tips.md

Tips

Change logging level

You can change the logging level by setting the LOG_LEVEL environment variable. For example,

export LOG_LEVEL=DEBUG 
ai2-kit ...

Use custom tags to simplify YAML configuration

ai2-kit implement some customized tags for YAML parser to simplify the configuration.

!load_text

!load_text can be used to read a file and use its content as the value of the tag. It accepts a string value or a list of strings as the argument. The strings will be joined together to form the path of the file to be read. For example,

data: !load_text /path/to/data/data.csv
# or
data: !load_text [/path/to/data, data.csv]

!load_yaml

!load_yaml is same as !load_text except that it will parse content of the file as a YAML document. For example,

data: !load_yaml /path/to/data/data.yml
data: !load_yaml /path/to/data/data.json
# or
data: !load_yaml [/path/to/data, data.yml]
data: !load_yaml [/path/to/data, data.json]

Note: it also support JSON format as it is a subset of YAML.

!join

!join can be used to join elements in a list into a single string. This is useful when you have to use a lot of absolution paths that shares the same based directory in your configuration. For example,

Note: this is string join not path join, so you need to add / manually when you want to join paths.

.data_dir: &data_dir /data/in/a/very/long/path/
data1: !join [*data_dir, data1.csv]
data2: !join [*data_dir, data2.csv]

which is equivalent to

data1: /data/in/a/very/long/path/data1.csv
data2: /data/in/a/very/long/path/data2.csv

Use nglview to visualize atoms structures in Jupyter Notebook

You can use the ase.visualize.view function to view atoms structures in Jupyter Notebook. If you would like to use nglview as your viewer, you need to take some extra steps to make it work.

# Install nglview
pip install nglview

# Enable Jupyter Notebook extension
jupyter nbextension enable --py widgetsnbextension