Main Geometry Menu

In the headline of this menu you can see the current number of atoms and molecular symmetry (we use an input for PH₃ as example). The commands in this menu will now be described briefly:

sy

Definition of the Schönflies symbol of the molecular point group symmetry. If you enter only sy, define will ask you to enter the symbol, but you may also directly enter sy c3v. define will symmetrize the geometry according to the new Schönflies symbol and will create new nuclei if necessary. You therefore have to take care that you enter the correct symbol and that your molecule is properly oriented. All TURBOMOLE programs require the molecule to be in a standard orientation depending on its point group. For the groups C_n, C_nv, C_nh, D_n, D_nh and D_nd the z-axis has to be the main rotational axis, secondary (twofold) rotational axis is always the x-axis, σ_v is always the xz-plane and σ_h the xy-plane. O_h is oriented as D_4h. For T_d, the threefold rotational axis points in direction (1,1,1) and the z-axis is one of the twofold axes bisecting one vertex of the tetrahedron.

desy

desy allows you to determine the molecular symmetry automatically. The geometry does not need to be perfectly symmetric for this command to work. If there are small deviations from some point group symmetry (as they occur in experimentally determined structures), desy will recognize the higher symmetry and symmetrize the molecule properly. If symmetry is lower than expected, use a larger threshold: up to 1.0 is possible.

susy

susy leads you through the complete subgroup structure if you want to lower symmetry, e.g. to investigate Jahn-Teller distortions. The molecule is automatically reoriented if necessary.
Example: Td→D2d→C2v→Cs.

ai

You may enter Cartesian atomic coordinates and atomic symbols interactively. After entering an atomic symbol, you will be asked for Cartesian coordinates for this type of atom until you enter *. If you enter &, the atom counter will be decremented and you may re-define the last atom (but you surely won't make mistakes, will you?). After entering *, define asks for the next atom type. Entering & here will allow you to re-define the last atom type and * to leave this mode and return to the geometry main menu. Enter q as atom symbol if you want to use a dummy center without nuclear charge. Symmetry equivalent atoms are created immediately after you entered a set of coordinates.

This is a convenient tool to provide e.g. rings: exploit symmetry group D_nh to create an n-membered planar ring by putting an atom on the x-axis.

a file

You may also read atomic coordinates (and possibly internal coordinates) from file, where file must have the same format as the data group $coord in file control.

The Cartesian coordinates and the definitions of the internal coordinates are read in free format; you only have to care for the keywords $coord and (optionally) $intdef and (important!) for the $end at the end of the file. The atomic symbol follows the Cartesian coordinates separated by (at least) one blank. For a description of the internal coordinate definitions refer to 4.1.2.

Entering `!' as first character of file will tell define to take file from the structure library. (The name following the `!' actually does not need to be a filename in this case but rather a search string referenced in the structure library contents file, see Section 4.1).

aa file

same as a, but assumes the atomic coordinates to be in Å rather than a.u.

sub

This command allows you to replace one atom in your molecule by another molecule. For example, if you have methane and you want to create ethane, you could just substitute one hydrogen atom by another methane molecule. The only requirement to be met by the substituted atom is that it must have exactly one bond partner. The substituting molecule must have an atom at the substituting site; in the example above it would not be appropriate to use CH3 instead of CH4 for substitution. Upon substitution, two atoms will be deleted and the two ones forming the new bond will be put to a standard distance. define will then ask you to specify a dihedral angle between the old and the new unit. It is also possible to use a part of your molecule as substituting unit, e.g. if you have some methyl groups in your molecule, you can create further ones by substitution. Some attention is required for the specification of this substituting unit, because you have to specify the atom which will be deleted upon bond formation, too. If you enter the filename from which the structure is to be read starting with `!', the file will be taken from the structure library (see Section 4.1). Definitions of internal coordinates will be adjusted after substitution, but no new internal coordinates are created.

i

This command offers a submenu which contains everything related to internal coordinates. It is further described in Section 4.1.2.

m

This command offers a submenu which allows you to manipulate the molecular geometry, i.e. to move and rotate the molecule or parts of it. It is further described in Section 4.1.3.

frag

Here, the fragments will be defined as being used by the jobbsse script in order to do a calculation osing the counter-poise correction scheme. In this menu, up to three monomers can be defined, together with their charges and their symmetry. When assigning atom numbers to fragments, if x is entered instead of a number, the program will request the first and last atoms of a range. This will be useful for very large fragments.

w file

The command w writes your molecular geometry and your internal coordinates to file. Afterwards you will be back in the geometry main menu. If the filename entered starts with `!', the structure will be written to the structure library.

name

name allows you to change atomic identifiers turning, e.g. oxygen atoms into sulfur atoms. After entering the identifier to be changed (remember the double quotation marks : "c ring"), you will be asked to enter the new one. You can use question marks for characters not to be changed, e.g. you enter "??ring" to change c chain to c ring. If you do not enter eight characters, your input will be filled up with trailing blanks.

del

The command del allows you to delete one or more atoms. After you entered the atomic list, define will show you a list of all atoms concerned and will ask you to confirm deleting these atoms. If any internal coordinate definitions exist, which rely on some of the deleted atoms, these definitions will be deleted, too.

banal

The command banal allows you to perform a bonding analysis, that is, define will try to decide which atoms are bonded and which are not (according to a table of standard bond lengths which is included in the code of define). You must have performed this command before you can use the display commands disb (display bonding information) or disa (display bond angle information). The standard bond lengths (and the bonding analysis available from these) are also needed for the commands sub and iaut (see internal coordinate menu, Section 4.1.2). If you want to change the standard bond lengths (or define more bond lengths, because not for all possible combinations of elements a standard length is available) you can do that by creating your own file with the non-default values and by specifying its full pathname in file .sys.data. The file has the following simple format:

c - h  2.2
h - h  2.0
. - .  ...

The format of the entries is almost arbitrary: the two element symbols have to be separated by a bar, the new bond distance follows in free format (in atomic units). If the file cannot be read properly, a warning message is displayed.

*

This command leaves this first main menu and writes all data generated so far to file. The default output file is the file you choose in the first question during your define session (usually control). Now the data groups $coord and $intdef will be written to file. After leaving this menu, you will enter the atomic attributes menu, which is described in Section 4.2.