is this a bug #1303

ThibaultTOTH · 2025-06-04T14:47:42Z

ThibaultTOTH
Jun 4, 2025

I'm a brand new user of xtb and I wanted to check how does it work. So I installed it with conda and i tried a very simple mollecule (water) with this command : (QM_descriptors) thibault@DESKTOP-K9I54CN:~/QM_desc_autodE$ xtb "/mnt/c/Users/Thibault/Desktop/UROP/Quantum linked fp/eau.xyz" --opt. I acknowledge the xyz file

eau.xyz :
3

O 0.0000 0.0000 0.0000
H 0.7586 0.0000 0.5043
H -0.7586 0.0000 0.5043

And i get :

 |                   =====================                   |
 |                           x T B                           |
 |                   =====================                   |
 |                         S. Grimme                         |
 |          Mulliken Center for Theoretical Chemistry        |
 |                    University of Bonn                     |
  -----------------------------------------------------------

xtb version 6.7.1 (edcfbbe) compiled by 'conda@afd1a870197c' on 2025-04-11

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 2025/06/04 at 16:34:44.071
ID Z sym. atoms
1 8 O 1
2 1 H 2, 3
```
    -------------------------------------------------
   |                Calculation Setup                |
    -------------------------------------------------

   program call               : xtb /mnt/c/Users/Thibault/Desktop/UROP/Quantum linked fp/eau.xyz --opt
   coordinate file            : /mnt/c/Users/Thibault/Desktop/UROP/Quantum linked fp/eau.xyz
   omp threads                :                     8


    -------------------------------------------------
   |                 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
  
  ...................................................
  : SETUP :
  :.................................................:
  : # basis functions 6 :
  : # atomic orbitals 6 :
  : # shells 4 :
  : # electrons 8 :
  : max. iterations 250 :
  : Hamiltonian GFN2-xTB :
  : restarted? false :
  : GBSA solvation false :
  : 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 :
  : net charge 0 :
  : unpaired electrons 0 :
  ...................................................

iter E dE RMSdq gap omega full diag
1 -5.1186444 -0.511864E+01 0.452E+00 16.53 0.0 T
2 -5.1191815 -0.537012E-03 0.267E+00 16.37 1.0 T
3 -5.1193556 -0.174101E-03 0.291E-01 16.22 1.0 T
4 -5.1193902 -0.346047E-04 0.875E-02 16.36 1.0 T
5 -5.1193937 -0.356338E-05 0.433E-02 16.31 1.3 T
6 -5.1193942 -0.476306E-06 0.102E-03 16.33 56.6 T
7 -5.1193942 -0.428241E-09 0.464E-04 16.33 124.5 T
8 -5.1193942 -0.813651E-10 0.972E-06 16.33 5940.1 T

*** convergence criteria satisfied after 8 iterations ***

     #    Occupation            Energy/Eh            Energy/eV
  -------------------------------------------------------------
     1        2.0000           -0.6845149             -18.6266
     2        2.0000           -0.5759723             -15.6730
     3        2.0000           -0.5039742             -13.7138
     4        2.0000           -0.4465089             -12.1501 (HOMO)
     5                          0.1534816               4.1764 (LUMO)
     6                          0.3825421              10.4095
  -------------------------------------------------------------
              HL-Gap            0.5999905 Eh           16.3266 eV
         Fermi-level           -0.1465137 Eh           -3.9868 eV

SCC (total) 0 d, 0 h, 0 min, 0.025 sec
SCC setup ... 0 min, 0.004 sec ( 16.510%)
Dispersion ... 0 min, 0.000 sec ( 1.165%)
classical contributions ... 0 min, 0.002 sec ( 7.619%)
integral evaluation ... 0 min, 0.002 sec ( 8.321%)
iterations ... 0 min, 0.011 sec ( 45.099%)
molecular gradient ... 0 min, 0.003 sec ( 13.331%)
printout ... 0 min, 0.002 sec ( 7.642%)

     :::::::::::::::::::::::::::::::::::::::::::::::::::::
     ::                     SUMMARY                     ::
     :::::::::::::::::::::::::::::::::::::::::::::::::::::
     :: total energy              -5.065774615094 Eh    ::
     :: gradient norm              0.097078630114 Eh/a0 ::
     :: HOMO-LUMO gap             16.326572583456 eV    ::
     ::.................................................::
     :: SCC energy                -5.119394196151 Eh    ::
     :: -> isotropic ES            0.031661124381 Eh    ::
     :: -> anisotropic ES         -0.000242580307 Eh    ::
     :: -> anisotropic XC         -0.001548811691 Eh    ::
     :: -> dispersion             -0.000139643559 Eh    ::
     :: repulsion energy           0.053619581058 Eh    ::
     :: add. restraining           0.000000000000 Eh    ::
     :: total charge              -0.000000000000 e     ::
     :::::::::::::::::::::::::::::::::::::::::::::::::::::

  -----------------------------------------------------------
 |                   =====================                   |
 |                        A N C O P T                        |
 |                   =====================                   |
 |               Approximate Normal Coordinate               |
 |                Rational Function Optimizer                |
  -----------------------------------------------------------
  -----------------------------------------------------------
 |                   =====================                   |
 |                        A N C O P T                        |
 |                   =====================                   |
 |               Approximate Normal Coordinate               |
 |                Rational Function Optimizer                |
  -----------------------------------------------------------

      ...................................................
      :                      SETUP                      :
      :.................................................:
      :   optimization level            normal          :
      :   max. optcycles                   200          :
      :   ANC micro-cycles                  20          :
      :   degrees of freedom                 3          :
      :.................................................:
      :   RF solver                   davidson          :
      :   write xtbopt.log                true          :
      :   linear?                        false          :
      :   energy convergence         0.5000000E-05 Eh   :
      :   grad. convergence          0.1000000E-02 Eh/α :
      :   maxmium RF displ.          1.0000000          :
      :   Hlow (freq-cutoff)         0.1000000E-01      :
      :   Hmax (freq-cutoff)         5.0000000          :
      :   S6 in model hess.         20.0000000          :
      ...................................................

generating ANC from exact Hessian ...
Using Lindh-Hessian (1995)
Shifting diagonal of input Hessian by 0.0000000000000000
Lowest eigenvalues of input Hessian
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.430345 1.374499 1.690819
Highest eigenvalues
0.000000 0.000000 0.000000 0.430345 1.374499 1.690819

........................................................................
.............................. CYCLE 1 ..............................
........................................................................

iter E dE RMSdq gap omega full diag
1 -5.1193942 -0.511939E+01 0.195E-08 16.33 0.0 T
2 -5.1193942 0.177636E-14 0.112E-08 16.33 100000.0 T
3 -5.1193942 -0.888178E-15 0.279E-09 16.33 100000.0 T
SCC iter. ... 0 min, 0.003 sec
gradient ... 0 min, 0.001 sec

total energy : -5.0657746 Eh change -0.3197442E-13 Eh
gradient norm : 0.0970785 Eh/α predicted 0.0000000E+00At line 852 of file ../src/optimizer.f90 (unit = 6, file = 'stdout')
Fortran runtime error: Missing comma between descriptors
(1x,"("f7.2"%)")
^

Error termination. Backtrace:
#0 0x7b8e77756b83 in parse_format_list
at ../../../libgfortran/io/format.c:1240
#1 0x7b8e77762ef5 in data_transfer_init
at ../../../libgfortran/io/transfer.c:3298
#2 0x5e722117d113 in ???
#3 0x5e72211806b7 in ???
#4 0x5e72211386e4 in ???
#5 0x5e7220f87253 in ???
#6 0x5e7220f74244 in ???
#7 0x7b8e7722a1c9 in ???
#8 0x7b8e7722a28a in ???
#9 0x5e7220f742e6 in ???
#10 0xffffffffffffffff in ???

The things that concern me is speciffycally this error in the log : Fortran runtime error: Missing comma between descriptors
(1x,"("f7.2"%)")

I notice that i used xtb on a ubuntu run in WSL?

Thank you by advance for your help

Thibault

PS if somone know if the ram prerequisites in autodE is hardcoded or if we could dodge it, It would help me

toxtran · 2025-06-08T06:17:54Z

toxtran
Jun 8, 2025

Fixed in #1278.

0 replies

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is this a bug #1303

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ThibaultTOTH Jun 4, 2025

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toxtran Jun 8, 2025

ThibaultTOTH
Jun 4, 2025

toxtran
Jun 8, 2025