Dear yt user, I try to use Generic UnicGrid Data (256^3 gas density cube + position of particle that is subset of a huge simulation). It is preliminary work, but I still have some questions. 1. In order to set density unit as cgs, I made following script: ...... data = dict(density = (map, "g/cm**3")) #map is 256^3 density data array bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) ..... Then, I got the following error message: Traceback (most recent call last): File "cutout2.py", line 62, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 461, in load_uniform_grid psize = get_psize(np.array(data[key].shape), nprocs) AttributeError: 'tuple' object has no attribute 'shape' Hence, I modify "data = dict(density = (map, "g/cm**3"))" --> "data = dict(density = map)" and it work. If this is the case, how can I define the density unit and show it when I make Slice/Projection? In addition, I would like to know how I can set the unit in Generic UnicGrid Data in general? The length unit can be provide to script in load_uniform_grid(... 3.086e24 ....) but I do not know how to set other units. 2. When I add particle information as follow: ..... npart = 100000 # number of particles data = dict(density = map, number_of_particles = npart, particle_position_x = posx, particle_position_y = posy, particle_position_z = posz) bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) ... I got the following error message: Traceback (most recent call last): File "cutout.py", line 107, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 519, in load_uniform_grid assign_particle_data(spf, pdata) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 371, in assign_particle_data pdata.pop("number_of_particles") KeyError: 'number_of_particles' So, I change "number_of_particles = npart," --> "number_of_particles = 100000," and it works. How could it happen? 3. Can I do halo finder (hop/fof) using the above particle data? Or, what information do I need to provide to do grouping? In this case, how can I set the units and linking length? 4. Can I make particle distribution to particle data like data['Dark_Matter_position_x']? This process will allow me additional analysis such as profile and obtaining total value. I may ask too many for new tool, but it will help a lot to use yt for general data set. Thank you, Junhwan
Hi Junhwan, Just to clarify (since the answers you receive will be different depending on your response) is this for the in-development yt 3.0 release or the current stable release? Nathan On Friday, May 16, 2014, Junhwan Choi (최준환) <choi.junhwan@gmail.com> wrote:
Dear yt user,
I try to use Generic UnicGrid Data (256^3 gas density cube + position of particle that is subset of a huge simulation). It is preliminary work, but I still have some questions.
1. In order to set density unit as cgs, I made following script: ...... data = dict(density = (map, "g/cm**3")) #map is 256^3 density data array bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) .....
Then, I got the following error message: Traceback (most recent call last): File "cutout2.py", line 62, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 461, in load_uniform_grid psize = get_psize(np.array(data[key].shape), nprocs) AttributeError: 'tuple' object has no attribute 'shape'
Hence, I modify "data = dict(density = (map, "g/cm**3"))" --> "data = dict(density = map)" and it work. If this is the case, how can I define the density unit and show it when I make Slice/Projection? In addition, I would like to know how I can set the unit in Generic UnicGrid Data in general? The length unit can be provide to script in load_uniform_grid(... 3.086e24 ....) but I do not know how to set other units.
2. When I add particle information as follow: ..... npart = 100000 # number of particles data = dict(density = map, number_of_particles = npart, particle_position_x = posx, particle_position_y = posy, particle_position_z = posz) bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) ...
I got the following error message: Traceback (most recent call last): File "cutout.py", line 107, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 519, in load_uniform_grid assign_particle_data(spf, pdata) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 371, in assign_particle_data pdata.pop("number_of_particles") KeyError: 'number_of_particles'
So, I change "number_of_particles = npart," --> "number_of_particles = 100000," and it works. How could it happen?
3. Can I do halo finder (hop/fof) using the above particle data? Or, what information do I need to provide to do grouping? In this case, how can I set the units and linking length?
4. Can I make particle distribution to particle data like data['Dark_Matter_position_x']? This process will allow me additional analysis such as profile and obtaining total value.
I may ask too many for new tool, but it will help a lot to use yt for general data set.
Thank you, Junhwan _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <javascript:;> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Nathan, I think that I am using the yt 3.0 unless there is stabke yt 3.0 version. Junhwan
On May 15, 2014, at 11:29 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Junhwan,
Just to clarify (since the answers you receive will be different depending on your response) is this for the in-development yt 3.0 release or the current stable release?
Nathan
On Friday, May 16, 2014, Junhwan Choi (최준환) <choi.junhwan@gmail.com> wrote: Dear yt user,
I try to use Generic UnicGrid Data (256^3 gas density cube + position of particle that is subset of a huge simulation). It is preliminary work, but I still have some questions.
1. In order to set density unit as cgs, I made following script: ...... data = dict(density = (map, "g/cm**3")) #map is 256^3 density data array bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) .....
Then, I got the following error message: Traceback (most recent call last): File "cutout2.py", line 62, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 461, in load_uniform_grid psize = get_psize(np.array(data[key].shape), nprocs) AttributeError: 'tuple' object has no attribute 'shape'
Hence, I modify "data = dict(density = (map, "g/cm**3"))" --> "data = dict(density = map)" and it work. If this is the case, how can I define the density unit and show it when I make Slice/Projection? In addition, I would like to know how I can set the unit in Generic UnicGrid Data in general? The length unit can be provide to script in load_uniform_grid(... 3.086e24 ....) but I do not know how to set other units.
2. When I add particle information as follow: ..... npart = 100000 # number of particles data = dict(density = map, number_of_particles = npart, particle_position_x = posx, particle_position_y = posy, particle_position_z = posz) bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) ...
I got the following error message: Traceback (most recent call last): File "cutout.py", line 107, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 519, in load_uniform_grid assign_particle_data(spf, pdata) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 371, in assign_particle_data pdata.pop("number_of_particles") KeyError: 'number_of_particles'
So, I change "number_of_particles = npart," --> "number_of_particles = 100000," and it works. How could it happen?
3. Can I do halo finder (hop/fof) using the above particle data? Or, what information do I need to provide to do grouping? In this case, how can I set the units and linking length?
4. Can I make particle distribution to particle data like data['Dark_Matter_position_x']? This process will allow me additional analysis such as profile and obtaining total value.
I may ask too many for new tool, but it will help a lot to use yt for general data set.
Thank you, Junhwan _______________________________________________ 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
Junhwan, Can you post your script somewhere? It might be easier to debug it that way. Best, John Z On May 16, 2014, at 12:46 AM, Junhwan Choi <choi.junhwan@gmail.com> wrote:
Hi Nathan,
I think that I am using the yt 3.0 unless there is stabke yt 3.0 version.
Junhwan
On May 15, 2014, at 11:29 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Junhwan,
Just to clarify (since the answers you receive will be different depending on your response) is this for the in-development yt 3.0 release or the current stable release?
Nathan
On Friday, May 16, 2014, Junhwan Choi (최준환) <choi.junhwan@gmail.com> wrote: Dear yt user,
I try to use Generic UnicGrid Data (256^3 gas density cube + position of particle that is subset of a huge simulation). It is preliminary work, but I still have some questions.
1. In order to set density unit as cgs, I made following script: ...... data = dict(density = (map, "g/cm**3")) #map is 256^3 density data array bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) .....
Then, I got the following error message: Traceback (most recent call last): File "cutout2.py", line 62, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 461, in load_uniform_grid psize = get_psize(np.array(data[key].shape), nprocs) AttributeError: 'tuple' object has no attribute 'shape'
Hence, I modify "data = dict(density = (map, "g/cm**3"))" --> "data = dict(density = map)" and it work. If this is the case, how can I define the density unit and show it when I make Slice/Projection? In addition, I would like to know how I can set the unit in Generic UnicGrid Data in general? The length unit can be provide to script in load_uniform_grid(... 3.086e24 ....) but I do not know how to set other units.
2. When I add particle information as follow: ..... npart = 100000 # number of particles data = dict(density = map, number_of_particles = npart, particle_position_x = posx, particle_position_y = posy, particle_position_z = posz) bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) ...
I got the following error message: Traceback (most recent call last): File "cutout.py", line 107, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 519, in load_uniform_grid assign_particle_data(spf, pdata) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 371, in assign_particle_data pdata.pop("number_of_particles") KeyError: 'number_of_particles'
So, I change "number_of_particles = npart," --> "number_of_particles = 100000," and it works. How could it happen?
3. Can I do halo finder (hop/fof) using the above particle data? Or, what information do I need to provide to do grouping? In this case, how can I set the units and linking length?
4. Can I make particle distribution to particle data like data['Dark_Matter_position_x']? This process will allow me additional analysis such as profile and obtaining total value.
I may ask too many for new tool, but it will help a lot to use yt for general data set.
Thank you, Junhwan _______________________________________________ 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
Here, I post my script in http://paste.yt-project.org/show/4641 Thank you, Junhwan On Thu, May 15, 2014 at 11:56 PM, John ZuHone <jzuhone@gmail.com> wrote:
Junhwan,
Can you post your script somewhere? It might be easier to debug it that way.
Best,
John Z
On May 16, 2014, at 12:46 AM, Junhwan Choi <choi.junhwan@gmail.com> wrote:
Hi Nathan,
I think that I am using the yt 3.0 unless there is stabke yt 3.0 version.
Junhwan
On May 15, 2014, at 11:29 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Junhwan,
Just to clarify (since the answers you receive will be different depending on your response) is this for the in-development yt 3.0 release or the current stable release?
Nathan
On Friday, May 16, 2014, Junhwan Choi (최준환) <choi.junhwan@gmail.com> wrote:
Dear yt user,
I try to use Generic UnicGrid Data (256^3 gas density cube + position of particle that is subset of a huge simulation). It is preliminary work, but I still have some questions.
1. In order to set density unit as cgs, I made following script: ...... data = dict(density = (map, "g/cm**3")) #map is 256^3 density data array bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) .....
Then, I got the following error message: Traceback (most recent call last): File "cutout2.py", line 62, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 461, in load_uniform_grid psize = get_psize(np.array(data[key].shape), nprocs) AttributeError: 'tuple' object has no attribute 'shape'
Hence, I modify "data = dict(density = (map, "g/cm**3"))" --> "data = dict(density = map)" and it work. If this is the case, how can I define the density unit and show it when I make Slice/Projection? In addition, I would like to know how I can set the unit in Generic UnicGrid Data in general? The length unit can be provide to script in load_uniform_grid(... 3.086e24 ....) but I do not know how to set other units.
2. When I add particle information as follow: ..... npart = 100000 # number of particles data = dict(density = map, number_of_particles = npart, particle_position_x = posx, particle_position_y = posy, particle_position_z = posz) bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) ...
I got the following error message: Traceback (most recent call last): File "cutout.py", line 107, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 519, in load_uniform_grid assign_particle_data(spf, pdata) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 371, in assign_particle_data pdata.pop("number_of_particles") KeyError: 'number_of_particles'
So, I change "number_of_particles = npart," --> "number_of_particles = 100000," and it works. How could it happen?
3. Can I do halo finder (hop/fof) using the above particle data? Or, what information do I need to provide to do grouping? In this case, how can I set the units and linking length?
4. Can I make particle distribution to particle data like data['Dark_Matter_position_x']? This process will allow me additional analysis such as profile and obtaining total value.
I may ask too many for new tool, but it will help a lot to use yt for general data set.
Thank you, Junhwan _______________________________________________ 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
Hi, I have read more about the "generic array data" from the document in yt webpage. I found that the the how to set data dict and call "load_uniform_grid" by yt-2.6 and yt-3.0 are quite different, and it looks that yt-3.0 supports better unit treatment. However, my yt-3.0 looks use old formate for load_uniform_grid as follow: ..... def load_uniform_grid(data, domain_dimensions, sim_unit_to_cm, bbox=None, nprocs=1, sim_time=0.0, periodicity=(True, True, True)): .... This load_uniform_grid arguments are different with those presented in yt-3.0 document. I think this is part of the reason that I have a difficulty. How can I use that load_uniform_grid for the version shown in yt-3.0 document? Thank you, Junhwan On Fri, May 16, 2014 at 11:28 AM, Junhwan Choi (최준환) <choi.junhwan@gmail.com> wrote:
Here, I post my script in http://paste.yt-project.org/show/4641
Thank you, Junhwan
On Thu, May 15, 2014 at 11:56 PM, John ZuHone <jzuhone@gmail.com> wrote:
Junhwan,
Can you post your script somewhere? It might be easier to debug it that way.
Best,
John Z
On May 16, 2014, at 12:46 AM, Junhwan Choi <choi.junhwan@gmail.com> wrote:
Hi Nathan,
I think that I am using the yt 3.0 unless there is stabke yt 3.0 version.
Junhwan
On May 15, 2014, at 11:29 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Junhwan,
Just to clarify (since the answers you receive will be different depending on your response) is this for the in-development yt 3.0 release or the current stable release?
Nathan
On Friday, May 16, 2014, Junhwan Choi (최준환) <choi.junhwan@gmail.com> wrote:
Dear yt user,
I try to use Generic UnicGrid Data (256^3 gas density cube + position of particle that is subset of a huge simulation). It is preliminary work, but I still have some questions.
1. In order to set density unit as cgs, I made following script: ...... data = dict(density = (map, "g/cm**3")) #map is 256^3 density data array bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) .....
Then, I got the following error message: Traceback (most recent call last): File "cutout2.py", line 62, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 461, in load_uniform_grid psize = get_psize(np.array(data[key].shape), nprocs) AttributeError: 'tuple' object has no attribute 'shape'
Hence, I modify "data = dict(density = (map, "g/cm**3"))" --> "data = dict(density = map)" and it work. If this is the case, how can I define the density unit and show it when I make Slice/Projection? In addition, I would like to know how I can set the unit in Generic UnicGrid Data in general? The length unit can be provide to script in load_uniform_grid(... 3.086e24 ....) but I do not know how to set other units.
2. When I add particle information as follow: ..... npart = 100000 # number of particles data = dict(density = map, number_of_particles = npart, particle_position_x = posx, particle_position_y = posy, particle_position_z = posz) bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) ...
I got the following error message: Traceback (most recent call last): File "cutout.py", line 107, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 519, in load_uniform_grid assign_particle_data(spf, pdata) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 371, in assign_particle_data pdata.pop("number_of_particles") KeyError: 'number_of_particles'
So, I change "number_of_particles = npart," --> "number_of_particles = 100000," and it works. How could it happen?
3. Can I do halo finder (hop/fof) using the above particle data? Or, what information do I need to provide to do grouping? In this case, how can I set the units and linking length?
4. Can I make particle distribution to particle data like data['Dark_Matter_position_x']? This process will allow me additional analysis such as profile and obtaining total value.
I may ask too many for new tool, but it will help a lot to use yt for general data set.
Thank you, Junhwan _______________________________________________ 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
Hi Junhwan, Sorry, I kind of got lost in some other things--I'll have a look at your script tonight and get back to you. Best, John Z On May 22, 2014, at 6:17 PM, Junhwan Choi (최준환) <choi.junhwan@gmail.com> wrote:
Hi,
I have read more about the "generic array data" from the document in yt webpage. I found that the the how to set data dict and call "load_uniform_grid" by yt-2.6 and yt-3.0 are quite different, and it looks that yt-3.0 supports better unit treatment.
However, my yt-3.0 looks use old formate for load_uniform_grid as follow: ..... def load_uniform_grid(data, domain_dimensions, sim_unit_to_cm, bbox=None, nprocs=1, sim_time=0.0, periodicity=(True, True, True)): ....
This load_uniform_grid arguments are different with those presented in yt-3.0 document. I think this is part of the reason that I have a difficulty.
How can I use that load_uniform_grid for the version shown in yt-3.0 document?
Thank you, Junhwan
On Fri, May 16, 2014 at 11:28 AM, Junhwan Choi (최준환) <choi.junhwan@gmail.com> wrote:
Here, I post my script in http://paste.yt-project.org/show/4641
Thank you, Junhwan
On Thu, May 15, 2014 at 11:56 PM, John ZuHone <jzuhone@gmail.com> wrote:
Junhwan,
Can you post your script somewhere? It might be easier to debug it that way.
Best,
John Z
On May 16, 2014, at 12:46 AM, Junhwan Choi <choi.junhwan@gmail.com> wrote:
Hi Nathan,
I think that I am using the yt 3.0 unless there is stabke yt 3.0 version.
Junhwan
On May 15, 2014, at 11:29 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Junhwan,
Just to clarify (since the answers you receive will be different depending on your response) is this for the in-development yt 3.0 release or the current stable release?
Nathan
On Friday, May 16, 2014, Junhwan Choi (최준환) <choi.junhwan@gmail.com> wrote:
Dear yt user,
I try to use Generic UnicGrid Data (256^3 gas density cube + position of particle that is subset of a huge simulation). It is preliminary work, but I still have some questions.
1. In order to set density unit as cgs, I made following script: ...... data = dict(density = (map, "g/cm**3")) #map is 256^3 density data array bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) .....
Then, I got the following error message: Traceback (most recent call last): File "cutout2.py", line 62, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 461, in load_uniform_grid psize = get_psize(np.array(data[key].shape), nprocs) AttributeError: 'tuple' object has no attribute 'shape'
Hence, I modify "data = dict(density = (map, "g/cm**3"))" --> "data = dict(density = map)" and it work. If this is the case, how can I define the density unit and show it when I make Slice/Projection? In addition, I would like to know how I can set the unit in Generic UnicGrid Data in general? The length unit can be provide to script in load_uniform_grid(... 3.086e24 ....) but I do not know how to set other units.
2. When I add particle information as follow: ..... npart = 100000 # number of particles data = dict(density = map, number_of_particles = npart, particle_position_x = posx, particle_position_y = posy, particle_position_z = posz) bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) ...
I got the following error message: Traceback (most recent call last): File "cutout.py", line 107, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 519, in load_uniform_grid assign_particle_data(spf, pdata) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 371, in assign_particle_data pdata.pop("number_of_particles") KeyError: 'number_of_particles'
So, I change "number_of_particles = npart," --> "number_of_particles = 100000," and it works. How could it happen?
3. Can I do halo finder (hop/fof) using the above particle data? Or, what information do I need to provide to do grouping? In this case, how can I set the units and linking length?
4. Can I make particle distribution to particle data like data['Dark_Matter_position_x']? This process will allow me additional analysis such as profile and obtaining total value.
I may ask too many for new tool, but it will help a lot to use yt for general data set.
Thank you, Junhwan _______________________________________________ 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
On Thu, May 22, 2014 at 3:17 PM, Junhwan Choi (최준환) <choi.junhwan@gmail.com>wrote:
Hi,
I have read more about the "generic array data" from the document in yt webpage. I found that the the how to set data dict and call "load_uniform_grid" by yt-2.6 and yt-3.0 are quite different, and it looks that yt-3.0 supports better unit treatment.
However, my yt-3.0 looks use old formate for load_uniform_grid as follow: ..... def load_uniform_grid(data, domain_dimensions, sim_unit_to_cm, bbox=None, nprocs=1, sim_time=0.0, periodicity=(True, True, True)): ....
This load_uniform_grid arguments are different with those presented in yt-3.0 document. I think this is part of the reason that I have a difficulty.
Sorry for the difficulty - we're in the middle of updating the docs so there is still come confusing incorrect information in the 3.0-dev documentation.
How can I use that load_uniform_grid for the version shown in yt-3.0 document?
Thank you, Junhwan
On Fri, May 16, 2014 at 11:28 AM, Junhwan Choi (최준환) <choi.junhwan@gmail.com> wrote:
Here, I post my script in http://paste.yt-project.org/show/4641
Thank you, Junhwan
On Thu, May 15, 2014 at 11:56 PM, John ZuHone <jzuhone@gmail.com> wrote:
Junhwan,
Can you post your script somewhere? It might be easier to debug it that way.
Best,
John Z
On May 16, 2014, at 12:46 AM, Junhwan Choi <choi.junhwan@gmail.com> wrote:
Hi Nathan,
I think that I am using the yt 3.0 unless there is stabke yt 3.0 version.
Junhwan
On May 15, 2014, at 11:29 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Junhwan,
Just to clarify (since the answers you receive will be different depending on your response) is this for the in-development yt 3.0 release or the current stable release?
Nathan
On Friday, May 16, 2014, Junhwan Choi (최준환) <choi.junhwan@gmail.com> wrote:
Dear yt user,
I try to use Generic UnicGrid Data (256^3 gas density cube + position of particle that is subset of a huge simulation). It is preliminary work, but I still have some questions.
1. In order to set density unit as cgs, I made following script: ...... data = dict(density = (map, "g/cm**3")) #map is 256^3 density data
array
bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) .....
Then, I got the following error message: Traceback (most recent call last): File "cutout2.py", line 62, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File
"/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py",
line 461, in load_uniform_grid psize = get_psize(np.array(data[key].shape), nprocs) AttributeError: 'tuple' object has no attribute 'shape'
Hence, I modify "data = dict(density = (map, "g/cm**3"))" --> "data = dict(density = map)" and it work. If this is the case, how can I define the density unit and show it when I make Slice/Projection? In addition, I would like to know how I can set the unit in Generic UnicGrid Data in general? The length unit can be provide to script in load_uniform_grid(... 3.086e24 ....) but I do not know how to set other units.
2. When I add particle information as follow: ..... npart = 100000 # number of particles data = dict(density = map, number_of_particles = npart, particle_position_x = posx, particle_position_y = posy, particle_position_z = posz) bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) ...
I got the following error message: Traceback (most recent call last): File "cutout.py", line 107, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File
"/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py",
line 519, in load_uniform_grid assign_particle_data(spf, pdata) File
"/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py",
line 371, in assign_particle_data pdata.pop("number_of_particles") KeyError: 'number_of_particles'
So, I change "number_of_particles = npart," --> "number_of_particles = 100000," and it works. How could it happen?
3. Can I do halo finder (hop/fof) using the above particle data? Or, what information do I need to provide to do grouping? In this case, how can I set the units and linking length?
4. Can I make particle distribution to particle data like data['Dark_Matter_position_x']? This process will allow me additional analysis such as profile and obtaining total value.
I may ask too many for new tool, but it will help a lot to use yt for general data set.
Thank you, Junhwan _______________________________________________ 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
Junhwan, Can you post your script somewhere? It might be easier to debug it that way. Best, John Z
On May 16, 2014, at 12:46 AM, Junhwan Choi <choi.junhwan@gmail.com> wrote:
Hi Nathan,
I think that I am using the yt 3.0 unless there is stabke yt 3.0 version.
Junhwan
On May 15, 2014, at 11:29 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Junhwan,
Just to clarify (since the answers you receive will be different depending on your response) is this for the in-development yt 3.0 release or the current stable release?
Nathan
On Friday, May 16, 2014, Junhwan Choi (최준환) <choi.junhwan@gmail.com> wrote: Dear yt user,
I try to use Generic UnicGrid Data (256^3 gas density cube + position of particle that is subset of a huge simulation). It is preliminary work, but I still have some questions.
1. In order to set density unit as cgs, I made following script: ...... data = dict(density = (map, "g/cm**3")) #map is 256^3 density data array bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) .....
Then, I got the following error message: Traceback (most recent call last): File "cutout2.py", line 62, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 461, in load_uniform_grid psize = get_psize(np.array(data[key].shape), nprocs) AttributeError: 'tuple' object has no attribute 'shape'
Hence, I modify "data = dict(density = (map, "g/cm**3"))" --> "data = dict(density = map)" and it work. If this is the case, how can I define the density unit and show it when I make Slice/Projection? In addition, I would like to know how I can set the unit in Generic UnicGrid Data in general? The length unit can be provide to script in load_uniform_grid(... 3.086e24 ....) but I do not know how to set other units.
2. When I add particle information as follow: ..... npart = 100000 # number of particles data = dict(density = map, number_of_particles = npart, particle_position_x = posx, particle_position_y = posy, particle_position_z = posz) bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) ...
I got the following error message: Traceback (most recent call last): File "cutout.py", line 107, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 519, in load_uniform_grid assign_particle_data(spf, pdata) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 371, in assign_particle_data pdata.pop("number_of_particles") KeyError: 'number_of_particles'
So, I change "number_of_particles = npart," --> "number_of_particles = 100000," and it works. How could it happen?
3. Can I do halo finder (hop/fof) using the above particle data? Or, what information do I need to provide to do grouping? In this case, how can I set the units and linking length?
4. Can I make particle distribution to particle data like data['Dark_Matter_position_x']? This process will allow me additional analysis such as profile and obtaining total value.
I may ask too many for new tool, but it will help a lot to use yt for general data set.
Thank you, Junhwan _______________________________________________ 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
participants (4)
-
John ZuHone -
Junhwan Choi -
Junhwan Choi (최준환)
-
Nathan Goldbaum