Mailman 3 July 2014 - yt-users

Mass Flux Across Surface Binned By Velocity
by Melinda Soares-Furtado 07 Jul '14

07 Jul '14

Hello, folks. I have a code that is computing the flux across a sphere of a given radius, as shown below. This code provides me with the summed flux across the surface, however what I am hoping to do is to bin this flux up into various velocities ranging from v_min to v_max. Thus, determine the mass flux across the surface for a chosen velocity bin. Does anyone know of a simple way to read out flux for a given velocity (normal to the surface) rather than the summed total? Code: from yt.mods import * pf=load("/trove/msoares/50Stars_LRefine5_Derefine0.05_velocity/50Stars_hdf5_plt_cnt_0200") rad=0.1/pf['pc'] sp = pf.h.sphere([0,0,0],2.0*rad) surf = pf.h.surface(sp,"Radius",rad) flux = surf.calculate_flux("x-velocity","y-velocity","z-velocity","Density") print flux Regards, Melinda Soares-Furtado

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ART data with no gas mesh
by Miguel Rocha 07 Jul '14

07 Jul '14

Hi yt-users! Has anyone successfully read with yt ART files that only contain dark matter particle data, without a gas mesh file. I am trying to load some Bolshoi snapshots which are single files in unformatted fortran format. YT supports loading ART snapshots from hydro runs in which you have multiple files for each snapshot, one file for the gas, one for the stars, one for the dark matter etc... Thus I would guess that build within the current ART frontend there must be all you need to read only one file for the dark matter. Has anyone tried to use the current ART frontend to read only a single DM file? Thanks! Miguel Rocha

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Flush_data_to_grids glitch
by David Collins 07 Jul '14

07 Jul '14

Hi, everybody-- In data_containers.py, around line 2664, there's a routine flush_data_to_grids. It seems like the line that says "np = pointI[0].ravel().size" is an error, as np refers to the numpy package. Does that seem right? I expect that should be number_of_points, or something? def _flush_data_to_grids(self, field, default_val, dtype='float32'): """ A dangerous, thusly underscored, thing to do to a data object, we can flush back any changes in a given field that have been made with a default value for the rest of the grid. """ i = 0 for grid in self._grids: pointI = self._get_point_indices(grid) np = pointI[0].ravel().size if grid.has_key(field): new_field = grid[field] else: new_field = np.ones(grid.ActiveDimensions, dtype=dtype) * default_val new_field[pointI] = self[field][i:i+np] grid[field] = new_field i += np -- -- Sent from a computer.

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GadgetDataset InternalEnergy Units
by Daniel 04 Jul '14

04 Jul '14

Hi, I noticed that the GadgetDataset read does not have units set. This should be fairly simple fix in the following file: ~/yt-3.0/yt/frontends/sph/fields.py -Line 58: ("InternalEnergy", ("", ["thermal_energy"], None)), +Line 58: ("InternalEnergy", ("code_length**2 / code_time**2", ["thermal_energy"], None)), Kind Regards, Daniel

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save phase plot data
by Maike Schmidt 04 Jul '14

04 Jul '14

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Clump Finding in yt-3.0
by Sendonaris, Elina 03 Jul '14

03 Jul '14

Hi all, I'm working with data from a simulation and would like to find the gravitationally bound regions of particles in the data. I'm using yt-3.0, and the documentation says that the code is broken in this version. Have any of you used this feature in this version, and if so, could you explain how using it is different from past versions? Thank you, Elina

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Field list when loading GadgetStaticOutput
by Daniel 03 Jul '14

03 Jul '14

Hi there, I am loading in a gadget binary snapshot successfully like so: pf = GadgetStaticOutput("snapshot_050", unit_base = unit_base, bounding_box = bbox) However I do not seem to be loading all the fields. The InternalEnergy, Density and SmoothingLength fields are listed in io.py but don't seemed to be getting called. ~/yt-3.0/yt/frontends/sph/io.py: _fields = ( "Coordinates", "Velocities", "ParticleIDs", "Mass", ("InternalEnergy", "Gas"), ("Density", "Gas"), ("SmoothingLength", "Gas"), ) Any advice would be greatly appreciated. Kind Regards, Daniel

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Unstructured grid yt support
by Ariadna Murguia 03 Jul '14

03 Jul '14

Hi, I wanted to visualize a dataset in an unstructured grid with AMR and a vtk output file. I went into the live chat and I was told the NSCA was working on a simple visualization. Could you please send me a sample script to visualize the data? Thank you very much, Ariadna Murguia

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Abort trap error upon launching yt on Mac OSX
by kiran narayanan 02 Jul '14

02 Jul '14

Hello, I've recently installed the stable version of yt on my MacBook, which is running OSX 10.6.8. The install script ran through normally without an problems. Upon sourcing activate, cloning yt-doc and running "yt help" or just "yt" even, I get an Abort Trap. Please help. Thanks, Kiran

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Callbacks, plot.data.center
by David Collins 02 Jul '14

02 Jul '14

Hi, everyone-- I"m trying to run a callback on a projected sphere, and I'm running into a missing piece of data. I'm doing the following: >>> sph = pf.h.sphere( c, w) >>> proj = pf.h.proj(1,'Density',source = sph) >>> pw=proj.to_pw( center= c, width=2) this works fine, and reproduces the plot I want. I have this callback that accesses "plot.data.center", but that seems to be an empty object. This callback is based on the ParticlesCallback, so it's accessing a sub region in the following manner below. So the plot object doesn't seem to be getting the center information any more. Is there a way to access this information now? Thanks! d. A snap from the relevant callback, the line that chokes is the access to data.center, and pdb says that the structure is None. def __call__(self, plot): data = plot.data # we construct a recantangular prism x0, x1 = plot.xlim y0, y1 = plot.ylim xx0, xx1 = plot._axes.get_xlim() yy0, yy1 = plot._axes.get_ylim() reg = self._get_region((x0,x1), (y0,y1), plot.data.axis, data) def _get_region(self, xlim, ylim, axis, data): LE, RE = [None]*3, [None]*3 xax = x_dict[axis] yax = y_dict[axis] zax = axis LE[xax], RE[xax] = xlim LE[yax], RE[yax] = ylim LE[zax] = data.center[zax] - self.width*0.5 RE[zax] = data.center[zax] + self.width*0.5 if self.region is not None \ and np.all(self.region.left_edge <= LE) \ and np.all(self.region.right_edge >= RE): return self.region self.region = data.pf.h.periodic_region( data.center, LE, RE) return self.region -- -- Sent from a computer.

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