Comments below.
Steve
2010/9/25 JhonY. I. <[email protected]...>:
Hello, Steve?
First many thanks for your helps really.
I'd like to perform simulation in which diamond material part is treated as
rigid body and rotational motion of this rigid body is discarded, while
other parts are
considered commonly.
For carbon in this system, airebo poetential will be applied but I don't
want to interaction between atoms (carbon) in diamond, as usual.I've read fix/rigid section for it following your advice.
However, there are some confused points in it as follows.1. In the manual, when I reduce degree of freedom by excluding rotational
motion of rigid body, the degree of freedom in calculating temperature
should remain as if
there is no change and I have to correct this point manually by using
"temperature compute" (specifically speaking, maybe, it will be concerned
with total kinetic energy for it).It is supposed that following command will be required for NVT simulation.
fix 1 rigid/nvt diamond temp 298. 298. 0.002 torque 1 off off off
(here, "diamond" is group ID for diamond rigid body and unit of metal is
assumed)
I'm not sure what you're asking. If you use fix rigid/nvt, then you don't have
to worry about DOF - the fix takes care of it, as well as computing
the temperature
of the rigid body.
Then, will it be not sufficient?
Should I use compute/temperature command additionally?
If so, where should I insert commpute temperature command in input file
(mabye, "commpute 1 diamond temp")?
fix rigid/nvt command performs temperature control and integration together
and I don't know how I can affect it by additional temperature calculation.
You can define your own computes however you wish. They will not
affect fix rigid/nvt.
What should I do for it in detail?
2. It is written that I should use "neigh_modify exclude" and "delete_bonds
commands" to avoid interaction calculation between atoms included in rigid
body.
An airebo potential assumes no bonded configuration between atoms prior to
interaction calculation.Thus, if I use airebo potential for carbon of diamond (rigid body), I think
that it will be sufficient to use only "meigh_modify exlude" command without
considering "delete bonds".
Is it right?
yes, there are no bonds (in a LAMMPS sense) in an AIREBO model
initially, I wouldn't worry about excluding the pairwise interactions
from your rigid body - it's just an efficiency issue - so I'd see if
you can get your model to work correctly first
Otherwise, would you advise me on what commands should be taken for it,
please?3. Incidentally asking, it seems that there is no option of Berendsen
thermostat in rigid/nvt.
I'd like to use Berendsen thermostat for non-rigid part and I think that
temperature control is performed independently to each other for rigid part
and
non-rigid part.
Will it be all right even if two kinds of thermostat are used together?
You can use whatever thermostat you want on parts of your model
that aren't the rigid body. You should not use a 2nd thermostat
on the rigid body if you are using fix rigid/nvt.