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grimme-lab
GFN-FF: NaN bonded atm energy
Describe the bug In xtb 6.7.1, I get a NaN bonded atm term leading to a NaN total energy. With xtb 6.5.0, there are no problems.
To Reproduce Steps to reproduce the behaviour:
xtb struc.xyz --gfnff --chrg -1 for this geometry:
struc.xyz
11
H -0.84462814585543 -0.19500848845119 -2.48547158646135
H 1.83637313711558 0.32029935415578 -2.31306886307104
H 0.63552535605618 -1.55032128951911 -0.75326557722882
B -0.74841410766123 2.25010029621782 0.49609111572967
B 0.65237417313343 2.34235529778879 1.32523058882990
C 0.01259204134162 0.97671570943565 0.11229036999530
C -0.00707928897868 1.02237755668225 1.74394842781084
Al 2.08821989368887 0.85437513894389 1.14906134317571
Al 0.46435632988754 -0.05828849495688 -1.56080644053513
Al -1.95124532722693 0.64540091537625 1.31655138764930
Al 0.13342493849906 -0.90776629567326 1.02360433410561
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 09:27:44.065
ID Z sym. atoms
1 1 H 1-3
2 5 B 4, 5
3 6 C 6, 7
4 13 Al 8-11
-------------------------------------------------
| Calculation Setup |
-------------------------------------------------
program call : xtb struc.xyz --gff --chrg -1
hostname : fs7
coordinate file : struc.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 : 5 EN : 2.04
Z : 6 EN : 2.55
Z :13 EN : 1.61
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 36
# H in HB 2
doing iterative Hueckel for 1 subsystem(s) ...
atom neighbors erfCN metchar sp-hybrid imet pi qest coordinates
1 H 1 0.94 0.02 0 0 0 -0.130 -1.596116 -0.368513 -4.696861
2 H 1 0.94 0.02 0 0 0 -0.130 3.470242 0.605278 -4.371067
3 H 2 1.31 0.08 1 0 0 -0.114 1.200969 -2.929683 -1.423466
4 B 4 3.29 0.09 3 0 0 -0.240 -1.414298 4.252073 0.937476
5 B 4 3.27 0.09 3 0 0 -0.240 1.232809 4.426410 2.504323
6 C 3 4.25 0.00 2 0 1 -0.033 0.023796 1.845725 0.212198
7 C 3 4.14 0.00 2 0 1 -0.042 -0.013378 1.932014 3.295585
8 Al 4 3.34 0.43 3 1 0 -0.044 3.946164 1.614535 2.171411
9 Al 5 3.90 0.20 3 1 0 0.046 0.877506 -0.110149 -2.949497
10 Al 4 3.26 0.33 3 1 0 -0.044 -3.687319 1.219631 2.487922
11 Al 6 3.99 0.23 3 1 0 -0.028 0.252137 -1.715430 1.934332
#atoms : 11
#bonds : 22
#angl : 53
#tors : 161
#nmol : 1
#optfrag : 1
-------------------------------------------------
| G F N - F F |
| A general generic force-field |
| Version 1.0.3 |
-------------------------------------------------
Number of HB bonds (bound hydrogen) 12
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 ( 0.421%)
non bonded repulsion ... 0 min, 0.000 sec ( 9.244%)
dCN ... 0 min, 0.000 sec ( 1.343%)
EEQ energy and q ... 0 min, 0.000 sec ( 9.765%)
D3 ... 0 min, 0.000 sec ( 10.588%)
EEQ gradient ... 0 min, 0.000 sec ( 8.663%)
bonds ... 0 min, 0.000 sec ( 18.669%)
bend and torsion ... 0 min, 0.000 sec ( 17.666%)
bonded ATM ... 0 min, 0.000 sec ( 8.823%)
HB/XB (incl list setup) ... 0 min, 0.000 sec ( 10.006%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy NaN Eh ::
:: gradient norm NaN Eh/a0 ::
::.................................................::
:: bond energy -1.291075068176 Eh ::
:: angle energy 0.153943522313 Eh ::
:: torsion energy 0.089622127749 Eh ::
:: repulsion energy 0.041082150669 Eh ::
:: electrostat energy -1.113127397168 Eh ::
:: dispersion energy -0.008973046013 Eh ::
:: HB energy 0.000000000000 Eh ::
:: XB energy 0.000000000000 Eh ::
:: bonded atm energy NaN 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: -0.292 -1.852 -0.070 4.768
-------------------------------------------------
| TOTAL ENERGY NaN Eh |
| GRADIENT NORM NaN Eh/α |
-------------------------------------------------
########################################################################
[WARNING] Runtime exception occurred
-1- gfnff_setup: Could not read topology file.
########################################################################
------------------------------------------------------------------------
* finished run on 2025/04/11 at 09:27:44.116
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.050 sec
* cpu-time: 0 d, 0 h, 0 min, 0.671 sec
* ratio c/w: 13.376 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.002 sec
* cpu-time: 0 d, 0 h, 0 min, 0.024 sec
* ratio c/w: 14.912 speedup
