[group[,]]atom, , , , , , ,
[group[,]]atom, , , ,
All atoms, including those related by symmetry transformations, should be specified in the Z-matrix. Note that for the first atom, no coordinates need be given, for the second atom only are needed, whilst for the third atom may be omitted. The 6 missing coordinates are obtained automatically by the program, which translates and re-orients the molecule such that the origin is at the centre of mass, and the axes correspond to the eigenvectors of the inertia tensor (see also CHARGE option above).
Variable names, and in general expressions that are linear in all dependent variables, may be used as well as fixed numerical values for the parameters , and . These expressions are evaluated as late as possible, so that it is possible, for example, to set up loops in which these parameters are changed; the geometry optimizer also understands this construction, and will optimize the energy with respect to the value of the variables. Non-linear expressions should not be used, because the geometry optimization module is unable to differentiate them.
Once the reorientation has been done, the program then looks for symmetry ( and subgroups), unless the NOSYM option has been given. It is possible to request that reduced symmetry be used by using appropriate combinations of the options X,Y,Z,XY,XZ,YZ,XYZ. These specify symmetry operations, the symbol defining which coordinate axes change sign under the operation. The point group is constructed by taking all combinations of specified elements. If symmetry is explicitly specified in this way, the program checks to see that the group requested can be used, swapping the coordinate axes if necessary. This provides a mechanism for ensuring that the same point group is used, for example, at all points in the complete generation of a potential energy surface, allowing the safe re-utilization of neighbouring geometry molecular orbitals as starting guesses, etc..
Note that symmetry is not implemented in density fitting methods, and in these cases the NOSYM option is implied automatically.
Also note that by default the automatic orientation of the molecule only takes place if the geometry is defined by internal (Z-matrix) coordinates. In case of XYZ Input the orientation is unchanged, unless the MASS option is specified in the geometry block.