csiborgtools/README.md

# 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 simulations (full support),
- CSiBORG2 dark matter-only Gadget4 simulations (planned full support),
- Quijote dark matter-only Gadget2 simulations (partial support),
however with little effort it can support other simulations as well.


## TODO
- [x] Prune old CSiBORG1 merger tree things.
- [ ] Add visualiastion of the density field.
- [ ] Add full support for CSiBORG2 suite of simulations.
- [ ] Add SPH field calculation from cosmotools.


## Adding a new simulation suite

box units
paths
readsim
halo_cat
Add README 2023-05-14 11:48:18 +00:00			`# CSiBORG Tools`

Add pynbody and other support (#92) * Simplify box units * Move old scripts * Add printing * Update readers * Disable boundscheck * Add new ordering * Clean up imports * Enforce dtype and add mass to quijote * Simplify print statements * Fix little typos * Fix key bug * Bug fixing * Delete boring comments * Improve ultimate clumps for PHEW * Delete boring comments * Add basic reading * Remove 0th index HID * Add flipping of X and Z * Updates to halo catalogues * Add ordered caching * Fix flipping * Add new flags * Fix PHEW empty clumps * Stop over-wrriting * Little improvements to angular neighbours * Add catalogue masking * Change if-else statements * Cache only filtered data * Add PHEW cats * Add comments * Sort imports * Get Quijote workign * Docs * Add HMF calculation * Move to old * Fix angular * Add great circle distance * Update imports * Update impotrts * Update docs * Remove unused import * Fix a quick bug * Update compatibility * Rename files * Renaming * Improve compatiblity * Rename snapsht * Fix snapshot bug * Update interface * Finish updating interface * Update all paths * Add old scripts * Add basic halo * Update imports * Improve snapshot processing * Update ordering * Fix how CM positions accessed * Add merger paths * Add imports * Add merger reading * Add making a merger tree * Add a basic merger tree reader * Add imports * Add main branch walking + comments + debuggin * Get tree running * Add working merger tree walking along main branch * Add units conversion for merger data * Add hid_to_array_index * Update merger tree * Add mergertree mass to PHEWcat * Edit comments * Add this to track changes... * Fix a little bug * Add mergertree mass * Add cache clearing * Improve summing substructure code * Littbe bug * Little updates to the merger tree reader * Update .giignore * Add box selection * Add optional deletingf of a group * add to keep track of changes * Update changes * Remove * Add manual tracker * Fix bug * Add m200c_to_r200c * Add manual halo tracking * Remove skipped snapshots * update cosmo params to match csiborg * remove old comments * Add SDSSxALFALFA * Fix bugs * Rename * Edit paths * Updates * Add comments * Add comment * Add hour conversion * Add imports * Add new observation class * Add selection * Add imports * Fix small bug * Add field copying for safety * Add matching to survey without masking * Add P(k) calculation * Add nb * Edit comment * Move files * Remove merger import * Edit setup.yp * Fix typo * Edit import warnigns * update nb * Update README * Update README * Update README * Add skeleton * Add skeleton 2023-12-07 14:23:32 +00:00			`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 simulations (full support),`
			`- CSiBORG2 dark matter-only Gadget4 simulations (planned full support),`
			`- Quijote dark matter-only Gadget2 simulations (partial support),`
			`however with little effort it can support other simulations as well.`


			`## TODO`
Remove old merger tree (#93) * Edit docs * Delete merger tree files * Edit README * Edit docs 2023-12-07 14:45:06 +00:00			`- [x] Prune old CSiBORG1 merger tree things.`
Update README 2023-12-08 12:41:02 +00:00			`- [ ] Add visualiastion of the density field.`
Add pynbody and other support (#92) * Simplify box units * Move old scripts * Add printing * Update readers * Disable boundscheck * Add new ordering * Clean up imports * Enforce dtype and add mass to quijote * Simplify print statements * Fix little typos * Fix key bug * Bug fixing * Delete boring comments * Improve ultimate clumps for PHEW * Delete boring comments * Add basic reading * Remove 0th index HID * Add flipping of X and Z * Updates to halo catalogues * Add ordered caching * Fix flipping * Add new flags * Fix PHEW empty clumps * Stop over-wrriting * Little improvements to angular neighbours * Add catalogue masking * Change if-else statements * Cache only filtered data * Add PHEW cats * Add comments * Sort imports * Get Quijote workign * Docs * Add HMF calculation * Move to old * Fix angular * Add great circle distance * Update imports * Update impotrts * Update docs * Remove unused import * Fix a quick bug * Update compatibility * Rename files * Renaming * Improve compatiblity * Rename snapsht * Fix snapshot bug * Update interface * Finish updating interface * Update all paths * Add old scripts * Add basic halo * Update imports * Improve snapshot processing * Update ordering * Fix how CM positions accessed * Add merger paths * Add imports * Add merger reading * Add making a merger tree * Add a basic merger tree reader * Add imports * Add main branch walking + comments + debuggin * Get tree running * Add working merger tree walking along main branch * Add units conversion for merger data * Add hid_to_array_index * Update merger tree * Add mergertree mass to PHEWcat * Edit comments * Add this to track changes... * Fix a little bug * Add mergertree mass * Add cache clearing * Improve summing substructure code * Littbe bug * Little updates to the merger tree reader * Update .giignore * Add box selection * Add optional deletingf of a group * add to keep track of changes * Update changes * Remove * Add manual tracker * Fix bug * Add m200c_to_r200c * Add manual halo tracking * Remove skipped snapshots * update cosmo params to match csiborg * remove old comments * Add SDSSxALFALFA * Fix bugs * Rename * Edit paths * Updates * Add comments * Add comment * Add hour conversion * Add imports * Add new observation class * Add selection * Add imports * Fix small bug * Add field copying for safety * Add matching to survey without masking * Add P(k) calculation * Add nb * Edit comment * Move files * Remove merger import * Edit setup.yp * Fix typo * Edit import warnigns * update nb * Update README * Update README * Update README * Add skeleton * Add skeleton 2023-12-07 14:23:32 +00:00			`- [ ] Add full support for CSiBORG2 suite of simulations.`
			`- [ ] Add SPH field calculation from cosmotools.`


			`## Adding a new simulation suite`

			`box units`
			`paths`
			`readsim`
			`halo_cat`