ExtXYZ.jl

This package provides Julia bindings for the extxyz C library which implements a parser and writer for the extended XYZ file format used in materials and molecular modelling, following the specification set out in the extxyz repo. Moreover the ExtXYZ.Atoms object directly adheres to the AtomsBase common interface for atomistic structures.

Maintainer: James Kermode (@jameskermode).

Installation

This package is registered in the General registry, so installation of the latest stable release is as simple as pressing ] to enter pkg> mode in the Julia REPL, and then entering:

pkg> add ExtXYZ

or for the development version:

pkg> dev https://github.com/libAtoms/ExtXYZ.jl

Related packages

• The JuLIP.jl package is an optional - but recommended - companion. JuLIP can use ExtXYZ.jl to read and write extended XYZ files to/from JuLIP.Atoms instances, using the functions JuLIP.read_extxyz() and JuLIP.write_extxyz().
• The package is integrated with AtomsIO.jl to provide a uniform interface (based on AtomsBase) for reading and writing a large range of atomistic structure files.

Please open issues/PRs here with suggestions of other packages it would be useful to provide interfaces to.

Basic Usage

Four key functions are exported: read_frame() and write_frame() for reading and writing single configurations (snapshots), respectively, and read_frames() and write_frames() for reading and writing trajectories. Moreover ExtXYZ.Atoms provides a datastructure to expose the read configurations in an AtomsBase-compatible manner. All read and write functions can work with string filenames, an open Base.IO instance or (intended primarily for internal use) a C FILE* pointer, stored as a Ptr{Cvoid} type.

using ExtXYZ

frame = read_frame("input.xyz")  # single atomic configuration, represented as a Dict{String}{Any}
write_frame("output.xyz", frame) # write a single frame to `output.xyz`. 

frame10 = read_frame("input.xyz", 10) # read a specific frame, counting from 1 for first frame in file

all_frames = read_frames("seq.xyz")  # read all frames, returns Vector{Dict{String}{Any}}
frames = read_frames("seq.xyz", 1:4) # specific range of frames

write_frames("output.xyz", frames, append=true) # append four frames to output

# Get a frame as AtomsBase-compatible ExtXYZ.Atoms object:
Atoms(read_frame("input.xyz"))

# Get list of frames as AtomsBase-compatible ExtXYZ.Atoms object:
Atoms.(read_frames("seq.xyz", 1:4)

The function iread_frames() provides lazy file-reading using a Channel:

for frame in iread_frames("input.xyz")
    process(frame) # do something with each frame
do

write_frames() can also be used for asynchronous writing by passing in a Channel:

Channel() do ch
    @async write_frames(outfile, ch)
    
    for frame in frames
        put!(ch, frame)
    end
end

Atoms data structure

In lieu of a package-independent data structure for representing atomic structures (i.e. an equivalent to ASE's Atoms class in the Python ecosystem), this package uses a Dict{String}{Any}. For the extended XYZ file:

8
Lattice="5.44 0.0 0.0 0.0 5.44 0.0 0.0 0.0 5.44" Properties=species:S:1:pos:R:3 Time=0.0
Si        0.00000000      0.00000000      0.00000000
Si        1.36000000      1.36000000      1.36000000
Si        2.72000000      2.72000000      0.00000000
Si        4.08000000      4.08000000      1.36000000
Si        2.72000000      0.00000000      2.72000000
Si        4.08000000      1.36000000      4.08000000
Si        0.00000000      2.72000000      2.72000000
Si        1.36000000      4.08000000      4.08000000

The internal representation, shown in JSON format for readability, is as follows:

{
   "N_atoms": 8,
   "arrays": {
      "pos": [
         [
            0.0,
            0.0,
            0.0
         ],
         [
            1.36,
            1.36,
            1.36
         ],
         [
            2.72,
            2.72,
            0.0
         ],
         [
            4.08,
            4.08,
            1.36
         ],
         [
            2.72,
            0.0,
            2.72
         ],
         [
            4.08,
            1.36,
            4.08
         ],
         [
            0.0,
            2.72,
            2.72
         ],
         [
            1.36,
            4.08,
            4.08
         ]
      ],
      "species": [
         "Si",
         "Si",
         "Si",
         "Si",
         "Si",
         "Si",
         "Si",
         "Si"
      ]
   },
   "info": {
      "Time": 0.0
   },
   "cell": [
      [
         5.44,
         0.0,
         0.0
      ],
      [
         0.0,
         5.44,
         0.0
      ],
      [
         0.0,
         0.0,
         5.44
      ]
   ]
}

Important dictionary keys include:

• N_atoms - the number of atoms (mandatory)
• cell - the unit cell, a 3x3 matrix of floats containing the cell vectors as rows, i.e. the same as ASE (mandatory)
• pbc - periodic boundary conditions, Vector{Bool} of length 3 (optional)
• info - dictionary containing per-configuration key/value pairs parsed from the comment (line #2 in each frame). These can include scalars, vectors and matrices of integer, real, bool and string scalars or vectors. (mandatory, can be empty)
• arrays - dictionary containing per-atom properties as a N_component x N_atoms matrix, reduced to a vector for the case N_component = 1. These represent scalar (N_component = 1) or vector (N_component > 1) per-atom properties, of integer (I), real (R), bool, (L) or string (S, scalars only) type. The set of properties is extracted from the special Properties key in the comment line. (mandatory, and must contain at least a string property "species" containing atomic symbols and a 3-column vector property