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Different types of calculation (protocols) are implemented in separate executables. The basic input (method specification, etc.) is shared between these modules, and in simple cases, it is possible to use the same input file for different modules. On the other hand, each type of calculation may require additional setup that is specific for the given module and will be ignored by other ones.

Alternatively, the executable cuby can be used to run any of these calculations, the calculation type is specified by keyword job. Some less frequent protocols can be run only this way.

cuby_energySinglepoint calculation of energy.
cuby_chargesCalculation of atomic charges.
cuby_interactionCalculation of interaction energy.
cuby_optimizeGeometry optimization.
cuby_mdMolecular dynamics
cuby_freqVibrational frequencies
cuby_nebNudged elastic band - minimum energy path search
cuby_datasetAutomated calculations on predefined datasets
cuby_scanPerform a calculation along trajectory of geometries
cuby_shellInteractive ruby shell (based on irb) with preloaded cuby framework.

Common features

All the modules (except cuby_shell) share the same commandline syntax and options. The executables need two arguments, first is name of the input file, second is the geometry file (see File formats):

cuby_energy input.yaml

The output is printed to standard output, you may want to redirect it to a file to save the results for further use.

Several commandline options are available for these modules:

-hPrint help and exit
-v valueVerbosity level
-pPrepare the calculation directory(ies) and exit
-k listExtra keywords added to input, format is keyword:value,keyword:value,...
-tPrint timing information