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

csiborgtools/io/__init__.py

@@ -17,6 +17,7 @@ from .readsim import (get_csiborg_ids, get_sim_path, get_snapshots,  # noqa
                       get_snapshot_path, read_info, nparts_to_start_ind,  # noqa
                       open_particle, open_unbinding, read_particle,  # noqa
                       drop_zero_indx,  # noqa
-                      read_clumpid, read_clumps, read_mmain)  # noqa
+                      read_clumpid, read_clumps, read_mmain,  # noqa
+                      merge_mmain_to_clumps)  # noqa
 from .readobs import (read_planck2015, read_2mpp)  # noqa
 from .outsim import (dump_split, combine_splits)  # noqa

csiborgtools/io/outsim.py

@@ -85,9 +85,6 @@ def combine_splits(Nsplits, Nsim, Nsnap, outdir, cols_add, remove_splits=False,
     out : structured array
         Clump array with appended results from the splits.
     """
-    # Will be grabbing these columns from each split
-    cols_add = [("npart", I64), ("totpartmass", F64), ("logRs", F64),
-                ("rho0", F64)]
     # Load clumps to see how many there are and will add to this array
     simpath = get_sim_path(Nsim)
     clumps = read_clumps(Nsnap, simpath, cols=None)

csiborgtools/io/readsim.py

@@ -23,7 +23,7 @@ from os.path import (join, isfile)
 from glob import glob
 from tqdm import tqdm
 
-from ..utils import cols_to_structured
+from ..utils import (cols_to_structured, add_columns)
 
 
 F16 = numpy.float16
@@ -495,3 +495,30 @@ def read_mmain(n, srcdir, fname="Mmain_{}.npy"):
         out[name] = arr[:, i]
 
     return out
+
+
+def merge_mmain_to_clumps(clumps, mmain):
+    """
+    Merge columns from the `mmain` files to the `clump` file, matches them
+    by their halo index while assuming that the indices `index` in both arrays
+    are sorted.
+
+    Parameters
+    ----------
+    clumps : structured array
+        Clumps structured array.
+    mmain : structured array
+        Parent halo array whose information is to be merged into `clumps`.
+
+    Returns
+    -------
+    out : structured array
+        Array with added columns.
+    """
+    X = numpy.full((clumps.size, 2), numpy.nan)
+    # Mask of which clumps have a mmain index
+    mask = numpy.isin(clumps["index"], mmain["index"])
+
+    X[mask, 0] = mmain["mass_cl"]
+    X[mask, 1] = mmain["sub_frac"]
+    return add_columns(clumps, X, ["mass_mmain", "sub_frac"])