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.
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: scan.xyz # 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) measurements: # 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)