[BUG] - QCG Terminates with Backtrace

[coltonbh]

Describe the bug
Running a quantum cluster growth calculation terminates with what appears to be a an issue reading structures.

To Reproduce
crest solute.xyz --qcg solvent.xyz --nsolv 10 --keepdir --gfnff --chrg 0 --uhf 0

solute.xyz

57
qcio_charge=0 qcio_multiplicity=1 Etot= -110.6313818486
N  -0.72310484590000002 0.66682730909999999 -0.54501433450000003
C  -1.87169979450000001 1.19360751919999997 -0.95321806580000001
S  -1.97129138300000006 2.79283969019999967 -1.57649585970000006
N  -2.94530890739999984 0.40956234990000001 -0.95195686089999998
C  -4.18621362399999963 0.65751521089999998 -1.66105095770000011
C  -4.16981029230000022 -0.09468512040000000 -2.99185852120000018
H  -5.08689994109999954 0.10067461250000000 -3.54018849159999949
C  0.26180396800000000 1.36771634599999992 0.05119279150000000
H  -0.48797811540000002 -0.95079148020000004 0.39474888089999999
H  -2.81448767709999981 -0.55778700709999995 -0.66930063760000003
H  -4.08733984479999979 -1.16333749489999994 -2.80801514739999991
H  -3.32540944749999978 0.23069547979999999 -3.60050555330000011
H  -4.24793115800000010 1.73559105110000012 -1.84303114740000007
C  -5.35023178039999969 0.20718259750000001 -0.78535404450000001
H  -5.34714631629999992 0.74548881680000001 0.15970374360000000
H  -5.27007377899999963 -0.85834452240000003 -0.58210172250000003
H  -6.29263612380000037 0.39965374660000003 -1.29043919439999999
O  -1.90662621459999992 -4.19268810949999970 0.55602488859999999
C  -1.83353074260000004 -3.36595508829999979 -0.47297442929999994
O  -2.70597174039999988 -2.56333910710000001 -0.69147216580000004
H  -0.36182517120000002 -6.71058824699999956 2.09947854169999992
C  -1.19212430430000005 -6.03902245929999992 1.90310497310000004
H  -2.05017745979999999 -6.62614431919999980 1.58691676379999991
H  -1.44686225289999992 -5.49372943379999956 2.80696703809999981
C  -0.79885923709999995 -5.06338844059999982 0.80696559050000005
H  0.05914673530000000 -4.44754011060000032 1.12122921700000000
C  -0.61286592200000001 -3.56347345989999997 -1.37459513530000010
H  0.24878601440000001 -3.12006319759999995 -0.85300079760000003
O  -0.37664519610000002 -4.96602777649999982 -1.55731918940000003
C  -0.41319693880000002 -5.76725236470000002 -0.49720021910000001
O  -0.16965793670000001 -6.93950624460000043 -0.59019043540000005
C  -0.78873448450000017 -2.93342560249999984 -2.74767156129999979
H  -1.65105047429999985 -3.36709303300000018 -3.24734534089999993
H  -0.94080994129999995 -1.86249130399999996 -2.63426329910000012
H  0.09769584770000000 -3.12238550349999988 -3.34633290499999969
O  -0.31270587709999997 -1.72908744209999998 0.96222987169999996
C  -0.75639768029999999 -1.41562626900000010 2.26570853620000001
H  -0.48053002800000000 -2.24861458190000008 2.91119042929999994
H  -0.27953495010000001 -0.50415289610000003 2.63805106130000011
H  -1.84335077949999993 -1.28882117770000004 2.29006576190000022
Na 0.32472673889999998 1.86108953960000001 -2.55904222440000062
C  1.59437988690000010 0.95251278650000004 -0.11900194240000000
C  2.62798630969999980 1.60470832070000013 0.52971551090000002
C  2.39738014130000021 2.66860490969999997 1.38924900060000001
C  1.07462962530000006 3.06100906630000003 1.58479759759999994
C  0.02722214700000000 2.44753363100000021 0.93182787649999999
H  1.79667058959999992 0.07812474300000000 -0.72427869379999998
H  3.20646641519999998 3.16906125620000001 1.89608601299999990
C  4.02242677450000041 1.13432563070000003 0.23739594440000000
C  0.79714348099999988 4.21848637510000035 2.49966740180000002
H  -0.98917202859999998 2.76478783479999990 1.11494240200000005
F  4.98155598309999981 1.85775123160000000 0.82310144169999999
F  4.27770141500000012 1.17451972130000004 -1.09261876559999993
F  4.23038156880000038 -0.14445611950000001 0.60183740860000001
F  0.93531460619999995 5.40534407600000044 1.86909261979999997
F  1.63171354739999996 4.26697994790000035 3.55306484169999992
F  -0.44489063280000002 4.21295314450000014 3.00783101180000001

solvent.xyz

5
qcio_charge=0 qcio_multiplicity=1 Etot= -12.2459681537
Cl 1.46122853990000001 0.17199287420000001 0.04406414020000000
C  -0.00104032490000000 -0.82797907320000008 0.02872366960000000
Cl -1.46079607739999995 0.17219286340000001 -0.05600426540000000
H  0.02909363750000000 -1.46634110380000005 -0.85247231329999995
H  -0.03269974490000000 -1.40366280469999993 0.95203640290000002

CREST Stdout

       ╔════════════════════════════════════════════╗
       ║            ___ ___ ___ ___ _____           ║
       ║           / __| _ \ __/ __|_   _|          ║
       ║          | (__|   / _|\__ \ | |            ║
       ║           \___|_|_\___|___/ |_|            ║
       ║                                            ║
       ║  Conformer-Rotamer Ensemble Sampling Tool  ║
       ║          based on the xTB methods          ║
       ║                                            ║
       ╚════════════════════════════════════════════╝
       Version 3.0.2, Sun, 25 August 20:02:44, 08/25/2024
       commit (af7eb99) compiled by 'usr@fv-az732-492'

   Cite work conducted with this code as

   • P.Pracht, F.Bohle, S.Grimme, PCCP, 2020, 22, 7169-7192.
   • S.Grimme, JCTC, 2019, 15, 2847-2862.
   • P.Pracht, S.Grimme, C.Bannwarth, F.Bohle, S.Ehlert,
     G.Feldmann, J.Gorges, M.Müller, T.Neudecker, C.Plett,
     S.Spicher, P.Steinbach, P.Wesołowski, F.Zeller,
     J. Chem. Phys., 2024, 160, 114110.

   for works involving QCG cite

   • S.Spicher, C.Plett, P.Pracht, A.Hansen, S.Grimme,
     JCTC, 2022, 18 (5), 3174-3189.
   • C.Plett, S. Grimme,
     Angew. Chem. Int. Ed. 2023, 62, e202214477.

   for works involving MECP screening cite

   • P.Pracht, C.Bannwarth, JCTC, 2022, 18 (10), 6370-6385.

   Original code
     P.Pracht, S.Grimme, Universität Bonn, MCTC
   with help from (alphabetical order):
     C.Bannwarth, F.Bohle, S.Ehlert, G.Feldmann, J.Gorges,
     S.Grimme, C.Plett, P.Pracht, S.Spicher, P.Steinbach,
     P.Wesolowski, F.Zeller

   Online documentation is available at
   https://crest-lab.github.io/crest-docs/

   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. See the
   GNU Lesser General Public License (LGPL) for more details.

 Command line input:
 $ crest solute.xyz -qcg solvent.xyz --nsolv 10 --keepdir --gfnff --chrg 0 --uhf 0

  --gfnff : Use of GFN-FF requested.
  --chrg 0
  --uhf 0

> Setting up backup calculator ... done.
 ----------------
 Calculation info
 ----------------
> User-defined calculation level:
 : GFN-FF calculation via GFNFF lib
 :   Molecular charge    : 0


  ========================================
  |           ----------------           |
  |                 Q C G                |
  |           ----------------           |
  |        Quantum Cluster Growth        |
  |       University of Bonn, MCTC       |
  ========================================
   S. Grimme, S. Spicher, C. Plett.

   Cite work conducted with this code as

   S. Spicher, C. Plett, P. Pracht, A. Hansen, S. Grimme, JCTC, 2022, 18, 3174-3189.


   The use of the aISS algorithm is requested (recommend).
   This requires xtb version 6.6.0 or newer.
   xTB-IFF can still be used with the --xtbiff flag.


  =========================================
  |   quantum cluster growth: INPUT       |
  =========================================

  QCG: Only Cluster Generation

  input parameters     
  solute                 : solute.xyz
  charge                 : 0
  uhf                    : 0
  solvent                : solvent.xyz
  # of solvents to add   : 10
  Cluster generated that are above 10 % populated 
  # of CPUs used         : 1
  Solvation model        : 
  xtb opt level          : normal
  System temperature [K] : 298.1
  RRHO scaling factor    : 0.75


 Solute geometry
  molecular radius (Bohr**1):   10.19
  molecular area   (Bohr**2): 2013.72
  molecular volume (Bohr**3): 4427.45
 Solvent geometry
  molecular radius (Bohr**1):    5.59
  molecular area   (Bohr**2):  429.00
  molecular volume (Bohr**3):  732.83

  radius of solute    :    16.42
  radius of solvent   :     9.02

  =========================================
  |            Preoptimization            |
  =========================================
 Total Energy of solute not found
 Total Energy of solvent not found

  ________________________________________________________________________

  __________________     Solute Cluster Generation   _____________________

  ________________________________________________________________________


  =========================================
  |   quantum cluster growth: GROW        |
  =========================================

 Solute:
       unit ellipsoid axis a,b,c     :   0.333   0.333   0.333
 Solvent:
       unit ellipsoid axis a,b,c     :   0.333   0.333   0.333

  solvent anisotropy            :     1.000
  solute anisotropy             :     1.000
  roff inner wall               :     0.000
  solute max dist               :    23.878
  solvent max dist              :     5.525
  inner unit axis               :     0.333     0.333     0.333
  inner ellipsoid/Bohr          :     2.388     2.388     2.388
  scaling factor outer ellipsoid:     1.000
  outer ellipsoid/Bohr          :     2.763     2.763     2.763

  Size       E        De       Detot      Density     Eatom    av. R  Rlast   Volume    Opt
            [Eh]    [kcal]     [kcal]     [u/Å^3]     [kcal]   [bohr] [bohr] [bohr^3]
Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
ERROR STOP error while reading input coordinates

Error termination. Backtrace:
#0  0xced1d0 in ???
#1  0xced479 in ???
#2  0xcee587 in ???
#3  0x845de4 in __strucrd_MOD_rdxmol
	at /home/runner/work/crest/crest/src/strucreader.f90:1028
#4  0x846c83 in __strucrd_MOD_rdcoord
	at /home/runner/work/crest/crest/src/strucreader.f90:936
#5  0x6a94d3 in qcg_grow_
	at /home/runner/work/crest/crest/src/qcg/solvtool.f90:661
#6  0x6b3e68 in crest_solvtool_
	at /home/runner/work/crest/crest/src/qcg/solvtool.f90:87
#7  0x40e52b in crest
	at /home/runner/work/crest/crest/src/crest_main.f90:261
#8  0x408f7e in main
	at /home/runner/work/crest/crest/src/crest_main.f90:26

Expected behavior
The QCG algorithm would execute correctly.

[coltonbh]

Also, I can confirm the same error when running example 2 on the documentation website found here. I'm using crest 3.0.2.

[coltonbh]

Also can confirm this isn't a /n issue. Tried solvent and solute with/without /n characters to terminate their xyz files.

[cplett]

Hi, which version of xtb are you using for the CREST runs? In version 6.7.1, there was a bug that caused a segmentation fault in the docking module, which might be the reason for the error you encountered. If you're using this version, I recommend switching to 6.7.1 or to the bleeding edge version of xtb to avoid this issue.

[coltonbh]

I'm not using an xtb binary. I'm using the CREST 3.0.2 binary available here on GitHub, which I believe uses tblite under the hood (though I could be mistaken!).

[pprcht]

QCG still uses xtb, there is a disclaimer in the README.md. It will have uses whatever binary it has found as there should be a error stop if none is present.

[coltonbh]

I see! That could be the issue! Really appreciate the feedback here to know what's going on.

It would be excellent if the program communicated these types of messages (ERROR: no xtb executable found.) or something like that. Then I'd know how to proceed without harassing you here :)

Much thanks! Lemme try to run in an environment with an xtb executable and see if that fixes it...

[pprcht]

It actually already does that, here's the relevant part in QCG:

crest/src/qcg/solvtool.f90

Lines 56 to 71 in a12cb48

	!> Check, if xtb is present
	call checkprog_silent(env%ProgName,.true.,iostat=io)
	if(io /= 0 ) error stop 'No xtb found'
	!> Check, if xtbiff is present (if it is required)
	if (env%use_xtbiff) then
	call checkprog_silent(env%ProgIFF,.true.,iostat=io)
	if(io /= 0 ) error stop 'No xtbiff found'
	else
	write (*, *)
	write (*, *) ' The use of the aISS algorithm is requested (recommend).'
	write (*, *) ' This requires xtb version 6.6.0 or newer.'
	write (*, *) ' xTB-IFF can still be used with the --xtbiff flag.'
	write (*, *)
	end if

Are you sure there wasn't an xtb somewhere in path?

[coltonbh]

Ah. I see. And yes, I have xtb-python installed, version 22.1 (though if you check xtb.__version__ it will say 20.2 due to this issue, the fix for which never got published to pypi).

Is there some reason you'd expect this executable to not work?