Interface dummy_filter

This interface serves as a filter for geometries containing dummy atoms (element = "X"), passing a geometry with dummy atoms removed for the actual calculation. In the other direction, the dummy atoms are added back to the results, with zero gradient on them.

Methods and capabilities

The interface implements a single unnamed method; 'method' keyword not necessary

Input structure

The interface requires following blocks in the input:

Keywords used

This interface does not use any specific keywords


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

# Dummy filter example 1

# Geometry optimization model geometry with dummy atoms
job: optimize

# The dummy atoms have to be named "X"
geometry: |
  O    0.000000000   0.000000000  -0.000000000
  H   -0.991859594  -0.050734173   0.116792934
  H    0.329900831  -0.845847733  -0.419174252
  X    0.434954299   0.121552446   0.892210603
  X    0.226998698   0.774964818  -0.589831435

# The filter is used as an interface
interface: dummy_filter

# And it passes the geometry without dummy atoms to the calculation defined
# in a separate block:
  # PM6 in Mopac as an example
  interface: mopac
  method: PM6
  charge: 0