Mailman 3 September 2018 - yt-users

How to make the new drived-fields work?
by lianxiaoli87＠sjtu.edu.cn 17 Sep '18

17 Sep '18

Hi, I write some new fields in yt/yt/fields named as XXX.py, but I have no idea about how to make it work correctly like yt's density, temperature etc which can be projected or sliced plots.

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Re: yt-users Digest, Vol 127, Issue 6
by Guido granda muñoz 13 Sep '18

13 Sep '18

Hello Mat, Ok. I will report it on the github site. Cheers, El jue., 13 sept. 2018 a las 11:01, <yt-users-request(a)python.org> escribió: > Send yt-users mailing list submissions to > yt-users(a)python.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.python.org/mm3/mailman3/lists/yt-users.python.org/ > or, via email, send a message with subject or body 'help' to > yt-users-request(a)python.org > > You can reach the person managing the list at > yt-users-owner(a)python.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > Today's Topics: > > 1. Point function not working for negative coordinates > (Guido granda muñoz) > 2. Re: Point function not working for negative coordinates > (Matthew Turk) > > > ---------------------------------------------------------------------- > > Date: Wed, 12 Sep 2018 17:47:31 -0500 > From: Guido granda muñoz <guidogranda(a)gmail.com> > Subject: [yt-users] Point function not working for negative > coordinates > To: yt-users(a)python.org > Message-ID: > < > CALOHZ_28Yh_4gVR53jZhdNUzCCM9C4PsU2-5UineUcyQdexGQA(a)mail.gmail.com> > Content-Type: multipart/alternative; > boundary="000000000000e2ae280575b46045" > > --000000000000e2ae280575b46045 > Content-Type: text/plain; charset="UTF-8" > > Hello yt users, > > I have been trying to obtain density values at different points using point > data object. The problem is that this function does not work for negative > coordinates regardless the fact that the computational domain contains > those coordinates. > > This is the error I got: > > Entering folder ./lr_teq_p_3_nk4 > Using rho_0: 6.372606e-24 > Using 5.0 snapshots > yt : [INFO ] 2018-09-12 17:34:34,371 Parameters: current_time > = 0.0 > yt : [INFO ] 2018-09-12 17:34:34,371 Parameters: domain_dimensions > = [256 256 256] > yt : [INFO ] 2018-09-12 17:34:34,372 Parameters: domain_left_edge > = [ -1.54283920e+19 -1.54283920e+19 -1.54283920e+19] > yt : [INFO ] 2018-09-12 17:34:34,372 Parameters: domain_right_edge > = [ 1.54283920e+19 1.54283920e+19 1.54283920e+19] > yt : [INFO ] 2018-09-12 17:34:34,372 Parameters: > cosmological_simulation = 0.0 > domain: [ 10.00000265 10.00000265 10.00000265] pc > YTPoint (lr_hdf5_plt_cnt_0000): , p=[ 1. 1. -0.001] cm > [] g/cm**3 > --------------------------------------------------------------------------- > ValueError Traceback (most recent call last) > /share/Part1/guido/w_profile2.py in <module>() > 84 print(point) > 85 print(point['gas','density']) > ---> 86 > dens_array[snap_order,ipoint]=point['gas','density'] > 87 ipoint=ipoint+1 > 88 print("time :",time) > > ValueError: setting an array element with a sequence. > > As you can see, the point p=[ 1. 1. -0.001] cm belongs to the > computational domain. When I only use positive coordinates the code runs > well. Correct me if I am wrong, but I think this is a bug. Do you guys know > another way to get values of any field at a fixed point? > > Cheers, > -- > Guido > > --000000000000e2ae280575b46045 > Content-Type: text/html; charset="UTF-8" > Content-Transfer-Encoding: quoted-printable > > <div dir=3D"ltr"><div dir=3D"ltr">Hello yt users,<div><br></div><div>I > have= > been trying to obtain density values at different points using point data > = > object. The problem is that this function does not work for negative > coordi= > nates regardless the fact that the computational domain contains those > coor= > dinates.</div><div><br></div><div>This is the error I > got:</div><div><br></= > div><div><div>Entering folder ./lr_teq_p_3_nk4</div><div>Using rho_0: > 6.372= > 606e-24=C2=A0</div><div>Using 5.0 snapshots</div><div>yt : [INFO=C2=A0 =C2= > =A0 =C2=A0] 2018-09-12 17:34:34,371 Parameters: current_time=C2=A0 =C2=A0 = > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =3D 0.0</div><div>yt : [INFO=C2=A0 =C2= > =A0 =C2=A0] 2018-09-12 17:34:34,371 Parameters: domain_dimensions=C2=A0 > =C2= > =A0 =C2=A0 =C2=A0 =C2=A0=3D [256 256 256]</div><div>yt : [INFO=C2=A0 > =C2=A0= > =C2=A0] 2018-09-12 17:34:34,372 Parameters: domain_left_edge=C2=A0 =C2=A0 > = > =C2=A0 =C2=A0 =C2=A0 =3D [ -1.54283920e+19=C2=A0 -1.54283920e+19=C2=A0 > -1.5= > 4283920e+19]</div><div>yt : [INFO=C2=A0 =C2=A0 =C2=A0] 2018-09-12 > 17:34:34,= > 372 Parameters: domain_right_edge=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=3D > [=C2= > =A0 1.54283920e+19=C2=A0 =C2=A01.54283920e+19=C2=A0 > =C2=A01.54283920e+19]</= > div><div>yt : [INFO=C2=A0 =C2=A0 =C2=A0] 2018-09-12 17:34:34,372 > Parameters= > : cosmological_simulation=C2=A0 =C2=A0=3D 0.0</div><div>domain: [ > 10.000002= > 65=C2=A0 10.00000265=C2=A0 10.00000265] pc</div><div>YTPoint > (lr_hdf5_plt_c= > nt_0000): , p=3D[ 1.=C2=A0 =C2=A0 =C2=A01.=C2=A0 =C2=A0 -0.001] > cm</div><di= > v>[] > g/cm**3</div><div>----------------------------------------------------= > -----------------------</div><div>ValueError=C2=A0 =C2=A0 =C2=A0 =C2=A0 > =C2= > =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = > =C2=A0 Traceback (most recent call > last)</div><div>/share/Part1/guido/w_pro= > file2.py in <module>()</div><div>=C2=A0 =C2=A0 =C2=A084=C2=A0 =C2=A0 > = > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= > =A0 print(point)</div><div>=C2=A0 =C2=A0 =C2=A085=C2=A0 =C2=A0 =C2=A0 =C2= > =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 > print(po= > int['gas','density'])</div><div>---> 86=C2=A0 =C2=A0 > =C2= > =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 > d= > > ens_array[snap_order,ipoint]=3Dpoint['gas','density']</div>= > <div>=C2=A0 =C2=A0 =C2=A087=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 > =C2=A0= > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ipoint=3Dipoint+1</div><div>=C2= > =A0 =C2=A0 =C2=A088=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0print("time > :&quo= > t;,time)</div><div><br></div><div>ValueError: setting an array element > with= > a sequence.</div><div><br></div><div>As you can see, the point p=3D[ > 1.=C2= > =A0 =C2=A0 =C2=A01.=C2=A0 =C2=A0 -0.001] cm belongs to the computational > do= > main. When I only use positive coordinates the code runs well. Correct me > i= > f I am wrong, but I think this is a bug. Do you guys know another way to > ge= > t values of any field at a fixed > point?</div><div><br></div><div>Cheers,</d= > iv>-- <br><div dir=3D"ltr" > class=3D"gmail_signature">Guido</div></div></div= > ></div> > > --000000000000e2ae280575b46045-- > > ------------------------------ > > Date: Thu, 13 Sep 2018 10:53:29 -0500 > From: Matthew Turk <matthewturk(a)gmail.com> > Subject: [yt-users] Re: Point function not working for negative > coordinates > To: Discussion of the yt analysis package <yt-users(a)python.org> > Message-ID: > <CALO3=5E21MrkThu+MQPK4EFsoBLBEybUNzF35bHRnDG= > Y9f5gQ(a)mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi Guido, > > This looks like a bug to me! Can you file an issue and we'll discuss > there? I think I have an idea how to fix it, but having the issue to > discuss would be great. > > https://github.com/yt-project/yt/issues/new > > -Matt > On Wed, Sep 12, 2018 at 5:49 PM Guido granda muñoz > <guidogranda(a)gmail.com> wrote: > > > > Hello yt users, > > > > I have been trying to obtain density values at different points using > point data object. The problem is that this function does not work for > negative coordinates regardless the fact that the computational domain > contains those coordinates. > > > > This is the error I got: > > > > Entering folder ./lr_teq_p_3_nk4 > > Using rho_0: 6.372606e-24 > > Using 5.0 snapshots > > yt : [INFO ] 2018-09-12 17:34:34,371 Parameters: current_time > = 0.0 > > yt : [INFO ] 2018-09-12 17:34:34,371 Parameters: domain_dimensions > = [256 256 256] > > yt : [INFO ] 2018-09-12 17:34:34,372 Parameters: domain_left_edge > = [ -1.54283920e+19 -1.54283920e+19 -1.54283920e+19] > > yt : [INFO ] 2018-09-12 17:34:34,372 Parameters: domain_right_edge > = [ 1.54283920e+19 1.54283920e+19 1.54283920e+19] > > yt : [INFO ] 2018-09-12 17:34:34,372 Parameters: > cosmological_simulation = 0.0 > > domain: [ 10.00000265 10.00000265 10.00000265] pc > > YTPoint (lr_hdf5_plt_cnt_0000): , p=[ 1. 1. -0.001] cm > > [] g/cm**3 > > > --------------------------------------------------------------------------- > > ValueError Traceback (most recent call > last) > > /share/Part1/guido/w_profile2.py in <module>() > > 84 print(point) > > 85 print(point['gas','density']) > > ---> 86 > dens_array[snap_order,ipoint]=point['gas','density'] > > 87 ipoint=ipoint+1 > > 88 print("time :",time) > > > > ValueError: setting an array element with a sequence. > > > > As you can see, the point p=[ 1. 1. -0.001] cm belongs to the > computational domain. When I only use positive coordinates the code runs > well. Correct me if I am wrong, but I think this is a bug. Do you guys know > another way to get values of any field at a fixed point? > > > > Cheers, > > -- > > Guido > > _______________________________________________ > > yt-users mailing list -- yt-users(a)python.org > > To unsubscribe send an email to yt-users-leave(a)python.org > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list -- yt-users(a)python.org > To unsubscribe send an email to yt-users-leave(a)python.org > > > ------------------------------ > > End of yt-users Digest, Vol 127, Issue 6 > **************************************** > -- Guido

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Point function not working for negative coordinates
by Guido granda muñoz 13 Sep '18

13 Sep '18

Hello yt users, I have been trying to obtain density values at different points using point data object. The problem is that this function does not work for negative coordinates regardless the fact that the computational domain contains those coordinates. This is the error I got: Entering folder ./lr_teq_p_3_nk4 Using rho_0: 6.372606e-24 Using 5.0 snapshots yt : [INFO ] 2018-09-12 17:34:34,371 Parameters: current_time = 0.0 yt : [INFO ] 2018-09-12 17:34:34,371 Parameters: domain_dimensions = [256 256 256] yt : [INFO ] 2018-09-12 17:34:34,372 Parameters: domain_left_edge = [ -1.54283920e+19 -1.54283920e+19 -1.54283920e+19] yt : [INFO ] 2018-09-12 17:34:34,372 Parameters: domain_right_edge = [ 1.54283920e+19 1.54283920e+19 1.54283920e+19] yt : [INFO ] 2018-09-12 17:34:34,372 Parameters: cosmological_simulation = 0.0 domain: [ 10.00000265 10.00000265 10.00000265] pc YTPoint (lr_hdf5_plt_cnt_0000): , p=[ 1. 1. -0.001] cm [] g/cm**3 --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /share/Part1/guido/w_profile2.py in <module>() 84 print(point) 85 print(point['gas','density']) ---> 86 dens_array[snap_order,ipoint]=point['gas','density'] 87 ipoint=ipoint+1 88 print("time :",time) ValueError: setting an array element with a sequence. As you can see, the point p=[ 1. 1. -0.001] cm belongs to the computational domain. When I only use positive coordinates the code runs well. Correct me if I am wrong, but I think this is a bug. Do you guys know another way to get values of any field at a fixed point? Cheers, -- Guido

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yt load strangeness
by romeeld＠gmail.com 11 Sep '18

11 Sep '18

I'm trying to load in two Gizmo cosmo simulations that are exactly identical except that one has a 25 Mpc/h size (call it sim) and the other has 100 Mpc/h (sim2). Weirdly, the 100 Mpc/h loads fine, but the 25 Mpc/h doesn't load any of its particle data, it seems. Below are some outputs from an ipython session to show what I mean. Any thoughts/pointers on what could be going wrong with the 25 box would be much appreciated. thanks, romeel In [4]: sim2 = yt.load("/cosma/home/dc-dave2/data/m25n1024/s43/snap_m25n1024_042.hdf5") yt : [INFO ] 2018-09-11 19:22:52,554 Calculating time from 1.660e-01 to be 3.729e+16 seconds yt : [INFO ] 2018-09-11 19:22:52,554 Assuming length units are in kpc/h (comoving) yt : [INFO ] 2018-09-11 19:22:52,565 Parameters: current_time = 3.72864881334e+16 s yt : [INFO ] 2018-09-11 19:22:52,565 Parameters: domain_dimensions = [2 2 2] yt : [INFO ] 2018-09-11 19:22:52,565 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2018-09-11 19:22:52,566 Parameters: domain_right_edge = [ 25000. 25000. 25000.] yt : [INFO ] 2018-09-11 19:22:52,566 Parameters: cosmological_simulation = 1 yt : [INFO ] 2018-09-11 19:22:52,566 Parameters: current_redshift = 5.02438675155 yt : [INFO ] 2018-09-11 19:22:52,566 Parameters: omega_lambda = 0.7 yt : [INFO ] 2018-09-11 19:22:52,566 Parameters: omega_matter = 0.3 yt : [INFO ] 2018-09-11 19:22:52,566 Parameters: hubble_constant = 0.68 In [6]: sim2 = yt.load("/cosma/home/dc-dave2/data/m100n1024/s43/snap_m100n1024_042.hdf5") yt : [INFO ] 2018-09-11 19:23:33,838 Calculating time from 1.660e-01 to be 3.729e+16 seconds yt : [INFO ] 2018-09-11 19:23:33,838 Assuming length units are in kpc/h (comoving) yt : [INFO ] 2018-09-11 19:23:33,847 Parameters: current_time = 3.72864881334e+16 s yt : [INFO ] 2018-09-11 19:23:33,847 Parameters: domain_dimensions = [2 2 2] yt : [INFO ] 2018-09-11 19:23:33,847 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2018-09-11 19:23:33,848 Parameters: domain_right_edge = [ 100000. 100000. 100000.] yt : [INFO ] 2018-09-11 19:23:33,848 Parameters: cosmological_simulation = 1 yt : [INFO ] 2018-09-11 19:23:33,848 Parameters: current_redshift = 5.02438675155 yt : [INFO ] 2018-09-11 19:23:33,848 Parameters: omega_lambda = 0.7 yt : [INFO ] 2018-09-11 19:23:33,848 Parameters: omega_matter = 0.3 yt : [INFO ] 2018-09-11 19:23:33,848 Parameters: hubble_constant = 0.68 In [23]: sim.dataset_type Out[23]: 'gadget_hdf5' In [24]: sim2.dataset_type Out[24]: 'gadget_hdf5' *********** all looks good so far In [17]: sim.parameters Out[17]: {'BoxSize': 25000.0, 'Flag_Cooling': 1, 'Flag_DoublePrecision': 0, 'Flag_Feedback': 1, 'Flag_IC_Info': 3, 'Flag_Metals': 11, 'Flag_Sfr': 1, 'Flag_StellarAge': 1, 'HubbleParam': 0.68000000000000005, 'MassTable': array([ 0., 0., 0., 0., 0., 0.]), 'Massarr': array([ 0., 0., 0., 0., 0., 0.]), 'NumFiles': 1, 'NumFilesPerSnapshot': 1, 'NumPart_ThisFile': array([1072810110, 1073741824, 0, 0, 931728, 5], dtype=int32), 'NumPart_Total': array([1072810110, 1073741824, 0, 0, 931728, 5], dtype=uint32), 'NumPart_Total_HighWord': array([0, 0, 0, 0, 0, 0], dtype=uint32), 'Omega0': 0.29999999999999999, 'OmegaLambda': 0.69999999999999996, 'Redshift': 5.0243867515502965, 'Time': 0.16599199905993139} In [18]: sim2.parameters Out[18]: {'BoxSize': 100000.0, 'Flag_Cooling': 1, 'Flag_DoublePrecision': 0, 'Flag_Feedback': 1, 'Flag_IC_Info': 3, 'Flag_Metals': 11, 'Flag_Sfr': 1, 'Flag_StellarAge': 1, 'HubbleParam': 0.68000000000000005, 'MassTable': array([ 0., 0., 0., 0., 0., 0.]), 'Massarr': array([ 0., 0., 0., 0., 0., 0.]), 'NumFiles': 1, 'NumFilesPerSnapshot': 1, 'NumPart_ThisFile': array([1071819062, 1073741824, 0, 0, 1922044, 482], dtype=int32), 'NumPart_Total': array([1071819062, 1073741824, 0, 0, 1922044, 482], dtype=uint32), 'NumPart_Total_HighWord': array([0, 0, 0, 0, 0, 0], dtype=uint32), 'Omega0': 0.29999999999999999, 'OmegaLambda': 0.69999999999999996, 'Redshift': 5.0243867515502965, 'Time': 0.16599199905993139} ************** both look reasonable. Now we look at the loaded data .... In [31]: sim.particle_types Out[31]: () In [32]: sim2.particle_types Out[32]: ('PartType4', 'PartType5', 'PartType0', 'PartType1', 'all') ********** sim has no particle_types! Why? In [19]: sim.field_info Out[19]: {('gas', 'cell_volume'): Alias Field for "('index', 'cell_volume')" (gas, cell_volume): (units: code_length**3), ('gas', 'dx'): Alias Field for "('index', 'dx')" (gas, dx): (units: code_length), ('gas', 'dy'): Alias Field for "('index', 'dy')" (gas, dy): (units: code_length), ('gas', 'dz'): Alias Field for "('index', 'dz')" (gas, dz): (units: code_length), ('gas', 'path_element_x'): Alias Field for "('index', 'path_element_x')" (gas, path_element_x): (units: code_length), ('gas', 'path_element_y'): Alias Field for "('index', 'path_element_y')" (gas, path_element_y): (units: code_length), ('gas', 'path_element_z'): Alias Field for "('index', 'path_element_z')" (gas, path_element_z): (units: code_length), ('gas', 'vertex_x'): Alias Field for "('index', 'vertex_x')" (gas, vertex_x): (units: code_length), ('gas', 'vertex_y'): Alias Field for "('index', 'vertex_y')" (gas, vertex_y): (units: code_length), ('gas', 'vertex_z'): Alias Field for "('index', 'vertex_z')" (gas, vertex_z): (units: code_length), ('gas', 'x'): Alias Field for "('index', 'x')" (gas, x): (units: code_length), ('gas', 'y'): Alias Field for "('index', 'y')" (gas, y): (units: code_length), ('gas', 'z'): Alias Field for "('index', 'z')" (gas, z): (units: code_length), ('index', 'cell_volume'): Derived Field (index, cell_volume): (units: code_length**3), ('index', 'cylindrical_r'): Derived Field (index, cylindrical_r): (units: cm), ('index', 'cylindrical_radius'): Derived Field (index, cylindrical_radius): (units: cm), ('index', 'cylindrical_theta'): Derived Field (index, cylindrical_theta): (units: ), ('index', 'cylindrical_z'): Derived Field (index, cylindrical_z): (units: cm), ('index', 'disk_angle'): Derived Field (index, disk_angle): (units: ), ('index', 'dx'): Derived Field (index, dx): (units: code_length), ('index', 'dy'): Derived Field (index, dy): (units: code_length), ('index', 'dz'): Derived Field (index, dz): (units: code_length), ('index', 'grid_indices'): Derived Field (index, grid_indices): (units: ), ('index', 'grid_level'): Derived Field (index, grid_level): (units: ), ('index', 'height'): Derived Field (index, height): (units: cm), ('index', 'morton_index'): Derived Field (index, morton_index): (units: ), ('index', 'ones'): Derived Field (index, ones): (units: ), ('index', 'ones_over_dx'): Derived Field (index, ones_over_dx): (units: 1/cm), ('index', 'path_element_x'): Derived Field (index, path_element_x): (units: code_length), ('index', 'path_element_y'): Derived Field (index, path_element_y): (units: code_length), ('index', 'path_element_z'): Derived Field (index, path_element_z): (units: code_length), ('index', 'radius'): Derived Field (index, radius): (units: cm), ('index', 'spherical_phi'): Derived Field (index, spherical_phi): (units: ), ('index', 'spherical_r'): Derived Field (index, spherical_r): (units: cm), ('index', 'spherical_radius'): Derived Field (index, spherical_radius): (units: cm), ('index', 'spherical_theta'): Derived Field (index, spherical_theta): (units: ), ('index', 'vertex_x'): Derived Field (index, vertex_x): (units: code_length), ('index', 'vertex_y'): Derived Field (index, vertex_y): (units: code_length), ('index', 'vertex_z'): Derived Field (index, vertex_z): (units: code_length), ('index', 'virial_radius_fraction'): Derived Field (index, virial_radius_fraction): (units: ), ('index', 'x'): Derived Field (index, x): (units: code_length), ('index', 'y'): Derived Field (index, y): (units: code_length), ('index', 'z'): Derived Field (index, z): (units: code_length), ('index', 'zeros'): Derived Field (index, zeros): (units: )} In [20]: sim2.field_info --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-20-7ba53e5d35de> in <module>() ----> 1 sim2.field_info AttributeError: 'GizmoDataset' object has no attribute 'field_info' ********* So sim2 (which is behaving properly) appears to be a GizmoDataset, as expected. But sim isn't? Then what is it? In [21]: sim.field_list Out[21]: [] In [22]: sim2.field_list yt : [INFO ] 2018-09-11 19:33:26,796 Allocating for 2.147e+09 particles (index particle type 'all') yt : [INFO ] 2018-09-11 19:39:02,984 Identified 1.516e+08 octs Out[22]: [('PartType0', 'AGS-Softening'), ('PartType0', 'Coordinates'), ('PartType0', 'DelayTime'), ('PartType0', 'Density'), ('PartType0', 'Dust_Masses'), ('PartType0', 'Dust_Metallicity'), ('PartType0', 'ElectronAbundance'), ('PartType0', 'FractionH2'), ('PartType0', 'GrackleHI'), ('PartType0', 'GrackleHII'), ('PartType0', 'GrackleHM'), ('PartType0', 'GrackleHeI'), ('PartType0', 'GrackleHeII'), ('PartType0', 'GrackleHeIII'), ('PartType0', 'HaloID'), ('PartType0', 'InternalEnergy'), ('PartType0', 'Masses'), ('PartType0', 'Metallicity_00'), ('PartType0', 'Metallicity_01'), ('PartType0', 'Metallicity_02'), ('PartType0', 'Metallicity_03'), ('PartType0', 'Metallicity_04'), ('PartType0', 'Metallicity_05'), ('PartType0', 'Metallicity_06'), ('PartType0', 'Metallicity_07'), ('PartType0', 'Metallicity_08'), ('PartType0', 'Metallicity_09'), ('PartType0', 'Metallicity_10'), ('PartType0', 'NWindLaunches'), ('PartType0', 'NeutralHydrogenAbundance'), ('PartType0', 'ParticleIDs'), ('PartType0', 'Potential'), ('PartType0', 'Sigma'), ('PartType0', 'SmoothingLength'), ('PartType0', 'StarFormationRate'), ('PartType0', 'Velocities'), ('PartType1', 'AGS-Softening'), ('PartType1', 'Coordinates'), ('PartType1', 'HaloID'), ('PartType1', 'Masses'), ('PartType1', 'ParticleIDs'), ('PartType1', 'Potential'), ('PartType1', 'Velocities'), ('PartType4', 'AGS-Softening'), ('PartType4', 'Coordinates'), ('PartType4', 'Dust_Masses'), ('PartType4', 'Dust_Metallicity'), ('PartType4', 'HaloID'), ('PartType4', 'Masses'), ('PartType4', 'Metallicity_00'), ('PartType4', 'Metallicity_01'), ('PartType4', 'Metallicity_02'), ('PartType4', 'Metallicity_03'), ('PartType4', 'Metallicity_04'), ('PartType4', 'Metallicity_05'), ('PartType4', 'Metallicity_06'), ('PartType4', 'Metallicity_07'), ('PartType4', 'Metallicity_08'), ('PartType4', 'Metallicity_09'), ('PartType4', 'Metallicity_10'), ('PartType4', 'ParticleIDs'), ('PartType4', 'Potential'), ('PartType4', 'StellarFormationTime'), ('PartType4', 'Velocities'), ('PartType5', 'AGS-Softening'), ('PartType5', 'BH_AccretionLength'), ('PartType5', 'BH_Mass'), ('PartType5', 'BH_Mass_AlphaDisk'), ('PartType5', 'BH_Mdot'), ('PartType5', 'BH_NProgs'), ('PartType5', 'Coordinates'), ('PartType5', 'HaloID'), ('PartType5', 'Masses'), ('PartType5', 'ParticleIDs'), ('PartType5', 'Potential'), ('PartType5', 'StellarFormationTime'), ('PartType5', 'Velocities'), ('all', 'AGS-Softening'), ('all', 'Coordinates'), ('all', 'HaloID'), ('all', 'Masses'), ('all', 'ParticleIDs'), ('all', 'Potential'), ('all', 'Velocities')] *********** sim2 has all the right fields. sim has no fields?!?

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Internal memory usage
by Nick Gnedin 07 Sep '18

07 Sep '18

Folks, I would like to test the integrity of a large dataset, for example by finding the max value of some data field. The dataset is too large to be fully loaded into memory, so I would like to read it slice by slice and compute max in each slice, and then combine them together. To that end I wrote the following script: import yt, yt.funcs import sys import numpy as np f = sys.argv[1] ds = yt.load(f) n = ds.domain_dimensions[0] dmax = np.zeros((n,)) for i in range(n): d = ds.r[i:(i+1),:,:][('artio', 'HVAR_GAS_DENSITY')] dmax[i] = np.amax(d) print(i,dmax[i],yt.funcs.get_memory_usage()) del d print(np.amax(dmax)) However, when I run it, I get: yt : [INFO ] 2018-08-28 10:52:58,075 Created 4945 chunks for ARTIO 0 16945762.0 202.5546875 yt : [INFO ] 2018-08-28 10:52:59,388 Created 1232 chunks for ARTIO 1 2416576.25 221.36328125 yt : [INFO ] 2018-08-28 10:53:01,599 Created 9635 chunks for ARTIO 2 10419311.0 269.06640625 ... yt : [INFO ] 2018-08-28 10:53:23,397 Created 1474 chunks for ARTIO 13 2395590.5 698.91015625 yt : [INFO ] 2018-08-28 10:53:25,594 Created 9747 chunks for ARTIO 14 11139424.0 739.16015625 The number of chunks created varies in each iteration of the loop, but the total memory usage is still steadily climbing up. Could you advise what I am doing wrong? Many thanks, Nick

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Does yt fully support eagle and illustris data?
by qinyuxian＠163.com 02 Sep '18

02 Sep '18

I just want to use yt to make a sliceplot of eagle data. ds = yt.load('/scratch/eagle/AGNdT9L0050N0752/snapshot_015_z002p012/snap_015_z002p012.0.hdf5') slc = yt.SlicePlot(ds, "z", ['density', 'temperature', 'xray_emissivity']) yt : [INFO ] 2018-09-02 10:17:48,333 Allocating for 8.505e+08 particles (index particle type 'all') yt : [INFO ] 2018-09-02 10:24:50,335 Identified 5.640e+07 octs yt : [INFO ] 2018-09-02 10:26:12,532 Attempting to download ~ 30 Mb of owls ion data from http://yt-project.org/data to ./. Downloading owls_ion_data.tar.gz to . : 33%|?.. | 1/3 [00:05<00:10, 0.18iDownloading owls_ion_data.tar.gz to . : 67%|?..?.. | 2/3 [00:09<00:05, 0Downloading owls_ion_data.tar.gz to . : 100%|?..?..?. 3/3 [00:12<00:00, Downloading owls_ion_data.tar.gz to . : 4it [00:13, 1.76it/s] yt : [INFO ] 2018-09-02 10:49:20,110 xlim = 0.000000 33.885000 yt : [INFO ] 2018-09-02 10:49:20,111 ylim = 0.000000 33.885000 yt : [INFO ] 2018-09-02 10:49:20,113 xlim = 0.000000 33.885000 yt : [INFO ] 2018-09-02 10:49:20,113 ylim = 0.000000 33.885000 yt : [INFO ] 2018-09-02 10:49:20,145 Making a fixed resolution buffer of (('gas', 'density')) 800 by 800 yt : [INFO ] 2018-09-02 10:49:20,149 Making a fixed resolution buffer of (('gas', 'temperature')) 800 by 800 yt : [INFO ] 2018-09-02 10:49:20,151 Making a fixed resolution buffer of (('gas', 'xray_emissivity')) 800 by 800 yt : [WARNING ] 2018-09-02 10:49:20,163 Plot image for field ('gas', 'temperature') has zero dynamic range. Min = Max = 0.000000. yt : [WARNING ] 2018-09-02 10:49:20,163 Switching to linear colorbar scaling. yt : [WARNING ] 2018-09-02 10:49:22,956 Plot image for field ('gas', 'density') has zero dynamic range. Min = Max = 0.000000. yt : [WARNING ] 2018-09-02 10:49:22,957 Switching to linear colorbar scaling. yt : [WARNING ] 2018-09-02 10:49:23,598 Plot image for field ('gas', 'xray_emissivity') has zero dynamic range. Min = Max = 0.000000. yt : [WARNING ] 2018-09-02 10:49:23,598 Switching to linear colorbar scaling. I get nothing in the figure. What's the matter?

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