Setup

Setting up CENSO

The easiest approach is to download a compiled CENSO binary from the release page: https://github.com/grimme-lab/CENSO/releases . There are two versions available censo and censo_w_cefine which contains the latest cefine version (for TURBOMOLE users). The compiled binaries are created with pyinstaller and are linked against GLIBC version 2.19 and will work for GLIBC version 2.19 and above.

Next make CENSO executable, create your global configuration file .censorc and adjust settings to your needs.

$ chmod +x censo_w_cefine
$ mv censo_w_cefine ~/bin/censo

$ cd ~/path_to_project/
$ censo -newconfig
$ mv censorc_new ~/.censorc

$ cat ~/.censorc
# shown in next tab

$CENSO global configuration file: .censorc
$VERSION:1.0.1 

ORCA: /path/excluding/binary/
ORCA version: 4.2.1
GFN-xTB: /path/including/binary/xtb-binary
CREST: /path/including/binary/crest-binary
mpshift: /path/including/binary/mpshift-binary
escf: /path/including/binary/escf-binary

#COSMO-RS
ctd = BP_TZVP_C30_1601.ctd cdir = "/software/cluster/COSMOthermX16/COSMOtherm/CTDATA-FILES" ldir = "/software/cluster/COSMOthermX16/COSMOtherm/CTDATA-FILES"
$ENDPROGRAMS

$CRE SORTING SETTINGS:
$GENERAL SETTINGS:
nconf: all                       # ['all', 'number e.g. 10 up to all conformers'] 
charge: 0                        # ['number e.g. 0'] 
unpaired: 0                      # ['number e.g. 0'] 
solvent: gas                     # ['gas', 'acetone', 'acetonitrile', 'aniline', 'benzaldehyde', 'benzene', 'ccl4', '...'] 
prog_rrho: xtb                   # ['xtb', 'prog'] 
temperature: 298.15              # ['temperature in K e.g. 298.15'] 
trange: [273.15, 378.15, 5]      # ['temperature range [start, end, step]'] 
multitemp: on                    # ['on', 'off'] 
evaluate_rrho: on                # ['on', 'off'] 
consider_sym: off                # ['on', 'off'] 
bhess: on                        # ['on', 'off'] 
imagthr: automatic               # ['automatic or e.g., -100    # in cm-1'] 
sthr: automatic                  # ['automatic or e.g., 50     # in cm-1'] 
scale: automatic                 # ['automatic or e.g., 1.0 '] 
rmsdbias: off                    # ['on', 'off'] 
sm_rrho: alpb                    # ['alpb', 'gbsa'] 
check: on                        # ['on', 'off'] 
prog: tm                         # ['tm', 'orca'] 
func: r2scan-3c                  # ['b97-3c', 'b97-d', 'b97-d3', 'pbe', 'pbeh-3c', 'r2scan-3c', 'tpss'] 
basis: automatic                 # ['automatic', 'def2-TZVP', 'def2-mSVP', 'def2-mTZVP', 'def2-mTZVP', '...'] 
maxthreads: 1                    # ['number of threads e.g. 2'] 
omp: 1                           # ['number cores per thread e.g. 4'] 
cosmorsparam: automatic          # ['automatic', '12-fine', '12-normal', '13-fine', '13-normal', '14-fine', '...'] 

$PART0 - CHEAP-PRESCREENING - SETTINGS:
part0: on                        # ['on', 'off'] 
func0: b97-d                     # ['b97-3c', 'b97-d', 'b97-d3', 'pbe', 'pbeh-3c', 'r2scan-3c', 'tpss'] 
basis0: def2-SV(P)               # ['automatic', 'def2-TZVP', 'def2-mSVP', 'def2-mTZVP', 'def2-mTZVP', '...'] 
part0_gfnv: gfn2                 # ['gfn1', 'gfn2', 'gfnff'] 
part0_threshold: 4.0             # ['number e.g. 4.0'] 

$PART1 - PRESCREENING - SETTINGS:
# func and basis is set under GENERAL SETTINGS
part1: on                        # ['on', 'off'] 
smgsolv1: cosmors                # ['alpb_gsolv', 'cosmo', 'cosmors', 'cosmors-fine', 'cpcm', 'dcosmors', '...'] 
part1_gfnv: gfn2                 # ['gfn1', 'gfn2', 'gfnff'] 
part1_threshold: 3.5             # ['number e.g. 5.0'] 

$PART2 - OPTIMIZATION - SETTINGS:
# func and basis is set under GENERAL SETTINGS
part2: on                        # ['on', 'off'] 
opt_limit: 2.5                   # ['number e.g. 4.0'] 
sm2: default                     # ['cosmo', 'cpcm', 'dcosmors', 'default', 'smd'] 
smgsolv2: cosmors                # ['alpb_gsolv', 'cosmo', 'cosmors', 'cosmors-fine', 'cpcm', 'dcosmors', '...'] 
part2_gfnv: gfn2                 # ['gfn1', 'gfn2', 'gfnff'] 
ancopt: on                       # ['on'] 
hlow: 0.01                       # ['lowest force constant in ANC generation, e.g. 0.01'] 
opt_spearman: on                 # ['on', 'off'] 
part2_threshold: 99              # ['Boltzmann sum threshold in %. e.g. 95 (between 1 and 100)'] 
optlevel2: automatic             # ['crude', 'sloppy', 'loose', 'lax', 'normal', 'tight', 'vtight', 'extreme', '...'] 
optcycles: 8                     # ['number e.g. 5 or 10'] 
spearmanthr: -4.0                # ['value between -1 and 1, if outside set automatically'] 
radsize: 10                      # ['number e.g. 8 or 10'] 
crestcheck: off                  # ['on', 'off'] 

$PART3 - REFINEMENT - SETTINGS:
part3: off                       # ['on', 'off'] 
prog3: prog                      # ['tm', 'orca', 'prog'] 
func3: pw6b95                    # ['b97-d3', 'dsd-blyp', 'pbe0', 'pw6b95', 'r2scan-3c', 'wb97x'] 
basis3: def2-TZVPD               # ['DZ', 'QZV', 'QZVP', 'QZVPP', 'SV(P)', 'SVP', 'TZVP', 'TZVPP', 'aug-cc-pV5Z', '...'] 
smgsolv3: cosmors                # ['alpb_gsolv', 'cosmo', 'cosmors', 'cosmors-fine', 'cpcm', 'dcosmors', '...'] 
part3_gfnv: gfn2                 # ['gfn1', 'gfn2', 'gfnff'] 
part3_threshold: 99              # ['Boltzmann sum threshold in %. e.g. 95 (between 1 and 100)'] 

$NMR PROPERTY SETTINGS:
$PART4 SETTINGS:
part4: off                       # ['on', 'off'] 
couplings: on                    # ['on', 'off'] 
progJ: prog                      # ['tm', 'orca', 'adf', 'prog'] 
funcJ: pbe0                      # ['pbe0', 'pbeh-3c', 'r2scan-3c', 'tpss'] 
basisJ: def2-TZVP                # ['DZ', 'QZV', 'QZVP', 'QZVPP', 'SV(P)', 'SVP', 'TZVP', 'TZVPP', 'aug-cc-pV5Z', '...'] 
sm4J: default                    # ['cosmo', 'cpcm', 'dcosmors', 'smd'] 
shieldings: on                   # ['on', 'off'] 
progS: prog                      # ['tm', 'orca', 'adf', 'prog'] 
funcS: pbe0                      # ['b97-3c', 'dsd-blyp', 'kt1', 'kt2', 'pbe0', 'pbeh-3c', 'r2scan-3c', 'tpss', '...'] 
basisS: def2-TZVP                # ['DZ', 'QZV', 'QZVP', 'QZVPP', 'SV(P)', 'SVP', 'TZVP', 'TZVPP', 'aug-cc-pV5Z', '...'] 
sm4S: default                    # ['cosmo', 'cpcm', 'dcosmors', 'smd'] 
reference_1H: TMS                # ['TMS'] 
reference_13C: TMS               # ['TMS'] 
reference_19F: CFCl3             # ['CFCl3'] 
reference_29Si: TMS              # ['TMS'] 
reference_31P: TMP               # ['TMP', 'PH3'] 
1H_active: on                    # ['on', 'off'] 
13C_active: on                   # ['on', 'off'] 
19F_active: off                  # ['on', 'off'] 
29Si_active: off                 # ['on', 'off'] 
31P_active: off                  # ['on', 'off'] 
resonance_frequency: 300.0       # ['MHz number of your experimental spectrometer setup'] 

$OPTICAL ROTATION PROPERTY SETTINGS:
$PART5 SETTINGS:
optical_rotation: off            # ['on', 'off'] 
funcOR: pbe                      # ['functional for opt_rot e.g. pbe'] 
funcOR_SCF: r2scan-3c            # ['functional for SCF in opt_rot e.g. r2scan-3c'] 
basisOR: def2-SVPD               # ['basis set for opt_rot e.g. def2-SVPD'] 
frequency_optical_rot: [589.0]   # ['list of freq in nm to evaluate opt rot at e.g. [589, 700]'] 
$END CENSORC

Upon the first usage of CENSO a folder '~/.censo_assets/' will be created. It contains a file ~/.censo_assets/censo_solvents.json with information on all available solvents and solvent models. If a solvent is not available with a certain solvent model, the user can then choose a replacement solvent, e.g. if benzene is not available choose toluene. This file is directly used in censo and typos will cause the calculation with the repective solvent to crash. For further information: Solvation.

$ cat ~/.censo_assets/censo_solvents.json
# shown in next tab

# CENSO solvents:
# example:
#{
#    "solvent_name_used_in_censo":{ 
#        "solvation_model": ["solvent_name_in_solvation_model", "solvent_name_in_solvation_model_which_is_applied"],
#        "solvation_model2": [null _if_solvent_is_not_available, "replacement_solvent_in_solvation_model2"],
#        "DC": 20.7 # dielectric constant used for COSMO + DCOSMO-RS
#    }
#}
# end example

{
    "acetone":{
        "cosmors": ["propanone_c0", "propanone_c0"],
        "dcosmors": ["propanone", "propanone"],
        "xtb": ["acetone", "acetone"],
        "cpcm": ["acetone", "acetone"],
        "smd": ["ACETONE", "ACETONE"],
        "DC": 20.7
    },
    "chcl3":{
        "cosmors": ["chcl3_c0", "chcl3_c0"],
        "dcosmors": ["chcl3", "chcl3"],
        "xtb": ["chcl3", "chcl3"],
        "cpcm": ["chloroform","chloroform"],
        "smd": ["CHLOROFORM", "CHLOROFORM"],
        "DC": 4.8
    },
    "acetonitrile":{
        "cosmors": ["acetonitrile_c0", "acetonitrile_c0"],
        "dcosmors": ["acetonitrile", "acetonitrile"],
        "xtb": ["acetonitrile", "acetonitrile"],
        "cpcm": ["acetonitrile", "acetonitrile"],
        "smd": ["ACETONITRILE", "ACETONITRILE"],
        "DC": 36.6
    },
    "ch2cl2":{
        "cosmors": ["ch2cl2_c0", "ch2cl2_c0"],
        "dcosmors": [null, "chcl3"],
        "xtb": ["ch2cl2", "ch2cl2"],
        "cpcm": ["CH2Cl2", "CH2Cl2"],
        "smd": ["DICHLOROMETHANE", "DICHLOROMETHANE"],
        "DC": 9.1
    },
    "dmso":{
        "cosmors": ["dimethylsulfoxide_c0", "dimethylsulfoxide_c0"],
        "dcosmors": ["dimethylsulfoxide", "dimethylsulfoxide"],
        "xtb": ["dmso", "dmso"],
        "cpcm": ["DMSO", "DMSO"],
        "smd": ["DIMETHYLSULFOXIDE", "DIMETHYLSULFOXIDE"],
        "DC": 47.2
    },
    "h2o":{
        "cosmors": ["h2o_c0", "h2o_c0"],
        "dcosmors": ["h2o", "h2o"],
        "xtb": ["h2o", "h2o"],
        "cpcm": ["Water", "Water"],
        "smd": ["WATER", "WATER"],
        "DC": 80.1
    },
    "methanol":{
        "cosmors": ["methanol_c0", "methanol_c0"],
        "dcosmors": ["methanol", "methanol"],
        "xtb": ["methanol", "methanol"],
        "cpcm": ["Methanol", "Methanol"],
        "smd": ["METHANOL", "METHANOL"],
        "DC": 32.7
    },
    "thf":{
        "cosmors": ["thf_c0", "thf_c0"],
        "dcosmors": ["thf", "thf"],
        "xtb": ["thf", "thf"],
        "cpcm": ["THF", "THF"],
        "smd": ["TETRAHYDROFURAN", "TETRAHYDROFURAN"],
        "DC": 7.6
    },
    "toluene":{
        "cosmors": ["toluene_c0", "toluene_c0"],
        "dcosmors": ["toluene", "toluene"],
        "xtb": ["toluene", "toluene"],
        "cpcm": ["Toluene", "Toluene"],
        "smd": ["TOLUENE", "TOLUENE"],
        "DC": 2.4
    },
    "octanol":{
        "cosmors": ["1-octanol_c0", "1-octanol_c0"],
        "dcosmors": ["octanol", "octanol"],
        "xtb": ["octanol", "octanol"],
        "cpcm": ["Octanol", "Octanol"],
        "smd": ["1-OCTANOL", "1-OCTANOL"],
        "DC": 9.9
    },
    "woctanol":{
        "cosmors": [null, "woctanol"],
        "dcosmors": ["wet-otcanol", "wet-octanol"],
        "xtb": ["woctanol", "woctanol"],
        "cpcm": [null, "Octanol"],
        "smd": [null, "1-OCTANOL"],
        "DC": 8.1
    },
    "hexadecane":{
        "cosmors": ["n-hexadecane_c0", "n-hexadecane_c0"],
        "dcosmors": ["hexadecane", "hexadecane"],
        "xtb": ["hexadecane", "hexadecane"],
        "cpcm": [null, "Hexane"],
        "smd": ["N-HEXADECANE", "N-HEXADECANE"],
        "DC": 2.1
    },
    "dmf":{
        "cosmors": ["dimethylformamide_c0","dimethylformamide_c0"],
        "dcosmors": [null, "dimethylsulfoxide"],
        "xtb": ["dmf", "dmf"],
        "cpcm": ["DMF", "DMF"],
        "smd": ["N,N-DIMETHYLFORMAMIDE", "N,N-DIMETHYLFORMAMIDE"],
        "DC": 38.3
    },
    "aniline":{
        "cosmors": ["aniline_c0", "aniline_c0"],
        "dcosmors": ["aniline", "aniline"],
        "xtb": ["aniline", "aniline"],
        "cpcm": [null,"Pyridine"],
        "smd": ["ANILINE", "ANILINE"],
        "DC": 6.9
    },
    "cyclohexane":{
        "cosmors": ["cyclohexane_c0", "cyclohexane_c0"],
        "dcosmors": ["cyclohexane", "cyclohexane"],
        "xtb": [null, "hexane"],
        "cpcm": ["Cyclohexane", "Cyclohexane"],
        "smd": ["CYCLOHEXANE", "CYCLOHEXANE"],
        "DC": 2.0
    },
    "ccl4":{
        "cosmors": ["ccl4_c0", "ccl4_c0"],
        "dcosmors": ["ccl4", "ccl4"],
        "xtb": ["ccl4", "ccl4"],
        "cpcm": ["CCl4", "CCl4"],
        "smd": ["CARBON TETRACHLORIDE", "CARBON TETRACHLORIDE"],
        "DC": 2.2
    },
    "diethylether":{
        "cosmors": ["diethylether_c0", "diethylether_c0"],
        "dcosmors": ["diethylether", "diethylether"],
        "xtb": ["ether", "ether"],
        "cpcm": [null, "THF"],
        "smd": ["DIETHYL ETHER", "DIETHYL ETHER"],
        "DC": 4.4
    },
    "ethanol":{
        "cosmors": ["ethanol_c0", "ethanol_c0"],
        "dcosmors": ["ethanol", "ethanol"],
        "xtb": ["ethanol", "ethanol"],
        "cpcm": [null, "Methanol"],
        "smd": ["ETHANOL", "ETHANOL"],
        "DC": 24.6
    },
    "hexane":{
        "cosmors": ["hexane_c0", "hexane_c0"],
        "dcosmors": ["hexane", "hexane"],
        "xtb": ["hexane", "hexane"],
        "cpcm": ["Hexane", "Hexane"],
        "smd": ["N-HEXANE", "N-HEXANE"],
        "DC": 1.9
    },
    "nitromethane":{
        "cosmors": ["nitromethane_c0", "nitromethane_c0"],
        "dcosmors": ["nitromethane", "nitromethane"],
        "xtb": ["nitromethane", "nitromethane"],
        "cpcm": [null, "methanol"],
        "smd": "",
        "DC": 38.2
    },
    "benzaldehyde":{
        "cosmors": ["benzaldehyde_c0", "benzaldehyde_c0"],
        "dcosmors": [null, "propanone"],
        "xtb": ["benzaldehyde", "benzaldehyde"],
        "cpcm": [null, "Pyridine"],
        "smd": ["BENZALDEHYDE", "BENZALDEHYDE"],
        "DC": 18.2
    },
    "benzene":{
        "cosmors": ["benzene_c0", "benzene_c0"],
        "dcosmors": [null, "toluene"],
        "xtb": ["benzene", "benzene"],
        "cpcm": ["Benzene", "Benzene"],
        "smd": ["BENZENE", "BENZENE"],
        "DC": 2.3
    },
    "cs2":{
        "cosmors": ["cs2_c0", "cs2_c0"],
        "dcosmors": [null, "ccl4"],
        "xtb": ["cs2", "cs2"],
        "cpcm": [null, "CCl4"],
        "smd": ["CARBON DISULFIDE", "CARBON DISULFIDE"],
        "DC": 2.6
    },
    "dioxane":{
        "cosmors": ["dioxane_c0", "dioxane_c0"],
        "dcosmors": [null, "diethylether"],
        "xtb": ["dioxane", "dioxane"],
        "cpcm": [null, "Cyclohexane"],
        "smd": ["1,4-DIOXANE", "1,4-DIOXANE"],
        "DC": 2.2
    },
    "ethylacetate":{
        "cosmors": ["ethylacetate_c0", "ethylacetate_c0"],
        "dcosmors": [null, "diethylether"],
        "xtb": ["ethylacetate", "ethylacetate"],
        "cpcm": [null, "THF"],
        "smd": ["ETHYL ETHANOATE", "ETHYL ETHANOATE"],
        "DC": 5.9
    },
    "furan":{
        "cosmors": ["furane_c0", "furane_c0"],
        "dcosmors": [null, "diethylether"],
        "xtb": ["furane", "furane"],
        "cpcm": [null, "THF"],
        "smd": [null, "THF"],
        "DC": 3.0
    },
    "phenol":{
        "cosmors": ["phenol_c0", "phenol_c0"],
        "dcosmors": [null, "thf"],
        "xtb": ["phenol", "phenol"],
        "cpcm": [null, "THF"],
        "smd": [null, "THIOPHENOL"],
        "DC": 8.0
    }
}

Get additional Information:

$ censo --help

# explaination of all possible command line arguments
# shown in next tab

         ______________________________________________________________
        |                                                              |
        |                                                              |
        |                   CENSO - Commandline ENSO                   |
        |                           v 1.0.1                            |
        |    energetic sorting of CREST Conformer Rotamer Ensembles    |
        |                    University of Bonn, MCTC                  |
        |                           Feb 2020                           |
        |                 based on ENSO version 2.0.1                  |
        |                     F. Bohle and S. Grimme                   |
        |                                                              |
        |______________________________________________________________|
        
        This program is 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.

optional arguments:
  -h, --help            show this help message and exit

GENERAL SETTINGS:
  -inp , --input        Input name of ensemble file: e.g. crest_conformers.xyz
  -nc , --nconf         Number of conformers which are going to be considered
                        (max number of conformers are all conformers from the
                        input file).
  -chrg , --charge      Charge of the investigated molecule.
  -u , --unpaired       Integer number of unpaired electrons of the
                        investigated molecule.
  -T , --temperature    Temperature in Kelvin for thermostatistical
                        evaluation.
  -multitemp , --multitemp 
                        Needs to be turned on if a temperature range should be
                        evaluated (flag trange). Options for multitemp are:
                        ['on' or 'off'].
  -trange start end step, --trange start end step
                        specify a temperature range [start, end, step] e.g.:
                        250.0 300.0 10.0 resulting in [250.0, 260.0, 270.0,
                        280.0, 290.0].
  -bhess , --bhess      Applies structure constraint to input/DFT geometry for
                        mRRHO calcuation.Options are: ['on' or 'off'].
  -consider_sym , ---consider_sym 
                        Consider symmetry in mRRHO calcuation (based on desy
                        xtb threshold).Options are: ['on' or 'off'].
  -rmsdbias , --rmsdbias 
                        Applies constraint to rmsdpot.xyz to be consistent to
                        CREST.Options are: ['on' or 'off'].
  -sm_rrho , --sm_rrho 
                        Solvation model used in xTB GmRRHO calculation.
                        Applied if not in gas-phase. Options are 'gbsa' or
                        'alpb'.
  -evaluate_rrho , --evaluate_rrho 
                        Evaluate mRRHO contribution. Options: on or off.
  -func , --functional 
                        Functional for geometry optimization (used in part2)
                        and single-points in part1
  -basis , --basis      Basis set employed together with the functional (func)
                        for the low level single point in part1 und
                        optimization in part2.
  -checkinput, --checkinput
                        Option to check if all necessary information for the
                        ENSO calculation are provided and check if certain
                        setting combinations make sence. Option to choose from
                        : ['on' or 'off']
  -solvent , --solvent 
                        Solvent the molecule is solvated in, available
                        solvents are: ['gas', 'acetone', 'acetonitrile',
                        'aniline', 'benzaldehyde', 'benzene', 'ccl4',
                        'ch2cl2', 'chcl3', 'cs2', 'cyclohexane',
                        'diethylether', 'dioxane', 'dmf', 'dmso', 'ethanol',
                        'ethylacetate', 'furan', 'h2o', 'hexadecane',
                        'hexane', 'methanol', 'nitromethane', 'octanol',
                        'phenol', 'thf', 'toluene', 'woctanol']. They can be
                        extended in the file
                        ~/.censo_assets/censo_solvents.json .
  -prog , --prog        QM-program used in part1 and part2 either 'orca' or
                        'tm'.
  -prog_rrho , --prog_rrho 
                        QM-program for mRRHO contribution in part1 2 and 3,
                        either 'xtb' or 'prog'.
  -crestcheck , --crestcheck 
                        Option to sort out conformers after DFT optimization
                        which CREST identifies as identical or rotamers of
                        each other. The identification/analysis is always
                        performed, but the removal of conformers has to be the
                        choice of the user. Options are: ['on' or 'off']
  -check {on,off}, --check {on,off}
                        Option to terminate the ENSO-run if too many
                        calculations/preparation steps fail. Options are:
                        ['on' or 'off'].
  -version, --version   Print CENSO version and exit.
  -part3only, --part3only
                        Option to turn off part1 and part2
  -cosmorsparam , --cosmorsparam 
                        Choose a COSMO-RS parametrization for possible COSMO-
                        RS G_solv calculations: e.g. 19-normal for
                        'BP_TZVP_19.ctd' or 16-fine for
                        'BP_TZVPD_FINE_C30_1601.ctd'.

SPECIAL RUN MODES:
  -logK, --logK         Automatically set required settings for logK
                        calculation. Of course charge, solvent etc. has to be
                        set by the user.

CRE CHEAP-PRESCREENING - PART0:
  -part0 , --part0      Option to turn the CHEAP prescreening evaluation
                        (part0) which improves description of ΔE 'on' or
                        'off'.
  -func0 , --func0      Functional for fast single-point (used in part0)
  -basis0 , --basis0    Basis set employed together with the functional
                        (func0) for the fast single point calculation in
                        part0.
  -part0_gfnv , --part0_gfnv 
                        GFNn-xTB version employed for calculating the gas
                        phase GFNn-xTB single point in part0. Allowed values
                        are [gfn1, gfn2, gfnff]
  -part0_threshold , -thrpart0 , --thresholdpart0 
                        Threshold in kcal/mol. All conformers in part0 (cheap
                        single-point) with a relativ energy below the
                        threshold are considered for part1.

CRE PRESCREENING - PART1:
  -part1 , --part1      Option to turn the prescreening evaluation (part1)
                        'on' or 'off'.
  -smgsolv1 , --smgsolv1 
                        Solvent model for the Gsolv evaluation in part1. This
                        can either be an implicit solvation or an additive
                        solvation model. Allowed values are [alpb_gsolv,
                        cosmo, cosmors, cosmors-fine, cpcm, dcosmors,
                        gbsa_gsolv, sm2, smd, smd_gsolv]
  -part1_gfnv , --part1_gfnv 
                        GFNn-xTB version employed for calculating the mRRHO
                        contribution in part1. Allowed values are [gfn1, gfn2,
                        gfnff]
  -part1_threshold , -thrpart1 , --thresholdpart1 
                        Threshold in kcal/mol. All conformers in part1
                        (lax_single-point) with a relativ energy below the
                        threshold are considered for part2.

CRE OPTIMIZATION - PART2:
  -part2 , --part2      Option to turn the full optimization (part2) 'on' or
                        'off'.
  -sm2 , --solventmodel2 
                        Solvent model employed during the geometry
                        optimization part2.The solvent model sm2 is not used
                        for Gsolv evaluation, but for the implicit effect on a
                        property (e.g. the optimization).
  -smgsolv2 , --smgsolv2 
                        Solvent model for the Gsolv calculation in part2.
                        Either the solvent model of the optimization (sm) or
                        an additive solvation model. Allowed values are
                        [alpb_gsolv, cosmo, cosmors, cosmors-fine, cpcm,
                        dcosmors, gbsa_gsolv, sm2, smd, smd_gsolv]
  -part2_gfnv , --part2_gfnv 
                        GFNn-xTB version employed for calculating the mRRHO
                        contribution in part2. Allowed values are [gfn1, gfn2,
                        gfnff]
  -ancopt               Option to use xtb as driver for the xTB-optimizer in
                        part2.
  -opt_spearman         Option to use an optimizer which checks if the
                        hypersurface of DFT andxTB is parallel and optimizes
                        mainly low lying conformers
  -optlevel2 , --optlevel2 
                        Option to set the optlevel in part2, only if
                        optimizing with the xTB-optimizer!Allowed values are
                        crude, sloppy, loose, lax, normal, tight, vtight,
                        extreme, automatic
  -optcycles , --optcycles 
                        number of cycles in ensemble optimizer.
  -hlow , --hlow        Lowest force constant in ANC generation (real), used
                        by xTB-optimizer.
  -spearmanthr , --spearmanthr 
                        Value between -1 and 1 for the spearman correlation
                        coeffient threshold
  -opt_limit , --opt_limit 
                        Lower limit Threshold in kcal/mol. If the GFNn and DFT
                        hypersurfaces areassumed parallel, the conformers
                        above the threshold are removed and not optimized
                        further.The conformers in part2 with a relativ free
                        energy below the threshold are fully optimized.
  -thrpart2 , --thresholdpart2 , -part2_threshold 
                        Boltzmann population sum threshold for part2 in %. The
                        conformers with the highest Boltzmann weigths are
                        summed up until the threshold is reached.E.g. all
                        conformers up to a Boltzmann population of 90 % are
                        considered.Example usage: "-thrpart2 99" --> considers
                        a population of 99 %
  -radsize , --radsize 
                        Radsize used in optimization and only for r2scan-3c!

CRE REFINEMENT - PART3:
  -part3 , --part3      Option to turn the high level free energy evaluation
                        (part3) 'on' or 'off'.
  -prog3 , --prog3      QM-program used in part3 either 'orca' or 'tm'.
  -func3 , --functionalpart3 
                        Functional for the COSMO-RS calculation, use
                        functional names as recognized by cefine.
  -basis3 , --basis3    Basis set employed together with the functional
                        (func3) for the high level single point in part3.
  -smgsolv3 , --smgsolv3 
                        Solvent model for the Gsolv calculation in part3.
                        Either the solvent model of the optimization (sm2) or
                        an additive solvation model.
  -part3_gfnv , --part3_gfnv 
                        GFNn-xTB version employed for calculating the mRRHO
                        contribution in part3. Allowed values are [gfn1, gfn2,
                        gfnff]
  -thrpart3 , --thresholdpart3 
                        Boltzmann population sum threshold for part3 in %. The
                        conformers with the highest Boltzmann weigths are
                        summed up until the threshold is reached.E.g. all
                        conformers up to a Boltzmann population of 90 % are
                        consideredExample usage: "-thrpart3 99" --> considers
                        a population of 99 %

NMR Mode:
  -part4 , --part4      Option to turn the NMR property calculation mode
                        (part4) 'on' or 'off'.
  -couplings , --couplings 
                        Option to run coupling constant calculations. Options
                        are 'on' or 'off'.
  -prog4J , --prog4J    QM-program for the calculation of coupling constants.
  -funcJ , --funcJ      Functional for the coupling constant calculation.
  -basisJ , --basisJ    Basis set for the calculation of coupling constants.
  -sm4_j , --sm4_j      Solvation model used in the coupling constant
                        calculation.
  -shieldings , --shieldings 
                        Option to run shielding constant calculations. Options
                        are 'on' or 'off'.
  -prog4S , --prog4S    QM-program for the calculation of shielding constants.
  -funcS , --funcS      Functional for shielding constant calculation.
  -basisS , --basisS    Basis set for the calculation of shielding constants.
  -sm4_s , --sm4_s      Solvation model used in the shielding constant
                        calculation.
  -hactive , --hactive 
                        Investigates hydrogen nuclei in coupling and shielding
                        calculations.choices=['on', 'off']
  -cactive , --cactive 
                        Investigates carbon nuclei in coupling and shielding
                        calculations.choices=['on', 'off']
  -factive , --factive 
                        Investigates fluorine nuclei in coupling and shielding
                        calculations.choices=['on', 'off']
  -siactive , --siactive 
                        Investigates silicon nuclei in coupling and shielding
                        calculations.choices=['on', 'off']
  -pactive , --pactive 
                        Investigates phosophorus nuclei in coupling and
                        shielding calculations.choices=['on', 'off']

OPTICAL ROTATION MODE:
  -OR , --OR , -part5   Do optical rotation calculation.
  -funcOR , --funcOR    Functional for optical rotation calculation.
  -funcOR_SCF , --funcOR_SCF 
                        Functional used in SCF for optical rotation
                        calculation.
  -basisOR , --basisOR 
                        Basis set for optical rotation calculation.
  -freqOR [ [ ...]], --freqOR [ [ ...]]
                        Frequencies to evaluate specific rotation at in nm.
                        E.g. 589 Or 589 700 to evaluate at 598 nm and 700 nm.

OPTIONS FOR PARALLEL CALCULATIONS:
  -O , --omp            Number of cores each thread can use. E.g. (maxthreads)
                        5 threads with each (omp) 4 cores --> 20 cores need to
                        be available on the machine.
  -P , --maxthreads     Number of independent calculations during the ENSO
                        calculation. E.g. (maxthreads) 5 independent
                        calculation- threads with each (omp) 4 cores --> 20
                        cores need to be available on the machine.

Concerning overall mRRHO calculations:
  -imagthr , --imagthr 
                        threshold for inverting imaginary frequencies for
                        thermo in cm-1. (e.g. -30.0)
  -sthr , --sthr        Rotor cut-off for thermo in cm-1. (e.g. 50.0)
  -scale , --scale      scaling factor for frequencies (e.g. 1.0)

CREATION/DELETION OF FILES:
  --cleanup, -cleanup   Delete unneeded files from current working directory.
  --cleanup_all, -cleanup_all
                        Delete all unneeded files from current working
                        directory. Stronger than -cleanup !
  -newconfig, -write_censorc, --write_censorc
                        Write new configuration file, which is placed into the
                        current directory.
  -inprc INPRCPATH, --inprc INPRCPATH
                        Path to the destination of the configuration file
                        .censorc
  -tutorial, --tutorial
                        Start interactive CENSO documentation.

$ censo -tutorial

# general explainations
# shown in next tab


         ______________________________________________________________
        |                                                              |
        |                                                              |
        |                   CENSO - Commandline ENSO                   |
        |                           v 1.0.1                            |
        |    energetic sorting of CREST Conformer Rotamer Ensembles    |
        |                    University of Bonn, MCTC                  |
        |                           Feb 2020                           |
        |                 based on ENSO version 2.0.1                  |
        |                     F. Bohle and S. Grimme                   |
        |                                                              |
        |______________________________________________________________|
        
        This program is 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.

This is the CENSO tutorial / interactive documentation:

Topic options are:
    general
    censorc
    setup
    thresholds
    solvation
    examples
    files
    jobscript
    everything

To exit please type one of the following: exit or q

Please input your information request:

....

Requirements:

CENSO needs other programs in certain versions and will not work properly without them:

xTB in version 6.4.0 or above
TM in version 7.5.x or above (when using r2scan-3c)
ORCA in version 4.x or above
cefine in the newest version, when using TURBOMOLE (or use censo_w_cefine)

Run CENSO on a cluster:

When submitting a calculation on a cluster architecture the following points have to be considered:

Are the program paths in your .censorc file correct (ORCA, xTB, CREST, COSMO-RS)
Is the correct TURBOMOLE version sourced in your job-submission file and are the correct environment variables for parallelization set?
CENSO can not be parallelized over several nodes!
provide the correct number of available cores to CENSO (P, maxthreads) * (O,omp) = number of cores
CENSO will generate a lot of data for each conformer. This data is stored in the CONFX (X=number) folders. If you restart and resubmit a calculation to the cluster, you have to tell your submission script to copy these folders.

Example job-submission script:

cat job
# output shown in other tab

#!/bin/bash
# PBS Job
#PBS -V
#PBS -N JOB_NAME
#PBS -m ae
#PBS -q batch
#PBS -l nodes=1:ppn=28
# 
cd $PBS_O_WORKDIR

### setup programs
## XTB
export OMP_NUM_THREADS=1
export MKL_NUM_THREADS=1
ulimit -s unlimited
export OMP_STACKSIZE=1000m

## TM
export PARA_ARCH=SMP
source /home/$USER/bin/.turbo751
export PARNODES=4  ## omp 
export TM_PAR_FORK=1

### ORCA4.2.1
ORCAPATH="/tmp1/orca_4_2_1_linux_x86-64_openmpi216";
MPIPATH="/software/openmpi-2.1.5/bin";
MPILIB="/software/openmpi-2.1.5/lib64";
PATH=${ORCAPATH}:${MPIPATH}:$PATH 
LD_LIBRARY_PATH=${ORCAPATH}:${MPILIB}:$LD_LIBRARY_PATH
LD_LIBRARY_PATH=/software/intel/parallel_studio_xe_2017.1/parallel_studio_xe_2017.4.056/compilers_and_libraries_2017/linux/compiler/lib/intel64_lin:$LD_LIBRARY_PATH
LD_LIBRARY_PATH=/software/intel/parallel_studio_xe_2017/mkl/lib/intel64:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH

## PATH
PATH=/home/$USER/bin:$PATH
export PATH
### end programs + PATH

export HOSTS_FILE=$PBS_NODEFILE
cat $HOSTS_FILE>hosts_file

TMP_DIR=/tmp1/$USER
DIR1=$PWD

mkdir -p $TMP_DIR/$PBS_JOBID

#check file system access
if [ ! -d $TMP_DIR/$PBS_JOBID ]; then
 echo "Unable to create $TMP_DIR/$PBS_JOBID  on $HOSTNAME. Must stop."
 exit
fi

#check current location
if [ "$PWD" == "$HOME" ]; then
 echo "Cowardly refusing to copy the whole home directory"
 exit
fi

#copy everything to node (will NOT copy directories for safety reasons.
#Add an 'r' only if absolutely sure what you are doing)
#bwlimit limits bandwidth to 5000 kbytes/sec

 rsync -q --bwlimit=5000 $DIR1/* $TMP_DIR/$PBS_JOBID/
 rsync -rq --ignore-missing-args --bwlimit=5000 $DIR1/CONF* $TMP_DIR/$PBS_JOBID/
 rsync -q --bwlimit=5000 $DIR1/.* $TMP_DIR/$PBS_JOBID/
 cd $TMP_DIR/$PBS_JOBID

####################################################################################
#Gettimings
start=$(date +%s)
#####################################################################################
#jobs start here (if you have no idea what this script does, only edit this part...)

echo "Calculation from $(date)" >> RUNTIME
export PYTHONUNBUFFERED=1

censo -inp inputfile.xyz -P 7 -O 4 > censo.out

#end of job      (....and stop editing here.)
#####################################################################################
#Print timings to file
end=$(date +%s)
secs=$(expr $end - $start)
printf '%dh:%dm:%02ds\n' $(($secs/3600)) $(($secs%3600/60)) $(($secs%60)) >> RUNTIME
#####################################################################################
#copy everything back that is smaller than 5 gbytes

 rsync -rq --bwlimit=5000 --max-size=5G $TMP_DIR/$PBS_JOBID/* $DIR1/
 rsync -q --bwlimit=5000 --max-size=5G $TMP_DIR/$PBS_JOBID/.* $DIR1/

#to be safe, get mos alpha and beta seperately. 
#Note that the rsync syntax is strange; you need to first include everything, 
#then exclude the rest ("*" includes subdirectories)

 rsync -rq --bwlimit=5000 --include="*/" --include="mos" --include="alpha" --include="beta" --exclude=* $TMP_DIR/$PBS_JOBID/* $DIR1/

#if you want the large files as well, comment in the following

#rsync -r --bwlimit=1000 --min-size=5G $TMP_DIR/$PBS_JOBID/* $DIR1/

 cd $DIR1
 rm -r $TMP_DIR/$PBS_JOBID

PreviousCENSO NextCensorc keyword definitions

Last updated 4 years ago

#!/bin/bash # PBS Job #PBS -V #PBS -N JOB_NAME #PBS -m ae #PBS -q batch #PBS -l nodes=1:ppn=28 # cd $PBS_O_WORKDIR ### setup programs ## XTB export OMP_NUM_THREADS=1 export MKL_NUM_THREADS=1 ulimit -s unlimited export OMP_STACKSIZE=1000m ## TM export PARA_ARCH=SMP source /home/$USER/bin/.turbo751 export PARNODES=4 ## omp export TM_PAR_FORK=1 ### ORCA4.2.1 ORCAPATH="/tmp1/orca_4_2_1_linux_x86-64_openmpi216"; MPIPATH="/software/openmpi-2.1.5/bin"; MPILIB="/software/openmpi-2.1.5/lib64"; PATH=${ORCAPATH}:${MPIPATH}:$PATH LD_LIBRARY_PATH=${ORCAPATH}:${MPILIB}:$LD_LIBRARY_PATH LD_LIBRARY_PATH=/software/intel/parallel_studio_xe_2017.1/parallel_studio_xe_2017.4.056/compilers_and_libraries_2017/linux/compiler/lib/intel64_lin:$LD_LIBRARY_PATH LD_LIBRARY_PATH=/software/intel/parallel_studio_xe_2017/mkl/lib/intel64:$LD_LIBRARY_PATH export LD_LIBRARY_PATH ## PATH PATH=/home/$USER/bin:$PATH export PATH ### end programs + PATH export HOSTS_FILE=$PBS_NODEFILE cat $HOSTS_FILE>hosts_file TMP_DIR=/tmp1/$USER DIR1=$PWD mkdir -p $TMP_DIR/$PBS_JOBID #check file system access if [ ! -d $TMP_DIR/$PBS_JOBID ]; then echo "Unable to create $TMP_DIR/$PBS_JOBID on $HOSTNAME. Must stop." exit fi #check current location if [ "$PWD" == "$HOME" ]; then echo "Cowardly refusing to copy the whole home directory" exit fi #copy everything to node (will NOT copy directories for safety reasons. #Add an 'r' only if absolutely sure what you are doing) #bwlimit limits bandwidth to 5000 kbytes/sec rsync -q --bwlimit=5000 $DIR1/* $TMP_DIR/$PBS_JOBID/ rsync -rq --ignore-missing-args --bwlimit=5000 $DIR1/CONF* $TMP_DIR/$PBS_JOBID/ rsync -q --bwlimit=5000 $DIR1/.* $TMP_DIR/$PBS_JOBID/ cd $TMP_DIR/$PBS_JOBID #################################################################################### #Gettimings start=$(date +%s) ##################################################################################### #jobs start here (if you have no idea what this script does, only edit this part...) echo "Calculation from $(date)" >> RUNTIME export PYTHONUNBUFFERED=1 censo -inp inputfile.xyz -P 7 -O 4 > censo.out #end of job (....and stop editing here.) ##################################################################################### #Print timings to file end=$(date +%s) secs=$(expr $end - $start) printf '%dh:%dm:%02ds\n' $(($secs/3600)) $(($secs%3600/60)) $(($secs%60)) >> RUNTIME ##################################################################################### #copy everything back that is smaller than 5 gbytes rsync -rq --bwlimit=5000 --max-size=5G $TMP_DIR/$PBS_JOBID/* $DIR1/ rsync -q --bwlimit=5000 --max-size=5G $TMP_DIR/$PBS_JOBID/.* $DIR1/ #to be safe, get mos alpha and beta seperately. #Note that the rsync syntax is strange; you need to first include everything, #then exclude the rest ("*" includes subdirectories) rsync -rq --bwlimit=5000 --include="*/" --include="mos" --include="alpha" --include="beta" --exclude=* $TMP_DIR/$PBS_JOBID/* $DIR1/ #if you want the large files as well, comment in the following #rsync -r --bwlimit=1000 --min-size=5G $TMP_DIR/$PBS_JOBID/* $DIR1/ cd $DIR1 rm -r $TMP_DIR/$PBS_JOBID

hashtagSetting up CENSO

hashtagGet additional Information:

hashtagRequirements:

hashtagRun CENSO on a cluster:

Setting up CENSO

Get additional Information:

Requirements:

Run CENSO on a cluster: