mirror of
https://github.com/Richard-Sti/csiborgtools.git
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Particle init CM separation (#17)
* Rename * rename module * add new_ic_ids * Add to_new support * rm unnecessary comment * Remove JUlia! * add new package attempt * add dump script * simplify positions getter * Remove unused code * change dumpdirs * update project * Add sorting * fix indexing bug * add comment * Add particle dumping * Delete blank line * Delete Julia things * Update README * add working script * fix assignment bug * fix bug * save temp to temp folder * fix indexing bug & path * do not always crreate folder * Rename file * add initcm reader * add x0, y0, z0 transforms * add initcm to halo cat * docs update * add initial KNN * add attempt at init match * add initial fiducial radius * rm blank space * Add further KNN Init pos support * Add init radius support * Remove message about the bug * Get rid of an error msg * purge mention of knn_init * Add init CM distance calc
This commit is contained in:
Richard Stiskalek
GitHub
parent
c3c686fa60
commit
13a9d11afe
12 changed files with 409 additions and 525 deletions
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||||||
deps = ["Random", "SHA"]
|
|
||||||
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
|
|
||||||
|
|
||||||
[[deps.Unicode]]
|
|
||||||
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
|
|
||||||
|
|
||||||
[[deps.VersionParsing]]
|
|
||||||
git-tree-sha1 = "58d6e80b4ee071f5efd07fda82cb9fbe17200868"
|
|
||||||
uuid = "81def892-9a0e-5fdd-b105-ffc91e053289"
|
|
||||||
version = "1.3.0"
|
|
||||||
|
|
||||||
[[deps.ZMQ]]
|
|
||||||
deps = ["FileWatching", "Sockets", "ZeroMQ_jll"]
|
|
||||||
git-tree-sha1 = "356d2bdcc0bce90aabee1d1c0f6d6f301eda8f77"
|
|
||||||
uuid = "c2297ded-f4af-51ae-bb23-16f91089e4e1"
|
|
||||||
version = "1.2.2"
|
|
||||||
|
|
||||||
[[deps.ZeroMQ_jll]]
|
|
||||||
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "libsodium_jll"]
|
|
||||||
git-tree-sha1 = "fe5c65a526f066fb3000da137d5785d9649a8a47"
|
|
||||||
uuid = "8f1865be-045e-5c20-9c9f-bfbfb0764568"
|
|
||||||
version = "4.3.4+0"
|
|
||||||
|
|
||||||
[[deps.ZipFile]]
|
|
||||||
deps = ["Libdl", "Printf", "Zlib_jll"]
|
|
||||||
git-tree-sha1 = "ef4f23ffde3ee95114b461dc667ea4e6906874b2"
|
|
||||||
uuid = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea"
|
|
||||||
version = "0.10.0"
|
|
||||||
|
|
||||||
[[deps.Zlib_jll]]
|
|
||||||
deps = ["Libdl"]
|
|
||||||
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
|
|
||||||
version = "1.2.12+3"
|
|
||||||
|
|
||||||
[[deps.libblastrampoline_jll]]
|
|
||||||
deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
|
|
||||||
uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
|
|
||||||
version = "5.1.1+0"
|
|
||||||
|
|
||||||
[[deps.libsodium_jll]]
|
|
||||||
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
|
|
||||||
git-tree-sha1 = "848ab3d00fe39d6fbc2a8641048f8f272af1c51e"
|
|
||||||
uuid = "a9144af2-ca23-56d9-984f-0d03f7b5ccf8"
|
|
||||||
version = "1.0.20+0"
|
|
||||||
|
|
||||||
[[deps.nghttp2_jll]]
|
|
||||||
deps = ["Artifacts", "Libdl"]
|
|
||||||
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
|
|
||||||
version = "1.48.0+0"
|
|
||||||
|
|
||||||
[[deps.p7zip_jll]]
|
|
||||||
deps = ["Artifacts", "Libdl"]
|
|
||||||
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
|
|
||||||
version = "17.4.0+0"
|
|
||||||
|
|
@ -1,12 +0,0 @@
|
||||||
name = "JuliaCSiBORGTools"
|
|
||||||
uuid = "6ceada58-95f6-416f-bef9-d16b3bb7d5db"
|
|
||||||
authors = ["rstiskalek <richard.stiskalek@protonmail.com>"]
|
|
||||||
version = "0.1.0"
|
|
||||||
|
|
||||||
[deps]
|
|
||||||
BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
|
|
||||||
IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a"
|
|
||||||
NPZ = "15e1cf62-19b3-5cfa-8e77-841668bca605"
|
|
||||||
PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
|
|
||||||
Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
|
|
||||||
StaticLint = "b3cc710f-9c33-5bdb-a03d-a94903873e97"
|
|
||||||
|
|
@ -1,22 +0,0 @@
|
||||||
# Copyright (C) 2022 Richard Stiskalek
|
|
||||||
# This program is free software; you can redistribute it and/or modify it
|
|
||||||
# under the terms of the GNU General Public License as published by the
|
|
||||||
# Free Software Foundation; either version 3 of the License, or (at your
|
|
||||||
# option) any later version.
|
|
||||||
#
|
|
||||||
# This program is distributed in the hope that it will be useful, but
|
|
||||||
# WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
||||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
|
|
||||||
# Public License for more details.
|
|
||||||
#
|
|
||||||
# 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.
|
|
||||||
|
|
||||||
module JuliaCSiBORGTools
|
|
||||||
|
|
||||||
include("./particles_match.jl")
|
|
||||||
|
|
||||||
export halo_parts
|
|
||||||
|
|
||||||
end # module JuliaCSiBORGTools
|
|
||||||
|
|
@ -1,29 +0,0 @@
|
||||||
# Copyright (C) 2022 Richard Stiskalek
|
|
||||||
# This program is free software; you can redistribute it and/or modify it
|
|
||||||
# under the terms of the GNU General Public License as published by the
|
|
||||||
# Free Software Foundation; either version 3 of the License, or (at your
|
|
||||||
# option) any later version.
|
|
||||||
#
|
|
||||||
# This program is distributed in the hope that it will be useful, but
|
|
||||||
# WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
||||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
|
|
||||||
# Public License for more details.
|
|
||||||
#
|
|
||||||
# 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.
|
|
||||||
|
|
||||||
|
|
||||||
"""
|
|
||||||
halo_parts(clumpid::Int, partids::Vector{<:Int}, clumpids::Vector{<:Int})
|
|
||||||
|
|
||||||
Return particle IDs belonging to a given clump.
|
|
||||||
|
|
||||||
# Arguments
|
|
||||||
- `clumpid::Integer`: the ID of the clump.
|
|
||||||
- `partids::Vector{<:Integer}`: vector of shape `(n_particles,)` with the particle IDs.
|
|
||||||
- `clumpids::Vector{<:Integer}`: vector of shape `(n_particles, )` with the particles' clump IDs.
|
|
||||||
"""
|
|
||||||
function halo_parts(clumpid::Integer, partids::Vector{<:Integer}, clumpids::Vector{<:Integer})
|
|
||||||
return partids[clumpids .== clumpid]
|
|
||||||
end
|
|
||||||
|
|
@ -20,8 +20,4 @@
|
||||||
|
|
||||||
## Open questions
|
## Open questions
|
||||||
- What scaling of the search region? No reason for it to be a multiple of $R_{200c}$.
|
- What scaling of the search region? No reason for it to be a multiple of $R_{200c}$.
|
||||||
- Begin extracting the DM environmental properties at galaxy positions?
|
- Begin extracting the DM environmental properties at galaxy positions?
|
||||||
|
|
||||||
|
|
||||||
## Notes
|
|
||||||
- New sims with part files in initial snapshot: `/mnt/extraspace/hdesmond/ramses_out_7468_new`. Also numbers 7588, 8020, 8452, 8836.
|
|
||||||
|
|
@ -14,7 +14,7 @@
|
||||||
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
|
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
|
||||||
|
|
||||||
import numpy
|
import numpy
|
||||||
from tqdm import tqdm
|
from tqdm import (tqdm, trange)
|
||||||
from astropy.coordinates import SkyCoord
|
from astropy.coordinates import SkyCoord
|
||||||
from ..read import CombinedHaloCatalogue
|
from ..read import CombinedHaloCatalogue
|
||||||
|
|
||||||
|
|
@ -125,7 +125,7 @@ class RealisationsMatcher:
|
||||||
def cosine_similarity(self, x, y):
|
def cosine_similarity(self, x, y):
|
||||||
r"""
|
r"""
|
||||||
Calculate the cosine similarity between two Cartesian vectors. Defined
|
Calculate the cosine similarity between two Cartesian vectors. Defined
|
||||||
as :math:`\Sum_{i} x_i y_{i} / (|x| |y|)`.
|
as :math:`\Sum_{i} x_i y_{i} / (|x| * |y|)`.
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
|
|
@ -152,8 +152,8 @@ class RealisationsMatcher:
|
||||||
return out[0]
|
return out[0]
|
||||||
return out
|
return out
|
||||||
|
|
||||||
def cross_knn_position_single(self, n_sim, nmult=5, dlogmass=2,
|
def cross_knn_position_single(self, n_sim, nmult=5, dlogmass=None,
|
||||||
verbose=True):
|
init_dist=False, verbose=True):
|
||||||
r"""
|
r"""
|
||||||
Find all neighbours within :math:`n_{\rm mult} R_{200c}` of halos in
|
Find all neighbours within :math:`n_{\rm mult} R_{200c}` of halos in
|
||||||
the `nsim`th simulation. Also enforces that the neighbours'
|
the `nsim`th simulation. Also enforces that the neighbours'
|
||||||
|
|
@ -168,21 +168,28 @@ class RealisationsMatcher:
|
||||||
Multiple of :math:`R_{200c}` within which to return neighbours. By
|
Multiple of :math:`R_{200c}` within which to return neighbours. By
|
||||||
default 5.
|
default 5.
|
||||||
dlogmass : float, optional
|
dlogmass : float, optional
|
||||||
Tolerance on mass logarithmic mass difference. By default 2 dex.
|
Tolerance on mass logarithmic mass difference. By default `None`.
|
||||||
|
init_dist : bool, optional
|
||||||
|
Whether to calculate separation of the initial CMs. By default
|
||||||
|
`False`.
|
||||||
|
verbose : bool, optional
|
||||||
|
Iterator verbosity flag. By default `True`.
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
matches : composite array
|
matches : composite array
|
||||||
Array, indices are `(n_sims - 1, 2, n_halos, n_matches)`. The
|
Array, indices are `(n_sims - 1, 3, n_halos, n_matches)`. The
|
||||||
2nd axis is `index` of the neighbouring halo in its catalogue and
|
2nd axis is `index` of the neighbouring halo in its catalogue,
|
||||||
`dist`, which is the 3D distance to the halo whose neighbours are
|
`dist`, which is the 3D distance to the halo whose neighbours are
|
||||||
searched.
|
searched, and `dist0` which is the separation of the initial CMs.
|
||||||
|
The latter is calculated only if `init_dist` is `True`.
|
||||||
"""
|
"""
|
||||||
# R200c, M200c and positions of halos in `n_sim` IC realisation
|
# Radius, M200c and positions of halos in `n_sim` IC realisation
|
||||||
r200 = self.cats[n_sim]["r200"]
|
|
||||||
logm200 = numpy.log10(self.cats[n_sim]["m200"])
|
logm200 = numpy.log10(self.cats[n_sim]["m200"])
|
||||||
|
R = self.cats[n_sim]["r200"]
|
||||||
pos = self.cats[n_sim].positions
|
pos = self.cats[n_sim].positions
|
||||||
|
if init_dist:
|
||||||
|
pos0 = self.cats[n_sim].positions0 # These are CM positions
|
||||||
matches = [None] * (self.cats.N - 1)
|
matches = [None] * (self.cats.N - 1)
|
||||||
# Verbose iterator
|
# Verbose iterator
|
||||||
if verbose:
|
if verbose:
|
||||||
|
|
@ -191,19 +198,30 @@ class RealisationsMatcher:
|
||||||
iters = enumerate(self.search_sim_indices(n_sim))
|
iters = enumerate(self.search_sim_indices(n_sim))
|
||||||
# Search for neighbours in the other simulations
|
# Search for neighbours in the other simulations
|
||||||
for count, i in iters:
|
for count, i in iters:
|
||||||
dist, indxs = self.cats[i].radius_neigbours(pos, r200 * nmult)
|
dist, indxs = self.cats[i].radius_neigbours(pos, R * nmult)
|
||||||
# Get rid of neighbors whose mass is too off
|
# Get rid of neighbors whose mass is too off
|
||||||
for j, indx in enumerate(indxs):
|
if dlogmass is not None:
|
||||||
match_logm200 = numpy.log10(self.cats[i][indx]["m200"])
|
for j, indx in enumerate(indxs):
|
||||||
mask = numpy.abs(match_logm200 - logm200[j]) < dlogmass
|
match_logm200 = numpy.log10(self.cats[i]["m200"][indx])
|
||||||
dist[j] = dist[j][mask]
|
mask = numpy.abs(match_logm200 - logm200[j]) < dlogmass
|
||||||
indxs[j] = indx[mask]
|
dist[j] = dist[j][mask]
|
||||||
|
indxs[j] = indx[mask]
|
||||||
|
# Find distance to the between the initial CM
|
||||||
|
dist0 = [numpy.asanyarray([], dtype=numpy.float64)] * dist.size
|
||||||
|
if init_dist:
|
||||||
|
with_neigbours = numpy.where([ii.size > 0 for ii in indxs])[0]
|
||||||
|
# Fill the pre-allocated array on positions with neighbours
|
||||||
|
for k in with_neigbours:
|
||||||
|
dist0[k] = numpy.linalg.norm(
|
||||||
|
pos0[k] - self.cats[i].positions0[indxs[k]], axis=1)
|
||||||
|
|
||||||
# Append as a composite array
|
# Append as a composite array
|
||||||
matches[count] = numpy.asarray([indxs, dist], dtype=object)
|
matches[count] = numpy.asarray([indxs, dist, dist0], dtype=object)
|
||||||
|
|
||||||
return numpy.asarray(matches, dtype=object)
|
return numpy.asarray(matches, dtype=object)
|
||||||
|
|
||||||
def cross_knn_position_all(self, nmult=5, dlogmass=2):
|
def cross_knn_position_all(self, nmult=5, dlogmass=None,
|
||||||
|
init_dist=False, verbose=True):
|
||||||
r"""
|
r"""
|
||||||
Find all neighbours within :math:`n_{\rm mult} R_{200c}` of halos in
|
Find all neighbours within :math:`n_{\rm mult} R_{200c}` of halos in
|
||||||
all simulations listed in `self.cats`. Also enforces that the
|
all simulations listed in `self.cats`. Also enforces that the
|
||||||
|
|
@ -215,7 +233,12 @@ class RealisationsMatcher:
|
||||||
Multiple of :math:`R_{200c}` within which to return neighbours. By
|
Multiple of :math:`R_{200c}` within which to return neighbours. By
|
||||||
default 5.
|
default 5.
|
||||||
dlogmass : float, optional
|
dlogmass : float, optional
|
||||||
Tolerance on mass logarithmic mass difference. By default 2 dex.
|
Tolerance on mass logarithmic mass difference. By default `None`.
|
||||||
|
init_dist : bool, optional
|
||||||
|
Whether to calculate separation of the initial CMs. By default
|
||||||
|
`False`.
|
||||||
|
verbose : bool, optional
|
||||||
|
Iterator verbosity flag. By default `True`.
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
|
|
@ -226,6 +249,7 @@ class RealisationsMatcher:
|
||||||
N = self.cats.N # Number of catalogues
|
N = self.cats.N # Number of catalogues
|
||||||
matches = [None] * N
|
matches = [None] * N
|
||||||
# Loop over each catalogue
|
# Loop over each catalogue
|
||||||
for i in range(N):
|
for i in trange(N) if verbose else range(N):
|
||||||
matches[i] = self.cross_knn_position_single(i, nmult, dlogmass)
|
matches[i] = self.cross_knn_position_single(
|
||||||
|
i, nmult, dlogmass, init_dist)
|
||||||
return matches
|
return matches
|
||||||
|
|
|
||||||
|
|
@ -13,7 +13,7 @@
|
||||||
# with this program; if not, write to the Free Software Foundation, Inc.,
|
# with this program; if not, write to the Free Software Foundation, Inc.,
|
||||||
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
|
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
|
||||||
|
|
||||||
from .readsim import (CSiBORGPaths, ParticleReader, read_mmain, get_positions) # noqa
|
from .readsim import (CSiBORGPaths, ParticleReader, read_mmain, read_initcm, get_positions) # noqa
|
||||||
from .make_cat import (HaloCatalogue, CombinedHaloCatalogue) # noqa
|
from .make_cat import (HaloCatalogue, CombinedHaloCatalogue) # noqa
|
||||||
from .readobs import (PlanckClusters, MCXCClusters, TwoMPPGalaxies, # noqa
|
from .readobs import (PlanckClusters, MCXCClusters, TwoMPPGalaxies, # noqa
|
||||||
TwoMPPGroups, SDSS) # noqa
|
TwoMPPGroups, SDSS) # noqa
|
||||||
|
|
|
||||||
|
|
@ -15,13 +15,12 @@
|
||||||
"""
|
"""
|
||||||
Functions to read in the particle and clump files.
|
Functions to read in the particle and clump files.
|
||||||
"""
|
"""
|
||||||
|
|
||||||
import numpy
|
import numpy
|
||||||
from os.path import join
|
from os.path import join
|
||||||
from tqdm import trange
|
from tqdm import trange
|
||||||
from copy import deepcopy
|
from copy import deepcopy
|
||||||
from sklearn.neighbors import NearestNeighbors
|
from sklearn.neighbors import NearestNeighbors
|
||||||
from .readsim import read_mmain
|
from .readsim import (read_mmain, read_initcm)
|
||||||
from ..utils import (flip_cols, add_columns)
|
from ..utils import (flip_cols, add_columns)
|
||||||
from ..units import (BoxUnits, cartesian_to_radec)
|
from ..units import (BoxUnits, cartesian_to_radec)
|
||||||
|
|
||||||
|
|
@ -45,6 +44,7 @@ class HaloCatalogue:
|
||||||
_data = None
|
_data = None
|
||||||
_knn = None
|
_knn = None
|
||||||
_positions = None
|
_positions = None
|
||||||
|
_positions0 = None
|
||||||
|
|
||||||
def __init__(self, paths, min_m500=None, max_dist=None):
|
def __init__(self, paths, min_m500=None, max_dist=None):
|
||||||
self._box = BoxUnits(paths)
|
self._box = BoxUnits(paths)
|
||||||
|
|
@ -117,7 +117,7 @@ class HaloCatalogue:
|
||||||
@property
|
@property
|
||||||
def n_sim(self):
|
def n_sim(self):
|
||||||
"""
|
"""
|
||||||
The initiali condition (IC) realisation ID.
|
The initial condition (IC) realisation ID.
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
|
|
@ -142,6 +142,12 @@ class HaloCatalogue:
|
||||||
# Cut on number of particles and finite m200
|
# Cut on number of particles and finite m200
|
||||||
data = data[(data["npart"] > 100) & numpy.isfinite(data["m200"])]
|
data = data[(data["npart"] > 100) & numpy.isfinite(data["m200"])]
|
||||||
|
|
||||||
|
# Now also load the initial positions
|
||||||
|
initcm = read_initcm(self.n_sim, self.paths.initmatch_path)
|
||||||
|
if initcm is not None:
|
||||||
|
data = self.merge_initmatch_to_clumps(data, initcm)
|
||||||
|
flip_cols(data, "x0", "z0")
|
||||||
|
|
||||||
# Calculate redshift
|
# Calculate redshift
|
||||||
pos = [data["peak_{}".format(p)] - 0.5 for p in ("x", "y", "z")]
|
pos = [data["peak_{}".format(p)] - 0.5 for p in ("x", "y", "z")]
|
||||||
vel = [data["v{}".format(p)] for p in ("x", "y", "z")]
|
vel = [data["v{}".format(p)] for p in ("x", "y", "z")]
|
||||||
|
|
@ -171,9 +177,14 @@ class HaloCatalogue:
|
||||||
# Cut on separation
|
# Cut on separation
|
||||||
data = data[data["dist"] < max_dist]
|
data = data[data["dist"] < max_dist]
|
||||||
|
|
||||||
# Pre-allocate the positions array
|
# Pre-allocate the positions arrays
|
||||||
self._positions = numpy.vstack(
|
self._positions = numpy.vstack(
|
||||||
[data["peak_{}".format(p)] for p in ("x", "y", "z")]).T
|
[data["peak_{}".format(p)] for p in ("x", "y", "z")]).T
|
||||||
|
# And do the unit transform
|
||||||
|
if initcm is not None:
|
||||||
|
data = self.box.convert_from_boxunits(data, ["x0", "y0", "z0"])
|
||||||
|
self._positions0 = numpy.vstack(
|
||||||
|
[data["{}0".format(p)] for p in ("x", "y", "z")]).T
|
||||||
|
|
||||||
self._data = data
|
self._data = data
|
||||||
|
|
||||||
|
|
@ -203,10 +214,39 @@ class HaloCatalogue:
|
||||||
X[mask, 1] = mmain["sub_frac"]
|
X[mask, 1] = mmain["sub_frac"]
|
||||||
return add_columns(clumps, X, ["mass_mmain", "sub_frac"])
|
return add_columns(clumps, X, ["mass_mmain", "sub_frac"])
|
||||||
|
|
||||||
|
def merge_initmatch_to_clumps(self, clumps, initcat):
|
||||||
|
"""
|
||||||
|
Merge columns from the `init_cm` files to the `clump` file.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
clumps : structured array
|
||||||
|
Clumps structured array.
|
||||||
|
initcat : structured array
|
||||||
|
Catalog with the clumps initial centre of mass at z = 70.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
out : structured array
|
||||||
|
"""
|
||||||
|
# There are more initcat clumps, so check which ones have z = 0
|
||||||
|
# and then downsample
|
||||||
|
mask = numpy.isin(initcat["ID"], clumps["index"])
|
||||||
|
initcat = initcat[mask]
|
||||||
|
# Now the index ordering should match
|
||||||
|
if not numpy.alltrue(initcat["ID"] == clumps["index"]):
|
||||||
|
raise ValueError(
|
||||||
|
"Ordering of `initcat` and `clumps` is inconsistent.")
|
||||||
|
|
||||||
|
X = numpy.full((clumps.size, 3), numpy.nan)
|
||||||
|
for i, p in enumerate(['x', 'y', 'z']):
|
||||||
|
X[:, i] = initcat[p]
|
||||||
|
return add_columns(clumps, X, ["x0", "y0", "z0"])
|
||||||
|
|
||||||
@property
|
@property
|
||||||
def positions(self):
|
def positions(self):
|
||||||
"""
|
"""
|
||||||
3D positions of halos.
|
3D positions of halos in comoving units of Mpc.
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
|
|
@ -216,6 +256,21 @@ class HaloCatalogue:
|
||||||
"""
|
"""
|
||||||
return self._positions
|
return self._positions
|
||||||
|
|
||||||
|
@property
|
||||||
|
def positions0(self):
|
||||||
|
r"""
|
||||||
|
3D positions of halos in the initial snapshot in comoving units of Mpc.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
X : 2-dimensional array
|
||||||
|
Array of shape `(n_halos, 3)`, where the latter axis represents
|
||||||
|
`x`, `y` and `z`.
|
||||||
|
"""
|
||||||
|
if self._positions0 is None:
|
||||||
|
raise RuntimeError("Initial positions are not set!")
|
||||||
|
return self._positions0
|
||||||
|
|
||||||
@property
|
@property
|
||||||
def velocities(self):
|
def velocities(self):
|
||||||
"""
|
"""
|
||||||
|
|
@ -240,6 +295,26 @@ class HaloCatalogue:
|
||||||
"""
|
"""
|
||||||
return numpy.vstack([self["L{}".format(p)] for p in ("x", "y", "z")]).T
|
return numpy.vstack([self["L{}".format(p)] for p in ("x", "y", "z")]).T
|
||||||
|
|
||||||
|
@property
|
||||||
|
def init_radius(self):
|
||||||
|
r"""
|
||||||
|
A fiducial initial radius of particles that are identified as a single
|
||||||
|
halo in the final snapshot. Estimated to be
|
||||||
|
|
||||||
|
..math:
|
||||||
|
R = (3 N / 4 \pi)^{1 / 3} * \Delta
|
||||||
|
|
||||||
|
where :math:`N` is the number of particles and `Delta` is the initial
|
||||||
|
inter-particular distance :math:`Delta = 1 / 2^{11}` in box units. The
|
||||||
|
output fiducial radius is in comoving units of Mpc.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
R : float
|
||||||
|
"""
|
||||||
|
delta = self.box.box2mpc(1 / 2**11)
|
||||||
|
return (3 * self["npart"] / (4 * numpy.pi))**(1/3) * delta
|
||||||
|
|
||||||
def radius_neigbours(self, X, radius):
|
def radius_neigbours(self, X, radius):
|
||||||
"""
|
"""
|
||||||
Return sorted nearest neigbours within `radius` or `X`.
|
Return sorted nearest neigbours within `radius` or `X`.
|
||||||
|
|
@ -272,6 +347,9 @@ class HaloCatalogue:
|
||||||
return self.data.dtype.names
|
return self.data.dtype.names
|
||||||
|
|
||||||
def __getitem__(self, key):
|
def __getitem__(self, key):
|
||||||
|
initpars = ["x0", "y0", "z0"]
|
||||||
|
if key in initpars and key not in self.keys:
|
||||||
|
raise RuntimeError("Initial positions are not set!")
|
||||||
return self._data[key]
|
return self._data[key]
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -299,8 +377,9 @@ class CombinedHaloCatalogue:
|
||||||
|
|
||||||
def __init__(self, paths, min_m500=None, max_dist=None, verbose=True):
|
def __init__(self, paths, min_m500=None, max_dist=None, verbose=True):
|
||||||
# Read simulations and their maximum snapshots
|
# Read simulations and their maximum snapshots
|
||||||
# NOTE remove this later and take all cats
|
# NOTE later change this back to all simulations
|
||||||
self._n_sims = paths.ic_ids[:10]
|
self._n_sims = [7468, 7588, 8020, 8452, 8836]
|
||||||
|
# self._n_sims = paths.ic_ids
|
||||||
n_snaps = [paths.get_maximum_snapshot(i) for i in self._n_sims]
|
n_snaps = [paths.get_maximum_snapshot(i) for i in self._n_sims]
|
||||||
self._n_snaps = numpy.asanyarray(n_snaps)
|
self._n_snaps = numpy.asanyarray(n_snaps)
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -18,10 +18,11 @@ Functions to read in the particle and clump files.
|
||||||
|
|
||||||
import numpy
|
import numpy
|
||||||
from scipy.io import FortranFile
|
from scipy.io import FortranFile
|
||||||
from os import listdir
|
import gc
|
||||||
from os.path import (join, isfile, isdir)
|
from os.path import (join, isfile, isdir)
|
||||||
from glob import glob
|
from glob import glob
|
||||||
from tqdm import tqdm
|
from tqdm import tqdm
|
||||||
|
from warnings import warn
|
||||||
from ..utils import (cols_to_structured, extract_from_structured)
|
from ..utils import (cols_to_structured, extract_from_structured)
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -56,22 +57,40 @@ class CSiBORGPaths:
|
||||||
mmain_path : str, optional
|
mmain_path : str, optional
|
||||||
Path to where mmain files are stored. By default
|
Path to where mmain files are stored. By default
|
||||||
`/mnt/zfsusers/hdesmond/Mmain`.
|
`/mnt/zfsusers/hdesmond/Mmain`.
|
||||||
|
initmatch_path : str, optional
|
||||||
|
Path to where match between the first and final snapshot is stored. By
|
||||||
|
default `/mnt/extraspace/rstiskalek/csiborg/initmatch/`.
|
||||||
|
to_new : bool, optional
|
||||||
|
Whether the paths should point to `new` files, for example
|
||||||
|
`ramses_out_8452_new`.
|
||||||
"""
|
"""
|
||||||
_srcdir = None
|
_srcdir = None
|
||||||
_n_sim = None
|
_n_sim = None
|
||||||
_n_snap = None
|
_n_snap = None
|
||||||
_dumpdir = None
|
_dumpdir = None
|
||||||
_mmain_path = None
|
_mmain_path = None
|
||||||
|
_initmatch_path = None
|
||||||
|
_to_new = None
|
||||||
|
|
||||||
def __init__(self, n_sim=None, n_snap=None,
|
# NOTE deuglify this stuff
|
||||||
srcdir="/mnt/extraspace/hdesmond/",
|
def __init__(self, n_sim=None, n_snap=None, srcdir=None, dumpdir=None,
|
||||||
dumpdir="/mnt/extraspace/rstiskalek/csiborg/",
|
mmain_path=None, initmatch_path=None, to_new=False):
|
||||||
mmain_path="/mnt/zfsusers/hdesmond/Mmain"):
|
if srcdir is None:
|
||||||
|
srcdir = "/mnt/extraspace/hdesmond/"
|
||||||
self.srcdir = srcdir
|
self.srcdir = srcdir
|
||||||
|
if dumpdir is None:
|
||||||
|
dumpdir = "/mnt/extraspace/rstiskalek/csiborg/"
|
||||||
self.dumpdir = dumpdir
|
self.dumpdir = dumpdir
|
||||||
|
if mmain_path is None:
|
||||||
|
mmain_path = "/mnt/zfsusers/hdesmond/Mmain"
|
||||||
self.mmain_path = mmain_path
|
self.mmain_path = mmain_path
|
||||||
|
if initmatch_path is None:
|
||||||
|
initmatch_path = "/mnt/extraspace/rstiskalek/csiborg/initmatch/"
|
||||||
|
self.initmatch_path = initmatch_path
|
||||||
|
self.to_new = to_new
|
||||||
if n_sim is not None and n_snap is not None:
|
if n_sim is not None and n_snap is not None:
|
||||||
self.set_info(n_sim, n_snap)
|
self.set_info(n_sim, n_snap)
|
||||||
|
# "/mnt/extraspace/rstiskalek/csiborg/initmatch/clump_cm_7468.npy"
|
||||||
|
|
||||||
@property
|
@property
|
||||||
def srcdir(self):
|
def srcdir(self):
|
||||||
|
|
@ -147,6 +166,45 @@ class CSiBORGPaths:
|
||||||
raise IOError("Invalid directory `{}`!".format(mmain_path))
|
raise IOError("Invalid directory `{}`!".format(mmain_path))
|
||||||
self._mmain_path = mmain_path
|
self._mmain_path = mmain_path
|
||||||
|
|
||||||
|
@property
|
||||||
|
def initmatch_path(self):
|
||||||
|
"""
|
||||||
|
Path to where match between the first and final snapshot is stored.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
initmach_path : str
|
||||||
|
"""
|
||||||
|
return self._initmatch_path
|
||||||
|
|
||||||
|
@initmatch_path.setter
|
||||||
|
def initmatch_path(self, initmatch_path):
|
||||||
|
"""
|
||||||
|
Set `initmatch_path`, check that the directory exists.
|
||||||
|
"""
|
||||||
|
if not isdir(initmatch_path):
|
||||||
|
raise IOError("Invalid directory `{}`!".format(initmatch_path))
|
||||||
|
self._initmatch_path = initmatch_path
|
||||||
|
|
||||||
|
@property
|
||||||
|
def to_new(self):
|
||||||
|
"""
|
||||||
|
Flag whether paths should point to `new` files, for example
|
||||||
|
`ramses_out_8452_new`.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
to_new : bool
|
||||||
|
"""
|
||||||
|
return self._to_new
|
||||||
|
|
||||||
|
@to_new.setter
|
||||||
|
def to_new(self, to_new):
|
||||||
|
"""Set `to_new`."""
|
||||||
|
if not isinstance(to_new, bool):
|
||||||
|
raise TypeError("`to_new` must be be a bool")
|
||||||
|
self._to_new = to_new
|
||||||
|
|
||||||
@property
|
@property
|
||||||
def n_sim(self):
|
def n_sim(self):
|
||||||
"""
|
"""
|
||||||
|
|
@ -236,14 +294,26 @@ class CSiBORGPaths:
|
||||||
def ic_ids(self):
|
def ic_ids(self):
|
||||||
"""
|
"""
|
||||||
CSiBORG initial condition (IC) simulation IDs from the list of folders
|
CSiBORG initial condition (IC) simulation IDs from the list of folders
|
||||||
in `self.srcdir`. Assumes that the folders look like `ramses_out_X`
|
in `self.srcdir`.
|
||||||
and extracts the `X` integer. Removes `5511` from the list of IDs.
|
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
ids : 1-dimensional array
|
ids : 1-dimensional array
|
||||||
Array of CSiBORG simulation IDs.
|
Array of CSiBORG simulation IDs.
|
||||||
"""
|
"""
|
||||||
|
if self.to_new:
|
||||||
|
return self._ic_ids_new
|
||||||
|
return self._ic_ids
|
||||||
|
|
||||||
|
@property
|
||||||
|
def _ic_ids(self):
|
||||||
|
"""
|
||||||
|
IC simulation IDs.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
ids : 1-dimensional array
|
||||||
|
"""
|
||||||
files = glob(join(self.srcdir, "ramses_out*"))
|
files = glob(join(self.srcdir, "ramses_out*"))
|
||||||
# Select only file names
|
# Select only file names
|
||||||
files = [f.split("/")[-1] for f in files]
|
files = [f.split("/")[-1] for f in files]
|
||||||
|
|
@ -260,6 +330,25 @@ class CSiBORGPaths:
|
||||||
pass
|
pass
|
||||||
return numpy.sort(ids)
|
return numpy.sort(ids)
|
||||||
|
|
||||||
|
@property
|
||||||
|
def _ic_ids_new(self):
|
||||||
|
"""
|
||||||
|
ICs simulation IDs denoted as `new` with recoved :math:`z = 70`
|
||||||
|
particle information.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
ids : 1-dimensional array
|
||||||
|
"""
|
||||||
|
files = glob(join(self.srcdir, "ramses_out*"))
|
||||||
|
# Select only file names
|
||||||
|
files = [f.split("/")[-1] for f in files]
|
||||||
|
# Only _new files
|
||||||
|
files = [f for f in files if "_new" in f]
|
||||||
|
# Take the ICs
|
||||||
|
ids = [int(f.split("_")[2]) for f in files]
|
||||||
|
return numpy.sort(ids)
|
||||||
|
|
||||||
def ic_path(self, n_sim=None):
|
def ic_path(self, n_sim=None):
|
||||||
"""
|
"""
|
||||||
Path to `n_sim`th CSiBORG IC realisation.
|
Path to `n_sim`th CSiBORG IC realisation.
|
||||||
|
|
@ -276,6 +365,8 @@ class CSiBORGPaths:
|
||||||
"""
|
"""
|
||||||
n_sim = self.get_n_sim(n_sim)
|
n_sim = self.get_n_sim(n_sim)
|
||||||
fname = "ramses_out_{}"
|
fname = "ramses_out_{}"
|
||||||
|
if self.to_new:
|
||||||
|
fname += "_new"
|
||||||
return join(self.srcdir, fname.format(n_sim))
|
return join(self.srcdir, fname.format(n_sim))
|
||||||
|
|
||||||
def get_snapshots(self, n_sim=None):
|
def get_snapshots(self, n_sim=None):
|
||||||
|
|
@ -291,7 +382,6 @@ class CSiBORGPaths:
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
snapshots : 1-dimensional array
|
snapshots : 1-dimensional array
|
||||||
Array of snapshot IDs.
|
|
||||||
"""
|
"""
|
||||||
n_sim = self.get_n_sim(n_sim)
|
n_sim = self.get_n_sim(n_sim)
|
||||||
simpath = self.ic_path(n_sim)
|
simpath = self.ic_path(n_sim)
|
||||||
|
|
@ -314,7 +404,6 @@ class CSiBORGPaths:
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
maxsnap : float
|
maxsnap : float
|
||||||
Maximum snapshot.
|
|
||||||
"""
|
"""
|
||||||
n_sim = self.get_n_sim(n_sim)
|
n_sim = self.get_n_sim(n_sim)
|
||||||
return max(self.get_snapshots(n_sim))
|
return max(self.get_snapshots(n_sim))
|
||||||
|
|
@ -332,7 +421,6 @@ class CSiBORGPaths:
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
minsnap : float
|
minsnap : float
|
||||||
Minimum snapshot.
|
|
||||||
"""
|
"""
|
||||||
n_sim = self.get_n_sim(n_sim)
|
n_sim = self.get_n_sim(n_sim)
|
||||||
return min(self.get_snapshots(n_sim))
|
return min(self.get_snapshots(n_sim))
|
||||||
|
|
@ -353,7 +441,6 @@ class CSiBORGPaths:
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
snappath : str
|
snappath : str
|
||||||
Path to the CSiBORG IC realisation snapshot.
|
|
||||||
"""
|
"""
|
||||||
n_snap = self.get_n_snap(n_snap)
|
n_snap = self.get_n_snap(n_snap)
|
||||||
n_sim = self.get_n_sim(n_sim)
|
n_sim = self.get_n_sim(n_sim)
|
||||||
|
|
@ -455,15 +542,6 @@ class ParticleReader:
|
||||||
print("Reading in output `{}` with ncpu = `{}`."
|
print("Reading in output `{}` with ncpu = `{}`."
|
||||||
.format(nout, ncpu))
|
.format(nout, ncpu))
|
||||||
|
|
||||||
# Check whether the unbinding file exists.
|
|
||||||
snapdirlist = listdir(snappath)
|
|
||||||
unbinding_file = "unbinding_{}.out00001".format(nout)
|
|
||||||
if unbinding_file not in snapdirlist:
|
|
||||||
raise FileNotFoundError(
|
|
||||||
"Couldn't find `{}` in `{}`. Use mergertreeplot.py -h or "
|
|
||||||
"--help to print help message."
|
|
||||||
.format(unbinding_file, snappath))
|
|
||||||
|
|
||||||
# First read the headers. Reallocate arrays and fill them.
|
# First read the headers. Reallocate arrays and fill them.
|
||||||
nparts = numpy.zeros(ncpu, dtype=int)
|
nparts = numpy.zeros(ncpu, dtype=int)
|
||||||
partfiles = [None] * ncpu
|
partfiles = [None] * ncpu
|
||||||
|
|
@ -761,25 +839,46 @@ def read_mmain(n, srcdir, fname="Mmain_{}.npy"):
|
||||||
return out
|
return out
|
||||||
|
|
||||||
|
|
||||||
def get_positions(n_sim, n_snap, get_clumpid, verbose=True,
|
def read_initcm(n, srcdir, fname="clump_cm_{}.npy"):
|
||||||
srcdir="/mnt/extraspace/hdesmond/"):
|
"""
|
||||||
|
Read `clump_cm`, i.e. the center of mass of a clump at redshift z = 70.
|
||||||
|
If the file does not exist returns `None`.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
n : int
|
||||||
|
The index of the initial conditions (IC) realisation.
|
||||||
|
srcdir : str
|
||||||
|
The path to the folder containing the files.
|
||||||
|
fname : str, optional
|
||||||
|
The file name convention. By default `clump_cm_{}.npy`, where the
|
||||||
|
substituted value is `n`.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
out : structured array
|
||||||
|
"""
|
||||||
|
fpath = join(srcdir, fname.format(n))
|
||||||
|
try:
|
||||||
|
return numpy.load(fpath)
|
||||||
|
except FileNotFoundError:
|
||||||
|
warn("File {} does not exist.".format(fpath))
|
||||||
|
return None
|
||||||
|
|
||||||
|
|
||||||
|
def get_positions(paths, get_clumpid, verbose=True):
|
||||||
"""
|
"""
|
||||||
Shortcut to get particle IDs, positions, masses and optionally clump
|
Shortcut to get particle IDs, positions, masses and optionally clump
|
||||||
indices.
|
indices.
|
||||||
|
|
||||||
Parameters
|
Parameters
|
||||||
----------
|
----------
|
||||||
n_sim : int
|
paths : py:class`csiborgtools.read.CSiBORGPaths`
|
||||||
CSiBORG IC realisation index.
|
CSiBORG paths-handling object with set `n_sim` and `n_snap`.
|
||||||
n_snap : int
|
|
||||||
Snapshot index.
|
|
||||||
get_clumpid : bool
|
get_clumpid : bool
|
||||||
Whether to also return the clump indices.
|
Whether to also return the clump indices.
|
||||||
verbose : bool, optional
|
verbose : bool, optional
|
||||||
Verbosity flag. By default `True`.
|
Verbosity flag. By default `True`.
|
||||||
srcdir : str, optional
|
|
||||||
The file path to the folder where realisations of the ICs are stored.
|
|
||||||
By default `/mnt/extraspace/hdesmond/`.
|
|
||||||
|
|
||||||
Returns
|
Returns
|
||||||
-------
|
-------
|
||||||
|
|
@ -793,9 +892,6 @@ def get_positions(n_sim, n_snap, get_clumpid, verbose=True,
|
||||||
Particles' clump IDs of shape `(n_particles, )`. Returned only if
|
Particles' clump IDs of shape `(n_particles, )`. Returned only if
|
||||||
`get_clumpid` is `True`.
|
`get_clumpid` is `True`.
|
||||||
"""
|
"""
|
||||||
# Setup the paths
|
|
||||||
paths = CSiBORGPaths(srcdir)
|
|
||||||
paths.set_info(n_sim, n_snap)
|
|
||||||
# Extract particles
|
# Extract particles
|
||||||
reader = ParticleReader(paths)
|
reader = ParticleReader(paths)
|
||||||
pars_extract = ["ID", "x", "y", "z", "M"]
|
pars_extract = ["ID", "x", "y", "z", "M"]
|
||||||
|
|
@ -805,8 +901,10 @@ def get_positions(n_sim, n_snap, get_clumpid, verbose=True,
|
||||||
pids = extract_from_structured(particles, "ID")
|
pids = extract_from_structured(particles, "ID")
|
||||||
ppos = extract_from_structured(particles, ["x", "y", "z"])
|
ppos = extract_from_structured(particles, ["x", "y", "z"])
|
||||||
pmass = extract_from_structured(particles, "M")
|
pmass = extract_from_structured(particles, "M")
|
||||||
|
|
||||||
# Force early memory release
|
# Force early memory release
|
||||||
del particles
|
del particles
|
||||||
|
gc.collect()
|
||||||
|
|
||||||
out = (pids, ppos, pmass)
|
out = (pids, ppos, pmass)
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -26,7 +26,7 @@ from ..read import ParticleReader
|
||||||
# Map of unit conversions
|
# Map of unit conversions
|
||||||
CONV_NAME = {
|
CONV_NAME = {
|
||||||
"length": ["peak_x", "peak_y", "peak_z", "Rs", "rmin", "rmax", "r200",
|
"length": ["peak_x", "peak_y", "peak_z", "Rs", "rmin", "rmax", "r200",
|
||||||
"r500"],
|
"r500", "x0", "y0", "z0"],
|
||||||
"mass": ["mass_cl", "totpartmass", "m200", "m500", "mass_mmain"],
|
"mass": ["mass_cl", "totpartmass", "m200", "m500", "mass_mmain"],
|
||||||
"density": ["rho0"]
|
"density": ["rho0"]
|
||||||
}
|
}
|
||||||
|
|
@ -414,7 +414,7 @@ class BoxUnits:
|
||||||
"Conversion of `{}` is not defined.".format(name))
|
"Conversion of `{}` is not defined.".format(name))
|
||||||
|
|
||||||
# Center at the observer
|
# Center at the observer
|
||||||
if name in ["peak_x", "peak_y", "peak_z"]:
|
if name in ["peak_x", "peak_y", "peak_z", "x0", "y0", "z0"]:
|
||||||
data[name] -= transforms["length"](0.5)
|
data[name] -= transforms["length"](0.5)
|
||||||
|
|
||||||
return data
|
return data
|
||||||
|
|
|
||||||
|
|
@ -1,49 +0,0 @@
|
||||||
# Copyright (C) 2022 Richard Stiskalek
|
|
||||||
# This program is free software; you can redistribute it and/or modify it
|
|
||||||
# under the terms of the GNU General Public License as published by the
|
|
||||||
# Free Software Foundation; either version 3 of the License, or (at your
|
|
||||||
# option) any later version.
|
|
||||||
#
|
|
||||||
# This program is distributed in the hope that it will be useful, but
|
|
||||||
# WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
||||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
|
|
||||||
# Public License for more details.
|
|
||||||
#
|
|
||||||
# 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.
|
|
||||||
|
|
||||||
using Pkg: activate, build
|
|
||||||
activate("../JuliaCSiBORGTools/")
|
|
||||||
|
|
||||||
using JuliaCSiBORGTools
|
|
||||||
using NPZ: npzread
|
|
||||||
using PyCall: pyimport
|
|
||||||
csiborgtools = pyimport("csiborgtools")
|
|
||||||
|
|
||||||
verbose = true
|
|
||||||
paths = csiborgtools.read.CSiBORGPaths()
|
|
||||||
nsims = paths.ic_ids[:1]
|
|
||||||
|
|
||||||
for nsim in nsims
|
|
||||||
nsnap_min = convert(Int64, paths.get_minimum_snapshot(nsim))
|
|
||||||
nsnap_max = convert(Int64, paths.get_maximum_snapshot(nsim))
|
|
||||||
|
|
||||||
# Get the maximum snapshot properties
|
|
||||||
verbose ? println("Loading snapshot $nsnap_max from simulation $nsim") : nothing
|
|
||||||
pids, ppos, pmass, clumpids = csiborgtools.read.get_positions(nsim, nsnap_max, get_clumpid=true, verbose=false)
|
|
||||||
|
|
||||||
println("Sizes are: ")
|
|
||||||
println(size(pids))
|
|
||||||
println(size(ppos))
|
|
||||||
println(size(pmass))
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
# # Get the minimum snapshot properties
|
|
||||||
# verbose ? println("Loading snapshot $nsnap_min from simulation $nsim") : nothing
|
|
||||||
# pids, ppos, pmass = csiborgtools.read.get_positions(nsim, nsnap_max, get_clumpid=false, verbose=false)
|
|
||||||
|
|
||||||
JuliaCSiBORGTools.halo_parts(0, partids, clumpids)
|
|
||||||
|
|
||||||
end
|
|
||||||
143
scripts/run_initmatch.py
Normal file
143
scripts/run_initmatch.py
Normal file
|
|
@ -0,0 +1,143 @@
|
||||||
|
# Copyright (C) 2022 Richard Stiskalek
|
||||||
|
# This program is free software; you can redistribute it and/or modify it
|
||||||
|
# under the terms of the GNU General Public License as published by the
|
||||||
|
# Free Software Foundation; either version 3 of the License, or (at your
|
||||||
|
# option) any later version.
|
||||||
|
#
|
||||||
|
# This program is distributed in the hope that it will be useful, but
|
||||||
|
# WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
|
||||||
|
# Public License for more details.
|
||||||
|
#
|
||||||
|
# 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.
|
||||||
|
"""
|
||||||
|
A script to calculate the centre of mass of particles at redshift 70 that
|
||||||
|
are grouped in a clump at present redshift.
|
||||||
|
|
||||||
|
Optionally also dumps the clumps information, however watch out as this will
|
||||||
|
eat up a lot of memory.
|
||||||
|
"""
|
||||||
|
from argparse import ArgumentParser
|
||||||
|
import numpy
|
||||||
|
from datetime import datetime
|
||||||
|
from mpi4py import MPI
|
||||||
|
from distutils.util import strtobool
|
||||||
|
from os.path import join, isdir
|
||||||
|
from os import mkdir
|
||||||
|
from os import remove
|
||||||
|
from sys import stdout
|
||||||
|
from gc import collect
|
||||||
|
try:
|
||||||
|
import csiborgtools
|
||||||
|
except ModuleNotFoundError:
|
||||||
|
import sys
|
||||||
|
sys.path.append("../")
|
||||||
|
import csiborgtools
|
||||||
|
|
||||||
|
parser = ArgumentParser()
|
||||||
|
parser.add_argument("--dump_clumps", default=False,
|
||||||
|
type=lambda x: bool(strtobool(x)))
|
||||||
|
args = parser.parse_args()
|
||||||
|
|
||||||
|
# Get MPI things
|
||||||
|
comm = MPI.COMM_WORLD
|
||||||
|
rank = comm.Get_rank()
|
||||||
|
nproc = comm.Get_size()
|
||||||
|
|
||||||
|
init_paths = csiborgtools.read.CSiBORGPaths(to_new=True)
|
||||||
|
fin_paths = csiborgtools.read.CSiBORGPaths(to_new=False)
|
||||||
|
nsims = init_paths.ic_ids
|
||||||
|
|
||||||
|
# Output files
|
||||||
|
dumpdir = "/mnt/extraspace/rstiskalek/csiborg/initmatch"
|
||||||
|
ftemp = join(dumpdir, "temp", "temp_{}_{}.npy")
|
||||||
|
fperm = join(dumpdir, "clump_cm_{}.npy")
|
||||||
|
|
||||||
|
for nsim in nsims:
|
||||||
|
if rank == 0:
|
||||||
|
print("{}: reading simulation {}.".format(datetime.now(), nsim))
|
||||||
|
stdout.flush()
|
||||||
|
# Check that the output folder for this sim exists
|
||||||
|
clumpdumpdir = join(dumpdir, "out_{}".format(nsim))
|
||||||
|
if args.dump_clumps and rank == 0 and not isdir(clumpdumpdir):
|
||||||
|
mkdir(clumpdumpdir)
|
||||||
|
|
||||||
|
# Barrier to make sure we created the directory with the rank 0
|
||||||
|
comm.Barrier()
|
||||||
|
|
||||||
|
# Set the snapshot numbers
|
||||||
|
init_paths.set_info(nsim, init_paths.get_minimum_snapshot(nsim))
|
||||||
|
fin_paths.set_info(nsim, fin_paths.get_maximum_snapshot(nsim))
|
||||||
|
# Set the readers
|
||||||
|
init_reader = csiborgtools.read.ParticleReader(init_paths)
|
||||||
|
fin_reader = csiborgtools.read.ParticleReader(fin_paths)
|
||||||
|
|
||||||
|
# Read and sort the initial particle files by their particle IDs
|
||||||
|
part0 = init_reader.read_particle(["x", "y", "z", "M", "ID"],
|
||||||
|
verbose=False)
|
||||||
|
part0 = part0[numpy.argsort(part0["ID"])]
|
||||||
|
|
||||||
|
# Order the final snapshot clump IDs by the particle IDs
|
||||||
|
pid = fin_reader.read_particle(["ID"], verbose=False)["ID"]
|
||||||
|
clump_ids = fin_reader.read_clumpid(verbose=False)
|
||||||
|
clump_ids = clump_ids[numpy.argsort(pid)]
|
||||||
|
|
||||||
|
del pid
|
||||||
|
collect()
|
||||||
|
|
||||||
|
# Get rid of the clumps whose index is 0 -- those are unassigned
|
||||||
|
mask = clump_ids > 0
|
||||||
|
clump_ids = clump_ids[mask]
|
||||||
|
part0 = part0[mask]
|
||||||
|
del mask
|
||||||
|
collect()
|
||||||
|
|
||||||
|
if rank == 0:
|
||||||
|
print("{}: dumping clumps for simulation.".format(datetime.now()))
|
||||||
|
stdout.flush()
|
||||||
|
|
||||||
|
# Grab unique clump IDs and loop over them
|
||||||
|
unique_clumpids = numpy.unique(clump_ids)
|
||||||
|
|
||||||
|
njobs = unique_clumpids.size
|
||||||
|
jobs = csiborgtools.fits.split_jobs(njobs, nproc)[rank]
|
||||||
|
for i in jobs:
|
||||||
|
n = unique_clumpids[i]
|
||||||
|
x0 = part0[clump_ids == n]
|
||||||
|
|
||||||
|
# Center of mass
|
||||||
|
cm = numpy.asanyarray(
|
||||||
|
[numpy.average(x0[p], weights=x0["M"]) for p in ('x', 'y', 'z')])
|
||||||
|
# Dump the center of mass
|
||||||
|
with open(ftemp.format(nsim, n), 'wb') as f:
|
||||||
|
numpy.save(f, cm)
|
||||||
|
# Optionally dump the entire clump
|
||||||
|
if args.dump_clumps:
|
||||||
|
fout = join(clumpdumpdir, "clump_{}.npy".format(n))
|
||||||
|
stdout.flush()
|
||||||
|
with open(fout, "wb") as f:
|
||||||
|
numpy.save(f, x0)
|
||||||
|
|
||||||
|
comm.Barrier()
|
||||||
|
if rank == 0:
|
||||||
|
print("Collecting CM files...")
|
||||||
|
stdout.flush()
|
||||||
|
# Collect the centre of masses and dump them
|
||||||
|
dtype = {"names": ['x', 'y', 'z', "ID"],
|
||||||
|
"formats": [numpy.float32] * 3 + [numpy.int32]}
|
||||||
|
out = numpy.full(njobs, numpy.nan, dtype=dtype)
|
||||||
|
|
||||||
|
for i, n in enumerate(unique_clumpids):
|
||||||
|
with open(ftemp.format(nsim, n), 'rb') as f:
|
||||||
|
fin = numpy.load(f)
|
||||||
|
out['x'][i] = fin[0]
|
||||||
|
out['y'][i] = fin[1]
|
||||||
|
out['z'][i] = fin[2]
|
||||||
|
out["ID"][i] = n
|
||||||
|
remove(ftemp.format(nsim, n))
|
||||||
|
|
||||||
|
print("Dumping CM files to .. `{}`.".format(fperm.format(nsim)))
|
||||||
|
with open(fperm.format(nsim), 'wb') as f:
|
||||||
|
numpy.save(f, out)
|
||||||
Loading…
Reference in a new issue