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Add cleaner paths (#43)

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* ignore venv

* ignore pylians if unavaible

* Edit loading paths

* Edit paths

* Stop having default paths

* Add nb

* Add glamdring paths

---------

Co-authored-by: Richard Stiskalek <dc-stis1@login8b.pri.cosma7.alces.network>
Co-authored-by: Richard Stiskalek <dc-stis1@login8a.pri.cosma7.alces.network>
This commit is contained in:
Richard Stiskalek 2023-04-14 23:24:52 +01:00 • committed by GitHub
parent 1344fa40b6
commit e0d3854277
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GPG key ID: 4AEE18F83AFDEB23
15 changed files with 1421 additions and 50 deletions
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2
scripts/crosspk.py
View file

@ -46,7 +46,7 @@ rank = comm.Get_rank()
nproc = comm.Get_size()
MAS = "CIC" # mass asignment scheme
paths = csiborgtools.read.CSiBORGPaths()
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
box = csiborgtools.units.BoxUnits(paths)
reader = csiborgtools.read.ParticleReader(paths)
ics = paths.ic_ids(tonew=False)

2
scripts/fieldprop.py
View file

@ -60,7 +60,7 @@ fperm = join(dumpdir, "fields", fname + ".npy")
dtype = {"names": ["delta", "phi"], "formats": [numpy.float32] * 2}
# CSiBORG simulation paths
paths = csiborgtools.read.CSiBORGPaths()
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
ics = paths.ic_ids(tonew=False)
nsims = len(ics)

5
scripts/fit_halos.py
View file

@ -34,7 +34,7 @@ comm = MPI.COMM_WORLD
rank = comm.Get_rank()
nproc = comm.Get_size()
paths = csiborgtools.read.CSiBORGPaths()
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
dumpdir = "/mnt/extraspace/rstiskalek/csiborg/"
loaddir = join(dumpdir, "temp")
cols_collect = [("npart", numpy.int64), ("totpartmass", numpy.float64),
@ -118,8 +118,7 @@ for i, nsim in enumerate(paths.ic_ids(tonew=False)):
out_collected = csiborgtools.read.combine_splits(
utils.Nsplits, nsnap, nsim, partreader, cols_collect,
remove_splits=True, verbose=False)
fname = join(paths.dumpdir, "ramses_out_{}_{}.npy"
.format(str(nsim).zfill(5), str(nsnap).zfill(5)))
fname = paths.hcat_path(nsim)
print("Saving results to `{}`.".format(fname))
numpy.save(fname, out_collected)

12
scripts/initmatch.py
View file

@ -44,25 +44,23 @@ parser = ArgumentParser()
parser.add_argument("--dump_clumps", type=lambda x: bool(strtobool(x)))
args = parser.parse_args()
paths = csiborgtools.read.CSiBORGPaths()
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
nsims = paths.ic_ids(tonew=True)
# Output files
dumpdir = "/mnt/extraspace/rstiskalek/csiborg/"
ftemp = join(dumpdir, "temp_initmatch", "temp_{}_{}_{}.npy")
fpermcm = join(dumpdir, "initmatch", "clump_{}_cm.npy")
fpermpart = join(dumpdir, "initmatch", "clump_{}_particles.npy")
ftemp = join(paths.dumpdir, "temp_initmatch", "temp_{}_{}_{}.npy")
fpermcm = join(paths.dumpdir, "initmatch", "clump_{}_cm.npy")
fpermpart = join(paths.dumpdir, "initmatch", "clump_{}_particles.npy")
for nsim in nsims:
if rank == 0:
print("{}: reading simulation {}.".format(datetime.now(), nsim),
flush=True)
nsnap_min = min(paths.get_snapshots(nsim))
nsnap_max = max(paths.get_snapshots(nsim))
reader = csiborgtools.read.ParticleReader(paths)
# Read and sort the initial particle files by their particle IDs
part0 = reader.read_particle(nsnap_min, nsim, ["x", "y", "z", "M", "ID"],
part0 = reader.read_particle(1, nsim, ["x", "y", "z", "M", "ID"],
verbose=False)
part0 = part0[numpy.argsort(part0["ID"])]

2
scripts/knn_auto.py
View file

@ -60,7 +60,7 @@ ics = [7444, 7468, 7492, 7516, 7540, 7564, 7588, 7612, 7636, 7660, 7684,
9820, 9844]
dumpdir = "/mnt/extraspace/rstiskalek/csiborg/knn"
fout = join(dumpdir, "auto", "knncdf_{}_{}.p")
paths = csiborgtools.read.CSiBORGPaths()
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
knncdf = csiborgtools.clustering.kNN_CDF()
###############################################################################

2
scripts/knn_cross.py
View file

@ -58,7 +58,7 @@ ics = [7444, 7468, 7492, 7516, 7540, 7564, 7588, 7612, 7636, 7660, 7684,
9292, 9316, 9340, 9364, 9388, 9412, 9436, 9460, 9484, 9508, 9532,
9556, 9580, 9604, 9628, 9652, 9676, 9700, 9724, 9748, 9772, 9796,
9820, 9844]
paths = csiborgtools.read.CSiBORGPaths()
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
dumpdir = "/mnt/extraspace/rstiskalek/csiborg/knn"
fout = join(dumpdir, "cross", "knncdf_{}_{}_{}.p")
knncdf = csiborgtools.clustering.kNN_CDF()

2
scripts/singlematch.py
View file

@ -35,7 +35,7 @@ parser.add_argument("--sigma", type=float)
args = parser.parse_args()
# File paths
paths = csiborgtools.read.CSiBORGPaths()
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
fout = join(utils.dumpdir, "overlap",
"cross_{}_{}.npz".format(args.nsim0, args.nsimx))
smooth_kwargs = {"sigma": args.sigma, "mode": "constant", "cval": 0.0}

2
scripts/split_halos.py
View file

@ -32,7 +32,7 @@ comm = MPI.COMM_WORLD
rank = comm.Get_rank()
nproc = comm.Get_size()
paths = csiborgtools.read.CSiBORGPaths()
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
sims = paths.ic_ids(False)
partcols = ["x", "y", "z", "vx", "vy", "vz", "M", "level"]