ReaxTools

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ReaxTools is a local post-processing toolkit for ReaxFF, machine-learning-potential, AIMD, and other reactive molecular dynamics trajectories. It reads XYZ or LAMMPS dump files, identifies bonds and molecules, counts species, reaction events, and atom transfers by structure, and writes auditable CSV files and figures.

Core features

Feature	Example
Species abundance
Bond counts
Coordination number
Ring counts
Reaction frequency
Reaction pathway
Transfer network
Key structures

Installation and quick start

git clone https://github.com/tgraphite/reax_tools
cd reax_tools
bash install_reax_tools.sh

Dependencies:

• CMake 3.14+ and a C++17 compiler.
• Python 3.8+ with numpy, pandas, matplotlib, and PyYAML.
• Graphviz and PyGraphviz for network figures.
• RDKit is optional; it is used by the molecules command and by the 2D key-structure figures from plot.

The C++ core can also be built directly:

cmake -S . -B build -DCMAKE_BUILD_TYPE=Release
cmake --build build -j
./bin/reax_tools_core -f test/energetic.xyz -o output

Typical usage:

reax_tools -f test/energetic.xyz -o output
reax_tools plot -f output

LAMMPS dump files require a type mapping:

reax_tools -f dump.lammpstrj -t C,H,O,N -o output

Common options:

Option	Description
-f, --traj	Input trajectory, .xyz or .lammpstrj
-o, --output	Output directory
-t, --types	LAMMPS dump type order, e.g. C,H,O,N
-r, --rescale-vdw	Global vdW radius scale, default 1.2
-tr, --type-radius	Per-element radius override, e.g. N:1.5 O:1.6
-tv, --type-valence	Per-element maximum valence override, e.g. N:4 O:3
-nt, --threads	Number of frame-processing threads
--no-rings	Disable ring detection
--no-reactions	Disable transfer-flow analysis
--no-track-reactions	Disable reaction-event tracking

Plotting commands:

reax_tools plot -f output
reax_tools counts -f output
reax_tools events -f output
reax_tools network -f output
reax_tools flow -f output
reax_tools focus -f output
reax_tools molecules -f output
reax_tools summary -f output

plot generates all recommended figures in one pass.

Current limitations

1. Triclinic cells and per-axis periodicity are not supported.
2. Electronic structure is not included.
3. Only constitutional isomers of small and medium molecules are resolved.

Community publications

As of October 2026, the community has published more than 20 related works. A selection is listed below.

System	Paper	Link
Thermal degradation of amine solutions for CO2 capture	Thermal degradation and inhibition of long-chain triamines for CO2 capture, Chem. Eng. J. 2026	DOI
Plasma graphene nanoflakes	Experimental and ReaxFF MD simulation study on plasma gas-phase synthesis of graphene nanoflakes, Diamond Relat. Mater. 2025	DOI
Three-phase gel foam for fire suppression	Optimization and performance assessment of an eco-friendly three-phase gel foam for liquid fires, Colloids Surf. A 2026	DOI
Ethanol on Al(111)	Adsorption and thermal decomposition mechanisms of ethanol on Al(111), J. Anal. Appl. Pyrolysis 2026	DOI
Pulsed-potential restructuring of Cu surfaces	Atomistic Origin of Non-equilibrium Surface Restructuring on Copper under Pulsed Potentials, JACS 2026	DOI
Huadian oil shale kerogen pyrolysis	A ReaxFF molecular dynamics study on the bond cleavage priority in the pyrolysis process of Huadian oil shale kerogen, Fuel 2026	DOI
Cellulose steam gasification	Fe2O3-assisted steam gasification of cellulose: a ReaxFF molecular dynamics study, Process Saf. Environ. Prot. 2026	DOI

Citation

Hanxiang Chen, ReaxTools: A high-performance ReaxFF/AIMD trajectory analysis tool based on graph theory. https://github.com/tgraphite/reax_tools [Computer Software], retrieved on [date], or a similar citation.