Usage examples

CENSO can be used for several applications / target quantities. Some are listed below:

CENSO has sorting "parts" which can be turned on and off. The parts are run in sequence and the sorting-results are influenced by the choice of sorting-parts employed.

If for example the optimization part (part2) is not performed, then all subsequent parts will calculate free energies or properties on the input SQM/FF geometries (not DFT optimized geometries)!

Each part contains thresholds (see Thresholds ) and choosing to low (free) energy windows (in the early sorting parts) will affect your final ensemble / averaged free energy / property.

For the demonstration purpose it is assumed that all parts are turned 'off' in the global configuration file of the user!

Calculate fast DFT (B97-D3(0)/def2-SV(P)+gcp) single-point energies on GFNn-xTB input geometries:

Useful in case of large structure ensembles (SE). Very efficient (fast) improvement on the electronic energy description compared to the initial SQM/FF energies. Conformers high lying in energy are quickly sorted out.

input

$ censo -inp ensemble.xyz -part0 on -chrg 1 -solvent h2o > censo.out &

output

example censorc

input-ensemble.xyz

Calculate free energies in solution phase (CHCl3) on GFNn-xTB geometries:

There are two options available:

• Using part1 (prescreening)

• or only using part3 and do not calculate part2 (optimization)

input

$ censo -inp ensemble.xyz -part1 on -chrg 1 -solvent chcl3 -smgsolv1 cosmors -func r2scan-3c -basis automatic -P 4 -O 2  > censo.out &

output

example censorc

input-ensemble.xyz

Calculate free energies on populated, DFT optimized conformers

• Using sorting parts: part0 and part1 in order to reduce the number of computational costly DFT geometry optimizations

• example settings are read from .censorc file

input

$ censo -inp ensemble.xyz -inprc /path/to/.censorc > censo.out &

output

example censorc

input-ensemble.xyz

Restarting calculations

CENSO keeps track of all performed calculations, if they succeed, fail or are pending. The data is stored in enso.json and enables restarting of CENSO runs. Restarting a calculation is useful if you only considered few conformers in the first run and want to increase the number of investigated conformers (e.g., start from 30 and go to 100 conformers). Or if after the calculation of an ensemble free energy a property, for example OR should be calculated, this can be done by first calculating the free energy, checking the results and the final ensemble and then restart to calculate the property (OR). Some restart limitations are given though: You can not change anything that concerns the geometry optimization, since all results have to be created with the same method-combination.

When restarting CENSO, files with information of the previous calculation (enso.json, enso_ensemble_partx.xyz, ...) are automatically backed up.

Restarting a calculation is performed by calling censo and adjusting the new settings by command line:

$ censo -restart -nc 200 > censo-restart.out &