The input of (initial) atomic positions as Cartesian coordinates has been mentioned already in the minimal-input examples in Chapter 2.1. Alternatively they may be given in z-matrix form.
ATOMS {Cartesian / Zmatrix / MOPAC}
{N} Atom Coords {F=Fragment}
...
End
Cartesian or Zmatrix or MOPAC
Specifies the type of coordinates. Default (no specification) is Cartesian. Instead of Zmatrix you may also type internal.
MOPAC is a special variety: the subsequent records in the data block are mopac style Z-matrix input for the atomic system, see example
below.
N
This is an optional integer by which you may number the atoms. The numbers should be 1,2,3, et cetera if any reference is made to them in other parts of input. The reason for this restriction is that ADF numbers the atoms internally according to their occurrence in the input file and it applies this internal numbering when any subsequent references are interpreted.
Atom
The name of an atom type. It must begin with the standard one- or two-character symbol for the chemical element: H, He, Li, and so on. Optionally it may be appended by .text, where text is any string (not containing delimiters). Examples: H, Mn.3, Cu.dz-new.
Dummy atoms may be useful in the construction of a Z-matrix, for instance
to obtain a set of internal coordinates that reflect the symmetry of
the molecule better. They may also be useful in a Z-matrix to avoid an
ill-defined dihedral angle, which occurs when three (almost) co-linear atoms
span either of the two planes that define the angle. In geometry optimizations
this must absolutely be avoided if such internal coordinates are used
as optimization parameters.
Dummy atoms are input with the chemical
symbol xx. XX-type atoms can be inserted in
the list of atoms like any other atom types. The name (xx) can have a suffix of the form .text. No fragment files must be supplied for dummies. There
are no symmetry constraints on the positions of the dummies. The dummies serve
only to set up the Z-matrix in a proper way.
Coords
This specifies he coordinates of the atom. If Cartesian
coordinates are used the x, y, z values must be given. For Z-matrix coordinates
you put first the three connection numbers, then the values of the bond
length, bond angle and dihedral angle. Example:
Ge 2 1
5 2.1 95.3 24.8
defines that a Germanium atom is located with a distance 2.1 Angstrom from the second
atom in the input list, that the angle (Ge-atom2-atom1) is 95.3 degrees and
that the dihedral angle between the planes (Ge-atom2-atom1) and
(atom2-atom1-atom5) is 24.8 degrees.
To avoid any confusion as regards the direction (sign) of the dihedral angle,
here is the definition used in ADF: Let the connection numbers for an atom P
refer to the atoms Q, R and S, in that order. Choose a local coordinate frame
such that Q is at the origin, R on the positive z-axis and S in the
xz-plane with a positive x-value. The three Z-matrix coordinates bond
length, bond angle and dihedral angle of P are then precisely its spherical
coordinates r, q, and -f: the distance to the origin, the angle that
PQ makes with the positive z-axis (0.π) and the negative
of the angle that the projection of PQ on the
xy-plane makes with the positive x-axis (0..2π, or -π..+π).
The connection numbers and internal coordinate values of the first atom in a
Z-matrix have no meaning. Similarly, the second atom requires only a
bond-length specification and the third atom only a bond length and a bond
angle. However, for each atom three connection numbers are read from input
and interpreted, and you must therefore supply zeros for them if they don't refer to any atoms. The
corresponding meaningless Z-matrix coordinate values can be omitted. More in general: missing
coordinate values are set to zero (also for Cartesian coordinates input).
Z-matrix values that are meaningless because they correspond to zero connection
numbers are ignored, whatever their value is in the input file.
In a Z-matrix definition the three reference atoms, with respectively 3,
2, and 1 connection numbers equal to zero, do not have to be the first three in
the input list. The program will scan the list for any atom that has
3 connection numbers zero, then for one that has only a bond length
specification, etc. If the Z-matrix is not properly defined, for instance if
more than one atom occurs with all three connection numbers equal to zero,
or when not every atom is somehow connected to all others, the program will
abort.
F=Fragment
Specifies that the atom belongs to a particular fragment. The fragment name must be of the form fragtype/n, where fragtype is the name of one of the types of fragments in the molecule. The integer n, after the slash, counts the individual fragments of that type. The numbering suffix /n is not required if there is only one fragment of that type.
When f=fragment is omitted altogether,
the fragment type is taken to be the atom type that was specified earlier on the same line. (The numbering /n is then added automatically by the
program, by counting the number of times that this single-atom fragment type
occurs in the list of atoms).
Mopac
The MOPAC style input requires that the records in the data block have the following format:
atomtype distance idist angle iangle dihedral idehedral
The three internal coordinate values (distance, angle, dihedral) are each followed directly by the connection number.
Atom type is not identical to chemical element: an atom type is defined by all characteristics of the basic atom to which it in fact refers: the nuclear charge, the basis functions, the frozen core, the density functional and any other features that were applied in generating that basic atom.
As mentioned before, the point group symmetry specified in input with a Schönfliess type symbol puts restrictions on the orientation of the atomic system. Unless the input-specified symmetry equals the true symmetry of the nuclear frame (in which case adf will adjust the orientation of the molecule, if necessary), the user must take care of this by supplying the Cartesian coordinates (in the appropriate orientation). If a subgroup of the true nuclear symmetry is used and Z-matrix format is used for the coordinates, the program will place the atoms in the standard Z-matrix frame: first atom at the origin, second on the positive x-axis, third in the xy-plane with positive y-value.
Dummy atoms may be placed asymmetrically. If the atomic coordinates are input as Cartesians, any dummy atoms are irrelevant. Their coordinates will be printed but otherwise they are ignored.
Input items are generally case insensitive. Exceptions are the names of files and directories. Since (to be discussed below) the name of the fragment type as it is defined under atoms (explicitly with the f=option, or implicitly as the name of the atom type) might also directly indicate the fragment file, the specification of fragment types is in principle case-sensitive. Errors may occur if you are sloppy in this respect.
However, you must not give different fragment types names that differ only by case: at various places in the program fragment type names are compared in a case-insensitive way.
Mixed Cartesian and Z-matrix coordinates
