ReaxTools Pro

ReaxTools Pro Tutorial : Studying combustion of ethanol.

Introduction

This tutorial explores the combustion of ethanol (C₂H₆O) in oxygen:

C₂H₆O + 3O₂ → 2CO₂ + 3H₂O

While stoichiometrically simple, actual combustion involves complex reaction networks. Marinov's study identified over 300 elementary reactions in this system.

Modern reactive MD methods now enable efficient analysis of such complex systems, reducing computation time from months to ~30 minutes.

Software Requirements

Packmol - System initialization
GPUMD - GPU-accelerated MD simulations
ReaxTools - Analysis and reporting

1. System Preparation

We construct a simulation box containing:

100 ethanol molecules
300 oxygen molecules
Total: 1500 atoms in 236 nm³ (density = 0.1 g/mL)

Packmol Input:

            filetype xyz
            output model.xyz
            tolerance 4.0
            structure ethanol.xyz
            number 100
            inside box 0 0 0 67.18 67.18 67.18
            end structure
            structure oxygen.xyz
            number 300
            inside box 0 0 0 67.18 67.18 67.18
            end structure

Execution:

packmol < packmol.inp

The final periodic system XYZ file includes boundary conditions:

            1500
            Lattice="67.18 0.0 0.0 0.0 67.18 0.0 0.0 0.0 67.18" Origin="0.026168 0.001867 0.024439" Properties=id:I:1:species:S:1:pos:R:3
            1 C 49.2771926179 25.3604183225 27.8483112501
            2 H 49.4570955095 25.3162389282 28.928943456
            ...

Initial system configuration

2. Simulation

When system prepared, we will use GPUMD to perform a 200 ps molecular dynamics simulation. According to the adiabatic combustion temperature of ethanol, which is 2082 ℃, ~2350 K, we will set the simulation temperature as 2350 K. And the ensemble is NVT, using langevin thermostat.

The GPUMD running parameter file run.in as below:

            potential    nep.txt
            velocity     2350 
            time_step    0.2
            
            ensemble     nvt_lan 2350 2350 100
            dump_thermo   10  
            dump_exyz     500
            run           1000000

We will use the newest Neuroevolution Potential (NEP) parameter set NEP-89 for simulation. Before simulation, the working directory contains files below:

run.in nep.txt model.xyz

Use command gpumd directly to invoke an automatic GPUMD task in current directory.

The simulation cost 10~20 minutes on GTX 4090D machine, after simulation terminated, the system structure looks like below:

System configuration after simulation.

3. ReaxTools Analysis

After simulation completion, GPUMD outputs a standard trajectory file (dump.xyz) in the current directory. This file is compatible with ReaxTools (File format reference).

Analysis steps:

Load the file on the main page
Click "Run" (typically completes within 1 minute)
View clearly presented results on the website

Configuration tip: For this case, we use -r 1 to apply stricter bond cutoff criteria for molecular identification. For advanced customization, see Input options reference.