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README.md

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 # CSiBORG Tools
 
-Tools for analysing the suite of Constrained Simulations in BORG (CSiBORG) simulations. The interface is designed to work with the following suites of simulations: *CSiBORG1* (dark matter-only RAMSES), *CSiBORG2* (dark matter-only Gadget4), *Quijote* (dark-matter only Gadget2), however with little effort it can support other simulations as well.
+Tools for analysing constrained cosmological simulations.
 
 
 ## TODO
-- [ ] In flow models test in a script that indeed the parallelization is working.
+- [ ] Remove Gaussian priors and switch to uniform. Can the beta preference be a volume effect?
-- [ ] Extend the parallelization to supernovae/simple distances.
+- [ ] Verify the effects of resolution (compare how Carrick worsens) and what happens to the LG velocity.
-
-## Ongoing projects
-
-### Data to calculate
-- [x] Process all CSiBORG1 snapshots (running).
-- [ ] Calculate halo properties for CSiBORG1
-- [x] Calculate initial properties for CSiBORG1
-- [ ] Calculate halo properties for CSiBORG2
-- [x] Calculate initial properties for CSiBORG2
-- [ ] Process all Quijote simulations.
-- [ ] Calculate halo properties for Quijote
-- [ ] Calculate initial properties for Quijote
-
-
-### General
-- [ ] Add new halo properties to the catalogues.
-- [x] Add initial halo properties to the catalogues.
-- [x] Add a new flag for flipping x- and z-coordinates fro catalogues, snapshots and field readers.
-- [x] Add radial velocity field loader.
-
-### Consistent halo reconstruction
-- [ ] Make a sketch of the overlap definition and add it to the paper.
-- [ ] Re-calculate the overlaps for CSiBORG1, Quijote and CSiBORG2
-- [x] Fix the script to calculate the initial lagrangian positions etc.
-
-### Enviromental dependence of galaxy properties
-- [x] Prepare the CSiBORG one particle files for SPH.
-- [ ] Transfer, calculate the SPH density field for CSiBORG1 and transfer back.
-- [x] Check that the velocity-field flipping of x and z coordinates is correct.
-- [x] Evaluate and share the density field for SDSS and SDSSxALFALFA for both CSiBORG2 and random fields.
-- [x] Check and verify the density field of galaxy colours (cannot do this now! Glamdring is super slow.)
-- [x] Calculate the radial velocity field for random realizations (submitted)
-- [x] Send Catherine concatenated data.
-- [ ] Start analyzing DiSPERSE results.
-
-
-### Mass-assembly of massive clusters
-- [ ] Make a list of nearby most-massive clusters.
-- [ ] Write code to identify a counterpart of such clusters.
-- [ ] Write code to make a plot of mass-assembly of all clusters within a certain mass range from the random simulations.
-- [ ] Write code to compare mass-assembly of a specific cluster with respect to random ones.
-
-
-### Effect of small-scale noise
-- [ ] Study how the small-scale noise variation affects the overlap measure, halo concentration and spin.
-- [ ] Add uncertainty on the halo concentration.
-
-### Gravitational-wave and large-scale structure
-- [ ] Validate the velocity field results agains Supranta data sets.
-- [x] Write code to estimate the enclosed mass and bulk flow.
-- [ ] Write code to estimate the average radial velocity in a spherical shell.
-- [ ] Write code to calculate the power spectrum of velocities.
-- [ ] Estimate the amplitude of the velocity field in radial shells around the observer, estimate analogous results for random simulations, and see if they agree within cosmic variance.
-- [ ] Calculate power spectra of velocities and maybe velocity dispersion.
-- [ ] Make the velocity field data available.
-
-
-### CSiBORG meets X-ray
-- [x] Make available one example snapshot from the simulation. Mention the issue with x- and z-coordinates.
-- [ ] Answer Johan and make a comparison to the Planck clusters.
-
-### CSiBORG advertising
-- [ ] Decide on the webpage design and what to store there.
-- [ ] Write a short letter describing the simulations.
-
-
-### Calculated data
-
-#### Enclosed mass & bulk velocity
-- *CSiBORG2_main*, *CSiBORG2_varysmall*, *CSiBORG2_arandom*
-
-#### SPH-density & velocity field
-- *CSiBORG2_main*, *CSiBORG2_random*, *CSiBORG2_varysmall*
-- Evaluated for SDSS and SDSSxALFALFA in: *CSiBORG2_main*, *CSiBORG2_random*
-
-#### Radial velocity field
-- *CSiBORG2_main, *CSiBORG2_random*