General MOLECULE input

In the general input section of the MOLECULE input file, we will consider such information as molecular symmetry, number of symmetry distinct atoms, generators of a given molecular point group, and so on. This information usually constitutes the four/five first lines of the input.

The input is best described by an example. The following is the first lines of an input for tetrahedrane, treated in $C_{2v}$ symmetry, with a 4-31G** basis. The line numbers are for convenience in the subsequent input description and should not appear in the actual input. Note also that in order to fit the example across the page some liberties have been taken with column spacings.

 1:INTGRL
 2:        Tetrahedrane, Td_symmetric geometry
 3:                 4-31G** basis
 4:Atomtypes=2 Generators=2 X Y Integrals=1.00D-15

We now define the input line-by-line. The FORMAT is given in parenthesis.

1

The word INTGRL (A6).

2-3

Two arbitrary title lines (A72).

4

General instructions about the molecule.

This line is keyword-driven. The general structure of the input is Keyword=. The input is case sensitive, but DALTON will recognize the keywords whether specified with only three characters (minimum) or the full name (or any intermediate option). The order of the keywords is arbitrary. The following keywords are recognized for this line:

Angstrom

Indicates that the atomic Cartesian coordinates are given in Ångström, and not in bohr (atomic units) which is the default.

Atomtypes

(Integer). This keyword is required. Number of atom types (number of atoms specified in separate blocks). For a Z-matrix input this will be the total number of atoms in the molecule, the Z-matrix module will then extract the number of atom types.

Cartesian

Indicates that a Cartesian Gaussian basis set will be used in the calculations.

Charge

(Integer). The charge of the molecule. Will be used by the program to determine the Hartree-Fock occupation.

Generators

(Integer+Character). Number of symmetry generators. If this keyword is not specified (and Nosymmetry not invoked) the automatic symmetry detection routines of the program will be invoked. Symmetry can be turned off (needed for instance if starting a walk at a highly symmetric structure which one knows will break symmetry) using the keyword Nosymmetry. DALTON is restricted to the Abelian subgroups of D$_{2h}$, and thus there can be 1 to 3 generating elements.

The number of generators is followed the equally many blocks of characters specifying which Cartesian axis change sign during each of the generators. X is reflection in the $yz$-plane, XY is rotation about the $z$-axis, and XYZ denotes inversion. Due to the handling of symmetry in the program, it is recommended to use mirror planes as symmetry generating elements if possible.

Integrals

(Real). Indicates the threshold for which integrals smaller than this will be considered to be zero. If not specified, a threshold of 1.0D-15 will be used. A threshold of 1.0D-15 will give integrals correct to approximately 1.0D-13.

Nosymmetry

Indicates that the calculation is to be run without the use of point-group symmetry. Automatic symmetry detection will also be disabled.

Own

Indicates that a user-supplied scheme for generating transformed angular momentum basis functions will be used.

Spherical

Default. Indicates that a spherical Gaussian basis set will be used in the calculations.

Note that if one wants to use the basis set library, there are two options. One option is to use a common basis set for the entire molecule in which the first line should be replaced by two lines, which for a calculation using the 4-31G** basis would look like:

 1:BASIS
 2:4-31G**

This option will not be active with customizable basis sets like the ANO or NQvD sets.

Alternatively you may specify different basis sets for different atoms, in which case the first line should read

 1:ATOMBASIS

The fourth line (fifth in a calculation using the basis set library) looks a bit devastating. However, for ordinary Hartree-Fock or MP2 calculations, only the number of different atom types and the charge need to be given (if the molecule is charged), as symmetry and Hartree-Fock occupation will be taken care of by the program. Thus this line could in the above example be reduced to

 4:Atomtypes=2

or even more concisely (though not more readable) as

 4:Ato=2

Let us finally give some remarks about the symmetry detection routines. These routines will detect any symmetry of a molecule by explicit testing for the occurrence of rotation axes, mirror planes and center of inversion. The occurrence of a symmetry element is tested in the program against a threshold which may be adjusted by the keyword .SYMTHR in the *READIN input section. By default, the program will require geometries that are correct to the sixth decimal place in order to detect all symmetry elements.

The program will translate and rotate the molecule into a suitable reference geometry before testing for the occurrence of symmetry operations. The program will not, due to the handling of symmetry in the program, transform the molecule back to original input coordinates. Furthermore, if there are symmetry equivalent nuclei, these will be removed from the input, and a new, standardized molecule input file will be generated and used in subsequent iterations of for instance a geometry optimization. This standardized input file (including basis set) is printed to the file DALTON.BAS, which is among the files copied back after the end of a calculation.

DALTON can only take advantage of point groups that are subgroups of D$_{2h}$. If symmetry higher than that is detected, the program will use the highest common subgroup of the symmetry group detected and D$_{2h}$.

We recommend that the automatic symmetry detection feature is not used when doing MCSCF calculations, as symmetry generators and their order in the input determines the order of the irreducible representations needed when specifying active spaces. Thus, for MCSCF calculations we recommend that the symmetry is explicitly specified through the appropriate symmetry generators, as well as the explicit Hartree-Fock occupation numbers.