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grimme-lab
GFN-FF: Wrong number of hydrogen bonds and therefore errors in energies
Describe the bug In xtb 6.7.1, the number of bound hydrogens is wrong and therefore the energies are probably also erroneous. In xtb 6.5.0, it seems to be more reasonable.
To Reproduce Steps to reproduce the behaviour:
xtb struc.xyz --gfnff --chrg 1 with the following geometry:
2.
3. start xtb with (all the options here)
4. run xtb with your options and the --verbose flag
5. output showing the error
struc.xyz
11
N -0.50092885765285 -1.43619780271398 -0.54472045972726
C 0.48802227158383 1.42850143520850 0.64900817141844
C -1.24446115854489 -0.82674425640188 0.58230671987245
C -0.78935639775705 -2.05567076686531 0.64831133727514
H -0.60930541092851 -2.99638145773496 1.14321984120870
Sn -1.68094207605292 1.33353414409303 0.71503139888144
Sn 0.08357735264444 -1.46520817937375 -2.53119981842309
H -0.18031024173011 0.47216680459566 -2.30245147300150
H 0.92370413500231 0.75600974372100 1.40187658632209
Sn 1.52891541154427 0.75532209824029 -1.14954864175881
H 0.82985387189149 2.44693283723143 0.8582279379323
xTB 6.5.0 output
-----------------------------------------------------------
| ===================== |
| x T B |
| ===================== |
| S. Grimme |
| Mulliken Center for Theoretical Chemistry |
| University of Bonn |
-----------------------------------------------------------
* xtb version 6.5.0 (746241f) compiled by 'ehlert@majestix' on 2022-05-15
xtb is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
xtb 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. See the
GNU Lesser General Public License for more details.
Cite this work as:
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht,
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11,
e01493. DOI: 10.1002/wcms.1493
for GFN2-xTB:
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
for GFN1-xTB:
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
for GFN0-xTB:
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint.
DOI: 10.26434/chemrxiv.8326202.v1
for GFN-FF:
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673.
DOI: 10.1002/anie.202004239
for ALPB and GBSA implicit solvation:
* S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput.,
2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471
for DFT-D4:
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017,
147, 034112. DOI: 10.1063/1.4993215
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher,
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122.
DOI: 10.1063/1.5090222
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys.
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A
for sTDA-xTB:
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103.
DOI: 10.1063/1.4959605
in the mass-spec context:
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879.
DOI: 10.1039/c7sc00601b
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133.
DOI: 10.1021/acsomega.9b02011
for metadynamics refer to:
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862
DOI: 10.1021/acs.jctc.9b00143
for SPH calculations refer to:
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714
DOI: 10.1021/acs.jctc.0c01306
with help from (in alphabetical order)
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, C. Hölzer
A. Katbashev, J. Koopman, C. Lavigne, S. Lehtola, F. März, M. Müller,
F. Musil, H. Neugebauer, J. Pisarek, C. Plett, P. Pracht, F. Pultar,
J. Seibert, P. Shushkov, S. Spicher, M. Stahn, M. Steiner, T. Strunk,
J. Stückrath, T. Rose, and J. Unsleber
* started run on 2025/04/11 at 09:33:31.266
-------------------------------------------------
| Calculation Setup |
-------------------------------------------------
program call : xtb struc.xyz --gfnff
hostname : fs7
coordinate file : struc.xyz
omp threads : 16
ID Z sym. atoms
1 7 N 1
2 6 C 2-4
3 1 H 5, 8, 9, 11
4 50 Sn 6, 7, 10
charge from .CHRG file: 1
==================== Thresholds ====================
CN : 150.00000
rep : 500.00000
disp: 2500.00000
HB1 : 250.00000
HB2 : 450.00000
Pauling EN used:
Z : 1 EN : 2.20
Z : 6 EN : 2.55
Z : 7 EN : 3.04
Z :50 EN : 1.96
electric field strengths (au): 0.000
-------------------------------------------------
| Force Field Initialization |
-------------------------------------------------
distances ...
----------------------------------------
generating topology and atomic info file ...
pair mat ...
computing topology distances matrix with Floyd-Warshall algo ...
making topology EEQ charges ...
#fragments for EEQ constrain: 1
----------------------------------------
generating topology and atomic info file ...
pair mat ...
computing topology distances matrix with Floyd-Warshall algo ...
making topology EEQ charges ...
#fragments for EEQ constrain: 1
rings ...
# BATM 74
# H in HB 3
doing iterative Hueckel for 1 subsystem(s) ...
atom neighbors erfCN metchar sp-hybrid imet pi qest coordinates
1 N 3 2.82 0.00 2 0 1 -0.131 -0.946618 -2.714021 -1.029372
2 C 4 3.46 0.00 3 0 0 -0.111 0.922228 2.699476 1.226448
3 C 3 2.76 0.00 2 0 1 0.016 -2.351691 -1.562320 1.100400
4 C 3 2.79 0.00 2 0 1 0.021 -1.491667 -3.884655 1.225131
5 H 1 0.97 0.00 0 0 0 0.109 -1.151420 -5.662340 2.160372
6 Sn 2 1.98 0.11 2 0 0 0.335 -3.176520 2.520014 1.351214
7 Sn 3 2.48 0.20 3 0 0 0.306 0.157938 -2.768842 -4.783274
8 H 2 1.28 0.09 1 0 0 -0.002 -0.340737 0.892266 -4.351003
9 H 1 0.98 0.01 0 0 0 0.097 1.745548 1.428651 2.649163
10 Sn 3 2.43 0.31 2 0 0 0.264 2.889231 1.427352 -2.172332
11 H 1 0.97 0.01 0 0 0 0.097 1.568197 4.624033 1.621816
#atoms : 11
#bonds : 13
#angl : 23
#tors : 30
#nmol : 1
#optfrag : 1
-------------------------------------------------
| G F N - F F |
| A general generic force-field |
| Version 1.0.3 |
-------------------------------------------------
Number of HB bonds (bound hydrogen) 9
Number of HB bonds (unbound hydrogen) 0
Number of XB bonds 0
E+G (total) 0 d, 0 h, 0 min, 0.000 sec
distance/D3 list ... 0 min, 0.000 sec ( 1.528%)
non bonded repulsion ... 0 min, 0.000 sec ( 16.862%)
dCN ... 0 min, 0.000 sec ( 4.024%)
EEQ energy and q ... 0 min, 0.000 sec ( 14.722%)
D3 ... 0 min, 0.000 sec ( 9.424%)
EEQ gradient ... 0 min, 0.000 sec ( 4.483%)
bonds ... 0 min, 0.000 sec ( 4.483%)
bend and torsion ... 0 min, 0.000 sec ( 14.060%)
bonded ATM ... 0 min, 0.000 sec ( 5.756%)
HB/XB (incl list setup) ... 0 min, 0.000 sec ( 7.947%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy 0.063842102145 Eh ::
:: gradient norm 0.326238860984 Eh/a0 ::
::.................................................::
:: bond energy -1.582254561999 Eh ::
:: angle energy 0.317478049105 Eh ::
:: torsion energy 0.011161159138 Eh ::
:: repulsion energy 0.065607637654 Eh ::
:: electrostat energy 1.262500844126 Eh ::
:: dispersion energy -0.010062693553 Eh ::
:: HB energy 0.000000000000 Eh ::
:: XB energy 0.000000000000 Eh ::
:: bonded atm energy -0.000588332325 Eh ::
:: external energy 0.000000000000 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge 1.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
-------------------------------------------------
| Property Printout |
-------------------------------------------------
-------------------------------------------------
| TOTAL ENERGY 0.063842102145 Eh |
| GRADIENT NORM 0.326238860984 Eh/α |
-------------------------------------------------
########################################################################
[WARNING] Runtime exception occurred
-1- gfnff_setup: Could not read topology file.
########################################################################
------------------------------------------------------------------------
* finished run on 2025/04/11 at 09:33:31.322
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.056 sec
* cpu-time: 0 d, 0 h, 0 min, 0.609 sec
* ratio c/w: 10.869 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.001 sec
* cpu-time: 0 d, 0 h, 0 min, 0.021 sec
* ratio c/w: 15.113 speedup
xTB 6.7.1 output
-----------------------------------------------------------
| ===================== |
| x T B |
| ===================== |
| S. Grimme |
| Mulliken Center for Theoretical Chemistry |
| University of Bonn |
-----------------------------------------------------------
* xtb version 6.7.1 (edcfbbe) compiled by 'albert@albert-system' on 2024-07-22
xtb is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
xtb 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. See the
GNU Lesser General Public License for more details.
Cite this work as:
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht,
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11,
e01493. DOI: 10.1002/wcms.1493
for GFN2-xTB:
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
for GFN1-xTB:
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
for GFN0-xTB:
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint.
DOI: 10.26434/chemrxiv.8326202.v1
for GFN-FF:
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673.
DOI: 10.1002/anie.202004239
for ALPB and GBSA implicit solvation:
* S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput.,
2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471
for ddCOSMO and CPCM-X implicit solvation:
* M. Stahn, S. Ehlert, S. Grimme, J. Phys. Chem. A,
2023, XX, XXXX-XXXX. DOI: 10.1021/acs.jpca.3c04382
for DFT-D4:
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017,
147, 034112. DOI: 10.1063/1.4993215
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher,
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122.
DOI: 10.1063/1.5090222
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys.
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A
for sTDA-xTB:
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103.
DOI: 10.1063/1.4959605
in the mass-spec context:
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879.
DOI: 10.1039/c7sc00601b
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133.
DOI: 10.1021/acsomega.9b02011
for metadynamics refer to:
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862
DOI: 10.1021/acs.jctc.9b00143
for SPH calculations refer to:
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714
DOI: 10.1021/acs.jctc.0c01306
for ONIOM refer to:
* C. Plett, A. Katbashev, S. Ehlert, S. Grimme, M. Bursch,
Phys. Chem. Chem. Phys., 2023, 25, 17860-17868. DOI: 10.1039/D3CP02178E
for DIPRO refer to:
* J. Kohn, N. Gildemeister, S. Grimme, D. Fazzi, A. Hansen,
J. Chem. Phys., 2023, just accepted.
for PTB refer to:
* S. Grimme, M. Mueller, A. Hansen, J. Chem. Phys., 2023, 158, 124111.
DOI: 10.1063/5.0137838
with help from (in alphabetical order)
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, C. Hölzer
A. Katbashev, J. Kohn, J. Koopman, C. Lavigne, S. Lehtola, F. März, M. Müller,
F. Musil, H. Neugebauer, J. Pisarek, C. Plett, P. Pracht, F. Pultar,
J. Seibert, P. Shushkov, S. Spicher, M. Stahn, M. Steiner, T. Strunk,
J. Stückrath, T. Rose, and J. Unsleber
* started run on 2025/04/11 at 09:33:10.609
ID Z sym. atoms
1 7 N 1
2 6 C 2-4
3 1 H 5, 8, 9, 11
4 50 Sn 6, 7, 10
-------------------------------------------------
| Calculation Setup |
-------------------------------------------------
program call : xtb struc.xyz --gfnff
hostname : fs7
coordinate file : struc.xyz
omp threads : 16
charge from .CHRG file: 1
==================== Thresholds ====================
CN : 150.00000
rep : 500.00000
disp: 2500.00000
HB1 : 250.00000
HB2 : 450.00000
Pauling EN used:
Z : 1 EN : 2.20
Z : 6 EN : 2.55
Z : 7 EN : 3.04
Z :50 EN : 1.96
electric field strengths (au): 0.000
-------------------------------------------------
| Force Field Initialization |
-------------------------------------------------
distances ...
----------------------------------------
generating topology and atomic info file ...
pair mat ...
computing topology distances matrix with Floyd-Warshall algo ...
making topology EEQ charges ...
#fragments for EEQ constrain: 1
----------------------------------------
generating topology and atomic info file ...
pair mat ...
computing topology distances matrix with Floyd-Warshall algo ...
making topology EEQ charges ...
#fragments for EEQ constrain: 1
rings ...
# BATM 74
# H in HB 3
doing iterative Hueckel for 1 subsystem(s) ...
WARNING: probably wrong pi occupation for system 1. Second attempt with Nel=Nel-1!
at,nb,topo%hyb,Npiel: 1 N 3 2 1
at,nb,topo%hyb,Npiel: 3 C 3 2 1
at,nb,topo%hyb,Npiel: 4 C 3 2 1
eigenvalues
# : 1 2 3
occ. : 2.000 0.000 0.000
eps : -4.214 1.703 2.953
atom neighbors erfCN metchar sp-hybrid imet pi qest coordinates
1 N 3 2.82 0.00 2 0 1 -0.131 -0.946618 -2.714021 -1.029372
2 C 4 3.46 0.00 3 0 0 -0.111 0.922228 2.699476 1.226448
3 C 3 2.76 0.00 2 0 1 0.016 -2.351691 -1.562320 1.100400
4 C 3 2.79 0.00 2 0 1 0.021 -1.491667 -3.884655 1.225131
5 H 1 0.97 0.00 0 0 0 0.109 -1.151420 -5.662340 2.160372
6 Sn 2 1.98 0.11 2 0 0 0.335 -3.176520 2.520014 1.351214
7 Sn 3 2.48 0.20 3 0 0 0.306 0.157938 -2.768842 -4.783274
8 H 2 1.28 0.09 1 0 0 -0.002 -0.340737 0.892266 -4.351003
9 H 1 0.98 0.01 0 0 0 0.097 1.745548 1.428651 2.649163
10 Sn 3 2.43 0.31 2 0 0 0.264 2.889231 1.427352 -2.172332
11 H 1 0.97 0.01 0 0 0 0.097 1.568197 4.624033 1.621816
#atoms : 11
#bonds : 13
#angl : 23
#tors : 30
#nmol : 1
#optfrag : 1
-------------------------------------------------
| G F N - F F |
| A general generic force-field |
| Version 1.0.3 |
-------------------------------------------------
Number of HB bonds (bound hydrogen) 54
Number of HB bonds (unbound hydrogen) 0
Number of XB bonds 0
E+G (total) 0 d, 0 h, 0 min, 0.001 sec
distance/D3 list ... 0 min, 0.000 sec ( 0.741%)
non bonded repulsion ... 0 min, 0.000 sec ( 16.429%)
dCN ... 0 min, 0.000 sec ( 2.135%)
EEQ energy and q ... 0 min, 0.000 sec ( 15.658%)
D3 ... 0 min, 0.000 sec ( 16.311%)
EEQ gradient ... 0 min, 0.000 sec ( 13.049%)
bonds ... 0 min, 0.000 sec ( 15.065%)
bend and torsion ... 0 min, 0.000 sec ( 2.847%)
bonded ATM ... 0 min, 0.000 sec ( 4.004%)
HB/XB (incl list setup) ... 0 min, 0.000 sec ( 5.457%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -0.017862799392 Eh ::
:: gradient norm 0.271075313342 Eh/a0 ::
::.................................................::
:: bond energy -1.664380282533 Eh ::
:: angle energy 0.317478049105 Eh ::
:: torsion energy 0.011581978134 Eh ::
:: repulsion energy 0.065607637654 Eh ::
:: electrostat energy 1.262500844126 Eh ::
:: dispersion energy -0.010062693553 Eh ::
:: HB energy 0.000000000000 Eh ::
:: XB energy 0.000000000000 Eh ::
:: bonded atm energy -0.000588332325 Eh ::
:: external energy 0.000000000000 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge 1.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
-------------------------------------------------
| Property Printout |
-------------------------------------------------
molecular dipole:
x y z tot (Debye)
q only: -0.022 0.353 -1.162 3.088
-------------------------------------------------
| TOTAL ENERGY -0.017862799392 Eh |
| GRADIENT NORM 0.271075313342 Eh/α |
-------------------------------------------------
########################################################################
[WARNING] Runtime exception occurred
-1- gfnff_setup: Could not read topology file.
########################################################################
------------------------------------------------------------------------
* finished run on 2025/04/11 at 09:33:10.644
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.034 sec
* cpu-time: 0 d, 0 h, 0 min, 0.431 sec
* ratio c/w: 12.666 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.001 sec
* cpu-time: 0 d, 0 h, 0 min, 0.017 sec
* ratio c/w: 14.842 speedup
Note that the bond energy and torsion energy change. Also note that the total energy for 6.5.0 is positive. This might be caused by a bug in the EEQ electrostatic energy for charged systems.
I've tested this input with #1362. The output is the following:
xtb #1362
``` ----------------------------------------------------------- | ===================== | | x T B | | ===================== | | S. Grimme | | Mulliken Center for Theoretical Chemistry | | University of Bonn | ----------------------------------------------------------- * xtb version 6.7.1 (4f62911ea5405dc1718721513619a287ee3d3df4) compiled by '@Linux' on 2025/12/02
xtb is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
xtb 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. See the
GNU Lesser General Public License for more details.
Cite this work as:
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht,
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11,
e01493. DOI: 10.1002/wcms.1493
for GFN2-xTB:
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
for GFN1-xTB:
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
for GFN0-xTB:
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint.
DOI: 10.26434/chemrxiv.8326202.v1
for GFN-FF:
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673.
DOI: 10.1002/anie.202004239
for ALPB and GBSA implicit solvation:
* S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput.,
2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471
for ddCOSMO and CPCM-X implicit solvation:
* M. Stahn, S. Ehlert, S. Grimme, J. Phys. Chem. A,
2023, XX, XXXX-XXXX. DOI: 10.1021/acs.jpca.3c04382
for DFT-D4:
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017,
147, 034112. DOI: 10.1063/1.4993215
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher,
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122.
DOI: 10.1063/1.5090222
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys.
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A
for sTDA-xTB:
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103.
DOI: 10.1063/1.4959605
in the mass-spec context:
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879.
DOI: 10.1039/c7sc00601b
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133.
DOI: 10.1021/acsomega.9b02011
for metadynamics refer to:
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862
DOI: 10.1021/acs.jctc.9b00143
for SPH calculations refer to:
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714
DOI: 10.1021/acs.jctc.0c01306
for ONIOM refer to:
* C. Plett, A. Katbashev, S. Ehlert, S. Grimme, M. Bursch,
Phys. Chem. Chem. Phys., 2023, 25, 17860-17868. DOI: 10.1039/D3CP02178E
for DIPRO refer to:
* J. Kohn, N. Gildemeister, S. Grimme, D. Fazzi, A. Hansen,
J. Chem. Phys. 159, 144106 (2023). DOI: 10.1063/5.0167484
for PTB refer to:
* S. Grimme, M. Mueller, A. Hansen, J. Chem. Phys., 2023, 158, 124111.
DOI: 10.1063/5.0137838
with help from (in alphabetical order)
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, C. Hölzer
A. Katbashev, J. Kohn, J. Koopman, C. Lavigne, S. Lehtola, F. März, M. Müller,
F. Musil, H. Neugebauer, J. Pisarek, C. Plett, P. Pracht, F. Pultar,
J. Seibert, P. Shushkov, S. Spicher, M. Stahn, M. Steiner, T. Strunk,
J. Stückrath, T. Rose, and J. Unsleber
* started run on 2025/12/12 at 07:41:07.974
ID Z sym. atoms
1 7 N 1
2 6 C 2-4
3 1 H 5, 8, 9, 11
4 50 Sn 6, 7, 10
-------------------------------------------------
| Calculation Setup |
-------------------------------------------------
program call : ../xtb sstruc.xyz --gfnff --chrg 1
hostname : vn01
coordinate file : sstruc.xyz
omp threads : 16
==================== Thresholds ====================
CN : 150.00000
rep : 500.00000
disp: 2500.00000
HB1 : 250.00000
HB2 : 450.00000
Pauling EN used:
Z : 1 EN : 2.20
Z : 6 EN : 2.55
Z : 7 EN : 3.04
Z :50 EN : 1.96
electric field strengths (au): 0.000
-------------------------------------------------
| Force Field Initialization |
-------------------------------------------------
distances ...
----------------------------------------
generating topology and atomic info file ...
pair mat ...
computing topology distances matrix with Floyd-Warshall algo ...
making topology EEQ charges ...
#fragments for EEQ constrain: 1
----------------------------------------
generating topology and atomic info file ...
pair mat ...
computing topology distances matrix with Floyd-Warshall algo ...
making topology EEQ charges ...
#fragments for EEQ constrain: 1
rings ...
# BATM 74
# H in HB 3
doing iterative Hueckel for 1 subsystem(s) ...
WARNING: probably wrong pi occupation for system 1. Second attempt with Nel=Nel-1!
at,nb,topo%hyb,Npiel: 1 N 3 2 1
at,nb,topo%hyb,Npiel: 3 C 3 2 1
at,nb,topo%hyb,Npiel: 4 C 3 2 1
eigenvalues
# : 1 2 3
occ. : 2.000 0.000 0.000
eps : -4.214 1.703 2.953
atom neighbors erfCN metchar sp-hybrid imet pi qest coordinates
1 N 3 2.82 0.00 2 0 1 -0.131 -0.946618 -2.714021 -1.029372
2 C 4 3.46 0.00 3 0 0 -0.111 0.922228 2.699476 1.226448
3 C 3 2.76 0.00 2 0 1 0.016 -2.351691 -1.562320 1.100400
4 C 3 2.79 0.00 2 0 1 0.021 -1.491667 -3.884655 1.225131
5 H 1 0.97 0.00 0 0 0 0.109 -1.151420 -5.662340 2.160372
6 Sn 2 1.98 0.11 2 0 0 0.335 -3.176520 2.520014 1.351214
7 Sn 3 2.48 0.20 3 0 0 0.306 0.157938 -2.768842 -4.783274
8 H 2 1.28 0.09 1 0 0 -0.002 -0.340737 0.892266 -4.351003
9 H 1 0.98 0.01 0 0 0 0.097 1.745548 1.428651 2.649163
10 Sn 3 2.43 0.31 2 0 0 0.264 2.889231 1.427352 -2.172332
11 H 1 0.97 0.01 0 0 0 0.097 1.568197 4.624033 1.621816
#atoms : 11
#bonds : 13
#angl : 23
#tors : 30
#nmol : 1
#optfrag : 1
-------------------------------------------------
| G F N - F F |
| A general generic force-field |
| Version 1.0.3 |
-------------------------------------------------
Number of HB bonds (bound hydrogen) 9
Number of HB bonds (unbound hydrogen) 0
Number of XB bonds 0
9 0 0
3 1 5 1 1
3 1 9 1 1
3 1 11 1 1
4 1 5 1 1
4 1 9 1 1
4 1 11 1 1
4 3 5 1 1
4 3 9 1 1
4 3 11 1 1
9 0 0
3 1 5 1 1
3 1 9 1 1
3 1 11 1 1
4 1 5 1 1
4 1 9 1 1
4 1 11 1 1
4 3 5 1 1
4 3 9 1 1
4 3 11 1 1
E+G (total) 0 d, 0 h, 0 min, 0.001 sec
distance/D3 list ... 0 min, 0.000 sec ( 0.841%)
non bonded repulsion ... 0 min, 0.000 sec ( 5.360%)
dCN ... 0 min, 0.000 sec ( 2.081%)
EEQ energy and q ... 0 min, 0.000 sec ( 4.934%)
D3 ... 0 min, 0.000 sec ( 18.427%)
EEQ gradient ... 0 min, 0.000 sec ( 3.288%)
bonds ... 0 min, 0.000 sec ( 5.984%)
bend and torsion ... 0 min, 0.000 sec ( 11.931%)
bonded ATM ... 0 min, 0.000 sec ( 1.658%)
HB/XB (incl list setup) ... 0 min, 0.000 sec ( 40.745%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -0.017862799392 Eh ::
:: gradient norm 0.271075313342 Eh/a0 ::
::.................................................::
:: bond energy -1.664380282533 Eh ::
:: angle energy 0.317478049105 Eh ::
:: torsion energy 0.011581978134 Eh ::
:: repulsion energy 0.065607637654 Eh ::
:: electrostat energy 1.262500844126 Eh ::
:: dispersion energy -0.010062693553 Eh ::
:: HB energy 0.000000000000 Eh ::
:: XB energy 0.000000000000 Eh ::
:: bonded atm energy -0.000588332325 Eh ::
:: external energy 0.000000000000 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge 1.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
-------------------------------------------------
| Property Printout |
-------------------------------------------------
molecular dipole:
x y z tot (Debye)
q only: -0.022 0.353 -1.162 3.088
-------------------------------------------------
| TOTAL ENERGY -0.017862799392 Eh |
| GRADIENT NORM 0.271075313342 Eh/α |
-------------------------------------------------
########################################################################
[WARNING] Runtime exception occurred
-1- gfnff_setup: Could not read topology file.
########################################################################
------------------------------------------------------------------------
* finished run on 2025/12/12 at 07:41:08.037
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.063 sec
* cpu-time: 0 d, 0 h, 0 min, 0.382 sec
* ratio c/w: 6.104 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.004 sec
* cpu-time: 0 d, 0 h, 0 min, 0.032 sec
* ratio c/w: 8.898 speedup
```
Looks like the output has a proper number of bonds:
Number of HB bonds (bound hydrogen) 9
Number of HB bonds (unbound hydrogen) 0
Number of XB bonds 0
And normal energies:
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -0.017862799392 Eh ::
:: gradient norm 0.271075313342 Eh/a0 ::
::.................................................::
:: bond energy -1.664380282533 Eh ::
:: angle energy 0.317478049105 Eh ::
:: torsion energy 0.011581978134 Eh ::
:: repulsion energy 0.065607637654 Eh ::
:: electrostat energy 1.262500844126 Eh ::
:: dispersion energy -0.010062693553 Eh ::
:: HB energy 0.000000000000 Eh ::
:: XB energy 0.000000000000 Eh ::
:: bonded atm energy -0.000588332325 Eh ::
:: external energy 0.000000000000 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge 1.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
-------------------------------------------------
| TOTAL ENERGY -0.017862799392 Eh |
| GRADIENT NORM 0.271075313342 Eh/α |
-------------------------------------------------
