Configuration files

Chemfiles can be configured using TOML configuration files. By default, chemfiles will read configuration from any file named .chemfiles.toml or chemfiles.toml in the current directory or any parent directory. Data from directories higher in the filesystem will be used instead of the one lower in the filesystem. For example, with the following file organization:

$HOME
├── .chemfiles.toml (1)
└── work
    ├── chemfiles.toml (2)
    ├── test-1
    │   ├── trajectory.xyz
    │   └── ...
    └── test-2
        ├── .chemfiles.toml (3)
        ├── trajectory.nc
        └── ...

Running chemfiles from $HOME/ will only use the configuration file (1), running it from $HOME/work/test-1 will use the configuration file (2) first and then from (1), and running it from $HOME/work/test-2 will use configuration data from (3), then (2) and then (1).

Configuration files should be valid TOML files, and can contain various sections.

[types]: atomic type renaming

The [types] section of the configuration file allow to change atomic types to make sure they match element name. For example, in a simulation where water molecules are named Hw-Ow-Hw, one may use this section of the input file like this:

[types]
Ow = "O"
Hw = "H"

Renaming atomic type allow to ensure that bonds will be guessed right, and that the right atomic data can be accessed.

The [types] section contains multiple key which are the old atom type, associated with string values which are the new atom type.

[atoms]: Defining new atom types

When working with particles outside of the periodic table (for example coarse grained particles), it can be useful to define new atom types. This can be done in the [atom] section.

[atoms.CH3]
full_name = "methyl"
mass = 15.035
charge = 0
vdw_radius = 2.4
covalent_radius = 1.1

# One can also override element data
[atoms.Zn]
charge = 1.8

# TOML also supports inline tables
[atoms]
CH4 = {mass = 16.043, charge = 0, full_name = "methane"}
Ph = {mass = 77.106, full_name = "phenyl"}

The [atoms] section contains multiple tables, one for each new atom type. These tables can contains the following key/values (all keys are optional):

• full_name (string) : the full name of the atomic type;

• mass (number) : the mass of the atomic type in atomic units;

• charge (number) : the charge of the atomic type in multiples of e;

• vdw_radius (number) : the Van der Waals radius of the atomic type in Angstrom;

• covalent_radius (number) : the covalent radius of the atomic type in Angstrom;