ToDo: Write introduction to LAMMPS!

Building LAMMPS with VASPml patch

git clone https://github.com/vasp-dev/lammps

cd lammps

git checkout vasp-mlff

ln -s /path/to/vasp/build/std/vaspml lib/vasp/

cd src

make yes-ml-vasp

make mpi

Setting up a LAMMPS MD run

LAMMPS comes with its own powerful script language which allows the user to specify all relevant MD simulation parameters in a single file. Please consult the LAMMPS documentation for details. Within the LAMMPS script language the commands pair_style and pair_coeff are responsible for selecting a force field. The ML-VASP package introduces a new pair_style called vasp. The pair_style vasp command does not have any additional arguments, all configurable settings are given as arguments to the pair_coeff command in this format:

pair_style vasp
pair_coeff * * file types

The pair_coeff command must be followed by * *, then followed by the name of the VASP force field file, typically ML_FF. Finally, there comes a mapping from LAMMPS atom types to VASP force field types, e.g., H O Na Cl means that LAMMPS types 1, 2, 3 and 4 are mapped to VASP types H, O, Na and Cl, respectively. A valid example may look like this:

pair_style vasp
pair_coeff * * ML_FF Pb Br Cs

This will map the LAMMPS atom types 1, 2 and 3 in the input data file to the types Pb, Br and Cs for which a pre-trained machine-learned force field should be present in the ML_FF file in the execution directory. A summary of the type mapping is provided in the screen output and the log.lammps file, e.g. for the example above it looks like this:

   LAMMPS       pair_coeff      VASP      |             VASP force field
    types       names           subtypes  |     types       names        subtypes
----------------------------------------- | -------------------------------------
        1 <---> Pb        <---> 0         |         0 <---> Pb     <---> 0        
        2 <---> Br        <---> 1         |         1 <---> Br     <---> 1        
        3 <---> Cs        <---> 2         |         2 <---> Cs     <---> 2

On the left side we find the mapping, the right side gives an overview of types present in the force field file. In this example, there is a one-to-one mapping, hence, the table looks pretty obvious and contains somewhat redundant information. However, it is also possible to leave out a mapping from specified LAMMPS types by supplying NULL instead of a valid VASP type name. This can be helpful when multiple force fields should be combined, see pair_style hybrid. Furthermore, multiple LAMMPS types may be mapped to the same VASP types. Finally, the force field file may contain types which are not used in the current MD simulation. Therefore, a more complicated example may look like this:

pair_coeff * * vasp ML_FF NULL Cs NULL Br Pb Br

and the corresponding table could contain this information:

   LAMMPS       pair_coeff      VASP      |             VASP force field
    types       names           subtypes  |     types       names        subtypes
----------------------------------------- | -------------------------------------
        1 <---> unmapped! <---> unmapped! |         0 <---> Ca     <---> unused!
        2 <---> Cs        <---> 2         |         1 <---> Pb     <---> 0        
        3 <---> unmapped! <---> unmapped! |         2 <---> O      <---> unused!
        4 <---> Br        <---> 1         |         3 <---> Br     <---> 1        
        5 <---> Pb        <---> 0         |         4 <---> Cs     <---> 2        
        6 <---> Br        <---> 1         |

Mind: Always ensure that the type mapping is correctly set up because mixed-up types may not immediately result in errors. An MD simulation may still run and only post-processing may ultimately reveal inconsistencies which can be tedious to trace back to type-mapping mistakes.

The pair_style vasp expects input coordinates to be in the units of Ångström and returns energies and forces with the energy unit of eV. Hence, it is only compatible with the LAMMPS setting units metal in the input script, otherwise an error will occur.