Crash when optimizing a large amount of molecules

Hi ,
I want to congratulate Marcus for the work in stability on 0.9.8! It’s much
more stable to work on Avogadro.
But when I try to optimize a large number of molecules, it crashes. On Linux
it closes, and on Windows it throws a C++ runtime error. What could be
causing this? Is there something I can do?

Fernando Nakagawa

In Linux it throws:

terminate called after throwing an instance of 'std::bad_alloc’
what(): std::bad_alloc
Cancelado

Fernando Nakagawa

On Sun, Oct 4, 2009 at 4:34 PM, Fernando Nakagawa naka86@gmail.com wrote:

Hi ,
I want to congratulate Marcus for the work in stability on 0.9.8! It’s much
more stable to work on Avogadro.
But when I try to optimize a large number of molecules, it crashes. On
Linux it closes, and on Windows it throws a C++ runtime error. What could be
causing this? Is there something I can do?

Fernando Nakagawa

On Mon, Oct 5, 2009 at 8:05 PM, Fernando Nakagawa naka86@gmail.com wrote:

In Linux it throws:

terminate called after throwing an instance of 'std::bad_alloc’
what(): std::bad_alloc
Cancelado

Are you trying to minimize a molecule with more than 1000 atoms? The
current force field implementation tries to allocate memory for all
non-bonded interactions. With more than 1000 atoms, this usually
fails. This will be changed in the future, but there is no real
solution at the moment.

Tim

Fernando Nakagawa

On Sun, Oct 4, 2009 at 4:34 PM, Fernando Nakagawa naka86@gmail.com wrote:

Hi ,
I want to congratulate Marcus for the work in stability on 0.9.8! It’s
much more stable to work on Avogadro.
But when I try to optimize a large number of molecules, it crashes. On
Linux it closes, and on Windows it throws a C++ runtime error. What could be
causing this? Is there something I can do?
Fernando Nakagawa


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On Oct 5, 2009, at 2:38 PM, Tim Vandermeersch wrote:

Are you trying to minimize a molecule with more than 1000 atoms? The
current force field implementation tries to allocate memory for all
non-bonded interactions.

Tim, are you saying it allocates memory even for non-bonded
interactions beyond the distance cut-off?

-Geoff

On Mon, Oct 5, 2009 at 9:19 PM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

On Oct 5, 2009, at 2:38 PM, Tim Vandermeersch wrote:

Are you trying to minimize a molecule with more than 1000 atoms? The
current force field implementation tries to allocate memory for all
non-bonded interactions.

Tim, are you saying it allocates memory even for non-bonded interactions
beyond the distance cut-off?

Yes, the memory requirements are currently N^2, regardless of the cut-off…

-Geoff