mirror of
https://github.com/Richard-Sti/csiborgtools_public.git
synced 2025-05-12 05:38:42 +00:00
Within halo work and NFW fit (#4)
* add listing of snapshots * change distance to comoving * ignore cp files * rename nb * add str to list * add NFW profile shapes * add fits imports * Rename to Nsnap * in clumps_read only select props * make clumpid int * expand doc * add import * edit readme * distribute halos * add profile & posterior * add import * add import * add documentation * add rvs and init guess * update todo * update nb * add file * return end index too * change clump_ids format to int32 * skeleton of dump particle * update nb * add func to drop 0 clump indxs parts * add import * add halo dump * switch to float32 * Update TODO * update TODO * add func that loads a split * add halo object * Rename to clump * make post work with a clump * add optimiser * add Nsplits * ignore submission scripts * ignore .out * add dumppath * add job splitting * add split halos script * rename file * renaem files * rm file * rename imports * edit desc * add pick clump * add number of particles * update TODO * update todo * add script * add dumping * change dumpdir structure * change dumpdir * add import * Remove tqdm * Increase the number of splits * rm shuffle option * Change to remove split * add emojis * fix part counts in splits * change num of splits * rm with particle cut * keep splits * fit only if 10 part and more * add min distance * rm warning about not set vels * update TODO * calculate rho0 too * add results collection * add import * add func to combine splits * update TODO * add extract cols * update nb * update TODO
This commit is contained in:
Richard Stiskalek
GitHub
parent
85a6a6d58a
commit
8a56c22813
15 changed files with 3815 additions and 397 deletions
2484
scripts/concentration_fit.ipynb
Normal file
2484
scripts/concentration_fit.ipynb
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File diff suppressed because one or more lines are too long
92
scripts/run_fit_halos.py
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92
scripts/run_fit_halos.py
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@ -0,0 +1,92 @@
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# Copyright (C) 2022 Richard Stiskalek
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# This program is free software; you can redistribute it and/or modify it
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# under the terms of the GNU General Public License as published by the
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# Free Software Foundation; either version 3 of the License, or (at your
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# option) any later version.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
|
||||
# Public License for more details.
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||||
#
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||||
# 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.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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"""
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A script to fit halos (concentration, ...). The particle array of each CSiBORG
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realisation must have been split in advance by `run_split_halos`.
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"""
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import numpy
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from os.path import join
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from mpi4py import MPI
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try:
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import csiborgtools
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except ModuleNotFoundError:
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import sys
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sys.path.append("../")
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import csiborgtools
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import utils
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F64 = numpy.float64
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I64 = numpy.int64
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# Simulations and their snapshot to analyze
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Nsims = [9844]
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Nsnap = 1016
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# Get MPI things
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comm = MPI.COMM_WORLD
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rank = comm.Get_rank()
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nproc = comm.Get_size()
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dumpdir = utils.dumpdir
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loaddir = join(utils.dumpdir, "temp")
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cols_collect = [("npart", I64), ("totpartmass", F64), ("logRs", F64),
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("rho0", F64)]
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# NOTE later loop over sims too
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Nsim = Nsims[0]
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jobs = csiborgtools.fits.split_jobs(utils.Nsplits, nproc)[rank]
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for Nsplit in jobs:
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print("Rank {} working on {}.".format(rank, Nsplit))
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parts, part_clumps, clumps = csiborgtools.fits.load_split_particles(
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Nsplit, loaddir, Nsim, Nsnap, remove_split=False)
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N = clumps.size
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cols = [("index", I64), ("npart", I64), ("totpartmass", F64),
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("logRs", F64), ("rho0", F64)]
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out = csiborgtools.utils.cols_to_structured(N, cols)
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out["index"] = clumps["index"]
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for n in range(N):
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# Pick clump and its particles
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xs = csiborgtools.fits.pick_single_clump(n, parts, part_clumps, clumps)
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clump = csiborgtools.fits.Clump.from_arrays(*xs)
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out["npart"][n] = clump.Npart
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out["totpartmass"][n] = clump.total_particle_mass
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# NFW profile fit
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if clump.Npart > 10:
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nfwpost = csiborgtools.fits.NFWPosterior(clump)
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logRs = nfwpost.maxpost_logRs()
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if logRs.success:
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out["logRs"][n] = logRs.x
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out["rho0"][n] = nfwpost.rho0_from_logRs(logRs.x)
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csiborgtools.io.dump_split(out, Nsplit, Nsim, Nsnap, dumpdir)
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# Force all ranks to wait
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comm.Barrier()
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# Use the rank 0 to combine outputs for this CSiBORG realisation
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if rank == 0:
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print("Collecting results!")
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out_collected = csiborgtools.io.combine_splits(
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utils.Nsplits, Nsim, Nsnap, utils.dumpdir, cols_collect,
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remove_splits=True, verbose=False)
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fname = join(utils.dumpdir, "ramses_out_{}_{}.npy"
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.format(str(Nsim).zfill(5), str(Nsnap).zfill(5)))
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print("Saving results to `{}`.".format(fname))
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numpy.save(fname, out_collected)
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print("All finished! See ya!")
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51
scripts/run_split_halos.py
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51
scripts/run_split_halos.py
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@ -0,0 +1,51 @@
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# Copyright (C) 2022 Richard Stiskalek
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# This program is free software; you can redistribute it and/or modify it
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# under the terms of the GNU General Public License as published by the
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# Free Software Foundation; either version 3 of the License, or (at your
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# option) any later version.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
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||||
# Public License for more details.
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#
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# You should have received a copy of the GNU General Public License along
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||||
# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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"""
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Script to split particles into smaller files according to their clump
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membership for faster manipulation. Running this will require a lot of memory.
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"""
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from tqdm import tqdm
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from os.path import join
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try:
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import csiborgtools
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except ModuleNotFoundError:
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import sys
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sys.path.append("../")
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import csiborgtools
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import utils
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Nsims = [9844]
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Nsnap = 1016
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partcols = ["x", "y", "z", "M", "level"]
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dumpdir = join(utils.dumpdir, "temp")
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for Nsim in tqdm(Nsims):
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simpath = csiborgtools.io.get_sim_path(Nsim)
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# Load the clumps, particles' clump IDs and particles.
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clumps = csiborgtools.io.read_clumps(Nsnap, simpath)
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particle_clumps = csiborgtools.io.read_clumpid(Nsnap, simpath,
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verbose=False)
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particles = csiborgtools.io.read_particle(partcols, Nsnap, simpath,
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verbose=False)
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# Drop all particles whose clump index is 0 (not assigned to any halo)
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particle_clumps, particles = csiborgtools.io.drop_zero_indx(
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particle_clumps, particles)
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# Dump it!
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csiborgtools.fits.dump_split_particles(particles, particle_clumps, clumps,
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utils.Nsplits, dumpdir, Nsim, Nsnap,
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verbose=False)
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print("All finished!")
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@ -1,352 +0,0 @@
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{
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"cells": [
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{
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"cell_type": "code",
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||||
"execution_count": 2,
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||||
"id": "5a38ed25",
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||||
"metadata": {
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||||
"ExecuteTime": {
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||||
"end_time": "2022-10-20T21:53:10.387523Z",
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||||
"start_time": "2022-10-20T21:53:08.558627Z"
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}
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},
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"outputs": [],
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"source": [
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"import numpy as np\n",
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"try:\n",
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" import csiborgtools\n",
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"except ModuleNotFoundError:\n",
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" import sys\n",
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" sys.path.append(\"../\")\n",
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" import csiborgtools\n",
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" \n",
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" \n",
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"%load_ext autoreload\n",
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"%autoreload 2"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 23,
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||||
"id": "7accd798",
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||||
"metadata": {
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||||
"ExecuteTime": {
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||||
"end_time": "2022-10-20T22:00:25.350404Z",
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||||
"start_time": "2022-10-20T22:00:24.775748Z"
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}
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},
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"outputs": [],
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"source": [
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"simpath = csiborgtools.io.get_sim_path(9844)\n",
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"Nsnap = 1016\n",
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"# csiborgtools.io.read_info(1016, simpath)"
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]
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},
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{
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"cell_type": "code",
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||||
"execution_count": 59,
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||||
"id": "131c3107",
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||||
"metadata": {
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||||
"ExecuteTime": {
|
||||
"end_time": "2022-10-20T22:25:59.104572Z",
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||||
"start_time": "2022-10-20T22:25:59.074460Z"
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}
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},
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"outputs": [],
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"source": [
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"box = csiborgtools.units.BoxUnits(Nsnap, simpath)"
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]
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},
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{
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"cell_type": "code",
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||||
"execution_count": 61,
|
||||
"id": "b1a11aa6",
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2022-10-20T22:26:12.931468Z",
|
||||
"start_time": "2022-10-20T22:26:12.671686Z"
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||||
}
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||||
},
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||||
"outputs": [
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||||
{
|
||||
"data": {
|
||||
"text/plain": [
|
||||
"3.765003070876428e+19"
|
||||
]
|
||||
},
|
||||
"execution_count": 61,
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||||
"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"box.box2solarmass(1)"
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]
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||||
},
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||||
{
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||||
"cell_type": "code",
|
||||
"execution_count": 55,
|
||||
"id": "19f39a80",
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2022-10-20T22:24:59.563137Z",
|
||||
"start_time": "2022-10-20T22:24:59.530173Z"
|
||||
}
|
||||
},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"text/plain": [
|
||||
"3.749e+19"
|
||||
]
|
||||
},
|
||||
"execution_count": 55,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"3.749e19"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 57,
|
||||
"id": "5d1413fd",
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2022-10-20T22:25:17.251057Z",
|
||||
"start_time": "2022-10-20T22:25:17.223543Z"
|
||||
}
|
||||
},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"text/plain": [
|
||||
"0.9957495198343349"
|
||||
]
|
||||
},
|
||||
"execution_count": 57,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"box.solarmass2box(3.749e19)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "90cf9d61",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": []
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "b53e8166",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": []
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "b3eeca5b",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": []
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 49,
|
||||
"id": "93d32800",
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2022-10-20T22:09:12.915516Z",
|
||||
"start_time": "2022-10-20T22:09:12.856213Z"
|
||||
}
|
||||
},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"text/plain": [
|
||||
"0.9988759675724455"
|
||||
]
|
||||
},
|
||||
"execution_count": 49,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"box.kpc2box(677.7 / 0.705 * 1000)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 43,
|
||||
"id": "66d3e98f",
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2022-10-20T22:06:46.471218Z",
|
||||
"start_time": "2022-10-20T22:06:46.437023Z"
|
||||
}
|
||||
},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"text/plain": [
|
||||
"678.4626139789958"
|
||||
]
|
||||
},
|
||||
"execution_count": 43,
|
||||
"metadata": {},
|
||||
"output_type": "execute_result"
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"box.box2kpc(1) / 1000 * 0.705"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "ef00a04c",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": []
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "d201838b",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"filename = \"/mnt/extraspace/hdesmond/ramses_out_9844/output_01016/info_01016.txt\""
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "d012a21b",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": []
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "547f7944",
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2022-10-20T19:52:22.548299Z",
|
||||
"start_time": "2022-10-20T19:52:22.544342Z"
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"results_filepath = '/mnt/extraspace/deaglan/H-AGN/'\n",
|
||||
"sugata_filepath = '/mnt/extraspace/jeg/greenwhale/Sugata/'\n",
|
||||
"\n",
|
||||
"def info_dir():\n",
|
||||
" return sugata_filepath + 'INFO/'\n",
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||||
"\n",
|
||||
"def info_file(nout):\n",
|
||||
" return info_dir() + 'info_' + str(nout).zfill(5) + '.txt'\n",
|
||||
"\n",
|
||||
"def h_agn_particle_directory(nout):\n",
|
||||
" return sugata_filepath + 'H-AGN/output_' + str(nout).zfill(5) + '/'\n",
|
||||
"\n",
|
||||
"def cosmo_dir():\n",
|
||||
" return './data/'\n",
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||||
"\n",
|
||||
"def cosmo_file(nout):\n",
|
||||
" return cosmo_dir() + 'cosmo_table_' + str(nout).zfill(5) + '.txt'"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "30630635",
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2022-10-20T19:52:22.777853Z",
|
||||
"start_time": "2022-10-20T19:52:22.774584Z"
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"info_dir()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "a3fc21b2",
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2022-10-20T19:56:35.946185Z",
|
||||
"start_time": "2022-10-20T19:56:35.943643Z"
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"filename = \"/mnt/extraspace/hdesmond/ramses_out_9844/output_01016/info_01016.txt\""
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "fae40a32",
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2022-10-20T20:05:04.410987Z",
|
||||
"start_time": "2022-10-20T20:05:04.403721Z"
|
||||
},
|
||||
"scrolled": false
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"e"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "de7e3ae7",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": []
|
||||
}
|
||||
],
|
||||
"metadata": {
|
||||
"kernelspec": {
|
||||
"display_name": "Python 3.8.0 ('venv_galomatch': virtualenv)",
|
||||
"language": "python",
|
||||
"name": "python3"
|
||||
},
|
||||
"language_info": {
|
||||
"codemirror_mode": {
|
||||
"name": "ipython",
|
||||
"version": 3
|
||||
},
|
||||
"file_extension": ".py",
|
||||
"mimetype": "text/x-python",
|
||||
"name": "python",
|
||||
"nbconvert_exporter": "python",
|
||||
"pygments_lexer": "ipython3",
|
||||
"version": "3.8.0"
|
||||
},
|
||||
"vscode": {
|
||||
"interpreter": {
|
||||
"hash": "f29d02a8350410abc2a9fb79641689d10bf7ab64afc03ec87ca3cf6ed2daa499"
|
||||
}
|
||||
}
|
||||
},
|
||||
"nbformat": 4,
|
||||
"nbformat_minor": 5
|
||||
}
|
||||
|
|
@ -28,6 +28,10 @@ except ModuleNotFoundError:
|
|||
sys.path.append("../")
|
||||
|
||||
|
||||
Nsplits = 200
|
||||
dumpdir = "/mnt/extraspace/rstiskalek/csiborg/"
|
||||
|
||||
|
||||
def load_mmain_convert(n):
|
||||
srcdir = "/users/hdesmond/Mmain"
|
||||
arr = csiborgtools.io.read_mmain(n, srcdir)
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue