Chemfiles, an efficient IO library for chemistry file formats

Chemfiles is a multi-language library written in modern C++ for reading and writing from and to molecular trajectory files. These files are created by your favorite theoretical chemistry program, and contains informations about atomic or residues names and positions. Some format also have additional informations, such as velocities, forces, energy, …

The main targeted audience of chemfiles (libchemfiles) are chemistry researchers working on their own code to do some kind of awesome science, without wanting to bother about handling all the format that may exist in the world.

Running simulation (either Quantum Dynamic, Monte Carlo, Molecular Dynamic, or any other method) often produce enormous amounts of data, which had to be post-processed in order to extract informations. This post-processing step involve reading and parsing the data, and computing physical values with the help of statistical thermodynamic. Chemfiles tries to help you on the first point, by providing the same interface to all the trajectory formats. If you ever need to change your output format, your analysis tools will still work the same way. Chemfiles is efficient because it allow you to write and debug your code only once, and then to re-use it as needed.


Chemfiles is still is alpha stage, and no backward compatibility is assured. I hope I can reach a stable interface pretty soon, once it have been validated on various formats.

User manual

Even if chemfiles is written in C++, it can be used from the most popular scientific programming languages: C, Fortran, Python, … You can just pick up your favorite language to use it. This part of the documentation presents the data model used by chemfiles to store information about the trajectories, and how to acess that data in C and C++.

Basic usage of chemfiles looks like this in C++:

#include <iostream>

#include "chemfiles.cpp"
using namespace chemfiles;

int main() {
    Trajectory traj("");
    Frame frame;

    traj >> frame;
    std::cout << "There are " << frame.natoms() << " atoms in the frame" << std::endl;
    auto positions = frame.positions();

    // Do awesome science here with the positions

    if (frame.has_velocities()) {
        auto velocities = frame.velocities();

        // If the file contains information about the velocities, you will
        // find them here.

The documentation for the other languages interfaces to chemfiles are accessibles at the following places:

In the following parts, the documentation will cover how to install chemfiles, and how the data are organised.