# Configuration files¶

Chemfiles can be configured using TOML configuration files. By default, chemfiles will read configuration from any file named .chemfilesrc 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 filesystem:

$HOME ├── .chemfilesrc (1) └── work ├── .chemfilesrc (2) ├── test-1 │ ├── trajectory.xyz │ └── ... └── test-2 ├── .chemfilesrc (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 simulatiion 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 wich are the old atom type, associated with string values wich are the new atom type.