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Tutorial 2 — CINEB + LAMMPS

Tutorial 2: CINEB using LAMMPS

This tutorial gives a set of example input files and instructions for a CINEB calculation which uses the ReaxFF forcefield through LAMMPS.

In this case, we are going to run a CINEB optimization of a reaction path representing association of water H2O onto a Pt atom which also has a pre-bound CO molecule. We will use the ReaxFF reactive force-field to model the potential energy surface, accessed through the LAMMPS molecular dynamics code.

The actual files to run this example can be found in the *~/cde/Tutorials/Tutorial_2 directory.

In this directory, you will find several input files:

  input
  path.xyz
  CHOPtNiX.ff
  lmp.head
  lmp.min
  lmp_control

These files are all required in order to the run the CINEB/LAMMPS calculation defined in the input file.

In general, the input is similar to that given in Tutorial 1 (@ref Tutorial1). The key difference is that the setup of the PES evaluations is different - in Tutorial 1 we used ORCA, but here we use ReaxFF via LAMMPS. As a result, the PES input block of the input file looks like the following in this case:

pestype  lammps
pesfile   lmp.head
pesopttype  lammps
pesoptfile lmp.min
pesexecutable '/Users/scott/code/lammps-22Aug18/src/lmp_serial'
pesoptexecutable '/Users/scott/code/lammps-22Aug18/src/lmp_serial'

There are a few important things to note about running calculations with ReaxFF/LAMMPS:

  • Here, the pestype and pestoptype have both been set to lammps, and the paths to the relevant LAMMPS executable have also been specified.

  • To get this example running, you MUST modify the executables to point to the LAMMPS executable on your own system.

  • Another difference with Tutorial 1 is that the PES template files are different. In this case, the template files lmp.head and lmp.min are LAMMPS template files. More information can be found in the PES templates (@ref Templates) section of the documentation.

  • Finally, as also noted in the PES templates (@ref Templates) section, the LAMMPS code requires two additional files to be present in the run directory. These are: (1) A .ff file, containing the ReaxFF parameters which should be used. In our case, this is called CHOPtNiX.ff. (2) A lmp_control* file, which contains additional control parameters used by LAMMPS!