5.1 Geometry specification

The simplest way to specify the coordinates of the atoms is to use cartesian coordinates and the XYZ input format, which is standard in many programs. In this case the geometry input looks as follows (example for formaldehyde).

geomtyp=xyz
geometry
   4
  FORMALDEHYDE
C          0.0000000000        0.0000000000       -0.5265526741
O          0.0000000000        0.0000000000        0.6555124750
H          0.0000000000       -0.9325664988       -1.1133424527
H          0.0000000000        0.9325664988       -1.1133424527
end

As seen in the example, the geometry is specified within the geometry block, enclosed by geometry and end. The first line of the xyz geometry block holds the number of atoms (anywhere, free format). The second line is an arbitrary title. Finally there is one line for each atom specifying the cartesian coordinates ($x, y, z$) in Ångstrøm.

Alternatively, the geometry can be specified in the Z-matrix form, which is also used in many other programs, and is the default in MOLPRO (i.e., the line geomtyp=zmat shown below can be omitted). In this case, the geometry is defined by distances and angles. This is a little more involved, and here we give only a simple example, again for formaldehyde.

geomtyp=zmat
geometry
ang
C
O   C  1.182
H1  C  1.102  O  122.1789
H2  C  1.102  O  122.1789  H1  180
end

Here, 1.182 and 1.102 are the C-O and the C-H bond distances, respectively. 122.1789 is the H-O-C angle, and 180 is the angle between the H1-C-O and H2-C-O planes (dihedral angle). Note that by default the bond distances are in atomic units (bohr), but one can give the ang keyword to use Ångstrøm.

As an alternative to the xyz input explained above, it is also possible to specify cartesian coordinates in a Z-matrix. In this case the form is

geomtyp=zmat
geometry
ang
C,,        0.0000000000 ,     0.0000000000 ,    -0.5265526741
O,,        0.0000000000 ,     0.0000000000 ,     0.6555124750
H,,        0.0000000000 ,    -0.9325664988 ,    -1.1133424527
H,,        0.0000000000 ,     0.9325664988 ,    -1.1133424527
end

Again, atomic units are the default, other than for the xyz input, where the coordinates need to be given in Ångstrøm. In order to use Ångstrøm, the ang option must be given before any coordinates.

Instead of constant numbers it is also possible to use variables in the Z-matrix input. For instance, the input for formaldehyde can be written as

geomtyp=zmat
geometry
ang
C
O  , C , rco
H1 , C , rch , O , hco
H2 , C , rch , O , hco , H1 , 180
end

rco=1.182 Ang
rch=1.102 Ang
hco=122.1789 Degree

The values of the variables can be changed in the course of the calculations, so that calculations can be performed for different geometries in one run. This will be explained in more detail later.