Update units to be consistent. (#78)

* Fix Quijote units

* Updates to units

* Fix how things are loaded

* Updating definitions & conventions

* Clear up how fiducial observers in quijote work

* Refactorize array manip

* Move function definition

* More code refactoring

* Remove unused argument

* Remove `convert_from_box`

* Make a note

* Converting particle units

* Add notes about units

* Remove box constants

* Add rho_crit0

* Fix spherical overdensity mass units

* Refactor more code

* Edit catalogue kwargs

* Edit the docstring

* Edit bounds

* Add new checks for empty array

* Remove unused import

* Remove old code

* Remove old function

* Update real 2 redshift

* Clear up the RSP conv

* Add comments

* Add some units

scripts/fit_halos.py

@@ -99,12 +99,12 @@ def _main(nsim, simname, verbose):
     if simname == "csiborg":
         box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
         cat = csiborgtools.read.CSiBORGHaloCatalogue(
-            nsim, paths, with_lagpatch=False, load_initial=False, rawdata=True,
-            load_fitted=False)
+            nsim, paths, bounds=None, load_fitted=False, load_initial=False)
     else:
         box = csiborgtools.read.QuijoteBox(nsnap, nsim, paths)
         cat = csiborgtools.read.QuijoteHaloCatalogue(
-            nsim, paths, nsnap, load_initial=False, rawdata=True)
+            nsim, paths, nsnap, bounds=None, load_fitted=False,
+            load_initial=False)
 
     # Particle archive
     f = csiborgtools.read.read_h5(paths.particles(nsim, simname))
@@ -116,6 +116,7 @@ def _main(nsim, simname, verbose):
     for i in trange(len(cat)) if verbose else range(len(cat)):
         hid = cat["index"][i]
         out["index"][i] = hid
+        # print("i = ", i)
         part = csiborgtools.read.load_halo_particles(hid, particles, halo_map,
                                                      hid2map)
         # Skip if no particles.

scripts/fit_hmf.py

@@ -59,12 +59,12 @@ def get_counts(nsim, bins, paths, parser_args):
 
     if simname == "csiborg":
         cat = csiborgtools.read.CSiBORGHaloCatalogue(
-            nsim, paths, bounds=bounds, with_lagpatch=False,
-            load_initial=False)
+            nsim, paths, bounds=bounds, load_initial=False)
         logmass = numpy.log10(cat["totpartmass"])
         counts = csiborgtools.fits.number_counts(logmass, bins)
     elif simname == "quijote":
-        cat0 = csiborgtools.read.QuijoteHaloCatalogue(nsim, paths, nsnap=4)
+        cat0 = csiborgtools.read.QuijoteHaloCatalogue(nsim, paths, nsnap=4,
+                                                      load_initial=False)
         nmax = int(cat0.box.boxsize // (2 * parser_args.Rmax))**3
         counts = numpy.full((nmax, len(bins) - 1), numpy.nan,
                             dtype=numpy.float32)
@@ -74,7 +74,8 @@ def get_counts(nsim, bins, paths, parser_args):
             logmass = numpy.log10(cat["group_mass"])
             counts[nobs, :] = csiborgtools.fits.number_counts(logmass, bins)
     elif simname == "quijote_full":
-        cat = csiborgtools.read.QuijoteHaloCatalogue(nsim, paths, nsnap=4)
+        cat = csiborgtools.read.QuijoteHaloCatalogue(nsim, paths, nsnap=4,
+                                                     load_initial=False)
         logmass = numpy.log10(cat["group_mass"])
         counts = csiborgtools.fits.number_counts(logmass, bins)
     else:

scripts/fit_init.py

@@ -68,7 +68,8 @@ def _main(nsim, simname, verbose):
         cat = csiborgtools.read.CSiBORGHaloCatalogue(
             nsim, paths, rawdata=True, load_fitted=False, load_initial=False)
     else:
-        cat = csiborgtools.read.QuijoteHaloCatalogue(nsim, paths, nsnap=4)
+        cat = csiborgtools.read.QuijoteHaloCatalogue(
+            nsim, paths, nsnap=4, load_fitted=False, load_initial=False)
     hid2map = {hid: i for i, hid in enumerate(halo_map[:, 0])}
 
     # Initialise the overlapper.

scripts/pre_dumppart.py

@@ -11,11 +11,16 @@
 # You should have received a copy of the GNU General Public License along
 # with this program; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
-"""
+r"""
 Script to load in the simulation particles, sort them by their FoF halo ID and
 dump into a HDF5 file. Stores the first and last index of each halo in the
 particle array. This can be used for fast slicing of the array to acces
 particles of a single clump.
+
+Ensures the following units:
+    - Positions in box units.
+    - Velocities in :math:`\mathrm{km} / \mathrm{s}`.
+    - Masses in :math:`M_\odot / h`.
 """
 from argparse import ArgumentParser
 from datetime import datetime
@@ -118,6 +123,14 @@ def main(nsim, simname, verbose):
         pars_extract = None
     parts, pids = partreader.read_particle(
         nsnap, nsim, pars_extract, return_structured=False, verbose=verbose)
+
+    # In case of CSiBORG, we need to convert the mass and velocities from
+    # box units.
+    if simname == "csiborg":
+        box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
+        parts[:, [3, 4, 5]] = box.box2vel(parts[:, [3, 4, 5]])
+        parts[:, 6] = box.box2solarmass(parts[:, 6])
+
     # Now we in two steps save the particles and particle IDs.
     if verbose:
         print(f"{datetime.now()}: dumping particles from {nsim}.", flush=True)

scripts/pre_sortinit.py

@@ -12,9 +12,13 @@
 # You should have received a copy of the GNU General Public License along
 # with this program; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
-"""
+r"""
 Script to sort the initial snapshot particles according to their final
 snapshot ordering, which is sorted by the halo IDs.
+
+Ensures the following units:
+    - Positions in box units.
+    - Masses in :math:`M_\odot / h`.
 """
 from argparse import ArgumentParser
 from datetime import datetime
@@ -75,6 +79,13 @@ def _main(nsim, simname, verbose):
         nsnap = -1
     part0, pid0 = partreader.read_particle(
         nsnap, nsim, pars_extract, return_structured=False, verbose=verbose)
+
+    # In CSiBORG we need to convert particle masses from box units.
+    if simname == "csiborg":
+        box = csiborgtools.read.CSiBORGBox(
+            max(paths.get_snapshots(nsim, simname)), nsim, paths)
+        part0[:, 3] = box.box2solarmass(part0[:, 3])
+
     # Quijote's initial snapshot information also contains velocities but we
     # don't need those.
     if simname == "quijote":

scripts/utils.py

@@ -89,9 +89,13 @@ def read_single_catalogue(args, config, nsim, run, rmax, paths, nobs=None):
         raise KeyError(f"No configuration for run {run}.")
     # We first read the full catalogue without applying any bounds.
     if args.simname == "csiborg":
-        cat = csiborgtools.read.CSiBORGHaloCatalogue(nsim, paths)
+        cat = csiborgtools.read.CSiBORGHaloCatalogue(
+            nsim, paths, load_fitted=True, load_inital=True,
+            with_lagpatch=False)
     else:
-        cat = csiborgtools.read.QuijoteHaloCatalogue(nsim, paths, nsnap=4)
+        cat = csiborgtools.read.QuijoteHaloCatalogue(
+            nsim, paths, nsnap=4, load_fitted=True, load_initial=True,
+            with_lagpatch=False)
         if nobs is not None:
             # We may optionally already here pick a fiducial observer.
             cat = cat.pick_fiducial_observer(nobs, args.Rmax)