Computational chemistry

Computational chemistry results — method, basis set, and computed properties — in a structured syntax.

Syntax

calc(method/basis){
  property: value [units]
}

• method — computational method (e.g. b3lyp, mp2, hf)
• basis — basis set (e.g. 6-31G*, cc-pVTZ)
• Each property line: title: value [units]

Example: DFT energy

Source Rendered

calc(b3lyp/6-31G*){ energy: -234.5 Hartree dipole: [0.1, 0.2, 0.3] Debye }

$\mathrm{calc}\left[\text{b3lyp/6-31G*}\right]\begin{array}{ccc}\mathrm{energy}& -234.5& \mathrm{Hartree}\\ \mathrm{dipole}& \mathrm{[0.1,}& \mathrm{0.2,}\end{array}$

Example: HF optimisation

Source Rendered

calc(hf/sto-3g){ energy: -76.0 Hartree HOMO: -0.5 Hartree LUMO: 0.2 Hartree }

$\mathrm{calc}\left[\text{hf/sto-3g}\right]\begin{array}{ccc}\mathrm{energy}& -76.0& \mathrm{Hartree}\\ \mathrm{HOMO}& -0.5& \mathrm{Hartree}\\ \mathrm{LUMO}& 0.2& \mathrm{Hartree}\end{array}$

Property fields

Field	Required	Example
title	yes	energy, dipole, HOMO
value	yes	-234.5
units	no	Hartree, Debye, eV

Validation (v0.18+)

Each property line must have a : separator. Malformed entries raise ParseError at parse time.

CML wire (v0.11+)

Emits as <molecule> with <propertyList> of <property> children:

<molecule title="b3lyp/6-31G*">
  <propertyList>
    <property title="energy">
      <scalar units="Hartree">-234.5</scalar>
    </property>
  </propertyList>
</molecule>