geom(1)

💖 geom(1) — bestie, let's analyze some molecular geometry 💖

okay so this is the page for geom, section 1 of the manual, and honestly? it's a whole vibe. it reads a molecular geometry input in Cartesian coordinates and tells you everything about it. iconic behavior fr fr. 🦋

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✨ NAME ✨

geom — analyzes a molecular geometry input in Cartesian coordinates. periodt. 💅

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🌸 DESCRIPTION 🌸

so the program geom reads a set of Cartesian coordinates and, from them, figures out:

• bond distances (in Bohr and angstrom, she gives you both, queen)
• bond angles
• torsional angles
• out-of-plane angles (optional, only if you ask nicely)
• moments of inertia
• rotational constants

that's the whole gig. no cap. 🔥

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🎀 FILES REQUIRED 🎀

bestie you need this:

    input.dat          - Input file

and one of the following:

    geom.dat           - geometry file
    file11.dat         - PSI-format geometry/gradient file

like, pick one, either is fine, we're flexible. 🫶

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🌈 FILES GENERATED 🌈

she makes you this:

    geom.out           - file containing the analysis

that's your receipt, keep it. 🧾✨

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👑 INPUT OPTIONS 👑

the geom program has the following options, and yes we're going through all of them because every single one matters:

• -h — print help information (aka these very options). your little safety net. 💜
• -aces [filename] — read the input in an ACES output format, where each line has the atomic symbol, the atomic number, and Cartesian coordinates (in Bohr). the optional argument is the name of the geometry input file, and it defaults to geom.dat.
• -qchem [filename] — read the input in a QCHEM output format, with each line made of the atom number, the atomic symbol, and Cartesian coordinates (in Angstroms). the optional argument is the geometry input file name, defaulting to geom.dat.
• -xyz [filename] — read the input in an XYZ output format. first line = the number of atoms, second line = a comment line, and then every line after that has the atomic symbol plus the Cartesian X, Y and Z coordinates (in Angstroms). the optional argument is the geometry input file name, and yeah, it defaults to geom.dat too.
• -oop — print out-of-plane angles. the angle a-b-c-d is defined as the angle formed by the vector a-d and the plane defined by atoms b, c, and d. geometry girlies stay winning. 📐
• DO_OOP = boolean — same thing as the command-line switch -oop up above. twin sisters basically.
• ISOTOPES = matrix of reals/strings — used to specify masses for the calculation of the center of mass and rotational constants. one array is provided for each isotopomer to be calculated. the arrays can mix floating point numbers with strings that designate isotopes. if this array isn't given and file11.dat is present, then the masses get obtained by converting the atomic numbers in file11. and if masses aren't given by ISOTOPES or by file11, then no mass-related quantities will be calculated. so like, give her the masses or she's not doing the mass math, simple as that. 💀
• -g [filename] — read Cartesian coordinates from a file other than file11.dat. if you don't give a filename, the default is geom.dat. the alternative file is assumed to be in a format similar to that of PSI's geom.dat. heads up though: since such files don't contain atomic numbers, the moments of inertia and rotational constants are not calculated if this option is used. so you're trading vibes for data, iykyk. 🙈
• READ_GEOM = boolean — this option in input.dat tells geom to read the geometry from geom.dat in the PSI geom.dat format.
• -a — print parameters for all pair distances. all of them. every pair. she's thorough. 🔥
• PRINT_ALL_DIST = boolean — same as the -a flag described above.
• -d distance — only print parameters involving pairs of atoms that are less than distance Bohr apart. the default value is 4.0 Bohr. (so -d = keep it close, bestie.)
• PRINT_DISTANCE = value — same as the -d flag described above.
• -angstrom — the input coordinates are in angstroms, not bohr. speak her language. 📏
• ANGSTROM = boolean — if TRUE, the input coordinates are in angstroms instead of bohr. the default is FALSE.

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🧚 the little example (aka the moment) 🧚

the following example is for calculating the geometrical information for water with several different isotopes. the geometry is read from geom.dat rather than from file11.dat.

geom: (
   read_geom = true
   isotopes = (
      (O H H)
      (O D D)
      (O18 1.007825 1.007825)
    ) )

look at her. three isotopomers, one adorable little input block. slay. 💖✨

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tiny reminder: if you skip ISOTOPES and file11.dat isn't around either, those mass-related quantities just… don't happen. not a bug, just the rules. 🫶

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and that's the whole page, bestie!! this was geom(1) from the manual, dated 5 June, 1998 — yes she's a 90s baby and she ATE 💅👑. go analyze something gorgeous. mwah. 🎀🦋💜