`SIGTRAP`/`SIGBUS` Errors For Hessian Calculation #1148

corinwagen · 2024-12-13T17:09:44Z

Describe the bug
I'm trying to run a Hessian calculation on AlCl3, but I get crazy errors instead.

To Reproduce
Steps to reproduce the behaviour:

happens with input (include input files):
xtb-in.xyz:

4
charge 0, multiplicity 1, autogenerated by Rowan at 2024-12-13 17:01:01
Al   -0.03696237   0.00433323   0.09896223
Cl   -1.78680134  -1.02582061   0.93010306
Cl   -0.09332046   2.06976748  -0.66597611
Cl    1.91708422  -1.04828012   0.02098519

start xtb with xtb xtb-in.xyz --gfn 2 --hess --iterations 1000 -P 1
run xtb with your options and the --verbose flag
output showing the error

      -----------------------------------------------------------
     |                   =====================                   |
     |                           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 2024/12/13 at 12:04:59.321

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

          program call               : /Users/cwagen/.pixi/envs/xtb/bin/xtb xtb-in.xyz --gfn 2 --hess --iterations 1000 -P 1 --verbose
          coordinate file            : xtb-in.xyz
          xtbhome directory          : /Users/cwagen
          path for xtb               : /Users/cwagen/.xtb-parameters/
          xcontrol input file        : xtb-in.xyz
          omp threads                :                     1

$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
 CONSTRAINTS & SCANS: DEBUG SECTION
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
   ID    Z sym.   atoms
    1   13 Al     1
    2   17 Cl     2-4
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$

           -------------------------------------------------
          |                 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

q/qsh data taken from xtbrestart
CAMM data taken from xtbrestart

          ...................................................
          :                      SETUP                      :
          :.................................................:
          :  # basis functions                  40          :
          :  # atomic orbitals                  36          :
          :  # shells                           12          :
          :  # electrons                        24          :
          :  max. iterations                  1000          :
          :  Hamiltonian                  GFN2-xTB          :
          :  restarted?                       true          :
          :  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          :
          ...................................................

 iter      E             dE          RMSdq      gap      omega  full diag
   1    -14.9121083 -0.149121E+02  0.433E-05    3.58       0.0  T
   2    -14.9121083 -0.113864E-11  0.192E-05    3.58    2598.6  T
   3    -14.9121083 -0.268230E-12  0.179E-05    3.58    2796.7  T

   *** convergence criteria satisfied after 3 iterations ***

         #    Occupation            Energy/Eh            Energy/eV
      -------------------------------------------------------------
         1        2.0000           -1.0630719             -28.9277
       ...           ...                  ...                  ...
         6        2.0000           -0.4649821             -12.6528
         7        2.0000           -0.4629092             -12.5964
         8        2.0000           -0.4586011             -12.4792
         9        2.0000           -0.4566983             -12.4274
        10        2.0000           -0.4544687             -12.3667
        11        2.0000           -0.4508334             -12.2678
        12        2.0000           -0.4420747             -12.0295 (HOMO)
        13                         -0.3104469              -8.4477 (LUMO)
        14                         -0.2085242              -5.6742
        15                         -0.1342266              -3.6525
        16                         -0.1212887              -3.3004
        17                         -0.0903244              -2.4579
       ...                                ...                  ...
        36                          0.7687708              20.9193
      -------------------------------------------------------------
                  HL-Gap            0.1316278 Eh            3.5818 eV
             Fermi-level           -0.3762608 Eh          -10.2386 eV

 SCC (total)                   0 d,  0 h,  0 min,  0.009 sec
 SCC setup                      ...        0 min,  0.001 sec ( 15.771%)
 Dispersion                     ...        0 min,  0.000 sec (  0.106%)
 classical contributions        ...        0 min,  0.000 sec (  0.066%)
 integral evaluation            ...        0 min,  0.000 sec (  4.612%)
 iterations                     ...        0 min,  0.002 sec ( 22.337%)
 molecular gradient             ...        0 min,  0.001 sec (  8.218%)
 printout                       ...        0 min,  0.005 sec ( 48.860%)

         :::::::::::::::::::::::::::::::::::::::::::::::::::::
         ::                     SUMMARY                     ::
         :::::::::::::::::::::::::::::::::::::::::::::::::::::
         :: total energy             -14.902031044922 Eh    ::
         :: gradient norm              0.070380250951 Eh/a0 ::
         :: HOMO-LUMO gap              3.581775587646 eV    ::
         ::.................................................::
         :: HOMO orbital eigv.       -12.029464872793 eV    ::
         :: LUMO orbital eigv.        -8.447689285146 eV    ::
         ::.................................................::
         :: SCC energy               -14.912108335207 Eh    ::
         :: -> isotropic ES            0.038628474312 Eh    ::
         :: -> anisotropic ES          0.002047587522 Eh    ::
         :: -> anisotropic XC         -0.007089118575 Eh    ::
         :: -> dispersion             -0.003333589249 Eh    ::
         :: repulsion energy           0.010075311782 Eh    ::
         :: add. restraining           0.000000000000 Eh    ::
         :: total charge               0.000000000000 e     ::
         ::.................................................::
         :: atomisation energy         0.556383615263 Eh    ::
         :::::::::::::::::::::::::::::::::::::::::::::::::::::

           -------------------------------------------------
          |                Numerical Hessian                |
           -------------------------------------------------
step length          :   0.00500
SCC accuracy         :   0.30000
Hessian scale factor :   1.00000
frozen atoms in %    :   0.00000    0
RMS gradient         :   0.07038 !! INCOMPLETELY OPTIMIZED GEOMETRY !!
estimated CPU  time      0.00 min
estimated wall time      0.00 min

writing file <hessian>.

 projected vibrational frequencies (cm⁻¹)
eigval :       -0.00    -0.00    -0.00    -0.00     0.00     0.00
eigval :      132.90   135.30   224.97   260.90   342.13   370.04
           -------------------------------------------------
          |                Property Printout                |
           -------------------------------------------------

    * Orbital Energies and Occupations

         #    Occupation            Energy/Eh            Energy/eV
      -------------------------------------------------------------
         1        2.0000           -1.0630718             -28.9277
         2        2.0000           -1.0614470             -28.8834
         3        2.0000           -1.0581849             -28.7947
         4        2.0000           -0.5375668             -14.6279
         5        2.0000           -0.4653122             -12.6618
         6        2.0000           -0.4649821             -12.6528
         7        2.0000           -0.4629091             -12.5964
         8        2.0000           -0.4586011             -12.4792
         9        2.0000           -0.4566983             -12.4274
        10        2.0000           -0.4544687             -12.3667
        11        2.0000           -0.4508334             -12.2678
        12        2.0000           -0.4420747             -12.0295 (HOMO)
        13                         -0.3104468              -8.4477 (LUMO)
        14                         -0.2085241              -5.6742
        15                         -0.1342266              -3.6525
        16                         -0.1212887              -3.3004
        17                         -0.0903243              -2.4578
        18                         -0.0821263              -2.2348
        19                         -0.0022809              -0.0621
        20                          0.0019512               0.0531
        21                          0.0042570               0.1158
        22                          0.0066332               0.1805
        23                          0.0072263               0.1966
       ...                                ...                  ...
        36                          0.7687709              20.9193
      -------------------------------------------------------------
                  HL-Gap            0.1316279 Eh            3.5818 eV
             Fermi-level           -0.3762607 Eh          -10.2386 eV

     #   Z          covCN         q      C6AA      α(0)
     1  13 Al       2.287     0.422   110.337    22.726
     2  17 Cl       0.763    -0.129   103.007    15.525
     3  17 Cl       0.763    -0.138   103.281    15.546
     4  17 Cl       0.761    -0.154   103.783    15.583

 Mol. C6AA /au·bohr⁶  :       1643.725854
 Mol. C8AA /au·bohr⁸  :      87529.313427
 Mol. α(0) /au        :         69.379687


Wiberg/Mayer (AO) data.
largest (>0.10) Wiberg bond orders for each atom

 ---------------------------------------------------------------------------
     #   Z sym  total        # sym  WBO       # sym  WBO       # sym  WBO
 ---------------------------------------------------------------------------
     1  13 Al   3.802 --     2 Cl   1.285     3 Cl   1.271     4 Cl   1.246
     2  17 Cl   1.457 --     1 Al   1.285
     3  17 Cl   1.443 --     1 Al   1.271
     4  17 Cl   1.418 --     1 Al   1.246
 ---------------------------------------------------------------------------

Topologies differ in total number of bonds
Writing topology from bond orders to xtbtopo.mol

molecular dipole:
                 x           y           z       tot (Debye)
 q only:       -0.126       0.019       0.019
   full:       -0.113       0.017       0.018       0.294
molecular quadrupole (traceless):
                xx          xy          yy          xz          yz          zz
 q only:       -1.596       0.530      -1.153       1.065       1.701       2.749
  q+dip:       -0.521       0.466      -0.285       0.166       0.372       0.807
   full:       -1.868       0.675      -1.357       1.237       1.980       3.225

           -------------------------------------------------
          |               Frequency Printout                |
           -------------------------------------------------
 projected vibrational frequencies (cm⁻¹)
eigval :       -0.00    -0.00    -0.00    -0.00     0.00     0.00
eigval :      132.90   135.30   224.97   260.90   342.13   370.04
 reduced masses (amu)
   1: 35.19   2: 35.31   3: 34.16   4: 34.07   5: 34.19   6: 34.65   7: 34.63   8: 34.69
   9: 35.43  10: 28.70  11: 29.54  12: 29.47
 IR intensities (km·mol⁻¹)
   1:  0.03   2:  0.02   3:  0.01   4:  0.01   5:  0.02   6:  0.01   7:  4.49   8:  4.66
   9:  0.37  10:  5.67  11:121.08  12:122.08
 Raman intensities (amu)
   1:  0.00   2:  0.00   3:  0.00   4:  0.00   5:  0.00   6:  0.00   7:  0.00   8:  0.00
   9:  0.00  10:  0.00  11:  0.00  12:  0.00
 output can be read by thermo (or use thermo option).
 writing <g98.out> molden fake output.
 recommended (thermochemical) frequency scaling factor: 1.0
           -------------------------------------------------
          |             Thermodynamic Functions             |
           -------------------------------------------------

Molecule has the following symmetry elements: 2*(C2) 3*(sigma)
WARNING: These symmetry elements match no point group I know of. Sorry.
Trying fallback mode to highest recognized Axis...

Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:

Program received signal SIGBUS: Access to an undefined portion of a memory object.

Backtrace for this error:
^Crecieved SIGINT, terminating...
external termination of xtb
Note: The following floating-point exceptions are signalling: IEEE_DIVIDE_BY_ZERO IEEE_UNDERFLOW_FLAG
ERROR STOP

Error termination. Backtrace:

As requested, here are the additional files generated:

hessian:

$hessian                                                                        
        0.0889256013   0.0038870748  -0.0097661810  -0.0399719848  -0.0184645898
        0.0123212326  -0.0101896587  -0.0000693931  -0.0020630823  -0.0387639578
        0.0146469081  -0.0004919694
        0.0038870748   0.0892343220  -0.0137729172  -0.0185078694  -0.0215040859
        0.0055642640  -0.0000216007  -0.0489094535   0.0113468370   0.0146423953
       -0.0188207826  -0.0031381838
       -0.0097661810  -0.0137729172   0.0630663732   0.0122056681   0.0054973927
       -0.0242991660  -0.0020665183   0.0114407574  -0.0223775368  -0.0003729689
       -0.0031652329  -0.0163896703
       -0.0399719848  -0.0185078694   0.0122056681   0.0451266468   0.0204275882
       -0.0173942634   0.0007802298  -0.0004317870   0.0015932178  -0.0059348918
       -0.0014879318   0.0035953775
       -0.0184645898  -0.0215040859   0.0054973927   0.0204275882   0.0213567849
       -0.0107251152  -0.0042718327  -0.0023807784   0.0044351649   0.0023088343
        0.0025280794   0.0007925575
        0.0123212326   0.0055642640  -0.0242991660  -0.0173942634  -0.0107251152
        0.0150255466   0.0030033103   0.0034364875   0.0043497438   0.0020697205
        0.0017243637   0.0049238756
       -0.0101896587  -0.0000216007  -0.0020665183   0.0007802298  -0.0042718327
        0.0030033103   0.0098373494  -0.0020396556  -0.0001207250  -0.0004279205
        0.0063330890  -0.0008160670
       -0.0000693931  -0.0489094535   0.0114407574  -0.0004317870  -0.0023807784
        0.0034364875  -0.0020396556   0.0551294343  -0.0179503665   0.0025408357
       -0.0038392024   0.0030731216
       -0.0020630823   0.0113468370  -0.0223775368   0.0015932178   0.0044351649
        0.0043497438  -0.0001207250  -0.0179503665   0.0130547695   0.0005905895
        0.0021683646   0.0049730235
       -0.0387639578   0.0146423953  -0.0003729689  -0.0059348918   0.0023088343
        0.0020697205  -0.0004279205   0.0025408357   0.0005905895   0.0451267701
       -0.0194920653  -0.0022873412
        0.0146469081  -0.0188207826  -0.0031652329  -0.0014879318   0.0025280794
        0.0017243637   0.0063330890  -0.0038392024   0.0021683646  -0.0194920653
        0.0201319055  -0.0007274954
       -0.0004919694  -0.0031381838  -0.0163896703   0.0035953775   0.0007925575
        0.0049238756  -0.0008160670   0.0030731216   0.0049730235  -0.0022873412
       -0.0007274954   0.0064927712

vibspectrum:

$vibrational spectrum
#  mode     symmetry     wave number   IR intensity    selection rules
#                         cm**(-1)      (km*mol⁻¹)       IR     RAMAN
     1                      -0.00         0.00000        -       - 
     2                      -0.00         0.00000        -       - 
     3                      -0.00         0.00000        -       - 
     4                      -0.00         0.00000        -       - 
     5                       0.00         0.00000        -       - 
     6                       0.00         0.00000        -       - 
     7        a            132.90         4.49331       YES     YES
     8        a            135.30         4.66203       YES     YES
     9        a            224.97         0.37200       YES     YES
    10        a            260.90         5.66771       YES     YES
    11        a            342.13       121.08038       YES     YES
    12        a            370.04       122.07996       YES     YES
$end

wbo:

           1           2   1.2850872128189181     
           1           3   1.2711298340908297     
           1           4   1.2457572184566110

charges:

    0.42174073
   -0.12946196
   -0.13817876
   -0.15410001

g98.out:

 Entering Gaussian System

xtbrestart (I presume this is a binary file):

0��������������������������������������������������0���`���?˚ü±–"?6{A¸��⁄?w�CªΩ Ôøûû˙DæÅ®?∂aÎ/‘¢∆øoG�ljû?øCÔ“πAØß?œ∫ÿdåã«ø|Ç¶w¨�@ø¢Ïâã≈H¶?eı2Q∂:…ø�µ‰g3�Aø`���`����¯è �Ãìøì¨���p\?ñå¸„Ó�=?d∫q�„>≈øw�·ë≤vªøÌ�@4C\µ?�“‚{ NÅ?m
j �â…?Z9ñ∏;é≥ø¶�{‘sM»?7˜�›*¢∏ø⁄Û3Ñ[aÇø`���¿���Ò∏ë3ïØıø†/ˆ8T�À?˚ŸÒ^Q;ÒøsA�i¬8Ò?éçAOÇ‹˘?b…AIsu�@s˘kºfza?‡AaÖ<mn?�ú’`M--?¥�!<–Ωhø¬Æ=´Áçeøfwyí;McøÔë£/=∫iø4ñ�€(U?ë¥∂¢�5|?�Õ-Ì•Rø�Ÿ√Ê�Ótø$≠…�‘Ønø®ˇ\âì¯Ç?∂æé�,Ë|øE~�müZø˘3¸íÌÂYøÛQ�$åµKøµ÷πœKI�ø¿���

xtbtopo.mol:

 xtb: 6.6.1 (8d0f1dd)
          12132412053D

  4  3  0     0  0            999 V2000
   -0.0370    0.0043    0.0990 Al  0  0  0  0  0  0  0  0  0  0  0  0
   -1.7868   -1.0258    0.9301 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.0933    2.0698   -0.6660 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.9171   -1.0483    0.0210 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
M  END

Expected behaviour
I would like xTB to run without giving these errors.

Additional context
(none)

The text was updated successfully, but these errors were encountered:

toxtran · 2024-12-19T14:56:06Z

@corinwagen, could you please check later versions of xtb? 6.7.0, for example

corinwagen · 2024-12-19T15:01:20Z

Ah good point. xTB 6.7.1 works fine at this test, apologies.

      -----------------------------------------------------------
     |                   =====================                   |
     |                           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 2024/12/19 at 14:59:31.799
   ID    Z sym.   atoms
    1   13 Al     1
    2   17 Cl     2-4

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

          program call               : ../src/peregrine/utils/binaries/xtb-6_7_1/bin/xtb xtb-in.xyz --gfn 2 --hess --iterations 1000 -P 1
          coordinate file            : xtb-in.xyz
          omp threads                :                     1


           -------------------------------------------------
          |                 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                  40          :
          :  # atomic orbitals                  36          :
          :  # shells                           12          :
          :  # electrons                        24          :
          :  max. iterations                  1000          :
          :  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    -14.8435492 -0.148435E+02  0.213E+01    4.56       0.0  T
   2    -14.9020896 -0.585404E-01  0.129E+01    3.42       1.0  T
   3    -14.8957895  0.630015E-02  0.347E+00    3.97       1.0  T
   4    -14.9115757 -0.157863E-01  0.927E-01    3.49       1.0  T
   5    -14.9093863  0.218940E-02  0.212E+00    3.78       1.0  T
   6    -14.9117320 -0.234567E-02  0.908E-01    3.65       1.0  T
   7    -14.9117946 -0.626728E-04  0.593E-01    3.64       1.0  T
   8    -14.9120841 -0.289429E-03  0.145E-01    3.60       1.0  T
   9    -14.9120923 -0.821451E-05  0.121E-01    3.57       1.0  T
  10    -14.9121078 -0.155504E-04  0.218E-02    3.58       2.3  T
  11    -14.9121082 -0.326283E-06  0.812E-03    3.58       6.2  T
  12    -14.9121083 -0.163296E-06  0.268E-03    3.58      18.7  T
  13    -14.9121083 -0.116175E-07  0.157E-03    3.58      31.9  T
  14    -14.9121083 -0.360181E-08  0.116E-03    3.58      43.2  T
  15    -14.9121083  0.581746E-09  0.607E-04    3.58      82.4  T
  16    -14.9121083 -0.136182E-08  0.537E-05    3.58     931.9  T

   *** convergence criteria satisfied after 16 iterations ***

         #    Occupation            Energy/Eh            Energy/eV
      -------------------------------------------------------------
         1        2.0000           -1.0630719             -28.9277
       ...           ...                  ...                  ...
         6        2.0000           -0.4649822             -12.6528
         7        2.0000           -0.4629092             -12.5964
         8        2.0000           -0.4586011             -12.4792
         9        2.0000           -0.4566983             -12.4274
        10        2.0000           -0.4544687             -12.3667
        11        2.0000           -0.4508334             -12.2678
        12        2.0000           -0.4420747             -12.0295 (HOMO)
        13                         -0.3104470              -8.4477 (LUMO)
        14                         -0.2085246              -5.6742
        15                         -0.1342269              -3.6525
        16                         -0.1212891              -3.3004
        17                         -0.0903246              -2.4579
       ...                                ...                  ...
        36                          0.7687704              20.9193
      -------------------------------------------------------------
                  HL-Gap            0.1316277 Eh            3.5818 eV
             Fermi-level           -0.3762608 Eh          -10.2386 eV

 SCC (total)                   0 d,  0 h,  0 min,  0.022 sec
 SCC setup                      ...        0 min,  0.002 sec (  7.478%)
 Dispersion                     ...        0 min,  0.000 sec (  0.841%)
 classical contributions        ...        0 min,  0.000 sec (  0.047%)
 integral evaluation            ...        0 min,  0.005 sec ( 21.886%)
 iterations                     ...        0 min,  0.012 sec ( 57.987%)
 molecular gradient             ...        0 min,  0.002 sec (  9.657%)
 printout                       ...        0 min,  0.000 sec (  1.988%)

         :::::::::::::::::::::::::::::::::::::::::::::::::::::
         ::                     SUMMARY                     ::
         :::::::::::::::::::::::::::::::::::::::::::::::::::::
         :: total energy             -14.902031044917 Eh    ::
         :: gradient norm              0.070380417295 Eh/a0 ::
         :: HOMO-LUMO gap              3.581771989054 eV    ::
         ::.................................................::
         :: SCC energy               -14.912106356699 Eh    ::
         :: -> isotropic ES            0.038628113207 Eh    ::
         :: -> anisotropic ES          0.002047573079 Eh    ::
         :: -> anisotropic XC         -0.007089135359 Eh    ::
         :: -> dispersion             -0.003333588925 Eh    ::
         :: repulsion energy           0.010075311782 Eh    ::
         :: add. restraining           0.000000000000 Eh    ::
         :: total charge              -0.000000000000 e     ::
         :::::::::::::::::::::::::::::::::::::::::::::::::::::

           -------------------------------------------------
          |                Numerical Hessian                |
           -------------------------------------------------
step length          :   0.00500
SCC accuracy         :   0.30000
Hessian scale factor :   1.00000
frozen atoms in %    :   0.00000    0
RMS gradient         :   0.07038 !! INCOMPLETELY OPTIMIZED GEOMETRY !!
estimated CPU  time      0.00 min
estimated wall time      0.00 min

writing file <hessian>.

 projected vibrational frequencies (cm⁻¹)
eigval :       -0.00    -0.00    -0.00     0.00     0.00     0.00
eigval :      132.84   135.23   224.40   260.85   340.48   368.66
           -------------------------------------------------
          |                Property Printout                |
           -------------------------------------------------

    * Orbital Energies and Occupations

         #    Occupation            Energy/Eh            Energy/eV
      -------------------------------------------------------------
         1        2.0000           -1.0630719             -28.9277
         2        2.0000           -1.0614470             -28.8834
         3        2.0000           -1.0581849             -28.7947
         4        2.0000           -0.5375669             -14.6279
         5        2.0000           -0.4653122             -12.6618
         6        2.0000           -0.4649822             -12.6528
         7        2.0000           -0.4629092             -12.5964
         8        2.0000           -0.4586011             -12.4792
         9        2.0000           -0.4566983             -12.4274
        10        2.0000           -0.4544687             -12.3667
        11        2.0000           -0.4508334             -12.2678
        12        2.0000           -0.4420747             -12.0295 (HOMO)
        13                         -0.3104469              -8.4477 (LUMO)
        14                         -0.2085243              -5.6742
        15                         -0.1342268              -3.6525
        16                         -0.1212889              -3.3004
        17                         -0.0903245              -2.4579
        18                         -0.0821264              -2.2348
        19                         -0.0022809              -0.0621
        20                          0.0019512               0.0531
        21                          0.0042570               0.1158
        22                          0.0066332               0.1805
        23                          0.0072263               0.1966
       ...                                ...                  ...
        36                          0.7687707              20.9193
      -------------------------------------------------------------
                  HL-Gap            0.1316278 Eh            3.5818 eV
             Fermi-level           -0.3762608 Eh          -10.2386 eV

     #   Z          covCN         q      C6AA      α(0)
     1  13 Al       2.287     0.422   110.337    22.726
     2  17 Cl       0.763    -0.129   103.007    15.525
     3  17 Cl       0.763    -0.138   103.281    15.546
     4  17 Cl       0.761    -0.154   103.783    15.583

 Mol. C6AA /au·bohr⁶  :       1643.725842
 Mol. C8AA /au·bohr⁸  :      87529.313867
 Mol. α(0) /au        :         69.379687


Wiberg/Mayer (AO) data.
largest (>0.10) Wiberg bond orders for each atom

 ---------------------------------------------------------------------------
     #   Z sym  total        # sym  WBO       # sym  WBO       # sym  WBO
 ---------------------------------------------------------------------------
     1  13 Al   3.802 --     2 Cl   1.285     3 Cl   1.271     4 Cl   1.246
     2  17 Cl   1.457 --     1 Al   1.285
     3  17 Cl   1.443 --     1 Al   1.271
     4  17 Cl   1.418 --     1 Al   1.246
 ---------------------------------------------------------------------------

Topologies differ in total number of bonds
Writing topology from bond orders to xtbtopo.mol

molecular dipole:
                 x           y           z       tot (Debye)
 q only:       -0.126       0.019       0.019
   full:       -0.113       0.017       0.018       0.294
molecular quadrupole (traceless):
                xx          xy          yy          xz          yz          zz
 q only:       -1.596       0.530      -1.153       1.065       1.701       2.749
  q+dip:       -0.521       0.466      -0.285       0.166       0.372       0.807
   full:       -1.868       0.675      -1.357       1.237       1.980       3.225

           -------------------------------------------------
          |               Frequency Printout                |
           -------------------------------------------------
 projected vibrational frequencies (cm⁻¹)
eigval :       -0.00    -0.00    -0.00     0.00     0.00     0.00
eigval :      132.84   135.23   224.40   260.85   340.48   368.66
 reduced masses (amu)
   1: 34.55   2: 34.56   3: 34.61   4: 34.96   5: 34.84   6: 34.07   7: 34.64   8: 34.69
   9: 35.43  10: 28.70  11: 29.53  12: 29.46
 IR intensities (km·mol⁻¹)
   1:  0.01   2:  0.00   3:  0.00   4:  0.00   5:  0.01   6:  0.00   7:  4.76   8:  4.90
   9:  0.37  10:  5.34  11:111.47  12:112.68
 Raman intensities (Ä⁴*amu⁻¹)
   1:  0.00   2:  0.00   3:  0.00   4:  0.00   5:  0.00   6:  0.00   7:  0.00   8:  0.00
   9:  0.00  10:  0.00  11:  0.00  12:  0.00
 output can be read by thermo (or use thermo option).
 writing <g98.out> molden fake output.
 recommended (thermochemical) frequency scaling factor: 1.0
           -------------------------------------------------
          |             Thermodynamic Functions             |
           -------------------------------------------------

Molecule has the following symmetry elements: 2*(C2) 3*(sigma)
WARNING: These symmetry elements match no point group I know of. Sorry.
Trying fallback mode to highest recognized Axis...
c2  symmetry found (for desy threshold:  0.10E+00) used in thermo

          ...................................................
          :                      SETUP                      :
          :.................................................:
          :  # frequencies                           6      :
          :  # imaginary freq.                       0      :
          :  linear?                             false      :
          :  only rotor calc.                    false      :
          :  symmetry                               c2      :
          :  rotational number                       2      :
          :  scaling factor                  1.0000000      :
          :  rotor cutoff                   50.0000000 cm⁻¹ :
          :  imag. cutoff                  -20.0000000 cm⁻¹ :
          :.................................................:

    mode    ω/cm⁻¹     T·S(HO)/kcal·mol⁻¹    T·S(FR)/kcal·mol⁻¹   T·S(vib)
   ------------------------------------------------------------------------
       1    132.84    -0.86600 ( 98.03%)    -0.76699 (  1.97%)    -0.86405
       2    135.23    -0.85579 ( 98.17%)    -0.76170 (  1.83%)    -0.85406
       3    224.40    -0.57344 ( 99.75%)    -0.61171 (  0.25%)    -0.57353
       4    260.85    -0.49376 ( 99.87%)    -0.56712 (  0.13%)    -0.49385
   ------------------------------------------------------------------------

   temp. (K)  partition function   enthalpy   heat capacity  entropy
                                   cal/mol     cal/K/mol   cal/K/mol   J/K/mol
 298.15  VIB   13.9                 1914.603     10.480     11.639
         ROT  0.225E+06              888.752      2.981     27.469
         INT  0.312E+07             2803.355     13.461     39.107
         TR   0.149E+28             1481.254      4.968     40.557
         TOT                        4284.6091    18.4288    79.6645   333.3165

       T/K    H(0)-H(T)+PV         H(T)/Eh          T*S/Eh         G(T)/Eh
   ------------------------------------------------------------------------
    298.15    0.682796E-02    0.101597E-01    0.378512E-01   -0.276915E-01
   ------------------------------------------------------------------------

         :::::::::::::::::::::::::::::::::::::::::::::::::::::
         ::                  THERMODYNAMIC                  ::
         :::::::::::::::::::::::::::::::::::::::::::::::::::::
         :: total free energy         -14.929722573792 Eh   ::
         ::.................................................::
         :: total energy              -14.902031044921 Eh   ::
         :: zero point energy           0.003331709435 Eh   ::
         :: G(RRHO) w/o ZPVE           -0.031023238306 Eh   ::
         :: G(RRHO) contrib.           -0.027691528871 Eh   ::
         :::::::::::::::::::::::::::::::::::::::::::::::::::::

           -------------------------------------------------
          | TOTAL ENERGY              -14.902031044921 Eh   |
          | TOTAL ENTHALPY            -14.891871376229 Eh   |
          | TOTAL FREE ENERGY         -14.929722573792 Eh   |
          | GRADIENT NORM               0.070380314082 Eh/α |
          | HOMO-LUMO GAP               3.581773588652 eV   |
           -------------------------------------------------
########################################################################
[WARNING] Runtime exception occurred
-1- hessian_numhess: Hessian on incompletely optimized geometry!
########################################################################

------------------------------------------------------------------------
 * finished run on 2024/12/19 at 14:59:31.977
------------------------------------------------------------------------
 total:
 * wall-time:     0 d,  0 h,  0 min,  0.178 sec
 *  cpu-time:     0 d,  0 h,  0 min,  0.159 sec
 * ratio c/w:     0.894 speedup
 SCF:
 * wall-time:     0 d,  0 h,  0 min,  0.022 sec
 *  cpu-time:     0 d,  0 h,  0 min,  0.014 sec
 * ratio c/w:     0.650 speedup
 analytical hessian:
 * wall-time:     0 d,  0 h,  0 min,  0.134 sec
 *  cpu-time:     0 d,  0 h,  0 min,  0.133 sec
 * ratio c/w:     0.992 speedup

normal termination of xtb

corinwagen added the unconfirmed This report has not yet been confirmed by the developers label Dec 13, 2024

corinwagen closed this as completed Dec 19, 2024

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`SIGTRAP`/`SIGBUS` Errors For Hessian Calculation #1148

`SIGTRAP`/`SIGBUS` Errors For Hessian Calculation #1148

corinwagen commented Dec 13, 2024

toxtran commented Dec 19, 2024

corinwagen commented Dec 19, 2024

SIGTRAP/SIGBUS Errors For Hessian Calculation #1148

SIGTRAP/SIGBUS Errors For Hessian Calculation #1148

Comments

corinwagen commented Dec 13, 2024

toxtran commented Dec 19, 2024

corinwagen commented Dec 19, 2024

`SIGTRAP`/`SIGBUS` Errors For Hessian Calculation #1148

`SIGTRAP`/`SIGBUS` Errors For Hessian Calculation #1148