[lammps-users] The parameter setting for ellipse

Dear all,

There are several parameters need to be set for ellipse as follows:

GB(sigma_ee/sigma_ss,epsilon_ss/epsilon_ee,upsilon,mu) (3,5,3,1)1

shape 1 3 1 1
pair_style gayberne 1.0 3.0 1.0 4
pair_coeff 1 1 1 1 1 1 0.2 1 1 0.2 4

This time the parameter for GB(sigma_ee/sigma_ss,epsilon_ss/epsilon_ee,upsilon,mu) (3,5,3,1) will be needed. But I am totally confused with the introduction from Lammps manual. It is the relationship between “shape” and “pair_coeff”.

When a longest axis is set to x-axis as the “shape” command set, it means the original ellipse orients to x-axis. Then the “end to end “ parameter would be set in the x-axis. But whether “pair_coeff” know which direction is the orientation? Different potential curves were gotten with “shape 1 3 1 and “shape 1 even if the “pair_coeff 1 1 1 1 1 1 0.2 1 1 0.2 were same. So it looks like that “pair_coeff” does not know which direction is the orientation. The curve from“shape 1 would be more similar to article report however the value was just half to that in the article.

Then how should I set these parameters? Please help me out! Thanks a million.

The coefficients can be set as they are present in the equations in the references describing the potential. The shape gives the values for sigma along the x, y, and z axes in the body frame. The pair_coeff gives the epsilon ratios for the interactions for ellipsoids if they are alligned along the corresponding axes, two alignments in 2D for example:

1 2
1 2
1 2


1 1 1 2 2 2

The ordering for the pair_coeff does matter and should be consistent with the shape command. Setting shape to 1 1 3 and pair_coeff to 1 1 0.2 would make sense. 1 1 3 and 0.2 1 1 would set the energy higher when ellipsoids are aligned along one of the shorter axes (as defined by the shape command), which probably does not make sense for most cases. The reasons for the complication are that LAMMPS allows for biaxial ellipsoids where all 3 semiaxes have independent lengths and also allows the distance and energy parameters to be set independently. This is the same as in the Berardi reference which is cited in the documentation and can be used for details. Hope that helps.

  • Mike