Bugs item #3529127, was opened at 2012-05-23 09:00
Message generated for change (Comment added) made by ghutchis
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>Category: Open Babel
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Dana Reinemann (dnreinem)
>Assigned to: Geoff Hutchison (ghutchis)
Summary: Cannot open Gaussian 09 output files
Initial Comment:
I recently downloaded v1.0.3 for the purpose of animating frequencies of output
files in addition to programs like Molden and GaussView, and I cannot open
anything. I've tried Gaussian 09 output files, g09 fchk files, and even g98W
fch files. Each time I try to open something, it says Reading molecular file
failed, and then the path to the file. However, in a futile attempt to open
anything, I tried opening a .txt version of one of my output files. The
program responded with Opening multi-molecule file, it could take awhile, and
then shortly after seeing that, it says that Reading molecular file failed.
I'm on Windows XP 64 bit. I've attached what I tried to open. Thanks for your
help!
----------------------------------------------------------------------
>Comment By: Geoff Hutchison (ghutchis)
Date: 2012-06-13 18:38
Message:
This works for me -- just make sure you have the latest Open Babel. We just
need to get a new version out there for Dana.
----------------------------------------------------------------------
Comment By: Marcus D. Hanwell (cryosuk)
Date: 2012-06-06 13:45
Message:
With master I can load the file, but get a segfault when clicking on any
vibration in the panel. It looks like an issue with loading the vibrational
data using OB, the backtrace is included below.
rogram received signal SIGSEGV, Segmentation fault.
0x00007ffff5b3bb8c in Avogadro::Molecule::OBMol (this=0x1563540)
at /home/marcus/src/avogadro/libavogadro/src/molecule.cpp:1284
1284 obmol.SetData(d->obvibdata->Clone(&obmol));
(gdb) bt
#0 0x00007ffff5b3bb8c in Avogadro::Molecule::OBMol (this=0x1563540)
at /home/marcus/src/avogadro/libavogadro/src/molecule.cpp:1284
#1 0x00007fffdd9ea297 in Avogadro::VibrationExtension::updateMode (this=
0x1299df0, mode=2)
at
/home/marcus/src/avogadro/libavogadro/src/extensions/spectra/vibrationextension.cpp:190
#2 0x00007fffdd9f8320 in Avogadro::VibrationExtension::qt_static_metacall
(_o=
0x1299df0, _c=QMetaObject::InvokeMetaMethod, _id=0, _a=0x7fffffffc1c0)
at
/home/marcus/build/avogadro/libavogadro/src/extensions/spectra/moc_vibrationextension.cxx:61
#3 0x00007ffff6420dcf in QMetaObject::activate(QObject*, QMetaObject
const*, int, void**) () from /usr/lib/libQtCore.so.4
#4 0x00007fffdd9f8d82 in Avogadro::VibrationWidget::selectedMode (this=
0x1483010, _t1=2)
at
/home/marcus/build/avogadro/libavogadro/src/extensions/spectra/moc_vibrationwidget.cxx:151
#5 0x00007fffdd9f41ed in Avogadro::VibrationWidget::currentCellChanged
(this=
0x1483010, row=2)
at
/home/marcus/src/avogadro/libavogadro/src/extensions/spectra/vibrationwidget.cpp:224
#6 0x00007fffdd9f8b18 in Avogadro::VibrationWidget::qt_static_metacall
(_o=
0x1483010, _c=QMetaObject::InvokeMetaMethod, _id=11,
_a=0x7fffffffc390)
at
/home/marcus/build/avogadro/libavogadro/src/extensions/spectra/moc_vibrationwidget.cxx:94
#7 0x00007ffff6420dcf in QMetaObject::activate(QObject*, QMetaObject
const*, int, void**) () from /usr/lib/libQtCore.so.4
#8 0x00007ffff71d405a in QTableWidget::currentCellChanged(int, int, int,
int)
() from /usr/lib/libQtGui.so.4
#9 0x00007ffff6420dcf in QMetaObject::activate(QObject*, QMetaObject
const*, int, void**) () from /usr/lib/libQtCore.so.4
#10 0x00007ffff71bcfea in QItemSelectionModel::currentChanged(QModelIndex
const&, QModelIndex const&) () from /usr/lib/libQtGui.so.4
#11 0x00007ffff71bd0d9 in QItemSelectionModel::setCurrentIndex(QModelIndex
const&, QFlags<QItemSelectionModel::SelectionFlag>) () from
/usr/lib/libQtGui.so.4
#12 0x00007ffff716e3ba in QAbstractItemView::mousePressEvent(QMouseEvent*)
()
from /usr/lib/libQtGui.so.4
#13 0x00007ffff6cb2b33 in QWidget::event(QEvent*) ()
from /usr/lib/libQtGui.so.4
#14 0x00007ffff705cef6 in QFrame::event(QEvent*) () from
/usr/lib/libQtGui.so.4
#15 0x00007ffff716a593 in QAbstractItemView::viewportEvent(QEvent*) ()
from /usr/lib/libQtGui.so.4
#16 0x00007ffff640ba56 in
QCoreApplicationPrivate::sendThroughObjectEventFilters(QObject*, QEvent*)
() from /usr/lib/libQtCore.so.4
#17 0x00007ffff6c62f4c in QApplicationPrivate::notify_helper(QObject*,
QEvent*)
() from /usr/lib/libQtGui.so.4
#18 0x00007ffff6c67c5b in QApplication::notify(QObject*, QEvent*) ()
from /usr/lib/libQtGui.so.4
#19 0x00007ffff640b8ee in QCoreApplication::notifyInternal(QObject*,
QEvent*)
() from /usr/lib/libQtCore.so.4
#20 0x00007ffff6c63dbb in QApplicationPrivate::sendMouseEvent(QWidget*,
QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer<QWidget>&, bool) ()
from /usr/lib/libQtGui.so.4
#21 0x00007ffff6cde804 in ?? () from /usr/lib/libQtGui.so.4
#22 0x00007ffff6cdd591 in QApplication::x11ProcessEvent(_XEvent*) ()
from /usr/lib/libQtGui.so.4
#23 0x00007ffff6d03682 in ?? () from /usr/lib/libQtGui.so.4
#24 0x00007ffff40944a5 in g_main_context_dispatch ()
from /usr/lib/libglib-2.0.so.0
#25 0x00007ffff40947d8 in ?? () from /usr/lib/libglib-2.0.so.0
#26 0x00007ffff4094894 in g_main_context_iteration ()
from /usr/lib/libglib-2.0.so.0
#27 0x00007ffff6439ae6 in
QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>)
() from /usr/lib/libQtCore.so.4
#28 0x00007ffff6d032fe in ?? () from /usr/lib/libQtGui.so.4
#29 0x00007ffff640a63f in
QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) () from
/usr/lib/libQtCore.so.4
#30 0x00007ffff640a8c8 in
QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) () from
/usr/lib/libQtCore.so.4
#31 0x00007ffff640f568 in QCoreApplication::exec() ()
from /usr/lib/libQtCore.so.4
#32 0x0000000000427c77 in main (argc=1, argv=0x7fffffffe338)
at /home/marcus/src/avogadro/avogadro/src/main.cpp:251
----------------------------------------------------------------------
Comment By: Michael Banck (mbanck)
Date: 2012-05-30 10:30
Message:
For what's it worth, I can open the file fine.
----------------------------------------------------------------------
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