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grimme-lab / xtb

Semiempirical Extended Tight-Binding Program Package
https://xtb-docs.readthedocs.io/
GNU Lesser General Public License v3.0
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CREST QCG with xtb 6.7.1: error while reading input coordinates #1080

Closed lizhiq16 closed 1 week ago

lizhiq16 commented 1 month ago

Describe the bug when I run the following: crest mol0.xyz --qcg mol1.xyz --nsolv 2 --T 12 --ensemble --mdtime 50 --wscal 1.0

Solute geometry
  molecular radius (Bohr**1):    8.33
  molecular area   (Bohr**2): 1122.04
  molecular volume (Bohr**3): 2422.34
 Solvent geometry
  molecular radius (Bohr**1):    8.33
  molecular area   (Bohr**2): 1122.04
  molecular volume (Bohr**3): 2422.34

  radius of solute    :    13.43
  radius of solvent   :    13.43

  =========================================
  |            Preoptimization            |
  =========================================
  Total Energy of solute:     -53.3225785 Eh
  Total energy of solvent:    -53.3225785 Eh

  ________________________________________________________________________

  __________________     Solute Cluster Generation   _____________________

  ________________________________________________________________________

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

 Solute:
       unit ellipsoid axis a,b,c     :   0.371   0.334   0.295
 Solvent:
       unit ellipsoid axis a,b,c     :   0.371   0.334   0.295

  solvent anisotropy            :     1.108
  solute anisotropy             :     1.108
  roff inner wall               :     2.684
  solute max dist               :    23.243
  solvent max dist              :    23.243
  inner unit axis               :     0.409     0.333     0.259
  inner ellipsoid/Bohr          :    16.783    13.666    10.617
  scaling factor outer ellipsoid:     1.000
  outer ellipsoid/Bohr          :    25.283    22.815    20.109

  Size       E        De       Detot      Density     Eatom    av. R  Rlast   Volume    Opt
            [Eh]    [kcal]     [kcal]     [u/Å^3]     [kcal]   [bohr] [bohr] [bohr^3]
error while reading input coordinates

To Reproduce CREST 3.0.1 with xtb 6.7.1, the bug consistently occurs. However, CREST 3.0.1 with xtb 6.6.1, the process runs smoothly.

Please provide all input and output file such that we confirm your report Use any solute and solvent molecules can reproduce this bug.

marcelmbn commented 1 month ago

This should probably be moved to https://github.com/crest-lab/crest. Maybe, you can have a look, @cplett @pprcht?

lizhiq16 commented 1 month ago

As I mentioned, CREST 3.0.1 with xtb 6.6.1 runs smoothly. Therefore, the issue seems to be related to xtb 6.7.1.

pprcht commented 1 month ago

the error message originates from CREST, but I can't tell if something is wrong with the xtb output or with the I/O. However, can confirm xtb 6.6.1 runs through the algo smoothly... Did anything at all change with the input output of xtb 6.7.1?

marcelmbn commented 1 month ago

Maybe @Albkat can comment best on this topic.

cplett commented 3 weeks ago

This issue appears to be related to the problem reported in #1078 and #1079. In xtb version 6.7.1, the docking module yields a segmentation fault, which also affects QCG, causing it not to work properly. The bug should be fixed with #1089 and likely only occurs in xtb 6.7.1. Therefore, I recommend using xtb versions 6.7.0 or 6.6.1 for the QCG runs until the next xtb version comes up, or using a compiled version that includes the pull request #1089.

lizhiq16 commented 3 weeks ago

OK, I will use xtb versions 6.6.1. When the next xtb version comes up, I'll give it a try. Thanks for the help : )

marcelmbn commented 1 week ago

Should be resolved by https://github.com/grimme-lab/xtb/pull/1089.