compute temp/body command
compute ID group-ID temp/body keyword value ...
ID, group-ID are documented in compute command
temp/body = 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
compute 1 all temp/body compute myTemp mobile temp/body bias tempCOM compute myTemp mobile temp/body dof rotate
Define a computation that calculates the temperature of a group of body 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 body particles can be included in the group. For 3d particles, each has 6 degrees of freedom (3 translational, 3 rotational). For 2d body particles, each has 3 degrees of freedom (2 translational, 1 rotational).
This choice for degrees of freedom (dof) assumes that all body 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.
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.
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 the Howto thermostat doc page 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.
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 the Howto output doc page for an overview of LAMMPS output options.
The scalar value calculated by this compute is “intensive”. The vector values are “extensive”.