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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) is chemistry researcher 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.

• Goals of chemfiles
• Features
• Supported file formats
• Getting started
• Full documentation
• Python interface
• Fortran interface
• Julia interface
• Rust interface

The chemfiles library tries to:

• Be easy and simple to use. There are only five main classes, which are really easy to understand. No messy templates and uninformative functions names;
• Be a multi-languages library, usable from whatever language you prefer. If your favorite language is not supported, chemfiles have a clean C interface so that you can add a binding;
• Following the UNIX moto, do one thing, and do it well.
• Be cross-platform, and usable from Linux, OS X and Windows;
• Have high-quality code, using modern software building technics (unit testing, code coverage, git for code versioning, ...).

Chemfiles also have non goals, or explicitly refused goals:

• It will not contains any code for analysis. You can find implementation of some analysis algorithms and a ready-to-use command line program in the chrp repository.
• It will not contain molecular dynamics, Monte-Carlo, energy minimization or quantum chemistry code. If you want such code with access to the chemfiles features, please see the cymbalum molecular simulation engine, by the same author.

• Automatic recognition of file type based on filename extension;
• Support for a number of atoms which is not constant;
• Set custom UnitCell or Topology when reading/writing;
• Bindings to the most used scientific languages: Python, C, Fortran 95;
• Work with binary formats, if the corresponding libraries are available.
• Open-source and freely available under the Mozilla Public License;

The following formats are supported through the VMD molfile plugins, and are read-only:

See the issue list for planned formats. If you want a new format to be added to chemfiles, you can either do it by yourself (it is easy !) and create a pull-request to incorporate your changes, or create a new issue with a link to the format reference and some example of well-formed files.

The whole installation is documented here, this page only show the basic steps. Please refer to the link below in case of problem.

If you want to use chemfiles from one of the available bindings, please refer to the corresponding repository:

• Python interface
• Fortran interface
• Julia interface
• Rust interface

Long story made short, just use the right commands for your system:

# On apt-get based distributions
apt-get update
apt-get install cmake libnetcdf-dev

# On yum based distributions
yum install epel-release # The EPEL repository have the netcdf lib
yum install cmake netcdf-devel netcdf-cxx-devel

# On OS X with Homebrew (brew.sh)
brew tap homebrew/science
brew install cmake netcdf

You will also need a recent C++ compiler: gcc 4.9, clang 3.5 and icpc 14 are known to work.

Get the code from the release page, and extract the archive. Then in a terminal, go to the folder where you put the code (~/chemfiles is assumed here):

cd ~/chemfiles

Then, cmake is used to build the code. So, create a folder and go for the build:

mkdir build
cd build
cmake ..

Then, you can build install the library:

make
make install

For more informations about how to configure the build, please read the doc!

The documentation is hosted at readthedocs, but here are some examples of how the usage feels in c++ and in C:

// C++ version
#include <iostream>
#include "chemfiles.hpp"

int main() {
    chemfiles::Trajectory trajectory("filename.xyz");
    chemfiles::Frame frame;

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

    // Do awesome things with the positions here !
}

// C version
#include <stdint.h>
#include <stdio.h>

#include "chemfiles.h"

int main(){
    CHFL_TRAJECTORY * trajectory = chfl_trajectory_open("filename.xyz", "r");
    CHFL_FRAME * frame = chfl_frame(0);
    size_t natoms = 0;

    if (!traj) {
        printf("Error while opening file: %s", chfl_last_error());
    }

    if (!chfl_trajectory_read(trajectory, frame)){
        // handle error here
    }
    chfl_frame_atoms_count(frame, &natoms);
    printf("There are %d atoms in the frame", natoms);

    float (*positions)[3] = (float(*)[3])malloc(sizeof(float[natoms][3]));

    if (!chfl_frame_positions(frame, positions, natoms)){
        // handle error
    }

    // Do awesome things with the positions here !

    chfl_frame_free(frame);
    chfl_close(trajectory);
    free(positions);
}

Any contribution is very welcome, from feedback to pull request.

Please report any bug you find and any feature you may want as a github issue.

Chemfiles have been tested on the following platforms, with the following compilers :

• Linux (64 bit)
  • GCC: gcc/g++ 4.9.2
• OS X (64 bit)
  • GCC: gcc/g++ 4.9.2
  • LLVM: clang/clang++ 3.5
  • Intel: icc/icpc 14
• Windows (32 bit) (only the C++ and C interfaces have been tested)
  • MSVC 2015rc (MSVC 2013 DO NOT work)
  • mingw64 gcc/g++ 4.9.2

If you manage to compile chemfiles on any other OS/compiler/architecture combination, please let me know so that I can add it to this list.

All this code is copyrighted by Guillaume Fraux, and put to your disposition under the terms of the Mozilla Public License v2.0.