Documentation

TurboGAP is a program and associated collection of routines designed for carrying out atomistic calculations based on machine learning interatomic potentials. This page deals with the technical aspects of using TurboGAP; to learn more about the underlying theory, check the GAP theory page.

Calculation mode

There are two basic modes for running a TurboGAP calculation, turbogap predict and turbogap md. They are invoked by simply typing turbogap predict or turbogap md in the command line or a bash script (e.g., to run MD in parallel on 8 CPU cores: mpirun -np 8 turbogap md). Both execution modes require an input file with TurboGAP options, a gap_files directory with the GAP potential to be used in the calculation, and an XYZ file in ASE's extended XYZ format with atomic positions, lattice vectors and chemical species information (for MD, also atomic velocities are needed).

turbogap predict

turbogap predict performs single-point calculation (i.e., the atomic positions are not updated during the simulation) for total energy, local energy, forces and virial pressure. When available for the specific potential, it can also perform a Hirshfeld volume prediction. If the atoms file contains more than one configuration, in the form of concatenated individual atomic structures, TurboGAP will perform predictions for all of them.

tubogap md

turbogap md performs molecular dynamics according to the options specified in the input file.

Files

Input file (input)

The input file contains the keywords that tell TurboGAP how to perform the single-point or MD calculation requested by the user. A minimal input file (without MD options) contains only information about the structure XYZ file, the location of the potential, and chemical species. An example looks like this:

! Species-specific info
atoms_file = 'atoms.xyz'
pot_file = 'gap_files/cho.gap'
n_species = 3
species = H C O
masses = 1.01 12.01 16.00 ! this is optional for single point, mandatory for MD
e0 = 0. 0. 0. ! this is optional, to specify per-species energy offsets

For a single-point turbogap predict calculation, something like the above is all that is needed. For running MD and other specilized simulations one needs to additionally specify the appropriate keywords. Check MD options for a complete list.