Optimization of the LAMMPS

OpenMP scaling benchmark inputs: 4,000-atom and 32,000-atom FCC Ar systems (lj/cut, NVE ensemble). Compiler-flag benchmark logs (Baseline / AVX2 / fp:fast / LTO / AVX2+fp:fast). 2. FEP case-study data (tools/fep/) LAMMPS input files for thermodynamic integration (TI) of Li⁺ desolvation in three battery solvents: ethylene carbonate (EC, ε = 89.8), propylene carbonate (PC, ε = 64.9), and 1,2-dimethoxyethane (DME, ε = 7.2). 21 λ-window simulation outputs (λ = 0.00–1.00, step 0.05) for both 40 ps/window (logs_opls/) and 200 ps/window (logs_opls_long/) production runs.

OPLS-AA force field parameter files for Li⁺, EC, PC, and DME. Joung–Cheatham Li⁺ ion parameters. 3. Analysis and figure scripts (tools/plots/, tools/bench/) Run-Benchmark.ps1 — PowerShell harness that automates multi-run LAMMPS execution, parses MPI timing output, and appends to summary.csv. fig1_workflow.py – fig7_fep_casestudy.py — Python scripts (matplotlib) reproducing all six main figures and three supplementary figures in the manuscript. fig_s1_omp_scaling.py, fig_s2_nve_energy.py — Supplementary figure scripts. 4.

Modified LAMMPS source files The 35 new OpenMP pair-style variants (A-1) and the 225 A-3 restrict/accumulator-patched files are submitted as pull requests to the upstream LAMMPS repository (github.com/lammps/lammps) upon journal acceptance. The exact commit SHA and PR numbers are listed in the manuscript. The source files are also mirrored at github.com/mirryou-maker/lammps-CO.

Software versions used: LAMMPS: develop branch, commit stable_29Aug2024 baseline + this work's patches Python 3.11, NumPy 2.4, SciPy 1.17, Matplotlib 3.11 OVITO 3.15 (structural visualization, supplementary) Operating system: Windows 11 / Linux (iREMB HPC cluster, PBS Pro) Compiler: MSVC 19.x (Windows benchmarks); GCC 8.5 + OpenMPI 4.1.4 (HPC runs)