Crystallography

Crystallography extends AsciiChem beyond molecules to periodic crystal structures. The crystal keyword captures the unit cell and asymmetric unit in a compact ASCII notation.

Syntax

crystal[<name>](
  a=<float>, b=<float>, c=<float>,
  alpha=<float>, beta=<float>, gamma=<float>,
  sg=<spacegroup>
) {
  <atoms with @f(x,y,z) fractional coords>
}

• crystal is a keyword (lowercase, doesn’t conflict with element symbols which are uppercase).
• [name] is an optional crystal name (e.g., the mineral or compound name).
• (params) carries unit cell parameters as key=value pairs.
• {atoms} carries the asymmetric unit atoms using fractional coordinates (@f(x,y,z)).

Worked examples

Sodium chloride (NaCl)

Source Rendered

crystal[NaCl](a=5.64,b=5.64,c=5.64,alpha=90,beta=90,gamma=90,sg=Fm-3m){ Na@f(0,0,0) Cl@f(0.5,0.5,0.5) }

$\mathrm{crystal}\left[\text{NaCl}\right]\begin{array}{cc}\mathrm{a}& 5.64\\ \mathrm{b}& 5.64\\ \mathrm{c}& 5.64\\ \mathrm{\alpha }& 90\\ \mathrm{\beta }& 90\\ \mathrm{\gamma }& 90\end{array}\begin{array}{cc}1& \mathrm{Na}\\ 2& \mathrm{Cl}\end{array}$

Silicon (diamond structure)

Source Rendered

crystal[Si](a=5.43,b=5.43,c=5.43,alpha=90,beta=90,gamma=90,sg=Fd-3m){ Si@f(0,0,0) Si@f(0.25,0.25,0.25) }

$\mathrm{crystal}\left[\text{Si}\right]\begin{array}{cc}\mathrm{a}& 5.43\\ \mathrm{b}& 5.43\\ \mathrm{c}& 5.43\\ \mathrm{\alpha }& 90\\ \mathrm{\beta }& 90\\ \mathrm{\gamma }& 90\end{array}\begin{array}{cc}1& \mathrm{Si}\\ 2& \mathrm{Si}\end{array}$

Without space group

Source Rendered

crystal[test](a=10,b=10,c=10){ C@f(0.1,0.1,0.1) O@f(0.5,0.5,0.5) }

$\mathrm{crystal}\left[\text{test}\right]\begin{array}{cc}\mathrm{a}& 10\\ \mathrm{b}& 10\\ \mathrm{c}& 10\end{array}\begin{array}{cc}1& \mathrm{C}\\ 2& \mathrm{O}\end{array}$

Unit cell parameters

Parameter	Symbol	Unit	Example
a	a-axis length	Å	5.64
b	b-axis length	Å	5.64
c	c-axis length	Å	5.64
alpha	α angle	degrees	90
beta	β angle	degrees	90
gamma	γ angle	degrees	90
sg	Space group (Hermann-Mauguin)	—	Fm-3m

Fractional coordinates

Atoms inside a crystal use @f(x,y,z) for fractional coordinates (relative to the unit cell). These map to CML xFract/yFract/ zFract attributes.

See Atoms for the full atom annotation syntax.

CML wire (v0.9.0+)

AsciiChem v0.9.0 migrates Crystal to native CML wire. The output is a <molecule> containing a native <crystal> child plus an <atomArray> with fractional coordinates — readable by any CML-aware tool without needing the AsciiChem extension namespace.

<molecule title="NaCl">
  <atomArray>
    <atom elementType="Na" xFract="0" yFract="0" zFract="0"/>
    <atom elementType="Cl" xFract="0.5" yFract="0.5" zFract="0.5"/>
  </atomArray>
  <crystal>
    <scalar title="a">5.64</scalar>
    <scalar title="b">5.64</scalar>
    <scalar title="c">5.64</scalar>
    <scalar title="alpha">90</scalar>
    <scalar title="beta">90</scalar>
    <scalar title="gamma">90</scalar>
    <symmetry spaceGroup="Fm-3m"/>
  </crystal>
</molecule>

Backwards compat

CML files written by older AsciiChem versions (using the <aci:crystal> text-carrier form) still parse correctly. The new emit always prefers native wire; the parse accepts either form.

Roadmap

Crystallography is Phase 1 of the beyond-formulas expansion. Future phases (documented in TODO.beyond-formulas/) will add:

• Spectroscopy (NMR, IR, MS)
• Computational chemistry results
• Z-Matrix internal coordinates
• Reaction mechanisms with spectator ions