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compute temp/region command

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Syntax

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compute ID group-ID temp/region region-ID
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  • ID, group-ID are documented in compute command
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  • temp/region = style name of this compute command
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  • region-ID = ID of region to use for choosing atoms
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Examples

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compute mine flow temp/region boundary
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Description

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Define a computation that calculates the temperature of a group of + + +

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compute temp/region command +

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Syntax: +

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compute ID group-ID temp/region region-ID 
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  • 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 +
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Examples: +

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compute mine flow temp/region boundary 
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Description: +

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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. E.g. 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, etc.

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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 T varies with time.

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The temperature is calculated by the formula KE = dim/2 N k T, where +e.g. thermo_modify, fix +temp/rescale, etc. +

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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 T varies with time. +

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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 = 2 or 3 = dimensionality of the simulation, N = number of atoms in both the group and region, k = Boltzmann constant, and T = -temperature.

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A kinetic energy tensor, stored as a 6-element vector, is also +temperature. +

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A kinetic energy tensor, stored as a 6-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 vx*vy for the xy component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz.

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The number of atoms contributing to the temperature is calculated each +zz, xy, xz, yz. +

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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.

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The removal of atoms outside the region by this fix is essentially -computing the temperature after a “bias” has been removed, which in +enter/leave the region. Thus there is no need to use the dynamic +option of the compute_modify command for this +compute style. +

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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 any of the thermostatting -fixes can operate on a geometric region of atoms, as defined by this -compute.

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Unlike other compute styles that calculate temperature, this compute +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. +

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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 +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.

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See this howto section of the manual for +explicitly using the extra option of the +compute_modify command. +

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See this howto section of the manual for a discussion of different ways to compute temperature and perform -thermostatting.

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Output info:

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This compute calculates a global scalar (the temperature) and a global +thermostatting. +

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Output info: +

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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 this section for an overview of LAMMPS output -options.

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The scalar value calculated by this compute is “intensive”. The -vector values are “extensive”.

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The scalar value will be in temperature units. The -vector values will be in energy units.

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Restrictions

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none
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