Commit ed2c8ff
JOSS paper submission (#124)
* Record processing time for each halo
* Skip density check for satellites
* Use written chunks when restarting
* Store calculation time for each property
* Use lookup table for stellar ages
* Add links to footnotes
* Remove unneeded sort
* Squash sort bug
* Non iterative inertia tensors
* Catch io errors for chunk files
* Move filter to parameter file
* Remove VR FOFSubhalo halo type
* Remove GroupNr_all
* Descriptions for timing information
* Sort halos on chunk
* Report peak memory usage
* Copy values from smaller apertures
* Store filter metadata for properties
* Fix docs generation
* Add script for plotting timings
* Added wrong plot_time script
* Update plot time script
* Plot setup time
* Various minor fixes
* Wrap COM values
* Add Victor symmetric array script
* Set min read radius to be optional
* Matthieu documentation suggestions
* Change assigning of files to ranks
* Add MPI compression script
* Set compressed properties to be read-only
* Add vmax radius to SO properties
* Fix velocity scale factors
* First attempt at reading in EAGLE
* Calculate cell offsets
* Working metadata
* Working EAGLE conversion script
* Add L100 EAGLE
* Add license
* Add JOSS paper
* Fix tests
* Create SOAP package
* Run formatter
* Remove stray file
* Update formatter version
* Format all files
* Minor paper compilation updates
* Address pre-review comments (#133)
* Use pyproject.toml instead of setup.py
* Update packages
* List packages
* Find packages automatically
* Add small DMO example
* Test subhalo rank with HBT data
* Add scripts for running HBT/VR
* Make test helper script MPI-compatible
* Generate documentation for small test
* Move Rockstar test and read with numpy instead of pandas
* Add rockstar test
* Run formatter
* Move subfind test
* Update scripts
* Include neutrinos in omega_m
* Update dust fraction calculation (#134)
* Don't use hydrogen fraction for dust properties
* Typo footnote_dust.tex
* Update parameter file README (#136)
* Update parameter file README
* Mention pdf doco
* Check each halo type for valid properties (#137)
* Have central's HostHaloIndex point to themselves (#138)
* Allow for different alias for snipshots (#139)
* Adding a number of extra properties (#141)
* Add dust properties
* Add stellar CoM
* Update test
* Minor name update
* Remove references to centre of potential (#143)
* Calculate SOAP index of progenitor/descendant (#142)
* Small refactor
* Don't update skipped SOAP properties
* Format
* Calculate and store progenitor/descendant indices
* Update handling of named columns
* Format
* Add footnote
* Calculate fof radii (#144)
* Script v1
* Create files across ranks
* Update docs
* Create virtual file
* Use relative paths
* Format
* Add test
* Use absolute positions
* Proper no wrap
* FOF radii
* Update SOAP to read new values
* Add half-light radii for each GAMA band. (#145)
* Defined new half light radii property
* Copied get_half_mass_radius to start implementing luminosity weighting.
* Create general function to find radius enclosing half of a given quantity
* Defined half light radius.
* Fix a couple of bugs.
* Script to obtain the SOAP property evolution for specified HBT-HERONS subhaloes (#146)
* Add script
* Fix redshift saving in HDF5
* Update misc README.md
* Make the script load the TrackIds and properties from a text file.
* Fixing typos
* Skip assert check for ranks with no subhalos (#148)
* Luminosity-weighted angular momenta and inertia tensors (#135)
* Add shorthand to obtain grik luminosities.
* Add basic functions to measure disc to total luminosity in different bands.
* Make new properties not be computed by default
* Add call of unimplemented function that computes light weighted L quantities.
* Define function for luminosity weighted L quantities. Not implemented for now.
* Add docs on parameters for get_angular_momentum_and_kappa_corot_luminosity_weighted
* Make kappa_corot and counterotating mass give a value per GAMMA band
* Add counterrotating luminosity array
* Handle multiple luminosity bands when computing average angular momentum
* Compute projected angular momentum if we do_counterrot_luminosity
* We now compute if stars are counterrotating or not for each luminosity band.
Expanded description of unyt array shapes to keep track in each step.
* fix typo
* Basic implementation done.
* Add correct return and remove NotImplemented error
* Change variables assigned to subhaloes to prevent overwritting mass-weighted calculations
* Only return a single property, which includes all GAMMA bands.
* Return a mass and light-based D/T.
* Add kappa_corot for luminosity bands
* change variable name
* Add property to save all luminosity-weighted angular momentum
* Add property definition in the Aperture properties
* Added new properties to the property table
* Add properties to the subhalo properties parameter file of COLIBRE
* Remove lazy properties that were not needed anymore
* Update docstring
* Add luminosity-weighted angular momenta to bound subhalo properties
* Add properties to the ApertureProperties parameter file section
* Change output expected type
* Change condition to execute new properties.
Mainly because of an annoying inconsistent between how starless subhaloes are handled. Mstar = 0 but Luminosities = None.
* Fix some indicies and if condition
* Add important clarification
* Fix bug in kappa_corot definition.
* Formatting alignment
* Add luminosity-weighted quantities to SO apertures
* Clarification comment
* Individual angular momentum for particles is now correct for kinetic energy calculation
* Fix GAMA typo
* Remove mass term form average angular momentum
we keep it in the individual particle angular momentum to obtain the kinetic energy in rotation.
* Create copy of inertia tensor to implement luminosity weighting
* Update description and inputs of inertia tensor
* Mask luminosities if we mask other properties
* Add comment...
* Create correct shape for eigenval and eigenvec matricies
* Shapes for each luminosity band
* Add stopping criteria on a per band basis
* Define the luminosity-weighted inertia tensor for BoundSubhalos
* Compute particle positions for each band.
Perhaps unneccessary since they will have the same positions in every band... Check how to improve later on.
* Update break condition to be done on a luminosity band basis
* Assign luminosity-based weights
* is_converged is now a boolean array
* Remove comment that was already addressed
* Tensor for each band done.
Still need to check if it gives me the correct element ordering relative to the default calculation of the inertia tensor.
* Re-add removed calculation of inertia tensor eigenvalue/vectors
* Create variable to hold the number of provided luminosity bands
* Return flattened matricies for each band
* Remove bug in stopping criteria for iterative tensor
* Added missing np.abs() call
It was causing the new function to stop iterating early
* Add import of new function
* Fix to prevent overflows into negative values for eigenvectors of inertia tensor
* Defined luminosity weighted projected inertia tensor
* Add call to luminosity-weighted function (undefined yet)
* Define luminosity weighted function and pass luminosity arrays.
* Correct typo from main branch
* Finish implementation of get_projected_inertia_tensor_luminosity_weighted.
Directly taken from 3D inertia calculations. Will likely need some restructuring.
* Fix incorrect comment statement
* Bug: using 3D positions instead of projected...
* Change location of axis ratio transpose
* Handle q = 0 values when testing convergence.
* Handle 0 / 0 division.
* Make q be an array from the get go
* Only compute tensors for non converged bands
* Do not rely on disabling warnings to handle q = 0 cases.
* Make q = 0 tensors to have all matrix entries to be equal to 0.
* Formatting
* Update variable names and parameter files
* Make get_inertia_tensor_luminosity_weighted only do computations for non-converged bands
More similar to get_projected_inertia_tensor_luminosity_weighted
* Fix issue resulting from merging
* Make 3D inertia tensors general
* Fix typo en error message
* Make mass-weighted inertia tensor more self-evident
* Make projected inertia tensors general
* Two bugs: incorrect function call and units in reduced tensors
* Move inertia tensor functions into their own file
* Fix unyt array initialisation to specify unit registry
* Generalise kappa_corot
* Shorten the description of helper functions
* Update colibre test
* Reformat
* Add note on single particle
* Remove questions
---------
Co-authored-by: robjmcgibbon <[email protected]>
* Full SOAP EAGLE catalogues (#150)
* Add more EAGLE snapshot properties
* Add script to approximate H fractions
* Use proper index for SOAP EAGLE
* Update scripts
* Squash bugs
* Define apertures based on BoundSubhalo properties (#147)
* Add note on timing flags
* Allow for property defined apertures
* Add error messages if required radii are disabled
* Missing method
* Update pdf documentation
* Add massive halos for testing
* Format
* Add contribution guide (#151)
* JOSS - Stuart comments 1 (#154)
* Merge fof position test
* Update docs
* Add project scripts & fix tests
* Format
* Add venv script for strw
* Rerun pdf generation
* Update README.md
* Match subhalos using membership files (#156)
* Backbone broken
* Fix test in calculate_fof_pos
* Run matching
* Match to SOAP idx
* Check matches are consistent
* Output to file
* Squash bug when saving
* Update docs
* Centrals only
* Update README
* Add __main__
* Run formatter
* Require astropy >= 6
* Update README
* Generate pdf with all properties
* Set lower limit on dust mass fractions (#158)
* Set lower limit
* Format
* Add DM CoM (#159)
* Add sbatch script for calculating FoF radii (#162)
* Add sbatch script for FOF radii
* Skip assert for ranks with no halos
* Nicer check
* Read new names if present (#163)
* Add workflow to check code is formatted (#165)
* Add format workflow
* Add --check
* Run formatter
* COLIBRE core excision (#167)
* Exclude COLIBRE core
* HalfMassRadii H
* Binding energies and Vmax calculations (#132)
* Read binding energy from HBT
* Output TotalBindingEnergy
* Vmax for aperture properties
* Squash bug and format
* Stop ranks hanging when reading binding energy
* Read SnapshotIndexOfLastIsolation
* Read in potential energy instead of binding
* Remove duplicate line
* Use vCoM from all particles
* Move subhalo_properties check for Ntot
* Update COLIBRE test
* Remove Ntot warning
* Add documentation of SpecificPotentialEnergies
* Add parameter file option to read energy
* Review changes
* Editorial changes (#171)
* Editorial changes.
* Update paper.bib
* A couple of more changes
* Update title capitalization
* Set read_potential_energy default to false
* Add more references
* Read sorted HBT (#172)
* Add script to recalculate COLIBRE FOF (#166)
* Add sbatch script for FOF radii
* Skip assert for ranks with no halos
* Nicer check
* More logging
* Add option to copy datasets
* Add node requirements
---------
Co-authored-by: Victor J. Forouhar Moreno <[email protected]>
Co-authored-by: Ivelina Momcheva <[email protected]>1 parent ef559e3 commit ed2c8ff
File tree
178 files changed
+18331
-11194
lines changed- .github/workflows
- SOAP
- catalogue_readers
- core
- particle_filter
- particle_selection
- property_calculation
- compression
- documentation
- joss_paper
- misc
- parameter_files
- scripts
- COLIBRE
- FLAMINGO
- L1000N0900
- L1000N1800
- L1000N3600
- L5600N5040
- tests
- COLIBRE
- FLAMINGO
- generate_test_data
Some content is hidden
Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.
178 files changed
+18331
-11194
lines changed| Original file line number | Diff line number | Diff line change | |
|---|---|---|---|
| |||
| 1 | + | |
| 2 | + | |
| 3 | + | |
| 4 | + | |
| 5 | + | |
| 6 | + | |
| 7 | + | |
| 8 | + | |
| 9 | + | |
| 10 | + | |
| 11 | + | |
| 12 | + | |
| 13 | + | |
| 14 | + | |
| 15 | + | |
| 16 | + | |
| 17 | + | |
| 18 | + | |
| 19 | + | |
| 20 | + | |
| 21 | + | |
| 22 | + | |
| 23 | + | |
| 24 | + | |
| 25 | + | |
| 26 | + | |
| 27 | + | |
| 28 | + | |
| 29 | + | |
| 30 | + | |
| Original file line number | Diff line number | Diff line change | |
|---|---|---|---|
| |||
2 | 2 | | |
3 | 3 | | |
4 | 4 | | |
| 5 | + | |
| 6 | + | |
5 | 7 | | |
6 | 8 | | |
7 | 9 | | |
| |||
16 | 18 | | |
17 | 19 | | |
18 | 20 | | |
| 21 | + | |
| 22 | + | |
| Original file line number | Diff line number | Diff line change | |
|---|---|---|---|
| |||
| 1 | + | |
| 2 | + | |
| 3 | + | |
| 4 | + | |
| 5 | + | |
| 6 | + | |
| 7 | + | |
| 8 | + | |
| 9 | + | |
| 10 | + | |
| 11 | + | |
| 12 | + | |
| 13 | + | |
| 14 | + | |
| 15 | + | |
| 16 | + | |
| 17 | + | |
| 18 | + | |
| 19 | + | |
| 20 | + | |
| 21 | + | |
| 22 | + | |
| 23 | + | |
| 24 | + | |
| 25 | + | |
| 26 | + | |
| 27 | + | |
| 28 | + | |
| 29 | + | |
| 30 | + | |
| 31 | + | |
| 32 | + | |
| 33 | + | |
| 34 | + | |
| 35 | + | |
| 36 | + | |
| 37 | + | |
| 38 | + | |
| 39 | + | |
| 40 | + | |
| 41 | + | |
| 42 | + | |
| 43 | + | |
| 44 | + | |
| 45 | + | |
| 46 | + | |
| 47 | + | |
| 48 | + | |
| 49 | + | |
| 50 | + | |
| 51 | + | |
| 52 | + | |
| 53 | + | |
| 54 | + | |
| 55 | + | |
| 56 | + | |
| 57 | + | |
| 58 | + | |
| 59 | + | |
| 60 | + | |
| 61 | + | |
| 62 | + | |
| 63 | + | |
| 64 | + | |
| 65 | + | |
| 66 | + | |
| 67 | + | |
0 commit comments