Geometry Specification

The molecular geometry may be specified using either Cartesian a Z-matrix coordinates. Cartesian coordinates are specified via the keyword geometry:

  geometry = (
     atomname1 x1 y1 z1 
     atomname2 x2 y2 z2 
     atomname3 x3 y3 z3 
             ...
     atomnameN xN yN zN 
  )

where atomname$i$ can take the following values:

• The element symbol: H, He, Li, Be, B, etc.
• The full element name: hydrogen, helium, lithium, etc.
• As a ghost atom with the symbol, G, or name, ghost. A ghost atom has a formal charge 0.0, and can be useful to specify the location of the off-nucleus basis functions.
• As a dummy atom with the symbol, X. Dummy atoms can be useful only to specify Z-matrix coordinates of proper symmetry or which contain linear fragments.

Hence the following two examples are equivalent to one another:

  geometry = (
     H 0.0 0.0 0.0 
     f 1.0 0.0 0.0 
     Li 3.0 0.0 0.0 
     BE 6.0 0.0 0.0 
  )

  geometry = (
     hydrogen  0.0 0.0 0.0 
     FLUORINE  1.0 0.0 0.0 
     Lithium   3.0 0.0 0.0 
     beryllium 6.0 0.0 0.0 
  )

It is also possible to include an inner set of parentheses around each line containing atomname1 x1 y1 z1.

The keyword units specifies the units for the coordinates:

• units = angstrom - angstroms (Å), default;
• units = bohr - atomic units (Bohr);

Z-matrix coordinates are specified using the keyword zmat:

  zmat = (
     atomname1
     atomname2 ref21 bond_dist2
     atomname3 ref31 bond_dist3 ref32 bond_angle3 
     atomname4 ref41 bond_dist4 ref42 bond_angle4 ref43 tors_angle4 
     atomname5 ref51 bond_dist5 ref52 bond_angle5 ref53 tors_angle5 
                             ...                
     atomnameN refN1 bond_distN refN2 bond_angleN refN3 tors_angleN 
  )

where

• bond_dist$i$ is the distance (in units specified by keyword units) from nucleus number $i$ to nucleus number ref$i$1. The units
• bond_angle$i$ is the angle formed by nuclei $i$, ref$i$1, and ref$i$2;
• tors_angle$i$ is the torsion angle formed by nuclei $i$, ref$i$1, ref$i$2, and ref$i$3;