Avogadro — The Complete Guide: Building and Visualising Molecules and Crystals in 3D
Avogadro is an open-source (BSD-3-Clause) molecular editor and viewer developed within the OpenChemistry project. It serves as the workbench for anyone doing molecular modelling: build a structure with the mouse, clean it up, look at it from every angle and prepare an input file for a calculation. It runs on Windows, macOS and Linux.
Avogadro
Avogadro / OpenChemistry project
A 3D editor and viewer for molecules and crystals: build, optimise and analyse, and prepare input for computational chemistry codes.
Get it from the vendorWhat you get
- Molecule building — adding atoms and bonds, plus a library of ready-made fragments.
- Geometry optimisation — tidying the structure with force fields.
- Measurements — bond lengths, angles and dihedral angles.
- Crystals — working with unit cells and periodic structures.
- Input for computational codes — preparing files for quantum chemistry programs and opening their results.
How it relates to engineering
Chemical and materials engineers use it to understand a molecule’s structure, set up an energy or property calculation, or illustrate a structure in a lecture or report. It is not a process simulator and does not compute stream properties — other tools handle that.
Related tools
For thermodynamic properties and phase equilibria in scripts — thermo. For chemical kinetics and combustion — Cantera. For full process simulation — DWSIM.
thermo
Caleb Bell
A Python library for thermodynamic properties and phase equilibria of thousands of chemicals and mixtures: equations of state, activity models and flashes.
Get it from the vendor
Cantera
Cantera Developers
Chemical kinetics, thermodynamics and transport, callable from Python or MATLAB.
Get it from the vendor
DWSIM
DWSIM Project
Steady-state and dynamic process simulation for chemical plants.
Get it from the vendor
Reaktoro
Allan Leal and contributors
A C++ and Python framework for chemical equilibrium and kinetics of multiphase systems — water, gases and minerals.
Get it from the vendorThe bottom line
Avogadro is a basic, convenient tool for anyone who needs to see and build molecules. Open source and completely free, including for commercial use.