2026-10-15T17:56:51Z https://data.mendeley.com/oai

oai:data.mendeley.com/6h7gp5czfr.1 2026-07-23T22:38:28Z

You, Chun-Yeol Optimization of the LAMMPS Mendeley Data Title: Benchmark data, FEP results, and modified LAMMPS source files for "AI-Assisted Systematic Optimization of the LAMMPS Molecular Dynamics Simulator via Large Language Model Coding Agents" This dataset accompanies the manuscript submitted to Computer Physics Communications (2026). It contains all data required to reproduce the performance benchmarks, numerical verification results, and free-energy perturbation (FEP) case study reported in the paper. Contents: 1. Benchmarking data (tools/bench/) summary.csv — Consolidated loop-time and pair-time statistics for all benchmark runs (N = 3–5 independent runs per configuration). in.*_test / in.*_speed_test — LAMMPS input files for each of the 225 pair styles verified under the A-3 optimization protocol (50-step NVE thermo-comparison tests) and for serial/OMP speed benchmarks. port*_before.thermo / port*_after.thermo — Bit-level thermo output (step, temp, epair, etotal, press) before and after each modification, enabling line-by-line numerical verification. 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) Computer Science Physical Sciences Dataset doi:10.17632/6h7gp5czfr.1 oai:data.mendeley.com/6h7gp5czfr.1 Creative Commons Attribution 4.0 International http://creativecommons.org/licenses/by/4.0 https://data.mendeley.com/datasets/6h7gp5czfr 2026-07-23T22:38:28Z