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Update sectors extractions scripts

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This commit is contained in:
Noe Brucy
2023-05-05 18:11:31 +02:00
parent 85cfd71b66
commit 946f11725e
3 changed files with 197 additions and 2 deletions
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7
galsec.py
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@@ -229,6 +229,7 @@ class Galsec:
A dataset of cells in the following format:
header:
time float [Myr] time since the start of the simulation
fluids str list list of fluids included
gas:
position float array (Ngas, 3) [kpc], centered
volume float array (Ngas) [pc^3]
@@ -251,6 +252,8 @@ class Galsec:
"""
self.data = {}
if "fluids" in data["header"]:
self.fluids = data["header"]["fluids"]
for fluid in self.fluids:
self.data[fluid] = QTable(data[fluid], units=self.units[fluid], copy=copy)
@@ -406,8 +409,8 @@ class Galsec:
filtered_data = self.data[fluid][
(self.data[fluid]["r"] > rmin)
& (self.data[fluid]["r"] < rmax)
& (self.data[fluid]["z"] > zmin)
& (self.data[fluid]["z"] < zmax)
& (self.data[fluid]["position"][:, 2] > zmin)
& (self.data[fluid]["position"][:, 2] < zmax)
]
grouped_data[fluid] = filtered_data.group_by(["r_bin"])
self.rings[fluid] = hstack(

84
sectors_extraction_arepo.py Normal file
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@@ -0,0 +1,84 @@
# coding: utf-8
import numpy as np
import h5py
from astropy import units as u
def load_fields(path):
"""
Parameters
----------
path : _type_
_description_
output : _type_
_description_
Returns
-------
dict
A dataset of cells in the following format:
gas:
position (Ngas, 3) [kpc], centered
volume (Ngas) [pc^3]
velocity (Ngas, 3) [km/s]
mass (Ngas) [Msun]
stars:
position (Nstar, 3) [kpc], centered
velocity (Nstar, 3) [km/s]
mass (Nstar) [Msun]
birth_time (Nstar) [Myr]
dm:
position (Ngas, 3) [kpc], centered
velocity (Ngas, 3) [km/s]
mass (Ngas) [Msun]
maps:
extent (xmin, xmax, ymin, ymax) Coordinates of the edges of the map, centered
gas_coldens (Nx, Ny) [Msun/pc^2], map of column density
"""
snap = h5py.File(path)
info = snap["Header"].attrs
gas = snap["PartType0"]
stars = snap["PartType4"]
time = info["Time"]
box_size = info["BoxSize"]
UnitLength_in_kpc = info["UnitLength_in_cm"] * u.cm.to(u.kpc)
UnitVelocity_in_km_per_s = info["UnitVelocity_in_cm_per_s"] * u.cm.to(u.km)
UnitTime_in_Myr = (
info["UnitLength_in_cm"] / info["UnitVelocity_in_cm_per_s"]
) * u.s.to(u.Myr)
UnitMass_in_Msun = info["UnitMass_in_g"] * u.g.to(u.Msun)
# Create dataset
data = {
"header": {"time": time * UnitTime_in_Myr, "fluids": ["gas", "stars"]},
"gas": {
"position": (
np.asarray(gas["CenterOfMass"]) - np.array([0.5, 0.5, 0.5]) * box_size
)
* UnitLength_in_kpc,
"volume": (np.asarray(gas["Masses"]) / np.asarray(gas["Density"]))
* UnitLength_in_kpc**3,
"velocity": np.asarray(gas["Velocities"]) * UnitVelocity_in_km_per_s,
"mass": np.asarray(gas["Masses"]) * UnitMass_in_Msun,
},
"stars": {
"position": (
np.asarray(stars["Coordinates"]) - np.array([0.5, 0.5, 0.5]) * box_size
)
* UnitLength_in_kpc,
"velocity": np.asarray(stars["Velocities"]) * UnitVelocity_in_km_per_s,
"mass": np.asarray(stars["Masses"]) * UnitMass_in_Msun,
"birth_time": np.asarray(stars["StellarFormationTime"]) * UnitTime_in_Myr,
},
}
return data
if __name__ == "__main__":
from snapshotprocessor import SnapshotProcessor
data = load_fields(
"/home/nbrucy/Travail/Postdoc/Ecogal/MW/junia2_0.25kpc/OUTPUT_SN/snap_150.hdf5"
)

108
sectors_extraction_ramses.py Normal file
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@@ -0,0 +1,108 @@
# coding: utf-8
import numpy as np
from snapshotprocessor import U
from tables import NoSuchNodeError
def load_fields(pp):
"""
Parameters
----------
path : _type_
_description_
output : _type_
_description_
Returns
-------
dict
A dataset of cells in the following format:
gas:
position (Ngas, 3) [kpc], centered
volume (Ngas) [pc^3]
velocity (Ngas, 3) [km/s]
mass (Ngas) [Msun]
stars:
position (Nstar, 3) [kpc], centered
velocity (Nstar, 3) [km/s]
mass (Nstar) [Msun]
birth_time (Nstar) [Myr]
dm:
position (Ngas, 3) [kpc], centered
velocity (Ngas, 3) [km/s]
mass (Ngas) [Msun]
maps:
extent (xmin, xmax, ymin, ymax) Coordinates of the edges of the map, centered
gas_coldens (Nx, Ny) [Msun/pc^2], map of column density
"""
# Load arrays
pp.load_cells(keys=["pos", "vel", "dx", "rho"])
try:
pp.load_parts(keys=["pos", "vel", "mass", "epoch"])
except (KeyError, NoSuchNodeError):
pp.load_parts(keys=["pos", "vel", "mass"])
cells = pp.cells
parts = pp.parts
if "epoch" not in parts:
parts["epoch"] = np.zeros(len(pp.parts["mass"]))
# Compute extra fields and convert units
for dset in (cells, parts):
dset["position"] = dset["pos"] - np.array([0.5, 0.5, 0.5])
cells["mass"] = (
cells["rho"]
* cells["dx"] ** 3
* (pp.info["unit_density"] * pp.info["unit_length"] ** 3).express(U.Msun)
)
cells["volume"] = cells["dx"] ** 3 * (pp.info["unit_length"] ** 3).express(
U.kpc**3
)
# Separate DM from stars
mass_dm = np.max(parts["mass"])
mask_dm = parts["mass"] == mass_dm
mask_star = parts["mass"] < mass_dm
# Create dataset
data = {
"header": {"time": pp.time * pp.info["unit_time"].express(U.Myr)},
"gas": {
"position": cells["position"] * pp.info["unit_length"].express(U.kpc),
"volume": cells["volume"],
"velocity": cells["vel"] * pp.info["unit_velocity"].express(U.km_s),
"mass": cells["mass"],
},
"stars": {
"position": parts["position"][mask_star]
* pp.info["unit_length"].express(U.kpc),
"velocity": parts["vel"][mask_star]
* pp.info["unit_velocity"].express(U.km_s),
"mass": parts["mass"][mask_star] * pp.info["unit_mass"].express(U.Msun),
"birth_time": parts["epoch"][mask_star]
* pp.info["unit_time"].express(U.Myr),
},
"dm": {
"position": parts["position"][mask_dm]
* pp.info["unit_length"].express(U.kpc),
"velocity": parts["vel"][mask_dm]
* pp.info["unit_velocity"].express(U.km_s),
"mass": parts["mass"][mask_dm] * pp.info["unit_mass"].express(U.Msun),
},
}
return data
if __name__ == "__main__":
from snapshotprocessor import SnapshotProcessor
pp = SnapshotProcessor(
"/home/nbrucy/ecogal/galturb/F20H_7_1pc_frig", num=80, params="params_gal.yml"
)
data = load_fields(pp)