Segmentation fault when running QCxMS2 with qcxms2.toml input

[BK33333]

Description:

I'm experiencing a segmentation fault when executing QCxMS2 with the following command:

qcxms2 qcxms2.toml -notsgeo



System Information:

• Operating System: Ubuntu 22.04
• QCxMS2 Version: 1.0.0 (built from source on April 13, 2025)
• Compiler: gfortran 11.4.0
• Build System: CMake
• External Programs:
  • xtb 6.7.1
  • CREST 3.0.2
  • molbar 1.1.3
  • ORCA 6.0.0

Input Files:

• qcxms2.toml:

  [molecule]
  file = "qcxms2.xyz"
  charge = 1
  method = "xtb"

  [md]
  temperature = 6000
  time = 1000

  [general]
  nproc = 2
  tgeo = false



• qcxms2.xyz:

  21
  Optimized structure from CREST
  N         -3.2504431441        0.3627515194       -0.3356139268
  H         -3.6682159468       -0.1925732445       -1.0855999201
  H         -2.5987836578        1.1631073631       -0.7606145783
  ...



Error Output:

Optimizing starting structure at the gfn2 level
ERROR: Could not find file qcxms2.toml for spin determination
Compute IP at level gfn2
ERROR: Could not find file qcxms2.toml for spin determination
...
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.



Backtrace:

#0  __memcpy_avx_unaligned_erms_rtm () at ../sysdeps/x86_64/multiarch/memmove-vec-unaligned-erms.S:273
#1  0x563e6e9c3f07 in __utility_MOD_getsumform at /home/reillycharles/qcxms2/src/utility.f90:512
#2  0x563e6e9b85a0 in __qmmod_MOD_readoutqm at /home/reillycharles/qcxms2/src/qmmod.f90:211
#3  0x563e6e9bab93 in __charges_MOD_checkip at /home/reillycharles/qcxms2/src/charges.f90:419
#4  0x563e6e9bb87b in __charges_MOD_getip1 at /home/reillycharles/qcxms2/src/charges.f90:334
#5  0x563e6e97aa63 in qcxms2 at /home/reillycharles/qcxms2/src/main.f90:146
#6  0x563e6e97750e in main at /home/reillycharles/qcxms2/src/main.f90:6



Additional Notes:

• Running dos2unix on qcxms2.inp did not resolve the issue.
• The error message suggests that the program cannot find qcxms2.toml, despite it being present in the working directory.
• The segmentation fault occurs during the execution of getsumform in utility.f90.

---

[gorges97]

Thanks for opening this issue. qcxms2 doesn't support TOML input yet. It is currently only a dependency because mctc-lib depends on it. You need to provide an XYZ file as input and specify the settings with commandline flags. Please check the documentation before using qcxms2: https://xtb-docs.readthedocs.io/en/latest/qcxms2_doc/qcxms2.html
In addition, unlike its predecessor QCxMS, qcxms2 does not perform MDs but follows a static reaction network approach.
However, I agree that it would be a nice feature to support this and it may be implemented in future releases.