Support for Linking with External Codes

Using the ChIMES Calculator with LAMMPS

We are currently working toward ChIMES calculator implementation in LAMMPS as a USER package. In the interim, the following provides a guide to implementing the ChIMES calculator as a LAMMPS pairstyle.

Quick start

Provided a system with a C++11-compatible compiler and an MPI compatible compiler are available, LAMMPS can be downloaded, installed, linked to ChIMES, and compiled all at once by navigating to etc/lmp, adding Intel compilers to your path and executing ./install.sh. Once complete, the installation can be tested by navigating to etc/lmp/tests and running the example via ../exe/lmp_mpi_chimes -i in.lammps.

As with installation of the ChIMES Calculator itself, if you are on a HPC using module files, you may need to load them first. Module files are already configured for a handful of HPC - inspect the contents of modfiles to see if yours is listed. If it is (e.g., LLNL-LC.mod), execute export hosttype=LLNL-LC; ./install.sh to install. Otherwise, load the appropriate modules by hand before running the install script.

Note that Intel oneapi compilers (which are now free) can be used to properly configure your enviroment for all Intel capabilities (e.g., icc, mpiicpc, mkl, etc.) - simply locate and execute the setvars.sh script within your Intel installation.

Detailed Compilation Overview

Note

This example assumes users have downloaded the 29 Oct 2020 release of LAMMPS (stable version as of 10/29/20), which can be downloaded here.

To integrate the ChIMES calculator in LAMMPS, locate the following files, and place them in the following destination among the LAMMPS source code:

File

Location

Destination

Description

chimesFF.{h,cpp}

chimesFF/src

src/MANYBODY

ChIMES calculator files

pair_chimes.{h,cpp}

etc/lmp/src

src/MANYBODY

ChIMES pair_style definition files

pair.{h,cpp}

etc/lmp/etc

src

Updated LAMMPS pair files (new ev_tally definition added)

Makefile.mpi_chimes

etc/lmp/etc

src/MAKE

Makefile for compiling with ChIMES support

Following, compile from the base LAMMPS directory with:

make yes-manybody
make mpi_chimes

Note that a successful compilation should produce an executable named lmp_mpi_chimes.

Tip

If you are using an intel compiler, either delete the pair_list.* files that appear in the src folder following the make yes-manybody command, or add -restrict to CCFLAGS in MAKE/Makefile.mpi_chimes. Note that the presently provided Makefile.mpi_chimes utilizes the latter approach.

Running

To run a simulation using ChIMES parameters, a block like the following is needed in the main LAMMPS input file (i.e. in.lammps):

pair_style  chimesFF
pair_coeff  * *   some_standard_chimes_parameter_file.txt

Note that the following must also be set in the main LAMMPS input file, to use ChIMES:

units       real
newton      on
atom_style  atomic
atom_modify sort 0 0.0

Warning

  1. Implementation assumes outer cutoffs for (n+1)-body interactions are always \(\le\) those for n-body interactions

  2. This capability is still under testing - please let us know if you observe strange behavior

  3. Assumes user wants single-atom energies to be added to the system energy. If you don’t want to, zero the energy offsets in the parameter file