compute temp/com command
compute ID group-ID temp/com
ID, group-ID are documented in compute command
temp/com = style name of this compute command
compute 1 all temp/com compute myTemp mobile temp/com
Define a computation that calculates the temperature of a group of atoms, after subtracting out the center-of-mass velocity of the group. This is useful if the group is expected to have a non-zero net velocity for some reason. A compute of this style can be used by any command that computes a temperature, (e.g., thermo_modify, fix temp/rescale, fix npt).
After the center-of-mass velocity has been subtracted from each atom, the temperature is calculated by the formula
where KE is the total kinetic energy of the group of atoms (sum of \(\frac12 m v^2\)), dim = 2 or 3 is the dimensionality of the simulation, \(N\) is number of atoms in the group, \(k_B\) is the Boltzmann constant, and \(T\) is the absolute temperature.
A kinetic energy tensor, stored as a six-element vector, is also calculated by this compute for use in the computation of a pressure tensor. The formula for the components of the tensor is the same as the above formula, except that \(v^2\) is replaced by \(v_x v_y\) for the \(xy\) component, and so on. The six 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.
The removal of the center-of-mass velocity by this fix is essentially computing the temperature after a “bias” has been removed from the velocity of the atoms. If this compute is used with a fix command that performs thermostatting then this bias will be subtracted from each atom, thermostatting of the remaining thermal velocity will be performed, and the bias will be added back in. Thermostatting fixes that work in this way include fix nvt, fix temp/rescale, fix temp/berendsen, and fix langevin.
This compute subtracts out 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 page for a discussion of different ways to compute temperature and perform thermostatting.
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 page for an overview of LAMMPS output options.
The scalar value calculated by this compute is “intensive”. The vector values are “extensive”.