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10.1.2 XYZ input

Simple cartesian coordinates in Ångstrom units can be read as an alternative to a Z matrix. This facility is triggered by setting the MOLPRO variable GEOMTYP to the value XYZ before the geometry specification is given, but usually this does not need to be done, as a geometry specification where the first line is a single integer will be recognized as XYZ format, as will the case of the first line consisting of a chemical symbol followed by three cartesian coordinates. The geometry block should then contain the cartesian coordinates in Minnesota Computer Centre, Inc. XYZ format. Variable names, and in general expressions that are linear in all dependent variables, may be used as well as fixed numerical values. Non-linear expressions should not be used, because the geometry optimization module is unable to differentiate them.

The XYZ file format consists of two header lines, the first of which contains the number of atoms, and the second of which is a title. The remaining lines each specify the coordinates of one atom, with the chemical symbol in the first field, and the $x$, $y$, $z$ coordinates following. A sequence number may be appended to the chemical symbol; it is then interpreted as the atomic group number, which can be used when different basis sets are wanted for different atoms of the same kind. The basis set is then specified for this group number rather than the atomic symbol. As a further extension, the first two header lines can be omitted.

Note that for XYZ input the default is not to reorient the molecule. Orientation can be forced, however, by the MASS or CHARGE options on the ORIENT directive.

h2o_xyzinput.com

The XYZ format had been specified within the documentation distributed with the Minnesota Supercomputer Center's XMol package. Note that MOLPRO has the facility to write XYZ files with the PUT command (see section 10.3).


Next: 10.2 Symmetry specification Up: 10.1 Geometry specifications Previous: 10.1.1 Z-matrix input   Contents   Index   PDF

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