add galactica import scripts
This commit is contained in:
Noe Brucy
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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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# This file is part of the 'astrophysix' Python package.
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#
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# Copyright © Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA)
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#
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# FREE SOFTWARE LICENCING
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# -----------------------
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# This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free
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# software. You can use, modify and/or redistribute the software under the terms of the CeCILL license as circulated by
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# CEA, CNRS and INRIA at the following URL: "http://www.cecill.info". As a counterpart to the access to the source code
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# and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty
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# and the software's author, the holder of the economic rights, and the successive licensors have only limited
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# liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying
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# and/or developing or reproducing the software by the user in light of its specific status of free software, that may
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# mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and
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# experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the
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# software's suitability as regards their requirements in conditions enabling the security of their systems and/or data
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# to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that
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# you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms.
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#
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#
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# COMMERCIAL SOFTWARE LICENCING
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# -----------------------------
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# You can obtain this software from CEA under other licencing terms for commercial purposes. For this you will need to
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# negotiate a specific contract with a legal representative of CEA.
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#
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from __future__ import print_function, unicode_literals
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import os
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import numpy as N
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import h5py
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from astrophysix.simdm import SimulationStudy, Project, ProjectCategory
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from astrophysix.simdm.experiment import (
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Simulation,
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AppliedAlgorithm,
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ParameterSetting,
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ParameterVisibility,
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ResolvedPhysicalProcess,
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)
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from astrophysix.simdm.protocol import (
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SimulationCode,
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AlgoType,
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Algorithm,
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InputParameter,
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PhysicalProcess,
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Physics,
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)
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from astrophysix.simdm.results import GenericResult, Snapshot
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from astrophysix.simdm.datafiles import Datafile, PlotType, PlotInfo
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from astrophysix.utils.file import FileType
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from astrophysix import units as U
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from plotter import *
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import datetime
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from mpl_toolkits.axes_grid1 import AxesGrid, Grid
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from matplotlib import gridspec
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P.rcParams["text.usetex"] = False
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pp_params = default_params()
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pp_params.input.nml_filename = "disk.nml"
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# pp_params.out.interactive = True
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pp_params.pymses.map_size = 2048
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pp_params.pymses.zoom = 4
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pp_params.pymses.filter = False
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pp_params.pymses.variables = ["rho", "vel", "P", "g"]
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pp_params.pymses.multiprocessing = True
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pp_params.process.verbose = True
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pp_params.disk.enable = True
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pp_params.disk.nb_bin = 100
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pp_params.pdf.nb_bin = 100
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pp_params.process.num_process = 10
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in_dir = "/drf/projets/alfven-data/nbrucy/simus/fragdisk"
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out_dir = "/dsm/anais/storageA/nbrucy/visus/fragdisk/mnras"
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nml_key = "cloud_params/beta_cool"
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# --- Runs -----
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pp_params.astrophysix.simu_fmt = "beta{nml[cloud_params/beta_cool]:g}_{tag:.8}"
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pp_params.astrophysix.descr_fmt = (
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"Group {tag:.8}, $\\beta$ = {nml[cloud_params/beta_cool]}"
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)
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pl_orp = Plotter(
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in_dir,
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filter_name="104_beta4_jr13",
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in_nums="last",
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path_out=out_dir,
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pp_params=pp_params,
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)
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orp = cst.Unit.create_unit("ORP", base_unit=pl_orp.comp.info["unit_time"] * 0.79)
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# JR13_TIC
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runs = "*_jr13"
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pl_jr13 = Plotter(
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in_dir,
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filter_name=runs,
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in_nums="all",
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sort_run_by=nml_key,
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path_out=out_dir,
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tag="jr13_tic_mnras",
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pp_params=pp_params,
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unit_time=orp,
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)
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print("JR13_TIC defined")
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# JR12_TIC
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runs_12 = "0[0-9][0-9]_beta*_jr12"
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pl_jr12_tic = Plotter(
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in_dir,
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filter_name=runs_12,
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in_nums="all",
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sort_run_by=nml_key,
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filter_nml=("cloud_params", "!=", 7),
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path_out=out_dir,
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tag="jr12_tic_mnras",
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pp_params=pp_params,
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unit_time=orp,
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)
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pp_params.astrophysix.simu_fmt = "beta{nml[cloud_params/beta_cool]:g}_{tag:.4}"
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pp_params.astrophysix.descr_fmt = (
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"Group {tag:.4}, $\\beta$ = {nml[cloud_params/beta_cool]}"
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)
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print("JR12_TIC defined")
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# JR12
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in_dir_conv = "/drf/projets/alfven-data/nbrucy/simus/conv_disk"
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out_dir_conv = "/dsm/anais/storageA/nbrucy/visus/conv_disk"
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runs = "[7-8][0-9]_beta*_j*"
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pl_jr12 = Plotter(
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in_dir_conv,
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filter_name=runs,
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in_nums="all",
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sort_run_by=nml_key,
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path_out=out_dir,
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tag="jr12_mnras",
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pp_params=pp_params,
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unit_time=orp,
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)
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print("JR12 defined")
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# JR11
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runs = "*beta*_jr11"
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pl_l11 = Plotter(
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in_dir_conv,
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filter_name=runs,
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sort_run_by=nml_key,
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filter_nml=("cloud_params/beta_cool", ">", 3),
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path_out=out_dir_conv,
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tag="jr11_mnras",
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pp_params=pp_params,
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unit_time=orp,
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)
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print("JR11 defined")
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pls = [pl_l11, pl_jr12, pl_jr12_tic, pl_jr13]
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# ----------------------------------------------- Project creation --------------------------------------------------- #
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# Available project categories are :
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# - ProjectCategory.SolarMHD
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# - ProjectCategory.PlanetaryAtmospheres
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# - ProjectCategory.StarPlanetInteractions
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# - ProjectCategory.StarFormation
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# - ProjectCategory.Supernovae
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# - ProjectCategory.GalaxyFormation
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# - ProjectCategory.GalaxyMergers
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# - ProjectCategory.Cosmology
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proj = Project(
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category=ProjectCategory.StarPlanetInteractions,
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project_title="Fragdisk",
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alias="FRAGDISK",
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short_description="Fragmentation of self-gravitating disks",
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general_description="""
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Study of the fragmentation of self-gravitating disks. See Brucy & Hennebelle 2021 (submitted) for more details.
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This database is currently being completed.
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Abstract:
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Self-gravitating disks are believed to play an important role in astrophysics in particular regarding the star and planet formation process.
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In this context, disks subject to an idealized cooling process, characterized by a cooling timescale β expressed in unit of orbital timescale,
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have been extensively studied. We take advantage of the Riemann solver and the 3D Godunov scheme implemented in the code Ramses
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to perform high resolution simulations, complementing previous studies that have used Smoothed Particle Hydrodynamics (SPH) or 2D grid codes.
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""",
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data_description="""The data available for this project is the underlying data of the article Brucy & Hennebelle 2021.
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The data is not already fully uploaded. 3D datacube extraction on demand is planned""",
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directory_path="~nbrucy/simus/fragdisk",
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)
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print(proj)
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# -------------------------------------------------------------------------------------------------------------------- #
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# -------------------------------------------------------------------------------------------------------------------- #
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redo = True
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for pl in pls:
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pl.pp_params.process.verbose = True
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pl.comp.pp_params.process.verbose = True
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for run in pl.runs:
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simu = pl.simulations[run]
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proj.simulations.add(simu)
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# -------------------------------------------------------------------------------------------------------------------- #
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for pl in pls:
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select = {"time": 4.5}
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pl.coldens(
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"z",
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overwrite=redo,
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overwrite_dep=False,
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unit_space=cst.cm,
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unit_time=orp,
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nml_key="cloud_params/beta_cool",
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vmin=1e-2,
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vmax=1e2,
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put_units=False,
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select=select,
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label=r"$\Sigma$",
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)
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pl.coldens(
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"y",
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overwrite=redo,
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overwrite_dep=False,
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unit_space=cst.cm,
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unit_time=orp,
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nml_key="cloud_params/beta_cool",
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vmin=1e-2,
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vmax=1e2,
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put_units=False,
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select=select,
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label=r"$\Sigma$",
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)
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pl.slice_rho(
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"z",
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overwrite=redo,
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overwrite_dep=False,
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unit_space=cst.cm,
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unit_time=orp,
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nml_key="cloud_params/beta_cool",
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put_units=False,
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select=select,
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label=r"$\rho$",
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)
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pl.slice_rho(
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"y",
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overwrite=redo,
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overwrite_dep=False,
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unit_space=cst.cm,
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unit_time=orp,
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nml_key="cloud_params/beta_cool",
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put_units=False,
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select=select,
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label=r"$\rho$",
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)
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pl.slice_P(
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"z",
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overwrite=redo,
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overwrite_dep=False,
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unit_space=cst.cm,
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unit_time=orp,
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nml_key="cloud_params/beta_cool",
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put_units=False,
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select=select,
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label=r"$P$",
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)
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pl.pdf_coldens(
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"z",
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overwrite=redo,
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overwrite_dep=False,
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unit_time=orp,
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nml_key="cloud_params/beta_cool",
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label=r"$\log(\sigma)$",
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kind="step",
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color="k",
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select=select,
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)
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# -------------------------------------------------------------------------------------------------------------------- #
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# Create HDF5 files
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for simu in proj.simulations:
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for snap in simu.snapshots:
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for df in snap.datafiles:
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name = df[FileType.JPEG_FILE].filename
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name = os.path.splitext(name)[0] + ".h5"
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h5 = h5py.File(out_dir + "/" + name, "w")
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p = h5.create_group("plot")
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df.plot_info.hsp_save_to_h5(p)
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h5.close()
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df[FileType.HDF5_FILE] = out_dir + "/" + name
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for param in ramses.input_parameters:
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param.key = os.path.basename(param.key)
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study = SimulationStudy(project=proj)
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for sim in study.project.simulations:
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for snap in sim.snapshots:
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snap.time = (snap.time[0], cst.year)
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proj.galactica_validity_check()
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study.save_HDF5(out_dir + "/fragdisk_study.h5")
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