Describe the bug
The docs say that ALPB doesn't support methanol, but it actually does. This is confusing.
To Reproduce
Steps to reproduce the behaviour:
happens with input benzene.xyz
12
benzene
C -0.71618036 2.71883299 0.00000000
C 0.67897964 2.71883299 0.00000000
C 1.37651764 3.92658399 0.00000000
C 0.67886364 5.13509299 -0.00119900
C -0.71596136 5.13501499 -0.00167800
C -1.41356236 3.92680899 -0.00068200
H -1.26593936 1.76651599 0.00045000
H 1.22848764 1.76631999 0.00131500
H 2.47619764 3.92666399 0.00063400
H 1.22906364 6.08723599 -0.00125800
H -1.26608336 6.08729599 -0.00263100
H -2.51316636 3.92699199 -0.00086200
start xtb with xtb benzene.xyz --alpb methanol
run xtb with your options and the --verbose flag
output showing the error
$ xtb benzene.xyz --alpb methanol
-----------------------------------------------------------
| ===================== |
| x T B |
| ===================== |
| S. Grimme |
| Mulliken Center for Theoretical Chemistry |
| University of Bonn |
-----------------------------------------------------------
* xtb version 6.6.1 (8d0f1dd) compiled by 'runner@Mac-1690902418499.local' on 2023-08-01
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 2024/08/08 at 16:39:02.540
-------------------------------------------------
| Calculation Setup |
-------------------------------------------------
program call : xtb benzene.xyz --alpb methanol
coordinate file : benzene.xyz
omp threads : 11
ID Z sym. atoms
1 6 C 1-6
2 1 H 7-12
-------------------------------------------------
| G F N 2 - x T B |
-------------------------------------------------
Reference 10.1021/acs.jctc.8b01176
* Hamiltonian:
H0-scaling (s, p, d) 1.850000 2.230000 2.230000
zeta-weighting 0.500000
* Dispersion:
s8 2.700000
a1 0.520000
a2 5.000000
s9 5.000000
* Repulsion:
kExp 1.500000 1.000000
rExp 1.000000
* Coulomb:
alpha 2.000000
third order shell-resolved
anisotropic true
a3 3.000000
a5 4.000000
cn-shift 1.200000
cn-exp 4.000000
max-rad 5.000000
* Solvation model: ALPB
Solvent methanol
Parameter file internal GFN2-xTB/ALPB
Dielectric constant 3.2700E+01
Reference state gsolv [1 M gas/solution]
Free energy shift 3.9449E-03 Eh 2.4755E+00 kcal/mol
Temperature 2.9815E+02 K
Density 7.9200E-01 kg/L
Solvent mass 3.2040E+01 g/mol
Interaction kernel P16
Born radius scaling (c1) 1.6600E+00
Born radii integrator GBOBC
Born offset 0.0000E+00 a0 0.0000E+00 AA
H-bond correction true
Ion screening false
Surface tension 1.0000E-05 Eh 1.5569E+01 dyn/cm
Grid points 230 per atom
q/qsh data taken from xtbrestart
CAMM data taken from xtbrestart
...................................................
: SETUP :
:.................................................:
: # basis functions 30 :
: # atomic orbitals 30 :
: # shells 18 :
: # electrons 30 :
: max. iterations 250 :
: Hamiltonian GFN2-xTB :
: restarted? true :
: GBSA solvation true :
: PC potential false :
: electronic temp. 300.0000000 K :
: accuracy 1.0000000 :
: -> integral cutoff 0.2500000E+02 :
: -> integral neglect 0.1000000E-07 :
: -> SCF convergence 0.1000000E-05 Eh :
: -> wf. convergence 0.1000000E-03 e :
: Broyden damping 0.4000000 :
...................................................
iter E dE RMSdq gap omega full diag
1 -16.1729795 -0.161730E+02 0.265E-02 4.82 0.0 T
2 -16.1729823 -0.277105E-05 0.697E-03 4.82 4.1 T
3 -16.1729825 -0.197374E-06 0.975E-04 4.82 29.6 T
4 -16.1729825 -0.136637E-10 0.323E-05 4.82 892.6 T
*** convergence criteria satisfied after 4 iterations ***
# Occupation Energy/Eh Energy/eV
-------------------------------------------------------------
1 2.0000 -0.6387861 -17.3823
... ... ... ...
9 2.0000 -0.4747785 -12.9194
10 2.0000 -0.4747679 -12.9191
11 2.0000 -0.4719868 -12.8434
12 2.0000 -0.4212588 -11.4630
13 2.0000 -0.4212269 -11.4622
14 2.0000 -0.4011206 -10.9150
15 2.0000 -0.4010887 -10.9142 (HOMO)
16 -0.2238290 -6.0907 (LUMO)
17 -0.2237710 -6.0891
18 -0.0963909 -2.6229
19 0.0931512 2.5348
20 0.1090974 2.9687
... ... ...
30 0.6314559 17.1828
-------------------------------------------------------------
HL-Gap 0.1772597 Eh 4.8235 eV
Fermi-level -0.3124589 Eh -8.5024 eV
SCC (total) 0 d, 0 h, 0 min, 0.012 sec
SCC setup ... 0 min, 0.005 sec ( 44.202%)
Dispersion ... 0 min, 0.000 sec ( 1.434%)
classical contributions ... 0 min, 0.000 sec ( 2.186%)
integral evaluation ... 0 min, 0.000 sec ( 2.129%)
iterations ... 0 min, 0.005 sec ( 43.720%)
molecular gradient ... 0 min, 0.001 sec ( 5.601%)
printout ... 0 min, 0.000 sec ( 0.604%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -15.884463273254 Eh ::
:: total w/o Gsasa/hb -15.877731778659 Eh ::
:: gradient norm 0.029582367152 Eh/a0 ::
:: HOMO-LUMO gap 4.823482459110 eV ::
::.................................................::
:: SCC energy -16.172982484736 Eh ::
:: -> isotropic ES 0.000899885867 Eh ::
:: -> anisotropic ES 0.002841384874 Eh ::
:: -> anisotropic XC 0.013488766376 Eh ::
:: -> dispersion -0.007959599319 Eh ::
:: -> Gsolv -0.006901409875 Eh ::
:: -> Gelec -0.000169915280 Eh ::
:: -> Gsasa -0.010529873495 Eh ::
:: -> Ghb -0.000146540916 Eh ::
:: -> Gshift 0.003944919816 Eh ::
:: repulsion energy 0.288512102173 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge 0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
-------------------------------------------------
| Property Printout |
-------------------------------------------------
* Orbital Energies and Occupations
# Occupation Energy/Eh Energy/eV
-------------------------------------------------------------
1 2.0000 -0.6387861 -17.3823
... ... ... ...
3 2.0000 -0.6088429 -16.5675
4 2.0000 -0.5665475 -15.4165
5 2.0000 -0.5665371 -15.4163
6 2.0000 -0.5278458 -14.3634
7 2.0000 -0.4927274 -13.4078
8 2.0000 -0.4885022 -13.2928
9 2.0000 -0.4747785 -12.9194
10 2.0000 -0.4747679 -12.9191
11 2.0000 -0.4719868 -12.8434
12 2.0000 -0.4212588 -11.4630
13 2.0000 -0.4212269 -11.4622
14 2.0000 -0.4011206 -10.9150
15 2.0000 -0.4010887 -10.9142 (HOMO)
16 -0.2238290 -6.0907 (LUMO)
17 -0.2237710 -6.0891
18 -0.0963909 -2.6229
19 0.0931512 2.5348
20 0.1090974 2.9687
21 0.1478842 4.0241
22 0.1480109 4.0276
23 0.1744588 4.7473
24 0.1745143 4.7488
25 0.3830144 10.4224
26 0.3831519 10.4261
... ... ...
30 0.6314559 17.1828
-------------------------------------------------------------
HL-Gap 0.1772597 Eh 4.8235 eV
Fermi-level -0.3124589 Eh -8.5024 eV
# Z covCN q C6AA α(0)
1 6 C 2.910 -0.031 28.771 8.795
2 6 C 2.910 -0.031 28.770 8.795
3 6 C 2.910 -0.031 28.770 8.795
4 6 C 2.910 -0.031 28.771 8.795
5 6 C 2.910 -0.031 28.770 8.795
6 6 C 2.910 -0.031 28.770 8.795
7 1 H 0.923 0.031 2.574 2.509
8 1 H 0.923 0.031 2.574 2.509
9 1 H 0.923 0.031 2.574 2.509
10 1 H 0.923 0.031 2.574 2.509
11 1 H 0.923 0.031 2.574 2.509
12 1 H 0.923 0.031 2.574 2.509
Mol. C6AA /au·bohr⁶ : 1747.195309
Mol. C8AA /au·bohr⁸ : 42645.607312
Mol. α(0) /au : 67.826514
Wiberg/Mayer (AO) data.
largest (>0.10) Wiberg bond orders for each atom
---------------------------------------------------------------------------
# Z sym total # sym WBO # sym WBO # sym WBO
---------------------------------------------------------------------------
1 6 C 3.991 -- 6 C 1.441 2 C 1.440 7 H 0.970
4 C 0.114
2 6 C 3.991 -- 3 C 1.441 1 C 1.440 8 H 0.970
5 C 0.113
3 6 C 3.991 -- 2 C 1.441 4 C 1.440 9 H 0.970
6 C 0.114
4 6 C 3.991 -- 5 C 1.441 3 C 1.440 10 H 0.970
1 C 0.114
5 6 C 3.991 -- 4 C 1.441 6 C 1.440 11 H 0.970
2 C 0.113
6 6 C 3.991 -- 1 C 1.441 5 C 1.440 12 H 0.970
3 C 0.114
7 1 H 0.999 -- 1 C 0.970
8 1 H 0.999 -- 2 C 0.970
9 1 H 0.999 -- 3 C 0.970
10 1 H 0.999 -- 4 C 0.970
11 1 H 0.999 -- 5 C 0.970
12 1 H 0.999 -- 6 C 0.970
---------------------------------------------------------------------------
Topologies differ in total number of bonds
Writing topology from bond orders to xtbtopo.mol
molecular dipole:
x y z tot (Debye)
q only: -0.000 -0.000 0.000
full: -0.000 -0.000 0.000 0.000
molecular quadrupole (traceless):
xx xy yy xz yz zz
q only: 0.708 0.000 0.706 0.001 -0.001 -1.415
q+dip: 2.864 0.000 2.860 0.004 -0.004 -5.724
full: 1.454 0.000 1.452 0.002 -0.001 -2.906
-------------------------------------------------
| TOTAL ENERGY -15.884463273254 Eh |
| GRADIENT NORM 0.029582367152 Eh/α |
| HOMO-LUMO GAP 4.823482459110 eV |
-------------------------------------------------
------------------------------------------------------------------------
* finished run on 2024/08/08 at 16:39:02.562
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.020 sec
* cpu-time: 0 d, 0 h, 0 min, 0.030 sec
* ratio c/w: 1.478 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.012 sec
* cpu-time: 0 d, 0 h, 0 min, 0.021 sec
* ratio c/w: 1.699 speedup
normal termination of xtb
Expected behaviour
Docs say that ALPB methanol works
Additional context
xTB 6.6.1 from conda-forge run on MacBook Pro 2024 (Apple Silicon, M3 Pro)
Describe the bug The docs say that ALPB doesn't support methanol, but it actually does. This is confusing.
To Reproduce Steps to reproduce the behaviour:
benzene.xyzxtbwithxtb benzene.xyz --alpb methanolxtbwith your options and the--verboseflagExpected behaviour Docs say that ALPB methanol works
Additional context xTB 6.6.1 from conda-forge run on MacBook Pro 2024 (Apple Silicon, M3 Pro)