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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 {html}<pre><code># 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.</code></pre>{/html} !2) Interaction energy calculation using Turbomole RI-DFT The first input file uses some default settings, second one shows more detailed configuration {html}<pre><code># 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.</code></pre><br/>{/html} {html}<pre><code># 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</code></pre>{/html}
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