/Madam,
I am new in yt and trying to visualize my FLASH simulation data (3D) with volume rendering.
I followed the cookbook in:
http://hg.enzotools.org/cookbook/raw-file/tip/recipes/simple_volume_rende...
However I got an error message:
File "/home/kpan2/softwares/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/software_sampler.py", line 110, in ray_cast
LE = na.array(LE) - self.back_center
ValueError: shape mismatch: objects cannot be broadcast to a single shape
I looked the software_sampler.py file and found all LE, RE, self.bricks are empty lists ( = []), but self.back_center is not and correct.
I guess there are some problems when setting self.bricks.
If anyone has any suggestions, I would be very happy to hear.
Thank you.
Best regards,
Kuo-Chuan
8 years, 1 month
modify - radiation pressure
by Elizabeth Harper-Clark
Hi all,
I would like to plot radiation pressure vectors in the style of
p.modify["velocity"](). Now, my radiation pressure acceleration is in my
data as three baryon fields (they appear in pf.h.field_list) : RadAccel1,
RadAccel2, RadAccel3 for the three spacial dimensions.
Now I am embarrassed to admit I have not done much yt development in the
past so I was hoping someone more familiar with the code could point me in
the direction of where I can add code for this? I am hoping it will be as
simple as finding all the places code exists for p.modify["velocity"]() and
copy and paste it changing the fields used to the radiation pressure ones.
Will it be? Where is the code for p.modify["velocity"]()? Are there any
tricky bits I should be aware of?
Many thanks,
Libby
--
Elizabeth Harper-Clark MA MSci
PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT
Sciences and Engineering Coordinator, Teaching Assistants' Training Program,
UofT
www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark>
h-clark(a)cita.utoronto.ca
Astronomy office phone: +1-416-978-5759
8 years, 1 month
