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.
$ censo -inp ensemble.xyz -part0 on -chrg 1 -solvent h2o > censo.out &
______________________________________________________________
| |
| |
| CENSO - Commandline ENSO |
| v 1.0.3 |
| 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.
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PARAMETERS
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The configuration file .censorc is read from /home/bohle/1projects/from_tmp1/CENSO/documentation-calcs/1-part0/.censorc.
Reading conformer rotamer ensemble from: /home/bohle/1projects/from_tmp1/CENSO/documentation-calcs/1-part0/ensemble.xyz.
Reading file: censo_solvents.json
--------------------------------------------------
CRE SORTING SETTINGS
--------------------------------------------------
number of atoms in system: 25
number of considered conformers: 22
number of all conformers from input: 22
charge: 1
unpaired: 0
solvent: h2o
temperature: 298.15
evaluate at different temperatures: on
temperature range: 273.15, 278.15, 283.15, 288.15, ...
calculate mRRHO contribution: on
consider symmetry for mRRHO contribution: off
cautious checking for error and failed calculations: on
checking the DFT-ensemble using CREST: off
maxthreads: 2
omp: 2
--------------------------------------------------
CRE CHEAP-PRESCREENING - PART0
--------------------------------------------------
part0: on
starting number of considered conformers: 22
program for part0: tm
functional for fast single-point: b97-d
basis set for fast single-point: def2-SV(P)
threshold g_thr(0) for sorting in part0: 4.0
Solvent model used with xTB: alpb
short-notation:
b97-d-D3/def2-SV(P) // GFNn-xTB (Input geometry)
END of parameters
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PATHS of external QM programs
------------------------------------------------------------
The following program paths are used:
xTB: /home/abt-grimme/AK-bin/xtb
TURBOMOLE: /home/abt-grimme/TURBOMOLE.7.5.1/bin/em64t-unknown-linux-gnu_smp
Using cefine from /home/bohle/bin/cefine
PARNODES for TM or COSMO-RS calculation was set to 2
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Processing data from previous run (enso.json)
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INFORMATION: No restart information exists and is created during this run!
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CRE CHEAP-PRESCREENING - PART0
----------------------------------------------------------------------------------------------------
program: tm
functional for part0: b97-d
basis set for part0: def2-SV(P)
threshold g_thr(0): 4.0
starting number of considered conformers: 22
Calculating efficient gas-phase single-point energies:
The efficient gas-phase single-point is calculated for:
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF7, CONF8, CONF9, CONF10, CONF11
CONF12, CONF13, CONF14, CONF15, CONF16, CONF17, CONF18, CONF19, CONF20, CONF21, CONF22
Constructed folders!
Starting 22 ALPB-Gsolv calculations
Running single-point in CONF1/part0_sp
Running single-point in CONF2/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF1/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF2/part0_sp
Running single-point in CONF3/part0_sp
Running single-point in CONF4/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF3/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF4/part0_sp
Running single-point in CONF5/part0_sp
Running single-point in CONF6/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF5/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF6/part0_sp
Running single-point in CONF7/part0_sp
Running single-point in CONF8/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF7/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF8/part0_sp
Running single-point in CONF9/part0_sp
Running single-point in CONF10/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF9/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF10/part0_sp
Running single-point in CONF11/part0_sp
Running single-point in CONF12/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF11/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF12/part0_sp
Running single-point in CONF13/part0_sp
Running single-point in CONF14/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF13/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF14/part0_sp
Running single-point in CONF15/part0_sp
Running single-point in CONF16/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF15/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF16/part0_sp
Running single-point in CONF17/part0_sp
Running single-point in CONF18/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF17/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF18/part0_sp
Running single-point in CONF19/part0_sp
Running single-point in CONF20/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF19/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF20/part0_sp
Running single-point in CONF21/part0_sp
Running single-point in CONF22/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF21/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF22/part0_sp
Tasks completed!
The efficient gas-phase single-point was successful for CONF1/part0_sp: E(DFT) = -496.55110270 Gsolv = -0.12279245
The efficient gas-phase single-point was successful for CONF2/part0_sp: E(DFT) = -496.55473079 Gsolv = -0.12241044
The efficient gas-phase single-point was successful for CONF3/part0_sp: E(DFT) = -496.55551554 Gsolv = -0.12099969
The efficient gas-phase single-point was successful for CONF4/part0_sp: E(DFT) = -496.55384665 Gsolv = -0.12156811
The efficient gas-phase single-point was successful for CONF5/part0_sp: E(DFT) = -496.55341065 Gsolv = -0.12251050
The efficient gas-phase single-point was successful for CONF6/part0_sp: E(DFT) = -496.55368828 Gsolv = -0.12175678
The efficient gas-phase single-point was successful for CONF7/part0_sp: E(DFT) = -496.54759208 Gsolv = -0.12365913
The efficient gas-phase single-point was successful for CONF8/part0_sp: E(DFT) = -496.55118920 Gsolv = -0.12200372
The efficient gas-phase single-point was successful for CONF9/part0_sp: E(DFT) = -496.54970422 Gsolv = -0.12167549
The efficient gas-phase single-point was successful for CONF10/part0_sp: E(DFT) = -496.55157272 Gsolv = -0.12001541
The efficient gas-phase single-point was successful for CONF11/part0_sp: E(DFT) = -496.54991969 Gsolv = -0.12296934
The efficient gas-phase single-point was successful for CONF12/part0_sp: E(DFT) = -496.55212770 Gsolv = -0.11751864
The efficient gas-phase single-point was successful for CONF13/part0_sp: E(DFT) = -496.55077718 Gsolv = -0.11854291
The efficient gas-phase single-point was successful for CONF14/part0_sp: E(DFT) = -496.55028792 Gsolv = -0.12090071
The efficient gas-phase single-point was successful for CONF15/part0_sp: E(DFT) = -496.54987374 Gsolv = -0.12311773
The efficient gas-phase single-point was successful for CONF16/part0_sp: E(DFT) = -496.55360018 Gsolv = -0.11274054
The efficient gas-phase single-point was successful for CONF17/part0_sp: E(DFT) = -496.55289531 Gsolv = -0.11378052
The efficient gas-phase single-point was successful for CONF18/part0_sp: E(DFT) = -496.50423172 Gsolv = -0.16468285
The efficient gas-phase single-point was successful for CONF19/part0_sp: E(DFT) = -496.52384365 Gsolv = -0.14390846
The efficient gas-phase single-point was successful for CONF20/part0_sp: E(DFT) = -496.50481476 Gsolv = -0.16519450
The efficient gas-phase single-point was successful for CONF21/part0_sp: E(DFT) = -496.53860751 Gsolv = -0.13212346
The efficient gas-phase single-point was successful for CONF22/part0_sp: E(DFT) = -496.50938650 Gsolv = -0.15826546
----------------------------------------------------------------------------------------------------
Removing high lying conformers by improved energy description
----------------------------------------------------------------------------------------------------
CONF# G [Eh] ΔG [kcal/mol] E [Eh] Gsolv [Eh] Gtot ΔE(DFT) ΔGsolv ΔGtot
GFN2-xTB GFN2-xTB b97-d-D3(0)/def2-SV(P) alpb [Eh] [kcal/mol] [kcal/mol] [kcal/mol]
[ALPB] [ALPB] [gfn2]
CONF1 -34.1746819 0.00 -496.5511027 -0.1227924 -496.6738951 2.28 -0.24 2.04
CONF2 -34.1743917 0.18 -496.5547308 -0.1224104 -496.6771412 0.00 0.00 0.00 <------
CONF3 -34.1742792 0.25 -496.5555155 -0.1209997 -496.6765152 -0.49 0.89 0.39
CONF4 -34.1739821 0.44 -496.5538467 -0.1215681 -496.6754148 0.55 0.53 1.08
CONF5 -34.1740224 0.41 -496.5534106 -0.1225105 -496.6759212 0.83 -0.06 0.77
CONF6 -34.1736309 0.66 -496.5536883 -0.1217568 -496.6754451 0.65 0.41 1.06
CONF7 -34.1725555 1.33 -496.5475921 -0.1236591 -496.6712512 4.48 -0.78 3.70
CONF8 -34.1721876 1.57 -496.5511892 -0.1220037 -496.6731929 2.22 0.26 2.48
CONF9 -34.1719439 1.72 -496.5497042 -0.1216755 -496.6713797 3.15 0.46 3.62
CONF10 -34.1714765 2.01 -496.5515727 -0.1200154 -496.6715881 1.98 1.50 3.48
CONF11 -34.1712638 2.14 -496.5499197 -0.1229693 -496.6728890 3.02 -0.35 2.67
CONF12 -34.1704841 2.63 -496.5521277 -0.1175186 -496.6696463 1.63 3.07 4.70
CONF13 -34.1703687 2.71 -496.5507772 -0.1185429 -496.6693201 2.48 2.43 4.91
CONF14 -34.1694191 3.30 -496.5502879 -0.1209007 -496.6711886 2.79 0.95 3.74
CONF15 -34.1691431 3.48 -496.5498737 -0.1231177 -496.6729915 3.05 -0.44 2.60
CONF16 -34.1664418 5.17 -496.5536002 -0.1127405 -496.6663407 0.71 6.07 6.78
CONF17 -34.1661652 5.34 -496.5528953 -0.1137805 -496.6666758 1.15 5.42 6.57
CONF18 -34.1660003 5.45 -496.5042317 -0.1646828 -496.6689146 31.69 -26.53 5.16
CONF19 -34.1664801 5.15 -496.5238437 -0.1439085 -496.6677521 19.38 -13.49 5.89
CONF20 -34.1658387 5.55 -496.5048148 -0.1651945 -496.6700093 31.32 -26.85 4.48
CONF21 -34.1670164 4.81 -496.5386075 -0.1321235 -496.6707310 10.12 -6.10 4.02
CONF22 -34.1656180 5.69 -496.5093865 -0.1582655 -496.6676520 28.45 -22.50 5.95
----------------------------------------------------------------------------------------------------
--------------------------------------------------
Conformers considered further
--------------------------------------------------
These conformers are below the 4.000 kcal/mol g_thr(0) threshold.
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF7, CONF8, CONF9, CONF10, CONF11
CONF14, CONF15
Calculating Boltzmann averaged (free) energy of ensemble on input geometries (not DFT optimized)!
temperature /K: avE(T) /a.u. avG(T) /a.u.
----------------------------------------------------------------------------------------------------
298.15 -496.5544580 -496.6764445 <<==part0==
----------------------------------------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>END of Part0<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Ran part0 in 32.8727 seconds
Part : #conf time
--------------------------------------------------
Input : 22 -
Part0_all : 13 32.87s
--------------------------------------------------
All parts : 32.87s
CENSO all done!$CENSO global configuration file: .censorc
$VERSION:1.0.3
ORCA: /home/USER/orca_4_2_1_linux_x86-64_openmpi216
ORCA version: 4.2.1
GFN-xTB: xtb
CREST: crest
mpshift: mpshift
escf: escf
#COSMO-RS
ctd = BP_TZVPD_FINE_C30_1601.ctd cdir = "/home/USER/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES" ldir = "/home/USER/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES"
cosmothermversion: 19
$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', 'chcl3', 'acetonitrile', 'ch2cl2', 'dmso', 'h2o', 'methanol', 'thf', '...']
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 # ['pbe', 'b97-d', 'pbeh-3c', 'tpss', 'b97-d3', 'r2scan-3c', 'b97-3c']
basis: automatic # ['automatic', 'def2-mSVP', 'def2-mTZVP', 'def2-mTZVP', 'def2-TZVP', '...']
maxthreads: 2 # ['number of threads e.g. 2']
omp: 2 # ['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: off # ['on', 'off']
func0: b97-d # ['pbeh-3c', 'b97-3c', 'b97-d3', 'pbe', 'r2scan-3c', 'tpss', 'b97-d']
basis0: def2-SV(P) # ['automatic', 'def2-mSVP', 'def2-mTZVP', 'def2-mTZVP', 'def2-TZVP', '...']
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: off # ['on', 'off']
smgsolv1: cosmors # ['alpb_gsolv', 'dcosmors', 'cosmo', 'smd', 'cosmors-fine', 'cpcm', 'gbsa_gsolv', '...']
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: off # ['on', 'off']
opt_limit: 2.5 # ['number e.g. 4.0']
sm2: dcosmors # ['cosmo', 'cpcm', 'default', 'smd', 'dcosmors']
smgsolv2: cosmors # ['cosmors-fine', 'gbsa_gsolv', 'cosmo', 'cpcm', 'smd_gsolv', 'alpb_gsolv', 'smd', '...']
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 # ['dsd-blyp', 'pw6b95', 'b97-d3', 'r2scan-3c', 'pbe0', 'wb97x']
basis3: def2-TZVPD # ['SVP', 'SV(P)', 'TZVP', 'TZVPP', 'QZVP', 'QZVPP', 'def2-SV(P)', 'def2-mSVP', '...']
smgsolv3: cosmors # ['alpb_gsolv', 'dcosmors', 'cosmo', 'smd', 'cosmors-fine', 'cpcm', 'gbsa_gsolv', '...']
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 # ['tpss', 'pbe0', 'pbeh-3c']
basisJ: def2-TZVP # ['SVP', 'SV(P)', 'TZVP', 'TZVPP', 'QZVP', 'QZVPP', 'def2-SV(P)', 'def2-mSVP', '...']
sm4J: default # ['dcosmors', 'smd', 'cosmo', 'cpcm']
shieldings: on # ['on', 'off']
progS: prog # ['tm', 'orca', 'adf', 'prog']
funcS: pbe0 # ['dsd-blyp', 'pbeh-3c', 'tpss', 'pbe0', 'kt2']
basisS: def2-TZVP # ['SVP', 'SV(P)', 'TZVP', 'TZVPP', 'QZVP', 'QZVPP', 'def2-SV(P)', 'def2-mSVP', '...']
sm4S: default # ['dcosmors', 'smd', 'cosmo', 'cpcm']
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
25
-34.15995484
O -2.7404108553 -0.9210263756 0.0505546155
O -0.6532148483 -1.7303331963 0.1381884568
N -2.1811530948 1.4662136641 -0.3280604715
N 1.9999042791 -1.6115147219 -0.1737452561
C 1.2832974514 1.7494376339 0.2478643443
C 0.0382242755 1.0547713107 0.8044626435
C 2.1972182535 0.8461961224 -0.5852172042
C -0.9624505804 0.6276788621 -0.2713633850
C 2.7304045776 -0.3664138808 0.1827513585
C -1.5037598584 -0.8390454546 0.0048901917
H 1.8561477225 2.1402514306 1.0892838382
H 0.9852377848 2.6009114549 -0.3642611073
H -0.4518270956 1.7282098745 1.5089809935
H 0.3322545004 0.1775252924 1.3825123935
H 1.6820235078 0.5059218506 -1.4832357051
H 3.0380251642 1.4546200515 -0.9165284484
H -0.4868586610 0.6089411942 -1.2530945560
H 2.6388482788 -0.2021893439 1.2562535001
H 3.7853986884 -0.5188774904 -0.0473087348
H -2.2380899515 2.1426216511 0.4407329422
H -2.3218532286 1.9466721688 -1.2205963738
H 2.3394829642 -2.3992859458 0.3882351555
H 0.9350292280 -1.5547588441 -0.0165809300
H 2.1475890354 -1.8368760327 -1.1636223077
H -2.9328940343 0.6971914121 -0.1921053926
25
-34.15944839
O -2.5910945174 -0.7526707388 0.4737473250
O -0.5258609320 -1.6055473558 0.4259946366
N -2.1883047577 1.2429283468 -0.9276187078
N 2.0221224751 -1.5482527990 -0.3635876013
C 1.0959612422 0.9269941773 1.0928268792
C -0.1118183900 1.5287127427 0.3646185610
C 2.3883955950 0.8232150730 0.2771806877
C -0.9137052232 0.5859776609 -0.5447048684
C 2.3984857923 -0.1999516224 -0.8542391926
C -1.3796771114 -0.7342464594 0.2052799197
H 0.8202702309 -0.0346561349 1.5230052762
H 1.3150554091 1.5881707649 1.9329336393
H 0.2252898792 2.3837647705 -0.2251981715
H -0.7970460540 1.8894152433 1.1356879771
H 2.6174364896 1.7989347868 -0.1517789136
H 3.1942064704 0.5825472961 0.9724285437
H -0.3499369029 0.3059081761 -1.4335569624
H 3.4048136146 -0.2402683769 -1.2749539435
H 1.7122153210 0.0852818535 -1.6492945642
H -2.2438155060 2.2226460139 -0.6308218074
H -2.4094139539 1.1700691932 -1.9248068681
H 0.9927667520 -1.5675551657 -0.0428313977
H 2.1377830502 -2.2542373686 -1.0973459319
H 2.6054467969 -1.8083924261 0.4393088723
H -2.8796747565 0.6310313638 -0.3580585669
25
-34.15925304
O -2.6152400314 -1.0465052003 0.2378304729
O -0.5362082855 -1.4663149505 -0.4593671015
N -2.4557715395 1.4039918868 0.4362491058
N 2.1447268012 -1.5911295291 -0.0908488427
C 1.1849792140 1.1291603967 -0.7123125066
C 0.0549239500 1.3190958463 0.3109988160
C 2.5516538580 0.8614163999 -0.0796419105
C -1.2770304521 0.8481909298 -0.2699298296
C 2.6278492228 -0.4408272994 0.7143702153
C -1.4798499370 -0.7275247362 -0.1594413730
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C 2.0807266384 0.5903317386 -0.0312863938
C -1.4336452672 0.8124987799 -0.5833640723
C 2.0372506913 -0.6914975753 0.8153963432
C -1.1077721831 -0.6712596326 -0.1784565029
H 0.4772061571 1.3762504059 1.1769048440
H 1.3491352329 2.5796760629 0.2516191005
H 0.2519128515 1.1866703660 -1.8221067218
H -0.4443786804 2.6264492546 -1.1098247151
H 2.1069094344 0.3214704229 -1.0870338715
H 3.0133169149 1.1098047495 0.1839278312
H -2.0690635873 0.7917157945 -1.4696202320
H 1.1994207751 -0.6693189818 1.5132782369
H 2.9569334194 -0.7921592267 1.3922309558
H -1.6800036187 2.1679532791 1.0053931771
H -3.1334683512 1.6233161070 0.3791665015
H 2.6232513605 -1.9579134554 -0.7362257317
H 1.8912989959 -2.7525757838 0.5392212719
H 0.9273933706 -1.8444066710 -0.5257136187
H -2.1333692549 0.5050567581 1.2388793063
25
-34.15102491
O -2.7007099152 -1.6852260154 -0.4665848832
O -3.5578446821 0.0350414384 0.6950996250
N -1.7249631955 1.6316108345 0.4298941943
N 4.8503432460 -0.2765578553 0.0049566510
C 1.1047501969 0.4501828237 -0.3379055216
C -0.1445140391 -0.2886936630 0.1459845288
C 2.3741940866 -0.2828979224 0.0965187068
C -1.4339016427 0.3793165613 -0.3028003047
C 3.6160850376 0.4539254738 -0.3951671902
C -2.6934727541 -0.5488189533 -0.0039847520
H 1.1202182595 1.4641232269 0.0631636060
H 1.0744507790 0.5160807326 -1.4261342120
H -0.1466884742 -0.3764861277 1.2347858649
H -0.1614173698 -1.3033571375 -0.2567289346
H 2.3826839006 -0.3550960319 1.1849100754
H 2.3458274825 -1.2937888279 -0.3120785959
H -1.4193517541 0.5529473168 -1.3796978179
H 3.6476836700 1.4575725004 0.0303995802
H 3.5908364898 0.5356651831 -1.4823627548
H -1.7888195298 2.4639789876 -0.1581990321
H -2.7206446817 1.3385249836 0.8116492773
H 5.6915565940 0.2174183391 -0.3259194480
H 4.8962264202 -0.3605243899 1.0314916029
H 4.8443782262 -1.2261178281 -0.3963638456
H -1.0847775954 1.7904079765 1.2125175138
25
-34.15096274
O -3.0664396656 -0.6811514259 0.4732552569
O -1.1830540829 -1.6357953168 -0.2743493731
N -2.5677177347 1.6455787239 -0.0357930901
N 3.4161836207 -1.4947231742 0.0043983586
C 1.0526738400 0.4198619079 -0.3271341828
C -0.1392962419 1.1756334823 0.2601668795
C 2.3301787116 0.6870764296 0.4694516416
C -1.4374925629 0.7826136622 -0.4432938226
C 3.5433351448 -0.0155439223 -0.1263696890
C -1.9232732343 -0.6849210780 -0.0466890927
H 1.1914397265 0.7321338619 -1.3635085567
H 0.7858921189 -0.6373779302 -0.3204311762
H 0.0218209785 2.2505182304 0.1468292069
H -0.2266241551 0.9455046686 1.3247226359
H 2.5278796928 1.7590277621 0.4727119199
H 2.1882724928 0.3782271446 1.5058219746
H -1.3025118280 0.8032883597 -1.5259809861
H 4.4479425383 0.3027435209 0.3921583620
H 3.6346463266 0.2349775607 -1.1836334244
H -3.0211573542 2.1410074345 -0.8045922540
H -3.2218629847 0.8371482423 0.3587042034
H 4.2253281871 -1.9726822174 -0.4155872948
H 3.3489651634 -1.7581308116 0.9983748528
H 2.5570336567 -1.8144640232 -0.4679619280
H -2.3203269015 2.3008181314 0.7098687755
25
-34.15085064
O -3.5353488917 0.0322108098 0.4084906022
O -2.4254579214 -1.9084093375 0.6284254091
N -1.7744403653 1.3652775888 -0.6438663864
N 4.1843308757 -0.1227935311 -1.0149931633
C 1.2054477125 0.3338345853 -0.2573250215
C -0.0723683835 -0.0922253390 0.4701395235
C 2.4067626747 0.2476116899 0.6871054133
C -1.3095998224 -0.0201188789 -0.4106994862
C 3.6989393857 0.7735207317 0.0732627710
C -2.5481677099 -0.7347193516 0.2919952398
H 1.1039179513 1.3593179418 -0.6150772671
H 1.3305507433 -0.3269971917 -1.1156830038
H -0.2323641779 0.5179203592 1.3619095074
H 0.0148258366 -1.1272987239 0.8068454593
H 2.1939049448 0.8432977651 1.5748900270
H 2.5356727482 -0.7824695024 1.0211816116
H -1.1430786561 -0.5391980852 -1.3555500184
H 4.4681954117 0.8303339300 0.8434799998
H 3.5410323285 1.7707403176 -0.3387001734
H -2.7959421798 1.2370421526 -0.2418926774
H -1.2663143192 2.0543977636 -0.0827359543
H 4.3101055621 -1.0795234870 -0.6518667702
H 3.4997443822 -0.1538144186 -1.7841531054
H 5.0842467659 0.2120203831 -1.3873716549
H -1.8037773550 1.6476905491 -1.6249441216
25
-34.15048917
O -1.9774584219 -0.8822136242 -1.3447844876
O -0.7353222350 -1.3040874260 0.4712779300
N -1.2018711229 0.8204001109 1.6759883927
N 1.9464051556 -1.6923491374 0.3496868798
C 0.8058411616 1.0462579377 -0.9468506072
C -0.4754178942 1.7785998054 -0.5275051890
C 1.8226970853 0.7789686777 0.1752315710
C -1.5019161161 0.9155320919 0.2220611780
C 2.6576744598 -0.4659344426 -0.1177787426
C -1.4255171488 -0.5796126398 -0.2987743324
H 1.2927227489 1.6467822241 -1.7161034319
H 0.5115436171 0.1136959367 -1.4299162738
H -0.9626535770 2.1244807715 -1.4395462399
H -0.2313854006 2.6631384020 0.0636669169
H 2.4836824282 1.6401220787 0.2631946203
H 1.3379895832 0.6415415675 1.1385387246
H -2.5044279955 1.3042479639 0.0511624497
H 3.6220420553 -0.4105315490 0.3870533340
H 2.8346807725 -0.5412209492 -1.1903941633
H -0.5537202797 1.5469435382 2.0029686770
H -2.0510266978 0.8448716653 2.2497725116
H 0.8939724574 -1.6086997720 0.2334441992
H 2.2630899289 -2.5235198565 -0.1606712473
H 2.1155048181 -1.8450780227 1.3513380594
H -0.7798223195 -0.1709536166 1.7101046448
25
-34.15043307
O -3.3078583007 -0.3518099727 0.5480566241
O -1.8441149941 -2.0073969491 0.1397595703
N -1.9672328473 1.5403727742 -0.2372000800
N 3.6044925126 -0.8358440764 -0.6659647320
C 1.1684565146 1.0446332415 -0.4943940738
C 0.1082467096 0.2177955398 0.2395309885
C 2.4785715426 1.1657908669 0.2896724500
C -1.2458520269 0.2676289576 -0.4513144135
C 3.1696429470 -0.1592315605 0.5890169973
C -2.2263428078 -0.8414226742 0.1422529421
H 0.7932826990 2.0569151989 -0.6482792542
H 1.3354698371 0.6191303209 -1.4843783659
H -0.0031461344 0.5661490514 1.2686433794
H 0.3791631733 -0.8378892566 0.2841197320
H 3.1579098277 1.8188328559 -0.2597110183
H 2.2713923792 1.6478155935 1.2450536588
H -1.1432114953 0.0569418065 -1.5170262136
H 2.5004236326 -0.8240708177 1.1341470919
H 4.0493855213 0.0280822082 1.2049984895
H -1.5070190112 2.1488324010 0.4454597884
H -2.1837208522 2.0584218679 -1.0901715209
H 4.2094106392 -0.2068158824 -1.2153183037
H 4.1256865653 -1.6973771969 -0.4514692989
H 2.7834959501 -1.0854874671 -1.2358687369
H -2.8845837684 1.1083956166 0.2016053653
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)
$ censo -inp ensemble.xyz -part1 on -chrg 1 -solvent chcl3 -smgsolv1 cosmors -func r2scan-3c -basis automatic -P 4 -O 2 > censo.out &
______________________________________________________________
| |
| |
| CENSO - Commandline ENSO |
| v 1.0.3 |
| 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.
----------------------------------------------------------------------------------------------------
PARAMETERS
----------------------------------------------------------------------------------------------------
The configuration file .censorc is read from /home/bohle/1projects/from_tmp1/CENSO/documentation-calcs/2-part1/.censorc.
Reading conformer rotamer ensemble from: /home/bohle/1projects/from_tmp1/CENSO/documentation-calcs/2-part1/ensemble.xyz.
Reading file: censo_solvents.json
--------------------------------------------------
CRE SORTING SETTINGS
--------------------------------------------------
number of atoms in system: 25
number of considered conformers: 22
number of all conformers from input: 22
charge: 1
unpaired: 0
solvent: chcl3
temperature: 298.15
evaluate at different temperatures: on
temperature range: 273.15, 278.15, 283.15, 288.15, ...
calculate mRRHO contribution: on
consider symmetry for mRRHO contribution: off
cautious checking for error and failed calculations: on
checking the DFT-ensemble using CREST: off
maxthreads: 4
omp: 2
--------------------------------------------------
CRE PRESCREENING - PART1
--------------------------------------------------
part1: on
starting number of considered conformers: 22
program for part1: tm
functional for initial evaluation: r2scan-3c
basis set for initial evaluation: def2-mTZVPP
calculate mRRHO contribution: on
program for mRRHO contribution: xtb
GFN version for mRRHO and/or GBSA_Gsolv: gfn2
Apply constraint to input geometry during mRRHO calculation: on
solvent model applied with xTB: alpb
evaluate at different temperatures: off
threshold g_thr(1) and G_thr(1) for sorting in part1: 3.5
solvent model for Gsolv contribution of part1: cosmors
short-notation:
r2scan-3c + COSMORS[chcl3] + GmRRHO(GFN2[alpb]-bhess) // GFNn-xTB (Input geometry)
END of parameters
------------------------------------------------------------
PATHS of external QM programs
------------------------------------------------------------
The following program paths are used:
xTB: /home/abt-grimme/AK-bin/xtb
TURBOMOLE: /home/abt-grimme/TURBOMOLE.7.5.1/bin/em64t-unknown-linux-gnu_smp
Setup of COSMO-RS:
ctd = BP_TZVPD_FINE_C30_1601.ctd
cdir = "/home/bohle/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES"
ldir = "/home/bohle/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES"
Using /home/bohle/COSMOlogic/COSMOthermX19/COSMOtherm/DATABASE-COSMO/BP-TZVP-COSMO
as path to the COSMO-RS NORMAL DATABASE.
Using cefine from /home/bohle/bin/cefine
PARNODES for TM or COSMO-RS calculation was set to 2
Using COSMOtherm from /home/bohle/COSMOlogic/COSMOthermX19/COSMOtherm/BIN-LINUX/cosmotherm
----------------------------------------------------------------------------------------------------
Processing data from previous run (enso.json)
----------------------------------------------------------------------------------------------------
INFORMATION: No restart information exists and is created during this run!
----------------------------------------------------------------------------------------------------
CRE PRESCREENING - PART1
----------------------------------------------------------------------------------------------------
program: tm
functional for part1 and 2: r2scan-3c
basis set for part1 and 2: def2-mTZVPP
Solvent: chcl3
solvent model for Gsolv contribution: cosmors
threshold g_thr(1) and G_thr(1): 3.5
starting number of considered conformers: 22
calculate mRRHO contribution: on
program for mRRHO contribution: xtb
GFN version for mRRHO and/or GBSA_Gsolv: gfn2
Apply constraint to input geometry during mRRHO calculation: on
temperature: 298.15
Calculating single-point energies and solvation contribution (G_solv):
The prescreening COSMO-RS is calculated for:
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF7, CONF8, CONF9, CONF10, CONF11
CONF12, CONF13, CONF14, CONF15, CONF16, CONF17, CONF18, CONF19, CONF20, CONF21, CONF22
Constructed folders!
Constructed folders!
Starting 22 COSMO-RS-Gsolv calculations.
Running COSMO-RS calculation in CONF1/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF2/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF3/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF4/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF5/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF6/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF7/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF8/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF9/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF10/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF11/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF12/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF13/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF14/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF15/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF16/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF17/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF18/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF19/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF20/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF21/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF22/r2scan-3c/COSMO
Tasks completed!
prescreening COSMO-RS calculation was successful for CONF1/r2scan-3c/COSMO: -0.09391084
prescreening COSMO-RS calculation was successful for CONF2/r2scan-3c/COSMO: -0.09344716
prescreening COSMO-RS calculation was successful for CONF3/r2scan-3c/COSMO: -0.09189166
prescreening COSMO-RS calculation was successful for CONF4/r2scan-3c/COSMO: -0.09269361
prescreening COSMO-RS calculation was successful for CONF5/r2scan-3c/COSMO: -0.09328873
prescreening COSMO-RS calculation was successful for CONF6/r2scan-3c/COSMO: -0.09278491
prescreening COSMO-RS calculation was successful for CONF7/r2scan-3c/COSMO: -0.09457155
prescreening COSMO-RS calculation was successful for CONF8/r2scan-3c/COSMO: -0.09275254
prescreening COSMO-RS calculation was successful for CONF9/r2scan-3c/COSMO: -0.09316162
prescreening COSMO-RS calculation was successful for CONF10/r2scan-3c/COSMO: -0.09116989
prescreening COSMO-RS calculation was successful for CONF11/r2scan-3c/COSMO: -0.09348580
prescreening COSMO-RS calculation was successful for CONF12/r2scan-3c/COSMO: -0.08900263
prescreening COSMO-RS calculation was successful for CONF13/r2scan-3c/COSMO: -0.08998048
prescreening COSMO-RS calculation was successful for CONF14/r2scan-3c/COSMO: -0.09122770
prescreening COSMO-RS calculation was successful for CONF15/r2scan-3c/COSMO: -0.09272288
prescreening COSMO-RS calculation was successful for CONF16/r2scan-3c/COSMO: -0.08509833
prescreening COSMO-RS calculation was successful for CONF17/r2scan-3c/COSMO: -0.08598277
prescreening COSMO-RS calculation was successful for CONF18/r2scan-3c/COSMO: -0.13224220
prescreening COSMO-RS calculation was successful for CONF19/r2scan-3c/COSMO: -0.11057302
prescreening COSMO-RS calculation was successful for CONF20/r2scan-3c/COSMO: -0.13223689
prescreening COSMO-RS calculation was successful for CONF21/r2scan-3c/COSMO: -0.09915029
prescreening COSMO-RS calculation was successful for CONF22/r2scan-3c/COSMO: -0.12536341
--------------------------------------------------
Removing high lying conformers
--------------------------------------------------
CONF# E(GFNn-xTB) ΔE(GFNn-xTB) E [Eh] Gsolv [Eh] Gtot ΔGtot
[a.u.] [kcal/mol] r2scan-3c COSMO-RS-normal [Eh] [kcal/mol]
[r2scan-3c]
CONF1 -34.1599548 0.00 -497.3021467 -0.0939108 -497.3960575 1.82
CONF2 -34.1594484 0.32 -497.3049956 -0.0934472 -497.3984428 0.33
CONF3 -34.1592530 0.44 -497.3064930 -0.0918917 -497.3983847 0.36
CONF4 -34.1590954 0.54 -497.3049058 -0.0926936 -497.3975994 0.86
CONF5 -34.1589250 0.65 -497.3056747 -0.0932887 -497.3989634 0.00 <------
CONF6 -34.1587465 0.76 -497.3049670 -0.0927849 -497.3977519 0.76
CONF7 -34.1578065 1.35 -497.2983644 -0.0945716 -497.3929360 3.78
CONF8 -34.1571241 1.78 -497.3029570 -0.0927525 -497.3957096 2.04
CONF9 -34.1570372 1.83 -497.3008248 -0.0931616 -497.3939864 3.12
CONF10 -34.1563217 2.28 -497.3038986 -0.0911699 -497.3950685 2.44
CONF11 -34.1559251 2.53 -497.3008250 -0.0934858 -497.3943108 2.92
CONF12 -34.1554750 2.81 -497.3045828 -0.0890026 -497.3935854 3.37
CONF13 -34.1554585 2.82 -497.3036749 -0.0899805 -497.3936554 3.33
CONF14 -34.1537285 3.91 -497.3022176 -0.0912277 -497.3934453 3.46
CONF15 -34.1529637 4.39 -497.3009381 -0.0927229 -497.3936610 3.33
CONF16 -34.1514138 5.36 -497.3063638 -0.0850983 -497.3914621 4.71
CONF17 -34.1512255 5.48 -497.3047147 -0.0859828 -497.3906975 5.19
CONF18 -34.1510249 5.60 -497.2564102 -0.1322422 -497.3886524 6.47
CONF19 -34.1509627 5.64 -497.2746319 -0.1105730 -497.3852050 8.63
CONF20 -34.1508506 5.71 -497.2550494 -0.1322369 -497.3872863 7.33
CONF21 -34.1504892 5.94 -497.2896633 -0.0991503 -497.3888135 6.37
CONF22 -34.1504331 5.98 -497.2596139 -0.1253634 -497.3849773 8.78
--------------------------------------------------
Conformers considered further
--------------------------------------------------
Below the g_thr(1) threshold of 3.5 kcal/mol.
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF8, CONF9, CONF10, CONF11, CONF12
CONF13, CONF14, CONF15
--------------------------------------------------
Calculating prescreening G_mRRHO with implicit solvation!
The prescreening G_mRRHO calculation is now performed for:
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF8, CONF9, CONF10, CONF11, CONF12
CONF13, CONF14, CONF15
Constructed folders!
Starting 14 G_RRHO calculations.
Running GFN2-xTB mRRHO in CONF1/rrho_part1
Running GFN2-xTB mRRHO in CONF2/rrho_part1
Running GFN2-xTB mRRHO in CONF3/rrho_part1
Running GFN2-xTB mRRHO in CONF4/rrho_part1
Running GFN2-xTB mRRHO in CONF5/rrho_part1
Running GFN2-xTB mRRHO in CONF6/rrho_part1
Running GFN2-xTB mRRHO in CONF8/rrho_part1
Running GFN2-xTB mRRHO in CONF9/rrho_part1
Running GFN2-xTB mRRHO in CONF10/rrho_part1
Running GFN2-xTB mRRHO in CONF11/rrho_part1
Running GFN2-xTB mRRHO in CONF12/rrho_part1
Running GFN2-xTB mRRHO in CONF13/rrho_part1
Running GFN2-xTB mRRHO in CONF14/rrho_part1
Running GFN2-xTB mRRHO in CONF15/rrho_part1
Tasks completed!
The prescreening G_mRRHO calculation @ c1 was successful for CONF1/rrho_part1: 0.18236493
The prescreening G_mRRHO calculation @ c1 was successful for CONF2/rrho_part1: 0.18246714
The prescreening G_mRRHO calculation @ c1 was successful for CONF3/rrho_part1: 0.18235782
The prescreening G_mRRHO calculation @ c1 was successful for CONF4/rrho_part1: 0.18239049
The prescreening G_mRRHO calculation @ c1 was successful for CONF5/rrho_part1: 0.18241907
The prescreening G_mRRHO calculation @ c1 was successful for CONF6/rrho_part1: 0.18225430
The prescreening G_mRRHO calculation @ c1 was successful for CONF8/rrho_part1: 0.18193879
The prescreening G_mRRHO calculation @ c1 was successful for CONF9/rrho_part1: 0.18214342
The prescreening G_mRRHO calculation @ c1 was successful for CONF10/rrho_part1: 0.18217367
The prescreening G_mRRHO calculation @ c1 was successful for CONF11/rrho_part1: 0.18267361
The prescreening G_mRRHO calculation @ c1 was successful for CONF12/rrho_part1: 0.18167483
The prescreening G_mRRHO calculation @ c1 was successful for CONF13/rrho_part1: 0.18145764
The prescreening G_mRRHO calculation @ c1 was successful for CONF14/rrho_part1: 0.18268845
The prescreening G_mRRHO calculation @ c1 was successful for CONF15/rrho_part1: 0.18320604
--------------------------------------------------
* Gibbs free energies of part1 *
--------------------------------------------------
CONF# G(GFNn-xTB) ΔG(GFNn-xTB) E [Eh] Gsolv [Eh] GmRRHO [Eh] Gtot ΔGtot
[a.u.] [kcal/mol] r2scan-3c COSMO-RS-normal GFN2 [Eh] [kcal/mol]
[r2scan-3c] [alpb]-bhess
CONF1 -33.9775899 0.00 -497.3021467 -0.0939108 0.1823649 -497.2136926 1.79
CONF2 -33.9769813 0.38 -497.3049956 -0.0934472 0.1824671 -497.2159757 0.36
CONF3 -33.9768952 0.44 -497.3064930 -0.0918917 0.1823578 -497.2160268 0.32
CONF4 -33.9767049 0.56 -497.3049058 -0.0926936 0.1823905 -497.2152089 0.84
CONF5 -33.9765060 0.68 -497.3056747 -0.0932887 0.1824191 -497.2165444 0.00 <------
CONF6 -33.9764922 0.69 -497.3049670 -0.0927849 0.1822543 -497.2154976 0.66
CONF8 -33.9751853 1.51 -497.3029570 -0.0927525 0.1819388 -497.2137708 1.74
CONF9 -33.9748938 1.69 -497.3008248 -0.0931616 0.1821434 -497.2118430 2.95
CONF10 -33.9741480 2.16 -497.3038986 -0.0911699 0.1821737 -497.2128948 2.29
CONF11 -33.9732515 2.72 -497.3008250 -0.0934858 0.1826736 -497.2116372 3.08
CONF12 -33.9738002 2.38 -497.3045828 -0.0890026 0.1816748 -497.2119106 2.91
CONF13 -33.9740008 2.25 -497.3036749 -0.0899805 0.1814576 -497.2121977 2.73
CONF14 -33.9710400 4.11 -497.3022176 -0.0912277 0.1826885 -497.2107568 3.63
CONF15 -33.9697576 4.91 -497.3009381 -0.0927229 0.1832060 -497.2104549 3.82
Additional global 'fuzzy-threshold' based on the standard deviation of (G_mRRHO):
Std_dev(G_mRRHO) = 0.272 kcal/mol
Fuzzythreshold = 0.309 kcal/mol
Final sorting threshold G_thr(1) = 3.500 + 0.309 = 3.809 kcal/mol
Spearman correlation coefficient between (E + Solv) and (E + Solv + mRRHO) = 0.908
--------------------------------------------------
Conformers considered further
--------------------------------------------------
Considered CONF14 because of increased fuzzythr.
These conformers are below the 3.809 kcal/mol G_thr(1) threshold.
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF8, CONF9, CONF10, CONF11, CONF12
CONF13, CONF14
Calculating Boltzmann averaged free energy of ensemble on input geometries (not DFT optimized)!
temperature /K: avE(T) /a.u. avGmRRHO(T) /a.u. avGsolv(T) /a.u. avG(T) /a.u.
----------------------------------------------------------------------------------------------------
298.15 -497.3054054 0.1823775 -0.0928881 -497.2159160 <<==part1==
----------------------------------------------------------------------------------------------------
Calculating unbiased GFNn-xTB energy
Constructed folders!
Starting 13 xTB - single-point calculations.
gfn2-xTB energy for CONF1/GFN_unbiased = -34.1515395
gfn2-xTB energy for CONF2/GFN_unbiased = -34.1509941
gfn2-xTB energy for CONF3/GFN_unbiased = -34.1515326
gfn2-xTB energy for CONF4/GFN_unbiased = -34.1508491
gfn2-xTB energy for CONF5/GFN_unbiased = -34.1514366
gfn2-xTB energy for CONF6/GFN_unbiased = -34.1512893
gfn2-xTB energy for CONF8/GFN_unbiased = -34.1493072
gfn2-xTB energy for CONF9/GFN_unbiased = -34.1491025
gfn2-xTB energy for CONF10/GFN_unbiased = -34.1491972
gfn2-xTB energy for CONF11/GFN_unbiased = -34.1487085
gfn2-xTB energy for CONF12/GFN_unbiased = -34.1484725
gfn2-xTB energy for CONF13/GFN_unbiased = -34.1480733
gfn2-xTB energy for CONF14/GFN_unbiased = -34.1461266
Tasks completed!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>END of Part1<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Ran part1 in 277.0194 seconds
Part : #conf time
--------------------------------------------------
Input : 22 -
Part1_initial_sort : 14 -
Part1_all : 14 277.02s
--------------------------------------------------
All parts : 277.02s
CENSO all done!
$CENSO global configuration file: .censorc
$VERSION:1.0.3
ORCA: /home/USER/orca_4_2_1_linux_x86-64_openmpi216
ORCA version: 4.2.1
GFN-xTB: xtb
CREST: crest
mpshift: mpshift
escf: escf
#COSMO-RS
ctd = BP_TZVPD_FINE_C30_1601.ctd cdir = "/home/USER/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES" ldir = "/home/USER/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES"
cosmothermversion: 19
$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', 'chcl3', 'acetonitrile', 'ch2cl2', 'dmso', 'h2o', 'methanol', 'thf', '...']
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 # ['pbe', 'b97-d', 'pbeh-3c', 'tpss', 'b97-d3', 'r2scan-3c', 'b97-3c']
basis: automatic # ['automatic', 'def2-mSVP', 'def2-mTZVP', 'def2-mTZVP', 'def2-TZVP', '...']
maxthreads: 2 # ['number of threads e.g. 2']
omp: 2 # ['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: off # ['on', 'off']
func0: b97-d # ['pbeh-3c', 'b97-3c', 'b97-d3', 'pbe', 'r2scan-3c', 'tpss', 'b97-d']
basis0: def2-SV(P) # ['automatic', 'def2-mSVP', 'def2-mTZVP', 'def2-mTZVP', 'def2-TZVP', '...']
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: off # ['on', 'off']
smgsolv1: cosmors # ['alpb_gsolv', 'dcosmors', 'cosmo', 'smd', 'cosmors-fine', 'cpcm', 'gbsa_gsolv', '...']
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: off # ['on', 'off']
opt_limit: 2.5 # ['number e.g. 4.0']
sm2: dcosmors # ['cosmo', 'cpcm', 'default', 'smd', 'dcosmors']
smgsolv2: cosmors # ['cosmors-fine', 'gbsa_gsolv', 'cosmo', 'cpcm', 'smd_gsolv', 'alpb_gsolv', 'smd', '...']
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 # ['dsd-blyp', 'pw6b95', 'b97-d3', 'r2scan-3c', 'pbe0', 'wb97x']
basis3: def2-TZVPD # ['SVP', 'SV(P)', 'TZVP', 'TZVPP', 'QZVP', 'QZVPP', 'def2-SV(P)', 'def2-mSVP', '...']
smgsolv3: cosmors # ['alpb_gsolv', 'dcosmors', 'cosmo', 'smd', 'cosmors-fine', 'cpcm', 'gbsa_gsolv', '...']
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 # ['tpss', 'pbe0', 'pbeh-3c']
basisJ: def2-TZVP # ['SVP', 'SV(P)', 'TZVP', 'TZVPP', 'QZVP', 'QZVPP', 'def2-SV(P)', 'def2-mSVP', '...']
sm4J: default # ['dcosmors', 'smd', 'cosmo', 'cpcm']
shieldings: on # ['on', 'off']
progS: prog # ['tm', 'orca', 'adf', 'prog']
funcS: pbe0 # ['dsd-blyp', 'pbeh-3c', 'tpss', 'pbe0', 'kt2']
basisS: def2-TZVP # ['SVP', 'SV(P)', 'TZVP', 'TZVPP', 'QZVP', 'QZVPP', 'def2-SV(P)', 'def2-mSVP', '...']
sm4S: default # ['dcosmors', 'smd', 'cosmo', 'cpcm']
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
25
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25
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25
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N -1.9672328473 1.5403727742 -0.2372000800
N 3.6044925126 -0.8358440764 -0.6659647320
C 1.1684565146 1.0446332415 -0.4943940738
C 0.1082467096 0.2177955398 0.2395309885
C 2.4785715426 1.1657908669 0.2896724500
C -1.2458520269 0.2676289576 -0.4513144135
C 3.1696429470 -0.1592315605 0.5890169973
C -2.2263428078 -0.8414226742 0.1422529421
H 0.7932826990 2.0569151989 -0.6482792542
H 1.3354698371 0.6191303209 -1.4843783659
H -0.0031461344 0.5661490514 1.2686433794
H 0.3791631733 -0.8378892566 0.2841197320
H 3.1579098277 1.8188328559 -0.2597110183
H 2.2713923792 1.6478155935 1.2450536588
H -1.1432114953 0.0569418065 -1.5170262136
H 2.5004236326 -0.8240708177 1.1341470919
H 4.0493855213 0.0280822082 1.2049984895
H -1.5070190112 2.1488324010 0.4454597884
H -2.1837208522 2.0584218679 -1.0901715209
H 4.2094106392 -0.2068158824 -1.2153183037
H 4.1256865653 -1.6973771969 -0.4514692989
H 2.7834959501 -1.0854874671 -1.2358687369
H -2.8845837684 1.1083956166 0.2016053653
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
$ censo -inp ensemble.xyz -inprc /path/to/.censorc > censo.out &
______________________________________________________________
| |
| |
| CENSO - Commandline ENSO |
| v 1.0.3 |
| 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.
----------------------------------------------------------------------------------------------------
PARAMETERS
----------------------------------------------------------------------------------------------------
The configuration file .censorc is read from /home/bohle/1projects/from_tmp1/CENSO/documentation-calcs/3-part0-2/.censorc.
Reading conformer rotamer ensemble from: /home/bohle/1projects/from_tmp1/CENSO/documentation-calcs/3-part0-2/ensemble.xyz.
Reading file: censo_solvents.json
--------------------------------------------------
CRE SORTING SETTINGS
--------------------------------------------------
number of atoms in system: 25
number of considered conformers: 22
number of all conformers from input: 22
charge: 1
unpaired: 0
solvent: h2o
temperature: 298.15
evaluate at different temperatures: on
temperature range: 273.15, 278.15, 283.15, 288.15, ...
calculate mRRHO contribution: on
consider symmetry for mRRHO contribution: off
cautious checking for error and failed calculations: on
checking the DFT-ensemble using CREST: off
maxthreads: 4
omp: 2
--------------------------------------------------
CRE CHEAP-PRESCREENING - PART0
--------------------------------------------------
part0: on
starting number of considered conformers: 22
program for part0: tm
functional for fast single-point: b97-d
basis set for fast single-point: def2-SV(P)
threshold g_thr(0) for sorting in part0: 4.0
Solvent model used with xTB: alpb
short-notation:
b97-d-D3/def2-SV(P) // GFNn-xTB (Input geometry)
--------------------------------------------------
CRE PRESCREENING - PART1
--------------------------------------------------
part1: on
starting number of considered conformers: 22
program for part1: tm
functional for initial evaluation: r2scan-3c
basis set for initial evaluation: def2-mTZVPP
calculate mRRHO contribution: on
program for mRRHO contribution: xtb
GFN version for mRRHO and/or GBSA_Gsolv: gfn2
Apply constraint to input geometry during mRRHO calculation: on
solvent model applied with xTB: alpb
evaluate at different temperatures: off
threshold g_thr(1) and G_thr(1) for sorting in part1: 3.5
solvent model for Gsolv contribution of part1: cosmors
short-notation:
r2scan-3c + COSMORS[h2o] + GmRRHO(GFN2[alpb]-bhess) // GFNn-xTB (Input geometry)
--------------------------------------------------
CRE OPTIMIZATION - PART2
--------------------------------------------------
part2: on
program: tm
functional for part2: r2scan-3c
basis set for part2: def2-mTZVPP
using xTB-optimizer for optimization: on
using the new ensemble optimizer: on
optimize all conformers below this G_thr(opt,2) threshold: 2.5
spearmanthr: 0.935
optimization level in part2: lax
solvent model applied in the optimization: dcosmors
solvent model for Gsolv contribution: cosmors
evaluate at different temperatures: on
Boltzmann sum threshold G_thr(2) for sorting in part2: 99.0
calculate mRRHO contribution: on
program for mRRHO contribution: xtb
GFN version for mRRHO and/or GBSA_Gsolv: gfn2
Apply constraint to input geometry during mRRHO calculation: on
solvent model applied with xTB: alpb
short-notation:
r2scan-3c + COSMORS[h2o] + GmRRHO(GFN2[alpb]-bhess) // r2scan-3c[DCOSMORS]
END of parameters
------------------------------------------------------------
PATHS of external QM programs
------------------------------------------------------------
The following program paths are used:
xTB: /home/abt-grimme/AK-bin/xtb
TURBOMOLE: /home/abt-grimme/TURBOMOLE.7.5.1/bin/em64t-unknown-linux-gnu_smp
Setup of COSMO-RS:
ctd = BP_TZVPD_FINE_C30_1601.ctd
cdir = "/home/bohle/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES"
ldir = "/home/bohle/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES"
Using /home/bohle/COSMOlogic/COSMOthermX19/COSMOtherm/DATABASE-COSMO/BP-TZVP-COSMO
as path to the COSMO-RS NORMAL DATABASE.
Using cefine from /home/bohle/bin/cefine
PARNODES for TM or COSMO-RS calculation was set to 2
Using COSMOtherm from /home/bohle/COSMOlogic/COSMOthermX19/COSMOtherm/BIN-LINUX/cosmotherm
----------------------------------------------------------------------------------------------------
Processing data from previous run (enso.json)
----------------------------------------------------------------------------------------------------
INFORMATION: No restart information exists and is created during this run!
----------------------------------------------------------------------------------------------------
CRE CHEAP-PRESCREENING - PART0
----------------------------------------------------------------------------------------------------
program: tm
functional for part0: b97-d
basis set for part0: def2-SV(P)
threshold g_thr(0): 4.0
starting number of considered conformers: 22
Calculating efficient gas-phase single-point energies:
The efficient gas-phase single-point is calculated for:
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF7, CONF8, CONF9, CONF10, CONF11
CONF12, CONF13, CONF14, CONF15, CONF16, CONF17, CONF18, CONF19, CONF20, CONF21, CONF22
Constructed folders!
Starting 22 ALPB-Gsolv calculations
Running single-point in CONF1/part0_sp
Running single-point in CONF2/part0_sp
Running single-point in CONF3/part0_sp
Running single-point in CONF4/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF1/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF3/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF2/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF4/part0_sp
Running single-point in CONF5/part0_sp
Running single-point in CONF6/part0_sp
Running single-point in CONF7/part0_sp
Running single-point in CONF8/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF5/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF6/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF7/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF8/part0_sp
Running single-point in CONF9/part0_sp
Running single-point in CONF11/part0_sp
Running single-point in CONF10/part0_sp
Running single-point in CONF12/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF9/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF10/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF11/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF12/part0_sp
Running single-point in CONF13/part0_sp
Running single-point in CONF15/part0_sp
Running single-point in CONF14/part0_sp
Running single-point in CONF16/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF13/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF15/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF14/part0_sp
Running single-point in CONF17/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF16/part0_sp
Running single-point in CONF18/part0_sp
Running single-point in CONF19/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF17/part0_sp
Running single-point in CONF20/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF18/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF19/part0_sp
Running single-point in CONF21/part0_sp
Running single-point in CONF22/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF20/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF22/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF21/part0_sp
Tasks completed!
The efficient gas-phase single-point was successful for CONF1/part0_sp: E(DFT) = -496.55110270 Gsolv = -0.12279245
The efficient gas-phase single-point was successful for CONF2/part0_sp: E(DFT) = -496.55473079 Gsolv = -0.12241044
The efficient gas-phase single-point was successful for CONF3/part0_sp: E(DFT) = -496.55551554 Gsolv = -0.12099969
The efficient gas-phase single-point was successful for CONF4/part0_sp: E(DFT) = -496.55384665 Gsolv = -0.12156811
The efficient gas-phase single-point was successful for CONF5/part0_sp: E(DFT) = -496.55341065 Gsolv = -0.12251050
The efficient gas-phase single-point was successful for CONF6/part0_sp: E(DFT) = -496.55368828 Gsolv = -0.12175678
The efficient gas-phase single-point was successful for CONF7/part0_sp: E(DFT) = -496.54759208 Gsolv = -0.12365913
The efficient gas-phase single-point was successful for CONF8/part0_sp: E(DFT) = -496.55118920 Gsolv = -0.12200372
The efficient gas-phase single-point was successful for CONF9/part0_sp: E(DFT) = -496.54970422 Gsolv = -0.12167549
The efficient gas-phase single-point was successful for CONF10/part0_sp: E(DFT) = -496.55157272 Gsolv = -0.12001541
The efficient gas-phase single-point was successful for CONF11/part0_sp: E(DFT) = -496.54991969 Gsolv = -0.12296934
The efficient gas-phase single-point was successful for CONF12/part0_sp: E(DFT) = -496.55212770 Gsolv = -0.11751864
The efficient gas-phase single-point was successful for CONF13/part0_sp: E(DFT) = -496.55077718 Gsolv = -0.11854291
The efficient gas-phase single-point was successful for CONF14/part0_sp: E(DFT) = -496.55028792 Gsolv = -0.12090071
The efficient gas-phase single-point was successful for CONF15/part0_sp: E(DFT) = -496.54987374 Gsolv = -0.12311773
The efficient gas-phase single-point was successful for CONF16/part0_sp: E(DFT) = -496.55360018 Gsolv = -0.11274054
The efficient gas-phase single-point was successful for CONF17/part0_sp: E(DFT) = -496.55289531 Gsolv = -0.11378052
The efficient gas-phase single-point was successful for CONF18/part0_sp: E(DFT) = -496.50423172 Gsolv = -0.16468285
The efficient gas-phase single-point was successful for CONF19/part0_sp: E(DFT) = -496.52384365 Gsolv = -0.14390846
The efficient gas-phase single-point was successful for CONF20/part0_sp: E(DFT) = -496.50481476 Gsolv = -0.16519450
The efficient gas-phase single-point was successful for CONF21/part0_sp: E(DFT) = -496.53860751 Gsolv = -0.13212346
The efficient gas-phase single-point was successful for CONF22/part0_sp: E(DFT) = -496.50938650 Gsolv = -0.15826546
----------------------------------------------------------------------------------------------------
Removing high lying conformers by improved energy description
----------------------------------------------------------------------------------------------------
CONF# G [Eh] ΔG [kcal/mol] E [Eh] Gsolv [Eh] Gtot ΔE(DFT) ΔGsolv ΔGtot
GFN2-xTB GFN2-xTB b97-d-D3(0)/def2-SV(P) alpb [Eh] [kcal/mol] [kcal/mol] [kcal/mol]
[ALPB] [ALPB] [gfn2]
CONF1 -34.1746819 0.00 -496.5511027 -0.1227924 -496.6738951 2.28 -0.24 2.04
CONF2 -34.1743917 0.18 -496.5547308 -0.1224104 -496.6771412 0.00 0.00 0.00 <------
CONF3 -34.1742792 0.25 -496.5555155 -0.1209997 -496.6765152 -0.49 0.89 0.39
CONF4 -34.1739821 0.44 -496.5538467 -0.1215681 -496.6754148 0.55 0.53 1.08
CONF5 -34.1740224 0.41 -496.5534106 -0.1225105 -496.6759212 0.83 -0.06 0.77
CONF6 -34.1736309 0.66 -496.5536883 -0.1217568 -496.6754451 0.65 0.41 1.06
CONF7 -34.1725555 1.33 -496.5475921 -0.1236591 -496.6712512 4.48 -0.78 3.70
CONF8 -34.1721876 1.57 -496.5511892 -0.1220037 -496.6731929 2.22 0.26 2.48
CONF9 -34.1719439 1.72 -496.5497042 -0.1216755 -496.6713797 3.15 0.46 3.62
CONF10 -34.1714765 2.01 -496.5515727 -0.1200154 -496.6715881 1.98 1.50 3.48
CONF11 -34.1712638 2.14 -496.5499197 -0.1229693 -496.6728890 3.02 -0.35 2.67
CONF12 -34.1704841 2.63 -496.5521277 -0.1175186 -496.6696463 1.63 3.07 4.70
CONF13 -34.1703687 2.71 -496.5507772 -0.1185429 -496.6693201 2.48 2.43 4.91
CONF14 -34.1694191 3.30 -496.5502879 -0.1209007 -496.6711886 2.79 0.95 3.74
CONF15 -34.1691431 3.48 -496.5498737 -0.1231177 -496.6729915 3.05 -0.44 2.60
CONF16 -34.1664418 5.17 -496.5536002 -0.1127405 -496.6663407 0.71 6.07 6.78
CONF17 -34.1661652 5.34 -496.5528953 -0.1137805 -496.6666758 1.15 5.42 6.57
CONF18 -34.1660003 5.45 -496.5042317 -0.1646828 -496.6689146 31.69 -26.53 5.16
CONF19 -34.1664801 5.15 -496.5238437 -0.1439085 -496.6677521 19.38 -13.49 5.89
CONF20 -34.1658387 5.55 -496.5048148 -0.1651945 -496.6700093 31.32 -26.85 4.48
CONF21 -34.1670164 4.81 -496.5386075 -0.1321235 -496.6707310 10.12 -6.10 4.02
CONF22 -34.1656180 5.69 -496.5093865 -0.1582655 -496.6676520 28.45 -22.50 5.95
----------------------------------------------------------------------------------------------------
--------------------------------------------------
Conformers considered further
--------------------------------------------------
These conformers are below the 4.000 kcal/mol g_thr(0) threshold.
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF7, CONF8, CONF9, CONF10, CONF11
CONF14, CONF15
Calculating Boltzmann averaged (free) energy of ensemble on input geometries (not DFT optimized)!
temperature /K: avE(T) /a.u. avG(T) /a.u.
----------------------------------------------------------------------------------------------------
298.15 -496.5544580 -496.6764445 <<==part0==
----------------------------------------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>END of Part0<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Ran part0 in 25.3156 seconds
----------------------------------------------------------------------------------------------------
CRE PRESCREENING - PART1
----------------------------------------------------------------------------------------------------
program: tm
functional for part1 and 2: r2scan-3c
basis set for part1 and 2: def2-mTZVPP
Solvent: h2o
solvent model for Gsolv contribution: cosmors
threshold g_thr(1) and G_thr(1): 3.5
starting number of considered conformers: 13
calculate mRRHO contribution: on
program for mRRHO contribution: xtb
GFN version for mRRHO and/or GBSA_Gsolv: gfn2
Apply constraint to input geometry during mRRHO calculation: on
temperature: 298.15
Calculating single-point energies and solvation contribution (G_solv):
The prescreening COSMO-RS is calculated for:
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF7, CONF8, CONF9, CONF10, CONF11
CONF14, CONF15
Constructed folders!
Constructed folders!
Starting 13 COSMO-RS-Gsolv calculations.
Running COSMO-RS calculation in CONF1/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF2/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF3/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF4/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF5/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF6/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF7/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF8/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF9/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF10/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF11/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF14/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF15/r2scan-3c/COSMO
Tasks completed!
prescreening COSMO-RS calculation was successful for CONF1/r2scan-3c/COSMO: -0.10999518
prescreening COSMO-RS calculation was successful for CONF2/r2scan-3c/COSMO: -0.10920229
prescreening COSMO-RS calculation was successful for CONF3/r2scan-3c/COSMO: -0.10753681
prescreening COSMO-RS calculation was successful for CONF4/r2scan-3c/COSMO: -0.10829026
prescreening COSMO-RS calculation was successful for CONF5/r2scan-3c/COSMO: -0.10936797
prescreening COSMO-RS calculation was successful for CONF6/r2scan-3c/COSMO: -0.10838241
prescreening COSMO-RS calculation was successful for CONF7/r2scan-3c/COSMO: -0.11058677
prescreening COSMO-RS calculation was successful for CONF8/r2scan-3c/COSMO: -0.10882956
prescreening COSMO-RS calculation was successful for CONF9/r2scan-3c/COSMO: -0.10889910
prescreening COSMO-RS calculation was successful for CONF10/r2scan-3c/COSMO: -0.10665800
prescreening COSMO-RS calculation was successful for CONF11/r2scan-3c/COSMO: -0.10960927
prescreening COSMO-RS calculation was successful for CONF14/r2scan-3c/COSMO: -0.10711489
prescreening COSMO-RS calculation was successful for CONF15/r2scan-3c/COSMO: -0.10994652
--------------------------------------------------
Removing high lying conformers
--------------------------------------------------
CONF# E(GFNn-xTB) ΔE(GFNn-xTB) E [Eh] Gsolv [Eh] Gtot ΔGtot
[a.u.] [kcal/mol] r2scan-3c COSMO-RS-normal [Eh] [kcal/mol]
[r2scan-3c]
CONF1 -34.1599548 0.00 -497.3021467 -0.1099952 -497.4121419 1.82
CONF2 -34.1594484 0.32 -497.3049956 -0.1092023 -497.4141979 0.53
CONF3 -34.1592530 0.44 -497.3064930 -0.1075368 -497.4140298 0.64
CONF4 -34.1590954 0.54 -497.3049058 -0.1082903 -497.4131961 1.16
CONF5 -34.1589250 0.65 -497.3056747 -0.1093680 -497.4150427 0.00 <------
CONF6 -34.1587465 0.76 -497.3049670 -0.1083824 -497.4133494 1.06
CONF7 -34.1578065 1.35 -497.2983644 -0.1105868 -497.4089512 3.82
CONF8 -34.1571241 1.78 -497.3029570 -0.1088296 -497.4117866 2.04
CONF9 -34.1570372 1.83 -497.3008248 -0.1088991 -497.4097239 3.34
CONF10 -34.1563217 2.28 -497.3038986 -0.1066580 -497.4105566 2.82
CONF11 -34.1559251 2.53 -497.3008250 -0.1096093 -497.4104343 2.89
CONF14 -34.1537285 3.91 -497.3022176 -0.1071149 -497.4093325 3.58
CONF15 -34.1529637 4.39 -497.3009381 -0.1099465 -497.4108846 2.61
--------------------------------------------------
Conformers considered further
--------------------------------------------------
Below the g_thr(1) threshold of 3.5 kcal/mol.
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF8, CONF9, CONF10, CONF11, CONF15
--------------------------------------------------
Calculating prescreening G_mRRHO with implicit solvation!
The prescreening G_mRRHO calculation is now performed for:
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF8, CONF9, CONF10, CONF11, CONF15
Constructed folders!
Starting 11 G_RRHO calculations.
Running GFN2-xTB mRRHO in CONF1/rrho_part1
Running GFN2-xTB mRRHO in CONF2/rrho_part1
Running GFN2-xTB mRRHO in CONF3/rrho_part1
Running GFN2-xTB mRRHO in CONF4/rrho_part1
Running GFN2-xTB mRRHO in CONF5/rrho_part1
Running GFN2-xTB mRRHO in CONF6/rrho_part1
Running GFN2-xTB mRRHO in CONF8/rrho_part1
Running GFN2-xTB mRRHO in CONF9/rrho_part1
Running GFN2-xTB mRRHO in CONF10/rrho_part1
Running GFN2-xTB mRRHO in CONF11/rrho_part1
Running GFN2-xTB mRRHO in CONF15/rrho_part1
Tasks completed!
The prescreening G_mRRHO calculation @ c1 was successful for CONF1/rrho_part1: 0.18287159
The prescreening G_mRRHO calculation @ c1 was successful for CONF2/rrho_part1: 0.18311981
The prescreening G_mRRHO calculation @ c1 was successful for CONF3/rrho_part1: 0.18287068
The prescreening G_mRRHO calculation @ c1 was successful for CONF4/rrho_part1: 0.18270975
The prescreening G_mRRHO calculation @ c1 was successful for CONF5/rrho_part1: 0.18272101
The prescreening G_mRRHO calculation @ c1 was successful for CONF6/rrho_part1: 0.18277331
The prescreening G_mRRHO calculation @ c1 was successful for CONF8/rrho_part1: 0.18239977
The prescreening G_mRRHO calculation @ c1 was successful for CONF9/rrho_part1: 0.18270475
The prescreening G_mRRHO calculation @ c1 was successful for CONF10/rrho_part1: 0.18264350
The prescreening G_mRRHO calculation @ c1 was successful for CONF11/rrho_part1: 0.18284194
The prescreening G_mRRHO calculation @ c1 was successful for CONF15/rrho_part1: 0.18323466
--------------------------------------------------
* Gibbs free energies of part1 *
--------------------------------------------------
CONF# G(GFNn-xTB) ΔG(GFNn-xTB) E [Eh] Gsolv [Eh] GmRRHO [Eh] Gtot ΔGtot
[a.u.] [kcal/mol] r2scan-3c COSMO-RS-normal GFN2 [Eh] [kcal/mol]
[r2scan-3c] [alpb]-bhess
CONF1 -33.9770832 0.00 -497.3021467 -0.1099952 0.1828716 -497.2292703 1.91
CONF2 -33.9763286 0.47 -497.3049956 -0.1092023 0.1831198 -497.2310781 0.78
CONF3 -33.9763824 0.44 -497.3064930 -0.1075368 0.1828707 -497.2311591 0.73
CONF4 -33.9763856 0.44 -497.3049058 -0.1082903 0.1827098 -497.2304863 1.15
CONF5 -33.9762040 0.55 -497.3056747 -0.1093680 0.1827210 -497.2323217 0.00 <------
CONF6 -33.9759732 0.70 -497.3049670 -0.1083824 0.1827733 -497.2305761 1.10
CONF8 -33.9747243 1.48 -497.3029570 -0.1088296 0.1823998 -497.2293868 1.84
CONF9 -33.9743324 1.73 -497.3008248 -0.1088991 0.1827047 -497.2270192 3.33
CONF10 -33.9736782 2.14 -497.3038986 -0.1066580 0.1826435 -497.2279131 2.77
CONF11 -33.9730831 2.51 -497.3008250 -0.1096093 0.1828419 -497.2275923 2.97
CONF15 -33.9697290 4.61 -497.3009381 -0.1099465 0.1832347 -497.2276500 2.93
Additional global 'fuzzy-threshold' based on the standard deviation of (G_mRRHO):
Std_dev(G_mRRHO) = 0.142 kcal/mol
Fuzzythreshold = 0.096 kcal/mol
Final sorting threshold G_thr(1) = 3.500 + 0.096 = 3.596 kcal/mol
Spearman correlation coefficient between (E + Solv) and (E + Solv + mRRHO) = 0.973
All relative (free) energies are below the initial G_thr(1) threshold of 3.5 kcal/mol.
All conformers are considered further.
Calculating Boltzmann averaged free energy of ensemble on input geometries (not DFT optimized)!
temperature /K: avE(T) /a.u. avGmRRHO(T) /a.u. avGsolv(T) /a.u. avG(T) /a.u.
----------------------------------------------------------------------------------------------------
298.15 -497.3054081 0.1827983 -0.1089068 -497.2315166 <<==part1==
----------------------------------------------------------------------------------------------------
Calculating unbiased GFNn-xTB energy
Constructed folders!
Starting 11 xTB - single-point calculations.
gfn2-xTB energy for CONF1/GFN_unbiased = -34.1764957
gfn2-xTB energy for CONF2/GFN_unbiased = -34.1762055
gfn2-xTB energy for CONF3/GFN_unbiased = -34.1760929
gfn2-xTB energy for CONF4/GFN_unbiased = -34.1757959
gfn2-xTB energy for CONF5/GFN_unbiased = -34.1758362
gfn2-xTB energy for CONF6/GFN_unbiased = -34.1754446
gfn2-xTB energy for CONF8/GFN_unbiased = -34.1740014
gfn2-xTB energy for CONF9/GFN_unbiased = -34.1737577
gfn2-xTB energy for CONF10/GFN_unbiased = -34.1732903
gfn2-xTB energy for CONF11/GFN_unbiased = -34.1730775
gfn2-xTB energy for CONF15/GFN_unbiased = -34.1709569
Tasks completed!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>END of Part1<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Ran part1 in 166.4199 seconds
----------------------------------------------------------------------------------------------------
CRE OPTIMIZATION - PART2
----------------------------------------------------------------------------------------------------
program: tm
functional for part2: r2scan-3c
basis set for part2: def2-mTZVPP
using the xTB-optimizer for optimization: on
using the new ensemble optimizer: on
optimize all conformers below this G_thr(opt,2) threshold: 2.5
Spearman threshold: 0.935
number of optimization iterations: 8
radsize: 10
optimization level in part2: lax
solvent: h2o
solvent model applied in the optimization: dcosmors
solvent model for Gsolv contribution: cosmors
temperature: 298.15
evalulate at different temperatures: on
temperature range: 273.15, 278.15, 283.15, 288.15, ...
Boltzmann sum threshold G_thr(2) for sorting in part2: 99.0
calculate mRRHO contribution: on
program for mRRHO contribution: xtb
GFN version for mRRHO and/or GBSA_Gsolv: gfn2
Apply constraint to input geometry during mRRHO calculation: on
Optimizing geometries at DFT level with implicit solvation!
The optimization is calculated for:
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF8, CONF9, CONF10, CONF11, CONF15
Constructed folders!
Preparing 11 calculations.
Tasks completed!
************************Starting optimizations************************
Starting threshold is set to 2.5 + 60.0 % = 4.0 kcal/mol
Lower limit is set to G_thr(opt,2) = 2.5 kcal/mol
*******************************CYCLE 1********************************
Starting 11 optimizations.
Running optimization in CONF1/r2scan-3c
Running optimization in CONF2/r2scan-3c
Running optimization in CONF3/r2scan-3c
Running optimization in CONF4/r2scan-3c
Running optimization in CONF5/r2scan-3c
Running optimization in CONF6/r2scan-3c
Running optimization in CONF8/r2scan-3c
Running optimization in CONF9/r2scan-3c
Running optimization in CONF10/r2scan-3c
Running optimization in CONF11/r2scan-3c
Running optimization in CONF15/r2scan-3c
Tasks completed!
Constructed folders!
Starting 11 G_RRHO calculations.
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Tasks completed!
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF1/r2scan-3c/rrho_crude: 0.18253283
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF2/r2scan-3c/rrho_crude: 0.18217211
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF3/r2scan-3c/rrho_crude: 0.18223212
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF4/r2scan-3c/rrho_crude: 0.18258415
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF5/r2scan-3c/rrho_crude: 0.18245612
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF6/r2scan-3c/rrho_crude: 0.18170042
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF8/r2scan-3c/rrho_crude: 0.18260313
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF9/r2scan-3c/rrho_crude: 0.18272834
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF10/r2scan-3c/rrho_crude: 0.18229001
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF11/r2scan-3c/rrho_crude: 0.18150537
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF15/r2scan-3c/rrho_crude: 0.18100199
Max number of performed iterations: 8
Spearman rank evaluation is performed in the next cycle.
CONF1 initial ΔG = 2.13 kcal/mol and current ΔG = 2.59 kcal/mol. (not_converged)
CONF2 initial ΔG = 0.86 kcal/mol and current ΔG = 0.46 kcal/mol. (not_converged)
CONF3 initial ΔG = 0.97 kcal/mol and current ΔG = 1.47 kcal/mol. (not_converged)
CONF4 initial ΔG = 1.62 kcal/mol and current ΔG = 1.40 kcal/mol. (not_converged)
CONF5 initial ΔG = 0.00 kcal/mol and current ΔG = 0.42 kcal/mol. (not_converged)
CONF6 initial ΔG = 0.60 kcal/mol and current ΔG = 1.15 kcal/mol. (not_converged)
CONF8 initial ΔG = 2.26 kcal/mol and current ΔG = 2.31 kcal/mol. (not_converged)
CONF9 initial ΔG = 3.90 kcal/mol and current ΔG = 4.42 kcal/mol. (not_converged)
CONF10 initial ΔG = 2.86 kcal/mol and current ΔG = 2.92 kcal/mol. (not_converged)
CONF11 initial ΔG = 2.26 kcal/mol and current ΔG = 3.43 kcal/mol. (not_converged)
CONF15 initial ΔG = 0.23 kcal/mol and current ΔG = 0.00 kcal/mol. (not_converged)
CONF9 is above 4.0 kcal/mol and gradient norm (0.004056375026) is below 0.01.
CONF9 is above threshold, dont optimize further and remove conformer.
CYCLE 1 performed in 1310.1062 seconds
*******************************CYCLE 2********************************
Starting 10 optimizations.
Running optimization in CONF1/r2scan-3c
Running optimization in CONF2/r2scan-3c
Running optimization in CONF3/r2scan-3c
Running optimization in CONF4/r2scan-3c
Running optimization in CONF5/r2scan-3c
Running optimization in CONF6/r2scan-3c
Running optimization in CONF8/r2scan-3c
Running optimization in CONF10/r2scan-3c
Running optimization in CONF11/r2scan-3c
Running optimization in CONF15/r2scan-3c
Tasks completed!
Geometry optimization converged for: CONF3 within 12 cycles
Max number of performed iterations: 16
CONF1 previous ΔG = 2.59 kcal/mol and current ΔG = 2.54 kcal/mol. (not_converged)
CONF2 previous ΔG = 0.46 kcal/mol and current ΔG = 0.00 kcal/mol. (not_converged)
CONF3 previous ΔG = 1.47 kcal/mol and current ΔG = 1.92 kcal/mol. (converged)
CONF4 previous ΔG = 1.40 kcal/mol and current ΔG = 10.87 kcal/mol. (not_converged)
CONF5 previous ΔG = 0.42 kcal/mol and current ΔG = 0.99 kcal/mol. (not_converged)
CONF6 previous ΔG = 1.15 kcal/mol and current ΔG = 1.57 kcal/mol. (not_converged)
CONF8 previous ΔG = 2.31 kcal/mol and current ΔG = 1.85 kcal/mol. (not_converged)
CONF10 previous ΔG = 2.92 kcal/mol and current ΔG = 3.68 kcal/mol. (not_converged)
CONF11 previous ΔG = 3.43 kcal/mol and current ΔG = 3.29 kcal/mol. (not_converged)
CONF15 previous ΔG = 0.00 kcal/mol and current ΔG = 0.03 kcal/mol. (not_converged)
Spearman coeff. from 8 --> 11 = 0.9758
Spearman coeff. from 9 --> 12 = 0.9879
Spearman coeff. from 10 --> 13 = 0.7455
Spearman coeff. from 11 --> 14 = 1.0000
Evaluating Spearman coeff. from 12 --> 15 = 0.9515
Evaluating Spearman coeff. from 13 --> 16 = 0.8667
Final averaged Spearman correlation coefficient: 0.9091
CONF4 is above 4.0 kcal/mol but gradient norm (0.108293192291) is above 0.01 --> not sorted out!
CYCLE 2 performed in 980.4814 seconds
*******************************CYCLE 3********************************
Starting 9 optimizations.
Running optimization in CONF1/r2scan-3c
Running optimization in CONF2/r2scan-3c
Running optimization in CONF4/r2scan-3c
Running optimization in CONF5/r2scan-3c
Running optimization in CONF6/r2scan-3c
Running optimization in CONF8/r2scan-3c
Running optimization in CONF10/r2scan-3c
Running optimization in CONF11/r2scan-3c
Running optimization in CONF15/r2scan-3c
Tasks completed!
Geometry optimization converged for: CONF5 within 23 cycles
Geometry optimization converged for: CONF11 within 21 cycles
Max number of performed iterations: 24
CONF1 previous ΔG = 2.54 kcal/mol and current ΔG = 2.38 kcal/mol. (not_converged)
CONF2 previous ΔG = 0.00 kcal/mol and current ΔG = 0.00 kcal/mol. (not_converged)
CONF3 previous ΔG = 1.92 kcal/mol and current ΔG = 2.09 kcal/mol. (converged)
CONF4 previous ΔG = 10.87 kcal/mol and current ΔG = 0.07 kcal/mol. (not_converged)
CONF5 previous ΔG = 0.99 kcal/mol and current ΔG = 1.25 kcal/mol. (converged)
CONF6 previous ΔG = 1.57 kcal/mol and current ΔG = 1.51 kcal/mol. (not_converged)
CONF8 previous ΔG = 1.85 kcal/mol and current ΔG = 1.89 kcal/mol. (not_converged)
CONF10 previous ΔG = 3.68 kcal/mol and current ΔG = 3.36 kcal/mol. (not_converged)
CONF11 previous ΔG = 3.29 kcal/mol and current ΔG = 3.30 kcal/mol. (converged)
CONF15 previous ΔG = 0.03 kcal/mol and current ΔG = 0.22 kcal/mol. (not_converged)
Spearman coeff. from 16 --> 19 = 0.6606
Spearman coeff. from 17 --> 20 = 0.6000
Spearman coeff. from 18 --> 21 = 0.7455
Spearman coeff. from 19 --> 22 = 0.8182
Evaluating Spearman coeff. from 20 --> 23 = 0.7091
Evaluating Spearman coeff. from 21 --> 24 = 1.0000
Final averaged Spearman correlation coefficient: 0.8545
CYCLE 3 performed in 830.9565 seconds
*******************************CYCLE 4********************************
Starting 7 optimizations.
Running optimization in CONF1/r2scan-3c
Running optimization in CONF2/r2scan-3c
Running optimization in CONF4/r2scan-3c
Running optimization in CONF6/r2scan-3c
Running optimization in CONF8/r2scan-3c
Running optimization in CONF10/r2scan-3c
Running optimization in CONF15/r2scan-3c
Tasks completed!
Geometry optimization converged for: CONF8 within 26 cycles
Geometry optimization converged for: CONF15 within 25 cycles
Max number of performed iterations: 32
CONF1 previous ΔG = 2.38 kcal/mol and current ΔG = 1.84 kcal/mol. (not_converged)
CONF2 previous ΔG = 0.00 kcal/mol and current ΔG = 0.00 kcal/mol. (not_converged)
CONF3 previous ΔG = 2.09 kcal/mol and current ΔG = 2.11 kcal/mol. (converged)
CONF4 previous ΔG = 0.07 kcal/mol and current ΔG = 0.01 kcal/mol. (not_converged)
CONF5 previous ΔG = 1.25 kcal/mol and current ΔG = 1.26 kcal/mol. (converged)
CONF6 previous ΔG = 1.51 kcal/mol and current ΔG = 1.57 kcal/mol. (not_converged)
CONF8 previous ΔG = 1.89 kcal/mol and current ΔG = 1.91 kcal/mol. (converged)
CONF10 previous ΔG = 3.36 kcal/mol and current ΔG = 6.58 kcal/mol. (not_converged)
CONF11 previous ΔG = 3.30 kcal/mol and current ΔG = 3.32 kcal/mol. (converged)
CONF15 previous ΔG = 0.22 kcal/mol and current ΔG = 0.23 kcal/mol. (converged)
Spearman coeff. from 24 --> 27 = 0.9636
Spearman coeff. from 25 --> 28 = 0.9879
Spearman coeff. from 26 --> 29 = 0.9758
Spearman coeff. from 27 --> 30 = 0.8424
Evaluating Spearman coeff. from 28 --> 31 = 0.9515
Evaluating Spearman coeff. from 29 --> 32 = 0.9636
Final averaged Spearman correlation coefficient: 0.9576
PES is assumed to be parallel
Updated optimization threshold to: 3.50 kcal/mol
CONF10 is above 3.5 kcal/mol but gradient norm (0.09473608827) is above 0.01 --> not sorted out!
CYCLE 4 performed in 613.0740 seconds
*******************************CYCLE 5********************************
Starting 5 optimizations.
Running optimization in CONF1/r2scan-3c
Running optimization in CONF2/r2scan-3c
Running optimization in CONF4/r2scan-3c
Running optimization in CONF6/r2scan-3c
Running optimization in CONF10/r2scan-3c
Tasks completed!
Geometry optimization converged for: CONF2 within 34 cycles
Geometry optimization converged for: CONF6 within 39 cycles
Max number of performed iterations: 40
CONF1 previous ΔG = 1.84 kcal/mol and current ΔG = 7.79 kcal/mol. (not_converged)
CONF2 previous ΔG = 0.00 kcal/mol and current ΔG = 0.38 kcal/mol. (converged)
CONF3 previous ΔG = 2.11 kcal/mol and current ΔG = 2.53 kcal/mol. (converged)
CONF4 previous ΔG = 0.01 kcal/mol and current ΔG = 0.35 kcal/mol. (not_converged)
CONF5 previous ΔG = 1.26 kcal/mol and current ΔG = 1.68 kcal/mol. (converged)
CONF6 previous ΔG = 1.57 kcal/mol and current ΔG = 1.94 kcal/mol. (converged)
CONF8 previous ΔG = 1.91 kcal/mol and current ΔG = 2.33 kcal/mol. (converged)
CONF10 previous ΔG = 6.58 kcal/mol and current ΔG = 0.00 kcal/mol. (not_converged)
CONF11 previous ΔG = 3.32 kcal/mol and current ΔG = 3.74 kcal/mol. (converged)
CONF15 previous ΔG = 0.23 kcal/mol and current ΔG = 0.65 kcal/mol. (converged)
Spearman coeff. from 32 --> 35 = 0.7333
Spearman coeff. from 33 --> 36 = 0.9273
Spearman coeff. from 34 --> 37 = 0.8182
Spearman coeff. from 35 --> 38 = 1.0000
Evaluating Spearman coeff. from 36 --> 39 = 0.9879
Evaluating Spearman coeff. from 37 --> 40 = 0.8545
Final averaged Spearman correlation coefficient: 0.9212
CONF1 is above 3.5 kcal/mol but gradient norm (0.083474094636) is above 0.01 --> not sorted out!
CYCLE 5 performed in 403.3400 seconds
*******************************CYCLE 6********************************
Starting 3 optimizations.
Running optimization in CONF1/r2scan-3c
Running optimization in CONF4/r2scan-3c
Running optimization in CONF10/r2scan-3c
Tasks completed!
Geometry optimization converged for: CONF4 within 44 cycles
Max number of performed iterations: 48
CONF1 previous ΔG = 7.79 kcal/mol and current ΔG = 2.37 kcal/mol. (not_converged)
CONF2 previous ΔG = 0.38 kcal/mol and current ΔG = 1.25 kcal/mol. (converged)
CONF3 previous ΔG = 2.53 kcal/mol and current ΔG = 3.40 kcal/mol. (converged)
CONF4 previous ΔG = 0.35 kcal/mol and current ΔG = 1.19 kcal/mol. (converged)
CONF5 previous ΔG = 1.68 kcal/mol and current ΔG = 2.55 kcal/mol. (converged)
CONF6 previous ΔG = 1.94 kcal/mol and current ΔG = 2.80 kcal/mol. (converged)
CONF8 previous ΔG = 2.33 kcal/mol and current ΔG = 3.20 kcal/mol. (converged)
CONF10 previous ΔG = 0.00 kcal/mol and current ΔG = 0.00 kcal/mol. (not_converged)
CONF11 previous ΔG = 3.74 kcal/mol and current ΔG = 4.61 kcal/mol. (converged)
CONF15 previous ΔG = 0.65 kcal/mol and current ΔG = 1.52 kcal/mol. (converged)
Spearman coeff. from 40 --> 43 = 0.8788
Spearman coeff. from 41 --> 44 = 0.6242
Spearman coeff. from 42 --> 45 = 0.9273
Spearman coeff. from 43 --> 46 = 1.0000
Evaluating Spearman coeff. from 44 --> 47 = 0.6485
Evaluating Spearman coeff. from 45 --> 48 = 0.9879
Final averaged Spearman correlation coefficient: 0.8182
CYCLE 6 performed in 296.2324 seconds
*******************************CYCLE 7********************************
Starting 2 optimizations.
Running optimization in CONF1/r2scan-3c
Running optimization in CONF10/r2scan-3c
Tasks completed!
Max number of performed iterations: 56
CONF1 previous ΔG = 2.37 kcal/mol and current ΔG = 2.60 kcal/mol. (not_converged)
CONF2 previous ΔG = 1.25 kcal/mol and current ΔG = 1.66 kcal/mol. (converged)
CONF3 previous ΔG = 3.40 kcal/mol and current ΔG = 3.81 kcal/mol. (converged)
CONF4 previous ΔG = 1.19 kcal/mol and current ΔG = 1.61 kcal/mol. (converged)
CONF5 previous ΔG = 2.55 kcal/mol and current ΔG = 2.97 kcal/mol. (converged)
CONF6 previous ΔG = 2.80 kcal/mol and current ΔG = 3.22 kcal/mol. (converged)
CONF8 previous ΔG = 3.20 kcal/mol and current ΔG = 3.61 kcal/mol. (converged)
CONF10 previous ΔG = 0.00 kcal/mol and current ΔG = 0.00 kcal/mol. (not_converged)
CONF11 previous ΔG = 4.61 kcal/mol and current ΔG = 5.02 kcal/mol. (converged)
CONF15 previous ΔG = 1.52 kcal/mol and current ΔG = 1.94 kcal/mol. (converged)
Spearman coeff. from 48 --> 51 = 1.0000
Spearman coeff. from 49 --> 52 = 1.0000
Spearman coeff. from 50 --> 53 = 1.0000
Spearman coeff. from 51 --> 54 = 1.0000
Evaluating Spearman coeff. from 52 --> 55 = 1.0000
Evaluating Spearman coeff. from 53 --> 56 = 1.0000
Final averaged Spearman correlation coefficient: 1.0000
PES is assumed to be parallel
Updated optimization threshold to: 3.00 kcal/mol
CYCLE 7 performed in 252.6446 seconds
*******************************CYCLE 8********************************
Starting 2 optimizations.
Running optimization in CONF1/r2scan-3c
Running optimization in CONF10/r2scan-3c
Tasks completed!
Max number of performed iterations: 64
CONF1 previous ΔG = 2.60 kcal/mol and current ΔG = 2.71 kcal/mol. (not_converged)
CONF2 previous ΔG = 1.66 kcal/mol and current ΔG = 1.87 kcal/mol. (converged)
CONF3 previous ΔG = 3.81 kcal/mol and current ΔG = 4.02 kcal/mol. (converged)
CONF4 previous ΔG = 1.61 kcal/mol and current ΔG = 1.81 kcal/mol. (converged)
CONF5 previous ΔG = 2.97 kcal/mol and current ΔG = 3.17 kcal/mol. (converged)
CONF6 previous ΔG = 3.22 kcal/mol and current ΔG = 3.42 kcal/mol. (converged)
CONF8 previous ΔG = 3.61 kcal/mol and current ΔG = 3.82 kcal/mol. (converged)
CONF10 previous ΔG = 0.00 kcal/mol and current ΔG = 0.00 kcal/mol. (not_converged)
CONF11 previous ΔG = 5.02 kcal/mol and current ΔG = 5.23 kcal/mol. (converged)
CONF15 previous ΔG = 1.94 kcal/mol and current ΔG = 2.14 kcal/mol. (converged)
Spearman coeff. from 56 --> 59 = 1.0000
Spearman coeff. from 57 --> 60 = 1.0000
Spearman coeff. from 58 --> 61 = 1.0000
Spearman coeff. from 59 --> 62 = 1.0000
Evaluating Spearman coeff. from 60 --> 63 = 1.0000
Evaluating Spearman coeff. from 61 --> 64 = 1.0000
Final averaged Spearman correlation coefficient: 1.0000
PES is assumed to be parallel
Updated optimization threshold to: 2.50 kcal/mol
CONF1 is above 2.5 kcal/mol and gradient norm (0.001262363132) is below 0.01.
CONF1 is removed because of the lowered threshold!
CONF1 is above threshold, dont optimize further and remove conformer.
CYCLE 8 performed in 251.6678 seconds
*******************************CYCLE 9********************************
Starting 1 optimizations.
Running optimization in CONF10/r2scan-3c
Tasks completed!
Max number of performed iterations: 72
CONF2 previous ΔG = 1.87 kcal/mol and current ΔG = 1.84 kcal/mol. (converged)
CONF3 previous ΔG = 4.02 kcal/mol and current ΔG = 3.99 kcal/mol. (converged)
CONF4 previous ΔG = 1.81 kcal/mol and current ΔG = 1.78 kcal/mol. (converged)
CONF5 previous ΔG = 3.17 kcal/mol and current ΔG = 3.14 kcal/mol. (converged)
CONF6 previous ΔG = 3.42 kcal/mol and current ΔG = 3.39 kcal/mol. (converged)
CONF8 previous ΔG = 3.82 kcal/mol and current ΔG = 3.79 kcal/mol. (converged)
CONF10 previous ΔG = 0.00 kcal/mol and current ΔG = 0.00 kcal/mol. (not_converged)
CONF11 previous ΔG = 5.23 kcal/mol and current ΔG = 5.20 kcal/mol. (converged)
CONF15 previous ΔG = 2.14 kcal/mol and current ΔG = 2.11 kcal/mol. (converged)
Spearman coeff. from 64 --> 67 = 1.0000
Spearman coeff. from 65 --> 68 = 1.0000
Spearman coeff. from 66 --> 69 = 1.0000
Spearman coeff. from 67 --> 70 = 1.0000
Evaluating Spearman coeff. from 68 --> 71 = 1.0000
Evaluating Spearman coeff. from 69 --> 72 = 1.0000
Final averaged Spearman correlation coefficient: 1.0000
PES is assumed to be parallel
Current optimization threshold: 2.50 kcal/mol
CYCLE 9 performed in 202.2149 seconds
*******************************CYCLE 10*******************************
Starting 1 optimizations.
Running optimization in CONF10/r2scan-3c
Tasks completed!
Geometry optimization converged for: CONF10 within 80 cycles
***********************Finished optimizations!************************
Timings:
Cycle: [s]
1 1310.11
2 980.48
3 830.96
4 613.07
5 403.34
6 296.23
7 252.64
8 251.67
9 202.21
10 200.34
sum: 5341.06
CONVERGED optimizations for the following remaining conformers:
Converged optimization for CONF2 after 34 cycles: -497.4508410
Converged optimization for CONF3 after 12 cycles: -497.4474711
Converged optimization for CONF4 after 44 cycles: -497.4513419
Converged optimization for CONF5 after 23 cycles: -497.4490457
Converged optimization for CONF6 after 39 cycles: -497.4478893
Converged optimization for CONF8 after 26 cycles: -497.4481610
Converged optimization for CONF10 after 80 cycles: -497.4538409
Converged optimization for CONF11 after 21 cycles: -497.4448166
Converged optimization for CONF15 after 25 cycles: -497.4492319
Calculating single-point energies and solvation contribution (G_solv)!
The low level gsolv calculation is now calculated for:
Constructed folders!
CONF2, CONF3, CONF4, CONF5, CONF6, CONF8, CONF10, CONF11, CONF15
Starting 9 COSMO-RS-Gsolv calculations.
Running COSMO-RS calculation in CONF2/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF3/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF4/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF5/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF6/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF8/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF10/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF11/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF15/r2scan-3c/COSMO
Tasks completed!
lowlevel COSMO-RS calculation was successful for CONF2/r2scan-3c/COSMO: -0.13589836
lowlevel COSMO-RS calculation was successful for CONF3/r2scan-3c/COSMO: -0.12865185
lowlevel COSMO-RS calculation was successful for CONF4/r2scan-3c/COSMO: -0.13533997
lowlevel COSMO-RS calculation was successful for CONF5/r2scan-3c/COSMO: -0.12940253
lowlevel COSMO-RS calculation was successful for CONF6/r2scan-3c/COSMO: -0.12980575
lowlevel COSMO-RS calculation was successful for CONF8/r2scan-3c/COSMO: -0.12959608
lowlevel COSMO-RS calculation was successful for CONF10/r2scan-3c/COSMO: -0.15938290
lowlevel COSMO-RS calculation was successful for CONF11/r2scan-3c/COSMO: -0.13131124
lowlevel COSMO-RS calculation was successful for CONF15/r2scan-3c/COSMO: -0.13806979
Calculating lowlevel G_mRRHO with implicit solvation on DFT geometry!
The lowlevel G_mRRHO calculation is now performed for:
CONF2, CONF3, CONF4, CONF5, CONF6, CONF8, CONF10, CONF11, CONF15
Constructed folders!
Starting 9 G_RRHO calculations.
Running GFN2-xTB mRRHO in CONF2/rrho_part2
Running GFN2-xTB mRRHO in CONF3/rrho_part2
Running GFN2-xTB mRRHO in CONF4/rrho_part2
Running GFN2-xTB mRRHO in CONF5/rrho_part2
Running GFN2-xTB mRRHO in CONF6/rrho_part2
Running GFN2-xTB mRRHO in CONF8/rrho_part2
Running GFN2-xTB mRRHO in CONF10/rrho_part2
Running GFN2-xTB mRRHO in CONF11/rrho_part2
Running GFN2-xTB mRRHO in CONF15/rrho_part2
Tasks completed!
The lowlevel G_mRRHO calculation @ c1 was successful for CONF2/rrho_part2: 0.18028469
The lowlevel G_mRRHO calculation @ c1 was successful for CONF3/rrho_part2: 0.18207391
The lowlevel G_mRRHO calculation @ c1 was successful for CONF4/rrho_part2: 0.18117449
The lowlevel G_mRRHO calculation @ c1 was successful for CONF5/rrho_part2: 0.18231888
The lowlevel G_mRRHO calculation @ c1 was successful for CONF6/rrho_part2: 0.18172189
The lowlevel G_mRRHO calculation @ c1 was successful for CONF8/rrho_part2: 0.18218769
The lowlevel G_mRRHO calculation @ c1 was successful for CONF10/rrho_part2: 0.17889859
The lowlevel G_mRRHO calculation @ c1 was successful for CONF11/rrho_part2: 0.18153296
The lowlevel G_mRRHO calculation @ c1 was successful for CONF15/rrho_part2: 0.18070768
--------------------------------------------------
* Gibbs free energies of part2 *
--------------------------------------------------
CONF# E(GFNn-xTB) ΔE(GFNn-xTB) E [Eh] Gsolv [Eh] GmRRHO [Eh] Gtot ΔGtot Boltzmannweight
[a.u.] [kcal/mol] r2scan-3c COSMO-RS-normal GFN2 [Eh] [kcal/mol] % at 298.15 K
[r2scan-3c] [alpb]-bhess
CONF2 -34.1594484 0.32 -497.2837810 -0.1358984 0.1802847 -497.2393947 0.17 21.10
CONF3 -34.1592530 0.44 -497.2915335 -0.1286518 0.1820739 -497.2381114 0.98 5.42
CONF4 -34.1590954 0.54 -497.2853431 -0.1353400 0.1811745 -497.2395086 0.10 23.80
CONF5 -34.1589250 0.65 -497.2917403 -0.1294025 0.1823189 -497.2388239 0.53 11.53
CONF6 -34.1587465 0.76 -497.2896963 -0.1298058 0.1817219 -497.2377802 1.19 3.82
CONF8 -34.1571241 1.78 -497.2905928 -0.1295961 0.1821877 -497.2380012 1.05 4.82
CONF10 -34.1563217 2.28 -497.2591855 -0.1593829 0.1788986 -497.2396698 0.00 28.23 <------
CONF11 -34.1559251 2.53 -497.2848139 -0.1313112 0.1815330 -497.2345922 3.19 0.13
CONF15 -34.1529637 4.39 -497.2792896 -0.1380698 0.1807077 -497.2366518 1.89 1.15
Calculating ALPB_Gsolv values for evaluation of the std. dev. of Gsolv.
Constructed folders!
Starting 9 ALPB-Gsolv calculations
Running ALPB_GSOLV calculation in 3-part0-2/CONF2/alpb_gsolv
Running ALPB_GSOLV calculation in 3-part0-2/CONF3/alpb_gsolv
Running ALPB_GSOLV calculation in 3-part0-2/CONF4/alpb_gsolv
Running ALPB_GSOLV calculation in 3-part0-2/CONF5/alpb_gsolv
Running ALPB_GSOLV calculation in 3-part0-2/CONF6/alpb_gsolv
Running ALPB_GSOLV calculation in 3-part0-2/CONF8/alpb_gsolv
Running ALPB_GSOLV calculation in 3-part0-2/CONF10/alpb_gsolv
Running ALPB_GSOLV calculation in 3-part0-2/CONF11/alpb_gsolv
Running ALPB_GSOLV calculation in 3-part0-2/CONF15/alpb_gsolv
Tasks completed!
ALPB_GSOLV calculation was successful for CONF2/alpb_gsolv: -0.14572423
ALPB_GSOLV calculation was successful for CONF3/alpb_gsolv: -0.14136373
ALPB_GSOLV calculation was successful for CONF4/alpb_gsolv: -0.14534319
ALPB_GSOLV calculation was successful for CONF5/alpb_gsolv: -0.14108828
ALPB_GSOLV calculation was successful for CONF6/alpb_gsolv: -0.14215086
ALPB_GSOLV calculation was successful for CONF8/alpb_gsolv: -0.14150861
ALPB_GSOLV calculation was successful for CONF10/alpb_gsolv: -0.16262359
ALPB_GSOLV calculation was successful for CONF11/alpb_gsolv: -0.14230853
ALPB_GSOLV calculation was successful for CONF15/alpb_gsolv: -0.14881714
SD of solvation models (all units in kcal/mol):
CONFX ΔG(COSMO-RS) ΔG(DCOSMO-RS_gsolv) ΔG(ALPB_gsolv) SD(COSMO-RS 40%, DCOSMO-RS_gsolv 40%, ALPB_gsolv 20%)
----------------------------------------------------------------------------------------------------
CONF2 14.74 17.32 10.60 3.01
CONF3 19.28 24.30 13.34 4.97
CONF4 15.09 17.98 10.84 3.21
CONF5 18.81 23.44 13.51 4.51
CONF6 18.56 22.88 12.85 4.53
CONF8 18.69 23.27 13.25 4.54
CONF10 0.00 0.00 0.00 0.00
CONF11 17.62 21.74 12.75 4.08
CONF15 13.37 15.51 8.66 3.06
----------------------------------------------------------------------------------------------------
Calculating Boltzmann averaged free energy of ensemble!
temperature /K: avE(T) /a.u. avGmRRHO(T) /a.u. avGsolv(T) /a.u. avG(T) /a.u.
----------------------------------------------------------------------------------------------------
273.15 -497.2736863 0.1842434 -0.1489372 -497.2383801
278.15 -497.2749007 0.1835285 -0.1471130 -497.2384852
283.15 -497.2760521 0.1828067 -0.1453716 -497.2386171
288.15 -497.2771316 0.1820765 -0.1437255 -497.2387805
293.15 -497.2781302 0.1813377 -0.1421818 -497.2389743
298.15 -497.2790497 0.1805897 -0.1407374 -497.2391974 <<==part2==
303.15 -497.2798874 0.1798315 -0.1393937 -497.2394496
308.15 -497.2806529 0.1790640 -0.1381406 -497.2397295
313.15 -497.2813425 0.1782861 -0.1369800 -497.2400363
318.15 -497.2819636 0.1774979 -0.1359037 -497.2403694
323.15 -497.2825199 0.1767001 -0.1349073 -497.2407270
328.15 -497.2830226 0.1758934 -0.1339792 -497.2411084
333.15 -497.2834731 0.1750769 -0.1331172 -497.2415134
338.15 -497.2838754 0.1742509 -0.1323164 -497.2419409
343.15 -497.2842354 0.1734163 -0.1315708 -497.2423900
348.15 -497.2845604 0.1725735 -0.1308732 -497.2428601
353.15 -497.2848497 0.1717219 -0.1302228 -497.2433506
358.15 -497.2851101 0.1708621 -0.1296129 -497.2438610
363.15 -497.2853448 0.1699946 -0.1290401 -497.2443904
368.15 -497.2855549 0.1691186 -0.1285027 -497.2449389
373.15 -497.2857417 0.1682355 -0.1279985 -497.2455047
----------------------------------------------------------------------------------------------------
--------------------------------------------------
Conformers considered further
--------------------------------------------------
Conformers that are below the Boltzmann threshold G_thr(2) of 99.0%:
CONF10, CONF4, CONF2, CONF5, CONF3, CONF8, CONF6, CONF15
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>END of Part2<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Ran part2 in 5486.1036 seconds
Part : #conf time
--------------------------------------------------
Input : 22 -
Part0_all : 13 25.32s
Part1_initial_sort : 11 -
Part1_all : 11 166.42s
Part2_opt : 9 -
Part2_all : 8 5486.10s
--------------------------------------------------
All parts : 5677.84s
CENSO all done!
$CENSO global configuration file: .censorc
$VERSION:1.0.3
ORCA: /home/$USER/orca_4_2_1_linux_x86-64_openmpi216
ORCA version: 4.2.1
GFN-xTB: /home/$USER/bin/xtb
CREST: /home/$USER/bin/crest
mpshift: mpshift
escf: escf
#COSMO-RS
ctd = BP_TZVPD_FINE_C30_1601.ctd cdir = "/home/$USER/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES" ldir = "/home/bohle/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES"
cosmothermversion: 19
$ENDPROGRAMS
$CRE SORTING SETTINGS:
$GENERAL SETTINGS:
nconf: all # ['all', 'number e.g. 10 up to all conformers']
charge: 1 # ['number e.g. 0']
unpaired: 0 # ['number e.g. 0']
solvent: h2o # ['gas', 'acetone', 'chcl3', 'acetonitrile', 'ch2cl2', 'dmso', 'h2o', 'methanol', 'thf', '...']
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 # ['pbe', 'b97-d', 'pbeh-3c', 'tpss', 'b97-d3', 'r2scan-3c', 'b97-3c']
basis: automatic # ['automatic', 'def2-mSVP', 'def2-mTZVP', 'def2-mTZVP', 'def2-TZVP', '...']
maxthreads: 4 # ['number of threads e.g. 2']
omp: 2 # ['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 # ['pbeh-3c', 'b97-3c', 'b97-d3', 'pbe', 'r2scan-3c', 'tpss', 'b97-d']
basis0: def2-SV(P) # ['automatic', 'def2-mSVP', 'def2-mTZVP', 'def2-mTZVP', 'def2-TZVP', '...']
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', 'dcosmors', 'cosmo', 'smd', 'cosmors-fine', 'cpcm', 'gbsa_gsolv', '...']
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: dcosmors # ['cosmo', 'cpcm', 'default', 'smd', 'dcosmors']
smgsolv2: cosmors # ['cosmors-fine', 'gbsa_gsolv', 'cosmo', 'cpcm', 'smd_gsolv', 'alpb_gsolv', 'smd', '...']
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 # ['dsd-blyp', 'pw6b95', 'b97-d3', 'r2scan-3c', 'pbe0', 'wb97x']
basis3: def2-TZVPD # ['SVP', 'SV(P)', 'TZVP', 'TZVPP', 'QZVP', 'QZVPP', 'def2-SV(P)', 'def2-mSVP', '...']
smgsolv3: cosmors # ['alpb_gsolv', 'dcosmors', 'cosmo', 'smd', 'cosmors-fine', 'cpcm', 'gbsa_gsolv', '...']
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 # ['tpss', 'pbe0', 'pbeh-3c']
basisJ: def2-TZVP # ['SVP', 'SV(P)', 'TZVP', 'TZVPP', 'QZVP', 'QZVPP', 'def2-SV(P)', 'def2-mSVP', '...']
sm4J: default # ['dcosmors', 'smd', 'cosmo', 'cpcm']
shieldings: on # ['on', 'off']
progS: prog # ['tm', 'orca', 'adf', 'prog']
funcS: pbe0 # ['dsd-blyp', 'pbeh-3c', 'tpss', 'pbe0', 'kt2']
basisS: def2-TZVP # ['SVP', 'SV(P)', 'TZVP', 'TZVPP', 'QZVP', 'QZVPP', 'def2-SV(P)', 'def2-mSVP', '...']
sm4S: default # ['dcosmors', 'smd', 'cosmo', 'cpcm']
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
25
-34.15995484
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25
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H 0.9927667520 -1.5675551657 -0.0428313977
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H 2.6054467969 -1.8083924261 0.4393088723
H -2.8796747565 0.6310313638 -0.3580585669
25
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H 0.9216680773 0.3153070715 -1.3864974308
H -0.0132519646 2.3752873127 0.5749134480
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25
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25
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N 2.0665657616 -1.5738488309 0.1665385721
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C 2.7727042231 -0.3622083435 -0.3226992137
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H 0.4155006230 0.3036523983 1.1797441237
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25
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25
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25
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H -2.8845837684 1.1083956166 0.2016053653Restarting 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 &Last updated
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