add galactica import scripts

fragdisk_galactica.py

@@ -0,0 +1,315 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# This file is part of the 'astrophysix' Python package.
+#
+# Copyright © Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA)
+#
+#  FREE SOFTWARE LICENCING
+#  -----------------------
+# This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free
+# software. You can use, modify and/or redistribute the software under the terms of the CeCILL license as circulated by
+# CEA, CNRS and INRIA at the following URL: "http://www.cecill.info". As a counterpart to the access to the source code
+# and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty
+# and the software's author, the holder of the economic rights, and the successive licensors have only limited
+# liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying
+# and/or developing or reproducing the software by the user in light of its specific status of free software, that may
+# mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and
+# experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the
+# software's suitability as regards their requirements in conditions enabling the security of their systems and/or data
+# to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that
+# you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms.
+#
+#
+# COMMERCIAL SOFTWARE LICENCING
+# -----------------------------
+# You can obtain this software from CEA under other licencing terms for commercial purposes. For this you will need to
+# negotiate a specific contract with a legal representative of CEA.
+#
+from __future__ import print_function, unicode_literals
+import os
+import numpy as N
+import h5py
+
+from astrophysix.simdm import SimulationStudy, Project, ProjectCategory
+from astrophysix.simdm.experiment import (
+    Simulation,
+    AppliedAlgorithm,
+    ParameterSetting,
+    ParameterVisibility,
+    ResolvedPhysicalProcess,
+)
+from astrophysix.simdm.protocol import (
+    SimulationCode,
+    AlgoType,
+    Algorithm,
+    InputParameter,
+    PhysicalProcess,
+    Physics,
+)
+from astrophysix.simdm.results import GenericResult, Snapshot
+from astrophysix.simdm.datafiles import Datafile, PlotType, PlotInfo
+from astrophysix.utils.file import FileType
+from astrophysix import units as U
+
+from plotter import *
+import datetime
+from mpl_toolkits.axes_grid1 import AxesGrid, Grid
+from matplotlib import gridspec
+
+P.rcParams["text.usetex"] = False
+
+
+pp_params = default_params()
+pp_params.input.nml_filename = "disk.nml"
+# pp_params.out.interactive = True
+pp_params.pymses.map_size = 2048
+pp_params.pymses.zoom = 4
+pp_params.pymses.filter = False
+pp_params.pymses.variables = ["rho", "vel", "P", "g"]
+pp_params.pymses.multiprocessing = True
+pp_params.process.verbose = True
+pp_params.disk.enable = True
+pp_params.disk.nb_bin = 100
+pp_params.pdf.nb_bin = 100
+pp_params.process.num_process = 10
+in_dir = "/drf/projets/alfven-data/nbrucy/simus/fragdisk"
+out_dir = "/dsm/anais/storageA/nbrucy/visus/fragdisk/mnras"
+nml_key = "cloud_params/beta_cool"
+
+# --- Runs  -----
+
+pp_params.astrophysix.simu_fmt = "beta{nml[cloud_params/beta_cool]:g}_{tag:.8}"
+pp_params.astrophysix.descr_fmt = (
+    "Group {tag:.8}, $\\beta$ = {nml[cloud_params/beta_cool]}"
+)
+
+pl_orp = Plotter(
+    in_dir,
+    filter_name="104_beta4_jr13",
+    in_nums="last",
+    path_out=out_dir,
+    pp_params=pp_params,
+)
+orp = cst.Unit.create_unit("ORP", base_unit=pl_orp.comp.info["unit_time"] * 0.79)
+
+# JR13_TIC
+runs = "*_jr13"
+pl_jr13 = Plotter(
+    in_dir,
+    filter_name=runs,
+    in_nums="all",
+    sort_run_by=nml_key,
+    path_out=out_dir,
+    tag="jr13_tic_mnras",
+    pp_params=pp_params,
+    unit_time=orp,
+)
+print("JR13_TIC defined")
+
+# JR12_TIC
+runs_12 = "0[0-9][0-9]_beta*_jr12"
+pl_jr12_tic = Plotter(
+    in_dir,
+    filter_name=runs_12,
+    in_nums="all",
+    sort_run_by=nml_key,
+    filter_nml=("cloud_params", "!=", 7),
+    path_out=out_dir,
+    tag="jr12_tic_mnras",
+    pp_params=pp_params,
+    unit_time=orp,
+)
+
+pp_params.astrophysix.simu_fmt = "beta{nml[cloud_params/beta_cool]:g}_{tag:.4}"
+pp_params.astrophysix.descr_fmt = (
+    "Group {tag:.4}, $\\beta$ = {nml[cloud_params/beta_cool]}"
+)
+print("JR12_TIC defined")
+
+# JR12
+in_dir_conv = "/drf/projets/alfven-data/nbrucy/simus/conv_disk"
+out_dir_conv = "/dsm/anais/storageA/nbrucy/visus/conv_disk"
+runs = "[7-8][0-9]_beta*_j*"
+pl_jr12 = Plotter(
+    in_dir_conv,
+    filter_name=runs,
+    in_nums="all",
+    sort_run_by=nml_key,
+    path_out=out_dir,
+    tag="jr12_mnras",
+    pp_params=pp_params,
+    unit_time=orp,
+)
+print("JR12 defined")
+
+# JR11
+runs = "*beta*_jr11"
+pl_l11 = Plotter(
+    in_dir_conv,
+    filter_name=runs,
+    sort_run_by=nml_key,
+    filter_nml=("cloud_params/beta_cool", ">", 3),
+    path_out=out_dir_conv,
+    tag="jr11_mnras",
+    pp_params=pp_params,
+    unit_time=orp,
+)
+
+print("JR11 defined")
+
+
+pls = [pl_l11, pl_jr12, pl_jr12_tic, pl_jr13]
+
+
+# ----------------------------------------------- Project creation --------------------------------------------------- #
+# Available project categories are :
+# - ProjectCategory.SolarMHD
+# - ProjectCategory.PlanetaryAtmospheres
+# - ProjectCategory.StarPlanetInteractions
+# - ProjectCategory.StarFormation
+# - ProjectCategory.Supernovae
+# - ProjectCategory.GalaxyFormation
+# - ProjectCategory.GalaxyMergers
+# - ProjectCategory.Cosmology
+proj = Project(
+    category=ProjectCategory.StarPlanetInteractions,
+    project_title="Fragdisk",
+    alias="FRAGDISK",
+    short_description="Fragmentation of self-gravitating disks",
+    general_description="""
+    Study of the fragmentation of self-gravitating disks. See Brucy & Hennebelle 2021 (submitted) for more details.
+
+    This database is currently being completed.
+
+    Abstract:
+
+    Self-gravitating disks are believed to play an important role in astrophysics in particular regarding the star and planet formation process.
+    In this context, disks subject to an idealized cooling process, characterized by a cooling timescale β expressed in unit of orbital timescale,
+    have been extensively studied. We take advantage of the Riemann solver and the 3D Godunov scheme implemented in the code Ramses
+    to perform high resolution simulations, complementing previous studies that have used Smoothed Particle Hydrodynamics (SPH) or 2D grid codes.
+    """,
+    data_description="""The data available for this project is the underlying data of the article Brucy & Hennebelle 2021.
+    The data is not already fully uploaded. 3D datacube extraction on demand is planned""",
+    directory_path="~nbrucy/simus/fragdisk",
+)
+print(proj)
+# -------------------------------------------------------------------------------------------------------------------- #
+
+# -------------------------------------------------------------------------------------------------------------------- #
+redo = True
+for pl in pls:
+    pl.pp_params.process.verbose = True
+    pl.comp.pp_params.process.verbose = True
+    for run in pl.runs:
+        simu = pl.simulations[run]
+        proj.simulations.add(simu)
+
+
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+for pl in pls:
+    select = {"time": 4.5}
+    pl.coldens(
+        "z",
+        overwrite=redo,
+        overwrite_dep=False,
+        unit_space=cst.cm,
+        unit_time=orp,
+        nml_key="cloud_params/beta_cool",
+        vmin=1e-2,
+        vmax=1e2,
+        put_units=False,
+        select=select,
+        label=r"$\Sigma$",
+    )
+
+    pl.coldens(
+        "y",
+        overwrite=redo,
+        overwrite_dep=False,
+        unit_space=cst.cm,
+        unit_time=orp,
+        nml_key="cloud_params/beta_cool",
+        vmin=1e-2,
+        vmax=1e2,
+        put_units=False,
+        select=select,
+        label=r"$\Sigma$",
+    )
+
+    pl.slice_rho(
+        "z",
+        overwrite=redo,
+        overwrite_dep=False,
+        unit_space=cst.cm,
+        unit_time=orp,
+        nml_key="cloud_params/beta_cool",
+        put_units=False,
+        select=select,
+        label=r"$\rho$",
+    )
+
+    pl.slice_rho(
+        "y",
+        overwrite=redo,
+        overwrite_dep=False,
+        unit_space=cst.cm,
+        unit_time=orp,
+        nml_key="cloud_params/beta_cool",
+        put_units=False,
+        select=select,
+        label=r"$\rho$",
+    )
+
+    pl.slice_P(
+        "z",
+        overwrite=redo,
+        overwrite_dep=False,
+        unit_space=cst.cm,
+        unit_time=orp,
+        nml_key="cloud_params/beta_cool",
+        put_units=False,
+        select=select,
+        label=r"$P$",
+    )
+
+    pl.pdf_coldens(
+        "z",
+        overwrite=redo,
+        overwrite_dep=False,
+        unit_time=orp,
+        nml_key="cloud_params/beta_cool",
+        label=r"$\log(\sigma)$",
+        kind="step",
+        color="k",
+        select=select,
+    )
+
+
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+# Create HDF5 files
+for simu in proj.simulations:
+    for snap in simu.snapshots:
+        for df in snap.datafiles:
+            name = df[FileType.JPEG_FILE].filename
+            name = os.path.splitext(name)[0] + ".h5"
+            h5 = h5py.File(out_dir + "/" + name, "w")
+            p = h5.create_group("plot")
+            df.plot_info.hsp_save_to_h5(p)
+            h5.close()
+            df[FileType.HDF5_FILE] = out_dir + "/" + name
+
+for param in ramses.input_parameters:
+    param.key = os.path.basename(param.key)
+
+study = SimulationStudy(project=proj)
+
+for sim in study.project.simulations:
+    for snap in sim.snapshots:
+        snap.time = (snap.time[0], cst.year)
+
+proj.galactica_validity_check()
+study.save_HDF5(out_dir + "/fragdisk_study.h5")

ismfeed_galactica.py

@@ -0,0 +1,325 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# This file is part of the 'astrophysix' Python package.
+#
+# Copyright © Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA)
+#
+#  FREE SOFTWARE LICENCING
+#  -----------------------
+# This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free
+# software. You can use, modify and/or redistribute the software under the terms of the CeCILL license as circulated by
+# CEA, CNRS and INRIA at the following URL: "http://www.cecill.info". As a counterpart to the access to the source code
+# and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty
+# and the software's author, the holder of the economic rights, and the successive licensors have only limited
+# liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying
+# and/or developing or reproducing the software by the user in light of its specific status of free software, that may
+# mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and
+# experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the
+# software's suitability as regards their requirements in conditions enabling the security of their systems and/or data
+# to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that
+# you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms.
+#
+#
+# COMMERCIAL SOFTWARE LICENCING
+# -----------------------------
+# You can obtain this software from CEA under other licencing terms for commercial purposes. For this you will need to
+# negotiate a specific contract with a legal representative of CEA.
+#
+from __future__ import print_function, unicode_literals
+import os
+import numpy as N
+
+from astrophysix.simdm import SimulationStudy, Project, ProjectCategory
+from astrophysix.simdm.experiment import (
+    Simulation,
+    AppliedAlgorithm,
+    ParameterSetting,
+    ParameterVisibility,
+    ResolvedPhysicalProcess,
+)
+from astrophysix.simdm.protocol import (
+    SimulationCode,
+    AlgoType,
+    Algorithm,
+    InputParameter,
+    PhysicalProcess,
+    Physics,
+)
+from astrophysix.simdm.results import GenericResult, Snapshot
+from astrophysix.simdm.datafiles import Datafile, PlotType, PlotInfo
+from astrophysix.utils.file import FileType
+from astrophysix import units as U
+
+# ----------------------------------------------- Project creation --------------------------------------------------- #
+# Available project categories are :
+# - ProjectCategory.SolarMHD
+# - ProjectCategory.PlanetaryAtmospheres
+# - ProjectCategory.StarPlanetInteractions
+# - ProjectCategory.StarFormation
+# - ProjectCategory.Supernovae
+# - ProjectCategory.GalaxyFormation
+# - ProjectCategory.GalaxyMergers
+# - ProjectCategory.Cosmology
+proj = Project(
+    category=ProjectCategory.StarFormation,
+    project_title="Ismfeed",
+    alias="ismfeed",
+    short_description="Impact of feedback and turbulence on star formation",
+    general_description="""Impact of feedback and turbulence on star formation. The simulation presented here are described in Brucy et al. 2020, ApJL, L38""",
+    data_description="The data available in this project...",
+    directory_path="~nbrucy/simus/ismfeed",
+)
+print(proj)
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+# --------------------------------------- Simulation code definition ------------------------------------------------- #
+ramses = SimulationCode(
+    name="Ramses 3 (MHD)",
+    code_name="Ramses",
+    code_version="3.10.1",
+    alias="RAMSES_3",
+    url="https://www.ics.uzh.ch/~teyssier/ramses/RAMSES.html",
+    description="Ramses MHD code",
+)
+# => Add algorithms : available algorithm types are :
+# - AlgoType.AdaptiveMeshRefinement
+# - AlgoType.VoronoiMovingMesh
+# - AlgoType.SmoothParticleHydrodynamics
+# - AlgoType.Godunov
+# - AlgoType.PoissonMultigrid
+# - AlgoType.PoissonConjugateGradient
+# - AlgoType.ParticleMesh
+# - AlgoType.FriendOfFriend
+# - AlgoType.HLLCRiemann
+# - AlgoType.RayTracer
+# amr = ramses.algorithms.add(Algorithm(algo_type=AlgoType.AdaptiveMeshRefinement, description="AMR"))
+ramses.algorithms.add(
+    Algorithm(algo_type=AlgoType.Godunov, description="Godunov scheme")
+)
+ramses.algorithms.add(
+    Algorithm(algo_type=AlgoType.HLLCRiemann, description="HLLC Riemann solver")
+)
+ramses.algorithms.add(
+    Algorithm(
+        algo_type=AlgoType.PoissonMultigrid, description="Multigrid Poisson solver"
+    )
+)
+ramses.algorithms.add(
+    Algorithm(algo_type=AlgoType.ParticleMesh, description="PM solver")
+)
+
+# => Add input parameters
+ramses.input_parameters.add(
+    InputParameter(
+        key="amr_params/levelmin",
+        name="Lmin",
+        description="min. level of AMR refinement",
+    )
+)
+ramses.input_parameters.add(
+    InputParameter(
+        key="amr_params/levelmax",
+        name="Lmax",
+        description="max. level of AMR refinement",
+    )
+)
+
+ramses.input_parameters.add(
+    InputParameter(
+        key="turb_params/turb_rms", name="f_rms", description="Amplitude of the driving"
+    )
+)
+ramses.input_parameters.add(
+    InputParameter(
+        key="cloud_params/dens0", name="n_0", description="Midplane density in cm**-3"
+    )
+)
+ramses.input_parameters.add(
+    InputParameter(
+        key="cloud_params/bx_bound",
+        name="bx_bound",
+        description="imposed magnetic field at the x boundary (1 implies that the magnetic pressure is equal to thermal pressure in WNM, which corresponds to about 5muG)",
+    )
+)
+
+
+# => Add physical processes : available physics are :
+# - Physics.SelfGravity
+# - Physics.Hydrodynamics
+# - Physics.MHD
+# - Physics.StarFormation
+# - Physics.SupernovaeFeedback
+# - Physics.AGNFeedback
+# - Physics.MolecularCooling
+ramses.physical_processes.add(
+    PhysicalProcess(
+        physics=Physics.StarFormation,
+        description="Star Formation is triggered when density overpass",
+    )
+)
+ramses.physical_processes.add(
+    PhysicalProcess(
+        physics=Physics.MHD, description="Magneto-hydrodynamical equations are solved"
+    )
+)
+ramses.physical_processes.add(
+    PhysicalProcess(physics=Physics.SelfGravity, description="Self-Gravity is applied.")
+)
+ramses.physical_processes.add(
+    PhysicalProcess(physics=Physics.SupernovaeFeedback, description="SN feedback")
+)
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+# -------------------------------------------- Simulation setup ------------------------------------------------------ #
+simu = Simulation(
+    simu_code=ramses,
+    name="Noturb_1",
+    alias="noturb_1",
+    description="Simulation without turbulence",
+    directory_path="~nbrucy/simus/turb/",
+)
+proj.simulations.add(simu)
+
+# Add applied algorithms implementation details. Warning : corresponding algorithms must have been added in the 'ramses'
+# simulation code.
+# simu.applied_algorithms.add(AppliedAlgorithm(algorithm=amr, details="My AMR implementation [Teyssier 2002]"))
+# simu.applied_algorithms.add(AppliedAlgorithm(algorithm=ramses.algorithms[AlgoType.HLLCRiemann.name],
+#                                             details="My Riemann solver implementation [Teyssier 2002]"))
+
+# Add parameter setting. Warning : corresponding input parameter must have been added in the 'ramses' simulation code.
+# Available parameter visibility options are :
+# - ParameterVisibility.NOT_DISPLAYED
+# - ParameterVisibility.ADVANCED_DISPLAY
+# - ParameterVisibility.BASIC_DISPLAY
+simu.parameter_settings.add(
+    ParameterSetting(
+        input_param=ramses.input_parameters["levelmin"],
+        value=8,
+        visibility=ParameterVisibility.BASIC_DISPLAY,
+    )
+)
+simu.parameter_settings.add(
+    ParameterSetting(
+        input_param=lmax, value=12, visibility=ParameterVisibility.BASIC_DISPLAY
+    )
+)
+
+# Add resolved physical process implementation details. Warning : corresponding physical process must have been added to
+# the 'ramses' simulation code
+simu.resolved_physics.add(
+    ResolvedPhysicalProcess(
+        physics=ramses.physical_processes[Physics.StarFormation.name],
+        details="Star formation specific implementation",
+    )
+)
+simu.resolved_physics.add(
+    ResolvedPhysicalProcess(
+        physics=grav, details="self-gravity specific implementation"
+    )
+)
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+# -------------------------------------- Simulation generic result and snapshots ------------------------------------- #
+# Generic result
+gres = GenericResult(
+    name="Key result 1 !",
+    description="My description",
+    directory_path="/my/path/to/result",
+)
+simu.generic_results.add(gres)
+
+# Simulation snapshot
+# In one-line
+sn = simu.snapshots.add(
+    Snapshot(
+        name="My best snapshot !",
+        description="My first snapshot description",
+        time=(125, U.kyr),
+        physical_size=(250.0, U.kpc),
+        directory_path="/path/to/snapshot1",
+        data_reference="OUTPUT_00056",
+    )
+)
+# Or create snapshot, then add it to the simulation
+sn2 = Snapshot(
+    name="My second best snapshot !",
+    description="My second snapshot description",
+    time=(0.26, U.Myr),
+    physical_size=(0.25, U.Mpc),
+    directory_path="/path/to/snapshot2",
+    data_reference="OUTPUT_00158",
+)
+simu.snapshots.add(sn2)
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+# ---------------------------------------------------- Result datafiles ---------------------------------------------- #
+# Datafile creation
+imf_df = sn.datafiles.add(
+    Datafile(
+        name="Initial mass function plot",
+        description="This is my plot detailed description",
+    )
+)
+
+# Add attached files to a datafile (1 per file type). Available file types are :
+# - FileType.HDF5_FILE
+# - FileType.PNG_FILE
+# - FileType.JPEG_FILE
+# - FileType.FITS_FILE
+# - FileType.TARGZ_FILE
+# - FileType.PICKLE_FILE
+# - FileType.JSON_FILE
+# - FileType.CSV_FILE
+# - FileType.ASCII_FILE
+imf_df[FileType.PNG_FILE] = os.path.join(
+    "/data", "io", "datafiles", "plot_image_IMF.png"
+)
+imf_df[FileType.JPEG_FILE] = os.path.join(
+    "/data", "io", "datafiles", "plot_with_legend.jpg"
+)
+imf_df[FileType.FITS_FILE] = os.path.join(
+    "/data", "io", "datafiles", "cassiopea_A_0.5-1.5keV.fits"
+)
+imf_df[FileType.TARGZ_FILE] = os.path.join("/data", "io", "datafiles", "archive.tar.gz")
+imf_df[FileType.JSON_FILE] = os.path.join(
+    "/data", "io", "datafiles", "test_header_249.json"
+)
+imf_df[FileType.ASCII_FILE] = os.path.join("/data", "io", "datafiles", "abstract.txt")
+imf_df[FileType.HDF5_FILE] = os.path.join("/data", "io", "HDF5", "study.h5")
+imf_df[FileType.PICKLE_FILE] = os.path.join(
+    "/data", "io", "datafiles", "dict_saved.pkl"
+)
+
+# Datafile plot information (for plot future updates and online interactive visualisation on Galactica web pages).
+# Available plot types are :
+# - LINE_PLOT
+# - SCATTER_PLOT
+# - HISTOGRAM
+# - HISTOGRAM_2D
+# - IMAGE
+# - MAP_2D
+imf_df.plot_info = PlotInfo(
+    plot_type=PlotType.LINE_PLOT,
+    xaxis_values=N.array([10.0, 20.0, 30.0, 40.0, 50.0]),
+    yaxis_values=N.array([1.256, 2.456, 3.921, 4.327, 5.159]),
+    xaxis_log_scale=False,
+    yaxis_log_scale=False,
+    xaxis_label="Mass",
+    yaxis_label="Probability",
+    xaxis_unit=U.Msun,
+    plot_title="Initial mass function",
+    yaxis_unit=U.Mpc,
+)
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+# Save study in HDF5 file
+study = SimulationStudy(project=proj)
+study.save_HDF5("./frig_study.h5")
+
+# Eventually reload it from HDF5 file to edit its content
+# study = SimulationStudy.load_HDF5("./frig_study.h5")