Z-matrix Examples#

Covalent Bonds#

[ZMATRIX]
NAME = covalent-bonds

$dist = dist 0.0 1.2

ROW = $*
ROW = $* 1 $dist

Water-Water Hydrogen Bonding#

[ZMATRIX]
NAME = water-hb

$O = attr atom_type OW
$H = attr atom_type HW1 HW2

# Covalent Bond, Hydrogen Bond, Angle
$CB = dist 0.0 1.2
$HB = dist 1.2 2.5
$A = angle 145 181

ROW = $O
ROW = $H 1 $CB
ROW = $O 2 $HB 1 $A

Octahedral Metal-Ligand Structure#

[ZMATRIX]
NAME = octa

$M = attr atom_type M
$L = attr atom_type L
$d = dist 0.0 2.0
$a90 = angle 89 91
$d90 = dihedral 89 91

ROW = $M
ROW = $L 1 $d
ROW = $L 1 $d 2 $a90
ROW = $L 1 $d 3 $a90 2 $d90 
ROW = $L 1 $d 4 $a90 3 $d90
ROW = $L 1 $d 5 $a90 4 $d90
ROW = $L 1 $d 6 $a90 5 $d90

Crystal Defects#

Structural defects can be found by specifying the correct structure, then using the boolean not operator to exclude/ignore the correct structures.

[ZMATRIX]
NAME = crystal_defect

$C = attr atom_type C
$d = dist 0.0 1.2
$good_angle = angle 108 110
$defect_angle = not $good_angle

ROW = $C
ROW = $C 1 $d
ROW = $C 1 $d 2 $defect_angle

Cyclic Water Pentamer#

[ZMATRIX]
NAME = cyclic-water-pentamer

$O = attr atom_type OW
$H = attr atom_type HW1 HW2
$CB = dist 0.0 1.2
$HB = dist 1.2 2.5

$aHOH = angle 98 118
$aOHO = angle 170 181
$cis = dihedral 0 20

ROW = $O
ROW = $H 1 $CB
ROW = $O 2 $HB 1 $aOHO
ROW = $H 3 $CB 2 $aHOH 1 $cis
ROW = $O 4 $HB 3 $aOHO 2 $cis
ROW = $H 5 $CB 4 $aHOH 3 $cis
ROW = $O 6 $HB 5 $aOHO 4 $cis
ROW = $H 7 $CB 6 $aHOH 5 $cis
ROW = $O 8 $HB 7 $aOHO 6 $cis
ROW = $H 9 $CB 8 $aHOH 7 $cis