Overlap fixing and more (#107)

* Update README

* Update density field reader

* Update name of SDSSxALFAFA

* Fix quick bug

* Add little fixes

* Update README

* Put back fit_init

* Add paths to initial snapshots

* Add export

* Remove some choices

* Edit README

* Add Jens' comments

* Organize imports

* Rename snapshot

* Add additional print statement

* Add paths to initial snapshots

* Add masses to the initial files

* Add normalization

* Edit README

* Update README

* Fix bug in CSiBORG1 so that does not read fof_00001

* Edit README

* Edit README

* Overwrite comments

* Add paths to init lag

* Fix Quijote path

* Add lagpatch

* Edit submits

* Update README

* Fix numpy int problem

* Update README

* Add a flag to keep the snapshots open when fitting

* Add a flag to keep snapshots open

* Comment out some path issue

* Keep snapshots open

* Access directly snasphot

* Add lagpatch for CSiBORG2

* Add treatment of x-z coordinates flipping

* Add radial velocity field loader

* Update README

* Add lagpatch to Quijote

* Fix typo

* Add setter

* Fix typo

* Update README

* Add output halo cat as ASCII

* Add import

* Add halo plot

* Update README

* Add evaluating field at radial distanfe

* Add field shell evaluation

* Add enclosed mass computation

* Add BORG2 import

* Add BORG boxsize

* Add BORG paths

* Edit run

* Add BORG2 overdensity field

* Add bulk flow clauclation

* Update README

* Add new plots

* Add nbs

* Edit paper

* Update plotting

* Fix overlap paths to contain simname

* Add normalization of positions

* Add default paths to CSiBORG1

* Add overlap path simname

* Fix little things

* Add CSiBORG2 catalogue

* Update README

* Add import

* Add TNG density field constructor

* Add TNG density

* Add draft of calculating BORG ACL

* Fix bug

* Add ACL of enclosed density

* Add nmean acl

* Add galaxy bias calculation

* Add BORG acl notebook

* Add enclosed mass calculation

* Add TNG300-1 dir

* Add TNG300 and BORG1 dir

* Update nb

README.md

@@ -4,24 +4,37 @@ Tools for analysing the suite of Constrained Simulations in BORG (CSiBORG) simul
 
 ## 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.
-- [ ] Improve the storage system for overlaps and calculate it for all simulations.
+- [ ] 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
-- [ ] Prepare the CSiBORG one particle files for SPH.
+- [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.
-- [ ] Check and verify the density field of galaxy colours (cannot do this now! Glamdring is super slow.)
-
-#### Calculated data
-##### 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
+- [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
@@ -33,13 +46,35 @@ Tools for analysing the suite of Constrained Simulations in BORG (CSiBORG) simul
 
 ### 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
-- [ ] Make available one example snapshot from the simulation. Mention the issue with x- and z-coordinates.
+- [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*