Segfault in orbital extension

[cryos]

The attached file crashes Avogadro for me on startup when the orbital extension is activated. Note that it contains no MO information, just vibrations.

The backtrace is:

Program received signal SIGSEGV, Segmentation fault.
0x00007fffcf1bcc2b in ?? () from /usr/lib/avogadro/1_1/extensions/orbitalextension.so
(gdb) bt
#0 0x00007fffcf1bcc2b in ?? () from /usr/lib/avogadro/1_1/extensions/orbitalextension.so
#1 0x00007fffcf1b6ead in ?? () from /usr/lib/avogadro/1_1/extensions/orbitalextension.so
#2 0x00007fffcf1b965b in ?? () from /usr/lib/avogadro/1_1/extensions/orbitalextension.so
#3 0x00007fffcf1b9d90 in ?? () from /usr/lib/avogadro/1_1/extensions/orbitalextension.so
#4 0x00007ffff5fd05b1 in Avogadro::Extension::qt_metacall(QMetaObject::Call, int, void**) () from /usr/lib/libavogadro.so.1
#5 0x00007fffcf1c4805 in ?? () from /usr/lib/avogadro/1_1/extensions/orbitalextension.so
#6 0x00007ffff67c62e6 in QMetaObject::activate(QObject_, QMetaObject const_, int, void**) () from /usr/lib/libQtCore.so.4
#7 0x0000000000436b7d in ?? ()
#8 0x0000000000446021 in ?? ()
#9 0x00000000004462e7 in ?? ()
#10 0x0000000000450308 in ?? ()
#11 0x00007ffff67c62e6 in QMetaObject::activate(QObject_, QMetaObject const_, int, void**) () from /usr/lib/libQtCore.so.4
#12 0x00007ffff5fd1534 in Avogadro::MoleculeFile::qt_metacall(QMetaObject::Call, int, void**) () from /usr/lib/libavogadro.so.1
#13 0x00007ffff67c2e29 in QObject::event(QEvent*) () from /usr/lib/libQtCore.so.4
#14 0x00007ffff6cc332c in QApplicationPrivate::notify_helper(QObject_, QEvent_) () from /usr/lib/libQtGui.so.4
#15 0x00007ffff6cc980b in QApplication::notify(QObject_, QEvent_) () from /usr/lib/libQtGui.so.4
#16 0x00007ffff67b309c in QCoreApplication::notifyInternal(QObject_, QEvent_) () from /usr/lib/libQtCore.so.4
#17 0x00007ffff67b6744 in QCoreApplicationPrivate::sendPostedEvents(QObject_, int, QThreadData_) () from /usr/lib/libQtCore.so.4
#18 0x00007ffff67dcb73 in ?? () from /usr/lib/libQtCore.so.4
#19 0x00007ffff42016f2 in g_main_context_dispatch () from /lib/libglib-2.0.so.0
#20 0x00007ffff4205568 in ?? () from /lib/libglib-2.0.so.0
#21 0x00007ffff420571c in g_main_context_iteration () from /lib/libglib-2.0.so.0
#22 0x00007ffff67dc6b3 in QEventDispatcherGlib::processEvents(QFlagsQEventLoop::ProcessEventsFlag) () from /usr/lib/libQtCore.so.4
#23 0x00007ffff6d7319e in ?? () from /usr/lib/libQtGui.so.4
#24 0x00007ffff67b6b8f in QCoreApplication::processEvents(QFlagsQEventLoop::ProcessEventsFlag) () from /usr/lib/libQtCore.so.4
#25 0x000000000046196d in ?? ()
#26 0x00007ffff7a9bc8d in __libc_start_main () from /lib/libc.so.6
#27 0x0000000000420129 in _start ()

Reported by: @mbanck

[cryos]

methane.molden

Original comment by: @mbanck

[cryos]

Just to be clear, openbabel seems to read this one in fine.

Original comment by: @mbanck

[cryos]

This file seems to expose a bug in Open Babel's molden support as well. When I successfully open the file, I see only 2 hydrogen atoms!

I submitted a patch to Gerrit which seems to fix the Avogadro side for me.
http://review.source.kitware.com/#/t/814

Original comment by: @ghutchis

[cryos]

• status: pending --> closed

Original comment by: @ghutchis