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AsciiC6hem

Z-Matrix

A Z-Matrix defines molecular geometry using internal coordinates: bond lengths, bond angles, and dihedral angles relative to previously-defined atoms.

Syntax

Section titled “Syntax”
zmatrix{
  atom
  atom  ref1  distance
  atom  ref1  distance  ref2  angle
  atom  ref1  distance  ref2  angle  ref3  dihedral
}

Each row defines one atom. The first row is the origin (no references). The second references one prior atom (distance only). The third references two (distance + angle). Subsequent rows reference three (distance + angle + dihedral).

Example: methane

Section titled “Example: methane”
Source Rendered
zmatrix{
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C1
C 1
H2 C1 1.09
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H3 C1 1.09 H2 109.5
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H4 C1 1.09 H2 109.5 H3 120.0
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}
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  • C1 is the origin
  • H2 is 1.09 Å from C1
  • H3 is 1.09 Å from C1, with angle H2-C1-H3 = 109.5°
  • H4 is 1.09 Å from C1, angle 109.5°, dihedral 120.0°

Units

Section titled “Units”
  • Distances: Angstroms (Å)
  • Angles: degrees

CML wire (v0.11+)

Section titled “CML wire (v0.11+)”

Emits as <zMatrix> inside a <molecule>:

<molecule>
  <zMatrix>zmatrix{...}</zMatrix>
</molecule>

Future enhancement: structural <length>, <angle>, <torsion> child elements per row.

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