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### compute temp/partial command

Syntax:

    compute ID group-ID temp/partial xflag yflag zflag

- ID, group-ID are documented in compute command
- temp/partial = style name of this compute command
- xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension

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.

The removal of velocity components 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 this howto section of the manual for a discussion of different ways to compute temperature and perform thermostatting.

Output info:

The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in the simulation.

Restrictions: none

Related commands:

compute temp, compute temp/region, compute pressure

Default: none