Tags: SWIFTSIM/SOAP
Tags
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]>