Manual:Basis:XYZ
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Introduction
When a .xyz file is given to PAM it will automatically detect how to handle this file. The actual .xyz file only contains the coordinates. Information about the atoms and the basis sets is given in the .inp file.
Coordinates
Coordinates are given in an .xyz file in the following way.
3 # Number of atoms Water with 90 degree angles # Comment line O 0.0 0.0 0.0 H 1.0 1.0 0.0 H 1.0 -1.0 0.0
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. In case you want to have a non-default basis set for a specific atom you should define this in the **MOLECULE block. E.g. treat atom H1 different from the other Hs
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
**MOLECULE
The description of the atomic properties (basis, nuclear charge) is given in the .INP file using the keyword **MOLECULE when using geometry (xyz) file input.
**DIRAC Specification of the calculation.
**MOLECULE Specification of the basis set and physical properties of nuclei (if different from the default).
In this section the following keywords are defined
*BASIS
Here the basis set information is specified.
- .DEFAULT
Specify 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 input
**MOLECULE *BASIS .DEFAULT cc-pVDZ .SPECIAL O BASIS cc-pVTZ .SPECIAL H1 BASIS cc-pVTZ *CENTERS .NUCLEUS H1 1.0 *END OF 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. In this special section other basis sets can be specified in the same way as in a .MOL file
*CENTERS
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
*UNITS
Here the units used for the coordinates in the XYZ files can be entered. If nothing is specified, angstroms are used (a real xyz file). If we specify 'AU' we use atomic units instead. E.g.
*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.
*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.
*UNITS nm 10.0 A
*SYMMETRY
With this keyword you can control symmetry recognition. To turn symmetry detection off and to force C1 symmetry use:
*SYMMETRY .NOSYM
