How to specify the molecule and basis set using xyz files¶
The actual xyz file only contains the number of centers, the atoms, and the corresponding coordinates. It could look like this one:
6 Methanol, identifying the alcoholic proton as H1 C -0.000000010000 0.138569980000 0.355570700000 O -0.000000010000 0.187935770000 -1.074466460000 H 0.882876920000 -0.383123830000 0.697839450000 H -0.882876940000 -0.383123830000 0.697839450000 H -0.000000010000 1.145042790000 0.750208830000 H1 -0.000000010000 -0.705300580000 -1.426986340000
The first line is the number of atoms. The second line can be blank or an arbitrary comment. It is not read by the program. If you ommit this line, then your molecule will be wrong, one atom will be missing! The following lines contain atom types and coordinates. The first entry on each line is the name of the atom. Any string up to eight characters will do, but if the name is present in the periodic table DIRAC will recognize the charge and can find the corresponding basis set.
From the xyz file DIRAC cannot know what basis set you want to use. For this reason, basis set and symmetry specification is then done in the input file using the keywords given below. This is in contrast to the traditional mol files. This means that the keywords below do not make sense when combined with a traditional mol file.
Here the basis set information is specified. .DEFAULT specifies the default large component basis set for all atoms. This can be modified for specific atom by the .SPECIAL keyword. For example, if we use the methanol.xyz file listed above, the following input specifies a cc-pVDZ on carbon and the 3 hydrogens labeled H, while oxygen and H1 will be treated with a cc-pVTZ basis:
**MOLECULE *BASIS .DEFAULT cc-pVDZ .SPECIAL O BASIS cc-pVTZ .SPECIAL H1 BASIS cc-pVTZ
Here the physical properties of the centers in our molecule can be specified. This is useful if the name of the center differs from the IUPAC element name or in case we want to use nuclei with fractional charges. This is controlled by the keyword nucleus that can be repeated as often as is needed. For the geometry file methanol.xyz we need to specify:
*CENTERS .NUCLEUS H1 1.0
Another reason to change the charge of the nucleus is to be able to run counterpoise calculations in which a ghost basis set is to be placed without adding a charge. This can be achieved by defining the ghost center as (for instance) O.Gh and then putting the nuclear charge to zero using:
*CENTERS .NUCLEUS O.Gh 0.0 8.0
the first number is the charge to be used, the second corresponds to the element number and is used to search the basis set library. In this example you can therefore simply specify the basis set name using the DEFAULT or SPECIAL keywords and the program will then find the corresponding oxygen basis.
Here you can specify the units to be used when reading the coordinates. If nothing is specified, angstrom is the default (this is then a real xyz file). If we specify ‘AU’ we use atomic units instead:
*COORDINATES .UNITS AU
We can also specify our own unit, by typing the name and the conversion factor when going from this new unit to atomic units:
*COORDINATES .UNITS nm 18.8972
Now all coordinates are entered in nanometer. If we add ‘A’ at the end, we can enter the new unit in angstrom:
*COORDINATES .UNITS nm 10.0 A
With this keyword we can control symmetry recognition. To turn symmetry detection off and to force C1 symmetry use: