diff --git a/cluster_examples/submit.sh b/cluster_examples/slurm_submit.sh similarity index 100% rename from cluster_examples/submit.sh rename to cluster_examples/slurm_submit.sh diff --git a/config/config_paper_1.yaml b/config/config_paper_1.yaml new file mode 100755 index 0000000..65301cc --- /dev/null +++ b/config/config_paper_1.yaml @@ -0,0 +1,69 @@ +# Config File of chemcomp paper 1 (Schneider & Bitsch 2021a) +# Can be used together with jobs/paper_1_disk.yaml, jobs/paper_1_growthtracks.yaml, jobs/paper_1_grid_thorngren.yaml +# to generate the data of Fig. 2, 3, 4, 11, 12, 13, 14, 15 + +# Take care of units here! Otherwise adapt in import_config.scale_units! +# Physical parameters +config_disk: + model: DiskLabDisk + M_STAR: 1.0 # mass of central star in sun massses + ALPHA: 5.0e-4 # Alpha viscosity + ALPHAHEIGHT: 1.0e-4 + M0: 0.128 # needed for DiskLabDisk + R0: 137 # needed for DiskLabDisk + DTG_total: 0.02 # Dust to gas ratios + static: False + evaporation: True + static_stokes: False + tau_disk: 1.0e4 + begin_photoevap: 3.0 # Myr + temp_evol: False + evap_width: 1.0e-3 + +chemistry: + FeH: 0.0 + use_FeH: False # use FeH proxy fit according to Bitsch, Battestini 2020 + C_frac: 0.0 # Fraction of C/H in C (will be reduced from CH4) + +config_planet: + model: BertPlanet + matter_removal: True + use_heat_torque: True + use_dynamical_torque: True + migration: True + M0_fact: 1 + a_p: 30.0 + t_0: 0.05 # time before planets start growing, total time: time_disk_0+t_0 + rho_c: 5.5 # density of the core (g/cm**3) + r_in: 0.2 + keep_peb_iso: True + use_pebiso_diffusion: False + +config_pebble_accretion: + u_frag: 5.0 # m/s + epsilon_p: 0.5 + +config_gas_accretion: + kappa_env: 0.05 + f_machida: 1 + f_disk_max: 1.0 + +config_planetesimal_accretion: + R_pla: 50 # Planetesimal radius in km + rho_pla: 1 # density of a single planetesimal (g/cm^3) = 1000 kg/m^3 + stirring: 1.0e-4 + efficiency: 0.00 + +# modelling parameters +defaults: + DEF_R_IN: 0.1 # inner r boundary (in AU) + DEF_R_OUT: 1000 # outer r boundary (in AU) + DEF_GRIDSIZE: 500 # radial gridsize + DEF_LIN_SPACING: False # Spacing of radial grid + DEF_T_END: 100 # Maximum simulation duration (in Myr), will cancel before if termination conditions are fulfilled + +output: + name: Bert + save_disk: True + save_interval: 5000 # time in years + save_disk_interval: 20 \ No newline at end of file diff --git a/config/config_paper_2_Jupiter.yaml b/config/config_paper_2_Jupiter.yaml new file mode 100755 index 0000000..fb1acdc --- /dev/null +++ b/config/config_paper_2_Jupiter.yaml @@ -0,0 +1,73 @@ +# Config File of the Jupiter model in chemcomp paper 2 (Schneider & Bitsch 2021b) +# Can be used together with jobs/paper_2_Jupiter.yaml +# to generate parts of the data for Jupiter in Fig. 4 and 5 + +# Take care of units here! Otherwise adapt in import_config.scale_units! +# Physical parameters +config_disk: + model: DiskLabDisk + M_STAR: 1.0 # mass of central star in sun massses + ALPHA: 1.0e-4 # Alpha viscosity + ALPHAHEIGHT: 1.0e-4 + M0: 0.0256 # needed for DiskLabDisk + R0: 137 # needed for DiskLabDisk + DTG_total: 0.015 # Dust to gas ratios + static: False + evaporation: True + static_stokes: False + tau_disk: 1.0e4 + begin_photoevap: 10.0 # Myr + temp_evol: False + evap_width: 1.0e-3 + +chemistry: + FeH: 0.0 + use_FeH: False # use FeH proxy fit according to Bitsch, Battestini 2020 + C_frac: 0.2 # Fraction of C/H in C (will be reduced from CH4) + +config_planet: + model: BertPlanet + matter_removal: True + use_heat_torque: True #True + use_dynamical_torque: True + migration: False + M0_fact: 1 + pebiso_start: True # start with pebiso + M_end: 1 + a_p: 5.0 + t_0: 1.0 # time before planets start growing, total time: time_disk_0+t_0 + rho_c: 5.5 # density of the core (g/cm**3) + r_in: 0.2 + keep_peb_iso: True + solid_frac: 1.0 + use_pebiso_diffusion: False + apply_gap_profile: True + +config_pebble_accretion: + u_frag: 5.0 # m/s + epsilon_p: 0.5 + +config_gas_accretion: + kappa_env: 0.05 + f_machida: 1 + f_disk_max: 1.0 + +config_planetesimal_accretion: + R_pla: 50 # Planetesimal radius in km + rho_pla: 1 # density of a single planetesimal (g/cm^3) = 1000 kg/m^3 + stirring: 1.0e-4 + efficiency: 0.00 + +# modelling parameters +defaults: + DEF_R_IN: 0.1 # inner r boundary (in AU) + DEF_R_OUT: 1000 # outer r boundary (in AU) + DEF_GRIDSIZE: 500 # radial gridsize + DEF_LIN_SPACING: False # Spacing of radial grid + DEF_T_END: 100 # Maximum simulation duration (in Myr), will cancel before if termination conditions are fulfilled + +output: + name: Bert + save_disk: False + save_interval: 500 # time in years + save_disk_interval: 20 \ No newline at end of file diff --git a/doc/source/Configuration/Config-File.rst b/doc/source/Configuration/Config-File.rst index 965371b..f4d68f0 100755 --- a/doc/source/Configuration/Config-File.rst +++ b/doc/source/Configuration/Config-File.rst @@ -1,6 +1,6 @@ config.yaml ^^^^^^^^^^^ -.. Note:: The code is build to use cgs units! Either use cgs values or set unit conversion with `scale` in `chemcomp/helpers/import_config.py` +.. warning:: The code is build to use cgs units internally. HOWEVER, most config entries come with a unit. If you want to introduce new parameters to the config file, either use cgs values or set unit conversion with `scale` in `chemcomp/helpers/import_config.py`. Example of unit conversion """""""""""""""""""""""""" diff --git a/doc/source/Disk-Only.rst b/doc/source/Disk-Only.rst new file mode 100644 index 0000000..88486cd --- /dev/null +++ b/doc/source/Disk-Only.rst @@ -0,0 +1,13 @@ +Disk only runs +"""""""""""""" +If you want to use ``chemcomp`` to run a disk model and don't care about a planet, you may use the following settings: + +In the ``config_planet`` section: + +* Set ``model`` to ``NoAccretion``. This will introduce a passive planet that ends the simulation, once planted into the disk. +* Set ``t_0`` to the value for how long you want to evolve the disk, before the planet ends the simulation. + +In the ``defaults`` section: + +* Set ``save_disk`` to ``True`` to make sure the disk is stored +* Set ``save_interval`` and ``save_disk_interval`` to a reasonable interval for which you require the disk quantities to be stored diff --git a/doc/source/FAQ.rst b/doc/source/FAQ.rst index 91f7bfb..f074141 100755 --- a/doc/source/FAQ.rst +++ b/doc/source/FAQ.rst @@ -5,6 +5,14 @@ How do I contribute? """""""""""""""""""" If you want to contribute feel free to create a pull request! This way others can profit from your contribution as well! +How do I do a disk only run? +"""""""""""""""""""""""""""" +Checkout the ``config/config_paper_1.yaml`` together with ``jobs/paper_1_disk.yaml`` for an example + +What happens, if I don't set a paramter +""""""""""""""""""""""""""""""""""""""" +A default value will be used in most cases. Make sure to set all parameters, so that you can be sure about its value! + Where do I find a list of Parameters? """"""""""""""""""""""""""""""""""""" Head over to the Configuration -> config.yaml diff --git a/doc/source/Publications.rst b/doc/source/Publications.rst new file mode 100755 index 0000000..39a41cd --- /dev/null +++ b/doc/source/Publications.rst @@ -0,0 +1,33 @@ +Publications +------------ + +Original Publications +^^^^^^^^^^^^^^^^^^^^^ + +* `Schneider & Bitsch (2021a) `_ + How drifting and evaporating pebbles shape giant planets. I. Heavy element content and atmospheric C/O +* `Schneider & Bitsch (2021b) `_ + How drifting and evaporating pebbles shape giant planets. II. Volatiles and refractories in atmospheres +* `Bitsch, Schneider & Kreidberg (2022) `_ + How drifting and evaporating pebbles shape giant planets. III. The formation of WASP-77A b and :math:`\tau` Boötis b + +Please cite `Schneider & Bitsch (2021a) `_, if you use ``chemcomp`` in your work. + +Publications using ``chemcomp`` +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +* `Bitsch et al. (2021) `_ + Dry or water world? How the water contents of inner sub-Neptunes constrain giant planet formation and the location of the water ice line +* `Hühn & Bitsch (2023) `_ + How accretion of planet-forming disks influences stellar abundances +* `Bitsch & Mah (2023) `_ + Enriching inner discs and giant planets with heavy elements +* `Mah & Bitsch (2023a) `_ + Forming super-Mercuries: Role of stellar abundances +* `Mah & Bitsch (2023b) `_ + Close-in ice lines and the super-stellar C/O ratio in discs around very low-mass stars +* `Savvidou & Bitsch (2023) `_ + How to make giant planets via pebble accretion +* `Danti, Bitsch & Mah (2023) `_ + Composition of giant planets: the roles of pebbles and planetesimals + +And several more in preperation (last updated: 22.11.2023) \ No newline at end of file diff --git a/doc/source/Usage.rst b/doc/source/Quick-Start.rst similarity index 55% rename from doc/source/Usage.rst rename to doc/source/Quick-Start.rst index d8e0a09..3f20deb 100644 --- a/doc/source/Usage.rst +++ b/doc/source/Quick-Start.rst @@ -40,3 +40,20 @@ Running chemcomp will create the following folders (if not existing) in the curr ├── zip_output # Storage of the ziped output files If you want to know how to open and plot these files, head over to :ref:`Output`! + +Examples +^^^^^^^^ + +You can find a few examples in the ``jobs`` and ``config`` folder. +These examples will help you to understand, how ``chemcomp`` has been used to create some figures in the original publications. + +These examples include: + +* ``jobs/paper_1_disk.yaml`` + Job file, used to generate the disk models in the first chemcomp paper (Schneider & Bitsch 2021a) +* ``jobs/paper_1_grid_thorngren.yaml`` + Job file, used to generate the grid of planets to compare the heavy element content in the first chemcomp paper (Schneider & Bitsch 2021a) +* ``jobs/paper_1_grid_thorngren.yaml`` + Job file, used to generate the growthtracks of planets in the first chemcomp paper (Schneider & Bitsch 2021a) +* ``jobs/paper_2_Jupiter.yaml`` + Job file, used to generate Jupiter like planets for the second chemcomp paper (Schneider & Bitsch 2021b) \ No newline at end of file diff --git a/doc/source/index.rst b/doc/source/index.rst index e837077..8b0de10 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -46,13 +46,21 @@ The physical model is in depth explained in `(Schneider & Bitsch 2021a)