Protocol measure

This protocol performs measurements on a series of geometries. The geometry should be in .xyz format, possibly with multiple entries.

The quantities that can be measured are demonstrated in the example.

Keywords used

Keywords specific for this protocol:

Other keywords used by this protocol:


The following examples, along with all other files needed to run them, can be found in the directory cuby4/protocols/measure/examples

# Protocol measure example 1

# Measurements on a benzene-ethylene complex

job: measure
geometry: # The file contains five geometries

# The list of measurements as name: expression pairs
# The name is printed in the output
# In the expressions, semicolons separate the arguments (atom selections)
  # Distance between two atoms
  dist_3_16: distance(3; 16) 
  # Distance between the centers of molecules
  dist_cc: distance(1-12; 13-18) 
  # Closest distance between molecules
  closest: closest_distance(%molecule(1); %molecule(2)) 
  # Angle between two atoms and a center of group atoms
  angle: angle(9; 3; 16,17,18)
  # Torsion angle
  torsion: torsion(9; 3; 16; 18)
  # Point - plane distance between the benzene ring and the other molecule
  # First argument is the point (center of molecule), remaining three define the plane
  point_plane: point_plane(13-18; 1; 5; 9)
  # Point-normal vector distance, takes arguments P,A,B,C
  # Calculates distance of P from a vector originating in A and perpendicular to AB and AC
  # Here, we calculate the displacement of the ethylene from the benzene ring center
  pp: point_normal(%molecule(2); %molecule(1); 1; 5)