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 u+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 see section 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:¶
Some information is already contained in censo and can be accessed by running:
$ 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 2021 |
| 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 2021 |
| 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¶
Note
CENSO interfaces to other codes (ORCA, TURBOMOLE, COSMOtherm). They are not part of CENSO!
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?
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.
Hint
CENSO can not be parallelized over several nodes!
Example job-submission script
#!/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
Hint
The program paths in your job-submission script have to be adjusted to your local environment