compute temp/region command
compute ID group-ID temp/region region-ID
ID, group-ID are documented in compute command
temp/region = style name of this compute command
region-ID = ID of region to use for choosing atoms
compute mine flow temp/region boundary
Define a computation that calculates the temperature of a group of atoms in a geometric region. This can be useful for thermostatting one portion of the simulation box. For example, a McDLT simulation where one side is cooled, and the other side is heated. A compute of this style can be used by any command that computes a temperature (e.g., thermo_modify, fix temp/rescale).
Note that a region-style temperature can be used to thermostat with fix temp/rescale or fix langevin, but should probably not be used with Nose–Hoover style fixes (fix nvt, fix npt, or fix nph) if the degrees of freedom included in the computed temperature vary with time.
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 the number of atoms in both the group and region, \(k_B\) is the Boltzmann constant, and \(T\) 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 calculated each time the temperature is evaluated since it is assumed atoms can enter/leave the region. Thus there is no need to use the dynamic option of the compute_modify command for this compute style.
The removal of atoms outside the region by this fix is essentially computing the temperature after a “bias” has been removed, which in this case is the velocity of any atoms outside the region. 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 means that when this compute is used to calculate the temperature for any of the thermostatting fixes via the fix modify temp command, the thermostat will operate only on atoms that are currently in the geometric region.
Unlike other compute styles that calculate temperature, this compute does not subtract out degrees-of-freedom due to fixes that constrain motion, such as fix shake and fix rigid. This is because those degrees of freedom (e.g., a constrained bond) could apply to sets of atoms that straddle the region boundary, and hence the concept is somewhat ill-defined. If needed the number of subtracted degrees of freedom can be set explicitly 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”.