Mailman 3 August 2021 - yt-users

Initialising simulation from outside directory
by sam.patrick＠ed.ac.uk Aug. 9, 2021

Aug. 9, 2021

Hello, I'm trying to run a some analysis code for an Enzo simulation from outside the simulation directory. I can initialise a simulation object easily enough with the line: sim = yt.load_simulation("/path/to/simulation/DD00xx/DD00xx", 'Enzo') but then when I try to load the time series with the line sim.get_time_series() it seems to assume that the Enzo files are within the current working directory and creates a null object. I was wondering if there was any way to modify this behaviour … [View More]

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Vertical axis in halo mass function
by Hamed Manouchehri Kousha Aug. 4, 2021

Aug. 4, 2021

Hi dear all, I want to plot a halo mass function, using a simulation's halo catalogue, with differential number density as vertical axis, i.e. "dn/d(logm)". But It seems that the only option is cumulative number density. Is there any way to do that? Regards, Hamed

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Facing difficulties in using yt 4.0.0
by basu Aug. 3, 2021

Aug. 3, 2021

Dear Sir/Ma'am, To introduce myself first, I am going to start my PhD at Max Planck Institute of Astrophysics in the group of Dr. Benedetta Ciardi in few months. For my ongoing project, I need to use yt package for which I have installed yt 4.0.0 via pip pipeline. But, I am facing a difficulty in processing the file successfully loaded and read by "yt.load". I am sharing 2-3 lines of my code and the errors I get. CODE: import yt import numpy as np import h5py ad=ds.all_data() ##[ERROR … [View More]1 here] fields = ['density'] le = ds.domain_left_edge re = ds.domain_right_edge ag = ds.arbitrary_grid(le,re,[256]*3) for f in fields: print(f) data[f] = ag[('gas', f)] bbox = np.array(list(zip(le.in_units('Mpccm/h'), re.in_units('Mpccm/h')))) ds_gridded = yt.load_uniform_grid(data, [256]*3, length_unit = ds.length_unit.to('Mpccm/h'), bbox=bbox) sp = yt.SlicePlot(ds_gridded,'z',('gas','density')) sp.save() ##[ERROR 2 here] ERROR:1: RuntimeError Traceback (most recent call last) <ipython-input-4-007efe033704> in <module> ----> 1 ad=ds.all_data() ~/.local/lib/python3.8/site-packages/yt/data_objects/static_output.py in all_data(self, find_max, **kwargs) 1039 which covers the entire simulation domain. 1040 """ -> 1041 self.index 1042 if find_max: 1043 c = self.find_max("density")[1] ~/.local/lib/python3.8/site-packages/yt/data_objects/static_output.py in index(self) 526 if self._index_class is None: 527 raise RuntimeError("You should not instantiate Dataset.") --> 528 self._instantiated_index = self._index_class( 529 self, dataset_type=self.dataset_type 530 ) ~/.local/lib/python3.8/site-packages/yt/geometry/particle_geometry_handler.py in __init__(self, ds, dataset_type) 22 self.dataset = weakref.proxy(ds) 23 self.float_type = np.float64 ---> 24 super().__init__(ds, dataset_type) 25 self._initialize_index() 26 ~/.local/lib/python3.8/site-packages/yt/geometry/geometry_handler.py in __init__(self, ds, dataset_type) 42 # potentially quite expensive, and should be done with the indexing. 43 mylog.debug("Detecting fields.") ---> 44 self._detect_output_fields() 45 46 @abc.abstractmethod ~/.local/lib/python3.8/site-packages/yt/geometry/particle_geometry_handler.py in _detect_output_fields(self) 296 fl, _units = field_cache[dom.filename] 297 else: --> 298 fl, _units = self.io._identify_fields(dom) 299 field_cache[dom.filename] = fl, _units 300 units.update(_units) ~/.local/lib/python3.8/site-packages/yt/frontends/gadget/ioKeyError Traceback (most recent call last) <ipython-input-6-97fe8b4b4ff8> in <module> 1 for f in fields: 2 print(f) ----> 3 data[f] = ag[('gas', f)] 4 bbox = np.array(list(zip(le.in_units('Mpccm/h'), re.in_units('Mpccm/h')))) 5 ds_gridded = yt.load_uniform_grid(data, [256]*3, length_unit = ds.length_unit.to('Mpccm/h'), bbox=bbox) ~/.local/lib/python3.8/site-packages/yt/data_objects/data_containers.py in __getitem__(self, key) 250 Returns a single field. Will add if necessary. 251 """ --> 252 f = self._determine_fields([key])[0] 253 if f not in self.field_data and key not in self.field_data: 254 if f in self._container_fields: ~/.local/lib/python3.8/site-packages/yt/data_objects/data_containers.py in _determine_fields(self, fields) 1450 ftype, fname = self._tupleize_field(field) 1451 # print(field, " : ",ftype, fname) -> 1452 finfo = self.ds._get_field_info(ftype, fname) 1453 1454 # really ugly check to ensure that this field really does exist somewhere, ~/.local/lib/python3.8/site-packages/yt/data_objects/static_output.py in _get_field_info(self, ftype, fname) 817 818 def _get_field_info(self, ftype, fname=None): --> 819 field_info, is_ambiguous = self._get_field_info_helper(ftype, fname) 820 821 if is_ambiguous: ~/.local/lib/python3.8/site-packages/yt/data_objects/static_output.py in _get_field_info_helper(self, ftype, fname) 833 834 def _get_field_info_helper(self, ftype, fname=None): --> 835 self.index 836 837 # store the original inputs in case we need to raise an error ~/.local/lib/python3.8/site-packages/yt/data_objects/static_output.py in index(self) 526 if self._index_class is None: 527 raise RuntimeError("You should not instantiate Dataset.") --> 528 self._instantiated_index = self._index_class( 529 self, dataset_type=self.dataset_type 530 ) ~/.local/lib/python3.8/site-packages/yt/geometry/particle_geometry_handler.py in __init__(self, ds, dataset_type) 22 self.dataset = weakref.proxy(ds) 23 self.float_type = np.float64 ---> 24 super().__init__(ds, dataset_type) 25 self._initialize_index() 26 ~/.local/lib/python3.8/site-packages/yt/geometry/geometry_handler.py in __init__(self, ds, dataset_type) 42 # potentially quite expensive, and should be done with the indexing. 43 mylog.debug("Detecting fields.") ---> 44 self._detect_output_fields() 45 46 @abc.abstractmethod ~/.local/lib/python3.8/site-packages/yt/geometry/particle_geometry_handler.py in _detect_output_fields(self) 296 fl, _units = field_cache[dom.filename] 297 else: --> 298 fl, _units = self.io._identify_fields(dom) 299 field_cache[dom.filename] = fl, _units 300 units.update(_units) ~/.local/lib/python3.8/site-packages/yt/frontends/gadget/io.py in _identify_fields(self, data_file) 290 else: 291 kk = k --> 292 if not hasattr(g[kk], "shape"): 293 continue 294 if len(g[kk].shape) > 1: h5py/_objects.pyx in h5py._objects.with_phil.wrapper() h5py/_objects.pyx in h5py._objects.with_phil.wrapper() ~/.local/lib/python3.8/site-packages/h5py/_hl/group.py in __getitem__(self, name) 286 raise ValueError("Invalid HDF5 object reference") 287 else: --> 288 oid = h5o.open(self.id, self._e(name), lapl=self._lapl) 289 290 otype = h5i.get_type(oid) h5py/_objects.pyx in h5py._objects.with_phil.wrapper() h5py/_objects.pyx in h5py._objects.with_phil.wrapper() h5py/h5o.pyx in h5py.h5o.open() KeyError: 'Unable to open object (bad object header version number)'.py in _identify_fields(self, data_file) 261 # -------------------------------------- 262 g = f[key] --> 263 if cname not in g: 264 continue 265 h5py/_objects.pyx in h5py._objects.with_phil.wrapper() h5py/_objects.pyx in h5py._objects.with_phil.wrapper() ~/.local/lib/python3.8/site-packages/h5py/_hl/group.py in __contains__(self, name) 437 def __contains__(self, name): 438 """ Test if a member name exists """ --> 439 return self._e(name) in self.id 440 441 def copy(self, source, dest, name=None, h5py/h5g.pyx in h5py.h5g.GroupID.__contains__() h5py/h5g.pyx in h5py.h5g.GroupID.__contains__() h5py/_objects.pyx in h5py._objects.with_phil.wrapper() h5py/_objects.pyx in h5py._objects.with_phil.wrapper() h5py/h5g.pyx in h5py.h5g._path_valid() h5py/_objects.pyx in h5py._objects.with_phil.wrapper() h5py/_objects.pyx in h5py._objects.with_phil.wrapper() h5py/h5l.pyx in h5py.h5l.LinkProxy.exists() RuntimeError: Unable to get link info (free block size is zero?) ERROR:2: KeyError Traceback (most recent call last) <ipython-input-6-97fe8b4b4ff8> in <module> 1 for f in fields: 2 print(f) ----> 3 data[f] = ag[('gas', f)] 4 bbox = np.array(list(zip(le.in_units('Mpccm/h'), re.in_units('Mpccm/h')))) 5 ds_gridded = yt.load_uniform_grid(data, [256]*3, length_unit = ds.length_unit.to('Mpccm/h'), bbox=bbox) ~/.local/lib/python3.8/site-packages/yt/data_objects/data_containers.py in __getitem__(self, key) 250 Returns a single field. Will add if necessary. 251 """ --> 252 f = self._determine_fields([key])[0] 253 if f not in self.field_data and key not in self.field_data: 254 if f in self._container_fields: ~/.local/lib/python3.8/site-packages/yt/data_objects/data_containers.py in _determine_fields(self, fields) 1450 ftype, fname = self._tupleize_field(field) 1451 # print(field, " : ",ftype, fname) -> 1452 finfo = self.ds._get_field_info(ftype, fname) 1453 1454 # really ugly check to ensure that this field really does exist somewhere, ~/.local/lib/python3.8/site-packages/yt/data_objects/static_output.py in _get_field_info(self, ftype, fname) 817 818 def _get_field_info(self, ftype, fname=None): --> 819 field_info, is_ambiguous = self._get_field_info_helper(ftype, fname) 820 821 if is_ambiguous: ~/.local/lib/python3.8/site-packages/yt/data_objects/static_output.py in _get_field_info_helper(self, ftype, fname) 833 834 def _get_field_info_helper(self, ftype, fname=None): --> 835 self.index 836 837 # store the original inputs in case we need to raise an error ~/.local/lib/python3.8/site-packages/yt/data_objects/static_output.py in index(self) 526 if self._index_class is None: 527 raise RuntimeError("You should not instantiate Dataset.") --> 528 self._instantiated_index = self._index_class( 529 self, dataset_type=self.dataset_type 530 ) ~/.local/lib/python3.8/site-packages/yt/geometry/particle_geometry_handler.py in __init__(self, ds, dataset_type) 22 self.dataset = weakref.proxy(ds) 23 self.float_type = np.float64 ---> 24 super().__init__(ds, dataset_type) 25 self._initialize_index() 26 ~/.local/lib/python3.8/site-packages/yt/geometry/geometry_handler.py in __init__(self, ds, dataset_type) 42 # potentially quite expensive, and should be done with the indexing. 43 mylog.debug("Detecting fields.") ---> 44 self._detect_output_fields() 45 46 @abc.abstractmethod ~/.local/lib/python3.8/site-packages/yt/geometry/particle_geometry_handler.py in _detect_output_fields(self) 296 fl, _units = field_cache[dom.filename] 297 else: --> 298 fl, _units = self.io._identify_fields(dom) 299 field_cache[dom.filename] = fl, _units 300 units.update(_units) ~/.local/lib/python3.8/site-packages/yt/frontends/gadget/io.py in _identify_fields(self, data_file) 290 else: 291 kk = k --> 292 if not hasattr(g[kk], "shape"): 293 continue 294 if len(g[kk].shape) > 1: h5py/_objects.pyx in h5py._objects.with_phil.wrapper() h5py/_objects.pyx in h5py._objects.with_phil.wrapper() ~/.local/lib/python3.8/site-packages/h5py/_hl/group.py in __getitem__(self, name) 286 raise ValueError("Invalid HDF5 object reference") 287 else: --> 288 oid = h5o.open(self.id, self._e(name), lapl=self._lapl) 289 290 otype = h5i.get_type(oid) h5py/_objects.pyx in h5py._objects.with_phil.wrapper() h5py/_objects.pyx in h5py._objects.with_phil.wrapper() h5py/h5o.pyx in h5py.h5o.open() KeyError: 'Unable to open object (bad object header version number)' What I feel is that there is a mismatch in the h5py version. What is that exact problem here? I have h5py 3.0.0, matplotlib 3.4.1,python 3.8,yt 4.0.0 in my machine. Please make me understand and suggest me a reasonable solution so that I can proceed smoothly to my next step. The length of this email seems large although most of it contains some outcomes of the codes. Waiting for your early reply. Regards, Arghyadeep Basu [View Less]

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ANN: ytree 3.0 released
by Britton Smith Aug. 3, 2021

Aug. 3, 2021

Greetings! I am extremely pleased to announce the release of ytree version 3.0! ytree is an extension of yt for analyzing merger trees. This is a major release that sees significant speed and memory use improvements, support for 5 new data formats, and several new features. New features and major enhancements are listed below. For a complete list of all changes, see the changelog <https://ytree.readthedocs.io/en/latest/changelog.html#version-3-0>. A special thanks to Manodeep Sinha … [View More]

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