The MOLECULE input file

We will not go into great detail here of the input format of the MOLECULE input file, as it is treated thoroughly in a separate chapter, Chapter 23. Here we only present two inputs for water; one using Cartesian coordinate input and automatic symmetry detection and the other using Cartesian coordinates and where we explicitly give the symmetry elements. Finally we show the MOLECULE input for H$_{2}$O$^{2+}$ using Z-matrix input. In all cases the basis set library of DALTON has been used, as we assume that most users will exploit the basis sets provided in the basis set library as opposed to punching them in. The punching format for basis sets are described in detail in Sec. 23.2.

Let us first start with an input for water using Cartesian coordinates in bohr, and the very popular 6-31G** basis set.

BASIS
6-31G**
Water
using the 6-31G** basis
Atomtypes=2
Charge=8.0 Atoms=1
O      .0000000000        -.2249058930         .0000000000
Charge=1.0 Atoms=2
H     1.4523499293         .8996235720         .0000000000
H    -1.4523499293         .8996235720         .0000000000

On the fifth line the number of different atomtypes or more correctly, the number of blocks of atoms, in this case two, oxygen and hydrogen, are given. There are one oxygen with charge 8, and two hydrogens with charge 1. The symmetry of the system will be detected by the program during the input processing unless turned off as shown in the last of the input examples for the MOLECULE input files.

We may also add the symmetry elements of the symmetry group ourselves. We must then remove any symmetry-dependent centers. For the above input this will result in, if we use the yz- (the x axis changes sign during the symmetry operation) and xy- (the $z$ axis changes sign) -planes as symmetry elements:

ATOMBASIS
Water
using ANOs specified for each atomtype
Atomtypes=2 Generators=2 X Y
Charge=8.0 Atoms=1 Basis=ano-1 5 4 3 1
O      .0000000000        -.2249058930         .0000000000
Charge=1.0 Atoms=1 Basis=ano-1 4 3 2
H     1.4523499293         .8996235720         .0000000000

In the above calculation we used the ANO set of Widmark and coworkers [18,19]. We use the contraction [5s4p3d1f/4s3p2d] for the oxygen and the hydrogens respectively. We also note the keyword ATOMBASIS which allows different basis functions to be used on different atoms.

Let us now proceed to an input for H$_{2}$O$^{2+}$ where we use Z-matrix input. The input will then look like:

BASIS
Sadlej-pVTZ
Water - geometry optimization with Sadlej's basis set
Project - Raman
Atomtypes=3  Charge=2 Nosymmetry
ZMAT
O   1 8.0
H   2 1 0.97 1.0
H   3 1 0.97 2 104.5 1.0

In addition to the number of atoms in the input (3), we have given the total charge of the molecule ($+2$), and the keyword Nosymmetry indicates that symmetry is not to be used in this calculation. Note that unlike Cartesian coordinate input, which by default is in atomic units, the Z-matrix input is always to be in Ångström.