Mailman 3 February 2016 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman 15 Aug '22

15 Aug '22

Hi All, I was curious if anyone has had any luck porting .ply files generated with yt into Blender with colors? It seems to port in the surfaces just fine, but they are a uniform color. From what I can gather, Blender imports .ply files with face color instead of vertex so I tried the surf.export_ply routine with "face" instead of "vertex" for sample_type, but no luck ("vertex" doesn't work either). Let me know if I can provide any more useful info. Thanks for any help, -J

3 2

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! 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 14

Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

6 8

Problem when run yt dev in parallel on Blue Waters
by Pengfei Chen 23 Aug '16

23 Aug '16

Hi all, I have trouble running yt in parallel on Blue Waters. I installed yt using miniconda, the version of yt is ~/miniconda/lib $yt version yt module located at: /u/sciteam/madcpf/miniconda/lib/python2.7/site-packages/yt-3.3.dev0-py2.7-linux-x86_64.egg The current version and changeset for the code is: --- Version = 3.3-dev Changeset = 90f900be7a36+ yt Then with miniconda/bin in PATH I installed mpi4py-2.0.0. But when I tried to make the following simple output in parallel, I get: import yt yt.enable_parallelism() from yt.utilities.parallel_tools.parallel_analysis_interface import\ parallel_objects, communication_system comm = communication_system.communicators[-1] print comm.rank, comm.size 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 ... When I run a similar code but with yt-2.x also on Blue Waters, I get what I expect: 7 16 15 16 6 16 9 16 11 16 8 16 0 16 4 16 ... I'm confused about it. Could anyone give me some suggestions please? Thanks, Pengfei

3 11

Covering Grid Dimensions: multiple refinement levels
by Carla Bernhardt 05 Apr '16

05 Apr '16

Dear YT Users, To better understand covering_grid (or smoothed_covering_grid), can someone explain what dimensions I should use when I have multiple levels of refinement? If I have 1 level of refinement from AMR data, the dimensions should be the same, I believe, but what if I have 2 or 3 levels of refinement? Should the fixed resolution region then have dimensions of dims*2^2 and dims*3^2 respectively? Here is one example from a tutorial <http://yt-project.org/doc/examining/low_level_inspection.html#examining-gri…> if that helps isolate my question: all_data_level_2 = ds.covering_grid(level=2, left_edge=[0,0.0,0.0], dims=ds.domain_dimensions * 2**2) Thanks in advance, Carla

3 14

gadget onto unigrid
by Desika Narayanan 29 Mar '16

29 Mar '16

Hi All, Is it possible to deposit the particles from a gadget data set onto a uniform grid in yt? Or, could it be possible to trick the octree deposition into doing it by forcing no refinements, but some sort of native grid resolution? thanks, desika

4 4

yt-3.2.1 installation error
by Muhammad Latif 08 Mar '16

08 Mar '16

Hi all, I'm getting the following error while installing yt-3.2.1 latest release. Any idea what is going on here? thanks in advance, cheers Latif Installing nose-1.3.6 Installing python-hglib-1.6 Installing sympy-0.7.6 Doing yt update, wiping local changes and updating to branch stable install_script.sh: line 1025: cd: /home/latif/YT/yt-x86_64/src/yt-hg/: No such file or directory Installing yt ******************************************** FAILURE REPORT: ******************************************** running install_data copying doc/man/isympy.1 -> /home/latif/YT/yt-x86_64/share/man/man1 running install_egg_info Writing /home/latif/YT/yt-x86_64/lib/python2.7/site-packages/sympy-0.7.6-py2.7.egg-info Collecting jinja2 Using cached Jinja2-2.8-py2.py3-none-any.whl Collecting MarkupSafe (from jinja2) Installing collected packages: MarkupSafe, jinja2 Successfully installed MarkupSafe-0.23 jinja2-2.8 /home/latif/YT/yt-x86_64/bin/python2.7: can't open file 'setup.py': [Errno 2] No such file or directory ******************************************** ******************************************** Failure. Check /home/latif/YT/yt-x86_64/yt_install.log. The last 10 lines are above.

2 1

Error in making light ray for a gadget dataset
by Bili Dong - Gmail 01 Mar '16

01 Mar '16

Hi yt users, I'm trying to make a light ray for a gadget dataset using this script: http://paste.yt-project.org/show/6234/ But I get the following error: ``` /Users/qobilidop/repos/yt/yt/geometry/geometry_handler.py in fcoords(self) 320 c = obj.select_fcoords(self.dobj) 321 if c.shape[0] == 0: continue--> 322 ci[ind:ind+c.shape[0], :] = c 323 ind += c.shape[0] 324 return ci ValueError: could not broadcast input array from shape (81,3) into shape (40,3) ``` My yt is on the changeset d47150dfbde6. I'm wondering if I'm doing it the correct way? And how could I solve the problem? Thanks, Bili

5 9

Google Summer of Code 2016
by Nathan Goldbaum 29 Feb '16

29 Feb '16

Hi all, Google announced today that yt has been accepted for Google Summer of Code 2016 as part of the OpenAstronomy organization! Please forward this message to students at any level who might be interested in getting paid to improve yt this summer. Ideas for yt projects are here: http://openastronomy.org/gsoc/gsoc2016/ideas.html#yt More details about applying to be a Google Summer of Code student are available here: https://summerofcode.withgoogle.com/ Students will be able to apply from March 14th until March 25th. Please feel free to contact me if you have any specific questions. -Nathan

1 0

phase plot and time series
by Mateusz Ruszkowski 29 Feb '16

29 Feb '16

Hi, Is there a simple way in yt to generate a "phase plot" of the gas density, with time and radius on the axes, using a time series of data files? Thanks, Mateusz

3 5

Compilation problem
by Mark Krumholz 25 Feb '16

25 Feb '16

Hi yt Users, I’m having a problem compiling the current development branch of yt on NASA pleiades, and I’m hoping that someone can suggest what could be going wrong. Here’s what I get when I try to compile: bridge4:yt mkrumhol$ /nasa/python/2.7.9/bin/python setup.py develop --prefix=/u/mkrumhol running develop running egg_info writing requirements to yt.egg-info/requires.txt writing yt.egg-info/PKG-INFO writing top-level names to yt.egg-info/top_level.txt writing dependency_links to yt.egg-info/dependency_links.txt writing entry points to yt.egg-info/entry_points.txt reading manifest file 'yt.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'scripts/pr_backport.py' no previously-included directories found matching 'doc/source/reference/api/generated' no previously-included directories found matching 'doc/build' writing manifest file 'yt.egg-info/SOURCES.txt' running build_ext pyrexc yt/analysis_modules/photon_simulator/utils.pyx --> yt/analysis_modules/photon_simulator/utils.c /home3/mkrumhol/yt/yt/analysis_modules/photon_simulator/utils.pyx:6:17: Syntax error in C variable declaration building 'yt.analysis_modules.photon_simulator.utils' extension gcc -fno-strict-aliasing -O2 -Wno-error -pipe -DHAVE_DB_185_H -pthread -I/usr/include -I/nasa/pkgsrc/2014Q4/include/db4 -I/nasa/pkgsrc/2014Q4/include -DNDEBUG -O2 -Wno-error -pipe -DHAVE_DB_185_H -pthread -I/usr/include -I/nasa/pkgsrc/2014Q4/include/db4 -I/nasa/pkgsrc/2014Q4/include -fPIC -I/nasa/pkgsrc/2014Q4/include/python2.7 -I/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/numpy/core/include -c yt/analysis_modules/photon_simulator/utils.c -o build/temp.linux-x86_64-2.7/yt/analysis_modules/photon_simulator/utils.o gcc: yt/analysis_modules/photon_simulator/utils.c: No such file or directory gcc: no input files error: command 'gcc' failed with exit status 1 I’m using python 2.7.9 and cython 0.23.4. The problem only occurs with the development branch; the stable branch compiles fine. I’d appreciate any suggestions. Thanks. -- Mark Krumholz http://www.mso.anu.edu.au/~krumholz/

3 3

Pyx + Tex
by John Regan 24 Feb '16

24 Feb '16

Hi All, I recently moved to working on a new machine and I've run into problems with eps_writer and pyx and tex. It seems pyx and tex are not talking to one another. I know pyx can sometimes have an iffy relationship with tex but does anyone know how to make them like each other? This is the output I get. yt : [INFO ] 2015-11-25 14:51:23,198 xlim = 0.456408 0.541884 yt : [INFO ] 2015-11-25 14:51:23,198 ylim = 0.482775 0.568251 yt : [INFO ] 2015-11-25 14:51:23,200 Making a fixed resolution buffer of (('gas', 'H_number_density')) 800 by 800 Create Multiplot.... yt : [WARNING ] 2015-11-25 14:51:24,085 No field specified. Choosing first field (('gas', 'H2_fraction')) yt : [WARNING ] 2015-11-25 14:51:24,955 No field specified. Choosing first field (('gas', 'H_number_density')) still waiting for tex after 5 (of 60) seconds... still waiting for tex after 10 (of 60) seconds... still waiting for tex after 15 (of 60) seconds... still waiting for tex after 20 (of 60) seconds... still waiting for tex after 25 (of 60) seconds... still waiting for tex after 30 (of 60) seconds... still waiting for tex after 35 (of 60) seconds... still waiting for tex after 40 (of 60) seconds... still waiting for tex after 45 (of 60) seconds... still waiting for tex after 50 (of 60) seconds... still waiting for tex after 55 (of 60) seconds... the timeout of 60 seconds expired and tex did not respond. We try to finish the dvi due to an unhandled tex error still waiting for tex after 5 (of 60) seconds... still waiting for tex after 10 (of 60) seconds... still waiting for tex after 15 (of 60) seconds... still waiting for tex after 20 (of 60) seconds... still waiting for tex after 25 (of 60) seconds... still waiting for tex after 30 (of 60) seconds... still waiting for tex after 35 (of 60) seconds... still waiting for tex after 40 (of 60) seconds... still waiting for tex after 45 (of 60) seconds... still waiting for tex after 50 (of 60) seconds... still waiting for tex after 55 (of 60) seconds... the timeout of 60 seconds expired and tex did not respond. Traceback (most recent call last): File "OnAxisMultiPlot_TimeSeries.py", line 173, in <module> figsize=(8,4), shrink_cb=1.8) File "/cosma/home/jregan/YT/yt-x86_64/src/yt-hg/yt/visualization/eps_writer.py", line 1164, in multiplot bbox = (100.0 * d.canvas.bbox().left().t, File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/canvas.py", line 156, in bbox obbox += cmd.bbox() File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 181, in bbox self.finish() File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 311, in finish self.doaxes() File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 588, in doaxes self.dolayout() File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 572, in dolayout self.doaxiscreate(axisname) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 248, in doaxiscreate self.axes[axisname].create() File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py", line 586, in create self.canvas = self.axis.create(self.data, self.positioner, self.graphtexrunner, self.errorname) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py", line 245, in create return _regularaxis._create(self, data, positioner, graphtexrunner, self.parter, self.rater, errorname) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py", line 146, in _create return layout(data) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py", line 141, in layout self.painter.paint(canvas, data, self, positioner) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/painter.py", line 258, in paint _title.paint(self, canvas, data, axis, axispos) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/painter.py", line 109, in paint title = canvas.layer("title").text_pt(x, y, axis.title, titleattrs) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/canvas.py", line 334, in text_pt return self.insert(self.texrunner.text_pt(x, y, atext, *args)) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py", line 1223, in text_pt return self.text(x * unit.t_pt, y * unit.t_pt, expr, *args, **kwargs) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py", line 1201, in text raise e pyx.text.TexResultError: TeX didn't respond as expected within the timeout period (60 seconds). The expression passed to TeX was: \scrollmode \raiseerror% \def\PyX{P\kern-.3em\lower.5ex\hbox{Y}\kern-.18em X}% \gdef\PyXBoxHAlign{0}% \newbox\PyXBox% \newbox\PyXBoxHAligned% \newdimen\PyXDimenHAlignLT% \newdimen\PyXDimenHAlignRT% \gdef\PyXFlushHAlign{0}% \def\PyXragged{% \leftskip=0pt plus \PyXFlushHAlign fil% \rightskip=0pt plus 1fil% \advance\rightskip0pt plus -\PyXFlushHAlign fil% \parfillskip=0pt% \pretolerance=9999% \tolerance=9999% \parindent=0pt% \hyphenpenalty=9999% \exhyphenpenalty=9999}% \newbox\PyXBoxVBox% \newdimen\PyXDimenVBox% \newbox\PyXBoxVAlign% \newdimen\PyXDimenVAlign% \newdimen\PyXDimenVShift% \long\def\ProcessPyXBox#1#2{% \setbox\PyXBox=\hbox{{#1}}% \PyXDimenHAlignLT=\PyXBoxHAlign\wd\PyXBox% \PyXDimenHAlignRT=\wd\PyXBox% \advance\PyXDimenHAlignRT by -\PyXDimenHAlignLT% \gdef\PyXBoxHAlign{0}% \immediate\write16{PyXBox:page=#2,lt=\the\PyXDimenHAlignLT,rt=\the\PyXDimenHAlignRT,ht=\the\ht\PyXBox,dp=\the\dp\PyXBox:}% \setbox\PyXBoxHAligned=\hbox{\kern-\PyXDimenHAlignLT\box\PyXBox}% \ht\PyXBoxHAligned0pt% {\count0=80\count1=121\count2=88\count3=#2\shipout\box\PyXBoxHAligned}}% \def\PyXInput#1{\immediate\write16{PyXInputMarker:executeid=#1:}}% \def\PyXMarker#1{\hskip0pt\special{PyX:marker #1}}%% \PyXInput{1}% After parsing the return message from TeX, the following was left: This is TeX, Version 3.14159265 (TeX Live 2015) (preloaded format=tex) Error in atexit._run_exitfuncs: Traceback (most recent call last): File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py", line 744, in _cleantmp texrunner.expectqueue.put_nowait(None) # do not expect any output anymore File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py", line 148, in put_nowait return self.put(item, False) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py", line 123, in put raise Full Full Error in sys.exitfunc: Traceback (most recent call last): File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py", line 744, in _cleantmp texrunner.expectqueue.put_nowait(None) # do not expect any output anymore File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py", line 148, in put_nowait return self.put(item, False) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py", line 123, in put raise Full Queue.Full The call I make is: multi = eps.multiplot(NCOLS, NROWS, projections, bare_axes=True,cb_labels=colorbar_label, figsize=(8,4), shrink_cb=1.8) Cheers, John

3 4

EnzoDatasetInMemory not working in parallel
by Britton Smith 24 Feb '16

24 Feb '16

Hi all, I've recently been trying to use yt's inline analysis functionality with Enzo and am having some difficultly getting it to work in parallel. I am using the development tip of yt. In serial, everything works fine, but in parallel, I get the following error: http://paste.yt-project.org/show/5694/ It seems that the issue is that yt is not correctly identifying which grids are available on a given processory for the EnzoDatasetInMemory object. Does anyone have an idea of how to fix this? Has anyone else seen this? For reference, my user_script is just this: import yt from yt.frontends.enzo.api import EnzoDatasetInMemory def main(): ds = EnzoDatasetInMemory() ad = ds.all_data() print ad.quantities.total_quantity("cell_mass") Thanks for any help, Britton

3 9

working with general hdf5 data from galaxy simulations
by D Mick 24 Feb '16

24 Feb '16

Hello all, yt has some of the greatest plotting capabilities, and I greatly enjoy working with yt! Recently I have begun to work with hdf5 data from a large scale galaxy simulation (illustris) and I was wondering how I can work with the data, is there a general munging procedure for getting it into the correct yt format? When I try to plot import yt ds = yt.load("Groups_hdf5_plt_cnt_0150") yt.SlicePlot(ds, 'x', "density", width = (800.0, 'kpc')).save() yt.SlicePlot(ds, 'y', "density", width = (800.0, 'kpc')).save() yt.SlicePlot(ds, 'z', "density", width = (800.0, 'kpc')).save() I get the following error: /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/yt/frontends/gadget_fof/data_structures.pyc in _parse_parameter_file(self) * 151* self.periodicity = (True, True, True) * 152* self.current_redshift = hvals["Redshift"] --> 153 self.omega_lambda = hvals["OmegaLambda"] * 154* self.omega_matter = hvals["Omega0"] * 155* self.hubble_constant = hvals["HubbleParam"] KeyError: 'OmegaLambda' I am guessing this is because the field entries do not match up. Any help is much appreciated! Dan

3 2

How to make a projection plot of a desirable thickness?
by Reju Sam John 22 Feb '16

22 Feb '16

Hi, I would like to make a projection of a field along 'z' axis centered at [0.5, 0.5, 0.5] with a thickness of 10Mpc (5 Mpc to +z dir and 5 Mpc to -z dir). How to select the above-mentioned region from the whole simulation volume? I am using YT Legacy 2.x. Thank you. -- Reju Sam John

2 1

Google summer of code ideas for yt
by Nathan Goldbaum 19 Feb '16

19 Feb '16

Hi all, This year yt is applying with the OpenAstronomy organization to participate in Google Summer of Code. The ideas we've put forward are here (scroll down the page a bit): http://openastronomy.org/gsoc/gsoc2016/ideas.html#yt If you know any students (undergrad, grad) who might be interested in getting paid by Google to work on yt over the summer, please forward them this message. I'm happy to answer questions about this here or off list. -Nathan

1 0

Problem making Plots
by Yuxiao Dai 19 Feb '16

19 Feb '16

Hi all, I tried to get some plots using a python code but got this error message. ======================= Traceback (most recent call last): File "ytplots_BMag_plot_dai.py", line 58, in <module> *pcb.save('plots/Bullet_BMag_'+str(i))* File "/home/yd742/software/withpysci/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py", line 173, in save override=override, force_save=force_save)) File "/home/yd742/software/withpysci/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 112, in save_image only_on_root(canvas.print_figure, fn) File "/home/yd742/software/withpysci/yt-x86_64/src/yt-hg/yt/funcs.py", line 368, in only_on_root return func(*args,**kwargs) File "/home/yd742/software/withpysci/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/backend_bases.py", line 2220, in print_figure **kwargs) File "/home/yd742/software/withpysci/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/backends/backend_agg.py", line 510, in print_png filename_or_obj = open(filename_or_obj, 'wb') IOError: [Errno 2] No such file or directory: 'plots/Bullet_BMag_0_Profile1D_0_RadiusMpc_BMag.png' ======================= I'm using yt Version = 2.6.1 Changeset = c994959ed3be ======================= I would very much appreciate it if anyone could help me on this. Thank you very much. Regards, Yuxiao

2 1

Add to list
by Azton I Wells 18 Feb '16

18 Feb '16

Can I please be added to the users list? Thanks, Azton

2 1

yt-2.x installation problem on Mac 10.11
by Pengfei Chen 18 Feb '16

18 Feb '16

Hi all, I'm trying to install yt-2.x on my Mac 10.11. I could use get_yt.sh to install yt-2.x. But I need to add "--enable-shared" while installing python, so that I could use inline python later on with yt. Is there a way that I could modify get_yt.sh to add the option "--enable-shared" while installing python? I also tried to install yt-2.x with install_script.sh, but I got the following error: Installing Python. This may take a while, but don't worry. yt loves you. ******************************************** FAILURE REPORT: ******************************************** -d /Users/madcpf/Documents/shared_yt2/lib/python2.7 -f \ -x 'bad_coding|badsyntax|site-packages|lib2to3/tests/data' \ /Users/madcpf/Documents/shared_yt2/lib/python2.7 Traceback (most recent call last): File "/Users/madcpf/Documents/shared_yt2/lib/python2.7/compileall.py", line 16, in <module> import struct File "/Users/madcpf/Documents/shared_yt2/lib/python2.7/struct.py", line 1, in <module> from _struct import * ImportError: No module named _struct make: *** [libinstall] Error 1 ******************************************** ******************************************** Failure. Check /Users/madcpf/Documents/shared_yt2/yt_install.log. The last 10 lines are above. Could someone please give me some suggestions about this? Thanks, Pengfei

1 0

yt install on mac 10.11.2
by Azton Wells 17 Feb '16

17 Feb '16

Hello all, I am trying to install yt on Mac 10.11.2. My most current efforts use ³yt² branch, and I am trying to install from the install_script.sh. We have modified the python installation section of the script from: ./configure --prefix=${DEST_DIR}/ ${PYCONF_ARGS} To: ./configure CPPFLAGS=-I/usr/local/opt/openssl/include --enable-shared --prefix=${DEST_DIR}/ ${PYCONF_ARGS} I have also added : export LD_LIBRARY_PATH=/usr/local/opt/openssl/lib:$LD_LIBRARY_PATH I have used: Brew install openssl Brew link force openssl My installation fails with: ******************************************** FAILURE REPORT: ******************************************** checking size of int... 0 checking size of long... 0 checking size of void *... 0 checking size of short... 0 checking size of float... 0 checking size of double... 0 checking size of fpos_t... 0 checking size of size_t... configure: error: in `/Users/Azton/Research/yt/src/Python-2.7.9': configure: error: cannot compute sizeof (size_t) See `config.log' for more details Using the get_yt.sh script that uses miniconda works, but I don¹t know if the ³conda install python² command will include ³--enable-shared² My question is two part: Does anyone have an idea for using the install_script.sh? (2) Failing using the install_script, would using the get_yt.sh install python with enable-shared? Thanks for any help, Azton

1 0

Default Units for new Enzo Fields
by Andrew James Emerick 17 Feb '16

17 Feb '16

Hi all, I wasn't sure if this should go in the yt-users list or Enzo-dev, as I'm not sure where the solution lies. I've defined some new fields in Enzo that have units of density that yt is reading as having dimensionless units. Are the units for fields defined and outputted somewhere in Enzo (to be read by yt)? Or does yt assume units depending on the name of the field? If the former, where do I tell the code that my field has density units when its written to file? I see "DataUnits" throughout the code, but I'm not sure if this is relevant or how to use it. If this is a yt-side thing, is there an easy way to just have yt read in my new fields with the correct units without me manually changing them once I've loaded a dataset? Andrew -- Graduate Student Columbia University Department of Astronomy

4 3

fontsize in ProfilePlot
by Alex Hill 16 Feb '16

16 Feb '16

Hi all, I’m trying to modify the font and/or figure size of a profile plot. ProfilePlot doesn’t appear to have a fontsize or figure_size option or any other option that would allow customization of these parameters (unlike, say, PhasePlot or SlicePlot). There is also no set_font_size or set_figure_size option I see to modify the font size after creating the plot. For example, with PhasePlot, I could do this: g = yt.PhasePlot(d.all_data(),'dens','temp',['cell_volume'], fontsize=18) g.set_figure_size(4) The equivalent options aren’t present in ProfilePlot: f = yt.ProfilePlot(d.all_data(),'dens',['cell_volume'], fontsize=18) TypeError: __init__() got an unexpected keyword argument ‘fontsize' How can I modify the font size of a profile plot? Cheers, Alex --------- Alex Hill Senior Postdoctoral Research Associate Office: KINSC Link L106 Department of Astronomy, Haverford College 370 Lancaster Ave, Haverford, PA 19041 USA phone: +1 484 297 2136 email/iMessage: ashill(a)haverford.edu

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problem with 0D point object
by Juan Camilo Ibanez Mejia 16 Feb '16

16 Feb '16

Hi all, I’m having problems using the 0D point object with a Flash dataset. When I try to retrieve the information from a coordinate with negative x or y coordinates I get an empty result. An example is given in http://paste.yt-project.org/show/6247/. ps: My dataset goes between +-500 pc in the x and y direction, so there is data there. Thanks for you help. Cheers, Juan

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Runtime Warning
by Sushilkumar 14 Feb '16

14 Feb '16

Dear yt: Upon running a script I get the following warning, which does not occur for other scripts. Could you let me know what this warning means and whether it is a cause of concern? /state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_modifications.py:387: RuntimeWarning: invalid value encountered in divide pixX /= nn /state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_modifications.py:388: RuntimeWarning: invalid value encountered in divide pixY /= nn Thanks in advance On Sat, Feb 13, 2016 at 12:52 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: Error in making light ray for a gadget dataset (Matthew Turk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 12 Feb 2016 14:42:08 -0600 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Error in making light ray for a gadget dataset > Message-ID: > <CALO3=5HRmi3919BJC9noCtCaS3BCV96== > HDxO1qwamxgnNE2Mw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Bili, > > Hm, I'm honestly not sure. This looks like an oddity in the way the octree > is being constructed in spatial dimensions. Any chance you can reproduce > this with a ray or ortho_ray object, which should simplify the number of > moving parts? > > On Tue, Feb 9, 2016 at 2:04 PM, Bili Dong - Gmail <qobilidop(a)gmail.com> > wrote: > > > Hi yt users, > > > > I'm trying to make a light ray for a gadget dataset using this script: > > http://paste.yt-project.org/show/6234/ > > > > But I get the following error: > > > > ``` > > > > /Users/qobilidop/repos/yt/yt/geometry/geometry_handler.py in > fcoords(self) 320 c = obj.select_fcoords(self.dobj) 321 > if c.shape[0] == 0: continue--> 322 > ci[ind:ind+c.shape[0], :] = c 323 ind += c.shape[0] 324 > return ci > > ValueError: could not broadcast input array from shape (81,3) into shape > (40,3) > > > > ``` > > > > > > My yt is on the changeset d47150dfbde6. > > > > > > I'm wondering if I'm doing it the correct way? And how could I solve the > problem? > > > > > > Thanks, > > > > Bili > > > > > > _______________________________________________ > > 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/201… > > > > ------------------------------ > > 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 96, Issue 18 > **************************************** > -- *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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yt errors
by tazkera haque 12 Feb '16

12 Feb '16

Hi , I am trying to run a python file with yt packages on STAMPEDE. and getting some errors each time. I think the error is due to some installation error of yt at first place. can you please look at both my code and error and send me the solutions to solve the problem. both the files are attached for your convenience. regards Tazkera

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yt help deriving new fields
by tazkera haque 11 Feb '16

11 Feb '16

Hi, I need a little help in defining a new derived field. my goal is to find if a stellar system eject some mass or not. I am attaching the derived_field_list from the file I have. I am trying to define the total energy of the system E=0.5*m*v**2+gravitational potential energy*m I am completely new to python and trying to get hold of the language through yt. I am attaching my efforts and the errors. please help me fix that. Thanks in advance. Tazkera

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ANN: yt 3.2.3 release
by Nathan Goldbaum 11 Feb '16

11 Feb '16

We are proud to announce the release of yt 3.2.3! yt (http://yt-project.org) is an open-source, community-developed toolkit for analysis and visualization of volumetric data of all types, with a particular emphasis on astrophysical and nuclear engineering simulations. Version 3.2.3 is a regularly scheduled bugfix release including fixes for a number of issues reported since the release of yt 3.2.2. The changes in this version are summarized below and include a number of bugfixes, performance improvements, and documentation improvements. We urge all users of prior versions to upgrade to yt 3.2.3 immediately. Summary of Changes ----------------------------- Fix an issue with parallel decomposition in the stream frontend under Python3. See PR 1862 <https://bitbucket.org/yt_analysis/yt/pull-requests/1862/bugfix-fix-python-3…> and PR 1927 <https://bitbucket.org/yt_analysis/yt/pull-requests/1927/improve-treatment-o…> Fix an issue with initializing LightRay objects with both start_position and a redshift range. See PR 1863 <https://bitbucket.org/yt_analysis/yt/pull-requests/1863/bugfix-close-loopho…> Work around an an issue the prevents compiling yt using Python 3.5.0 by disabling OpenMP support. This is fixed in Python 3.5.1. See PR 1871 <https://bitbucket.org/yt_analysis/yt/pull-requests/1871/do-not-try-to-inclu…> Fix an issue with parsing some parameters in NMSU ART datasets. See PR 1875 <https://bitbucket.org/yt_analysis/yt/pull-requests/1875> Ensure ARTIO frontend creates a metal_density when outputs contain both Ia and II metal production. See PR 1876 <https://bitbucket.org/yt_analysis/yt/pull-requests/1876/adding-checks-to-as…> Convert profile extrema to output_units instead of units, to be consistent with behavior of array_like_field. See PR 1882 <https://bitbucket.org/yt_analysis/yt/pull-requests/1882/bugfix-convert-prof…> Only set output_units after units has been set. See PR 1887 <https://bitbucket.org/yt_analysis/yt/pull-requests/1887/bugfix-only-set-out…> Fix casting errors in the SDF frontend under NumPy 1.10 and newer. See PR 1890 <https://bitbucket.org/yt_analysis/yt/pull-requests/1890/fixed-casting-error…> Improved Python3 compatibility. See PR 1899 <https://bitbucket.org/yt_analysis/yt/pull-requests/1899/bugfix-py3-compat/d…>, PR 1920 <https://bitbucket.org/yt_analysis/yt/pull-requests/1920/replace-iteritems-w…>, PR 1934 <https://bitbucket.org/yt_analysis/yt/pull-requests/1934/use-sixbytesio-inst…>, and PR 1931 <https://bitbucket.org/yt_analysis/yt/pull-requests/1931/use-bytesio-in-the-…> PlotWindow helpers for showing and hiding colorbars and axis annotations now return the PlotWindow instance. This improves viewing in the notebook. See PR 1905 <https://bitbucket.org/yt_analysis/yt/pull-requests/1905/making-plotwindow-s…> Corrected error in docstring for load_uniform_grid. See PR 1910 <https://bitbucket.org/yt_analysis/yt/pull-requests/1910/correct-docstring-f…> Fix sphinx syntax error in getting help guide. See PR 1928 <https://bitbucket.org/yt_analysis/yt/pull-requests/1928/fix-rst-syntax-erro…> Improve docs rendering on Firefox for Linux and possible other browsers. See PR 1929 <https://bitbucket.org/yt_analysis/yt/pull-requests/1929/docs-increase-margi…> Fix issues parsing GDF files under Python3. See PR 1930 <https://bitbucket.org/yt_analysis/yt/pull-requests/1930/ensure-gdf-unit-nam…> Produce better error message when load_uniform_grid is passed data with an incorrect shape. See PR 1933 <https://bitbucket.org/yt_analysis/yt/pull-requests/1933/fail-early-when-loa…> Fix issue with plotting cylindrical data. See PR 1940 <https://bitbucket.org/yt_analysis/yt/pull-requests/1940/reintroduce-sanitiz…> Fix issues with eps writer docs, rendering, and compatibility. See PR 1941 <https://bitbucket.org/yt_analysis/yt/pull-requests/1941/eps_writer-update/d…> and PR 1963 <https://bitbucket.org/yt_analysis/yt/pull-requests/1963/bugfix-removing-lar…> Produce a better error message with export_fits is not able to determine any output fields. See PR 1943 <https://bitbucket.org/yt_analysis/yt/pull-requests/1943/better-error-messag…> Fixed parameter parsing for reduced dimensionality Boxlib datasets. See PR 1947 <https://bitbucket.org/yt_analysis/yt/pull-requests/1947> Fix a number of issues with ds.find_field_values_at_point and ds.find_field_values_at_points. See PR 1950 <https://bitbucket.org/yt_analysis/yt/pull-requests/1950/fix-a-number-of-iss…> Adding a cache for selector object hashes. See PR 1965 <https://bitbucket.org/yt_analysis/yt/pull-requests/1965/adding-a-hash-cache…> Import HUGE from yt.utilities.physical_ratiois. See PR 1971 <https://bitbucket.org/yt_analysis/yt/pull-requests/1971> Compatible with upcoming NumPy 1.11 release. See PR 1969 <https://bitbucket.org/yt_analysis/yt/pull-requests/1969/compatible-with-upc…> Coming Soon! ------------------- The next major release of yt will be version 3.3, which is slated to include an overhaul of the volume rendering system, support for analyzing and visualizing unstructured mesh data, a new system for saving and restoring data objects, and a way to specify unit systems when loading data. Some of this functionality is already available on the development branch of yt. We welcome feedback from early testers. Standard Installation Methods ---------------------------------------- As with previous releases, you can install yt from source using one of the following methods. 1) From the install script (http://yt-project.org/#getyt ): If you previously installed yt from the install script, you can update your installation in-place using the following command: # Update $ yt update If you are on the “stable” branch, updating will bring you from an earlier version to 3.2.3, whereas if you are on the development “yt” branch, only the changes since your last update should be incorporated. To install from scratch, do the following: # Installation $ wget http://bitbucket.org/yt_analysis/yt/raw/stable/doc/install_script.sh $ bash install_script.sh 2) From pip (source or binary wheel, see below for more details): # Installation $ pip install yt # Update $ pip install -U yt 3) From the Anaconda Python Distribution (https://store.continuum.io/cshop/anaconda/): # Installation $ conda install yt # Update $ conda update yt Note that it might take up to a week for the conda package built by Continuum Analytics to be updated for yt 3.2.3. Installing Binary Packages via pip ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ If you do not have compilers available, it is also possible to install binary packages (“wheels”) using pip on Windows and Mac OS X (64-bit only for both). This has the advantage of not needing to install yt from source using a proper compiler setup, which has caused occasional problems on both of these platforms and prevented us from installing yt easily on other Python distributions. Note that it may take several days for binary wheels for yt 3.2.3 to be uploaded. We have so far been able to install and run the binary distribution via pip on the following platforms and Python stacks: Windows x86_64: Enthought Canopy Python (https://www.enthought.com/products/canopy/) WinPython (http://winpython.sourceforge.net/) Mac OS X x86_64: Enthought Canopy Python (https://www.enthought.com/products/canopy/) Homebrew Python (http://brew.sh/) Python.org Python Mac OS X’s system Python MacPorts Python (https://www.macports.org/) This is somewhat experimental, so other distributions may work (or not), please submit bug reports or successes to the mailing list or to the Bitbucket issues page (http://bitbucket.org/yt_analysis/yt/issues). Both Python 2.7 and Python 3.4 are supported. The dependencies for installing yt via this method are the same as from source: NumPy h5py HDF5 SymPy Matplotlib IPython (not required, but strongly recommended) To install a new version of yt on one of these platforms, simply do $ pip install yt and you should get the binary distribution automatically. Also, if your python installation is system-wide (e.g., the Mac system Python) you might need to run pip with administrator privileges. For more information, including more installation instructions, links to community resources, and information on contributing to yt’s development, please see the yt homepage at http://yt-project.org and the documentation for yt 3.2.3 at http://yt-project.org/doc. yt is the product of a large community of developers and users and we are extraordinarily grateful for and proud of their contributions. Please forward this announcement on to any interested parties. As always, if you have any questions, concerns, or run into any trouble updating please don't hesitate to send a message to the mailing list or stop by our IRC channel. All the best, Nathan Goldbaum, on behalf of the yt development team

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Google Summer of Code 2016, GSoC2016
by Raniere Silva 08 Feb '16

08 Feb '16

Hi all, Since yt is a NumFOCUS affiliated project and NumFOCUS will apply to be a mentoring organization on GSoC I want to know (1) if yt is planning to apply this year and (2) if want to apply under NumFOCUS umbrella. yt is welcome and encouraged to apply as separate mentoring organizations directly with Google. We're happy to help you fill out your application and improve your ideas pages, as well as link your page to help students find you. We may also be able to be a reference for you. It is totally fine if you want to use the NumFOCUS umbrella org as a backup plan in case you don't get selected and we do! Cheers, Raniere

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Can I annotate the redhsift on a volume rendering plot?
by Joseph Smidt 08 Feb '16

08 Feb '16

Hey everyone, If I want to append the redshift on a normal plot I can do so like: plot.annotate_timestamp(redshift=True) However, If with volume rendering I do something like cam = ds.camera(cc, L, W, Npixels, tf) im = cam.snapshot("my_vr.png", clip_ratio=6.0,transparent=True) there seems to be no such intermediate method like method cam.annotate_timestamp(redshift=True) I can do. Is there a way to add the redshift annotation to a volume rendering plot? Thanks. -- ------------------------------------------------------------------------ Joseph Smidt <josephsmidt(a)gmail.com> Theoretical Division P.O. Box 1663, Mail Stop B283 Los Alamos, NM 87545 Office: 505-665-9752 Fax: 505-667-1931

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SlicePlot(), How to write the plotted values to a file?
by Reju Sam John 07 Feb '16

07 Feb '16

Hi, I would like to know, how to write the plotted values of a 'SlicePlot()' to a file? For example, I made a slice plot with the following line. p = SlicePlot(pf,0,'My_Field',[0.5,0.5,0.5],(20,'Mpc')) But how can I write the plotted values to a file? Thankyou. Reju Sam John

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Quick question
by Kailash Faris 06 Feb '16

06 Feb '16

I havent been on yt in about a month and I receive this error message when I use the command 'yt notebook' http://paste.yt-project.org/show/6226/ Does anyone know how to fix it?

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Confusing distribution of the number of particles per octree node
by Bili Dong - Gmail 04 Feb '16

04 Feb '16

Hi all, I'm looking at the number of particles per octree node (n_p hereafter) (a.k.a. the ('deposit', 'all_count') field) and find the results confusing. To my understanding, an octree node is refined (into 8 sub-nodes) only when n_p (of that node) > n_ref, so eventually n_p.mean (the average value of n_p) should be greater than n_ref/8. But the number I get is much smaller. When n_ref = 64, I get n_p.mean approximately 2 for all my tests. I'm wondering if my understanding of the octree refining process if correct? And if so, how to explain the weird distribution of n_p? Here's the link to my tests: https://nbviewer.jupyter.org/gist/qobilidop/d8f4cb85f1b465770854 Thanks, Bili

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Re: [yt-users] yt-users Digest, Vol 96, Issue 2
by Slavin, Jonathan 04 Feb '16

04 Feb '16

Hi Nathan, Oddly when I just updated via conda ("conda update yt") I got version 3.2.2. Jon On Thu, Feb 4, 2016 at 11:15 AM, <yt-users-request(a)lists.spacepope.org> wrote: > Message: 1 > Date: Thu, 4 Feb 2016 10:14:46 -0600 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org>, " > yt-dev(a)lists.spacepope.org" > <yt-dev(a)lists.spacepope.org> > Subject: [yt-users] ANN: yt 3.2.3 release > Message-ID: > < > CAJXewOmW0BCr0Z9_kYdmeWamM90k0jJWCxJRYvkxgHRpkO1ziw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > We are proud to announce the release of yt 3.2.3! > > yt (http://yt-project.org) is an open-source, community-developed toolkit > for > > analysis and visualization of volumetric data of all types, with a > particular > > emphasis on astrophysical and nuclear engineering simulations. > > Version 3.2.3 is a regularly scheduled bugfix release including fixes for a > -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

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DM density profiles
by Junhwan Choi (최준환) 03 Feb '16

03 Feb '16

Hi yt user, I make a simple DM and gas density profile for my enzo simulation with following script: ====================== import matplotlib as matplotlib matplotlib.use('Agg') import yt import yt.units as units import numpy as np import matplotlib.pyplot as plt def _radiuspc(field, data): return data[('radius')].in_units('pc') yt.add_field('radiuspc', function=_radiuspc, units="pc") Nbin= 100 rmax = 4000 index = 60 ds = yt.load("../DD%04d/DD%04d" % (index,index)) ds.index ad= ds.all_data() center = ds.find_max(("gas", "density"))[1] my_sphere = ds.sphere(center, rmax*units.pc) rmin = max([1.0e-4,2.0*ds.index.get_smallest_dx().in_units('pc')]) profile = yt.Profile1D(my_sphere, 'radiuspc', Nbin, x_min=rmin, x_max=rmax, x_log=True, weight_field='cell_volume') profile.add_fields(('gas','density')) profile.add_fields(('gas','dark_matter_density')) profile.add_fields(('deposit','all_density')) plt.plot(np.log10(profile.x), np.log10(profile[('gas','density')]), label="('gas','density')", linestyle="-", color='g') plt.plot(np.log10(profile.x), np.log10(profile[('gas','dark_matter_density')]), label="('gas','dark_matter_density')", linestyle="-", color='r') plt.plot(np.log10(profile.x), np.log10(profile[('deposit','all_density')]), label="('deposit','all_density')", linestyle="-", color='b') plt.legend(loc=0,prop={'size':9}) plt.savefig('DMTest') ====================== The only particle in the simulation is the dark matter so that profile[('gas','dark_matter_density')] and profile[('deposit','all_density')] should be same. However, as shown in the attached figure, they are very different. I would like to ask a few questions regarding to this plot. 1) Why do profile[('gas','dark_matter_density')] and profile[('deposit','all_density')] show significant difference? 2) What limit the minimum r in profile[('deposit','all_density')]? 3) If I would like to make total density profile, what do I do? I think that profile[('deposit','all_density')] is more liable result. Can I add data[('gas','density')] and data[('deposit','all_density')], two different field types, in the derived field? Thank you in advance, Junhwan Choi _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Can I specify the particle type when loading data?
by Bili Dong - Gmail 03 Feb '16

03 Feb '16

Hi yt users, I'm working with a particle dataset and I'm wondering if it is possible to only load a certain type of particle fields from the snapshot as my dataset? For example, there might be 'PartType0' and 'PartType1' in the snapshot, but I only want to load 'PartType0'. The reason I want to do this is that, to my understanding, the octree of the particle dataset is constructed adaptively according to the number of particles, including all types of particles in the dataset. But I want the octree constructed only according to the type of particles I'm interested in. Is it possible? Thanks, Bili

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faster method for getting frbs?
by Slavin, Jonathan 03 Feb '16

03 Feb '16

Hi all, I've been using yt to handle FLASH AMR data stored in HDF5 files. I want to cycle through a series of images generated, plotting each as I go using matplotlib. To do this I have (somewhat simplified): for f in files: ds = yt.load(f) slc = ds.slice(2,0) # its 2D r-z data frb = slc.to_frb(width=(Rmax,'pc'), height=(Zmax, 'pc'), resolution=(NX,NY)) image = np.array(frb['temp']) imshow(img) etc. This works the way I want it to, but is very slow. Is there a way to speed it up? Thanks, Jon -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

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