Variables and Dummy Atoms in Jaguar Z‑Matrix Input

Bond lengths or angles can also be specified as variables below the Z‑matrix itself. This feature makes it easier to input equal values (such as C–H bond lengths or H–C–H bond angles for methane), and also makes it possible to keep several distances or angles the same as each other during an optimization.

To use variables, type the variable name (chbond, for instance) where you would type the corresponding value (such as a C–H bond length in Å) for each relevant occurrence of that value. You can prefix any variable with a + or − sign. After you type the full Z‑matrix, define the variables by adding one or more lines at the bottom, such as

chbond=1.09  HCHang=109.47

As for Cartesian input, you can separate the variable settings from the coordinates by a line containing the text Z‑variables.

Defining dummy atoms can make the assignment of bond lengths and angles easier. Dummy atoms are a way of describing a point in space in the format used for an atomic coordinate without placing an atom at that point. The symbols allowed for dummy atoms are X or Du. An example of the use of a dummy atom for CH₃OH input follows:

C  
O    C   1.421
H1   C   1.094    O   107.2
X1   C   1.000    O   129.9    H1  180.0
H2   C   1.094    X1   54.25   H1   90.0
H3   C   1.094    X1   54.25   H1  -90.0
H4   O   0.963    C   108.0    H1  180.0