Hi All, Is the accumulation flag working in 3.0? I tried to plot the enclosed mass in a sphere and I got some funny results. rpm = yt.create_profile(sp, 'radius', 'cell_mass', units = {'radius': 'pc', 'cell_mass' : 'Msun'}, weight_field='density', accumulation=True, fractional=False) print "Mass = ", rpm["gas", "cell_mass"] In this case bin[n-1] gives a mass of something like 0.5 Msun but when I print the totals quantity I get a value of several orders of magnitude higher and closer to what I would expect. sp.quantities.total_quantity(["cell_mass", "particle_mass"]) Cheers, John
Hi John, I think that if you want to compute "total" instead of mean you need to set weight_field to None in create_profile. Cheers, Kacper On Sat Nov 01 2014 at 6:10:50 AM John Regan <johnanthonyregan@gmail.com> wrote:
Hi All,
Is the accumulation flag working in 3.0? I tried to plot the enclosed mass in a sphere and I got some funny results.
rpm = yt.create_profile(sp, 'radius', 'cell_mass', units = {'radius': 'pc', 'cell_mass' : 'Msun'}, weight_field='density', accumulation=True, fractional=False)
print "Mass = ", rpm["gas", "cell_mass"]
In this case bin[n-1] gives a mass of something like 0.5 Msun but when I print the totals quantity I get a value of several orders of magnitude higher and closer to what I would expect.
sp.quantities.total_quantity(["cell_mass", "particle_mass"])
Cheers, John _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Kacper, Of course - I should have noticed that. Thanks for finding that. However, I notice that when I try to create a profile for the Dark (particle) matter I run into some trouble as well. rpm = yt.create_profile(sp, 'radius', ['particle_mass'], units = {'radius': 'pc', 'particle_mass' : 'Msun'}, n_bins=20, weight_field=None, accumulation=True, fractional=False) This gives the following error: Traceback (most recent call last): File "EnclosedMass.py", line 35, in <module> n_bins=20, weight_field=None, accumulation=True, fractional=False) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 1361, in create_profile obj.add_fields([field for field in fields]) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 782, in add_fields self._bin_chunk(chunk, fields, temp_storage) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 979, in _bin_chunk rv = self._get_data(chunk, fields) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 910, in _get_data arr[:,i] = chunk[field][filter] File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/units/yt_array.py", line 963, in __getitem__ ret = super(YTArray, self).__getitem__(item) ValueError: too many boolean indices Has anyone seen this before? For the 'cell_mass' everything works fine. Cheers, John On Sat, Nov 1, 2014 at 6:49 PM, Kacper Kowalik <xarthisius.kk@gmail.com> wrote:
Hi John, I think that if you want to compute "total" instead of mean you need to set weight_field to None in create_profile. Cheers, Kacper
On Sat Nov 01 2014 at 6:10:50 AM John Regan <johnanthonyregan@gmail.com> wrote:
Hi All,
Is the accumulation flag working in 3.0? I tried to plot the enclosed mass in a sphere and I got some funny results.
rpm = yt.create_profile(sp, 'radius', 'cell_mass', units = {'radius': 'pc', 'cell_mass' : 'Msun'}, weight_field='density', accumulation=True, fractional=False)
print "Mass = ", rpm["gas", "cell_mass"]
In this case bin[n-1] gives a mass of something like 0.5 Msun but when I print the totals quantity I get a value of several orders of magnitude higher and closer to what I would expect.
sp.quantities.total_quantity(["cell_mass", "particle_mass"])
Cheers, John _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi John, Try "particle_radius". Matt On Mon, Nov 3, 2014, 7:06 AM John Regan <johnanthonyregan@gmail.com> wrote:
Hi Kacper,
Of course - I should have noticed that. Thanks for finding that. However, I notice that when I try to create a profile for the Dark (particle) matter I run into some trouble as well.
rpm = yt.create_profile(sp, 'radius', ['particle_mass'], units = {'radius': 'pc', 'particle_mass' : 'Msun'}, n_bins=20, weight_field=None, accumulation=True, fractional=False)
This gives the following error:
Traceback (most recent call last): File "EnclosedMass.py", line 35, in <module> n_bins=20, weight_field=None, accumulation=True, fractional=False) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 1361, in create_profile obj.add_fields([field for field in fields]) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 782, in add_fields self._bin_chunk(chunk, fields, temp_storage) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 979, in _bin_chunk rv = self._get_data(chunk, fields) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 910, in _get_data arr[:,i] = chunk[field][filter] File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/units/yt_array.py", line 963, in __getitem__ ret = super(YTArray, self).__getitem__(item) ValueError: too many boolean indices
Has anyone seen this before? For the 'cell_mass' everything works fine.
Cheers, John
On Sat, Nov 1, 2014 at 6:49 PM, Kacper Kowalik <xarthisius.kk@gmail.com> wrote:
Hi John, I think that if you want to compute "total" instead of mean you need to set weight_field to None in create_profile. Cheers, Kacper
On Sat Nov 01 2014 at 6:10:50 AM John Regan <johnanthonyregan@gmail.com> wrote:
Hi All,
Is the accumulation flag working in 3.0? I tried to plot the enclosed mass in a sphere and I got some funny results.
rpm = yt.create_profile(sp, 'radius', 'cell_mass', units = {'radius': 'pc', 'cell_mass' : 'Msun'}, weight_field='density', accumulation=True, fractional=False)
print "Mass = ", rpm["gas", "cell_mass"]
In this case bin[n-1] gives a mass of something like 0.5 Msun but when I print the totals quantity I get a value of several orders of magnitude higher and closer to what I would expect.
sp.quantities.total_quantity(["cell_mass", "particle_mass"])
Cheers, John _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Hi Matt, Same result I'm afraid. Traceback (most recent call last): File "EnclosedMass.py", line 35, in <module> n_bins=20, weight_field=None, accumulation=True, fractional=False) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 1361, in create_profile obj.add_fields([field for field in fields]) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 782, in add_fields self._bin_chunk(chunk, fields, temp_storage) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 979, in _bin_chunk rv = self._get_data(chunk, fields) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 910, in _get_data arr[:,i] = chunk[field][filter] File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/units/yt_array.py", line 963, in __getitem__ ret = super(YTArray, self).__getitem__(item) ValueError: too many boolean indices John On Mon, Nov 3, 2014 at 1:16 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi John,
Try "particle_radius".
Matt
On Mon, Nov 3, 2014, 7:06 AM John Regan <johnanthonyregan@gmail.com> wrote:
Hi Kacper,
Of course - I should have noticed that. Thanks for finding that. However, I notice that when I try to create a profile for the Dark (particle) matter I run into some trouble as well.
rpm = yt.create_profile(sp, 'radius', ['particle_mass'], units = {'radius': 'pc', 'particle_mass' : 'Msun'}, n_bins=20, weight_field=None, accumulation=True, fractional=False)
This gives the following error:
Traceback (most recent call last): File "EnclosedMass.py", line 35, in <module> n_bins=20, weight_field=None, accumulation=True, fractional=False) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 1361, in create_profile obj.add_fields([field for field in fields]) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 782, in add_fields self._bin_chunk(chunk, fields, temp_storage) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 979, in _bin_chunk rv = self._get_data(chunk, fields) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 910, in _get_data arr[:,i] = chunk[field][filter] File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/units/yt_array.py", line 963, in __getitem__ ret = super(YTArray, self).__getitem__(item) ValueError: too many boolean indices
Has anyone seen this before? For the 'cell_mass' everything works fine.
Cheers, John
On Sat, Nov 1, 2014 at 6:49 PM, Kacper Kowalik <xarthisius.kk@gmail.com> wrote:
Hi John, I think that if you want to compute "total" instead of mean you need to set weight_field to None in create_profile. Cheers, Kacper
On Sat Nov 01 2014 at 6:10:50 AM John Regan <johnanthonyregan@gmail.com> wrote:
Hi All,
Is the accumulation flag working in 3.0? I tried to plot the enclosed mass in a sphere and I got some funny results.
rpm = yt.create_profile(sp, 'radius', 'cell_mass', units = {'radius': 'pc', 'cell_mass' : 'Msun'}, weight_field='density', accumulation=True, fractional=False)
print "Mass = ", rpm["gas", "cell_mass"]
In this case bin[n-1] gives a mass of something like 0.5 Msun but when I print the totals quantity I get a value of several orders of magnitude higher and closer to what I would expect.
sp.quantities.total_quantity(["cell_mass", "particle_mass"])
Cheers, John _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Hi John, It was exactly the same error, when you used particle_radius in both places that "radius" was used before? -Matt On Mon Nov 03 2014 at 7:06:44 AM John Regan <johnanthonyregan@gmail.com> wrote:
Hi Kacper,
Of course - I should have noticed that. Thanks for finding that. However, I notice that when I try to create a profile for the Dark (particle) matter I run into some trouble as well.
rpm = yt.create_profile(sp, 'radius', ['particle_mass'], units = {'radius': 'pc', 'particle_mass' : 'Msun'}, n_bins=20, weight_field=None, accumulation=True, fractional=False)
This gives the following error:
Traceback (most recent call last): File "EnclosedMass.py", line 35, in <module> n_bins=20, weight_field=None, accumulation=True, fractional=False) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 1361, in create_profile obj.add_fields([field for field in fields]) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 782, in add_fields self._bin_chunk(chunk, fields, temp_storage) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 979, in _bin_chunk rv = self._get_data(chunk, fields) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 910, in _get_data arr[:,i] = chunk[field][filter] File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/units/yt_array.py", line 963, in __getitem__ ret = super(YTArray, self).__getitem__(item) ValueError: too many boolean indices
Has anyone seen this before? For the 'cell_mass' everything works fine.
Cheers, John
On Sat, Nov 1, 2014 at 6:49 PM, Kacper Kowalik <xarthisius.kk@gmail.com> wrote:
Hi John, I think that if you want to compute "total" instead of mean you need to set weight_field to None in create_profile. Cheers, Kacper
On Sat Nov 01 2014 at 6:10:50 AM John Regan <johnanthonyregan@gmail.com> wrote:
Hi All,
Is the accumulation flag working in 3.0? I tried to plot the enclosed mass in a sphere and I got some funny results.
rpm = yt.create_profile(sp, 'radius', 'cell_mass', units = {'radius': 'pc', 'cell_mass' : 'Msun'}, weight_field='density', accumulation=True, fractional=False)
print "Mass = ", rpm["gas", "cell_mass"]
In this case bin[n-1] gives a mass of something like 0.5 Msun but when I print the totals quantity I get a value of several orders of magnitude higher and closer to what I would expect.
sp.quantities.total_quantity(["cell_mass", "particle_mass"])
Cheers, John _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Hi Matt, Ah I see what you mean now. Changing 'radius' to 'particle_radius' worked nicely. However, the results are bit weird. rpm = yt.create_profile(sp, ['particle_radius'], ['particle_mass'], units = {'particle_radius': 'pc', 'particle_mass' : 'Msun'}, n_bins=20, weight_field=None, accumulation=True, fractional=False) print "Particle Mass = ", rpm["particle_mass"] Particle Mass = [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 2.17730865e+47 2.39503952e+48 5.00780990e+48 9.36242721e+48 2.87404742e+49 8.03426893e+49 1.91385431e+50 4.44824158e+50 1.02681876e+51 2.28900459e+51 4.74174278e+51 1.05066029e+52 2.07602025e+52 3.49614805e+52 4.89060538e+52 6.82621100e+52 1.08907237e+53] Msun Any idea what is causing the crazy values? On Mon, Nov 3, 2014 at 4:23 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi John,
It was exactly the same error, when you used particle_radius in both places that "radius" was used before?
-Matt
On Mon Nov 03 2014 at 7:06:44 AM John Regan <johnanthonyregan@gmail.com> wrote:
Hi Kacper,
Of course - I should have noticed that. Thanks for finding that. However, I notice that when I try to create a profile for the Dark (particle) matter I run into some trouble as well.
rpm = yt.create_profile(sp, 'radius', ['particle_mass'], units = {'radius': 'pc', 'particle_mass' : 'Msun'}, n_bins=20, weight_field=None, accumulation=True, fractional=False)
This gives the following error:
Traceback (most recent call last): File "EnclosedMass.py", line 35, in <module> n_bins=20, weight_field=None, accumulation=True, fractional=False) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 1361, in create_profile obj.add_fields([field for field in fields]) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 782, in add_fields self._bin_chunk(chunk, fields, temp_storage) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 979, in _bin_chunk rv = self._get_data(chunk, fields) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 910, in _get_data arr[:,i] = chunk[field][filter] File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/units/yt_array.py", line 963, in __getitem__ ret = super(YTArray, self).__getitem__(item) ValueError: too many boolean indices
Has anyone seen this before? For the 'cell_mass' everything works fine.
Cheers, John
On Sat, Nov 1, 2014 at 6:49 PM, Kacper Kowalik <xarthisius.kk@gmail.com> wrote:
Hi John, I think that if you want to compute "total" instead of mean you need to set weight_field to None in create_profile. Cheers, Kacper
On Sat Nov 01 2014 at 6:10:50 AM John Regan <johnanthonyregan@gmail.com> wrote:
Hi All,
Is the accumulation flag working in 3.0? I tried to plot the enclosed mass in a sphere and I got some funny results.
rpm = yt.create_profile(sp, 'radius', 'cell_mass', units = {'radius': 'pc', 'cell_mass' : 'Msun'}, weight_field='density', accumulation=True, fractional=False)
print "Mass = ", rpm["gas", "cell_mass"]
In this case bin[n-1] gives a mass of something like 0.5 Msun but when I print the totals quantity I get a value of several orders of magnitude higher and closer to what I would expect.
sp.quantities.total_quantity(["cell_mass", "particle_mass"])
Cheers, John _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Yup, those sure are weird! Looks to me like a units issue -- any chance those could be in grams but reported in Msun? On Mon Nov 03 2014 at 11:15:23 AM John Regan <johnanthonyregan@gmail.com> wrote:
Hi Matt,
Ah I see what you mean now. Changing 'radius' to 'particle_radius' worked nicely. However, the results are bit weird.
rpm = yt.create_profile(sp, ['particle_radius'], ['particle_mass'], units = {'particle_radius': 'pc', 'particle_mass' : 'Msun'}, n_bins=20, weight_field=None, accumulation=True, fractional=False) print "Particle Mass = ", rpm["particle_mass"]
Particle Mass = [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 2.17730865e+47 2.39503952e+48 5.00780990e+48 9.36242721e+48 2.87404742e+49 8.03426893e+49 1.91385431e+50 4.44824158e+50 1.02681876e+51 2.28900459e+51 4.74174278e+51 1.05066029e+52 2.07602025e+52 3.49614805e+52 4.89060538e+52 6.82621100e+52 1.08907237e+53] Msun
Any idea what is causing the crazy values?
On Mon, Nov 3, 2014 at 4:23 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi John,
It was exactly the same error, when you used particle_radius in both places that "radius" was used before?
-Matt
On Mon Nov 03 2014 at 7:06:44 AM John Regan <johnanthonyregan@gmail.com> wrote:
Hi Kacper,
Of course - I should have noticed that. Thanks for finding that. However, I notice that when I try to create a profile for the Dark (particle) matter I run into some trouble as well.
rpm = yt.create_profile(sp, 'radius', ['particle_mass'], units = {'radius': 'pc', 'particle_mass' : 'Msun'}, n_bins=20, weight_field=None, accumulation=True, fractional=False)
This gives the following error:
Traceback (most recent call last): File "EnclosedMass.py", line 35, in <module> n_bins=20, weight_field=None, accumulation=True, fractional=False) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 1361, in create_profile obj.add_fields([field for field in fields]) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 782, in add_fields self._bin_chunk(chunk, fields, temp_storage) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 979, in _bin_chunk rv = self._get_data(chunk, fields) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 910, in _get_data arr[:,i] = chunk[field][filter] File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/units/yt_array.py", line 963, in __getitem__ ret = super(YTArray, self).__getitem__(item) ValueError: too many boolean indices
Has anyone seen this before? For the 'cell_mass' everything works fine.
Cheers, John
On Sat, Nov 1, 2014 at 6:49 PM, Kacper Kowalik <xarthisius.kk@gmail.com> wrote:
Hi John, I think that if you want to compute "total" instead of mean you need to set weight_field to None in create_profile. Cheers, Kacper
On Sat Nov 01 2014 at 6:10:50 AM John Regan <johnanthonyregan@gmail.com> wrote:
Hi All,
Is the accumulation flag working in 3.0? I tried to plot the enclosed mass in a sphere and I got some funny results.
rpm = yt.create_profile(sp, 'radius', 'cell_mass', units = {'radius': 'pc', 'cell_mass' : 'Msun'}, weight_field='density', accumulation=True, fractional=False)
print "Mass = ", rpm["gas", "cell_mass"]
In this case bin[n-1] gives a mass of something like 0.5 Msun but when I print the totals quantity I get a value of several orders of magnitude higher and closer to what I would expect.
sp.quantities.total_quantity(["cell_mass", "particle_mass"])
Cheers, John _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Yeah that's what I thought first but 1 Msun = 10^33 g. So that would put the inner DM mass at ~ 10^14 right? The total mass inside the sphere of 1kpc is only about 10^7 though. Something is not quite correct somewhere in the profiling calculation. On Mon, Nov 3, 2014 at 5:16 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Yup, those sure are weird! Looks to me like a units issue -- any chance those could be in grams but reported in Msun?
On Mon Nov 03 2014 at 11:15:23 AM John Regan <johnanthonyregan@gmail.com> wrote:
Hi Matt,
Ah I see what you mean now. Changing 'radius' to 'particle_radius' worked nicely. However, the results are bit weird.
rpm = yt.create_profile(sp, ['particle_radius'], ['particle_mass'], units = {'particle_radius': 'pc', 'particle_mass' : 'Msun'}, n_bins=20, weight_field=None, accumulation=True, fractional=False) print "Particle Mass = ", rpm["particle_mass"]
Particle Mass = [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 2.17730865e+47 2.39503952e+48 5.00780990e+48 9.36242721e+48 2.87404742e+49 8.03426893e+49 1.91385431e+50 4.44824158e+50 1.02681876e+51 2.28900459e+51 4.74174278e+51 1.05066029e+52 2.07602025e+52 3.49614805e+52 4.89060538e+52 6.82621100e+52 1.08907237e+53] Msun
Any idea what is causing the crazy values?
On Mon, Nov 3, 2014 at 4:23 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi John,
It was exactly the same error, when you used particle_radius in both places that "radius" was used before?
-Matt
On Mon Nov 03 2014 at 7:06:44 AM John Regan <johnanthonyregan@gmail.com> wrote:
Hi Kacper,
Of course - I should have noticed that. Thanks for finding that. However, I notice that when I try to create a profile for the Dark (particle) matter I run into some trouble as well.
rpm = yt.create_profile(sp, 'radius', ['particle_mass'], units = {'radius': 'pc', 'particle_mass' : 'Msun'}, n_bins=20, weight_field=None, accumulation=True, fractional=False)
This gives the following error:
Traceback (most recent call last): File "EnclosedMass.py", line 35, in <module> n_bins=20, weight_field=None, accumulation=True, fractional=False) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 1361, in create_profile obj.add_fields([field for field in fields]) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 782, in add_fields self._bin_chunk(chunk, fields, temp_storage) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 979, in _bin_chunk rv = self._get_data(chunk, fields) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 910, in _get_data arr[:,i] = chunk[field][filter] File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/units/yt_array.py", line 963, in __getitem__ ret = super(YTArray, self).__getitem__(item) ValueError: too many boolean indices
Has anyone seen this before? For the 'cell_mass' everything works fine.
Cheers, John
On Sat, Nov 1, 2014 at 6:49 PM, Kacper Kowalik <xarthisius.kk@gmail.com
wrote:
Hi John, I think that if you want to compute "total" instead of mean you need to set weight_field to None in create_profile. Cheers, Kacper
On Sat Nov 01 2014 at 6:10:50 AM John Regan < johnanthonyregan@gmail.com> wrote:
Hi All,
Is the accumulation flag working in 3.0? I tried to plot the enclosed mass in a sphere and I got some funny results.
rpm = yt.create_profile(sp, 'radius', 'cell_mass', units = {'radius': 'pc', 'cell_mass' : 'Msun'}, weight_field='density', accumulation=True, fractional=False)
print "Mass = ", rpm["gas", "cell_mass"]
In this case bin[n-1] gives a mass of something like 0.5 Msun but when I print the totals quantity I get a value of several orders of magnitude higher and closer to what I would expect.
sp.quantities.total_quantity(["cell_mass", "particle_mass"])
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Hi Matt, It looks like the particle mass is in grams but the unit assignment sets it to code_mass. Then when the units is set to Msun the numbers get crazy. I can't see easily where the units for the particle mass get set in the create_profile routine (in field/particle_fields the mass is set to g in particle_mass()). Any idea where this might be getting all mixed up or how to force the mass units to be grams in create_profile()? Cheers, John On Mon, Nov 3, 2014 at 5:18 PM, John Regan <johnanthonyregan@gmail.com> wrote:
Yeah that's what I thought first but 1 Msun = 10^33 g. So that would put the inner DM mass at ~ 10^14 right?
The total mass inside the sphere of 1kpc is only about 10^7 though. Something is not quite correct somewhere in the profiling calculation.
On Mon, Nov 3, 2014 at 5:16 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Yup, those sure are weird! Looks to me like a units issue -- any chance those could be in grams but reported in Msun?
On Mon Nov 03 2014 at 11:15:23 AM John Regan <johnanthonyregan@gmail.com> wrote:
Hi Matt,
Ah I see what you mean now. Changing 'radius' to 'particle_radius' worked nicely. However, the results are bit weird.
rpm = yt.create_profile(sp, ['particle_radius'], ['particle_mass'], units = {'particle_radius': 'pc', 'particle_mass' : 'Msun'}, n_bins=20, weight_field=None, accumulation=True, fractional=False) print "Particle Mass = ", rpm["particle_mass"]
Particle Mass = [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 2.17730865e+47 2.39503952e+48 5.00780990e+48 9.36242721e+48 2.87404742e+49 8.03426893e+49 1.91385431e+50 4.44824158e+50 1.02681876e+51 2.28900459e+51 4.74174278e+51 1.05066029e+52 2.07602025e+52 3.49614805e+52 4.89060538e+52 6.82621100e+52 1.08907237e+53] Msun
Any idea what is causing the crazy values?
On Mon, Nov 3, 2014 at 4:23 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi John,
It was exactly the same error, when you used particle_radius in both places that "radius" was used before?
-Matt
On Mon Nov 03 2014 at 7:06:44 AM John Regan <johnanthonyregan@gmail.com> wrote:
Hi Kacper,
Of course - I should have noticed that. Thanks for finding that. However, I notice that when I try to create a profile for the Dark (particle) matter I run into some trouble as well.
rpm = yt.create_profile(sp, 'radius', ['particle_mass'], units = {'radius': 'pc', 'particle_mass' : 'Msun'}, n_bins=20, weight_field=None, accumulation=True, fractional=False)
This gives the following error:
Traceback (most recent call last): File "EnclosedMass.py", line 35, in <module> n_bins=20, weight_field=None, accumulation=True, fractional=False) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 1361, in create_profile obj.add_fields([field for field in fields]) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 782, in add_fields self._bin_chunk(chunk, fields, temp_storage) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 979, in _bin_chunk rv = self._get_data(chunk, fields) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 910, in _get_data arr[:,i] = chunk[field][filter] File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/units/yt_array.py", line 963, in __getitem__ ret = super(YTArray, self).__getitem__(item) ValueError: too many boolean indices
Has anyone seen this before? For the 'cell_mass' everything works fine.
Cheers, John
On Sat, Nov 1, 2014 at 6:49 PM, Kacper Kowalik < xarthisius.kk@gmail.com> wrote:
Hi John, I think that if you want to compute "total" instead of mean you need to set weight_field to None in create_profile. Cheers, Kacper
On Sat Nov 01 2014 at 6:10:50 AM John Regan < johnanthonyregan@gmail.com> wrote:
> Hi All, > > Is the accumulation flag working in 3.0? > I tried to plot the enclosed mass in a sphere and I got some funny > results. > > rpm = yt.create_profile(sp, 'radius', 'cell_mass', > units = {'radius': 'pc', 'cell_mass' : > 'Msun'}, > weight_field='density', accumulation=True, > fractional=False) > > print "Mass = ", rpm["gas", "cell_mass"] > > In this case bin[n-1] gives a mass of something like 0.5 Msun but > when I print the totals quantity I get a value of several orders of > magnitude higher and closer to what I would expect. > > sp.quantities.total_quantity(["cell_mass", "particle_mass"]) > > Cheers, > John > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >
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Hi John, Do you have a short script using one of the test datasets on yt-project.org/data that reproduces this behavior? -Nathan On Tue, Nov 4, 2014 at 10:26 AM, John Regan <johnanthonyregan@gmail.com> wrote:
Hi Matt,
It looks like the particle mass is in grams but the unit assignment sets it to code_mass. Then when the units is set to Msun the numbers get crazy. I can't see easily where the units for the particle mass get set in the create_profile routine (in field/particle_fields the mass is set to g in particle_mass()). Any idea where this might be getting all mixed up or how to force the mass units to be grams in create_profile()?
Cheers, John
On Mon, Nov 3, 2014 at 5:18 PM, John Regan <johnanthonyregan@gmail.com> wrote:
Yeah that's what I thought first but 1 Msun = 10^33 g. So that would put the inner DM mass at ~ 10^14 right?
The total mass inside the sphere of 1kpc is only about 10^7 though. Something is not quite correct somewhere in the profiling calculation.
On Mon, Nov 3, 2014 at 5:16 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Yup, those sure are weird! Looks to me like a units issue -- any chance those could be in grams but reported in Msun?
On Mon Nov 03 2014 at 11:15:23 AM John Regan <johnanthonyregan@gmail.com> wrote:
Hi Matt,
Ah I see what you mean now. Changing 'radius' to 'particle_radius' worked nicely. However, the results are bit weird.
rpm = yt.create_profile(sp, ['particle_radius'], ['particle_mass'], units = {'particle_radius': 'pc', 'particle_mass' : 'Msun'}, n_bins=20, weight_field=None, accumulation=True, fractional=False) print "Particle Mass = ", rpm["particle_mass"]
Particle Mass = [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 2.17730865e+47 2.39503952e+48 5.00780990e+48 9.36242721e+48 2.87404742e+49 8.03426893e+49 1.91385431e+50 4.44824158e+50 1.02681876e+51 2.28900459e+51 4.74174278e+51 1.05066029e+52 2.07602025e+52 3.49614805e+52 4.89060538e+52 6.82621100e+52 1.08907237e+53] Msun
Any idea what is causing the crazy values?
On Mon, Nov 3, 2014 at 4:23 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi John,
It was exactly the same error, when you used particle_radius in both places that "radius" was used before?
-Matt
On Mon Nov 03 2014 at 7:06:44 AM John Regan < johnanthonyregan@gmail.com> wrote:
Hi Kacper,
Of course - I should have noticed that. Thanks for finding that. However, I notice that when I try to create a profile for the Dark (particle) matter I run into some trouble as well.
rpm = yt.create_profile(sp, 'radius', ['particle_mass'], units = {'radius': 'pc', 'particle_mass' : 'Msun'}, n_bins=20, weight_field=None, accumulation=True, fractional=False)
This gives the following error:
Traceback (most recent call last): File "EnclosedMass.py", line 35, in <module> n_bins=20, weight_field=None, accumulation=True, fractional=False) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 1361, in create_profile obj.add_fields([field for field in fields]) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 782, in add_fields self._bin_chunk(chunk, fields, temp_storage) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 979, in _bin_chunk rv = self._get_data(chunk, fields) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", line 910, in _get_data arr[:,i] = chunk[field][filter] File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/units/yt_array.py", line 963, in __getitem__ ret = super(YTArray, self).__getitem__(item) ValueError: too many boolean indices
Has anyone seen this before? For the 'cell_mass' everything works fine.
Cheers, John
On Sat, Nov 1, 2014 at 6:49 PM, Kacper Kowalik < xarthisius.kk@gmail.com> wrote:
> Hi John, > I think that if you want to compute "total" instead of mean you need > to set weight_field to None in create_profile. > Cheers, > Kacper > > On Sat Nov 01 2014 at 6:10:50 AM John Regan < > johnanthonyregan@gmail.com> wrote: > >> Hi All, >> >> Is the accumulation flag working in 3.0? >> I tried to plot the enclosed mass in a sphere and I got some funny >> results. >> >> rpm = yt.create_profile(sp, 'radius', 'cell_mass', >> units = {'radius': 'pc', 'cell_mass' : >> 'Msun'}, >> weight_field='density', accumulation=True, >> fractional=False) >> >> print "Mass = ", rpm["gas", "cell_mass"] >> >> In this case bin[n-1] gives a mass of something like 0.5 Msun but >> when I print the totals quantity I get a value of several orders of >> magnitude higher and closer to what I would expect. >> >> sp.quantities.total_quantity(["cell_mass", "particle_mass"]) >> >> Cheers, >> John >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Hi Nathan, Sure. Using the enzo_tiny_cosmology I see the same problem. Script attached. On Tue, Nov 4, 2014 at 6:29 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi John,
Do you have a short script using one of the test datasets on yt-project.org/data that reproduces this behavior?
-Nathan
On Tue, Nov 4, 2014 at 10:26 AM, John Regan <johnanthonyregan@gmail.com> wrote:
Hi Matt,
It looks like the particle mass is in grams but the unit assignment sets it to code_mass. Then when the units is set to Msun the numbers get crazy. I can't see easily where the units for the particle mass get set in the create_profile routine (in field/particle_fields the mass is set to g in particle_mass()). Any idea where this might be getting all mixed up or how to force the mass units to be grams in create_profile()?
Cheers, John
On Mon, Nov 3, 2014 at 5:18 PM, John Regan <johnanthonyregan@gmail.com> wrote:
Yeah that's what I thought first but 1 Msun = 10^33 g. So that would put the inner DM mass at ~ 10^14 right?
The total mass inside the sphere of 1kpc is only about 10^7 though. Something is not quite correct somewhere in the profiling calculation.
On Mon, Nov 3, 2014 at 5:16 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Yup, those sure are weird! Looks to me like a units issue -- any chance those could be in grams but reported in Msun?
On Mon Nov 03 2014 at 11:15:23 AM John Regan < johnanthonyregan@gmail.com> wrote:
Hi Matt,
Ah I see what you mean now. Changing 'radius' to 'particle_radius' worked nicely. However, the results are bit weird.
rpm = yt.create_profile(sp, ['particle_radius'], ['particle_mass'], units = {'particle_radius': 'pc', 'particle_mass' : 'Msun'}, n_bins=20, weight_field=None, accumulation=True, fractional=False) print "Particle Mass = ", rpm["particle_mass"]
Particle Mass = [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 2.17730865e+47 2.39503952e+48 5.00780990e+48 9.36242721e+48 2.87404742e+49 8.03426893e+49 1.91385431e+50 4.44824158e+50 1.02681876e+51 2.28900459e+51 4.74174278e+51 1.05066029e+52 2.07602025e+52 3.49614805e+52 4.89060538e+52 6.82621100e+52 1.08907237e+53] Msun
Any idea what is causing the crazy values?
On Mon, Nov 3, 2014 at 4:23 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi John,
It was exactly the same error, when you used particle_radius in both places that "radius" was used before?
-Matt
On Mon Nov 03 2014 at 7:06:44 AM John Regan < johnanthonyregan@gmail.com> wrote:
> Hi Kacper, > > Of course - I should have noticed that. Thanks for finding that. > However, I notice that when I try to create a profile for the Dark > (particle) matter I run into some trouble as well. > > rpm = yt.create_profile(sp, 'radius', ['particle_mass'], > units = {'radius': 'pc', 'particle_mass' : > 'Msun'}, > n_bins=20, weight_field=None, > accumulation=True, fractional=False) > > This gives the following error: > > Traceback (most recent call last): > File "EnclosedMass.py", line 35, in <module> > n_bins=20, weight_field=None, accumulation=True, > fractional=False) > File > "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", > line 1361, in create_profile > obj.add_fields([field for field in fields]) > File > "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", > line 782, in add_fields > self._bin_chunk(chunk, fields, temp_storage) > File > "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", > line 979, in _bin_chunk > rv = self._get_data(chunk, fields) > File > "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", > line 910, in _get_data > arr[:,i] = chunk[field][filter] > File > "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/units/yt_array.py", line > 963, in __getitem__ > ret = super(YTArray, self).__getitem__(item) > ValueError: too many boolean indices > > > Has anyone seen this before? For the 'cell_mass' everything works > fine. > > Cheers, > John > > On Sat, Nov 1, 2014 at 6:49 PM, Kacper Kowalik < > xarthisius.kk@gmail.com> wrote: > >> Hi John, >> I think that if you want to compute "total" instead of mean you >> need to set weight_field to None in create_profile. >> Cheers, >> Kacper >> >> On Sat Nov 01 2014 at 6:10:50 AM John Regan < >> johnanthonyregan@gmail.com> wrote: >> >>> Hi All, >>> >>> Is the accumulation flag working in 3.0? >>> I tried to plot the enclosed mass in a sphere and I got some funny >>> results. >>> >>> rpm = yt.create_profile(sp, 'radius', 'cell_mass', >>> units = {'radius': 'pc', 'cell_mass' : >>> 'Msun'}, >>> weight_field='density', accumulation=True, >>> fractional=False) >>> >>> print "Mass = ", rpm["gas", "cell_mass"] >>> >>> In this case bin[n-1] gives a mass of something like 0.5 Msun but >>> when I print the totals quantity I get a value of several orders of >>> magnitude higher and closer to what I would expect. >>> >>> sp.quantities.total_quantity(["cell_mass", "particle_mass"]) >>> >>> Cheers, >>> John >>> _______________________________________________ >>> yt-users mailing list >>> yt-users@lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >
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Dug into this a little bit. The issue is that querying the particle_mass field returns CGS values, but the field_info for particle_mass says it should be in code_mass. This is illustrated by the following script: https://bpaste.net/show/6ee56ae61fa6 Does anyone remember why this is the case? The reason this is coming up here is because the profiling code passes raw numpy arrays to the cython parallel profiling machinery, so the units that are attached to the data when we query the data source are stripped off. We're relying on the field_info units entry for all fields being identical to the units that get appended to the results of a field access on a data object. Unfortunately I don't have time right now to figure out where this inconsistency is coming from... -Nathan On Tue, Nov 4, 2014 at 10:42 AM, John Regan <johnanthonyregan@gmail.com> wrote:
Hi Nathan,
Sure. Using the enzo_tiny_cosmology I see the same problem. Script attached.
On Tue, Nov 4, 2014 at 6:29 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi John,
Do you have a short script using one of the test datasets on yt-project.org/data that reproduces this behavior?
-Nathan
On Tue, Nov 4, 2014 at 10:26 AM, John Regan <johnanthonyregan@gmail.com> wrote:
Hi Matt,
It looks like the particle mass is in grams but the unit assignment sets it to code_mass. Then when the units is set to Msun the numbers get crazy. I can't see easily where the units for the particle mass get set in the create_profile routine (in field/particle_fields the mass is set to g in particle_mass()). Any idea where this might be getting all mixed up or how to force the mass units to be grams in create_profile()?
Cheers, John
On Mon, Nov 3, 2014 at 5:18 PM, John Regan <johnanthonyregan@gmail.com> wrote:
Yeah that's what I thought first but 1 Msun = 10^33 g. So that would put the inner DM mass at ~ 10^14 right?
The total mass inside the sphere of 1kpc is only about 10^7 though. Something is not quite correct somewhere in the profiling calculation.
On Mon, Nov 3, 2014 at 5:16 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Yup, those sure are weird! Looks to me like a units issue -- any chance those could be in grams but reported in Msun?
On Mon Nov 03 2014 at 11:15:23 AM John Regan < johnanthonyregan@gmail.com> wrote:
Hi Matt,
Ah I see what you mean now. Changing 'radius' to 'particle_radius' worked nicely. However, the results are bit weird.
rpm = yt.create_profile(sp, ['particle_radius'], ['particle_mass'], units = {'particle_radius': 'pc', 'particle_mass' : 'Msun'}, n_bins=20, weight_field=None, accumulation=True, fractional=False) print "Particle Mass = ", rpm["particle_mass"]
Particle Mass = [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 2.17730865e+47 2.39503952e+48 5.00780990e+48 9.36242721e+48 2.87404742e+49 8.03426893e+49 1.91385431e+50 4.44824158e+50 1.02681876e+51 2.28900459e+51 4.74174278e+51 1.05066029e+52 2.07602025e+52 3.49614805e+52 4.89060538e+52 6.82621100e+52 1.08907237e+53] Msun
Any idea what is causing the crazy values?
On Mon, Nov 3, 2014 at 4:23 PM, Matthew Turk <matthewturk@gmail.com> wrote:
> Hi John, > > It was exactly the same error, when you used particle_radius in both > places that "radius" was used before? > > -Matt > > > On Mon Nov 03 2014 at 7:06:44 AM John Regan < > johnanthonyregan@gmail.com> wrote: > >> Hi Kacper, >> >> Of course - I should have noticed that. Thanks for finding that. >> However, I notice that when I try to create a profile for the Dark >> (particle) matter I run into some trouble as well. >> >> rpm = yt.create_profile(sp, 'radius', ['particle_mass'], >> units = {'radius': 'pc', 'particle_mass' : >> 'Msun'}, >> n_bins=20, weight_field=None, >> accumulation=True, fractional=False) >> >> This gives the following error: >> >> Traceback (most recent call last): >> File "EnclosedMass.py", line 35, in <module> >> n_bins=20, weight_field=None, accumulation=True, >> fractional=False) >> File >> "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", >> line 1361, in create_profile >> obj.add_fields([field for field in fields]) >> File >> "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", >> line 782, in add_fields >> self._bin_chunk(chunk, fields, temp_storage) >> File >> "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", >> line 979, in _bin_chunk >> rv = self._get_data(chunk, fields) >> File >> "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", >> line 910, in _get_data >> arr[:,i] = chunk[field][filter] >> File >> "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/units/yt_array.py", line >> 963, in __getitem__ >> ret = super(YTArray, self).__getitem__(item) >> ValueError: too many boolean indices >> >> >> Has anyone seen this before? For the 'cell_mass' everything works >> fine. >> >> Cheers, >> John >> >> On Sat, Nov 1, 2014 at 6:49 PM, Kacper Kowalik < >> xarthisius.kk@gmail.com> wrote: >> >>> Hi John, >>> I think that if you want to compute "total" instead of mean you >>> need to set weight_field to None in create_profile. >>> Cheers, >>> Kacper >>> >>> On Sat Nov 01 2014 at 6:10:50 AM John Regan < >>> johnanthonyregan@gmail.com> wrote: >>> >>>> Hi All, >>>> >>>> Is the accumulation flag working in 3.0? >>>> I tried to plot the enclosed mass in a sphere and I got some >>>> funny results. >>>> >>>> rpm = yt.create_profile(sp, 'radius', 'cell_mass', >>>> units = {'radius': 'pc', 'cell_mass' : >>>> 'Msun'}, >>>> weight_field='density', >>>> accumulation=True, fractional=False) >>>> >>>> print "Mass = ", rpm["gas", "cell_mass"] >>>> >>>> In this case bin[n-1] gives a mass of something like 0.5 Msun but >>>> when I print the totals quantity I get a value of several orders of >>>> magnitude higher and closer to what I would expect. >>>> >>>> sp.quantities.total_quantity(["cell_mass", "particle_mass"]) >>>> >>>> Cheers, >>>> John >>>> _______________________________________________ >>>> yt-users mailing list >>>> yt-users@lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>> >>> >>> _______________________________________________ >>> yt-users mailing list >>> yt-users@lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >>> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Hi Nathan, Ah, usually what we do is, on the way in to Cython, call convert_to_units(field.units). I think this will fix it here. -Matt On Tue Nov 04 2014 at 1:42:49 PM Nathan Goldbaum <nathan12343@gmail.com> wrote:
Dug into this a little bit.
The issue is that querying the particle_mass field returns CGS values, but the field_info for particle_mass says it should be in code_mass. This is illustrated by the following script: https://bpaste.net/show/6ee56ae61fa6
Does anyone remember why this is the case?
The reason this is coming up here is because the profiling code passes raw numpy arrays to the cython parallel profiling machinery, so the units that are attached to the data when we query the data source are stripped off. We're relying on the field_info units entry for all fields being identical to the units that get appended to the results of a field access on a data object.
Unfortunately I don't have time right now to figure out where this inconsistency is coming from...
-Nathan
On Tue, Nov 4, 2014 at 10:42 AM, John Regan <johnanthonyregan@gmail.com> wrote:
Hi Nathan,
Sure. Using the enzo_tiny_cosmology I see the same problem. Script attached.
On Tue, Nov 4, 2014 at 6:29 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi John,
Do you have a short script using one of the test datasets on yt-project.org/data that reproduces this behavior?
-Nathan
On Tue, Nov 4, 2014 at 10:26 AM, John Regan <johnanthonyregan@gmail.com> wrote:
Hi Matt,
It looks like the particle mass is in grams but the unit assignment sets it to code_mass. Then when the units is set to Msun the numbers get crazy. I can't see easily where the units for the particle mass get set in the create_profile routine (in field/particle_fields the mass is set to g in particle_mass()). Any idea where this might be getting all mixed up or how to force the mass units to be grams in create_profile()?
Cheers, John
On Mon, Nov 3, 2014 at 5:18 PM, John Regan <johnanthonyregan@gmail.com> wrote:
Yeah that's what I thought first but 1 Msun = 10^33 g. So that would put the inner DM mass at ~ 10^14 right?
The total mass inside the sphere of 1kpc is only about 10^7 though. Something is not quite correct somewhere in the profiling calculation.
On Mon, Nov 3, 2014 at 5:16 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Yup, those sure are weird! Looks to me like a units issue -- any chance those could be in grams but reported in Msun?
On Mon Nov 03 2014 at 11:15:23 AM John Regan < johnanthonyregan@gmail.com> wrote:
> Hi Matt, > > Ah I see what you mean now. Changing 'radius' to 'particle_radius' > worked nicely. However, the results are bit weird. > > rpm = yt.create_profile(sp, ['particle_radius'], ['particle_mass'], > units = {'particle_radius': 'pc', > 'particle_mass' : 'Msun'}, > n_bins=20, weight_field=None, > accumulation=True, fractional=False) > print "Particle Mass = ", rpm["particle_mass"] > > Particle Mass = [ 0.00000000e+00 0.00000000e+00 > 0.00000000e+00 2.17730865e+47 > 2.39503952e+48 5.00780990e+48 9.36242721e+48 2.87404742e+49 > 8.03426893e+49 1.91385431e+50 4.44824158e+50 1.02681876e+51 > 2.28900459e+51 4.74174278e+51 1.05066029e+52 2.07602025e+52 > 3.49614805e+52 4.89060538e+52 6.82621100e+52 > 1.08907237e+53] Msun > > Any idea what is causing the crazy values? > > On Mon, Nov 3, 2014 at 4:23 PM, Matthew Turk <matthewturk@gmail.com> > wrote: > >> Hi John, >> >> It was exactly the same error, when you used particle_radius in >> both places that "radius" was used before? >> >> -Matt >> >> >> On Mon Nov 03 2014 at 7:06:44 AM John Regan < >> johnanthonyregan@gmail.com> wrote: >> >>> Hi Kacper, >>> >>> Of course - I should have noticed that. Thanks for finding that. >>> However, I notice that when I try to create a profile for the Dark >>> (particle) matter I run into some trouble as well. >>> >>> rpm = yt.create_profile(sp, 'radius', ['particle_mass'], >>> units = {'radius': 'pc', 'particle_mass' : >>> 'Msun'}, >>> n_bins=20, weight_field=None, >>> accumulation=True, fractional=False) >>> >>> This gives the following error: >>> >>> Traceback (most recent call last): >>> File "EnclosedMass.py", line 35, in <module> >>> n_bins=20, weight_field=None, accumulation=True, >>> fractional=False) >>> File >>> "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", >>> line 1361, in create_profile >>> obj.add_fields([field for field in fields]) >>> File >>> "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", >>> line 782, in add_fields >>> self._bin_chunk(chunk, fields, temp_storage) >>> File >>> "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", >>> line 979, in _bin_chunk >>> rv = self._get_data(chunk, fields) >>> File >>> "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", >>> line 910, in _get_data >>> arr[:,i] = chunk[field][filter] >>> File >>> "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/units/yt_array.py", line >>> 963, in __getitem__ >>> ret = super(YTArray, self).__getitem__(item) >>> ValueError: too many boolean indices >>> >>> >>> Has anyone seen this before? For the 'cell_mass' everything works >>> fine. >>> >>> Cheers, >>> John >>> >>> On Sat, Nov 1, 2014 at 6:49 PM, Kacper Kowalik < >>> xarthisius.kk@gmail.com> wrote: >>> >>>> Hi John, >>>> I think that if you want to compute "total" instead of mean you >>>> need to set weight_field to None in create_profile. >>>> Cheers, >>>> Kacper >>>> >>>> On Sat Nov 01 2014 at 6:10:50 AM John Regan < >>>> johnanthonyregan@gmail.com> wrote: >>>> >>>>> Hi All, >>>>> >>>>> Is the accumulation flag working in 3.0? >>>>> I tried to plot the enclosed mass in a sphere and I got some >>>>> funny results. >>>>> >>>>> rpm = yt.create_profile(sp, 'radius', 'cell_mass', >>>>> units = {'radius': 'pc', 'cell_mass' : >>>>> 'Msun'}, >>>>> weight_field='density', >>>>> accumulation=True, fractional=False) >>>>> >>>>> print "Mass = ", rpm["gas", "cell_mass"] >>>>> >>>>> In this case bin[n-1] gives a mass of something like 0.5 Msun >>>>> but when I print the totals quantity I get a value of several orders of >>>>> magnitude higher and closer to what I would expect. >>>>> >>>>> sp.quantities.total_quantity(["cell_mass", "particle_mass"]) >>>>> >>>>> Cheers, >>>>> John >>>>> _______________________________________________ >>>>> yt-users mailing list >>>>> yt-users@lists.spacepope.org >>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>> >>>> >>>> _______________________________________________ >>>> yt-users mailing list >>>> yt-users@lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>> >>>> >>> _______________________________________________ >>> yt-users mailing list >>> yt-users@lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >
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Can you guys take a look at this? https://bitbucket.org/yt_analysis/yt/pull-request/1292/ensure-profiled-data-... On Tue, Nov 4, 2014 at 11:44 AM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Nathan,
Ah, usually what we do is, on the way in to Cython, call convert_to_units(field.units). I think this will fix it here.
-Matt
On Tue Nov 04 2014 at 1:42:49 PM Nathan Goldbaum <nathan12343@gmail.com> wrote:
Dug into this a little bit.
The issue is that querying the particle_mass field returns CGS values, but the field_info for particle_mass says it should be in code_mass. This is illustrated by the following script: https://bpaste.net/show/6ee56ae61fa6
Does anyone remember why this is the case?
The reason this is coming up here is because the profiling code passes raw numpy arrays to the cython parallel profiling machinery, so the units that are attached to the data when we query the data source are stripped off. We're relying on the field_info units entry for all fields being identical to the units that get appended to the results of a field access on a data object.
Unfortunately I don't have time right now to figure out where this inconsistency is coming from...
-Nathan
On Tue, Nov 4, 2014 at 10:42 AM, John Regan <johnanthonyregan@gmail.com> wrote:
Hi Nathan,
Sure. Using the enzo_tiny_cosmology I see the same problem. Script attached.
On Tue, Nov 4, 2014 at 6:29 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi John,
Do you have a short script using one of the test datasets on yt-project.org/data that reproduces this behavior?
-Nathan
On Tue, Nov 4, 2014 at 10:26 AM, John Regan <johnanthonyregan@gmail.com
wrote:
Hi Matt,
It looks like the particle mass is in grams but the unit assignment sets it to code_mass. Then when the units is set to Msun the numbers get crazy. I can't see easily where the units for the particle mass get set in the create_profile routine (in field/particle_fields the mass is set to g in particle_mass()). Any idea where this might be getting all mixed up or how to force the mass units to be grams in create_profile()?
Cheers, John
On Mon, Nov 3, 2014 at 5:18 PM, John Regan <johnanthonyregan@gmail.com
wrote:
Yeah that's what I thought first but 1 Msun = 10^33 g. So that would put the inner DM mass at ~ 10^14 right?
The total mass inside the sphere of 1kpc is only about 10^7 though. Something is not quite correct somewhere in the profiling calculation.
On Mon, Nov 3, 2014 at 5:16 PM, Matthew Turk <matthewturk@gmail.com> wrote:
> Yup, those sure are weird! Looks to me like a units issue -- any > chance those could be in grams but reported in Msun? > > > On Mon Nov 03 2014 at 11:15:23 AM John Regan < > johnanthonyregan@gmail.com> wrote: > >> Hi Matt, >> >> Ah I see what you mean now. Changing 'radius' to 'particle_radius' >> worked nicely. However, the results are bit weird. >> >> rpm = yt.create_profile(sp, ['particle_radius'], ['particle_mass'], >> units = {'particle_radius': 'pc', >> 'particle_mass' : 'Msun'}, >> n_bins=20, weight_field=None, >> accumulation=True, fractional=False) >> print "Particle Mass = ", rpm["particle_mass"] >> >> Particle Mass = [ 0.00000000e+00 0.00000000e+00 >> 0.00000000e+00 2.17730865e+47 >> 2.39503952e+48 5.00780990e+48 9.36242721e+48 2.87404742e+49 >> 8.03426893e+49 1.91385431e+50 4.44824158e+50 1.02681876e+51 >> 2.28900459e+51 4.74174278e+51 1.05066029e+52 2.07602025e+52 >> 3.49614805e+52 4.89060538e+52 6.82621100e+52 >> 1.08907237e+53] Msun >> >> Any idea what is causing the crazy values? >> >> On Mon, Nov 3, 2014 at 4:23 PM, Matthew Turk <matthewturk@gmail.com >> > wrote: >> >>> Hi John, >>> >>> It was exactly the same error, when you used particle_radius in >>> both places that "radius" was used before? >>> >>> -Matt >>> >>> >>> On Mon Nov 03 2014 at 7:06:44 AM John Regan < >>> johnanthonyregan@gmail.com> wrote: >>> >>>> Hi Kacper, >>>> >>>> Of course - I should have noticed that. Thanks for finding that. >>>> However, I notice that when I try to create a profile for the >>>> Dark (particle) matter I run into some trouble as well. >>>> >>>> rpm = yt.create_profile(sp, 'radius', ['particle_mass'], >>>> units = {'radius': 'pc', 'particle_mass' >>>> : 'Msun'}, >>>> n_bins=20, weight_field=None, >>>> accumulation=True, fractional=False) >>>> >>>> This gives the following error: >>>> >>>> Traceback (most recent call last): >>>> File "EnclosedMass.py", line 35, in <module> >>>> n_bins=20, weight_field=None, accumulation=True, >>>> fractional=False) >>>> File >>>> "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", >>>> line 1361, in create_profile >>>> obj.add_fields([field for field in fields]) >>>> File >>>> "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", >>>> line 782, in add_fields >>>> self._bin_chunk(chunk, fields, temp_storage) >>>> File >>>> "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", >>>> line 979, in _bin_chunk >>>> rv = self._get_data(chunk, fields) >>>> File >>>> "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/profiles.py", >>>> line 910, in _get_data >>>> arr[:,i] = chunk[field][filter] >>>> File >>>> "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/units/yt_array.py", line >>>> 963, in __getitem__ >>>> ret = super(YTArray, self).__getitem__(item) >>>> ValueError: too many boolean indices >>>> >>>> >>>> Has anyone seen this before? For the 'cell_mass' everything works >>>> fine. >>>> >>>> Cheers, >>>> John >>>> >>>> On Sat, Nov 1, 2014 at 6:49 PM, Kacper Kowalik < >>>> xarthisius.kk@gmail.com> wrote: >>>> >>>>> Hi John, >>>>> I think that if you want to compute "total" instead of mean you >>>>> need to set weight_field to None in create_profile. >>>>> Cheers, >>>>> Kacper >>>>> >>>>> On Sat Nov 01 2014 at 6:10:50 AM John Regan < >>>>> johnanthonyregan@gmail.com> wrote: >>>>> >>>>>> Hi All, >>>>>> >>>>>> Is the accumulation flag working in 3.0? >>>>>> I tried to plot the enclosed mass in a sphere and I got some >>>>>> funny results. >>>>>> >>>>>> rpm = yt.create_profile(sp, 'radius', 'cell_mass', >>>>>> units = {'radius': 'pc', 'cell_mass' : >>>>>> 'Msun'}, >>>>>> weight_field='density', >>>>>> accumulation=True, fractional=False) >>>>>> >>>>>> print "Mass = ", rpm["gas", "cell_mass"] >>>>>> >>>>>> In this case bin[n-1] gives a mass of something like 0.5 Msun >>>>>> but when I print the totals quantity I get a value of several orders of >>>>>> magnitude higher and closer to what I would expect. >>>>>> >>>>>> sp.quantities.total_quantity(["cell_mass", "particle_mass"]) >>>>>> >>>>>> Cheers, >>>>>> John >>>>>> _______________________________________________ >>>>>> yt-users mailing list >>>>>> yt-users@lists.spacepope.org >>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>>> >>>>> >>>>> _______________________________________________ >>>>> yt-users mailing list >>>>> yt-users@lists.spacepope.org >>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>> >>>>> >>>> _______________________________________________ >>>> yt-users mailing list >>>> yt-users@lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>> >>> >>> _______________________________________________ >>> yt-users mailing list >>> yt-users@lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >>> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >
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participants (4)
-
John Regan -
Kacper Kowalik -
Matthew Turk -
Nathan Goldbaum