8.6.1. Finite-size spherical and aspherical particles
Typical MD models treat atoms or particles as point masses. Sometimes it is desirable to have a model with finite-size particles such as spheroids or ellipsoids or generalized aspherical bodies. The difference is that such particles have a moment of inertia, rotational energy, and angular momentum. Rotation is induced by torque coming from interactions with other particles.
LAMMPS has several options for running simulations with these kinds of particles. The following aspects are discussed in turn:
computes, thermodynamics, and dump output
rigid bodies composed of finite-size particles
Example input scripts for these kinds of models are in the body, colloid, dipole, ellipse, line, peri, pour, and tri directories of the examples directory in the LAMMPS distribution.
There are several atom styles that allow for definition of finite-size particles: sphere, dipole, ellipsoid, line, tri, peri, and body.
The sphere style defines particles that are spheroids and each particle can have a unique diameter and mass (or density). These particles store an angular velocity (omega) and can be acted upon by torque. The “set” command can be used to modify the diameter and mass of individual particles, after then are created.
The dipole style does not actually define finite-size particles, but is often used in conjunction with spherical particles, via a command like
atom_style hybrid sphere dipole
This is because when dipoles interact with each other, they induce torques, and a particle must be finite-size (i.e. have a moment of inertia) in order to respond and rotate. See the atom_style dipole command for details. The “set” command can be used to modify the orientation and length of the dipole moment of individual particles, after then are created.
The ellipsoid style defines particles that are ellipsoids and thus can be aspherical. Each particle has a shape, specified by 3 diameters, and mass (or density). These particles store an angular momentum and their orientation (quaternion), and can be acted upon by torque. They do not store an angular velocity (omega), which can be in a different direction than angular momentum, rather they compute it as needed. The “set” command can be used to modify the diameter, orientation, and mass of individual particles, after then are created. It also has a brief explanation of what quaternions are.
The line style defines line segment particles with two end points and a mass (or density). They can be used in 2d simulations, and they can be joined together to form rigid bodies which represent arbitrary polygons.
The tri style defines triangular particles with three corner points and a mass (or density). They can be used in 3d simulations, and they can be joined together to form rigid bodies which represent arbitrary particles with a triangulated surface.
The body style allows for definition of particles which can represent complex entities, such as surface meshes of discrete points, collections of sub-particles, deformable objects, etc. The body style is discussed in more detail on the Howto body doc page.
Note that if one of these atom styles is used (or multiple styles via the atom_style hybrid command), not all particles in the system are required to be finite-size or aspherical.
For example, in the ellipsoid style, if the 3 shape parameters are set to the same value, the particle will be a sphere rather than an ellipsoid. If the 3 shape parameters are all set to 0.0 or if the diameter is set to 0.0, it will be a point particle. In the line or tri style, if the lineflag or triflag is specified as 0, then it will be a point particle.
Some of the pair styles used to compute pairwise interactions between finite-size particles also compute the correct interaction with point particles as well, e.g. the interaction between a point particle and a finite-size particle or between two point particles. If necessary, pair_style hybrid can be used to insure the correct interactions are computed for the appropriate style of interactions. Likewise, using groups to partition particles (ellipsoids versus spheres versus point particles) will allow you to use the appropriate time integrators and temperature computations for each class of particles. See the doc pages for various commands for details.
Also note that for 2d simulations, atom styles sphere and ellipsoid still use 3d particles, rather than as circular disks or ellipses. This means they have the same moment of inertia as the 3d object. When temperature is computed, the correct degrees of freedom are used for rotation in a 2d versus 3d system.
When a system with finite-size particles is defined, the particles will only rotate and experience torque if the force field computes such interactions. These are the various pair styles that generate torque:
The granular pair styles are used with spherical particles. The dipole pair style is used with the dipole atom style, which could be applied to spherical or ellipsoidal particles. The GayBerne and REsquared potentials require ellipsoidal particles, though they will also work if the 3 shape parameters are the same (a sphere). The Brownian and lubrication potentials are used with spherical particles. The line, tri, and body potentials are used with line segment, triangular, and body particles respectively.
There are several fixes that perform time integration on finite-size spherical particles, meaning the integrators update the rotational orientation and angular velocity or angular momentum of the particles:
Likewise, there are 3 fixes that perform time integration on ellipsoidal particles:
The advantage of these fixes is that those which thermostat the particles include the rotational degrees of freedom in the temperature calculation and thermostatting. The fix langevin command can also be used with its omgea or angmom options to thermostat the rotational degrees of freedom for spherical or ellipsoidal particles. Other thermostatting fixes only operate on the translational kinetic energy of finite-size particles.
These fixes perform constant NVE time integration on line segment, triangular, and body particles:
Note that for mixtures of point and finite-size particles, these integration fixes can only be used with groups which contain finite-size particles.
Computes, thermodynamics, and dump output
There are several computes that calculate the temperature or rotational energy of spherical or ellipsoidal particles:
These include rotational degrees of freedom in their computation. If you wish the thermodynamic output of temperature or pressure to use one of these computes (e.g. for a system entirely composed of finite-size particles), then the compute can be defined and the thermo_modify command used. Note that by default thermodynamic quantities will be calculated with a temperature that only includes translational degrees of freedom. See the thermo_style command for details.
These commands can be used to output various attributes of finite-size particles:
Attributes include the dipole moment, the angular velocity, the angular momentum, the quaternion, the torque, the end-point and corner-point coordinates (for line and tri particles), and sub-particle attributes of body particles.
Rigid bodies composed of finite-size particles
The fix rigid command treats a collection of particles as a rigid body, computes its inertia tensor, sums the total force and torque on the rigid body each timestep due to forces on its constituent particles, and integrates the motion of the rigid body.
If any of the constituent particles of a rigid body are finite-size particles (spheres or ellipsoids or line segments or triangles), then their contribution to the inertia tensor of the body is different than if they were point particles. This means the rotational dynamics of the rigid body will be different. Thus a model of a dimer is different if the dimer consists of two point masses versus two spheroids, even if the two particles have the same mass. Finite-size particles that experience torque due to their interaction with other particles will also impart that torque to a rigid body they are part of.
See the “fix rigid” command for example of complex rigid-body models it is possible to define in LAMMPS.
Note that the fix shake command can also be used to treat 2, 3, or 4 particles as a rigid body, but it always assumes the particles are point masses.
Also note that body particles cannot be modeled with the fix rigid command. Body particles are treated by LAMMPS as single particles, though they can store internal state, such as a list of sub-particles. Individual body particles are typically treated as rigid bodies, and their motion integrated with a command like fix nve/body. Interactions between pairs of body particles are computed via a command like pair_style body/nparticle.