Software Technical Information

The information in this section describes n2p2 and LAMMPS as a whole. Information specific to the additions in this module are in subsequent sections.

Name

n2p2, LAMMPS

Language

C++

Licence

GPL-3.0-or-later (n2p2), GPL-2.0 (LAMMPS)

Documentation Tool

Doxygen, Sphinx

Application Documentation

http://compphysvienna.github.io/n2p2/ (n2p2) https://lammps.sandia.gov/ (LAMMPS)

Relevant Training Material

http://compphysvienna.github.io/n2p2/ (n2p2) https://lammps.sandia.gov/ (LAMMPS)

Software Module Developed by

Andreas Singraber

n2p2 - Improved link to HPC MD software

This module documents efforts to improve the interaction of n2p2 with existing HPC software, in particular the molecular dynamics (MD) software package LAMMPS.

Purpose of Module

Although n2p2 was already shipped with source files for patching LAMMPS before, the build process required manual intervention of users. To avoid this in future versions of LAMMPS a pull request was created to include the n2p2/LAMMPS interface by default as a user package. In order to conform with LAMMPS contribution guidelines multiple issues were resolved, triggering these changes/additions to LAMMPS and n2p2:

• Modify the traditional build process (via makefiles) to include n2p2
• Modify the CMake build process to search and include n2p2
• Create additional documentation about the build settings
• Adapt documentation of the LAMMPS pair_style nnp command
• Create a suitable example which can be shipped with LAMMPS
• Change n2p2 to conform with LAMMPS bigbig settings (see here)
• Change the source files pair_nnp.(cpp/h) to conform with the LAMMPS coding style

Furthermore, the n2p2 build system was adapted to allow for multiple interfaces to other software packages, with an option to select only those of interest to the user. This can be achieved by providing the INTERFACES variable in the build stage, e.g. use

make libnnpif INTERFACES="LAMMPS CabanaMD"

to build both the LAMMPS and the CabanaMD interface and include it in the libnnpif library.

As a first application, the user contributed CabanaMD interface was integrated in the new build process. CabanaMD is an ECP proxy application which makes use of the Kokkos performance portability library and n2p2 to port neural network potentials in MD simulations to GPUs and other HPC hardware.

Background Information

This module is based on n2p2, a C++ code for generation and application of neural network potentials used in molecular dynamics simulations. The source code and documentation are located here:

• n2p2 documentation: http://compphysvienna.github.io/n2p2/
• n2p2 source code: http://github.com/CompPhysVienna/n2p2

In addition the source files for the LAMMPS patch are based on LAMMPS, a C++ code for massively parallelized molecular dynamics simulations. The source code and documentation are located here:

• LAMMPS documentation: https://lammps.sandia.gov/
• LAMMPS source code: http://github.com/lammps/lammps

Building and Testing

Important

By the time of reading these instructions the packages were most likely developed further and it cannot be guaranteed that the procedures given below will give the desired results. To retrieve the state of each software at the time of writing these lines please uncomment and use the lines with git checkout <commit-hash>.

LAMMPS user package

To test whether the LAMMPS user package USER-NNP works together with n2p2 as expected we have to download LAMMPS from the pair-style-nnp feature branch and use the current master version of n2p2. First, to get and compile n2p2:

git clone https://github.com/CompPhysVienna/n2p2
cd n2p2/src
# git checkout 428db3ee61f9943feaeedfaaeb5e096289983d46
make libnnpif -j
cd ../..

Next we retrieve the LAMMPS feature branch:

git clone -b pair-style-nnp --single-branch https://github.com/singraber/lammps
cd lammps
# git checkout ed53e2bbff2465dd05ba015a05843b2bb328360c

and compile the code with the USER-NNP package enabled using the CMake build approach:

mkdir build
cd build
cmake -D PKG_USER-NNP=yes -D N2P2_DIR=<path-to-n2p2> ../cmake
make -j

Alternatively, we could also use the traditional build process using makefiles:

cd src
make yes-user-nnp
make N2P2_DIR=<path-to-n2p2> mpi -j

In either case the LAMMPS binary should be created (lammps/build/lmp or lammps/src/lmp_mpi) and we can test if it works correctly with the provided example:

cd ../examples/USER/nnp
# Binary from CMake build process:
mpirun -np 4 ../../../build/lmp -in in.nnp
# or from the traditional build process:
# mpirun -np 4 ../../../src/lmp_mpi -in in.nnp

CabanaMD interface

While the n2p2 build process for the CabanaMD interface is trivial (it requires only the collection of some header files) the compilation steps on the CabanaMD side are not trivial. Furthermore, testing requires a suitable GPU with a compatible compiler environment. Hence it is not feasible to provide general build instructions for testing here. However, the n2p2 documentation offers an example build procedure for a specific hardware setup here.

Source Code

Changes in LAMMPS

The easiest way to view the source code changes in LAMMPS covered by this module is to use the GitHub pull request page. There, use the Files changed tab to review all changes.

Changes in n2p2

The following commits collect all changes required to follow the LAMMPS contribution guidelines:

• Updated makefiles for new LAMMPS build process
• Add flag information when n2p2 runs
• Changed build flags prefix from NNP_ to N2P2_
• Changed Atom::(Neighbor::)tag to int64_t

The commits which restructured the makefiles to allow multiple selectable interface library parts can be found here (they are part of the CabanaMD pull request):

• Restructured interface library
• Renamed source files and updated docs

The CabanaMD example build instructions were added to the n2p2 documentation in this commit:

• Add CabanaMD build example docs for reference