atomes(1)

📦
version 1.3.2 · 3 versions
, in fedora 43, fedora 44

🎀 atomes(1) 🎀

okay so bestie, welcome to the General Commands Manual page for atomes, and I need you to know upfront: it's a LOT of options, but every single one of them is iconic in its own way. grab a snack, we're doing this together 🫶

✨ NAME ✨

atomes — a toolbox to analyze, visualize and create/edit 3D atomic scale models 🧪✨

🦋 SYNOPSIS 🦋

atomes [OPTIONS] files...
atomes [IMAGES_OPTIONS] file...
atomes [CONVERSION_OPTIONS] file...

no cap, those three little lines are the whole personality of this program 💅

💖 DESCRIPTION 💖

This manual page documents briefly the atomes command. (yes, "briefly", and yet here we are, 40 options deep 😭)

atomes is a toolbox to analyze, visualize and create/edit 3D atomic scale models.

It offers a workspace to open and manage project(s) that can exchange data: analysis results, atomic coordinates ...

atomes also provides an advanced input preparation system for calculations using well know molecular dynamics codes:

  • Classical MD: DLPOLY and LAMMPS
  • Ab-initio MD: CPMD and CP2K
  • QM-MM MD: CPMD and CP2K

like, it's giving scientist who also does UX. obsessed. 🌸

🌈 OPTIONS 🌈

This program uses a set of custom options to specify the file formats for atomic coordinates (ex: -xyz), but otherwise follows the usual GNU command line syntax, with long options starting with two dashes (`-').

atomes will try to open a file based on its extension, however file type can be strictly enforced using the corresponding option.

A summary of options is presented below. it's long. breathe. you got this 💜

  • -h, --help — Show summary of options
  • -v, --version — Show version of program
  • -awf, -AWF — Open atomes workspace file
  • -apf, -APF — Open atomes project file(s)
  • -xyz, -XYZ — Import XYZ atomic coordinates(s)
  • -c3d, -C3D — Import Chem3D atomic coordinates(s)
  • -trj, -TRJ — Import CPMD atomic coordinates(s)
  • -xdatcar, -XDATCAR — Import VASP atomic coordinates(s)
  • -pdb, -PDB, -ent, -ENT — Import PDB atomic coordinates(s)
  • -cif, -CIF — Import CIF atomic coordinate(s)
  • -hist, -HIST — Import DL_POLY history file atomic coordinates(s)
  • -sml, -SML — Import atomes chemical library coordinates(s)
  • -ipf, -IPF — Import I.S.A.A.C.S. project

✨ EXEMPLES ✨

(i know, the heading says EXEMPLES, we respect it as it is, periodt 👑)

atomes project.apf file.xyz -pdb other_file
atomes -awf workspace -apf project -xyz file -pdb other_file

see? you can just stack them. main character energy fr fr.

🎀 IMAGE_OPTIONS 🎀

atomes can be used to generate image of atomic scale models directly from the command line, without using the graphical interface. yes bestie, no clicking required, straight-up terminal glamour 💅✨

  • -p, --png, --render-png — Render PNG image
  • -j, --jpg, --render-jpg — Render JPG image
  • -o, --output=[FILE] — Image name (default: image.png or image.jpg)
  • -W, --width=[X_SIZE] — Image width in pixels, X_SIZE must be > 0
  • -H, --height=[Y_SIZE] — Image height in pixels, Y_SIZE must be > 0

Depending on the file to be rendered, default parameters for the rendering are obtained:

  • For an atomes project file (*.apf): from the project file itself.
  • For any another type of atomic coordinates (ex: .xyz): from the user preferences in atomes.pml

In both cases some parameters can be momentarily overriden using command line options:

  • -s, --style=[STYLE] — Visual style, in:
    • Balls and sticks: balls_and_sticks, ball_and_stick, b_and_s, bs, b
    • Wireframes: wireframes, wireframe, wires, wire, wi, w
    • Covalent radius: covalent_radius, covalent, cov_rad, cov, co, cr
    • Ionic radius: ionic_radius, ionic_rad, ionic, ion, ir
    • van der Waals radius: van_der_waals_radius, van_der_waals, vdw_radius, vdw_rad, vdw, vr
    • In crystal radius: in_crystal_radius, crystal_radius, in_crystal, crystal, cryst, cr
    • Spheres: spheres, sphere, sph, sp, s
    • Cylinders: cylinders, cylinder, cyl, cy, c
    • Dots: dots, dot, d
  • -r, --rep=[REP] — Representation style, in:
    • Orthographic: orthograhpic, ortho, 0
    • Perpsective (default): perspective, persp, 1
  • -b, --box=[STYLE] — Trigger box representation, if any, and set box style. Style, in:
    • Wireframes: wireframes, wireframe, wires, wire, wi, w
    • Cylinders: cylinders, cylinder, cyl, cy, c
  • -a, --axis=[STYLE] — Trigger axis representation and set axis style. Style, in:
    • Wireframes: wireframes, wireframe, wires, wire, wi, w
    • Cylinders: cylinders, cylinder, cyl, cy, c
  • -e, --acolor=[MAP] — Set color map for atoms and bonds
    • Chemical specie(s): species, spec, sp, 0
    • Total coordination(s): total_coordiantion, total_coord, tc, 1
    • Partial coordination(s): partial_coordiantion, partial_coord, pc, 2
    • Fragment(s)*: fragment, frag, fg, 3
    • Molecule(s)*: molecule, mol, mo, 4
    • * if required trigger the corresponding analysis
  • -t, --pcolor=[MAP] — Trigger polyhedra representation, and set the corresponding color map
  • -C, --box_color=[COLOR] — Box color, COLOR in hexadecimal coding, 3 or 6 letters, with or without #
  • -G, --back_grad=[GRAD] — Background gradient type, in:
    • No gradient: none, no, 0
    • Linear: linear, lin, 1
    • Circular: circular, circ, 2
  • -B, --back_color=[COLOR] — Background color, COLOR in hexadecimal coding, 3 or 6 letters, with or without #. Trigger single color mode (no gradient) for the background
  • -D, --back_dir=[DIR] — Background gradient direction, in:
    • Linear gradient
      • Right to left: 0
      • Top to bottom: 1
      • Bottom right to top left: 2
      • Top right to bottom left: 3
    • Circular gradient
      • Right to left: 0
      • Left to right: 1
      • Top to bottom: 2
      • Bottom to top: 3
      • Bottom right to top left: 4
      • Bottom left to top right: 5
      • Top right to bottom left: 6
      • Top left to bottom righ: 7
      • From the center: 8
  • -P, --back_pos=[POS] — Gradient colors mixed position in [0.0 - 1.0]
  • -U, --grad_col_a=[COLOR] — Gradient initial color, COLOR in hexadecimal coding, 3 or 6 letters, with or without #
  • -V, --grad_col_b=[COLOR] — Gradient final color, COLOR in hexadecimal coding, 3 or 6 letters, with or without #

🌟 EXAMPLES 🌟

atomes --render-png --width=1920 -H 1024 --output=project.png project.apf
atomes -j --style=vdw -r ortho -e pc -t pc file.xyz

look at that second one. -e pc -t pc. it's giving coordinated. slay 🔥

🦋 CONVERSION_OPTIONS 🦋

atomes can be used to convert atomic coordinate(s) directly from the command line, without using the graphical interface. no GUI, just vibes ✨

  • -c, --convert=[FORMAT] — Format to convert coordinates, from atomes project file or any accepted atomic coordinates format (see above), to:
    • XYZ: xyz
    • Chem3D: c3d
    • atomes chemical library: sml

The output (Cartesian coordinates) will be found in a file which name starts with the name of the initial file and ends by -conv.FORMAT

🌟 EXAMPLES 🌟

atomes --convert=xyz project.apf
atomes -c sml file.pdb

🔭 SEE ALSO 🔭

<https://atomes.ipcms.fr/>

go look. it's cute. iykyk 🌈

👑 AUTHOR 👑

This manual page was created by Dr. Sébastien Le Roux <sebastien.leroux@ipcms.unistra.fr>

thank you for your service, king 🫡👑

💀 BUGS 💀

Report bugs at <https://github.com/Slookeur/atomes-GNU/issues>.

bestie, if something is broken, do NOT suffer in silence, go tell them. that's what the issue tracker is for 💖

and that's the whole thing! this page comes to you from the General Commands Manual and it's dated September 21 2026 — so yeah, atomes(1), freshly timestamped and everything. go render something gorgeous. bye bestie 🎀💖🦋

📦 where this page comes from