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November 2014

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42 discussions

access coarse raw data in the AMR simulation with yt
by Junhwan Choi (최준환) Nov. 4, 2014

Nov. 4, 2014

Hi yt user, Previously, I asked basic question how I can access raw data using yt. At that time, I confirm that the following script print the x, y, z,vx, vy, vz, and mass for all finest cells in the spherical region ================= from yt.mods import * pf = load("../DD%04d/DD%04d" % (snapshot,snapshot)) center = pf.h.find_max("Density")[1] sp = pf.h.sphere(center, (rmax,'pc')) for icell in range(0,sp["CellMassMsun"].size): print sp["x"][icell], sp["y"][icell], sp["z"][icell] print sp["x-velocity"][icell], sp["y-velocity"][icell], sp["z-velocity"][icell] print sp["CellMassMsun"][icell] ================ However, is there any way to access the coarse raw data? For example, the highest resolution of my simulation is say N_amr=10. But, I would like to access the data only up to N_amr=5 (from top grid to N_amr=5 grid). In this case, the grid information N_amr=6 to 10 is represented by its parent grid data. Is it possible? If so, how can I access these coarse data? Thank you in advance, Junhwan

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Fwd: [enzo-dev] A lightcone problem
by Britton Smith Nov. 3, 2014

Nov. 3, 2014

Hi GB, I am forwarding this over to the yt-users list as this is a yt issue and not an enzo issue. I am unable to reproduce the issue you're seeing when I use the light cone cookbook recipe. I'm guessing that you're running into a corner case with the light cone generator that is specific to your simulation data. Could you send along the light cone solution file? It should be named lightcone.dat. There might be some clues in there. Britton ---------- Forwarded message ---------- From: Gongbo Zhao <gong-bo.zhao(a)port.ac.uk> Date: Thu, Oct 23, 2014 at 11:35 PM Subject: [enzo-dev] A lightcone problem To: brittonsmith(a)gmail.com Cc: "enzo-dev(a)googlegroups.com" <enzo-dev(a)googlegroups.com> Hi Britton, I used the latest yt (version Version = 3.1-dev; Changeset = bf8f9f98b34a (yt) tip) but I am having problems with the lightcone analysis. When I ran it using the following script, > from yt.analysis_modules.cosmological_observation.api import \ > LightCone > > lc = LightCone('Example_Cosmology_Sim.param', > 'Enzo', 0., 0.1) > lc.calculate_light_cone_solution(seed=123456789, filename='lightcone.dat') > field = 'density' > field_of_view = (600.0, "arcmin") > resolution = (60.0, "arcsec") > lc.project_light_cone(field_of_view, resolution, > field, weight_field=None, > save_stack=True, > save_slice_images=True) I got these error messages, > yt : [INFO ] 2014-10-24 04:29:36,439 Parameters: domain_dimensions = [128 128 128] > yt : [INFO ] 2014-10-24 04:29:36,440 Parameters: domain_left_edge = [ 0. 0. 0.] > yt : [INFO ] 2014-10-24 04:29:36,440 Parameters: domain_right_edge = [ 1. 1. 1.] > yt : [INFO ] 2014-10-24 04:29:36,441 Parameters: initial_time = 1.1703706995e+15 s > yt : [INFO ] 2014-10-24 04:29:36,441 Parameters: final_time = 4.31424173577e+17 s > yt : [INFO ] 2014-10-24 04:29:36,441 Parameters: stop_cycle = 100000 > yt : [INFO ] 2014-10-24 04:29:36,441 Parameters: cosmological_simulation = 1 > yt : [INFO ] 2014-10-24 04:29:36,441 Parameters: box_size = 64.0 Mpccm/h > yt : [INFO ] 2014-10-24 04:29:36,441 Parameters: omega_lambda = 0.73 > yt : [INFO ] 2014-10-24 04:29:36,441 Parameters: omega_matter = 0.27 > yt : [INFO ] 2014-10-24 04:29:36,441 Parameters: hubble_constant = 0.71 > yt : [INFO ] 2014-10-24 04:29:36,441 Parameters: initial_redshift = 60.0 > yt : [INFO ] 2014-10-24 04:29:36,442 Parameters: final_redshift = 0.0 > yt : [INFO ] 2014-10-24 04:29:36,442 Total datasets: 313. > yt : [INFO ] 2014-10-24 04:29:49,842 create_cosmology_splice: Used 5 data dumps to get from z = 0.100000 to 0.000000. > yt : [ERROR ] 2014-10-24 04:29:49,978 Warning: box fraction required to go from z = 0.099445 to 0.077086 is 1.008644 > yt : [ERROR ] 2014-10-24 04:29:49,978 Full box delta z is 0.022168, but it is 0.022359 to the next data dump. > yt : [INFO ] 2014-10-24 04:29:50,042 Saving light cone solution to lightcone.dat. > yt : [INFO ] 2014-10-24 04:29:50,217 Parameters: current_time = 272.816550757 > yt : [INFO ] 2014-10-24 04:29:50,217 Parameters: domain_dimensions = [128 128 128] > yt : [INFO ] 2014-10-24 04:29:50,217 Parameters: domain_left_edge = [ 0. 0. 0.] > yt : [INFO ] 2014-10-24 04:29:50,218 Parameters: domain_right_edge = [ 1. 1. 1.] > yt : [INFO ] 2014-10-24 04:29:50,218 Parameters: cosmological_simulation = 1 > yt : [INFO ] 2014-10-24 04:29:50,218 Parameters: current_redshift = 0.0994652856936 > yt : [INFO ] 2014-10-24 04:29:50,218 Parameters: omega_lambda = 0.73 > yt : [INFO ] 2014-10-24 04:29:50,218 Parameters: omega_matter = 0.27 > yt : [INFO ] 2014-10-24 04:29:50,218 Parameters: hubble_constant = 0.71 > yt : [INFO ] 2014-10-24 04:29:50,220 Making projection at z = 0.099445 from DD0272/DD0272. > Parsing Hierarchy 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 > yt : [INFO ] 2014-10-24 04:29:51,714 Gathering a field list (this may take a moment.) > yt : [INFO ] 2014-10-24 04:29:52,622 Loading field plugins. > yt : [INFO ] 2014-10-24 04:29:52,622 Loaded angular_momentum (8 new fields) > yt : [INFO ] 2014-10-24 04:29:52,622 Loaded astro (14 new fields) > yt : [INFO ] 2014-10-24 04:29:52,623 Loaded cosmology (20 new fields) > yt : [INFO ] 2014-10-24 04:29:52,623 Loaded fluid (56 new fields) > yt : [INFO ] 2014-10-24 04:29:52,624 Loaded fluid_vector (88 new fields) > yt : [INFO ] 2014-10-24 04:29:52,624 Loaded geometric (102 new fields) > yt : [INFO ] 2014-10-24 04:29:52,624 Loaded local (102 new fields) > yt : [INFO ] 2014-10-24 04:29:52,625 Loaded magnetic_field (108 new fields) > yt : [INFO ] 2014-10-24 04:29:52,625 Loaded my_plugins (108 new fields) > yt : [INFO ] 2014-10-24 04:29:52,625 Loaded species (110 new fields) > Traceback (most recent call last): > File "lightcone.py", line 13, in <module> > save_slice_images=True) > File "/opt/apps/enzo/new/yt-x86_64/src/yt-hg/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py", line 322, in project_light_cone > weight_field=weight_field) > File "/opt/apps/enzo/new/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 267, in barrierize > return func(*args, **kwargs) > File "/opt/apps/enzo/new/yt-x86_64/src/yt-hg/yt/analysis_modules/cosmological_observation/light_cone/light_cone_projection.py", line 84, in _light_cone_projection > data_source=cut_region) > File "/opt/apps/enzo/new/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 245, in __init__ > self.get_data(field) > File "/opt/apps/enzo/new/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 285, in get_data > self._initialize_chunk(chunk, tree) > File "/opt/apps/enzo/new/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 369, in _initialize_chunk > tree.initialize_chunk(i1, i2, ilevel) > File "QuadTree.pyx", line 330, in yt.utilities.lib.QuadTree.QuadTree.initialize_chunk (yt/utilities/lib/QuadTree.c:4710) > ValueError: Buffer has wrong number of dimensions (expected 1, got 2) It seems to be a buffer dimension problem? Thanks, GB -- You received this message because you are subscribed to the Google Groups "enzo-dev" group. To unsubscribe from this group and stop receiving emails from it, send an email to enzo-dev+unsubscribe(a)googlegroups.com. To post to this group, send email to enzo-dev(a)googlegroups.com. Visit this group at http://groups.google.com/group/enzo-dev. For more options, visit https://groups.google.com/d/optout.

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