Section Geometry

Geometrical data such as number of atoms, coordinates, etc: Most variable names should be self-explanatory

grouplabel

Point group symmetry (string) used in the calculation, for instance O(H). This may be set in the input file.

Geometric Symmetry

Auto-determined ('true') symmetry (considering the nuclear frame and any external fields, but not taking into account any user-defined MO occupation numbers and hence the electronic charge distribution.

symmetry tolerance

Threshold for allowed deviation of input atomic coordinates from symmetry to be detected or verified.

orient

Affine transformation (3,4 matrix: rotation and translation) between the input coordinates and the frame in which the program processes the atoms. ADF has certain orientation requirements for all supported point group symmetries and may rotate and translate the input coordinates accordingly.

oinver

The inverse transformation of orient

lrotat

A logical flag to signal whether or not a rotation has been applied between the input frame and the internally used frame.

nr of fragmenttypes

The number of distinct types of fragments

nr of dummy fragmenttypes

Idem, but counting only dummy atom fragments. A dummy fragment, if it exists, must consist of one single (dummy) atom.

fragmenttype

Names (string) of the fragment types.

fragment mass

Sum of atomic masses in the fragment.

fragment charge

An array with 3 values per fragment type (nftypes,3): 1=sum of nuclear charges, 2=sum of effective nuclear charges (discounting for the frozen core shells), 3=nr of valence electrons

fframe

Signals whether or not special local coordinate frames are used for the atoms. Usually this is not so, in which case the variable has the value DEFAULT. fframe is an array that runs over the atoms. See the 'z=' option to the data in the ATOMS input key block.

cum nr of fragments

An array (0:nftyps) that gives the total number of fragments for the fragment types up to and including the indexed one. The ordering of fragments and fragment types is printed in the standard output file.

nr of fragments

The total number of fragments in the calculation
This equals the last element of the previous variable 'cum nr of fragments'

nr of dummy fragments

The total number of fragments that each consist of a single dummy atom.

fragment mapping

Affine transformation matrices (3,4: rotation and translation), one for each fragment in the molecule, that transform the fragment coordinates as they are on the fragment file(s), to the actual position of the fragments in the molecule.

cum nr of atomtypes

An array (0:fragmenttypes) that counts the number of atom types up to and including the indexed fragment type.

nr of atomtypes

Total number of atom types in the molecule. Must equal the last element of the 'cum nr of atomtypes' array

nr of dummy atomtypes

Similar, now counting only the atom types consisting of a dummy atom.

atomtype

Names (strings) of the atom types

mass

Atomic masses: array running over the atom types. Compare 'fragment mass'.

charge

Similar as for 'fragment charge', but now the values per atom type.

cum nr of atoms

An array (0:atomtypes) that counts the number of atoms up to and including the indexed atom type.

nr of atoms

Total number of atoms. Must equal the last element of the array 'cum nr of atoms'.

nr of dummy atoms

Total number of dummy atoms

atmcrd

Type of atomic coordinates in input: CART (Cartesian) or ZMAT (Internal).

kmatrix InputOrder

The connection matrix listing (and referencing) the atoms in the order as they were in the input file. This ordering aspect is significant because internally the program reorders the atoms and groups them together by atom type and fragment type. Hence it is relevant to know what ordering (input- or internal-) is assumed in data arrays.

zaxis

For each atom the direction of the local z-axis. Normally this is identical to the standard (0,0,1), but it may be different for analysis purposes. See the 'z=' option to the data records in the ATOMS block.

fragment and atomtype index

An integer array (natoms,2) that specifies for each atom the fragment and the atom type it belongs to.

atom order index

An integer array (natoms,2) that defines the re-ordering of atoms between the list in the input file and the internally used list (which is driven by fragment types, fragments, atom types; dummies come last). The internally used list can be derived from the printout of the fragments, early in the standard output.

kmatrix

The connection matrix using the internally applied ordering of atoms

xyz

Cartesian coordinates of the atoms, in the internally used ordering of atoms

xyz Inputorder

Similar, but now for the ordering of atoms as in the input file.

zmatrix

Internal (Z-matrix) atomic coordinates

zmatrix Inputorder

Internal coordinates in the input-order of atoms

Atomic Distances

Inter atomic distance matrix

ntyp

Number of atom types, not counting dummy atoms,

nqptr

A cumulative counting array, very similar to 'cum nr of atoms'
Differences: it runs only over 'ntyp' atom types (not including dummy atoms) and its indexing as well as its values are shifted by one: nqptr(k) is the total number of atoms plus one, counting the atom types up to and including #(k-1)

nnuc

Total number of non-dummy atoms

qtch

Nuclear charges of the non-dummy atoms

qeff

Effective nuclear charges (subtracting charge for the frozen core shells) of the non-dummy atoms

nfragm

Total number of non-dummy fragments

nofrag_1

Integer array specifying for each non-dummy atom the fragment it belongs to.

nofrag_2

Integer array specifying for each non-dummy atom the fragment type it belongs to

nuclab

Names of the non-dummy atom types.