yt-users April 2015

yt-users@python.org

29 participants
30 discussions

Simulation of Stellar Surface and protoplanetary disk interface
by Steven Alsheimer 13 Apr '15

13 Apr '15

Hi all I was wondering if there are certain presets or already made simulations or tweak-able sims from yt that I could use to simulate the point where a star and a protoplantary disk meet I'm new to yt and was wondering how one would go about this. Thanks, Steven _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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memory error for gadget visualization
by Junhwan Choi (최준환) 13 Apr '15

13 Apr '15

Hi yt users and developer, I tried to make a simple visualization for 244/h cMpc box with 512^3 DM and gas gadget simulation with following script ================================== import matplotlib as matplotlib matplotlib.use('Agg') import matplotlib.pylab as pylab import numpy as np import yt import yt.units as units index = 0 text_dict = {'color':'white', 'size':20} fname = ('../snap_vbc_%03d.hdf5' % index) unit_base = {'UnitLength_in_cm' : 3.08568e+21, 'UnitMass_in_g' : 1.989e+43, 'UnitVelocity_in_cm_per_s' : 100000} bbox_lim = 244000 #kpc bbox = [[0,bbox_lim], [0,bbox_lim], [0,bbox_lim]] ds = yt.load(fname,unit_base=unit_base,bounding_box=bbox) cen_center=np.array([122000,122000,122000]) pc = yt.ProjectionPlot(ds, "z", ('deposit', 'PartType0_density'), width = (244.0, 'Mpccm/h')) pc.annotate_text((0.8,0.9),'z=%4.2f' % ds.current_redshift, data_coords=False, text_args = text_dict) pc.save("all_view_%04d" % index) pc = yt.ProjectionPlot(ds, "z", ('deposit', 'PartType1_density'), width = (244.0, 'Mpccm/h')) pc.annotate_text((0.8,0.9),'z=%4.2f' % ds.current_redshift, data_coords=False, text_args = text_dict) pc.save("all_view_%04d" % index) pc = yt.ProjectionPlot(ds, "z", ('deposit', 'all_density'), width = (244.0, 'Mpccm/h')) pc.annotate_text((0.8,0.9),'z=%4.2f' % ds.current_redshift, data_coords=False, text_args = text_dict) pc.save("all_view_%04d" % index) pc = yt.ProjectionPlot(ds, "z", ('gas', 'density'), width = (244.0, 'Mpccm/h')) pc.annotate_text((0.8,0.9),'z=%4.2f' % ds.current_redshift, data_coords=False, text_args = text_dict) pc.save("all_view_%04d" % index) =================================== It initially works an make couple figures but it crash with following error message: ....... Traceback (most recent call last): File "viz.py", line 56, in <module> viz4(index) File "viz.py", line 50, in viz4 pc = yt.ProjectionPlot(ds, "z", ('gas', 'density'), width = (244.0, 'Mpccm/h')) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/visualization/plot_window.py", line 1228, in __init__ field_parameters = field_parameters, method = method) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/construction_data_containers.py", line 250, in __init__ self.get_data(field) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/construction_data_containers.py", line 295, in get_data chunk_fields, "io", local_only = True)): File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 507, in para llel_objects for obj_id, obj in oiter: File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py", line 592, in chunks self.get_data(fields) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py", line 693, in get_data self._generate_fields(fields_to_generate) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py", line 713, in _generate_fields fd = self._generate_field(field) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py", line 285, in _generate_field tr = self._generate_fluid_field(field) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py", line 303, in _generate_fluid_field rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py", line 319, in _generate_spatial_fluid ind += o.select(self.selector, self[field], rv, ind) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py", line 248, in __getitem__ self.get_data(f) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py", line 693, in get_data self._generate_fields(fields_to_generate) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py", line 713, in _generate_fields fd = self._generate_field(field) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py", line 285, in _generate_field tr = self._generate_fluid_field(field) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py", line 305, in _generate_fluid_field rv = finfo(gen_obj) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/fields/derived_field.py", line 184, in __call__ dd = self._function(self, data) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/fields/particle_fields.py", line 958, in _vol_weight dens = data[ptype, density_name].in_cgs() File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/octree_subset.py", line 77, in __getitem__ tr = super(OctreeSubset, self).__getitem__(key) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py", line 248, in __getitem__ self.get_data(f) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py", line 687, in get_data particles, self, self._current_chunk) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/geometry/geometry_handler.py", line 234, in _read_particle_fields fields_to_read) File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/utilities/io_handler.py", line 177, in _read_particle_selection for field_r, vals in self._read_particle_fields(chunks, ptf, selector): File "/work/00916/tg459470/common/anaconda/lib/python2.7/site-packages/yt-3.2dev-py2.7-linux-x86_64.egg/yt/frontends/owls/io.py", line 97, in _read_particle_fields coords = g["Coordinates"][:].astype("float64") MemoryError It looks there is a memory shortage. I use the stampede normal node which has ~32GB and I do not think 512^3 gas and DM particles require this amount memory. [But, I successfully made a visualization with 256^3 in 100/h cMpc run.] Is there any my possible mistake that leaks the memory? If so, could you inform me to overcome this memory issue. 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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Suppressing yt output
by Andrew James Emerick 11 Apr '15

11 Apr '15

Hello everyone, In general, is there any way to suppress the messages that yt prints to screen? Specifically, I am looping through many datasets in an ipython notebook and would like to stop the yt printout that happens with every "yt.load()" call. This ends up slowing down and occasionally crashing my notebook. I've tried normal means of suppressing stdout and stderr, but they don't seem to be working. Adding ";" at the end of the yt.load call doesn't work, and adding "%%capture" in the cell in the ipython notebook also does not work. Thanks, Andrew E. -- Graduate Student Columbia University Department of Astronomy _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Derived Field
by Chen Jingjing 10 Apr '15

10 Apr '15

Dear yt-users, I am trying to calculate the total HI mass within a sphere. I have a field called 'HI_Density'. And I tried to use the script HI_Mass = sphere['enzo','HI_Density'].in_units('Msun').sum() But I got an error that says the unit code_mass/code_length**3 cannot be converted to code_mass. So I thought I might need to create a derived_field called 'HI_Mass' which mutiplies the HI_Density with code_length**3. But I don't see that there is any existing field of cell length/volume. So how should I do this? Or is there an easier way to compute the total HI mass without deriving a field? Thanks, Jingjing -- Jingjing Chen [ chenjj235(a)gmail.com ] Department of Astronomy Columbia University 550 West 120th Street New York, New York 10027 Cell Phone: +1(347)5746709 _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Cold Gas
by Chen Jingjing 07 Apr '15

07 Apr '15

Dear yt-users, I was trying to calculate only the total mass of cold gas(<1e4.5) within a sphere and I tried the following script: ds=yt.load('RedshiftOutputxxxx') sp = ds.sphere(center,radius) *spcut = sp.cut_region(["obj['temperature']<1e4.5"])* *spcut.quantities.total_mass()* But I got an error that says: yt.utilities.exceptions.YTMixedCutRegion: Can't mix particle/discrete and fluid/mesh conditions or quantities. Field: ('all', 'particle_mass') and Conditions specified: obj['temperature']<1e4.5 Does anyone know how to fix it? Thanks, Jingjing -- Jingjing Chen [ chenjj235(a)gmail.com ] Department of Astronomy Columbia University 550 West 120th Street New York, New York 10027 Cell Phone: +1(347)5746709 _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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a problem switching versions of yt?
by Kathy Eastwood 07 Apr '15

07 Apr '15

Hi, I *think* I introduced this problem when switching from version 2 to version 3...I am currently running version 3.1. I define a derived field, number density, from the original density field, but something seems to be wrong with the units. I cannot make a sliceplot (as I used to be able to, in the old version), and I get other "unit conversion errors". thanks, kathy This cell works ok: def _numdens(field, data): return data["dens"]/(2.36*10**(-24)) ds.add_field("numdens", function=_numdens, units="1/cm**3") This cell does NOT work, and I get a very similar error when trying to do a sliceplot: maxval_numdens, maxloc_numdens = ds.find_max('numdens') print maxval_numdens print maxloc_numdens YTUnitConversionError Traceback (most recent call last)<ipython-input-12-8b3af9af1cf1> in <module>()----> 1 maxval_numdens, maxloc_numdens = ds.find_max('numdens') 2 print maxval_numdens 3 print maxloc_numdens /home/kde/yt-x86_64/src/yt-hg/yt/data_objects/static_output.pyc in find_max(self, field) 524 source = self.all_data() 525 max_val, maxi, mx, my, mz = \--> 526 source.quantities.max_location(field) 527 mylog.info("Max Value is %0.5e at %0.16f %0.16f %0.16f", 528 max_val, mx, my, mz) /home/kde/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.pyc in __call__(self, field) 524 525 def __call__(self, field):--> 526 rv = super(MaxLocation, self).__call__(field) 527 if len(rv) == 1: rv = rv[0] 528 return rv /home/kde/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.pyc in __call__(self, *args, **kwargs) 54 storage = {} 55 for sto, ds in parallel_objects(chunks, -1, storage = storage):---> 56 sto.result = self.process_chunk(ds, *args, **kwargs) 57 # Now storage will have everything, and will be done via pickling, so 58 # the units will be preserved. (Credit to Nathan for this /home/kde/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.pyc in process_chunk(self, data, field) 535 mz = array_like_field(data, -1, "z") 536 maxi = -1--> 537 if data[field].size > 0: 538 maxi = np.argmax(data[field]) 539 ma = data[field][maxi] /home/kde/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key) 246 return self.field_data[f] 247 else:--> 248 self.get_data(f) 249 # fi.units is the unit expression string. We depend on the registry 250 # hanging off the dataset to define this unit object. /home/kde/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields) 691 692 fields_to_generate += gen_fluids + gen_particles--> 693 self._generate_fields(fields_to_generate) 694 for field in self.field_data.keys(): 695 if field not in ofields: /home/kde/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _generate_fields(self, fields_to_generate) 717 raise RuntimeError 718 self.field_data[field] = fd--> 719 fd.convert_to_units(fi.units) 720 except GenerationInProgress as gip: 721 for f in gip.fields: /home/kde/yt-x86_64/src/yt-hg/yt/units/yt_array.pyc in convert_to_units(self, units) 387 388 """--> 389 new_units = self._unit_repr_check_same(units) 390 (conversion_factor, offset) = self.units.get_conversion_factor(new_units) 391 /home/kde/yt-x86_64/src/yt-hg/yt/units/yt_array.pyc in _unit_repr_check_same(self, units) 373 if not self.units.same_dimensions_as(units): 374 raise YTUnitConversionError(--> 375 self.units, self.units.dimensions, units, units.dimensions) 376 377 return units YTUnitConversionError: Unit dimensionalities do not match. Tried to convert between code_mass/code_length**3 (dim (mass)/(length)**3) and cm**(-3) (dim (length)**(-3)). -- Kathy DeGioia Eastwood, Ph.D. Professor of Physics and Astronomy Northern Arizona University Flagstaff, AZ 86011-6010 Ph: 928-523-7159 FX: 928-523-1371 Kathy.Eastwood(a)nau.edu deliveries: 602 S. Humphreys St., Bldg 19 Rm 209 _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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help! darkskysims(yt-dark)
by abasak＠miners.utep.edu 06 Apr '15

06 Apr '15

Hello, I am getting an error when I am trying to run examples given in darkskysims/darksky_tour. The examples uses yt to load the data. The script looks like this : import sys import matplotlib; matplotlib.use('Agg') from dark_loader import load_halo, prefix import yt if __name__ == "__main__": root_dir = prefix + 'ds14_a/' particles = root_dir + "ds14_a_1.0000" halos = root_dir + "halos/ds14_a_halos_1.0000" halo_num = 0 if len(sys.argv) > 1: halo_num = int(sys.argv[-1]) pds, halo, center, radius = load_halo(particles, halos, halo_num) p = yt.ProjectionPlot(pds, 0, "dark_matter_density", weight_field=None) p.annotate_sphere(center, radius, circle_args={'color':'r'}) p.annotate_title(r"$M_{200b} = %0.2e \mathrm{M_{\odot}/h}$" % halo['m200b']) p.set_cmap("all", "RdGy_r") p.set_axes_unit("Mpccm/h") p.set_zlim('all', 1.0e-3, 1.0) p.save('halo_%04i' % halo_num) And it gives me the following output: ... File "//anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py", line 1227, in __init__ field_parameters = field_parameters, method = method) File "//anaconda/lib/python2.7/site-packages/yt/data_objects/construction_data_containers.py", line 250, in __init__ self.get_data(field) File "//anaconda/lib/python2.7/site-packages/yt/data_objects/construction_data_containers.py", line 295, in get_data chunk_fields, "io", local_only = True)): File "//anaconda/lib/python2.7/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 506, in parallel_objects for obj_id, obj in oiter: File "//anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 588, in chunks self.get_data() # Ensure we have built ourselves File "//anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 622, in get_data self.index._identify_base_chunk(self) File "//anaconda/lib/python2.7/site-packages/yt/geometry/particle_geometry_handler.py", line 140, in _identify_base_chunk self.regions.identify_data_files(dobj.selector)] File "//anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 583, in selector self._selector = sclass(self) File "yt/geometry/selection_routines.pyx", line 721, in yt.geometry.selection_routines.RegionSelector.__init__ (build/src.macosx-10.5-x86_64-2.7/yt/geometry/selection_routines.c:14458) ValueError: Buffer dtype mismatch, expected 'float64_t' but got 'float' Can anyone please help me. I will really appreciate it. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Particle-Only Plots
by Andrew Myers 04 Apr '15

04 Apr '15

Dear yt users, I have a pull request open that implements plots of particle fields, as demonstrated in this <http://nbviewer.ipython.org/gist/atmyers/c965c769a488016c3299> notebook. It would be great to get some more eyes on this - the more people who try it before the pull request is merged, the better. Any comments, criticisms, or bug reports will only improve the version that gets merged, so please feel free to suggest improvements. The documentation for how to use the new features is here <http://tests.yt-project.org/job/py2.7-yt-3.0_docs/26/artifact/sandbox/doc/b…>, and cookbook recipes are here <http://tests.yt-project.org/job/py2.7-yt-3.0_docs/26/artifact/sandbox/doc/b…> . If you're interested, you can get the changesets from my yt fork by doing: 1. Make sure yt is activated 2. cd $YT_DEST/src/yt-hg/ 3. hg pull -b particle_plots https://bitbucket.org/atmyers/yt 4. hg update -C particle_plots 5. python setup.py develop WARNING: The "-C" option to hg update will wipe any uncommited changes in your working copy, so be wary. Thanks, Andrew _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Cannot seem to access the mailing list archive...
by Kathy Eastwood 01 Apr '15

01 Apr '15

anybody else having this problem? for example, I am trying to look at http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-October/01… and get the response Forbidden You don't have permission to access /pipermail/ yt-users-spacepope.org/2013-October/019534.html on this server. Additionally, a 404 Not Found error was encountered while trying to use an ErrorDocument to handle the request. thanks kathy -- Kathy DeGioia Eastwood, Ph.D. Professor of Physics and Astronomy Northern Arizona University Flagstaff, AZ 86011-6010 Ph: 928-523-7159 FX: 928-523-1371 Kathy.Eastwood(a)nau.edu deliveries: 602 S. Humphreys St., Bldg 19 Rm 209 _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Recenter Halo
by Chen Jingjing 01 Apr '15

01 Apr '15

Dear yt-users, I am having a little problem on finding the exact center of a halo. I used to do "hc = HaloCatalog(data_ds=data_ds, finder_method='hop')" to create a halo catalog. But I think the position in the catalog is a little bit off the exact center judging from the plots I made. I need the exact center to compute the angular momentum so the off-center result could cause some problem. I tried to recenter at the maximum gas density by adding this line "hc.sphere_field_max_recenter('density')" But I got an error, AttributeError: 'HaloCatalog' object has no attribute 'sphere_field_max_recenter'. Can anyone tell me what is the right way to find the center as the location of maximum gas density? Thanks, Jingjing -- Jingjing Chen [ chenjj235(a)gmail.com ] Department of Astronomy Columbia University 550 West 120th Street New York, New York 10027 Cell Phone: +1(347)5746709 _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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yt-users April 2015