This repository hosts the CENSO code for the refinement of Conformer Rotamer
Ensembles (CRE) as obtained from CREST.
There are several options possible. The easiest is to use the packaged censo programs (by use of Pyinstaller) which can be found at the release section. The packaged censo is linked against GLIBC version 2.19 and will work for GLIBC version 2.19 and above.
For the packaged "binary" of CENSO, download it from the release site, copy to your bin and make executable:
$ cp censo ~/bin/censo $ chmod u+x ~/bin/censo
Other options to use censo are shown below:
Download the git repository and run:
$ pip install --upgrade pip $ pip install --editable . $ censo arg1 arg2
Treating the censo directory as a package and as the main script:
$ python3 -m censo arg1 arg2
Using the censo-runner.py wrapper:
$ ./censo-runner.py arg1 arg2
After installation with pip:
$ censo arg1 arg2
Create the remote configuration file .censorc where the user can adjust default settings and provide paths to the external programs e.g. xtb, crest, orca ...
$ censo -newconfig $ cp censorc-new /home/$USER/.censorc # edit .censorc vi /home/$USER/.ensorc
Can be found following: https://xtb-docs.readthedocs.io/en/latest/CENSO_docs/censo.html
Interactive Documentation can be accessed:
$ censo -tutorial
Explainations on the commandline arguments can be printed by:
$ censo --help
- newest xtb (currently: https://github.com/grimme-lab/xtb/releases/tag/v6.4.0 )
- newest cefine https://github.com/grimme-lab/cefine/releases
- ORCA > version 4.1 and below 5.0.0 !!!
Further information (will be ordered later on):
- the file .censorc can be used in the current working directory and will be preferred to the global configuration file in ~/.censorc
- a folder ~/.censo_assets/ will be created upon usage of censo
- ORCA has not been tested extensively so please be careful, test calculations and report possible "bad" settings
- To be efficient COSMO-RS calculations are not performed with BP86 but whith the functionals for energy evaluation.
# check if setting-combinations match: $ censo -inp structure_ensemble.xyz -part2 on -solvent h2o --checkinput # start the calculation: $ censo -inp structure_ensemble.xyz -part2 on -solvent h2o > censo.out 2> error.censo &
The molecule numbering from the input structure ensemble is kept throughout the entire program. There are several program parts which can be used to filter a structure ensemble:
- Cheap prescreening (part0): Very fast DFT energies in order to improve upon the energy
- description of the SQM method used to generate the input structure ensemble. The (free) energies are evaluated on the input geometries (DFT unoptimized).
- Prescreening (part1): Improved DFT energies and accurate solvation energies (if needed).
- The free energies are evaluated on the input geometries (DFT unoptimized).
- Optimization (part2): efficient structure ensemble optimization and
- free energy calculation on DFT optimized geometries.
- Refinement (part3): Optional free energy refinement (on DFT optimized geometries).
- E.g. using hybrid DFA with large basis set.
- NMR properties (part4): Optional calculation of shielding and coupling constants on
- populated conformers.
- Optical Rotation (part5): Optional calculation of optical rotatory dispersion
- for the populated ensemble.
The amount of ricore for each calculation can be set in your .cefinerc. The same holds for maxcor and/or rpacor.
$ echo "ricore 4000" > .cefinerc $ echo "maxcor 4000" >> .cefinerc $ echo "rpacor 4000" >> .cefinercCENSO currently does not work with the new ORCA 5.x release. In the new ORCA release changes to the input have been introduced (e.g. DFT grids) and the input creation inside CENSO has to be updated.
Solvation models available for implicit effect on properties e.g. the geometry (SM). And "additive" solvation models which return a solvation contribution to free energy (Gibbs energy) of the choosen geometry (SMGSOLV).
programs solvation models comment Turbomole COSMO (SM) DCOSMO-RS (SM) COSMO-RS COSMO-RS (SMGSOLV) (only solvent model for evaluation at different temperatures) ORCA CPCM (SM) SMD (SM) SMD_GSOLV (SMGSOLV) xTB GBSA_Gsolv (SMGSOLV) ALPB_Gsolv (SMGSOLV) CENSO uses several QM-packages and not all solvents are available for all solvation models throughout the QM-packages. For this reason a user editable file is created in the folder:
$ ~/.censo_assets/censo_solvents.jsonwhich contains a dictionary of all available solvent models and solvents. If a solvent is not available with a certain solvent model, the user can then choose a replacement solvent. E.g. if CCl4 is not available choose CHCl3.
The solvent file is directly used in CENSO and typos will cause calculations to crash! Adding a new solvent is as easy as adding a new dictionary to the file.
General reference:
S. Grimme, F. Bohle, A. Hansen, P. Pracht, S. Spicher, and M. Stahn J. Phys. Chem. A 2021, 125 (19), 4039–4054.
DOI: 10.1021/acs.jpca.1c00971.
Reference is available in bibtex format.
CENSOis free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
CENSOis distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU Lesser General Public License for more details.