Hi, Axel,
please always keep the mailing list in cc: when replying.
Thank you. I want to calculate the energy change between two groups of
atoms. It involves the details of interactions of each atoms pair. I think I
can define two groups that only contain the pair atoms and
then iterates over all the pairs. It must be very computational consumed.
I'd like to try first. Thank you.
the is _far_ too complicated. compute group/group will already compute
the pairwise energy contributions (not only the forces) of the two
groups of atoms
so all you have to do is to retrieve it and monitor the changes.
axel.
Hi, Axel,
Yeah, I see. If I need the energy flux, may I simply divide the energy exchange by the time step? Thank you.
Regards,
Liang
Hi, Axel,
Yeah, I see. If I need the energy flux, may I simply divide the energy
exchange by the time step? Thank you.
hmmm... isn't "flux" in this context usually defined as transported
property per area per time? at least this is what is done when
people compute heat flux (i.e. the flux of kinetic energy). check out:
cheers,
axel.
Hi, Axel,
The “compute heat/flux” command will calculate the net heat flux in and out the the group of atoms. I have periodic boundaries, and I want to exclude the energy flux through the periodic boundaries. So it might not be appropriate to use this command. I think compute group/group can work.
Regards
Liang
Hi, Axel,
The "compute heat/flux" command will calculate the net heat flux in and out
the the group of atoms. I have periodic boundaries, and I want to exclude
the energy flux through the periodic boundaries. So it might not be
appropriate to use this command. I think compute group/group can work.
i only mentioned heat/flux as an example for "flux". it computes
something different than compute group/group. as far as PBC
are concerned, that is handled by "mirroring" the system. this
way you get twice the flux because of symmetry.
if you _are_ in fact after the heat flux, then you should read the
explanations and examples given very carefully. this is a topic
that has been discussed on this list many times and there are
some subtleties involved, so it will pay off to be careful.
axel.