yt-users May 2018

yt-users@python.org

13 participants
27 discussions

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

3-D Mass power spectra
by 梁家豪 03 Jun '19

03 Jun '19

Dear yt Can current yt calculate 3-D Mass power spectra? I checked the website but I didn't find any information. I think calculating 3-D Mass power spectra is a very useful for cosmological simulations. So I guess maybe yt supports this function now....? Thanks in advance

4 7

Question about deposited fields: follow up
by Nick Gnedin 01 Jun '18

01 Jun '18

I also have a follow-up question. My previous question was about the build-in deposited fields. But when I try to do that myself, units seem to be screwed up. ----------------------- import yt import numpy as np def StellarMass2(field,data): ms = data[('STAR','particle_mass')] if('FieldDetector' in str(type(data))): return ms else: return ms.in_units("Msun") d = yt.load("rei10_a0.1001/rei10_a0.1001.art") d.add_field(("STAR","mass2"),function=StellarMass2,sampling_type="particle",units="Msun") d.add_deposited_particle_field(("STAR","mass2"),"nearest",weight_field='particle_ones') xcen = d.arr([5,5,5],"Mpccm/h") s = d.sphere(xcen,(100,"kpc")) sf = ('STAR','mass2') df = ('deposit','STAR_nn_mass2') print(np.amax(s[sf]),np.amax(s[df])) ---------------------------- > 1625.2196373326824 Msun 1625.2196373326824 Msun I.e, the units of the deposited field are that of mass, rather than density. Even worse, if I treat the deposited field as the mass per cell rather than density, it does not add up: print("sum=%9.3e int=%9.3e"%(np.sum(s[sf].in_units("Msun")),np.sum(s[df].in_units("Msun")))) > sum=3.252e+04 int=1.521e+05 So, I am totally lost about what add_deposited_particle_field() function actually does. n

3 2

Error when loading "AmrEx/BoxLib" (plotfile) by yt
by caseywang777＠gmail.com 29 May '18

29 May '18

Hi, I run a code(Nyx) and it generates "AmrEx/BoxLib" (plotfile) files The code I run to generate "AmrEx/BoxLib" (plotfile) files is here. I have cloned these two code https://github.com/AMReX-Codes/amrex and https://github.com/AMReX-Astro/Nyx and follow the chapter 1 in Nyx User guide to run the most basic Lya example. It generates the several plotfile directories and I want to use yt to read the plotfile and visualize it. I have read these two links https://amrex-codes.github.io/amrex/docs_html/Visualization.html#yt http://yt-project.org/doc/examining/loading_data.html (Section of AMReX / BoxLib Data) and follow the instruction to load the one of the plotfile directory. The problem is here.... This is my python(yt) code to read the plotfile ("plt00302" is the plotfile directory) import yt print(yt.__version__) ds = yt.load("plt00302") print(ds.field_list) The first three lines is ok and no error. This line,"ds = yt.load("plt00302")", even print some information which looks reasonable. But the last line, "print(ds.field_list)" gives me the following error message. Traceback (most recent call last): File "boxlibTest.py", line 4, in <module> print(ds.field_list) File "/home/myUserName/anaconda3/lib/python3.6/site-packages/yt/data_objects/static_output.py", line 546, in field_list return self.index.field_list File "/home/myUserName/anaconda3/lib/python3.6/site-packages/yt/data_objects/static_output.py", line 504, in index self, dataset_type=self.dataset_type) File "/home/myUserName/anaconda3/lib/python3.6/site-packages/yt/frontends/boxlib/data_structures.py", line 1215, in __init__ super(NyxHierarchy, self).__init__(ds, dataset_type) File "/home/myUserName/anaconda3/lib/python3.6/site-packages/yt/frontends/boxlib/data_structures.py", line 337, in __init__ self._cache_endianness(self.grids[-1]) File "/home/myUserName/anaconda3/lib/python3.6/site-packages/yt/frontends/boxlib/data_structures.py", line 467, in _cache_endianness _header_pattern[self.dimensionality-1].search(header).groups() AttributeError: 'NoneType' object has no attribute 'groups' Any one has suggestion or solution about this? Thanks

3 4

Question about deposited fields
by Nick Gnedin 27 May '18

27 May '18

Guys, What are the implicit units of the deposited field? In the following script using implicit units returns an incorrect result, while setting them explicitly gives the correct one. import yt import numpy as np d = yt.load("rei10_a0.1001/rei10_a0.1001.art") xcen = d.arr([5,5,5],"Mpccm/h") s = d.sphere(xcen,(100,"kpc")) sf = ('STAR','particle_mass') df = ('deposit','STAR_density') print("sum=%9.3e int=%9.3e"%(np.sum(s[sf]),np.sum(s[df]*s[('gas','cell_volume')]))) print("sum=%9.3e int=%9.3e"%(np.sum(s[sf].in_units("Msun")),np.sum(s[df].in_units("Msun/kpc**3")*s[('gas','cell_volume')].in_units("kpc**3")))) > sum=6.894e-05 int=1.818e-31 sum=3.252e+04 int=3.252e+04 n

2 1

Re: Adding particle fields
by Nick Gnedin 27 May '18

27 May '18

Nathan, I think it was my bug - the field detector wants to see all the fields accessed inside the call. If I do the following, then the code works: def StellarLuminosity(field,data): ts = data[('STAR','age')] zs = data[('STAR','metallicity_snii')] + data[('STAR','metallicity_snia')] ms = data[('STAR','particle_mass')] if('FieldDetector' in str(type(data))): return ms else: #ts = data[('STAR','age')].in_units("yr").v #zs = (data[('STAR','metallicity_snii')]+data[('STAR','metallicity_snia')]).v return ms.in_units("Msun") # return sps.GetLnu(ts,zs)*data[('STAR','mass')].in_units("Msun") Thank you so much for all the help, sorry for keeping pestering you. n On 5/27/2018 1:37 PM, Nathan Goldbaum wrote: > So in this case you've written the field to behave one way during field > detection and another way during the real field evaluation. This is > confusing the field machinery. > > I think you're running into a bug in how the artio frontend handles some > of its particle fields, see this pull request I just opened: > > https://github.com/yt-project/yt/pull/1802 > <https://github.com/yt-project/yt/pull/1802> > > After applying that patch I think you'll be able to avoid the check to > see if you're in field detection. > > On Sun, May 27, 2018 at 1:20 PM, Nick Gnedin <ngnedin(a)gmail.com > <mailto:ngnedin@gmail.com>> wrote: > > > Nathan, > > I made progress with the real code, but then I hit another error > that leaves me dumbfounded: > > ---------------------------- > import yt > > def StellarLuminosity(field,data): > if(not 'FieldDetector' in str(type(data))): > ts = data[('STAR','age')].in_units("yr").v > zs = > (data[('STAR','metallicity_snii')]+data[('STAR','metallicity_snia')]).v > return data[('STAR','mass')].in_units("Msun") > else: > return data[('STAR','age')] > > > d = yt.load("rei10_a0.1001/rei10_a0.1001.art") > > > d.add_field(("STAR","luminosity"),function=StellarLuminosity,units="Msun",sampling_type="particle") > d.add_deposited_particle_field(("STAR","luminosity"),"nearest",weight_field='particle_ones') > > print(d.derived_field_list) > > print(d.all_data()[('STAR','metallicity_snii')]) > print(d.all_data()[("deposit","STAR_nn_luminosity")]) > -------------------------- > > Below is the error I get. ('STAR','metallicity_snii') certainly > exists, I can print it, but the deposited field seems to be unable > to find it. > > yt : [INFO ] 2018-05-27 13:15:16,205 Created 256 chunks for ARTIO > [ 5.39916630e-30 2.21650149e-22 2.95487393e-06 ..., > 1.23813297e-05 > 1.28902484e-05 1.42594863e-05] dimensionless > yt : [INFO ] 2018-05-27 13:15:16,396 Created 256 chunks for ARTIO > Traceback (most recent call last): > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", > line 335, in _generate_fluid_field > finfo.check_available(gen_obj) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/fields/derived_field.py", > line 199, in check_available > validator(data) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/fields/derived_field.py", > line 418, in __call__ > raise NeedsGridType(self.ghost_zones,self.fields) > yt.fields.field_exceptions.NeedsGridType: (0, None) > > During handling of the above exception, another exception occurred: > > Traceback (most recent call last): > File "debug.py", line 23, in <module> > print(d.all_data()[("deposit","STAR_nn_luminosity")]) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", > line 282, in __getitem__ > self.get_data(f) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", > line 1337, in get_data > self._generate_fields(fields_to_generate) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", > line 1357, in _generate_fields > fd = self._generate_field(field) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", > line 319, in _generate_field > tr = self._generate_fluid_field(field) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", > line 337, in _generate_fluid_field > rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", > line 357, in _generate_spatial_fluid > ind += o.select(self.selector, self[field], rv, ind) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", > line 282, in __getitem__ > self.get_data(f) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", > line 1337, in get_data > self._generate_fields(fields_to_generate) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", > line 1357, in _generate_fields > fd = self._generate_field(field) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", > line 319, in _generate_field > tr = self._generate_fluid_field(field) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", > line 339, in _generate_fluid_field > rv = finfo(gen_obj) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/fields/derived_field.py", > line 237, in __call__ > dd = self._function(self, data) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/static_output.py", > line 1274, in _deposit_field > fields = [data[ptype, deposit_field]] > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/octree_subset.py", > line 75, in __getitem__ > tr = super(OctreeSubset, self).__getitem__(key) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", > line 282, in __getitem__ > self.get_data(f) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", > line 1337, in get_data > self._generate_fields(fields_to_generate) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", > line 1357, in _generate_fields > fd = self._generate_field(field) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", > line 317, in _generate_field > tr = self._generate_particle_field(field) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", > line 402, in _generate_particle_field > rv = self.ds._get_field_info(*field)(gen_obj) > File > "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/fields/derived_field.py", > line 235, in __call__ > "for %s" % (self.name <http://self.name>,)) > RuntimeError: Something has gone terribly wrong, _function is > NullFunc for ('STAR', 'METALLICITY_SNII') > > > n > > > > > > On 5/27/2018 12:08 PM, Nathan Goldbaum wrote: > > Hi Nick, > > What you're seeing in those print statements is how yt's field > detection system works. Before we actually select and return > data, we pass your field function fake data to make sure it > doesn't raise errors or it doesn't select fields that aren't > available for your dataset. > > Here's a script I made based on yours that helps explain what's > going on: > > https://gist.github.com/ngoldbaum/4d27987bda8ecbce5c9bd9b98bbbbf49 > <https://gist.github.com/ngoldbaum/4d27987bda8ecbce5c9bd9b98bbbbf49> > > And here's the output of that script: > > https://gist.github.com/ngoldbaum/475fcd827a53e4d02e76cb25711ff5ea > <https://gist.github.com/ngoldbaum/475fcd827a53e4d02e76cb25711ff5ea> > > I made a couple modifications compared to your script. First, I > added a line at the end that selects your new field from a data > object, which causes real data to be fed into the field function > after field detection completes. I also specified "units='auto'" > in the call to add_field. The dimensions keyword is only used > when "units='auto'" is set. > > You can see that your field function is called twice. First with > a `FieldDetector` instance and then the second time with a real > yt data object. In general the field function might be called > several times before real data is supplied to it. One way I > commonly deal with this is the following hack to only see output > when the field definition is called with real data: > > def NewField(field, data): > q = data[('STAR', 'age')] > if 'FieldDetector' in str(type(data)): > print("BBB",data) > return q > > Although more often I use python's debugger via "import pdb; > pdb.set_trace()" instead of print statements. > > Hope that helps, > > Nathan > > On Sun, May 27, 2018 at 10:51 AM, Nick Gnedin <ngnedin(a)gmail.com > <mailto:ngnedin@gmail.com> <mailto:ngnedin@gmail.com > <mailto:ngnedin@gmail.com>>> wrote: > > > Guys, > > I am trying to add a new particle field, and apparently I > am doing > something wrong, but I could find the documentation for this: > > import yt > def NewField(field,data): > q = data[('STAR','age')] > print("BBB",data) > return q > d = yt.load("rei10_a0.1001/rei10_a0.1001.art") > print('AAA',d.all_data()[("STAR","age")]) > > d.add_field(("STAR","new-field"),function=NewField,dimensions="time",sampling_type="particle") > > The result is here: > > AAA [ 1.35689106e+08 1.29578798e+08 1.15241829e+08 ..., > 2.97175878e+07 > 2.04648908e+07 1.35365980e+07] yr > BBB defaultdict(<function > FieldDetector.__init__.<locals>.<lambda> > at 0x2b9e698e3598>, {('STAR', 'BIRTH_TIME'): YTArray([ 1.]) > (dimensionless), ('STAR', 'creation_time'): YTArray([ 1.]) > (dimensionless), ('STAR', 'age'): YTArray([ 1.]) > (dimensionless)}) > > It appears that the data object sent to > NewField(field,data) has all > its fields set to dimensionless. > > I tried omitting sampling_type="particle", but it does not > help, > just generates an incomprehensible warning. > > n > _______________________________________________ > yt-users mailing list -- yt-users(a)python.org > <mailto:yt-users@python.org> > <mailto:yt-users@python.org <mailto:yt-users@python.org>> > To unsubscribe send an email to yt-users-leave(a)python.org > <mailto:yt-users-leave@python.org> > <mailto:yt-users-leave@python.org > <mailto:yt-users-leave@python.org>> > > >

1 0

Re: Adding particle fields
by Nick Gnedin 27 May '18

27 May '18

Nathan, I made progress with the real code, but then I hit another error that leaves me dumbfounded: ---------------------------- import yt def StellarLuminosity(field,data): if(not 'FieldDetector' in str(type(data))): ts = data[('STAR','age')].in_units("yr").v zs = (data[('STAR','metallicity_snii')]+data[('STAR','metallicity_snia')]).v return data[('STAR','mass')].in_units("Msun") else: return data[('STAR','age')] d = yt.load("rei10_a0.1001/rei10_a0.1001.art") d.add_field(("STAR","luminosity"),function=StellarLuminosity,units="Msun",sampling_type="particle") d.add_deposited_particle_field(("STAR","luminosity"),"nearest",weight_field='particle_ones') print(d.derived_field_list) print(d.all_data()[('STAR','metallicity_snii')]) print(d.all_data()[("deposit","STAR_nn_luminosity")]) -------------------------- Below is the error I get. ('STAR','metallicity_snii') certainly exists, I can print it, but the deposited field seems to be unable to find it. yt : [INFO ] 2018-05-27 13:15:16,205 Created 256 chunks for ARTIO [ 5.39916630e-30 2.21650149e-22 2.95487393e-06 ..., 1.23813297e-05 1.28902484e-05 1.42594863e-05] dimensionless yt : [INFO ] 2018-05-27 13:15:16,396 Created 256 chunks for ARTIO Traceback (most recent call last): File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 335, in _generate_fluid_field finfo.check_available(gen_obj) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/fields/derived_field.py", line 199, in check_available validator(data) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/fields/derived_field.py", line 418, in __call__ raise NeedsGridType(self.ghost_zones,self.fields) yt.fields.field_exceptions.NeedsGridType: (0, None) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "debug.py", line 23, in <module> print(d.all_data()[("deposit","STAR_nn_luminosity")]) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 282, in __getitem__ self.get_data(f) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 1337, in get_data self._generate_fields(fields_to_generate) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 1357, in _generate_fields fd = self._generate_field(field) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 319, in _generate_field tr = self._generate_fluid_field(field) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 337, in _generate_fluid_field rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 357, in _generate_spatial_fluid ind += o.select(self.selector, self[field], rv, ind) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 282, in __getitem__ self.get_data(f) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 1337, in get_data self._generate_fields(fields_to_generate) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 1357, in _generate_fields fd = self._generate_field(field) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 319, in _generate_field tr = self._generate_fluid_field(field) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 339, in _generate_fluid_field rv = finfo(gen_obj) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/fields/derived_field.py", line 237, in __call__ dd = self._function(self, data) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/static_output.py", line 1274, in _deposit_field fields = [data[ptype, deposit_field]] File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/octree_subset.py", line 75, in __getitem__ tr = super(OctreeSubset, self).__getitem__(key) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 282, in __getitem__ self.get_data(f) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 1337, in get_data self._generate_fields(fields_to_generate) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 1357, in _generate_fields fd = self._generate_field(field) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 317, in _generate_field tr = self._generate_particle_field(field) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 402, in _generate_particle_field rv = self.ds._get_field_info(*field)(gen_obj) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/fields/derived_field.py", line 235, in __call__ "for %s" % (self.name,)) RuntimeError: Something has gone terribly wrong, _function is NullFunc for ('STAR', 'METALLICITY_SNII') n On 5/27/2018 12:08 PM, Nathan Goldbaum wrote: > Hi Nick, > > What you're seeing in those print statements is how yt's field detection > system works. Before we actually select and return data, we pass your > field function fake data to make sure it doesn't raise errors or it > doesn't select fields that aren't available for your dataset. > > Here's a script I made based on yours that helps explain what's going on: > > https://gist.github.com/ngoldbaum/4d27987bda8ecbce5c9bd9b98bbbbf49 > > And here's the output of that script: > > https://gist.github.com/ngoldbaum/475fcd827a53e4d02e76cb25711ff5ea > > I made a couple modifications compared to your script. First, I added a > line at the end that selects your new field from a data object, which > causes real data to be fed into the field function after field detection > completes. I also specified "units='auto'" in the call to add_field. The > dimensions keyword is only used when "units='auto'" is set. > > You can see that your field function is called twice. First with a > `FieldDetector` instance and then the second time with a real yt data > object. In general the field function might be called several times > before real data is supplied to it. One way I commonly deal with this is > the following hack to only see output when the field definition is > called with real data: > > def NewField(field, data): > q = data[('STAR', 'age')] > if 'FieldDetector' in str(type(data)): > print("BBB",data) > return q > > Although more often I use python's debugger via "import pdb; > pdb.set_trace()" instead of print statements. > > Hope that helps, > > Nathan > > On Sun, May 27, 2018 at 10:51 AM, Nick Gnedin <ngnedin(a)gmail.com > <mailto:ngnedin@gmail.com>> wrote: > > > Guys, > > I am trying to add a new particle field, and apparently I am doing > something wrong, but I could find the documentation for this: > > import yt > def NewField(field,data): > q = data[('STAR','age')] > print("BBB",data) > return q > d = yt.load("rei10_a0.1001/rei10_a0.1001.art") > print('AAA',d.all_data()[("STAR","age")]) > d.add_field(("STAR","new-field"),function=NewField,dimensions="time",sampling_type="particle") > > The result is here: > > AAA [ 1.35689106e+08 1.29578798e+08 1.15241829e+08 ..., > 2.97175878e+07 > 2.04648908e+07 1.35365980e+07] yr > BBB defaultdict(<function FieldDetector.__init__.<locals>.<lambda> > at 0x2b9e698e3598>, {('STAR', 'BIRTH_TIME'): YTArray([ 1.]) > (dimensionless), ('STAR', 'creation_time'): YTArray([ 1.]) > (dimensionless), ('STAR', 'age'): YTArray([ 1.]) (dimensionless)}) > > It appears that the data object sent to NewField(field,data) has all > its fields set to dimensionless. > > I tried omitting sampling_type="particle", but it does not help, > just generates an incomprehensible warning. > > n > _______________________________________________ > yt-users mailing list -- yt-users(a)python.org > <mailto:yt-users@python.org> > To unsubscribe send an email to yt-users-leave(a)python.org > <mailto:yt-users-leave@python.org> > >

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Re: Adding particle fields
by Nick Gnedin 27 May '18

27 May '18

Nathan, Thank you. If you care for a comment, I do not think this is a good idea. I sent you a snippet, my real field function looks like this: def StellarLuminosity(field,data): ts = data[('STAR','age')].in_units("yr").v zs = (data[('STAR', 'METALLICITY_SNII')]+data[('STAR', 'METALLICITY_SNIa')]).v return sps.GetLnu(ts,zs)*data[('STAR','mass')].in_units("Msun") The fake data caused an error in the statement ts = data[('STAR','age')].in_units("yr") because dimensionless data cannot be converted into years, and that was how I discovered that the incorrect data were sent to the field function. I can add a check "if 'FieldDetector' in str(type(data))" to the function, but think about what is going on in the actual calculation: a string comparison is going to be taking place every time that function is called, if it is called frequently, that will be a huge performance penalty. n On 5/27/2018 12:08 PM, Nathan Goldbaum wrote: > Hi Nick, > > What you're seeing in those print statements is how yt's field detection > system works. Before we actually select and return data, we pass your > field function fake data to make sure it doesn't raise errors or it > doesn't select fields that aren't available for your dataset. > > Here's a script I made based on yours that helps explain what's going on: > > https://gist.github.com/ngoldbaum/4d27987bda8ecbce5c9bd9b98bbbbf49 > > And here's the output of that script: > > https://gist.github.com/ngoldbaum/475fcd827a53e4d02e76cb25711ff5ea > > I made a couple modifications compared to your script. First, I added a > line at the end that selects your new field from a data object, which > causes real data to be fed into the field function after field detection > completes. I also specified "units='auto'" in the call to add_field. The > dimensions keyword is only used when "units='auto'" is set. > > You can see that your field function is called twice. First with a > `FieldDetector` instance and then the second time with a real yt data > object. In general the field function might be called several times > before real data is supplied to it. One way I commonly deal with this is > the following hack to only see output when the field definition is > called with real data: > > def NewField(field, data): > q = data[('STAR', 'age')] > if 'FieldDetector' in str(type(data)): > print("BBB",data) > return q > > Although more often I use python's debugger via "import pdb; > pdb.set_trace()" instead of print statements. > > Hope that helps, > > Nathan > > On Sun, May 27, 2018 at 10:51 AM, Nick Gnedin <ngnedin(a)gmail.com > <mailto:ngnedin@gmail.com>> wrote: > > > Guys, > > I am trying to add a new particle field, and apparently I am doing > something wrong, but I could find the documentation for this: > > import yt > def NewField(field,data): > q = data[('STAR','age')] > print("BBB",data) > return q > d = yt.load("rei10_a0.1001/rei10_a0.1001.art") > print('AAA',d.all_data()[("STAR","age")]) > d.add_field(("STAR","new-field"),function=NewField,dimensions="time",sampling_type="particle") > > The result is here: > > AAA [ 1.35689106e+08 1.29578798e+08 1.15241829e+08 ..., > 2.97175878e+07 > 2.04648908e+07 1.35365980e+07] yr > BBB defaultdict(<function FieldDetector.__init__.<locals>.<lambda> > at 0x2b9e698e3598>, {('STAR', 'BIRTH_TIME'): YTArray([ 1.]) > (dimensionless), ('STAR', 'creation_time'): YTArray([ 1.]) > (dimensionless), ('STAR', 'age'): YTArray([ 1.]) (dimensionless)}) > > It appears that the data object sent to NewField(field,data) has all > its fields set to dimensionless. > > I tried omitting sampling_type="particle", but it does not help, > just generates an incomprehensible warning. > > n > _______________________________________________ > yt-users mailing list -- yt-users(a)python.org > <mailto:yt-users@python.org> > To unsubscribe send an email to yt-users-leave(a)python.org > <mailto:yt-users-leave@python.org> > >

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Adding particle fields
by Nick Gnedin 27 May '18

27 May '18

Guys, I am trying to add a new particle field, and apparently I am doing something wrong, but I could find the documentation for this: import yt def NewField(field,data): q = data[('STAR','age')] print("BBB",data) return q d = yt.load("rei10_a0.1001/rei10_a0.1001.art") print('AAA',d.all_data()[("STAR","age")]) d.add_field(("STAR","new-field"),function=NewField,dimensions="time",sampling_type="particle") The result is here: AAA [ 1.35689106e+08 1.29578798e+08 1.15241829e+08 ..., 2.97175878e+07 2.04648908e+07 1.35365980e+07] yr BBB defaultdict(<function FieldDetector.__init__.<locals>.<lambda> at 0x2b9e698e3598>, {('STAR', 'BIRTH_TIME'): YTArray([ 1.]) (dimensionless), ('STAR', 'creation_time'): YTArray([ 1.]) (dimensionless), ('STAR', 'age'): YTArray([ 1.]) (dimensionless)}) It appears that the data object sent to NewField(field,data) has all its fields set to dimensionless. I tried omitting sampling_type="particle", but it does not help, just generates an incomprehensible warning. n

2 1

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