Quick Start Guide of Installing and Running RAPTOR for MS-RMD Simulations

Contents of Software Package

• USER-RAPTOR - The LAMMPS package folder with source codes of RAPTOR
• tests - Testing examples
• Makefile.mpi_EXAMPLE - An example Makefile to build LAMMPS/RAPTOR
• MANUAL.pdf - Raptor User Manual
• README - This file

Installation

1. RAPTOR is a plugin package to LAMMPS for running MS-RMD simulations. To run LAMMPS/RAPTOR, the first step is to download, configure and install LAMMPS distribute from its official website.

   • LAMMPS website: https://lammps.sandia.gov/
   • Download link: https://lammps.sandia.gov/download.html
   • Official manual: https://lammps.sandia.gov/doc/Manual.html

   A recommended version can be download directly via:

   • https://lammps.sandia.gov/tars/lammps-29Sep2021.tar.gz

   A quick installation guide can be found at:

   • https://lammps.sandia.gov/doc/Build_make.html

   User needs to configure the Makefile by providing customized system library dependencies. Following dependencies are required for building LAMMPS with the RAPTOR package:

   • MPI (IntelMPI or OpenMPI)
   • FFT (Intel/MKL or FFTW3)

   To use RAPTOR, following two LAMMPS packages need to be enabled:

   • MOLECULE
   • KSPACE

2. Here's an example of commands that can be used to build LAMMPS with RAPTOR:

   cd [LAMMPS]/src
   cp -rp [INSTALL]/USER-RAPTOR .
   cp -p [INSTALL]/Makefile.mpi_EXAMPLE MAKE/Makefile.mpi
   make yes-MOLECULE
   make yes-KSPACE
   make yes-USER-RAPTOR
   make mpi

   Explanation:

   • [LAMMPS] is the folder from unpacking the downloaded LAMMPS tar file
   • [INSTALL] is this folder that from unpacking VOTH-RAPTOR.tar.gz tar file

If everything runs successfully, an executable binary filewill be generated as [LAMMPS]/src/lmp_mpi

Tests and Usage

There are two examples provided in the tests folder in this package:

• single - Water box with one pair of H+ and CL-
• multi - Water box with 16 pairs of H+ and CL- (using MS-RMD-SCI method)

Both of them are using the newest RMD/3.2 parameters for excess protons in water. To run any of these test, run following command in the folder:

   mpirun -np [N] [LAMMPS]/src/lmp_mpi -in in.lmp

• [N] is the number of processes (cores) to run the simulation
• [LAMMPS] is the folder of LAMMPS distribute

Contact

For any questions, please contact Yuxing Peng at yuxing@uchicago.edu