Syntax:
compute ID group-ID temp/partial xflag yflag zflag
Examples:
compute newT flow temp/partial 1 1 0
Description:
Define a compute to calculate the temperature of a group of atoms, after excluding one or more velocity components. A compute of this style can be used by any command that computes a temperature, e.g. thermo_modify, fix temp/rescale, fix npt, etc.
The temperature is calculated by the formula KE = dim/2 N k T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature. The calculation of KE excludes the x, y, or z dimensions if xflag, yflag, or zflag = 0. The dim parameter is adjusted to give the correct number of degrees of freedom.
A 6-component kinetic energy tensor is also calculated by this compute for use in the calculation 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 vx * vy for the xy component, etc.
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 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.
Restrictions: none
Related commands:
compute temp, compute temp/region, compute pressure
Default: none