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?<br>
<br>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?<br>
<br>Thanks.<br>
<br><div class="gmail_quote">On 9 April 2010 05:16, Jean Bréfort <span dir="ltr"><<a href="mailto:jean.brefort@normalesup.org" target="_blank">jean.brefort@normalesup.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Getting a crash as well on debian.<br>
<br>
Here is a stack trace I get with an ethane molecule:<br>
<br>
#0 0x00007fffea65ff45 in *__GI_raise (sig=<value optimized out>)<br>
at ../nptl/sysdeps/unix/sysv/linux/raise.c:64<br>
#1 0x00007fffea662d80 in *__GI_abort () at abort.c:88<br>
#2 0x00007fffeaccc975 in __gnu_cxx::__verbose_terminate_handler() ()<br>
from /usr/lib/libstdc++.so.6<br>
#3 0x00007fffeaccada6 in ?? () from /usr/lib/libstdc++.so.6<br>
#4 0x00007fffeaccadd3 in std::terminate() () from /usr/lib/libstdc<br>
++.so.6<br>
#5 0x00007fffeaccaece in __cxa_throw () from /usr/lib/libstdc++.so.6<br>
#6 0x00007ffff1ec05ef in sc::Molecule::throw_if_atom_duplicated(int,<br>
double)<br>
() from /usr/lib/libSCmolecule.so.7<br>
#7 0x00007ffff1ec84f6 in sc::Molecule::Molecule(sc::Ref<sc::KeyVal><br>
const&) ()<br>
from /usr/lib/libSCmolecule.so.7<br>
#8 0x00007ffff1ecb0e9 in sc::DescribedClass*<br>
sc::create<sc::Molecule>(sc::Ref<sc::KeyVal> const&) ()<br>
from /usr/lib/libSCmolecule.so.7<br>
#9 0x00007ffff06fc150 in sc::StringKeyVal::key_value(char const*,<br>
sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7<br>
#10 0x00007ffff06ff1a5 in sc::PrefixKeyVal::key_value(char const*,<br>
sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7<br>
#11 0x00007ffff06f3afa in sc::KeyVal::key_describedclassvalue(char<br>
const*, sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7<br>
#12 0x00007ffff06f115a in sc::KeyVal::describedclassvalue(char const*,<br>
sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7<br>
#13 0x00007ffff1edd8b1 in<br>
sc::MolecularEnergy::MolecularEnergy(sc::Ref<sc::KeyVa---Type <return><br>
to continue, or q <return> to quit---<br>
l> const&) () from /usr/lib/libSCmolecule.so.7<br>
#14 0x00007ffff285916f in<br>
sc::Wavefunction::Wavefunction(sc::Ref<sc::KeyVal> const&) ()<br>
from /usr/lib/libSCwfn.so.7<br>
#15 0x00007ffff28625b3 in<br>
sc::OneBodyWavefunction::OneBodyWavefunction(sc::Ref<sc::KeyVal> const&)<br>
() from /usr/lib/libSCwfn.so.7<br>
#16 0x00007ffff2d8f55d in sc::SCF::SCF(sc::Ref<sc::KeyVal> const&) ()<br>
from /usr/lib/libSCscf.so.7<br>
#17 0x00007ffff2d9c1dd in sc::CLSCF::CLSCF(sc::Ref<sc::KeyVal> const&)<br>
()<br>
from /usr/lib/libSCscf.so.7<br>
#18 0x00007ffff2d9fa4e in sc::CLHF::CLHF(sc::Ref<sc::KeyVal> const&) ()<br>
from /usr/lib/libSCscf.so.7<br>
#19 0x00007ffff2da2509 in sc::DescribedClass*<br>
sc::create<sc::CLHF>(sc::Ref<sc::KeyVal> const&) ()<br>
from /usr/lib/libSCscf.so.7<br>
#20 0x00007ffff06fc150 in sc::StringKeyVal::key_value(char const*,<br>
sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7<br>
#21 0x00007ffff06ff1a5 in sc::PrefixKeyVal::key_value(char const*,<br>
sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7<br>
#22 0x00007ffff06f3afa in sc::KeyVal::key_describedclassvalue(char<br>
const*, sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7<br>
#23 0x00007ffff06f115a in sc::KeyVal::describedclassvalue(char const*,<br>
sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7<br>
#24 0x00007ffff370c5ad in eng1_qm_mpqc::eng1_qm_mpqc(setup*, unsigned<br>
int, unsigned int) () fr<br>
#25 0x00007ffff3709784 in setup1_qm::CreateEngineByIndex(unsigned int)<br>
()<br>
from /usr/lib/libghemical.so.5<br>
#26 0x00007ffff36e5515 in setup::CreateCurrentEngine() ()<br>
from /usr/lib/libghemical.so.5<br>
#27 0x00007ffff36e256f in model::DoEnergy() ()<br>
from /usr/lib/libghemical.so.5<br>
#28 0x00007ffff428a44e in g_closure_invoke ()<br>
from /usr/lib/libgobject-2.0.so.0<br>
#29 0x00007ffff429e513 in ?? () from /usr/lib/libgobject-2.0.so.0<br>
#30 0x00007ffff429f8cf in g_signal_emit_valist ()<br>
from /usr/lib/libgobject-2.0.so.0<br>
#31 0x00007ffff429fdd3 in g_signal_emit ()<br>
from /usr/lib/libgobject-2.0.so.0<br>
#32 0x00007ffff5fd9d43 in ?? () from /usr/lib/libgtk-x11-2.0.so.0<br>
#33 0x00007ffff428a44e in g_closure_invoke ()<br>
from /usr/lib/libgobject-2.0.so.0<br>
#34 0x00007ffff429de2c in ?? () from /usr/lib/libgobject-2.0.so.0<br>
#35 0x00007ffff429f8cf in g_signal_emit_valist ()<br>
from /usr/lib/libgobject-2.0.so.0<br>
#36 0x00007ffff429fdd3 in g_signal_emit ()<br>
from /usr/lib/libgobject-2.0.so.0<br>
#37 0x00007ffff61af46e in gtk_widget_activate ()<br>
from /usr/lib/libgtk-x11-2.0.so.0<br>
#38 0x00007ffff60af83d in gtk_menu_shell_activate_item ()<br>
from /usr/lib/libgtk-x11-2.0.so.0<br>
#39 0x00007ffff60b1039 in ?? () from /usr/lib/libgtk-x11-2.0.so.0<br>
#40 0x00007ffff60a1838 in ?? () from /usr/lib/libgtk-x11-2.0.so.0<br>
#41 0x00007ffff428a44e in g_closure_invoke ()<br>
from /usr/lib/libgobject-2.0.so.0<br>
<br>
Le jeudi 08 avril 2010 à 23:20 +1000, Glen Shennan a écrit :<br>
<div><div></div><div>> Hi,<br>
><br>
> I have just started trying to use Ghemical but I'm having problems<br>
> with it crashing every time I try to set the computation method to QM<br>
> (mopac7 or mpqc). I've been setting the computation method to QM and<br>
> then clicking "Compute...Energy" as the program says to do but it<br>
> simply crashes at this point. Does this sound familiar?<br>
><br>
> I'm running Ghemical on an AMD64 running Ubuntu.<br>
><br>
> Regards,<br>
> Glen Shennan<br>
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<br>
<br>
</blockquote></div><br>