Alpine.jl

About

Alpine is a Julia library for analyzing and processing the results of molecular dynamics simulations.

Overview

• Load and save a variety of molecular dynamics data/trajectory files (XYZ, LAMMPSTRJ, LAMMPSDAT, etc.)

• Work with extremely large (1 TB+) data files by indexing frames and loading only the relevant data

• Key/value property system supports arbitrary properties defined on atoms and simulation boxes

• Very fast computation of radial distribution functions (RDFs) with support for arbitrary binning functions

• Ability to generate 3D density distributions from atom position data

• Licensed under the MIT License

How to install

In Julia:

Pkg.clone("https://github.com/NickMcNutt/Alpine.jl")

Usage

Reading and writing molecular dynamics data/trajectory files

AtomFile(filename::AbstractString)

AtomFile(filetype::AtomFileType, filename::AbstractString)

Create a reference to a molecular dynamics data file. The file type is determined from the file extension. The second form of this function may be used to directly specify the file type, which can be one of:

• XYZ
• An XYZ file. The first line of this file must be an integer specifying the number of atoms. The second line of the file can be anything. Multiple frames can be contained in the XYZ file. Each frame must immediately follow the previous one.
• LAMMPSTRJ
• A LAMMPS trajectory file
• LAMMPSDAT
• A LAMMPS data file

Note that Alpine DOES NOT CHECK that the specified file format is correct, or even that the data file is error free. This is because a data integrity check would drastically slow down the reading of large files. To this end, ensure that your data is correct, otherwise the results will be unpredictable.

read_frame_headers(atom_file::AtomFile)

Collect header information from all of the simulation frames in a molecular dynamics trajectory file. This function indexes the location of each frame within the data file so that atom data can later be quickly read without searching the entire file. This function also reads any properties defined on the simulation box in each frame (e.g., current timestep, box dimensions, etc.).

read_atoms(atom_file::AtomFile; [frames::AbstractVector{Int}])

read_atoms(filename::AbstractString, [end_frames::Int])

Read atom data from an AtomFile.

The first form of this function takes an AtomFile and an optional keyword argument frames that specifies the indices of the frames that are to be read from a trajectory file.

The second form of this function is a shortcut that creates an AtomFile from a given filename and then reads the atom data from that file. The optional argument end_frames specifies that only the last end_frames frames in the trajectory file should be read.

write_atoms(atom_file::AtomFile, frame::Frame)

write_atoms(atom_file::AtomFile, frames::Vector{Frame})

write_atoms(filename::AbstractString, frame::Frame)

write_atoms(filename::AbstractString, frames::Vector{Frame})

Write one or more Frames to an atom file.

Analysis

Alpine includes a collection of tools for analyzing the results of MD simulations.

For computing radial distribution functions (RDFs), the following functions are provided:

rdf{T}(atoms::Atoms, xbw::T, ybw::T, zbw::T, radius::T, Δr::T)

Compute the RDF for a collection of atoms in a periodic rectangular prism box with dimensions (xbw, ybw, zbw) out to radius radius with bin size Δr.

rdf{T}(f::Function, nf::Int, atoms::Atoms, xbw::T, ybw::T, zbw::T, radius::T, Δr::T)

Compute the multiple RDFs simultaneous for a collection of atoms where each RDF consists of atoms that satisfy a particular condition.