Mailman 3 May 2016 - yt-users

error while submitting development queue job to STAMPEDE supercomputer
by turhan nasri May 27, 2016

May 27, 2016

Hi people, though I am not sure if this is the right place to ask this, but I have submitted a development queue job to STAMPEDE supercomputer and I was using yt toolkit in my script, I got the following error after around half an hour of running the job. [c557-702.stampede.tacc.utexas.edu:mpispawn_0][child_handler] MPI process (rank: 0, pid: 26868) terminated with signal 9 -> abort job [c557-702.stampede.tacc.utexas.edu:mpirun_rsh][process_mpispawn_connection] mpispawn_0 from node c557-702 aborted: MPI process error (1) TACC: MPI job exited with code: 1 can anyone please shed light on the error here? with the development queue the maximum code runtime is 2 hours. thanks in advance. -Turhan

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tilting disk issues
by Stephanie Tonnesen May 25, 2016

May 25, 2016

Hi all, I am simulating a single idealized galaxy and select a disk region to get the rotational velocity (see attached code below). My problem is that changing my angular momentum vector doesn't change the velocity profile! Can anyone tell me what is going on here? Thanks, Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes(a)gmail.com

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HaloMassFunction
by Io Odderskov May 23, 2016

May 23, 2016

Dear Yt-users. I have just started used Yt, which I find to be very useful. However, I am having trouble converting the units of the output of the HaloMassFcn-function to match other data sets. I have tried comparing the Tinker 2008 fitting function produced by HaloMassFcn to the halo mass function from the Halo Finder Comparison Project (https://arxiv.org/pdf/1104.0949v1.pdf) and to a halo catalogue from the DEUS consortium (http://www.deus-consortium.org/deuvo/#download). In these cases, the halo masses are given in Msun/h, and the cumulative halo number density in h^3/Mpc^3. According to the Yt-documentation, the masses output by the HaloMassFcn-function should be in Msun, and the number densities in 1/Mpc^3. To convert to Msun/h and h^3/Mpc^3, I multiply the masses by h, and divide the number densities with h^3. In the attached figure, this corresponds to the line labelled "Tinker2008 - masses multiplied by h", which does not match the other data sets very well. If I instead divide the masses by h, I get the line labelled Tinker2008 - masses divided by h", which looks much better. But I really can't see how to justify this conversion. I hope you can help me figure out what I'm doing wrong :-) Thanks in advance! Best regards, Io. script: http://paste.yt-project.org/show/6530/ image http://imgur.com/otWW3QJ version: Version = 3.2.3 Changeset = bdea84d95099 (stable) @ P.S. When I tried to do "yt upload_image", I got a 404 error. Perhaps imgur changed their API?

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xstick label in yt slice plot
by Jiang, Yanfei May 20, 2016

May 20, 2016

Hi, I am trying to make a slice plot with the new capability for spherical polar grid in Athena++ data John developed. The attached notebook.png shows what I am doing. I take a slice and the origin is set to "domain". The image.png is the image from the notebook. In the slice image, the empty space near the center corresponds to the inner radial boundary of the original spherical coordinate, which is 2 in this case. Therefore, I think the x stick where is 0 in the plot should be 2. Do you know any way to fix this? Thanks. -- Yan-Fei Jiang Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138

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Problem with gradient of a derived field
by José Utreras May 19, 2016

May 19, 2016

Hi everyone, I'm having the following problem: I want to calculate the gradient field of the angular velocity which I have defined as follows: >def _Omega(field,data): > if data.has_field_parameter("bulk_velocity"): > bv = data.get_field_parameter("bulk_velocity").in_units("cm/s") > else: > bv = data.ds.arr(np.zeros(3), "cm/s") > xv = data["gas","velocity_x"] - bv[0] > yv = data["gas","velocity_y"] - bv[1] > center = data.get_field_parameter('center') > x_hat = data["x"] - center[0] > y_hat = data["y"] - center[1] > r = np.sqrt(x_hat*x_hat+y_hat*y_hat) > x_hat /= r**2 > y_hat /= r**2 > > return np.sqrt((xv*y_hat-yv*x_hat)**2) >yt.add_field("Omega", function=_Omega,take_log=False, units=r"1/yr",validators=[ValidateParameter('bulk_velocity')]) This is the profile I have got using the SlicePlot tool: https://drive.google.com/file/d/0B43CkTTj8OeOcy16TkFaZlBhRE0/view?usp=shari… So, it is a function of radius. The density is also a function of radius. The problem is that if I use >grad_fields = ds.add_gradient_fields(("gas","Omega")) >slice = yt.SlicePlot(ds, 'z', "Omega_gradient_x") I get this https://drive.google.com/file/d/0B43CkTTj8OeOLUxGVUJSQ253TE0/view?usp=shari… the sign should only change across x=0. I did the same for the density field getting the correct behaviour. I've also tried to define the gradient field >def _vorticity_2(field, data): > f = (data[ftype, "Omega"][sl_right,sl_center,sl_center] - > data[ftype, "Omega"][sl_left,sl_center,sl_center]) \ > / (div_fac*just_one(data["index", "dx"])) > > new_field = data.ds.arr(np.zeros_like(data[ftype, "velocity_z"], > dtype=np.float64), > f.units) > new_field[sl_center, sl_center, sl_center] = f > return new_field But I got the same results. If I'm doing something wrong please let me know. Cheers! Jose Utreras

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ANN: Grackle 2.2 released
by Britton Smith May 18, 2016

May 18, 2016

Greetings everyone, I am pleased to announce the release of version 2.2 of the Grackle chemistry and cooling library. The Grackle is a library for chemistry and radiative cooling in astrophysical simulations and models. Grackle 2.2 is fully backward compatible with version 2.1. No changes to simulation code interfaces are required. Grackle 2.2 adds some exciting new features: * Test suite with continuous integration testing: Grackle now uses py.test to run a suite of unit and answer tests. The tests can be run locally by users/developers to verify proper behavior. The tests are also automatically run on drone.io whenever the main repository is updated. Thanks to Nathan Goldbaum for adding this! * OpenMP support: Grackle can now be run with OpenMP parallelism. All of the Grackle's solvers are now threaded and show significant speedup when called with >16^3 particles/cells. Thanks to Hsi-Yu Schive for this work! * Updated primordial chemistry rates: updated reactions rates for H ionization, H- formation/destruction, H2 dissociation, H2+ formation, H2 LTE cooling, and HD low density cooling. Added reactions for collisional ionization of H by H and H by He. Thanks to Simon Glover for this! * Added support for old-style cooling tables used in the original Cloudy cooling module in Enzo. Added a table for high density metal cooling, cloudy_metals_2008_3D.h5. Minor enhancements: * Pygrackle, Grackle's python interface, significantly upgraded, refactored, and cleaned up. * Fixed bug in comoving/proper conversion in calculation of temperature in tabulated mode. This only affected calls to calculate_temperature in tabulated mode, but not the actual cooling solver. * Documentation improvements. This is the last release with the current API. A number of new features are under development, such as adding new species to the solver, passing arrays of heating rates, and support for radiative transfer. All of these will require breaking backward compatibility. However, a new API is being developed that will allow for features to continue to be added without any further API break. This will likely be released as Grackle 3.0 some time this summer. The Grackle can be obtained at: https://bitbucket.org/grackle/grackle The documentation can be found here: http://grackle.readthedocs.io/ -The Grackle development team

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Drawing order of plot annotations
by Daniel Fenn May 16, 2016

May 16, 2016

Hi, Is it possible to control the order that plot annotations are drawn? For example, right now I'm plotting density contours, and I'd like to add a circle annotation on top. However, when I add the circle, it's drawn behind the density contours. This happens no matter the order that I add the annotations in my script. Is there a straightforward way to force the circle to be drawn on top of the density contours, so that it's not obscured? Thanks, Dan

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Total Active Particles?
by David Collins May 16, 2016

May 16, 2016

Hi, Everybody! Is there a field or function that totals the number of active particles? I see that I can get it from the grid, but I don't see anything for the whole ds. Thanks, d. -- -- Sent from a computer.

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path_element_z error
by David Collins May 13, 2016

May 13, 2016

Hi, Everybody! I have an odd error, I was wondering if this is pebkac or a yt glitch. If I try to do a projection, first it complains about 'creation_time' not existing, then on a subsequent call, it complains about 'path_element_z' not existing. The only difference between this run and other similar Enzo runs that do work is this one has a handful of active particles. Is there something else I need to do to get those to work? I'm running yt 3.2.3. Thanks! d. >>> ds = yt.load(path) >>> proj = yt.ProjectionPlot(ds,ax,field) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "p33_harry_plotter.py", line 40, in <module> proj = yt.ProjectionPlot(ds,ax,field) #,weight_field=weight_fields.get(field,None),method=methods.get(field,'integrate')) File "/u/sciteam/dcollins/local-yt-2016-04-12-nathan/src/yt-conda/lib/python2.7/site-packages/yt/visualization/plot_window.py", line 1437, in __init__ field_parameters = field_parameters, method = method) File "/u/sciteam/dcollins/local-yt-2016-04-12-nathan/src/yt-conda/lib/python2.7/site-packages/yt/data_objects/construction_data_containers.py", line 255, in __init__ field = self._determine_fields(ensure_list(field)) File "/u/sciteam/dcollins/local-yt-2016-04-12-nathan/src/yt-conda/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 518, in _determine_fields finfo = self.ds._get_field_info("unknown", fname) File "/u/sciteam/dcollins/local-yt-2016-04-12-nathan/src/yt-conda/lib/python2.7/site-packages/yt/data_objects/static_output.py", line 505, in _get_field_info self.index File "/u/sciteam/dcollins/local-yt-2016-04-12-nathan/src/yt-conda/lib/python2.7/site-packages/yt/data_objects/static_output.py", line 326, in index self.create_field_info() File "/u/sciteam/dcollins/local-yt-2016-04-12-nathan/src/yt-conda/lib/python2.7/site-packages/yt/data_objects/static_output.py", line 377, in create_field_info self.add_particle_union(pu) File "/u/sciteam/dcollins/local-yt-2016-04-12-nathan/src/yt-conda/lib/python2.7/site-packages/yt/data_objects/static_output.py", line 435, in add_particle_union funits = self._get_field_info(s, field).units File "/u/sciteam/dcollins/local-yt-2016-04-12-nathan/src/yt-conda/lib/python2.7/site-packages/yt/data_objects/static_output.py", line 543, in _get_field_info raise YTFieldNotFound((ftype, fname), self) yt.utilities.exceptions.YTFieldNotFound: Could not find field '('io', 'creation_time')' in DD0010. >>> proj = yt.ProjectionPlot(ds,ax,field) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "p33_harry_plotter.py", line 40, in <module> proj = yt.ProjectionPlot(ds,ax,field) #,weight_field=weight_fields.get(field,None),method=methods.get(field,'integrate')) File "/u/sciteam/dcollins/local-yt-2016-04-12-nathan/src/yt-conda/lib/python2.7/site-packages/yt/visualization/plot_window.py", line 1437, in __init__ field_parameters = field_parameters, method = method) File "/u/sciteam/dcollins/local-yt-2016-04-12-nathan/src/yt-conda/lib/python2.7/site-packages/yt/data_objects/construction_data_containers.py", line 258, in __init__ self.get_data(field) File "/u/sciteam/dcollins/local-yt-2016-04-12-nathan/src/yt-conda/lib/python2.7/site-packages/yt/data_objects/construction_data_containers.py", line 332, in get_data self._handle_chunk(chunk, fields, tree) File "/u/sciteam/dcollins/local-yt-2016-04-12-nathan/src/yt-conda/lib/python2.7/site-packages/yt/data_objects/construction_data_containers.py", line 424, in _handle_chunk dl = chunk["index", "path_element_%s" % (ax_name)] File "/u/sciteam/dcollins/local-yt-2016-04-12-nathan/src/yt-conda/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 253, in __getitem__ self.get_data(f) File "/u/sciteam/dcollins/local-yt-2016-04-12-nathan/src/yt-conda/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 702, in get_data fluids, self, self._current_chunk) File "/u/sciteam/dcollins/local-yt-2016-04-12-nathan/src/yt-conda/lib/python2.7/site-packages/yt/geometry/geometry_handler.py", line 239, in _read_fluid_fields fields_to_read, fields_to_generate = self._split_fields(fields) File "/u/sciteam/dcollins/local-yt-2016-04-12-nathan/src/yt-conda/lib/python2.7/site-packages/yt/geometry/geometry_handler.py", line 220, in _split_fields raise YTFieldNotFound((ftype,fname), self.ds) yt.utilities.exceptions.YTFieldNotFound: Could not find field '('index', 'path_element_z')' in DD0010. -- -- Sent from a computer.

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Camera/Off Axis Options
by Sushilkumar May 11, 2016

May 11, 2016

Dear Suoqing Ji: I could not find the script you attached neither in the email text nor in the google drive On Wed, May 11, 2016 at 2:12 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: Camera/Off Axis Optioons (Suoqing Ji) > 2. LightRay class (Fei Li) > 3. Re: LightRay class (Cameron Hummels) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 11 May 2016 11:25:53 -0700 > From: Suoqing Ji <suoqing(a)physics.ucsb.edu> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Camera/Off Axis Optioons > Message-ID: <3BCF6B56-E116-4C42-AED8-13E541829F86(a)physics.ucsb.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Sushil, > > I do not know which file in your google drive is the one you used to make > the plot, but I found some potential problems in a similar script > yt_frb_offaxis.py: > > 1. When you load the data, with data = dict(?), the key values should be > ?velocity_x/y/z? instead of ?cutting_plane_velocity_x/y/z?, since the later > can be derived from the velocity field you provided; > > 2. The data for stream plot should not be normalized; > > Here I attached the script, and you should be able to produce the figure > without problem. > > Best wishes, > -- > Suoqing JI > Ph.D Candidate > Department of Physics > University of California, Santa Barbara > http://web.physics.ucsb.edu/~suoqing > > > > On May 11, 2016, at 9:01 AM, Sushilkumar <sushil.sush19us(a)gmail.com> > wrote: > > > > Dear Suoqing JI: > > > > I tried with both factor=1 and deleting the ::factor (yt_frb_offaxis.py) > but the same issue still persist (L(1,0,0) N(0,1,1).png). The only > difference being that without the "factor" it takes longer time to compute > than for a "factor=20". > > > > For same data if I use "slc.annoate_streamline" gives approximately > proper results (UniformGridData_Slice_y_field_x_t000.png) but without the > offaxis > > > > Any suggestions. > > > > Thanks in advance > > > > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> > > -- > > 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." > > > > _______________________________________________ > > 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… > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: annotation.py > Type: text/x-python-script > Size: 1548 bytes > Desc: not available > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 2 > Date: Wed, 11 May 2016 19:06:49 +0000 > From: Fei Li <lif.li(a)mail.utoronto.ca> > To: "yt-users(a)lists.spacepope.org" <yt-users(a)lists.spacepope.org> > Subject: [yt-users] LightRay class > Message-ID: > < > CY1PR03MB2378B7748FFAB0F47A379797BF720(a)CY1PR03MB2378.namprd03.prod.outlook.com > > > > Content-Type: text/plain; charset="iso-8859-1" > > Hello yt users, > > I tried to use the LightRay class to generate a light ray for one of my > gridded simulation snapshots. The simulation is from the FIRE project which > used a heavily modified version of Gadget-3 called GIZMO written by Phil > Hopkins. And the error I got is: ValueError: need more than 1 value to > unpack. > > Here is my script: > > $ python > Python 2.7.11 |Continuum Analytics, Inc.| (default, Dec 6 2015, 18:08:32) > [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > Anaconda is brought to you by Continuum Analytics. > Please check out: http://continuum.io/thanks and https://anaconda.org > >>> import yt > >>> import trident > >>> fn='/cita/h/home-2/fli/FIRE/grid_190_256.hdf5' > >>> light_ray=trident.LightRay(fn,simulation_type='Gadget') > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File > "/home/fli/opt/yt-conda/lib/python2.7/site-packages/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py", > line 152, in __init__ > find_outputs=find_outputs) > File > "/home/fli/opt/yt-conda/lib/python2.7/site-packages/yt/analysis_modules/cosmological_observation/cosmology_splice.py", > line 34, in __init__ > find_outputs=find_outputs) > File > "/home/fli/opt/yt-conda/lib/python2.7/site-packages/yt/convenience.py", > line 153, in simulation > find_outputs=find_outputs) > File > "/home/fli/opt/yt-conda/lib/python2.7/site-packages/yt/frontends/gadget/simulation_handling.py", > line 75, in __init__ > find_outputs=find_outputs) > File > "/home/fli/opt/yt-conda/lib/python2.7/site-packages/yt/data_objects/time_series.py", > line 414, in __init__ > self._parse_parameter_file() > File > "/home/fli/opt/yt-conda/lib/python2.7/site-packages/yt/frontends/gadget/simulation_handling.py", > line 289, in _parse_parameter_file > param, vals = (i.strip() for i in line.split(None, 1)) > ValueError: need more than 1 value to unpack > > Thanks for your help, > > Fei Li > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 3 > Date: Wed, 11 May 2016 12:12:08 -0700 > From: Cameron Hummels <chummels(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] LightRay class > Message-ID: > <CACyTu7FeqQUkhdE034q182uvPYm= > 50p9J2qP509x+xQBuUYQZw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Fei Li, > > Since you're primarily trying to use Trident's functionality which wraps > around the LightRay class, you should probably direct questions of this > nature to the Trident mailing list. I'll start a discussion there on this > topic now and cc you. > > trident-project-users(a)googlegroups.com > > Cameron > > On Wed, May 11, 2016 at 12:06 PM, Fei Li <lif.li(a)mail.utoronto.ca> wrote: > > > Hello yt users, > > > > I tried to use the LightRay class to generate a light ray for one of my > > gridded simulation snapshots. The simulation is from the FIRE project > which > > used a heavily modified version of Gadget-3 called GIZMO written by Phil > > Hopkins. And the error I got is: ValueError: need more than 1 value to > > unpack. > > > > Here is my script: > > > > $ python > > Python 2.7.11 |Continuum Analytics, Inc.| (default, Dec 6 2015, > 18:08:32) > > [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 > > Type "help", "copyright", "credits" or "license" for more information. > > Anaconda is brought to you by Continuum Analytics. > > Please check out: http://continuum.io/thanks and https://anaconda.org > > >>> import yt > > >>> import trident > > >>> fn='/cita/h/home-2/fli/FIRE/grid_190_256.hdf5' > > >>> light_ray=trident.LightRay(fn,simulation_type='Gadget') > > Traceback (most recent call last): > > File "<stdin>", line 1, in <module> > > File > > > "/home/fli/opt/yt-conda/lib/python2.7/site-packages/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py", > > line 152, in __init__ > > find_outputs=find_outputs) > > File > > > "/home/fli/opt/yt-conda/lib/python2.7/site-packages/yt/analysis_modules/cosmological_observation/cosmology_splice.py", > > line 34, in __init__ > > find_outputs=find_outputs) > > File > > "/home/fli/opt/yt-conda/lib/python2.7/site-packages/yt/convenience.py", > > line 153, in simulation > > find_outputs=find_outputs) > > File > > > "/home/fli/opt/yt-conda/lib/python2.7/site-packages/yt/frontends/gadget/simulation_handling.py", > > line 75, in __init__ > > find_outputs=find_outputs) > > File > > > "/home/fli/opt/yt-conda/lib/python2.7/site-packages/yt/data_objects/time_series.py", > > line 414, in __init__ > > self._parse_parameter_file() > > File > > > "/home/fli/opt/yt-conda/lib/python2.7/site-packages/yt/frontends/gadget/simulation_handling.py", > > line 289, in _parse_parameter_file > > param, vals = (i.strip() for i in line.split(None, 1)) > > ValueError: need more than 1 value to unpack > > > > Thanks for your help, > > > > Fei Li > > > > > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > > > -- > Cameron Hummels > NSF Postdoctoral Fellow > Department of Astronomy > California Institute of Technology > http://chummels.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 99, Issue 29 > **************************************** > -- *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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