Mailman 3 August 2011 - yt-users

Re: [yt-users] passing parameters to 'ray'
by Elizabeth Tasker Aug. 17, 2011

Aug. 17, 2011

Hi Sam, OK, I've succeeded in breaking your improved script. When you try and set both parameter and spatial validators, the code stops recognising them. So: add_field("RayTest", function=_RayTest, validators=[ValidateParameter("disk_vector")]) works while add_field("RayTest", function=_RayTest, validators=[ValidateParameter("disk_vector"), ValidateParameter("disk_center"), ValidateSpatial(1, ["x-velocity", "y-velocity", "z-velocity", "x", "y", "z"])]) does not.Which it why it didn't … [View More]work in my longer script. Perhaps I've put the format in incorrectly? Elizabeth Elizabeth Tasker wrote: > Hi Sam, > > Thank you -- my test script now works fine but I've managed to break > my longer one so completely it's become impossible to test anything. > Oops. However, I think when I tried the method below originally, I put > the set_field_parameters in the wrong place, which would explain why > they didn't work. > > Thanks loads for the example. > > Elizabeth > > Sam Skillman wrote: >> Hi Elizabeth, >> >> So the problem is that when you add_field and ask to validate the >> height_vector, it doesn't exist yet. I believe you can get the >> desired behavior with: >> >> from yt.mods import * >> >> def _RayTest(field, data): >> >> center = data.get_field_parameter("center") >> h_vec = na.array(data.get_field_parameter("height_vector")) >> >> print "center :", center, "h_vec: ", h_vec >> >> return data["Density"] >> >> add_field("RayTest", function=_RayTest) >> >> # Grab data >> fn = "GravPotential/DD0301/GT_BTAccel_256AMR4_PeHeat_sf5_SNe_0301" >> pf = load(fn) >> ray1 = pf.h.ray((2.0, 2.0 ,2.0), (12.0, 12.0, 12.0)) >> ray1.set_field_parameter('height_vector',na.array([0.,0.,1.])) >> ray1.set_field_parameter('center',[0.5]*3) >> ray1["RayTest"] >> >> When I run this I get: center : [0.5, 0.5, 0.5] h_vec: [ 0. 0. 1.] >> >> I'm not sure what dd was in your dd.center since dd wasn't defined in >> that script, but you should be able to set center to whatever you >> want here. I also changed density to Density. >> Best, >> Sam >> >> On Wed, Aug 10, 2011 at 9:36 AM, Elizabeth Tasker >> <taskere(a)mcmaster.ca <mailto:taskere@mcmaster.ca>> wrote: >> >> Hi Matt, >> >> I think this script explains what I mean. When I run it, I get: >> >> /1/home/taskere/yt/yt/data_objects/field_info_container.py in >> __call__(self, data) >> 357 doesnt_have.append(p) >> 358 if len(doesnt_have) > 0: >> --> 359 raise NeedsParameter(doesnt_have) >> 360 return True >> 361 >> >> NeedsParameter: (['height_vector']) >> >> >> As a side note, I think 'ray' sets its own value for the field >> parameter, "center", making it the start of the ray. If that's >> true, does it have problems for calling radius? e.g. >> >> ray["Radius"] >> >> where radius would need to be the center of the object, not >> necessarily the start of the ray? (This particular issue wouldn't >> affect me, but I thought it might bite someone later). >> >> Elizabeth >> >> >> >> Matthew Turk wrote: >> >> >> Hi Elizabeth, >> >> Could you elaborate on what you mean, and provide an example >> script? >> >> Thanks, >> >> -Matt >> >> On Aug 10, 2011 7:22 AM, "Elizabeth Tasker" >> <taskere(a)mcmaster.ca <mailto:taskere@mcmaster.ca> >> <mailto:taskere@mcmaster.ca <mailto:taskere@mcmaster.ca>>> >> wrote: >> > Hi, >> > >> > I'm having problems passing parameters to a ray object. I'm >> trying: >> > >> > ray1 = pf.h.ray( com[c], com[nearestcore], field_parameters = >> > {'height_vector':na.array([0,0,1]), 'center':dd.center}) >> > Omega0 = ray1["Omega"] >> > >> > and I also tried out: >> > >> > ray1.set_field_parameter("height_vector", na.array([0,0,1])) >> > ray1.set_field_parameter("center", dd.center) >> > >> > But it can't recognise them. >> > >> > Elizabeth >> > _______________________________________________ >> > yt-users mailing list >> > yt-users(a)lists.spacepope.org >> <mailto:yt-users@lists.spacepope.org> >> <mailto:yt-users@lists.spacepope.org >> <mailto:yt-users@lists.spacepope.org>> >> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> ------------------------------------------------------------------------ >> >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> <mailto:yt-users@lists.spacepope.org> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org [View Less]

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ray objects
by Elizabeth Tasker Aug. 17, 2011

Aug. 17, 2011

Hi, When you create a ray object with yt, e.g. ray1 = pf.h.ray([10,16,16], [10.3,16.1,16]) I was expecting to get the values of the cells that lie inbetween those two sets of co-ordinates. Instead, it looks like the first two values back at the start and end points. .e.g.: -------> print(ray1["x"]) Warning: divide by zero encountered in divide Warning: invalid value encountered in multiply Warning: divide by zero encountered in divide Warning: invalid value encountered in multiply yt : … [View More]

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Trouble installing yt
by Nathan Goldbaum Aug. 16, 2011

Aug. 16, 2011

Hi all, I'm having trouble installing yt from the install script. This is on a small cluster here at UCSC. The install script fails while trying to install libpng The terminal output from my install session is located here: http://paste.enzotools.org/show/1746/ And the contents of my yt_install.log are located here: http://paste.enzotools.org/show/1747/ Any thoughts as to why the install script is failing? Best, Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC … [View More]

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Clump finding and mpi4py
by Eve Lee Aug. 15, 2011

Aug. 15, 2011

Hello, May I ask if the current version of yt supports parallelization of clump finding routine? When I use mpirun.py -np (whatever number) python (name of my clump finding routine) (some arguments my routine requires) --parallel, I keep getting the following error: Traceback (most recent call last): File "find_clumps.py", line 32, in <module> amods.level_sets.find_clumps(base, c_min, c_max, step) File "/home/jchong/yt/new_dev/xxx/yt-x86_64/src/yt-hg/yt/analysis_modules/… [View More]level_sets/clump_handling.py", line 188, in find_clumps elif (child._isValid()): File "/home/jchong/yt/new_dev/xxx/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", line 143, in _isValid self.function_value = eval(self.function) File "<string>", line 1, in <module> File "/home/jchong/yt/new_dev/xxx/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 86, in __call__ self.func(e, *args, **kwargs) File "/home/jchong/yt/new_dev/xxx/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 347, in _IsBound bv_x,bv_y,bv_z = data.quantities["BulkVelocity"]() AttributeError: 'FieldDetector' object has no attribute 'quantities' This version is updated to changeset 4457:bf868d1a8f02. I have no problem running the same routine serially but it would be nice if I can run parallel to save some time. Below is my clump finding routine if it helps: from yt.mods import * import sys #Find and save clumps #Read in the command-line-passed arguments datadir = sys.argv[1] pltdir = sys.argv[2] datanum_start = int(sys.argv[3]) datanum_end = int(sys.argv[4]) datanum_step = int(sys.argv[5]) for i in range(datanum_start, datanum_end, datanum_step): pf = load(datadir+"DD%04i/data%04i" %(i,i)) center = [0.5, 0.5, 0.5] radius = 1.0 sp = pf.h.sphere(center, radius) particles = pf.h.find_particles_by_type(4) if type(particles) != types.NoneType: field = "Matter_Density" #Use both new_function = 'self.data.quantities["IsBound"](truncate=True,include_thermal_energy=False) > 1.0' else: field = "Density" new_function = 'self.data.quantities["IsBound"](truncate=True,include_thermal_energy=False,include_particles=False) > 1.0' c_min = 10**na.floor(na.log10(sp[field]).min()+1) c_max = 10**na.floor(na.log10(sp[field]).max()+1) step = 10 #Find clumps base = amods.level_sets.Clump(sp, None, field, function=new_function) amods.level_sets.find_clumps(base, c_min, c_max, step) #Save clumps pf.h.save_object(base, "Clump") Thanks! Best Regards, Eve [View Less]

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change in add_projection/add_thin_projection for unweighted projections?
by Christine Simpson Aug. 15, 2011

Aug. 15, 2011

Hi all, Has there been a change to the add_projection or add_thin_projection routines for unweighted projections? I have some projection scripts from ~a month ago that are all off by like 20 orders of magnitude on the color bar limits for unweighted projections. The only thing that makes sense to me is that yt is now dividing the line of sight integration by the depth of the projection. So it is sum(f(i)*dl(i))/sum(dl(i)) instead of sum(f(i)*dl(i)). Is that right? I don't think it used to … [View More]

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pickle
by Elizabeth Tasker Aug. 11, 2011

Aug. 11, 2011

Hi, (Another day a different problem!): I'd like to pickle the results from extract_connected_sets, but I can't seem to retrieve what I pickle properly. I have: contours = dd.extract_connected_sets("NegEscapeVelocity", 1, 30.0, maxv, log_space=False) cloudcores = contours[1][0] #cores defined by contour 0 file = open('testa.pickle','wb') cPickle.dump(cloudcores,file,protocol=-1) file.close() file = open('testa.pickle','rb') core = cPickle.load(file) file.close() But while: In [76]: … [View More]

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Visualizing clumps in 3D?
by Eve Lee Aug. 11, 2011

Aug. 11, 2011

Hello, I'm using yt's clump find routine to locate clumps with embedded star particles in an Enzo stirred turbulent box with star formation, and I'm wondering if yt has the functionalities to visualize these clumps in 3D space rather than 2D projected contour lines. Is it possible to volume render just the clumps (not the whole box which seems like what yt's doing according to the documentation webpage) or better yet, make a 3D contour plot to visualize the clump hierarchy? Thanks. Best Regards, Eve

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passing parameters to 'ray'
by Elizabeth Tasker Aug. 10, 2011

Aug. 10, 2011

Hi, I'm having problems passing parameters to a ray object. I'm trying: ray1 = pf.h.ray( com[c], com[nearestcore], field_parameters = {'height_vector':na.array([0,0,1]), 'center':dd.center}) Omega0 = ray1["Omega"] and I also tried out: ray1.set_field_parameter("height_vector", na.array([0,0,1])) ray1.set_field_parameter("center", dd.center) But it can't recognise them. Elizabeth

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ART simulations
by Mark Danovich Aug. 10, 2011

Aug. 10, 2011

Hi, Is there any support for Daniel Ceverino's ART simulations and maybe some tutorial. I've seen code for reading in the data, but I don't know how to make it yt compatible. Thanks. -- Mark Danovich

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Re: [yt-users] data along rays
by Elizabeth Tasker Aug. 9, 2011

Aug. 9, 2011

Actually, I think it's because my covering_grid has no ghost zones. I'll add some in. E. Elizabeth Tasker wrote: > Hi Matt, > > Ah, great -- thank you. However, when I try to use it, the code chocks > on my 3d data. I have: > > add_field("Omega", function=_Omega, > validators=[ValidateParameter("height_vector"), > ValidateParameter("center"), ValidateSpatial(1, ["x-velocity", > "y-velocity", "z-velocity", "x", "y", "z"])]) > > and I get > > /1/home/… [View More]taskere/yt/yt/data_objects/field_info_container.py in > __call__(self, data) > 411 if self.ghost_zones <= data._num_ghost_zones: > 412 return True > --> 413 raise NeedsGridType(self.ghost_zones,self.fields) > 414 > 415 class ValidateGridType(FieldValidator): > > NeedsGridType: (1, ['x-velocity', 'y-velocity', 'z-velocity', 'x', > 'y', 'z']) > > Did I get the syntax wrong? > > Elizabeth > > > Matthew Turk wrote: >> >> Hi Elizabeth, >> >> You have to use the ValidateSpatial validator to ensure that the data >> handed to te subroutine is 3D. >> >> -Matt >> >> On Aug 9, 2011 11:50 AM, "Elizabeth Tasker" <taskere(a)mcmaster.ca >> <mailto:taskere@mcmaster.ca>> wrote: >> > Hi, >> > >> > I have a mystery: >> > >> > Creating a ray via: >> > >> > ray = pf.h.ray( com[c], com[nearestcore]) >> > >> > and I want to get the effective potential along it, for which I have a >> > subrountine for. However, yr gets stuck here: >> > >> > if data.pf <http://data.pf>["HydroMethod"] == 2: >> > xvel[0:-1,0:-1,0:-1] = >> > >> 0.5*(data["x-velocity"][slice(None,-1,None),0:-1,0:-1]+data["x-velocity"][slice(1,None,None),0:-1,0:-1]) >> >> > >> > >> > I thought the problem was because a ray is a 1D data set and I was >> > trying to treat it like a 3D array, but what confuses me is that: >> > >> > ray["DivV"] >> > >> > works just fine but as the same sort of line within its definition. >> > >> > http://yt.enzotools.org/doc/reference/field_list.html#divv >> > >> > To make matters more confusing, if I copy out the definition of DivV >> > directly from universal_fields.py and implement it imaginatively as >> > DivV2, the code doesn't work, giving me: >> > >> > /1/home/taskere/yt/scripts/iyt in _DivV2(field, data) >> > 211 div_fac = 2.0 >> > 212 ds = div_fac * data['dx'].flat[0] >> > --> 213 f = data["x-velocity"][sl_right,1:-1,1:-1]/ds >> > 214 f -= data["x-velocity"][sl_left ,1:-1,1:-1]/ds >> > 215 if data.pf.dimensionality > 1: >> > >> > IndexError: too many indices >> > >> > >> > What magic line does yt have to allow DivV to work for a ray? >> > >> > Thanks, >> > >> > Elizabeth >> > >> > _______________________________________________ >> > yt-users mailing list >> > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org [View Less]

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