Table of Contents

1. XYZ.jl
2. Getting Started
   • Prerequisites
   • Installation
3. Usage
4. License and acknowledgments

XYZ.jl

A Julia package for reading XYZ trajectory files.

It currently supports XYZ files with a constant number of atoms.

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Getting Started

Prerequisites

This package is a Julia parser for XYZ files. It works with Julia 1.5 or above.

It requires the DCD package. You should install the DCD parser first!

Installation (with set-up ssh keys)

Adding private packages to Julia requires a password-less access (see the manual in this organization for setup)

pkg> add git@github.com:laagegroup/XYZ_parser_jl.git

Installation (with https, RECOMMENDED)

This package can be directly added via https by running the following command from the Julia interface:

pkg> add https://github.com/laagegroup/XYZ_parser_jl.git

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Usage

This package can be used in the Julia REPL or within a Julia script. Here is an example of the main features:

using XYZ

xyz = load_xyz("foo.xyz")

na = natoms(xyz)  # Get the number of atoms.
nf = nframes(xyz) # Get the number of frames.
atoms = atomnames(xyz) # Get the list of atom names.

for frame in xyz  # Iterate over each frame.
  r = positions(frame)  # Get an array of all current positions with dimensions (3, na).

  # Work on the current frame.
end

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License and acknowledgments

This package is a modification of the DCD parser in this organization: https://github.com/laagegroup/DCD_parser_jl.git (The original development is due to Michael von Domaros, see https://github.com/mvondomaros/DCD.jl.git and the MIT license original_MIT_license).

Modifications are distributed under the GNU Affero General Public License v3.0. See LICENSE for more information.

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