compute temp/asphere command — LAMMPS 15 May 2015 version documentation

# compute temp/asphere command

## Syntax

    compute ID group-ID temp/asphere keyword value ...

- ID, group-ID are documented in compute command
- temp/asphere = style name of this compute command
- zero or more keyword/value pairs may be appended
- keyword = bias or dof

    bias value = bias-ID
      bias-ID = ID of a temperature compute that removes a velocity bias
    dof value = all or rotate
      all = compute temperature of translational and rotational degrees of freedom
      rotate = compute temperature of just rotational degrees of freedom

## Examples

    compute 1 all temp/asphere
    compute myTemp mobile temp/asphere bias tempCOM
    compute myTemp mobile temp/asphere dof rotate

## Description

Define a computation that calculates the temperature of a group of aspherical particles, including a contribution from both their translational and rotational kinetic energy. This differs from the usual compute temp command, which assumes point particles with only translational kinetic energy.

Only finite-size particles (aspherical or spherical) can be included in the group. For 3d finite-size particles, each has 6 degrees of freedom (3 translational, 3 rotational). For 2d finite-size particles, each has 3 degrees of freedom (2 translational, 1 rotational).

Warning

This choice for degrees of freedom (dof) assumes that all finite-size aspherical or spherical particles in your model will freely rotate, sampling all their rotational dof. It is possible to use a combination of interaction potentials and fixes that induce no torque or otherwise constrain some of all of your particles so that this is not the case. Then there are less dof and you should use the compute_modify extra command to adjust the dof accordingly.

For example, an aspherical particle with all three of its shape parameters the same is a sphere. If it does not rotate, then it should have 3 dof instead of 6 in 3d (or 2 instead of 3 in 2d). A uniaxial aspherical particle has two of its three shape parameters the same. If it does not rotate around the axis perpendicular to its circular cross section, then it should have 5 dof instead of 6 in 3d. The latter is the case for uniaxial ellipsoids in a GayBerne model since there is no induced torque around the optical axis. It will also be the case for biaxial ellipsoids when exactly two of the semiaxes have the same length and the corresponding relative well depths are equal.

The translational kinetic energy is computed the same as is described by the compute temp command. The rotational kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor for the aspherical particle and w is its angular velocity, which is computed from its angular momentum.

Warning

For 2d models, particles are treated as ellipsoids, not ellipses, meaning their moments of inertia will be the same as in 3d.

A kinetic energy tensor, stored as a 6-element vector, is also calculated by this compute. The formula for the components of the tensor is the same as the above formula, except that v^2 and w^2 are replaced by vx*vy and wx*wy for the xy component, and the appropriate elements of the inertia tensor are used. The 6 components of the vector are ordered xx, yy, zz, xy, xz, yz.

The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the dynamic option of the compute_modify command if this is not the case.

This compute subtracts out translational degrees-of-freedom due to fixes that constrain molecular motion, such as fix shake and fix rigid. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the extra option of the compute_modify command.

See this howto section of the manual for a discussion of different ways to compute temperature and perform thermostatting.

The keyword/value option pairs are used in the following ways.

For the bias keyword, bias-ID refers to the ID of a temperature compute that removes a “bias” velocity from each atom. This allows compute temp/sphere to compute its thermal temperature after the translational kinetic energy components have been altered in a prescribed way, e.g. to remove a flow velocity profile. Thermostats that use this compute will work with this bias term. See the doc pages for individual computes that calculate a temperature and the doc pages for fixes that perform thermostatting for more details.

For the dof keyword, a setting of all calculates a temperature that includes both translational and rotational degrees of freedom. A setting of rotate calculates a temperature that includes only rotational degrees of freedom.

Output info:

This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or vector values from a compute as input. See this section for an overview of LAMMPS output options.

The scalar value calculated by this compute is “intensive”. The vector values are “extensive”.

The scalar value will be in temperature units. The vector values will be in energy units.

## Restrictions

This compute is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.

This compute requires that atoms store angular momementum and a quaternion as defined by the atom_style ellipsoid command.

All particles in the group must be finite-size. They cannot be point particles, but they can be aspherical or spherical as defined by their shape attribute.

## Related commands

compute temp

Default: none