Chapter 4
Preparing your input file with DEFINE

define is the general interactive input generator of TURBOMOLE. During a session with define, you will create the control file which controls the actions of all other TURBOMOLE programs. During your define session you will be guided through four main menus:

1.
The geometry main menu: This first menu allows you to build your molecule, define internal coordinates for geometry optimizations, determine the point group symmetry of the molecule, adjust internal coordinates to the desired values and related operations. Beyond this one can perform a geometry optimization at a force field level to preoptimize the geometry and calculate a Cartesian analytical Hessian. After leaving this menu, your molecule to be calculated should be fully specified.
2.
The atomic attributes menu: Here you will have to assign basis sets and/or effective core potentials to all atoms. The SV(P) basis is assigned automatically as default, as well as ECPs (small core) beyond Kr.
3.
The occupation numbers and start vectors menu: In this menu you should choose eht to start from Extended Hückel MO vectors. Then you have to define the number of occupied orbitals in each irreducible representation.
4.
The general menu: The last menu manages a lot of control parameters for all TURBOMOLE programs.

Most of the menu commands are self-explanatory and will only be discussed briefly. Typing * (or q) terminates the current menu, writes data to control and leads to the next while typing & goes back to the previous menu.

  4.0.3 Universally Available Display Commands in DEFINE
  4.0.4 Specifying Atomic Sets
  4.0.5 control as Input and Output File
  4.0.6 Be Prepared
 4.1 The Geometry Main Menu
  4.1.1 Description of commands
  4.1.2 Internal Coordinate Menu
  4.1.3 Manipulating the Geometry
 4.2 The Atomic Attributes Menu
  4.2.1 Description of the commands
 4.3 Generating MO Start Vectors
  4.3.1 The MO Start Vectors Menu
  4.3.2 Assignment of Occupation Numbers
  4.3.3 Orbital Specification Menu
  4.3.4 Roothaan Parameters
  4.3.5 Start-MOs for broken symmetry treatments ("flip")
 4.4 The General Options Menu
  4.4.1 Important commands
  4.4.2 Special adjustments
  4.4.3 Relax Options
  4.4.4 Definition of External Electrostatic Fields
  4.4.5 Properties

4.0.3 Universally Available Display Commands in DEFINE

There are some commands which may be used at (almost) every stage of your define session. If you build up a complicated molecular geometry, you will find the dis command useful. It will bring you to the following little submenu:

ANY COMMAND WHICH STARTS WITH THE 3 LETTERS  dis  IS A  
DISPLAY COMMAND. AVAILABLE DISPLAY COMMANDS ARE :  
disc  <range> : DISPLAY CARTESIAN COORDINATES  
dist  <real>  : DISPLAY DISTANCE LIST  
disb  <range> : DISPLAY BONDING INFORMATION  
disa  <range> : DISPLAY BOND ANGLE INFORMATION  
disi  <range> : DISPLAY VALUES OF INTERNAL COORDINATES  
disg  <range> : GRAPHICAL DISPLAY OF MOL. GEOMETRY  
<range> IS A SET OF ATOMS REFERENCED  
<real>  IS AN OPTIONAL DISTANCE THRESHOLD (DEFAULT=5.0)  
AS AN EXAMPLE CONSIDER  disc  1,3-6,10,11  WHICH DISPLAYS  
THE CARTESIAN COORDINATES OF ATOMS 1,3,4,5,6,10,and 11 .  
HIT >return< TO CONTINUE OR ENTER ANY DISPLAY COMMAND

Of course, you may enter each of these display commands directly without entering the general command dis before. The option disg needs special adaption to the computational environment, however, and will normally not be available.

4.0.4 Specifying Atomic Sets

For many commands in define you will have to specify a set of atoms on which that command shall act. There are three ways to do that:

You should take into account that define also creates, from the atoms you entered, all others according to symmetry. If necessary, you will therefore have to lower the (formal) symmetry before executing a command.

4.0.5 control as Input and Output File

define may be used to update an existing control file, which is helpful if only the basis set has been changed. In this case just keep all data, i.e. reply with <enter> on all questions, and only specify new start MOs. The more general usage is described now.

At the beginning of each define session, you will be asked to enter the name of the file to be created. As mentioned earlier, all TURBOMOLE programs require their input to be on a file named control, but it may be useful at this moment to choose another name for this file (e.g. if you have an old input file control and you do not want to overwrite it). Next you will be asked to enter the name of an old file which you want to use as input for this session. This prevents you from creating the new input from scratch if you want to make only minor changes to an old control file. It is possible to use the same file as input and output file during a define session (which means that it will only be modified). This may lead to difficulties, however, because define reads from the input file when entering each main menu and writes the corresponding data when leaving this menu. Therefore the input file may be in an ill-defined status for the next main menu (this will be the case, for example, if you add or change atoms in the first menu so that the basis set information is wrong in the second menu). define takes care of most—but not all—of these problems.

For these reasons, it is recommended to use a different filename for the input and the output file of the define session if you change the molecule to be investigated. In most cases involving only changes in the last three of the four main menus no problem should arise when using the same file as input and output.

4.0.6 Be Prepared

Atomic Coordinates

Molecules and their structures are specified by coordinates of its atoms, within the program invariably by Cartesian coordinates in atomic units (Ångstrøm would also do). In TURBOMOLE these coordinates are contained in the file coord (see Section 22 “Sample control files” for an example).

Recommendation

We strongly recommend to create the coord file before calling define, only for small molecules one should use the interactive input feature of define. Set up the molecule by any program you like and write out coordinates in the xyz-format (XMol format), which is supported by most programs. Then use the TURBOMOLE tool x2t to convert it into a TURBOMOLE coord file (see Section 1.5.

Internal Coordinates

Structure optimizations, see jobex, are most efficient if carried out in internal coordinates and TURBOMOLE offers the following choices.

internals

based on bond distances and angles, see Section 4.1.2.

redundant internals


defined as linearly independent combinations of internals (see ref.  [27]), provided automatically by the command ired in the ‘geometry main menu’ in Section 4.1 below. This works in almost all cases and is efficient. The disadvantage is, that this is a black box procedure, the coordinates employed have no direct meaning and cannot be modified easily by the user.

cartesians


should always work but are inefficient (more cycles needed for convergence). Cartesians are the last resort if other options fail, they are assigned as default if one leaves the main geometry menu and no other internals have been defined.