Calculating the electrostatic potential surface crashes

[cryos]

When I start to calculate the electrostatic potential surface the whole programm chrashes. I use Mac OSX 10.6 and Avogadro 1.0.0.

email: [email protected]

Reported by: *anonymous

[cryos]

Could you provide an example?

Original comment by: @annulen

[cryos]

1.0.1 is available, in addition to nightlies and the upcoming 1.0.2.

Original comment by: @cryos

[cryos]

This bug should be reopened. I can reproduce this in 1.0.3 on linux with any simple molecule. Van der Waals works fine. I'll attach a stack trace, which shows the null cube that causes the crash.

Original comment by: kjslag

[cryos]

I couldn't figure out how to attach a file. So here is the trace:

Reading symbols from /home/k/Documents/usr/src/avogadro-1.0.3/build/bin/avogadro...done.
(gdb) run
Starting program: /home/k/Documents/usr/src/avogadro-1.0.3/build/bin/avogadro
[Thread debugging using libthread_db enabled]
"Avogadro version: 1.0.3 Git:
LibAvogadro version: 1.0.3 Git: "
Locale: "en_US"
Libavogadro translations not found.
"System has OpenGL support."
"About to test OpenGL capabilities."
"OpenGL capabilities found: "
"Double Buffering."
"Direct Rendering."
"Antialiasing."
In a build directory - loading alternative...
Searching for plugins in "/home/k/Documents/usr/src/avogadro-1.0.3/build/lib"
Loading plugins: "/home/k/Documents/usr/src/avogadro-1.0.3/build/bin/../lib/avogadro/1_0"
Searching for plugins in ""
Searching for plugins in ""
Searching for plugins in ""
Searching for plugins in ""
Searching for plugins in ""
Loading plugins: "/home/k/.avogadro/1_0/plugins"
Searching for plugins in ""
Searching for plugins in ""
Searching for plugins in ""
Searching for plugins in ""
Searching for plugins in ""
QStackedLayout::setCurrentWidget: Widget 0x15ce220 not contained in stack
[New Thread 0x7fffc44f4700 (LWP 10785)]
[New Thread 0x7fffc3cf3700 (LWP 10786)]
GLWidget initialisation...
GLWidget initialised...
createObjects()
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area
[New Thread 0x7fffc1ad0700 (LWP 10787)]
[Thread 0x7fffc1ad0700 (LWP 10787) exited]
read 1 molecules.
setOBMol called.
Old molecule deleted...
baseName: "cml"
Calculate called!
calculateMesh called 0.05 QObject(0x0)

Program received signal SIGSEGV, Segmentation fault.
0x00007ffff5c47f7e in Avogadro::Cube::lock (this=0x0) at /home/k/Documents/usr/src/avogadro-1.0.3/libavogadro/src/cube.cpp:321
321 return m_lock;
(gdb) where
#0 0x00007ffff5c47f7e in Avogadro::Cube::lock (this=0x0) at /home/k/Documents/usr/src/avogadro-1.0.3/libavogadro/src/cube.cpp:321
#1 0x00007fffdf8a1f33 in Avogadro::SurfaceExtension::calculateMesh (this=0x164eb80, cube=0x0, isoValue=0.050000000000000003)
at /home/k/Documents/usr/src/avogadro-1.0.3/libavogadro/src/extensions/surfaceextension.cpp:505
#2 0x00007fffdf8a30c2 in Avogadro::SurfaceExtension::calculate (this=0x164eb80) at /home/k/Documents/usr/src/avogadro-1.0.3/libavogadro/src/extensions/surfaceextension.cpp:676
#3 0x00007fffdf8ebbf9 in Avogadro::SurfaceExtension::qt_metacall (this=0x164eb80, c=QMetaObject::InvokeMetaMethod, id=0, a=0x7fffffffc0f0)
at /home/k/Documents/usr/src/avogadro-1.0.3/build/libavogadro/src/extensions/moc_surfaceextension.cxx:75
#4 0x00007ffff609829a in QMetaObject::activate(QObject, QMetaObject const, int, void**) () from /usr/lib/libQtCore.so.4
#5 0x00007fffdf8ec275 in Avogadro::SurfaceDialog::calculate (this=0x2238c40) at /home/k/Documents/usr/src/avogadro-1.0.3/build/libavogadro/src/extensions/moc_surfacedialog.cxx:110
#6 0x00007fffdf8aadd6 in Avogadro::SurfaceDialog::calculateClicked (this=0x2238c40) at /home/k/Documents/usr/src/avogadro-1.0.3/libavogadro/src/extensions/surfacedialog.cpp:329
#7 0x00007fffdf8ec208 in Avogadro::SurfaceDialog::qt_metacall (this=0x2238c40, c=QMetaObject::InvokeMetaMethod, id=7, a=0x7fffffffc290)
at /home/k/Documents/usr/src/avogadro-1.0.3/build/libavogadro/src/extensions/moc_surfacedialog.cxx:97
#8 0x00007ffff609829a in QMetaObject::activate(QObject, QMetaObject const, int, void**) () from /usr/lib/libQtCore.so.4
#9 0x00007ffff6f02992 in QAbstractButton::clicked(bool) () from /usr/lib/libQtGui.so.4
#10 0x00007ffff6c4ab0e in ?? () from /usr/lib/libQtGui.so.4
#11 0x00007ffff6c4be4b in ?? () from /usr/lib/libQtGui.so.4
#12 0x00007ffff6c4c0bc in QAbstractButton::mouseReleaseEvent(QMouseEvent) () from /usr/lib/libQtGui.so.4
#13 0x00007ffff68ec716 in QWidget::event(QEvent) () from /usr/lib/libQtGui.so.4
#14 0x00007ffff689c174 in QApplicationPrivate::notify_helper(QObject_, QEvent_) () from /usr/lib/libQtGui.so.4
#15 0x00007ffff68a18fb in QApplication::notify(QObject_, QEvent_) () from /usr/lib/libQtGui.so.4
#16 0x00007ffff608562c in QCoreApplication::notifyInternal(QObject_, QEvent_) () from /usr/lib/libQtCore.so.4
#17 0x00007ffff689d142 in QApplicationPrivate::sendMouseEvent(QWidget_, QMouseEvent_, QWidget_, QWidget_, QWidget*_, QPointer&, bool) () from /usr/lib/libQtGui.so.4
#18 0x00007ffff6919528 in ?? () from /usr/lib/libQtGui.so.4
#19 0x00007ffff691832a in QApplication::x11ProcessEvent(XEvent) () from /usr/lib/libQtGui.so.4
#20 0x00007ffff693f562 in ?? () from /usr/lib/libQtGui.so.4
#21 0x00007ffff31b36cd in g_main_context_dispatch () from /usr/lib/libglib-2.0.so.0
#22 0x00007ffff31b3ea8 in ?? () from /usr/lib/libglib-2.0.so.0
#23 0x00007ffff31b4139 in g_main_context_iteration () from /usr/lib/libglib-2.0.so.0
#24 0x00007ffff60b027f in QEventDispatcherGlib::processEvents(QFlagsQEventLoop::ProcessEventsFlag) () from /usr/lib/libQtCore.so.4
#25 0x00007ffff693f1fe in ?? () from /usr/lib/libQtGui.so.4
#26 0x00007ffff6084832 in QEventLoop::processEvents(QFlagsQEventLoop::ProcessEventsFlag) () from /usr/lib/libQtCore.so.4
#27 0x00007ffff6084a2f in QEventLoop::exec(QFlagsQEventLoop::ProcessEventsFlag) () from /usr/lib/libQtCore.so.4
#28 0x00007ffff6088c07 in QCoreApplication::exec() () from /usr/lib/libQtCore.so.4
#29 0x00000000004281bc in main (argc=1, argv=0x7fffffffddd8) at /home/k/Documents/usr/src/avogadro-1.0.3/avogadro/src/main.cpp:245

Original comment by: kjslag