ONIOM segfault - invalid memory reference

[camattelaer]

Describe the bug
A clear and concise description of what the bug is.

Getting segfault when trying to perform ONIOM calculation:

To Reproduce
Steps to reproduce the behaviour:

1. happens with input coordinates
   test_coords.txt

2. start xtb with (all the options here)
   xtb complex_dry_1.pdb --oniom 828-864 --chrg +1:+3

ulimit -s unlimited and export OMP_STACKSIZE=4G (also greater values) were tried
xtb complex_dry_1.pdb --chrg +3 runs without issues

4. run xtb with your options and the --verbose flag
   does not provide extra info

5. output showing the error
   `Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x149eabc7951f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#1 0x149eac2cde89 in ???
#2 0x149eac2e97e8 in ???
#3 0x149eac2ae340 in ???
#4 0x149eac4d6ea1 in ???
#5 0x149eac325c8f in ???
#6 0x55aabff03b79 in ???
#7 0x55aabfef2224 in ???
#8 0x149eabc60d8f in __libc_start_call_main
at ../sysdeps/nptl/libc_start_call_main.h:58
#9 0x149eabc60e3f in __libc_start_main_impl
at ../csu/libc-start.c:392
#10 0x55aabfef22c8 in ???
Segmentation fault (core dumped)`

Please provide all input and output file such that we confirm your report.

Expected behaviour
A clear and concise description of what you expected to happen.
no segfault

Additional context
Add any other context about the problem here.

Thanks in advance

CA

[alexamist]

Hi, I'm having the same problem in xtb version 6.7.1, but for a different type of calculation:
xtb open.POSCAR --opt --mcgfnff

Error:
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0xcb488623960 in ???
#1 0xcb488622ac5 in ???
#2 0xcb48744251f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3 0x58b63f8b6620 in ???
#4 0x58b63f8908d2 in ???
#5 0x58b63f8bd605 in ???
#6 0x58b63f85f878 in ???
#7 0x58b63f9020a7 in ???
#8 0x58b63f81f5b5 in ???
#9 0x58b63f810640 in ???
#10 0xcb487429d8f in __libc_start_call_main
at ../sysdeps/nptl/libc_start_call_main.h:58
#11 0xcb487429e3f in __libc_start_main_impl
at ../csu/libc-start.c:392
#12 0x58b63f8106c4 in ???
#13 0xffffffffffffffff in ???
Segmentation fault (core dumped)

If I change the method --mcgfnff to --gfn 1, the calculation runs without problems.

[foxtran]

@camattelaer, please check your .pdb file.

\f0\fs24 \cf0 ATOM      1  N   LYS A   1      26.987  27.129  33.104  1.00  0.00           N  \
ATOM      2  H1  LYS A   1      27.255  27.985  33.570  1.00  0.00           H  \

What is before ATOM 1? xtb has a limited support of pdb file format.

[foxtran]

@alexamist, please open a separate issue.