Hi Mr. Britton Smith, Thank you very much for your very polite reply the other day. When I executed the processing of Gadget2 data that you taught me as follows and prepared for Clump Finding, I got an error like this. I don't know the cause of this error and the solution. If you have any advice, could you please let me know? Tomoyuki Shiokawa -------------------------------------------------------------------- import numpy as np import yt from yt.data_objects.level_sets.api import * fname = "Gadget2.0090" unit_base = { "UnitLength_in_cm": 3.08568e21, "UnitMass_in_g": 1.989e43, "UnitVelocity_in_cm_per_s": 100000, } bbox_lim = 70 # kpc bbox = [[-bbox_lim, bbox_lim], [-bbox_lim, bbox_lim], [-bbox_lim, bbox_lim]] ds = yt.load(fname, unit_base=unit_base, bounding_box=bbox) sphere = ds.sphere([-2.13004994, 1.08833396, 0.87476391], (70, "kpc")) ds2 = sphere.save_as_dataset(fields=[("gas", "density"), ("all", "particle_mass")]) print(ds2) sphere_ds = yt.load(ds2) print(sphere_ds.data["grid", "density"]) data_source = sphere_ds.disk([0.5, 0.5, 0.5], [0.0, 0.0, 1.0], (8, "kpc"), (1, "kpc")) master_clump = Clump(data_source, ("gas", "density")) master_clump.add_validator("min_cells", 20) master_clump.add_info_item("center_of_mass") c_min = data_source["gas", "density"].min() c_max = data_source["gas", "density"].max() print(c_min) print(c_max) step = 2.0 find_clumps(master_clump, c_min, c_max, step) ---------------------------------------------------------------------------------------------------------------------------------------------------------- yt : [INFO ] 2021-11-01 12:05:14,115 Omega Lambda is 0.0, so we are turning off Cosmology. yt : [INFO ] 2021-11-01 12:05:14,245 Parameters: current_time = 10.68 yt : [INFO ] 2021-11-01 12:05:14,247 Parameters: domain_dimensions = [2 2 2] yt : [INFO ] 2021-11-01 12:05:14,253 Parameters: domain_left_edge = [-70. -70. -70.] yt : [INFO ] 2021-11-01 12:05:14,257 Parameters: domain_right_edge = [70. 70. 70.] yt : [INFO ] 2021-11-01 12:05:14,260 Parameters: cosmological_simulation = 0 yt : [INFO ] 2021-11-01 12:05:14,278 Allocating for 2.198e+06 particles (index particle type 'all') yt : [INFO ] 2021-11-01 12:05:14,705 Identified 1.478e+05 octs yt : [INFO ] 2021-11-01 12:06:02,589 Saving field data to yt dataset: Gadget2_sphere.h5. yt : [INFO ] 2021-11-01 12:06:03,130 Parameters: current_time = 10.68 code_time yt : [INFO ] 2021-11-01 12:06:03,132 Parameters: domain_dimensions = [2 2 2] Gadget2_sphere.h5 yt : [INFO ] 2021-11-01 12:06:03,138 Parameters: domain_left_edge = [-70. -70. -70.] code_length yt : [INFO ] 2021-11-01 12:06:03,149 Parameters: domain_right_edge = [70. 70. 70.] code_length yt : [INFO ] 2021-11-01 12:06:03,156 Parameters: cosmological_simulation = 0 yt : [INFO ] 2021-11-01 12:06:03,176 Allocating for 3.232e+06 particles (index particle type 'all') yt : [INFO ] 2021-11-01 12:06:04,515 Identified 8.938e+05 octs [0.00000000e+00 0.00000000e+00 2.01374744e-24 ... 0.00000000e+00 0.00000000e+00 0.00000000e+00] g/cm**3 yt : [INFO ] 2021-11-01 12:06:07,879 Finding clumps: min: 0.000000e+00, max: 3.546025e-16, step: 2.000000 0.0 g/cm**3 3.5460253791689846e-16 g/cm**3 --------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) <ipython-input-21-0dcc2997b138> in <module>() 36 print(c_max) 37 step = 2.0 ---> 38 find_clumps(master_clump, c_min, c_max, step) /home/salty1840/anaconda3/envs/yt3/lib/python2.7/site-packages/yt/data_objects/level_sets/clump_handling.pyc in find_clumps(clump, min_val, max_val, d_clump) 410 (min_val, max_val, d_clump)) 411 if min_val >= max_val: return --> 412 clump.find_children(min_val) 413 414 if len(clump.children) == 1: /home/salty1840/anaconda3/envs/yt3/lib/python2.7/site-packages/yt/data_objects/level_sets/clump_handling.pyc in find_children(self, min_val, max_val) 161 self.children = [] 162 if max_val is None: max_val = self.max_val --> 163 nj, cids = identify_contours(self.data, self.field, min_val, max_val) 164 # Here, cids is the set of slices and values, keyed by the 165 # parent_grid_id, that defines the contours. So we can figure out all /home/salty1840/anaconda3/envs/yt3/lib/python2.7/site-packages/yt/data_objects/level_sets/contour_finder.pyc in identify_contours(data_source, field, min_val, max_val, cached_fields) 34 DLE = data_source.ds.domain_left_edge 35 masks = dict((g.id, m) for g, m in data_source.blocks) ---> 36 for (g, node, (sl, dims, gi)) in data_source.tiles.slice_traverse(): 37 g.field_parameters.update(data_source.field_parameters) 38 node.node_ind = len(node_ids) /home/salty1840/anaconda3/envs/yt3/lib/python2.7/site-packages/yt/data_objects/data_containers.pyc in tiles(self) 1195 def tiles(self): 1196 if self._tree is not None: return self._tree -> 1197 self._tree = AMRKDTree(self.ds, data_source=self) 1198 return self._tree 1199 /home/salty1840/anaconda3/envs/yt3/lib/python2.7/site-packages/yt/utilities/amr_kdtree/amr_kdtree.pyc in __init__(self, ds, min_level, max_level, data_source) 155 156 if not issubclass(ds.index.__class__, GridIndex): --> 157 raise RuntimeError("AMRKDTree does not support particle or octree-based data.") 158 159 ParallelAnalysisInterface.__init__(self) RuntimeError: AMRKDTree does not support particle or octree-based data.