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, and is formatted.

The input is best described by an example. The following is the first lines of an input for tetrahedrane , treated in  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:    2    2  X  Y  Z   1.00D-15

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

1

The word INTGRL (A6).

2-3

Two arbitrary title lines (A72).

4

CRT,NONTYP,KCHARG,SYMTXT,((KASYM(I,J),I=1,3),J=1,3), ID3, THRS (A1,I4,I3,A2,10A1,D10.2).

CRT

By giving a small or capital 'C' in this position, the program will use Cartesian Gaussian basis functions  instead of the default, which is Spherical Gaussian basis functions  .

NONTYP

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.

KCHARG

The charge of the molecule . Will be used by the program to determine the Hartree-Fock occupation. A zero is assumed if no number is given here.

SYMTXT

Number of symmetry generators . If this field is left blank, 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) by typing a zero in this place. Any other number will be interpreted as the number of symmetry generators (1-3).

KASYM

Symmetry 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.

ID3

A number in this place indicates that the coordinates of the atoms will be read in Ångström , and not in atomic units which is the default.

THR

Threshold for neglect of final integrals. Default is 1.0D-15, which will be used if no input is given here. A threshold of 1.0D-15 will give integrals correct to approximately 1.0D-13.

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:    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 standarized input file (including basis set) can be printed to the file DALTON.BAS by using the keyword .MOLPRI   in the *READIN   submodule.

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

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 irreproducible 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.