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Update evaluate density scripts (#105)

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* Edit docs

* Updated interpolated field paths

* Update field sampling script

* Add comments about flipping fields

* Fix little typo

* Edit docs

* Edit hard-coded values

* Fix paths issue

* Add docs

* Switch uncorrected dist to corrected

* Improve error message

* Convert numpy int to Python int

* Add flip of x and z

* Update README

* Edit README

* Fix bug in velocity field calculation

* Fix simple bug

* Add checked axes flipping

* Fix field units

* Update README
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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 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.
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.
## Ongoing projects
### 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.
### Enviromental dependence of galaxy properties
- [ ] Calculate the SPH density field for CSiBORG1.
- [x] Check that the velocity-field flipping of x and z coordinates is correct.
- [ ] Evaluate and share the density field for SDSS & 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*
## TODO
- [x] Prune old CSiBORG1 merger tree things.
- [x] Add visualiastion of the density field.
- [ ] Clear out `density` support.
- [ ] Add sorting of Gadget4 initial snapshot like final snapshot.
- [ ] Add full support for CSiBORG2 suite of simulations.
- [ ] Add SPH field calculation from cosmotools.
### 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.
## Adding a new simulation suite
### Effect of small-scale noise
- [ ] Study how the small-scale noise variation affects the overlap measure, halo concentration and spin.
box units
paths
readsim
halo_cat
### Gravitational-wave and large-scale structure
- [ ] 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.
### CSiBORG advertising
- [ ] Decide on the webpage design and what to store there.
- [ ] Write a short letter describing the simulations.