Configuration

chemcomp
├── analysis              # sample python scripts for post-processing
├── chemcomp              # main directory of the code
│   ├── accretion_models  # modules for accretion
│   ├── disks             # disk modules
│   │   ├── _0pacity      # opacity files
│   ├── helpers           # helper (e.g. wrapper for multiprocessing, etc)
│   │   └── units         # units and other constants
│   └── planets           # planet modules
├── config                # config files
├── jobs                  # job files
├── output                # output files
└── zip_output            # ziped output files

There are several ways how you can use chemcomp. Upon installation of chemcomp, several scripts are added to your python environment. We will discuss these in more detail below.

Run configuration:

• config.yaml
• Job.yaml

chemcomp_main

Wrapper for running a single configuration. Execute with:

chemcomp_main [-h/--help][-c/--config_file]

• -c specifies the path to the config file.

• -h shows the help dialog.

Parameters that are set in the config file can be found here.

chemcomp_pipeline

Wrapper for running multiple configurations. Execute with:

chemcomp_pipeline [-h/--help][-c/--config_file][-d/--delete][-j/--job_file][-o/overwrite]

• -c specifies the path to the config file.

• -o specifies if you want to overwrite existing simulations. Use -o 1 if you want to overwrite all your already finished runs.

• -h shows the help dialog.

• -d specifies wether to delete (use -d 1) or not delete (use -d 0) the files in output after zipping.

• -j specifies the path to the job file.

Explanations about the config file can be found here. Explanations of the job file can be found here.

Note:

Your execution did not finish? Don’t worry. You can continue your runs with -o 0, which will only runs on those parameters again, that did not yet finish.

You can find an example of how to use chemcomp_pipeline in the cluster_examples folder.

The chemcomp directory

The chemcomp/chemcomp directory is the directory where the main code resides.

chemcomp/chemcomp
├── __init__.py
├── accretion_models
│   ├── __init__.py
│   ├── _accretion_class.py     # framework for accretion models
│   ├── gas.py                  # gas accretion model
│   ├── pebbles.py              # pebble accretion model
├── disks
│   ├── _0pacity
│   │   ├── __init__.py
│   │   ├── meanopac1_5050.dat  # opacity lookup table
│   │   ├── meanopac5.dat       # opacity lookup table
│   │   └── opacity_models.py   # delivers the opacities
│   ├── __init__.py
│   ├── _chemistry.py       # SchneiderBitsch2020 composition model
│   ├── _disk_class.py          # general disk model (parent of individual disks)
│   ├── kees.py                 # visc heating that works
│   ├── mmsn.py                 # simple mmsn disk with Hayashi H/R.
│   └── twopop.py               # disk used in twopop.
├── helpers
│   ├── __init__.py
│   ├── analysis_helper.py      # framework for post processing
│   ├── debugger_helper.py      # some useful functions for debugging during runtime
│   ├── import_config.py        # functions that are used for the import of the parameters in the config file.
│   ├── main_helpers.py         # functions that are used for main.py and pipeline.py.
│   ├── solvediffonedee.py      # functions used for visc disk evolution
│   ├── tridag.py               # functions used for visc disk evolution
│   └── units
│       ├── __init__.py
│       ├── berts_units.py      # Berts weird code units. Not used.
│       └── chemistry_const.py  # constants used for the _chemistry_new and _chemistry
└── planets
    ├── __init__.py
    ├── _planet_class.py        # main planet module (parent).
    ├── bertmigration.py        # P11 + K18 migration + feedback torques.
    ├── migration_1.py          # only Lindblad torque.
    ├── no_accretion.py         # no accretion, no migration -> only disk
    └── simple_planet.py        # no migration

The code is structured in four main modules:

Module	directory of parent class	Used for
Disk	_disk_class	Deals with the disk related physics (e.g. dust growth, visc evolution, etc.)
Chemistry	_chemistry	Chemical compositions used in Disk.
Planet	_planet_class	Controls the other modules. Grows and migrates.
Accretion	_accretion_class	Used in Planet. Calculates the accretion rates.

Other directories

The paths for output, zip_output, config and jobs can be adjusted in chemcomp/chemcomp/helpers/__init__.py

Path	Variable	Use of path
output	OUTPUT_PATH	storage path for the output files
zip_output	ZIP_OUTPUT_PATH	storage path for the zipped output files
jobs	JOB_PATH	path in which job configurations are stored
config	CONFIG_PATH	path in which configuration/parameter files are stored

The complete set of parameters in the config file is explained here. Explanations of the job file can be found here.