Examples

A set of basic examples is a part of cuby3 package. You'll find them in directory examples. Input files contains comments on what the keywords mean. Selected input files (but not the geometries) are also listed here:

1) Singlepoint energy calculation at SCC-DFTB level

# EXAMPLE 1: SCC-DFTB singlepoint calculation on water molecule
# to run the calculation, use:
# cuby_energy input.yaml water.xyz

interface: dftb
# We call DFTB interface to run the calculation

dftb_dispersion: no
# The dispersion correction is on by default, this keyword can be used to switch it off

charge: 0
# Total charge of the system is 0

job_cleanup: no
# Do not delete the directory with DFTB calculation, so we can look at the original
# files produced by the dftb+ program. By default, thse are deleted when calculation
# ends successfuly.

2) Interaction energy calculation using Turbomole RI-DFT

The first input file uses some default settings, second one shows more detailed configuration

# EXAMPLE 2: RI-DFT-D interaction energy calculated using Turbomole
# to run the calculation, use:
# cuby_interaction input_1.yaml water_dimer.xyz

# When XYZ geometry is used, the program attempts to find two molecules
# for interaction energy calculation from the connectivity.
# For manual selection of subsystem, see input_2.yaml.

interface: turbomole
# Call turbomole to do the calculation

tm_level: ridft
# use RI-DFT

charge: 0
basisset: TZVP
functional: tpss
# calculation setup

modifiers: dispersion
# Empirical dispersion is added to the DFT calculation.
# Default parameters for given basis set/functional are used.
# See input_2.yaml for custom setup of dispersion.

# EXAMPLE 2: RI-DFT-D interaction energy calculated using Turbomole
# to run the calculation, use:
# cuby_interaction input_2.yaml water_dimer.pdb

interface: turbomole
# Call turbomole to do the calculation

tm_level: ridft
# use RI-DFT

mem: 100
# Memory for RI procedure: 100 MB

basisset: TZVP
functional: tpss
# calculation setup

# custom specification of subsystems::freeze_atoms
molecule_a:
  charge: 0            # charge of monomer
  selection: 1-3       # Selection of atoms - by atom index
molecule_b:
  charge: 0
  selection: :2        # Selection: by residue number (in PDB only)

modifiers: dispersion
dispersion_para: 1.0, 25.0
# Custom damping function parameters:
# radii scaling factor sr: 1.0
# alpha (exponent): 25.0