[ghemical-users] Ghemical problems

[Glen Shennan]

Turns out I shouldn't have been trying ab initio QC on my laptop.  I was
trying to model thiophene when the crashes occured but when I try ethane I
can get through the energy calculation and geometry optimisation (slowly)
with no crashes, using MPQC STO-3G.  Assume lack of memory is to blame?

I want to use ghemical/mpqc to produce images of individual molecular
orbitals in organic species but I am really struggling to find
documentation.  Is there a reference that would get me up to speed?  I
understand this is possible with ghemical but I might be wrong?

Thanks.

On 9 April 2010 05:16, Jean Bréfort <jean.brefort at normalesup.org> wrote:

> Getting a crash as well on debian.
>
> Here is a stack trace I get with an ethane molecule:
>
> #0  0x00007fffea65ff45 in *__GI_raise (sig=<value optimized out>)
>    at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
> #1  0x00007fffea662d80 in *__GI_abort () at abort.c:88
> #2  0x00007fffeaccc975 in __gnu_cxx::__verbose_terminate_handler() ()
>   from /usr/lib/libstdc++.so.6
> #3  0x00007fffeaccada6 in ?? () from /usr/lib/libstdc++.so.6
> #4  0x00007fffeaccadd3 in std::terminate() () from /usr/lib/libstdc
> ++.so.6
> #5  0x00007fffeaccaece in __cxa_throw () from /usr/lib/libstdc++.so.6
> #6  0x00007ffff1ec05ef in sc::Molecule::throw_if_atom_duplicated(int,
> double)
>    () from /usr/lib/libSCmolecule.so.7
> #7  0x00007ffff1ec84f6 in sc::Molecule::Molecule(sc::Ref<sc::KeyVal>
> const&) ()
>   from /usr/lib/libSCmolecule.so.7
> #8  0x00007ffff1ecb0e9 in sc::DescribedClass*
> sc::create<sc::Molecule>(sc::Ref<sc::KeyVal> const&) ()
> from /usr/lib/libSCmolecule.so.7
> #9  0x00007ffff06fc150 in sc::StringKeyVal::key_value(char const*,
> sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
> #10 0x00007ffff06ff1a5 in sc::PrefixKeyVal::key_value(char const*,
> sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
> #11 0x00007ffff06f3afa in sc::KeyVal::key_describedclassvalue(char
> const*, sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
> #12 0x00007ffff06f115a in sc::KeyVal::describedclassvalue(char const*,
> sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
> #13 0x00007ffff1edd8b1 in
> sc::MolecularEnergy::MolecularEnergy(sc::Ref<sc::KeyVa---Type <return>
> to continue, or q <return> to quit---
> l> const&) () from /usr/lib/libSCmolecule.so.7
> #14 0x00007ffff285916f in
> sc::Wavefunction::Wavefunction(sc::Ref<sc::KeyVal> const&) ()
> from /usr/lib/libSCwfn.so.7
> #15 0x00007ffff28625b3 in
> sc::OneBodyWavefunction::OneBodyWavefunction(sc::Ref<sc::KeyVal> const&)
> () from /usr/lib/libSCwfn.so.7
> #16 0x00007ffff2d8f55d in sc::SCF::SCF(sc::Ref<sc::KeyVal> const&) ()
>   from /usr/lib/libSCscf.so.7
> #17 0x00007ffff2d9c1dd in sc::CLSCF::CLSCF(sc::Ref<sc::KeyVal> const&)
> ()
>   from /usr/lib/libSCscf.so.7
> #18 0x00007ffff2d9fa4e in sc::CLHF::CLHF(sc::Ref<sc::KeyVal> const&) ()
>   from /usr/lib/libSCscf.so.7
> #19 0x00007ffff2da2509 in sc::DescribedClass*
> sc::create<sc::CLHF>(sc::Ref<sc::KeyVal> const&) ()
> from /usr/lib/libSCscf.so.7
> #20 0x00007ffff06fc150 in sc::StringKeyVal::key_value(char const*,
> sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
> #21 0x00007ffff06ff1a5 in sc::PrefixKeyVal::key_value(char const*,
> sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
> #22 0x00007ffff06f3afa in sc::KeyVal::key_describedclassvalue(char
> const*, sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
> #23 0x00007ffff06f115a in sc::KeyVal::describedclassvalue(char const*,
> sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
> #24 0x00007ffff370c5ad in eng1_qm_mpqc::eng1_qm_mpqc(setup*, unsigned
> int, unsigned int) () fr
> #25 0x00007ffff3709784 in setup1_qm::CreateEngineByIndex(unsigned int)
> ()
>   from /usr/lib/libghemical.so.5
> #26 0x00007ffff36e5515 in setup::CreateCurrentEngine() ()
>   from /usr/lib/libghemical.so.5
> #27 0x00007ffff36e256f in model::DoEnergy() ()
> from /usr/lib/libghemical.so.5
> #28 0x00007ffff428a44e in g_closure_invoke ()
> from /usr/lib/libgobject-2.0.so.0
> #29 0x00007ffff429e513 in ?? () from /usr/lib/libgobject-2.0.so.0
> #30 0x00007ffff429f8cf in g_signal_emit_valist ()
>   from /usr/lib/libgobject-2.0.so.0
> #31 0x00007ffff429fdd3 in g_signal_emit ()
> from /usr/lib/libgobject-2.0.so.0
> #32 0x00007ffff5fd9d43 in ?? () from /usr/lib/libgtk-x11-2.0.so.0
> #33 0x00007ffff428a44e in g_closure_invoke ()
> from /usr/lib/libgobject-2.0.so.0
> #34 0x00007ffff429de2c in ?? () from /usr/lib/libgobject-2.0.so.0
> #35 0x00007ffff429f8cf in g_signal_emit_valist ()
>   from /usr/lib/libgobject-2.0.so.0
> #36 0x00007ffff429fdd3 in g_signal_emit ()
> from /usr/lib/libgobject-2.0.so.0
> #37 0x00007ffff61af46e in gtk_widget_activate ()
>   from /usr/lib/libgtk-x11-2.0.so.0
> #38 0x00007ffff60af83d in gtk_menu_shell_activate_item ()
>   from /usr/lib/libgtk-x11-2.0.so.0
> #39 0x00007ffff60b1039 in ?? () from /usr/lib/libgtk-x11-2.0.so.0
> #40 0x00007ffff60a1838 in ?? () from /usr/lib/libgtk-x11-2.0.so.0
> #41 0x00007ffff428a44e in g_closure_invoke ()
> from /usr/lib/libgobject-2.0.so.0
>
> Le jeudi 08 avril 2010 à 23:20 +1000, Glen Shennan a écrit :
> > Hi,
> >
> > I have just started trying to use Ghemical but I'm having problems
> > with it crashing every time I try to set the computation method to QM
> > (mopac7 or mpqc).  I've been setting the computation method to QM and
> > then clicking "Compute...Energy" as the program says to do but it
> > simply crashes at this point.  Does this sound familiar?
> >
> > I'm running Ghemical on an AMD64 running Ubuntu.
> >
> > Regards,
> > Glen Shennan
> > _______________________________________________
> > ghemical-users mailing list
> > ghemical-users at bioinformatics.org
> > http://www.bioinformatics.org/mailman/listinfo/ghemical-users
>
>
>
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