JAX and fix conc (#6)

* change to log10 initlogRs

* add uncertainty

* add check if hessian negative

* update TODO

* update TODO

* output the error too

* save e_logRs

* add concentration calculation

* calcul concentration

* missed comma in a list

* Update TODO

* fix bug

* add box units and pretty status

* make uncertainty optional

* add BIC function

* remove BIC again

* add new overdensity calculation

* change defualt values to max dist and mass

* change to r200

* new halo find

* speed up the calculation

* add commented fucn

* update TODO

* add check whether too close to outside boundary

* Update TODO

* extract velocity as well

* calculate m200 and m500

* update nb

* update TODO

README.md

@@ -1,11 +1,12 @@
 # CSiBORG tools
 
 ## :scroll: Short-term TODO
-- [x] Calculate $M_{\rm vir}, R_{\rm vir}, c$ from $R_s, \rho_0, \ldots$
-- [x] In `NFWPosterior` correct for the radius in which particles are fitted.
-- [x] Calculate $M_{\rm 500c}$ by sphere shrinking
-- [x] Change to log10 of the scale factor
-- [ ] Calculate uncertainty on $R_{\rm s}$, switch to `JAX` and get gradients.
+- [ ] Calculate mass functions
+- [ ] Add functions for converting the output file to box units.
+- [ ] Calculate catalogues for all realisations.
+- [x] Verify the bulk flow of particles and the clump
+- [x] Check why for some halos $M_{500c} > M_{200c}$
+
 
 
 ## :hourglass: Long-term TODO
@@ -13,4 +14,5 @@
 - [ ] Calculate the cross-correlation in CSiBORG. Should see the scale of the constraints?
 
 
-## :bulb: Open questions
+## :bulb: Open questions
+- Propagate uncertainty of $\log R_{\rm s}$ to concentration