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Overlap fixing and more (#107)
* Update README * Update density field reader * Update name of SDSSxALFAFA * Fix quick bug * Add little fixes * Update README * Put back fit_init * Add paths to initial snapshots * Add export * Remove some choices * Edit README * Add Jens' comments * Organize imports * Rename snapshot * Add additional print statement * Add paths to initial snapshots * Add masses to the initial files * Add normalization * Edit README * Update README * Fix bug in CSiBORG1 so that does not read fof_00001 * Edit README * Edit README * Overwrite comments * Add paths to init lag * Fix Quijote path * Add lagpatch * Edit submits * Update README * Fix numpy int problem * Update README * Add a flag to keep the snapshots open when fitting * Add a flag to keep snapshots open * Comment out some path issue * Keep snapshots open * Access directly snasphot * Add lagpatch for CSiBORG2 * Add treatment of x-z coordinates flipping * Add radial velocity field loader * Update README * Add lagpatch to Quijote * Fix typo * Add setter * Fix typo * Update README * Add output halo cat as ASCII * Add import * Add halo plot * Update README * Add evaluating field at radial distanfe * Add field shell evaluation * Add enclosed mass computation * Add BORG2 import * Add BORG boxsize * Add BORG paths * Edit run * Add BORG2 overdensity field * Add bulk flow clauclation * Update README * Add new plots * Add nbs * Edit paper * Update plotting * Fix overlap paths to contain simname * Add normalization of positions * Add default paths to CSiBORG1 * Add overlap path simname * Fix little things * Add CSiBORG2 catalogue * Update README * Add import * Add TNG density field constructor * Add TNG density * Add draft of calculating BORG ACL * Fix bug * Add ACL of enclosed density * Add nmean acl * Add galaxy bias calculation * Add BORG acl notebook * Add enclosed mass calculation * Add TNG300-1 dir * Add TNG300 and BORG1 dir * Update nb
This commit is contained in:
Richard Stiskalek
GitHub
parent
0984191dc8
commit
9e4b34f579
30 changed files with 10037 additions and 248 deletions
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@ -174,8 +174,7 @@ class CSiBORG1Reader:
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if which_snapshot == "initial":
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self.nsnap = 1
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raise RuntimeError("TODO not implemented")
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self.source_dir = None
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self.source_dir = f"/mnt/extraspace/rstiskalek/csiborg1/initial/ramses_out_{nsim}_new/output_00001" # noqa
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elif which_snapshot == "final":
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sourcedir = join(base_dir, f"ramses_out_{nsim}")
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self.nsnap = max([int(basename(f).replace("output_", ""))
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@ -195,7 +194,7 @@ class CSiBORG1Reader:
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self.sph_file = f"/mnt/extraspace/rstiskalek/csiborg1/sph_temp/chain_{self.nsim}.hdf5" # noqa
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def read_info(self):
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filename = glob(join(self.source_dir, "info_*"))
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filename = glob(join(self.source_dir, "info_*.txt"))
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if len(filename) > 1:
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raise ValueError("Found too many `info` files.")
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filename = filename[0]
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@ -675,6 +674,7 @@ def process_final_snapshot(nsim, simname):
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flush=True)
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# Lastly, create the halo mapping and default catalogue.
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print(f"{now()}: writing `{reader.output_cat}`.")
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print(f"{datetime.now()}: creating `GroupOffset`...")
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halo_map, unique_halo_ids = make_offset_map(halo_ids)
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# Dump the halo mapping.
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@ -744,8 +744,9 @@ def process_initial_snapshot(nsim, simname):
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del sort_indxs_final
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collect()
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print(f"{now()}: loading and sorting the initial particle position.")
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print(f"{now()}: loading and sorting the initial particle information.")
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pos = reader.read_snapshot("pos")[sort_indxs]
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mass = reader.read_snapshot("mass")[sort_indxs]
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del sort_indxs
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collect()
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@ -764,6 +765,8 @@ def process_initial_snapshot(nsim, simname):
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with File(reader.output_snap, 'w') as f:
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f.create_dataset("Coordinates", data=pos,
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**hdf5plugin.Blosc(**BLOSC_KWARGS))
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f.create_dataset("Masses", data=mass,
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**hdf5plugin.Blosc(**BLOSC_KWARGS))
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def process_initial_snapshot_csiborg2(nsim, simname):
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@ -836,39 +839,6 @@ def process_initial_snapshot_csiborg2(nsim, simname):
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**hdf5plugin.Blosc(**BLOSC_KWARGS))
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###############################################################################
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# Prepare CSiBORG1 RAMSES for SPH density field #
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###############################################################################
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def prepare_csiborg1_for_sph(nsim):
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"""
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Prepare a RAMSES snapshot for cosmotool SPH density & velocity field
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calculation.
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"""
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reader = CSiBORG1Reader(nsim, "final")
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print("------- Preparing CSiBORG1 for SPH -------")
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print(f"Simulation index: {nsim}")
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print(f"Output file: {reader.sph_file}")
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print("-------------------------------------------------")
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print(flush=True)
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with File(reader.sph_file, 'w') as dest:
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# We need to read pos first to get the dataset size
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pos = reader.read_snapshot("pos")
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dset = dest.create_dataset("particles", (len(pos), 7),
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dtype=numpy.float32)
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dset[:, :3] = pos
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del pos
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collect()
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dset[:, 3:6] = reader.read_snapshot("vel")
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dset[:, 6] = reader.read_snapshot("mass")
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###############################################################################
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# Command line interface #
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###############################################################################
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@ -883,8 +853,8 @@ if __name__ == "__main__":
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"csiborg2_random", "csiborg2_varysmall"],
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help="Simulation name.")
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parser.add_argument("--mode", type=int, required=True,
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choices=[0, 1, 2, 3],
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help="0: process final snapshot, 1: process initial snapshot, 2: process both, 3: prepare CSiBORG1 for SPH.") # noqa
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choices=[0, 1, 2],
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help="0: process final snapshot, 1: process initial snapshot, 2: process both") # noqa
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args = parser.parse_args()
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if "csiborg2" in args.simname and args.mode in [0, 2]:
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@ -897,8 +867,6 @@ if __name__ == "__main__":
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process_final_snapshot(args.nsim, args.simname)
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elif args.mode == 1:
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process_initial_snapshot(args.nsim, args.simname)
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elif args.mode == 2:
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else:
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process_final_snapshot(args.nsim, args.simname)
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process_initial_snapshot(args.nsim, args.simname)
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else:
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prepare_csiborg1_for_sph(args.nsim)
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