CODXYZ2ORTHO(1)

📦 version 3.12.0, in debian bookworm, debian trixie, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 CODXYZ2ORTHO — bestie edition 💖

okay so real talk, this is the manual page for codxyz2ortho, a lil General Commands Manual darling that takes your XYZ files and fixes their whole geometry situation. stay with me, it's giving chemistry but make it cute. ✨

🌸 NAME 🌸

codxyz2ortho — take an XYZ format [1] molecular file and convert coordinates to orthogonal ones (assuming that they were fractional in the original file). Unit cell constants can be given as command line option parameters. [1] https://en.wikipedia.org/wiki/XYZ_file_format

like. it literally does what it says on the tin, no cap. 🫶

🦋 SYNOPSIS 🦋

codxyz2ortho --options inputs*.xyz

codxyz2ortho --options < inp.xyz

two ways to feed her: throw a bunch of inputs*.xyz files at her as arguments, or pipe an inp.xyz straight into her stdin. pick your vibe. 💅

✨ DESCRIPTION ✨

Take an XYZ format [1] molecular file and convert coordinates to orthogonal ones (assuming that they were fractional in the original file). Unit cell constants can be given as command line option parameters.

[1] https://en.wikipedia.org/wiki/XYZ_file_format

so yeah — the file you hand over is assumed to have fractional coords, and she hands you back orthogonal ones. if she doesn't already know your unit cell, you gotta tell her, and that's what the command line options are for. main character energy, honestly. 👑

🎀 OPTIONS 🎀

  • -c, --cell "10 10 10 90 90 90" — specify unit cell for conversion.
  • -l, --lattice "0.1 0 0 0 0.2 0 0 0 0.15" — specify unit cell vectors in ortho frame for conversion.
  • -f, --float-format "%21.14e" — specify format for floating point output. For Perl, a usual "printf" format can be given.
  • -H, --human-readable — use format "%15.6f" for better human readability.
  • -M, --machine-readable — use format "%21.14e" to maintain precision. Default.
  • --help, --usage — output a short usage message (this message) and exit.
  • --version — output version information and exit.
ngl the -M default is the one that's always silently running the show. precision girlies, we see you. 🙈

😭 REPORTING BUGS 😭

Report codxyz2ortho bugs using e-mail: cod-bugs@ibt.lt

fr fr, if something's cursed, tell the devs. they wanna know. 💌

and that's the whole page bestie!! you just read CODXYZ2ORTHO(1) from the General Commands Manual — yes that's the actual title up top and the lil footer stamp at the bottom, iconic. slay, go convert some coordinates, mwah 💖🎀🦋✨🌸💅

📦 where this page comes from