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https://github.com/Richard-Sti/csiborgtools.git
synced 2024-10-18 16:25:06 +02:00
Add SWIFT SPH (#147)
* Add new params * Add manticore params * Add SWIFT reader * Update script * Simplify * Add comment * Update H0 values for the void * Update queue
This commit is contained in:
Richard Stiskalek
GitHub
parent
1fc9ca9306
commit
c2bc5a6398
@ -610,6 +610,8 @@ def sample_calibration(Vext_min, Vext_max, Vmono_min, Vmono_max, beta_min,
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if no_Vext:
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Vext = jnp.zeros(3)
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# 840 in the direction of (l, b) = (117, 4)
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# Vext = jnp.asarray([338.9478154 , -11.45056064, 768.49415294])
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else:
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Vext = sample("Vext", Uniform(Vext_min, Vext_max).expand([3]))
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@ -71,6 +71,7 @@ def simname2boxsize(simname):
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"csiborg2_varysmall": 676.6,
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"csiborg2_random": 676.6,
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"csiborg2X": 681.1,
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"manticore_2MPP_N128_DES_V1": 681.1,
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"borg1": 677.7,
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"borg2": 676.6,
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"borg2_all": 676.6,
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@ -97,6 +98,7 @@ def simname2Omega_m(simname):
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"csiborg2_random": 0.3111,
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"csiborg2_varysmall": 0.3111,
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"csiborg2X": 0.306,
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"manticore_2MPP_N128_DES_V1": 0.306,
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"borg1": 0.307,
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"borg2": 0.3111,
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"borg2_all": 0.3111,
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@ -131,4 +133,5 @@ paths_glamdring = {
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"tng300_1_dir": "/mnt/extraspace/rstiskalek/TNG300-1/",
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"aux_cat_dir": "/mnt/extraspace/rstiskalek/catalogs",
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"CF4_dir": "/mnt/extraspace/rstiskalek/catalogs/CF4",
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"manticore_dir": "/mnt/extraspace/rstiskalek/MANTICORE",
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}
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@ -50,6 +50,8 @@ class Paths:
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Path to the CSiBORG2 random simulation directory.
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csiborg2_varysmall_srcdir : str
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Path to the CSiBORG2 varysmall simulation directory.
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manticore_srcdir : str
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Path to the MANTICORE simulation directory.
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postdir : str
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Path to the CSiBORG post-processing directory.
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quijote_dir : str
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@ -70,6 +72,7 @@ class Paths:
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csiborg2_main_srcdir,
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csiborg2_random_srcdir,
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csiborg2_varysmall_srcdir,
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manticore_dir,
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postdir,
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quijote_dir,
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borg1_dir,
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@ -82,6 +85,7 @@ class Paths:
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self.csiborg2_main_srcdir = csiborg2_main_srcdir
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self.csiborg2_random_srcdir = csiborg2_random_srcdir
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self.csiborg2_varysmall_srcdir = csiborg2_varysmall_srcdir
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self.manticore_dir = manticore_dir
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self.quijote_dir = quijote_dir
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self.borg1_dir = borg1_dir
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self.borg2_dir = borg2_dir
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@ -108,6 +112,12 @@ class Paths:
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files = glob(join(self.csiborg2_varysmall_srcdir, "chain_*"))
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files = [int(search(r'chain_16417_(\d+)', f).group(1))
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for f in files]
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elif "manticore" in simname:
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fdir = self.manticore_dir
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if simname == "manticore_2MPP_N128_DES_V1":
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fdir = join(fdir, "2MPP_N128_DES_V1", "resimulations", "R512")
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files = glob(join(fdir, "mcmc_*"))
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files = [int(search(r'mcmc_(\d+)', f).group(1)) for f in files]
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elif simname == "csiborg2X":
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# NOTE this too is preliminary
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fname = "/mnt/extraspace/rstiskalek/MANTICORE/resimulations/fields/2MPP_N128_DES_PROD/R512" # noqa
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@ -173,6 +183,8 @@ class Paths:
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snaps = sorted(snaps)
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elif simname == "csiborg2X":
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raise ValueError("Snapshots not available for CSiBORG2X.")
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elif "manticore" in simname:
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raise ValueError("Snapshots not available for MANTICORE.")
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elif simname == "quijote":
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snaps = glob(join(self.quijote_dir, "fiducial_processed",
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f"chain_{nsim}", "snapshot_*"))
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@ -203,6 +215,8 @@ class Paths:
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f"snapshot_{str(nsnap).zfill(3)}.hdf5")
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elif simname == "csiborg2X":
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raise ValueError("Snapshots not available for CSiBORG2X.")
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elif "manticore" in simname:
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raise ValueError("Snapshots not available for MANTICORE.")
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elif simname == "quijote":
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fpath = join(self.quijote_dir, "fiducial_processed",
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f"chain_{nsim}",
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@ -28,7 +28,13 @@ from tqdm import trange
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def interpolate_indranil_void(kind, nsims, RA, dec, rmax, dr, dump_folder,
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catalogue):
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if kind not in ["exp", "gauss", "mb"]:
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if kind == "mb":
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h = 0.7615
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elif kind == "gauss":
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h = 0.7724
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elif kind == "exp":
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h = 0.7725
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else:
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raise ValueError(f"Unknown void kind: `{kind}`.")
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kind = kind.upper()
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@ -48,11 +54,10 @@ def interpolate_indranil_void(kind, nsims, RA, dec, rmax, dr, dump_folder,
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fname = join(fdir, f"v_pec_{kind}profile_rLG_{nsim}.dat")
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data = np.loadtxt(fname)
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# The grid is in Mpc
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r_grid = np.arange(0, 251)
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# The grid is in Mpc from 0 to 251 but we convert to Mpc / h
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r_grid = np.arange(0, 251) * h
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phi_grid = np.arange(0, 181)
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# The input is in Mpc/h, so we need to convert to Mpc
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r_eval = np.arange(0, rmax, dr).astype(float) / 0.674
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r_eval = np.arange(0, rmax, dr).astype(float)
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model_axis = SkyCoord(l=117, b=4, frame='galactic', unit='deg').icrs
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coords = SkyCoord(ra=RA, dec=dec, unit='deg').icrs
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@ -76,7 +81,7 @@ def interpolate_indranil_void(kind, nsims, RA, dec, rmax, dr, dump_folder,
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# Write the output, homogenous density.
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density = np.ones_like(result)
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with File(fname_out, 'a') as f_out:
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f_out.create_dataset(f"rdist_{k}", data=r_eval * 0.674)
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f_out.create_dataset(f"rdist_{k}", data=r_eval)
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f_out.create_dataset(f"density_{k}", data=density)
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f_out.create_dataset(f"velocity_{k}", data=result)
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@ -1,7 +1,7 @@
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nthreads=1
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memory=7
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memory=4
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on_login=${1}
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queue="berg"
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queue="cmb"
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env="/mnt/users/rstiskalek/csiborgtools/venv_csiborg/bin/python"
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file="field_los_indranil_void.py"
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@ -107,6 +107,33 @@ def prepara_gadget2(snapshot_path, temporary_output_path):
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return boxsize
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def prepare_swift(snapshot_path, temporary_output_path):
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"""
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Read in SWIFT Manticore files from Stuart.
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"""
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# Get some basic information about the snapshots.
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with File(snapshot_path, 'r') as src, File(temporary_output_path, 'w') as target: # noqa
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h = src["Cosmology"].attrs["h"][0]
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npart = src["Header"].attrs["NumPart_Total"][1]
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# Convert to Msun / h
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mpart = src["Header"].attrs["InitialMassTable"][1] * 1e10 * h
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# Convert to Mpc / h
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boxsize = src["Header"].attrs["BoxSize"][0] * h
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print(f"{'Boxsize':<20}: {boxsize}")
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print(f"{'Npart':<20}: {npart}")
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print(f"{'Mpart':<20}: {mpart}")
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dset = target.create_dataset("particles", (npart, 7), dtype=np.float32)
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dset[:, :3] = src["DMParticles/Coordinates"][:] * h # Mpc / h
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dset[:, 3:6] = src["DMParticles/Velocities"][:] # km/s
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dset[:, 6] = np.ones(npart, dtype=np.float32) * mpart
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return boxsize
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def run_sph_filter(particles_path, output_path, boxsize, resolution,
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SPH_executable):
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"""
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@ -171,7 +198,7 @@ def main(snapshot_path, output_path, resolution, scratch_space, SPH_executable,
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[1] https://bitbucket.org/glavaux/cosmotool/src/master/sample/simple3DFilter.cpp # noqa
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"""
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# First get the temporary file path.
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if snapshot_kind in ["gadget2", "gadget4"]:
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if snapshot_kind in ["gadget2", "gadget4", "swift"]:
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temporary_output_path = join(
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scratch_space, generate_unique_id(snapshot_path))
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elif snapshot_kind == "ramses":
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@ -206,10 +233,12 @@ def main(snapshot_path, output_path, resolution, scratch_space, SPH_executable,
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print(f"{now()}: preparing snapshot...", flush=True)
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boxsize = prepara_gadget2(snapshot_path, temporary_output_path)
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print(f"{now()}: wrote temporary data to {temporary_output_path}.")
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elif snapshot_kind == "swift":
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print(f"{now()}: preparing snapshot...", flush=True)
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boxsize = prepare_swift(snapshot_path, temporary_output_path)
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print(f"{now()}: wrote temporary data to {temporary_output_path}.")
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else:
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boxsize = 677.7 # Mpc/h
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print(f"{now()}: CAREFUL, forcefully setting the boxsize to {boxsize} Mpc / h.", # noqa
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flush=True)
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raise RuntimeError(f"Snapshot kind `{snapshot_kind}` not implemented.")
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# Run the SPH filter.
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run_sph_filter(temporary_output_path, output_path, boxsize, resolution,
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@ -237,7 +266,7 @@ if __name__ == "__main__":
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parser.add_argument("--SPH_executable", type=str, required=True,
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help="Path to the `simple3DFilter` executable.")
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parser.add_argument("--snapshot_kind", type=str, required=True,
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choices=["gadget4", "gadget2", "ramses"],
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choices=["gadget4", "gadget2", "ramses", "swift"],
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help="Kind of the simulation snapshot.")
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args = parser.parse_args()
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@ -1,5 +1,5 @@
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#!/bin/bash
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nthreads=28
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nthreads=12
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memory=7
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on_login=${1}
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queue="berg"
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@ -11,9 +11,10 @@ resolution=1024
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SPH_executable="/mnt/users/rstiskalek/cosmotool/bld/sample/simple3DFilter"
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scratch_space="/mnt/extraspace/rstiskalek/dump/"
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snapshot_kind="gadget2"
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snapshot_path="/mnt/extraspace/rstiskalek/CLONES/s8/cf2gvpecc1pt5elmo73_sig6distribsbvoldi_RZA3Derrv2_512_500_ss8_zinit60_000"
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output_path="/mnt/extraspace/rstiskalek/CLONES/s8/cf2gvpecc1pt5elmo73_sig6distribsbvoldi_RZA3Derrv2_512_500_ss8_zinit60_000.hdf5"
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# CLONES settings
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# snapshot_kind="gadget2"
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# snapshot_path="/mnt/extraspace/rstiskalek/CLONES/s8/cf2gvpecc1pt5elmo73_sig6distribsbvoldi_RZA3Derrv2_512_500_ss8_zinit60_000"
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# output_path="/mnt/extraspace/rstiskalek/CLONES/s8/cf2gvpecc1pt5elmo73_sig6distribsbvoldi_RZA3Derrv2_512_500_ss8_zinit60_000.hdf5"
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# Check if `on_login` is either 0 or 1
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@ -26,14 +27,36 @@ fi
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export OMP_NUM_THREADS={nthreads}
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export OMP_NESTED=true
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pythoncm="$env $file --snapshot_path $snapshot_path --output_path $output_path --resolution $resolution --scratch_space $scratch_space --SPH_executable $SPH_executable --snapshot_kind $snapshot_kind"
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if [ $on_login -eq 1 ]; then
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echo $pythoncm
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$pythoncm
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else
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cm="addqueue -s -q $queue -n 1x$nthreads -m $memory $pythoncm"
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echo "Submitting:"
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echo $cm
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echo
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eval $cm
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fi
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# pythoncm="$env $file --snapshot_path $snapshot_path --output_path $output_path --resolution $resolution --scratch_space $scratch_space --SPH_executable $SPH_executable --snapshot_kind $snapshot_kind"
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# if [ $on_login -eq 1 ]; then
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# echo $pythoncm
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# $pythoncm
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# else
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# cm="addqueue -s -q $queue -n 1x$nthreads -m $memory $pythoncm"
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# echo "Submitting:"
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# echo $cm
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# echo
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# eval $cm
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# fi
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# Manticore SWIFT submission loop
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snapshot_kind="swift"
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for k in {0..40}; do
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snapshot_path="/mnt/extraspace/rstiskalek/MANTICORE/2MPP_N128_DES_V1/resimulations/R512/mcmc_$k/swift_monofonic/snap_0001/snap_0001.hdf5"
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output_path="/mnt/extraspace/rstiskalek/MANTICORE/2MPP_N128_DES_V1/fields/R512/SPH_$k.hdf5"
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pythoncm="$env $file --snapshot_path $snapshot_path --output_path $output_path --resolution $resolution --scratch_space $scratch_space --SPH_executable $SPH_executable --snapshot_kind $snapshot_kind"
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if [ $on_login -eq 1 ]; then
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echo $pythoncm
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$pythoncm
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else
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cm="addqueue -s -q $queue -n 1x$nthreads -m $memory $pythoncm"
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echo "Submitting:"
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echo $cm
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echo
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eval $cm
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fi
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sleep 0.05
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done
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