Organize in submodules

2022-10-07 11:20:04 +02:00
parent 1f3b0762c9
commit 0d90179292
32 changed files with 231 additions and 510 deletions
@@ -0,0 +1,464 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+
+from __future__ import print_function, unicode_literals
+
+import os
+import h5py
+import numpy as np
+import matplotlib as mpl
+from astrophysix import units as U
+from astrophysix.simdm import Project, ProjectCategory, SimulationStudy
+from astrophysix.simdm.datafiles import PlotInfo, PlotType
+from astrophysix.utils.file import FileType
+
+from plotter import Plotter
+from params import default_params
+from ramses_astrophysix import ramses
+
+
+# ---------------------------------------------- Global parameters ------------------------------------------ #
+
+# groups = ["jr13_tic"]
+groups = ["jr11", "jr12", "jr12_tic", "jr13_tic"]
+keep_plot_info = False
+include_hdf5 = True
+replot = True
+nml_key = "cloud_params/beta_cool"
+select = {
+    "time": 4.5,
+    #    "filter_nml" : (nml_key, "=", 8),
+}
+
+
+params = default_params()
+params.input.nml_filename = "disk.nml"
+params.pymses.map_size = 2048
+params.pymses.zoom = 4
+params.pymses.filter = False
+params.pymses.variables = ["rho", "vel", "P", "g"]
+params.pymses.multiprocessing = True
+params.process.verbose = True
+params.disk.enable = True
+params.disk.nb_bin = 100
+params.pdf.nb_bin = 100
+params.process.num_process = 10
+in_dir = "/drf/projets/alfven-data/nbrucy/simus/fragdisk"
+out_dir = "/dsm/anais/storageA/nbrucy/visus/fragdisk/mnras"
+in_dir_conv = "/drf/projets/alfven-data/nbrucy/simus/conv_disk"
+out_dir_conv = "/dsm/anais/storageA/nbrucy/visus/conv_disk"
+
+
+# ---------------------------------------------- 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="""
+
+    <h4> Study of the fragmentation of self-gravitating disks</h4>
+    <p>
+    See Brucy & Hennebelle 2021 (submitted) for more details.
+    This database is currently being completed.
+    </p>
+
+    <h4>Abstract:</h4>
+
+    <p>
+    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
+    $\\beta$ 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.
+    </p>
+
+   <h4> Description of the simulations: </h4>
+
+    <p>
+    We simulate a disk of gas undergoing purely hydrodynamics forces,
+    its own gravity and the $\\beta$-cooling.
+    The simulation is ran with the 3D-grid code Ramses (Teyssier 2002) which uses a Godunov scheme.
+    The flux between each cell is computed with the HLLC Riemann solver.
+    The gravity potential is updated at each timestep with a Poisson solver,
+    and a source term is added to the energy equation to implement the $\\beta$-cooling.
+    </p>
+
+    <p>
+    The $\\beta$-cooling consists in removing internal energy from the gas with a cooling time:
+    $t_\\text{cool} = \\beta \\Omega^{-1}$ with $\\Omega$ the rotation frequency.
+    </p>
+
+    <p>
+    We use the same initial conditions as in Meru & Bate (2012) to allow comparison.
+    The specific disk setup for Ramses was inspired by Hennebelle et al. (2017).
+    The disk is initially close to equilibrium with an initial column density profile
+    $\\Sigma \\propto r^{-1}$ and a temperature profile $T \\propto r^{-1/2}$
+    where $r$ is the cylindrical radius.
+    The disk has a radius $r_d = 0.25$ (code units), after which the density is divided by 100.
+    The density and temperature at the disk radius $r_d$ are chosen so that the mass
+    of the disk $M_d = 0.1 M_\\star$, where $M_\\star$ is the mass of the central object,
+    and the initial value of the Toomre parameter at the disk radius is $Q_{0,d} = 2$.
+    The adiabatic index of the gas is $\\gamma = 5/3$.
+    </p>
+
+    <p>
+    The simulation is run within a cube of size $L=2$. Although the problem has a cylindrical symmetry,
+    we use Cartesian coordinates.
+    This prevents having a singularity at the centre of the box.
+    One caveat is the poor resolution on the centre of the cube but this is mitigated
+    by the use of the adaptive mesh refinement (AMR).
+    Another caveat is that having a cubic box may introduce spurious
+    reflection at the border of the simulation.
+    To avoid this, we maintain a dead zone over a radius of $0.875$ (in code units)
+    where all variables are replaced by their initial value at each timestep.
+    This method has been used in  Hennebelle et al. (2017) and has proven to be efficient.
+    </p>
+
+
+    <p>
+    The simulations presented here were run for several values of $\beta$ and several resolutions.
+    To reduce the computation time, we use the Ramses's Adaptative Mesh Refinement (AMR).
+    Only the parts of the simulation which are prone to form fragments are simulated with full resolution.
+    Each cell is refined until the Jeans's length is covered by at least 20 cells or it reaches the maximum
+    level of refinement $l_{\\max}$.
+    The level of refinement of a cell is the number of times the simulation box must be divided in eight
+    equal part to get the cell.
+    Thus, the resolution of a simulation is given by the value of $l_{\\max}$.
+
+    A first set of simulations with $l_{\\max} = 11$ to $l_{\\max} = 12$ are run until
+    about 5 Outer Rotation Periods (ORP),
+    that is that the gas at the border of the disk had 5 orbits around the star.
+    A second set of simulations, labelled tic, for Turbulent Initial Condition,
+    were run from relaxed initial conditions for $l_{\\max} = 12$ and $l_{\\max} = 13$.
+    More precisely, they were restarted from a simulation at $\beta = 20$ and $l_{\\max} = 12$
+    for which the whole disk reached a gravito-turbulent state (after 2 ORPs).
+    According to  Paardekooper et al. (2011) and Clarke et al.(2007), departing
+    from such turbulent condition should reduce spurious fragmentation.
+
+    </p>
+    """,
+    data_description="""
+    <p>The data available for this project is the underlying data of the article Brucy & Hennebelle 2021.</p>
+    <p>The data is not already fully uploaded. 3D datacube extraction on demand is planned</p>
+    """,
+    directory_path="~nbrucy/simus/fragdisk",
+)
+print(proj)
+# ------------------------------------------------------------------------------------------------------ #
+
+
+# ---- Units ----
+pl_units = Plotter(
+    in_dir,
+    filter_name="104_beta4_jr13",
+    in_nums="last",
+    path_out=out_dir,
+    params=params,
+)
+info = pl_units.comp.info
+rd = U.Unit.create_unit(
+    "r_d",
+    latex="r_\\mathrm{d}",
+    base_unit=0.25 * info["unit_length"] / info["boxlen"],
+)
+rhod = U.Unit.create_unit(
+    "rho_d",
+    latex="\\rho_\\mathrm{d}",
+    base_unit=6.36 * info["unit_density"],
+)
+rho_u = U.Unit.create_unit(
+    "rho_u",
+    latex="\mathrm{M}_\\star.r_\\mathrm{d}^{-3}",
+    base_unit=info["unit_mass"] * rd ** (-3),
+)
+orp = U.Unit.create_unit(
+    "ORP",
+    base_unit=2 * np.pi * np.sqrt(0.25 ** 3) * info["unit_time"],
+)
+vkd = U.Unit.create_unit(
+    "vkd",
+    latex="v_\\mathrm{k,d}",
+    base_unit=2 * np.pi * rd / orp,
+)
+Pd = U.Unit.create_unit(
+    "P_d",
+    base_unit=(0.2 * info["unit_velocity"]) ** 2 * rhod,
+)
+P_u = U.Unit.create_unit(
+    "P_u",
+    latex="v_\\mathrm{k,d}^2.\\mathrm{M}_\\star.r_\\mathrm{d}^{-3}",
+    base_unit=vkd ** 2 * rho_u,
+)
+
+Sigmad = U.Unit.create_unit(
+    "Sigma_d",
+    latex="\\Sigma_d",
+    base_unit=0.25 * info["unit_density"] * info["unit_length"] / info["boxlen"],
+)
+Sigma_u = U.Unit.create_unit(
+    "Sigma_u",
+    latex="M_\\star.r_d^{-2}",
+    base_unit=rd ** (-2) * info["unit_mass"],
+)
+
+
+# ---- Runs  -----
+
+pls = []
+
+for group in groups:
+    if group == "jr13_tic":
+        # JR13_TIC
+
+        params.astrophysix.simu_fmt = "beta{nml[cloud_params/beta_cool]:g}_{tag:.8}"
+        params.astrophysix.descr_fmt = """
+        <p>Group {tag:.8}, $\\beta$ = {nml[cloud_params/beta_cool]}.</p>
+        """
+
+        runs = "*_jr13"
+        pl = Plotter(
+            in_dir,
+            filter_name=runs,
+            in_nums="all",
+            sort_run_by=nml_key,
+            path_out=out_dir,
+            tag="jr13_tic_mnras",
+            params=params,
+            unit_time=orp,
+        )
+
+    if group == "jr12_tic":
+        # JR12_TIC
+        params.astrophysix.simu_fmt = "beta{nml[cloud_params/beta_cool]:g}_{tag:.8}"
+        params.astrophysix.descr_fmt = """
+        <p>Group {tag:.8}, $\\beta$ = {nml[cloud_params/beta_cool]}.</p>
+        """
+        runs_12 = "0[0-9][0-9]_beta*_jr12"
+        pl = 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",
+            params=params,
+            unit_time=orp,
+        )
+
+    if group == "jr12":
+
+        params.astrophysix.simu_fmt = "beta{nml[cloud_params/beta_cool]:g}_{tag:.4}"
+        params.astrophysix.descr_fmt = """
+        <p>Group {tag:.4}, $\\beta$ = {nml[cloud_params/beta_cool]}</p>
+        """
+
+        # JR12
+        runs = "[7-8][0-9]_beta*_j*"
+        pl = Plotter(
+            in_dir_conv,
+            filter_name=runs,
+            in_nums="all",
+            sort_run_by=nml_key,
+            path_out=out_dir,
+            tag="jr12_mnras",
+            params=params,
+            unit_time=orp,
+        )
+
+    if group == "jr11":
+
+        params.astrophysix.simu_fmt = "beta{nml[cloud_params/beta_cool]:g}_{tag:.4}"
+        params.astrophysix.descr_fmt = """
+        <p>Group {tag:.4}, $\\beta$ = {nml[cloud_params/beta_cool]}</p>
+        """
+
+        # JR11
+        runs = "*beta*_jr11"
+        pl = 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",
+            params=params,
+            unit_time=orp,
+        )
+
+    pls.append(pl)
+    print("{} defined".format(group.upper()))
+
+# -------------------------------------------------------------------------------------------------------------------- #
+
+for pl in pls:
+    pl.params.process.verbose = True
+    pl.comp.params.process.verbose = True
+    for run in pl.runs:
+        simu = pl.simulations[run]
+        proj.simulations.add(simu)
+
+
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+for pl in pls:
+    # Edit descriptions
+    pl.rules["slice_rho"].description = "Density slice"
+    pl.rules["slice_P"].description = "Pressure slice"
+    pl.rules["slice_velr"].description = "Radial velocity slice"
+    pl.rules["slice_velphi"].description = "Orthoradial velocity slice"
+    pl.rules[
+        "pdf_coldens"
+    ].description = """
+    Probability function of the logarithm of the column density fluctuations
+    $\\sigma = \\Sigma/\\overline{\\Sigma}$ with respect to its azimuthal average
+    """
+
+    # define plot parameters
+    map_kwargs = {
+        "overwrite": replot,
+        "overwrite_dep": False,
+        "unit_space": rd,
+        "center_space": True,
+        "unit_time": orp,
+        "nml_key": "cloud_params/beta_cool",
+        "select": select,
+    }
+
+    coldens_kwargs = {
+        **map_kwargs,
+        **{
+            "unit": Sigma_u,
+            "label": r"$\Sigma$",
+        },
+    }
+
+    rho_kwargs = {
+        **map_kwargs,
+        **{
+            "unit": rho_u,
+            "label": r"$\rho$",
+        },
+    }
+
+    P_kwargs = {
+        **map_kwargs,
+        **{
+            "unit": P_u,
+            "label": r"$P$",
+        },
+    }
+
+    vel_kwargs = {
+        **map_kwargs,
+        **{
+            "unit": vkd,
+        },
+    }
+
+    # do plots
+    pl.coldens("z", **coldens_kwargs)
+    pl.coldens("y", **coldens_kwargs)
+
+    pl.slice_rho("z", **rho_kwargs)
+    pl.slice_rho("y", **rho_kwargs)
+
+    pl.slice_velr(
+        "z",
+        label=r"$v_r$",
+        norm=mpl.colors.SymLogNorm(0.1, vmin=-2, vmax=2, base=10),
+        autoscale=False,
+        **vel_kwargs,
+    )
+    pl.slice_velphi("z", label=r"$v_\varphi$", **vel_kwargs)
+    pl.slice_velx("z", label=r"$v_x$", **vel_kwargs)
+
+    pl.slice_P("z", **P_kwargs)
+
+    pl.pdf_coldens(
+        "z",
+        overwrite=replot,
+        overwrite_dep=False,
+        unit_time=orp,
+        nml_key="cloud_params/beta_cool",
+        label=r"$\log(\Sigma / \overline{\Sigma})$",
+        kind="step",
+        color="k",
+        select=select,
+    )
+
+
+# ----------------------------------------------------------------------------------------------------------------- #
+
+# Light fake PlotInfo to replace real one to reduce size of the hdf5 file
+pi = PlotInfo(
+    plot_type=PlotType.LINE_PLOT,
+    xaxis_values=np.array([10.0, 20.0, 30.0, 40.0, 50.0]),
+    yaxis_values=np.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,
+)
+
+for simu in proj.simulations:
+    for snap in simu.snapshots:
+
+        # Change unit to things Galactica understands
+        snap.time = (snap.time[0], U.none)
+        snap.description = """
+        <p>Snapshot at {time:.3g} ORPs.</p>
+
+        <h5 class="sn_panel">Notations:</h5>
+
+        <p>
+        $r_d$ : radius of the disk <br />
+        ORP : outer rotation period, that is period of the gas at $r_d$ <br />
+        $M_\\star$ : Mass of the central object <br />
+        $v_{kepl}$ : Keplerian speed at $r_d$
+        </p>
+        <p>All slices are taken at $z=0$ or $y=0$.
+        """.format(
+            time=snap.time[0], kepl="{k,d}"
+        )
+
+        # Convert plotinfo into HDF5 file
+        for df in snap.datafiles:
+            name = df[FileType.JPEG_FILE].filename
+            name = os.path.splitext(name)[0] + ".h5"
+            if include_hdf5 and df.name not in ["slice_velphi_z", "slice_velr_z"]:
+                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
+            if not keep_plot_info:
+                df.plot_info = pi
+
+# Trim parameters name
+for param in ramses.input_parameters:
+    param.key = os.path.basename(param.key)
+
+# Validity check
+proj.galactica_validity_check()
+
+# Save
+study = SimulationStudy(project=proj)
+study.save_HDF5(out_dir + "/fragdisk_study.h5")
@@ -0,0 +1,326 @@
+#!/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 import units as U
+from astrophysix.simdm import Project, ProjectCategory, SimulationStudy
+from astrophysix.simdm.datafiles import Datafile, PlotInfo, PlotType
+from astrophysix.simdm.experiment import (
+    AppliedAlgorithm,
+    ParameterSetting,
+    ParameterVisibility,
+    ResolvedPhysicalProcess,
+    Simulation,
+)
+from astrophysix.simdm.protocol import (
+    Algorithm,
+    AlgoType,
+    InputParameter,
+    PhysicalProcess,
+    Physics,
+    SimulationCode,
+)
+from astrophysix.simdm.results import GenericResult, Snapshot
+from astrophysix.utils.file import FileType
+
+# ----------------------------------------------- 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")
@@ -0,0 +1,91 @@
+# coding: utf-8
+
+
+from astrophysix.simdm.protocol import (
+    Algorithm,
+    AlgoType,
+    InputParameter,
+    PhysicalProcess,
+    Physics,
+    SimulationCode,
+)
+
+# 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
+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"
+    )
+)
+# => 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="amr_params/jeans_refine",
+        name="jeans_refine",
+        description="Array, number of cells needed to resolve the Jeans lenght at each level from lmin",
+    )
+)
+ramses.input_parameters.add(
+    InputParameter(
+        key="cloud_params/beta_cool", name="beta", description="Cooling parameter"
+    )
+)
+
+
+# => 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.Hydrodynamics, description="Hydrodynamical equations are solved"
+    )
+)
+ramses.physical_processes.add(
+    PhysicalProcess(physics=Physics.SelfGravity, description="Self-Gravity is applied.")
+)