The Geometry Main Menu

After some preliminaries providing the title etc. you reach the geometry main menu:

SPECIFICATION OF MOLECULAR GEOMETRY ( #ATOMS=0     SYMMETRY=c1  )
YOU MAY USE ONE OF THE FOLLOWING COMMANDS :
sy <group> <eps> : DEFINE MOLECULAR SYMMETRY (default for eps=3d-1)
desy <eps>       : DETERMINE MOLECULAR SYMMETRY AND ADJUST
                    COORDINATES (default for eps=1d-6)
susy             : ADJUST COORDINATES FOR SUBGROUPS
ai               : ADD ATOMIC COORDINATES INTERACTIVELY
a <file>         : ADD ATOMIC COORDINATES FROM FILE <file>
aa <file>        : ADD ATOMIC COORDINATES IN ANGSTROEM UNITS FROM FILE <file>
sub              : SUBSTITUTE AN ATOM BY A GROUP OF ATOMS
i                : INTERNAL COORDINATE MENU
ired             : REDUNDANT INTERNAL COORDINATES
red_info         : DISPLAY REDUNDANT INTERNAL COORDINATES
ff               : UFF-FORCEFIELD CALCULATION
m                : MANIPULATE GEOMETRY
frag             : DEFINE FRAGMENTS FOR BSSE CALCULATION
w <file>         : WRITE MOLECULAR COORDINATES TO FILE <file>
r <file>         : RELOAD ATOMIC AND INTERNAL COORDINATES FROM FILE <file>
name             : CHANGE ATOMIC IDENTIFIERS
del              : DELETE ATOMS
dis              : DISPLAY MOLECULAR GEOMETRY
banal            : CARRY OUT BOND ANALYSIS
*                : TERMINATE MOLECULAR GEOMETRY SPECIFICATION
                    AND WRITE GEOMETRY DATA TO CONTROL FILE

IF YOU APPEND A QUESTION MARK TO ANY COMMAND AN EXPLANATION
OF THAT COMMAND MAY BE GIVEN

This menu allows you to build your molecule by defining the Cartesian coordinates interactively (ai) or by reading the coordinates from an external file (a, aa). The structure can be manipulated by the commands sub, m, name and del. The command sy allows you to define the molecular symmetry while desy tries to determine automatically the symmetry group of a given molecule.

There exists a structure library which contains the Cartesian coordinates of selected molecules, e.g. CH₄. These data can be obtained by typing for example a ! ch4 or a ! methane. The data files are to be found in the directory $TURBODIR/structures. The library can be extended.

You can perform a geometry optimization at a force field level to preoptimize the geometry. For this purpose the Universal Force Field (UFF) developed from Rappé et al. in 1992 [7] has been implemented in the uff module (see also Section 5.4). This can also be used to calculate an analytical approximate cartesian Hessian. If one does so, the start Hessian for the ab initio geometry optimization is this Hessian instead of the diagonal one ($forceinit on carthess for relax module).