Closed
Description
Describe the bug
The charge distribution is computed without using the neighbor list from the ffnb section in the input file. This is evident from the gfnff_charges file, but also in the output which reports #fragments for EEQ constrain: 1 although the bonds specified with ffnb give rise to two fragments.
The bug was seen with a build from March 5 2025 (xtb version 6.7.1 (04e5303))
To Reproduce
Steps to reproduce the behaviour:
- happens with input
example.xyz:
5
H2O and OH-
O 0.000000 0.000000 0.000000
H 0.757000 0.586000 0.000000
H -0.757000 0.586000 0.000000
O 2.200000 1.400000 0.000000
H 1.500000 0.800000 0.000000
control.inp:
$ffnb
nb = 1:2
nb = 2:1
nb = 3:4, 5
nb = 4:3
nb = 5:3
$end
- start
xtbwithexample.xyz --gfnff --input control.inp --charge -1 - output showing the error:
Content of gfnff_charges:
-0.63277778
0.07228187
0.08012365
-0.79885588
0.27922814
Full xtb output:
-----------------------------------------------------------
| ===================== |
| x T B |
| ===================== |
| S. Grimme |
| Mulliken Center for Theoretical Chemistry |
| University of Bonn |
-----------------------------------------------------------
* xtb version 6.7.1 (04e5303) compiled by 'runner@fv-az1705-474' on 2025-03-05
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 2025/03/12 at 13:08:50.166
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
CONSTRAINTS & SCANS: DEBUG SECTION
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
ID Z sym. atoms
1 8 O 1, 4
2 1 H 2, 3, 5
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
-------------------------------------------------
| Calculation Setup |
-------------------------------------------------
program call : xtb example.xyz --gfnff --input control.inp --charge -1 --verbose
coordinate file : example.xyz
xtbhome directory : /home/xxx
path for xtb : /home/xxx
xcontrol input file : control.inp
omp threads : 16
entering GFN-FF setup routine... 5
==================== 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 : 8 EN : 3.44
electric field strengths (au): 0.000
-------------------------------------------------
| Force Field Initialization |
-------------------------------------------------
distances ...
----------------------------------------
generating topology and atomic info file ...
The neighborlist has been adjusted according to the input 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 ...
The neighborlist has been adjusted according to the input file.
pair mat ...
computing topology distances matrix with Floyd-Warshall algo ...
making topology EEQ charges ...
#fragments for EEQ constrain: 1
rings ...
# BATM 0
# H in HB 1
doing iterative Hueckel for 2 subsystem(s) ...
iterative Hueckel run to get P ...
atom neighbors erfCN metchar sp-hybrid imet pi qest coordinates
1 O 1 1.92 0.00 3 0 0 -0.637 0.000000 0.000000 0.000000
2 H 1 1.77 0.07 1 0 0 0.170 1.430523 1.107380 0.000000
3 H 2 0.97 0.00 0 0 0 0.354 -1.430523 1.107380 0.000000
4 O 1 0.98 0.00 2 0 0 -0.668 4.157397 2.645617 0.000000
5 H 1 1.78 0.07 1 0 0 -0.219 2.834589 1.511781 0.000000
molecular fragment # atoms topo charge
1 5 -1.000
#atoms : 5
#bonds : 3
bond atoms type in ring R R0 piBO fqq kbond(tot) alp
O H 1 2 1 0 0.957 0.922 0.000 1.047 -0.041 0.583
H O 3 4 1 0 3.067 0.728 0.000 1.047 -0.149 0.657
H H 3 5 1 0 2.267 0.840 0.000 1.047 -0.055 0.402
#angl : 1
angle atoms phi0 phi FC pi rings
3 5 4 100.000 9.975 0.148 F 0
torsion atoms nrot rings phi0 phi FC
out-of-plane atoms phi0 phi FC
#tors : 0
#nmol : 1
#optfrag : 1
GFN-FF setup done.
-------------------------------------------------
| G F N - F F |
| A general generic force-field |
| Version 1.0.3 |
-------------------------------------------------
Number of HB bonds (bound hydrogen) 0
Number of HB bonds (unbound hydrogen) 6
Number of XB bonds 0
E+G (total) 0 d, 0 h, 0 min, 0.002 sec
distance/D3 list ... 0 min, 0.000 sec ( 0.496%)
non bonded repulsion ... 0 min, 0.000 sec ( 13.224%)
dCN ... 0 min, 0.000 sec ( 0.416%)
EEQ energy and q ... 0 min, 0.000 sec ( 11.221%)
D3 ... 0 min, 0.000 sec ( 11.182%)
EEQ gradient ... 0 min, 0.000 sec ( 7.276%)
bonds ... 0 min, 0.001 sec ( 27.647%)
bend and torsion ... 0 min, 0.000 sec ( 12.103%)
bonded ATM ... 0 min, 0.000 sec ( 0.169%)
HB/XB (incl list setup) ... 0 min, 0.000 sec ( 13.144%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -0.769440140696 Eh ::
:: gradient norm 0.790955614087 Eh/a0 ::
::.................................................::
:: bond energy -0.044340515347 Eh ::
:: angle energy 0.000014258410 Eh ::
:: torsion energy 0.000000000000 Eh ::
:: repulsion energy 0.545844072303 Eh ::
:: electrostat energy -1.270171709235 Eh ::
:: dispersion energy -0.000786246826 Eh ::
:: HB energy 0.000000000000 Eh ::
:: XB energy 0.000000000000 Eh ::
:: bonded atm energy 0.000000000000 Eh ::
:: external energy 0.000000000000 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge -1.000000000000 e ::
::.................................................::
:: atomisation energy 0.000000000000 Eh ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
-------------------------------------------------
| Property Printout |
-------------------------------------------------
molecular dipole:
x y z tot (Debye)
q only: -2.541 -1.523 0.000 7.529
-------------------------------------------------
| TOTAL ENERGY -0.769440140696 Eh |
| GRADIENT NORM 0.790955614087 Eh/α |
-------------------------------------------------
########################################################################
[WARNING] Runtime exception occurred
-1- gfnff_setup: Could not read topology file.
########################################################################
------------------------------------------------------------------------
unit open action filename
129 false : read control.inp
130 true : read control.inp
129 false : read example.xyz
129 false : read control.inp
129 false : written gfnff_topo
129 false : replaced gfnff_charges
------------------------------------------------------------------------
* finished run on 2025/03/12 at 13:08:50.187
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.021 sec
* cpu-time: 0 d, 0 h, 0 min, 0.029 sec
* ratio c/w: 1.423 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.004 sec
* cpu-time: 0 d, 0 h, 0 min, 0.008 sec
* ratio c/w: 2.043 speedup
Expected behaviour
The EEQ constraints are expected to respect the bonds that have been provided such that the bonds used and the charges assigned are consistent.
Input files
The files have been renamed to .txt files for uploading.
example.txt
control.txt