In the virial stress equation of Lammps, are the variables Va and Vb the value of thermal excitation velocity of atom or the absolute value of velocity?

Are they necessary in computing the stress, in the cases which we have rigid-body motion?

It depends on what temperature compute you assign to the

compute pressure command. See its doc page and
Section 6.16 of the manual for discussion of the
various temperature computes and how they
subtract off a “bias” to leave a thermal velocity.

For rigid bodies, fix rigid subtracts off the rigid body constraint
contribution to the virial stress, so that the pressure should
be correct. Nothing special is done with velocities in that
case.

I’m sorry, I meant that in compute stress/atom section in Lammps doc, are the velocities in the virial stress formula, the absolute value of velocity or the component of velocity related to the thermal excitation.

And as we know each displacement has two components; component due to the movement of center of mass and the component related to the deformations (strains). Now, I want to ask a question:
In computing the temperature we should exclude the kinetic energy of center of mass from the total kinetic energy.
Is there any similar process in computing stress? Or, after spatially averaging the compute stress/atom values, should we exclude the stress due to the center of mass movement? If yes, how?

Thank you very much
Mahdi Tavakol

It depends on what temperature compute you assign to the

compute pressure command. See its doc page and
Section 6.16 of the manual for discussion of the
various temperature computes and how they
subtract off a “bias” to leave a thermal velocity.

For rigid bodies, fix rigid subtracts off the rigid body constraint
contribution to the virial stress, so that the pressure should
be correct. Nothing special is done with velocities in that
case.

Compute pressure and compute stress/atom are different in this
respect. The former allows you to assign a temperature ID (a compute)
with a bias that subtracts a factor (like center of mass motion, see

Section 6.16). The latter (stress/atom) does not. If you include
the kinetic term in stress/atom it is always just vij for the individual
atom (see the formula on the doc page). However, you can exclude
the kinetic contribution all together if you like. And get the kinetic
contribution from compute temp/com or whatever temperature
compute you want.