The program SYMMOL symmetrizes a group of atoms whose coordinates are obtained from the name.INS file. It prints out information about the given set of atoms and information concerning its symmetry, the symmetrized orthogonal coordinates together with the point group (PG), the labels and the equivalent positions. Some quantities showing the goodness-of-fit are also printed: the RMS on the coordinates, the molecular RMS, the maximum deviation of the coordinates of the atom from the symmetrized ones and the continuous symmetry measure (CSM) for the whole PG and for the single elements of the PG.
For hexagonal PGs or for PGs different from the 32 crystallographic PGs, the program also prints out the symmetry group matrices in the orthogonal frame, the symmetry operations in hexagonal coordinates and the atom coordinates in the hexagonal system.
The symmetrization is performed within a tolerance based on a value given in input (DCM). The user may choose between different possible criteria of tolerance: the tolerance may be a constant, that is, the DCM input value, or a variable. In the latter case, the tolerance for each atom is DCM weighted by either the distance of the atom from the centre of mass or the mean standard uncertainty (s.u.) of the atom.
Computation of the inertia moments may be performed using atomic masses as weights or assigning unitary weights to the atoms or weigthing the atoms by the reciprocal of their mean square s.u.
Atoms with MOL less than 0 are not used to find the symmetry group, but, after symmetrization of atoms with MOL=I, the atoms with MOL=-I are examined to see if it is possible to symmetrize them in the same group, but according to the larger tolerance parameter DCME. The use of MOL less than 0 can be very useful when there is a PSEUDO DEGENERACY OF THE PRINCIPAL INERTIA AXES
All lines of input starting with # are interpreted as comment and ignored
1) CELL PARAMETERS (free format)
if orthogonal coordinates are given, cell must be: 1 1 1 90 90 90
2) INDWGH,INDTOL,DCM,DCME (free format)
INDWGH=0,1 moments of inertia are calculated with weights = atomic masses
INDWGH=2 moments of inertia are calculated with weights = 1.0
INDWGH=3 moments of inertia are calculated with weights = (1/s(i))**2
were s(i) = is the mean s.u. for the atom i as calculated from
atomic standard uncertainties (see below)
INDTOL=0,1 an element of symmetry of the molecular group is accepted only
if for any atom i exist an atom j for which
ABS[XO(i)-Mk*XO(j)] less than DCM
where XO are the inertial coordinates, Mk is the symmetry matrix
and DCM is a constant tolerance
INDTOL=2 as indtol=1 but the tolerance is now DCM*d(i)/dm
where d(i) is the distance of the atom i from the mass centre
and dm is the mean of the d(i) of all the considered atom
INDTOL=3 as indtol=1 but the tolerance is now DCM*s(i)
3) NAME(i) MOL(i) X(i) SX(i) for I=1 to NA=total number of atoms.
format(a6,i2,6f9.5)
NAME(i) = Label for the atom i. The first (1 or 2) non-blank letters must
be the symbol of the atomic species.
- the symbol may be in upper lower case or mixed
MOL(i) = group (molecule) of atom i
The program attempts to symmetrize all the groups
MOL(i) less than 0
This atom belongs to the group ABS(MOL(i)) but it weight is =0.0
and the tolerance for this atoms is DCME
MOL(i) = 0 This atom is completely ignored
X(i) = atom coordinates referred to the cell
SX(i) = atom standard uncertainties referred to the cell