Commandline options

Usually, Cuby calculation is run by calling the cuby4 script with a single argument, the name of the input file:

cuby4 input.yaml

Modifying the input

The calculation can be also modified from the commandline, the commandline options override the settings from the input (which is not modified).

The keywords used most often can be accessed with single-letter commandline options, e.g. the option "-g" can be used to specify the geometry:

cuby4 input.yaml -g geometryfile.xyz

The following keywords can be accessed this way:

Additional documenation
geometry-g
job_cleanup-c
job-j
prepare_only-p
queue_submit-q
selection-s
verbosity-v

Value of any keyword (at the root level of the input) can be changed from commandline by using the keyword itslf as an option, prepended with "--". For example, to change the charge of the system, use:

cuby4 input.yaml --charge 1

It is possible to set the value of keywords in specific blocks in the input. For example, to set the keyword charge in block calculation_a, following syntax is used:

cuby4 input.yaml --calculation_a:charge 1

The last feature allows changing the value of a keyword everywhere in the input (only in places where the keyword is already present). This is processed first, before individual changes are made. The syntax is:

cuby4 input.yaml --*:charge 1

Access to documentation

The cuby4 script also provides access to the automatically generated documentation:

List all keywords:
cuby4 kw
List of keywords accessible from commandline:
cuby4 kw commandline
Detailed information on specific keyword:
cuby4 kw keyword_name
List of interfaces:
cuby4 interface
Information on the selected interface:
cuby4 inteface interface_name
List of protocols:
cuby4 protocol
Information on a protocol (job type):
cuby4 protocol protocol_name
List of available methods:
cuby4 method
Information on a computational method:
cuby4 method method_name

Shell

The following commands opens interactive ruby shell (irb) with preloaded cuby libraries:

cuby4 shell

Other tasks

Options --info, --make and --test are described at the installation page.