csiborgtools/README.md

# CSiBORG tools

## :scroll: Short-term TODO
- [ ] 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
- [ ] Improve file naming system
- [ ] Calculate the cross-correlation in CSiBORG. Should see the scale of the constraints?


## :bulb: Open questions
- Propagate uncertainty of $\log R_{\rm s}$ to concentration
Mass enclosed in a sphere calculation (#5) * rename nb * add merge func * rm bug.. * add static methods * save rmin, rmax * add properties for box units * move radial info to the clump * add Npart explicit * move where rmin, rmax obtained * add box cosmo * add __getattr__ * add comments in units * add enclosed spherical mass * rm unused variables * add clump mass setter * add the halo index * add enclosed overdensity * add enclosed_overdensity * simplify loss func * opt result to nan * change Rs to log10 * change back to attribs * add H0 and h props * add setattrs * Remove global constants * move Msuncgs above * add crit density * add dots * add r200c and r500c * add M200 and M500 * make lowercase * output r200, r500, m200, m500 * update TODO * update README * fit NFW only up to r200 * add r178, m178 * add m178, r178 * update TODO 2022-11-01 10:10:54 +00:00			`# CSiBORG tools`
Within halo work and NFW fit (#4) * add listing of snapshots * change distance to comoving * ignore cp files * rename nb * add str to list * add NFW profile shapes * add fits imports * Rename to Nsnap * in clumps_read only select props * make clumpid int * expand doc * add import * edit readme * distribute halos * add profile & posterior * add import * add import * add documentation * add rvs and init guess * update todo * update nb * add file * return end index too * change clump_ids format to int32 * skeleton of dump particle * update nb * add func to drop 0 clump indxs parts * add import * add halo dump * switch to float32 * Update TODO * update TODO * add func that loads a split * add halo object * Rename to clump * make post work with a clump * add optimiser * add Nsplits * ignore submission scripts * ignore .out * add dumppath * add job splitting * add split halos script * rename file * renaem files * rm file * rename imports * edit desc * add pick clump * add number of particles * update TODO * update todo * add script * add dumping * change dumpdir structure * change dumpdir * add import * Remove tqdm * Increase the number of splits * rm shuffle option * Change to remove split * add emojis * fix part counts in splits * change num of splits * rm with particle cut * keep splits * fit only if 10 part and more * add min distance * rm warning about not set vels * update TODO * calculate rho0 too * add results collection * add import * add func to combine splits * update TODO * add extract cols * update nb * update TODO 2022-10-30 20:16:56 +00:00
Mass enclosed in a sphere calculation (#5) * rename nb * add merge func * rm bug.. * add static methods * save rmin, rmax * add properties for box units * move radial info to the clump * add Npart explicit * move where rmin, rmax obtained * add box cosmo * add __getattr__ * add comments in units * add enclosed spherical mass * rm unused variables * add clump mass setter * add the halo index * add enclosed overdensity * add enclosed_overdensity * simplify loss func * opt result to nan * change Rs to log10 * change back to attribs * add H0 and h props * add setattrs * Remove global constants * move Msuncgs above * add crit density * add dots * add r200c and r500c * add M200 and M500 * make lowercase * output r200, r500, m200, m500 * update TODO * update README * fit NFW only up to r200 * add r178, m178 * add m178, r178 * update TODO 2022-11-01 10:10:54 +00:00			`## :scroll: Short-term TODO`
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 2022-11-05 21:17:05 +00:00			`- [ ] 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 $M_{500c} > M_{200c}$`

Mass enclosed in a sphere calculation (#5) * rename nb * add merge func * rm bug.. * add static methods * save rmin, rmax * add properties for box units * move radial info to the clump * add Npart explicit * move where rmin, rmax obtained * add box cosmo * add __getattr__ * add comments in units * add enclosed spherical mass * rm unused variables * add clump mass setter * add the halo index * add enclosed overdensity * add enclosed_overdensity * simplify loss func * opt result to nan * change Rs to log10 * change back to attribs * add H0 and h props * add setattrs * Remove global constants * move Msuncgs above * add crit density * add dots * add r200c and r500c * add M200 and M500 * make lowercase * output r200, r500, m200, m500 * update TODO * update README * fit NFW only up to r200 * add r178, m178 * add m178, r178 * update TODO 2022-11-01 10:10:54 +00:00

			`## :hourglass: Long-term TODO`
Update TODO 2022-10-30 20:21:48 +00:00			`- [ ] Improve file naming system`
Mass enclosed in a sphere calculation (#5) * rename nb * add merge func * rm bug.. * add static methods * save rmin, rmax * add properties for box units * move radial info to the clump * add Npart explicit * move where rmin, rmax obtained * add box cosmo * add __getattr__ * add comments in units * add enclosed spherical mass * rm unused variables * add clump mass setter * add the halo index * add enclosed overdensity * add enclosed_overdensity * simplify loss func * opt result to nan * change Rs to log10 * change back to attribs * add H0 and h props * add setattrs * Remove global constants * move Msuncgs above * add crit density * add dots * add r200c and r500c * add M200 and M500 * make lowercase * output r200, r500, m200, m500 * update TODO * update README * fit NFW only up to r200 * add r178, m178 * add m178, r178 * update TODO 2022-11-01 10:10:54 +00:00			`- [ ] Calculate the cross-correlation in CSiBORG. Should see the scale of the constraints?`
Within halo work and NFW fit (#4) * add listing of snapshots * change distance to comoving * ignore cp files * rename nb * add str to list * add NFW profile shapes * add fits imports * Rename to Nsnap * in clumps_read only select props * make clumpid int * expand doc * add import * edit readme * distribute halos * add profile & posterior * add import * add import * add documentation * add rvs and init guess * update todo * update nb * add file * return end index too * change clump_ids format to int32 * skeleton of dump particle * update nb * add func to drop 0 clump indxs parts * add import * add halo dump * switch to float32 * Update TODO * update TODO * add func that loads a split * add halo object * Rename to clump * make post work with a clump * add optimiser * add Nsplits * ignore submission scripts * ignore .out * add dumppath * add job splitting * add split halos script * rename file * renaem files * rm file * rename imports * edit desc * add pick clump * add number of particles * update TODO * update todo * add script * add dumping * change dumpdir structure * change dumpdir * add import * Remove tqdm * Increase the number of splits * rm shuffle option * Change to remove split * add emojis * fix part counts in splits * change num of splits * rm with particle cut * keep splits * fit only if 10 part and more * add min distance * rm warning about not set vels * update TODO * calculate rho0 too * add results collection * add import * add func to combine splits * update TODO * add extract cols * update nb * update TODO 2022-10-30 20:16:56 +00:00

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 2022-11-05 21:17:05 +00:00			`## :bulb: Open questions`
			`- Propagate uncertainty of $\log R_{\rm s}$ to concentration`