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4.1 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).

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
}

As seen in the example, the geometry is specified within the geometry block, enclosed by geometry={ and }. The first line of the xyz geometry block holds the number of atoms (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. For simplicity, the first two lines can also be omitted.

Alternatively, the geometry can be specified in the Z-matrix form, which is also used in many other programs. 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.

angstrom
geometry={
C
O   C  1.182
H1  C  1.102  O  122.1789
H2  C  1.102  O  122.1789  H1  180
}

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 angstrom 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

angstrom
geometry={
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
}

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 angstrom command must be given before the geometry block.

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

geometry={
C
O  , C , rco
H1 , C , rch , O , hco
H2 , C , rch , O , hco , H1 , 180
}

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.

By default, the program repositions and rotates the molecule so that the coordinate axes have the centre of mass of the molecule as origin, and are aligned with the principal inertial axes. This behaviour is usually what is required, in order that the program can recognize and exploit point-group symmetry, but can be changed through parameters specified on the ORIENT command (see manual). By default, the program tries to find and use the maximum abelian point-group symmetry, but this behaviour can be controlled using the SYMMETRY command (see manual).



Next: 4.2 Basis set specification Up: 4 How to prepare Previous: 4 How to prepare   Contents   PDF

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