Initial guess fails for MoS2 cutout

[afdemoura]

Dear xtb developers,

I am trying to use xtb version 6.2 to optimize the geometry of a MoS2 model system and always get the error message:

#ERROR! (goedecker_solve) DSYSV failed
abnormal termination of xtb

I have tried different combinations of keywords, but error persists even for the simplest case (xtb mos2.xyz, no further options).

xtb runs fine for other systems I had already studied using previous versions, it seems specific to the system I am trying to run now.

I am pasting below the input and output files.

Regards

Andre

input file:

89

Mo     -1.90836      3.59421     -3.29351
Mo     -4.76701      5.00656     -3.18619
Mo      0.74351      5.33114     -2.93457
Mo     -2.11514      6.74348     -2.82724
Mo      3.39537      7.06806     -2.57563
Mo      0.53672      8.48040     -2.46830
Mo     -7.62566      6.41891     -3.07886
Mo    -10.48428      7.83123     -2.97154
Mo     -4.97379      8.15584     -2.71992
Mo     -7.83242      9.56815     -2.61260
Mo    -10.69107     10.98051     -2.50527
Mo     -2.32192      9.89277     -2.36098
Mo     -5.18055     11.30508     -2.25366
Mo     -8.03921     12.71744     -2.14633
Mo      6.04724      8.80498     -2.21669
Mo      3.18859     10.21733     -2.10936
Mo      5.84045     11.95425     -1.75042
Mo      0.32994     11.62969     -2.00204
Mo     -2.52869     13.04200     -1.89472
Mo     -5.38734     14.45437     -1.78739
Mo      2.98180     13.36661     -1.64310
Mo      0.12318     14.77893     -1.53577
Mo     -2.73548     16.19129     -1.42845
S      -0.82964      2.30636     -5.03115
S      -0.94345      1.84097     -1.93827
S      -3.68829      3.71871     -4.92383
S      -3.80210      3.25332     -1.83095
S      -6.54695      5.13107     -4.81650
S      -6.66076      4.66567     -1.72362
S       1.82222      4.04329     -4.67221
S       1.70842      3.57790     -1.57933
S      -1.03642      5.45564     -4.56489
S      -1.15023      4.99024     -1.47201
S      -3.89508      6.86799     -4.45756
S      -4.00889      6.40260     -1.36468
S       4.47408      5.78021     -4.31327
S       4.36028      5.31482     -1.22039
S       1.61544      7.19256     -4.20595
S       1.50163      6.72717     -1.11307
S      -1.24321      8.60492     -4.09862
S      -1.35702      8.13953     -1.00574
S      -9.40558      6.54341     -4.70918
S      -9.51939      6.07802     -1.61630
S     -12.26424      7.95577     -4.60185
S     -12.37804      7.49038     -1.50897
S      -6.75372      8.28033     -4.35024
S      -6.86753      7.81494     -1.25736
S      -9.61237      9.69269     -4.24291
S      -9.72618      9.22730     -1.15003
S     -12.47102     11.10505     -4.13558
S     -12.58483     10.63966     -1.04270
S      -4.10185     10.01726     -3.99130
S      -4.21566      9.55187     -0.89842
S      -6.96051     11.42962     -3.88397
S      -7.07431     10.96422     -0.79109
S      -9.81916     12.84197     -3.77664
S      -9.93297     12.37658     -0.68376
S       7.12595      7.51713     -3.95433
S       7.01214      7.05174     -0.86145
S       4.26730      8.92948     -3.84701
S       4.15350      8.46409     -0.75413
S       1.40865     10.34184     -3.73968
S       1.29484      9.87645     -0.64680
S       6.91916     10.66641     -3.48807
S       6.80536     10.20101     -0.39519
S       4.06052     12.07877     -3.38074
S       3.94671     11.61338     -0.28786
S       6.71241     13.81571     -3.02179
S       6.59861     13.35032      0.07109
S      -1.44999     11.75418     -3.63236
S      -1.56380     11.28879     -0.53947
S      -4.30864     13.16654     -3.52503
S      -4.42245     12.70115     -0.43215
S      -7.16729     14.57890     -3.41770
S      -7.28110     14.11351     -0.32482
S       1.20188     13.49111     -3.27341
S       1.08807     13.02572     -0.18053
S      -1.65678     14.90346     -3.16609
S      -1.77059     14.43807     -0.07321
S      -4.51543     16.31583     -3.05876
S      -4.62924     15.85043      0.03412
S       3.85374     15.22803     -2.91447
S       3.73993     14.76264      0.17841
S       0.99509     16.64039     -2.80715
S       0.88128     16.17500      0.28573
S      -1.86356     18.05275     -2.69982
S      -1.97737     17.58736      0.39306
S       1.50163      6.72717     -1.11307
S       1.50163      6.72717     -1.11307

output file:

$ xtb mos2.xyz 
      -----------------------------------------------------------      
     |                   =====================                   |     
     |                           x T B                           |     
     |                   =====================                   |     
     |                         S. Grimme                         |     
     |          Mulliken Center for Theoretical Chemistry        |     
     |                    University of Bonn                     |     
     |                  Version 6.2 (SAW190828)                  |     
      -----------------------------------------------------------      

   This program 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.
   
   FOR NON-COMMERCIAL, ACADEMIA USE ONLY.
   
   Cite this work as:
   * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
     13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
   * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
     15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
   * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint.
     DOI: 10.26434/chemrxiv.8326202.v1
   
   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
   
   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
   
   for metadynamics refer to:
   * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862
     DOI: 10.1021/acs.jctc.9b00143
   
   with help from (in alphabetical order)
   C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher, M. Checinski,
   S. Dohm, S. Ehlert, S. Ehrlich, F. März, H. Neugebauer, J. Pisarek,
   P. Pracht, P. Shushkov, and S. Spicher.
   
 * started run on 2019/10/21 at 09:46:47.821     

           -------------------------------------------------
          |                Calculation Setup                |
           -------------------------------------------------

          program call               : xtb mos2.xyz
          coordinate file            : mos2.xyz
          omp threads                :                     4
          number of atoms            :                    89
          number of electrons        :                   534
          charge                     :                     0
          spin                       :                   0.0
          first test random number   :      0.75364557330491


molecular fragmentation (1/2 indicates fragments):
111111111111111111111111111111111111111111111111111111111111111111112111
11111111122221211
# atoms in fragment 1/2:    83     6
 fragment masses (1/2) :     4130.22      192.36
CMA distance (Bohr)    :  14.796
constraining FC (au)   :  0.0500

########################################################################
# WARNING! Please study the warnings concerning your input carefully
#  - XTBHOME is not set, using HOME instead
########################################################################

           ------------------------------------------------- 
          |                 G F N 2 - x T B                 |
          | Geometry, Frequencies, Noncovalent interactions |
          |            JCTC 2019 parametrisation            |
           ------------------------------------------------- 
             k(s)              :                1.8500
             k(p)              :                2.2300
             k(d)              :                2.2300
             k(f)              :                2.0000
             kEN (H0ij)        :               -2.0000
             D4 a1             :                0.5200
             D4 a2             :                5.0000
             D4 s6             :                1.0000
             D4 s8             :                2.7000
             D4 s9             :                5.0000
             alphaj            :                2.0000

  Z AO/shell   Hii/eV     exponent
 16     Tue Apr 24 11:44:34 CEST 2018   EN: 2.580 GM2: 0.340  GM3:-0.0502  RAES: 3.10
     3s    -20.029654    1.981333
     3p    -11.377694    2.025643
     3d     -0.420282    1.702555
 42     Thu Apr 26 14:26:12 CEST 2018   EN: 2.160 GM2: 0.586  GM3: 0.0920  RAES: 5.00
     4d     -7.995133    1.777658
     5s     -7.336245    1.639917
     5p     -3.686225    1.159781

#ERROR! (goedecker_solve) DSYSV failed
abnormal termination of xtb

---

[awvwgk]

Thanks for reporting. This seems to an issue with the geometry input, to check your input run xtb mos2.xyz -v --define. The input check should report something like this:

 * 3 distinct bonds (by element types)

   Z      Z             #   av. dist./Å        max./Å        min./Å
  16 S   16 S           3     0.0000000     0.0000000     0.0000000
  16 S   42 Mo        144     2.4169342     2.4169670     2.4169058
  42 Mo  42 Mo          6     3.1903159     3.1903266     3.1902991

There are three very short sulphur-sulphur “bonds” present.

[afdemoura]

Thanks, Sebastian! Silly error indeed, I should have double checked that before reporting the error (xtb did what it was supposed to do). Andre

…

On Mon, Oct 21, 2019 at 10:52 AM Sebastian Ehlert ***@***.***> wrote: Thanks for reporting. This seems to an issue with the geometry input, to check your input run xtb mos2.xyz -v --define. The input check should report something like this: * 3 distinct bonds (by element types) Z Z # av. dist./Å max./Å min./Å 16 S 16 S 3 0.0000000 0.0000000 0.0000000 16 S 42 Mo 144 2.4169342 2.4169670 2.4169058 42 Mo 42 Mo 6 3.1903159 3.1903266 3.1902991 There are three *very short* sulphur-sulphur “bonds” present. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#27?email_source=notifications&email_token=ANRSQQP6NNP5WTZB2TQAHWLQPWX2VA5CNFSM4JC44OK2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEB2MUZA#issuecomment-544524900>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANRSQQJNBJFRIF7IBYRUJTTQPWX2VANCNFSM4JC44OKQ> .

--

_____________ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090

[awvwgk]

All right, I will close this issue than.

And of course welcome to github 🎉