# compute temp/deform command

Accelerator Variants: *temp/deform/kk*

## Syntax

``` LAMMPS
compute ID group-ID temp/deform
```

-   ID, group-ID are documented in [compute](compute) command
-   temp/deform = style name of this compute command

## Examples

``` LAMMPS
compute myTemp all temp/deform
```

## Description

Define a computation that calculates the temperature of a group of
atoms, after subtracting out a streaming velocity induced by the
simulation box changing size and/or shape, for example in a
non-equilibrium MD (NEMD) simulation. The size/shape change is induced
by use of the [fix deform](fix_deform) command. A compute of this style
is created by the [fix nvt/sllod](fix_nvt_sllod) command to compute the
thermal temperature of atoms for thermostatting purposes. A compute of
this style can also be used by any command that computes a temperature
(e.g., [thermo_modify](thermo_modify), [fix
temp/rescale](fix_temp_rescale), [fix npt](fix_nh)).

The deformation fix changes the box size and/or shape over time, so each
atom in the simulation box can be thought of as having a \"streaming\"
velocity. For example, if the box is being sheared in *x*, relative to
*y*, then atoms at the bottom of the box (low *y*) have a small *x*
velocity, while atoms at the top of the box (high *y*) have a large *x*
velocity. This position-dependent streaming velocity is subtracted from
each atom\'s actual velocity to yield a thermal velocity, which is then
used to compute the temperature.

:::: note
::: title
Note
:::

[Fix deform](fix_deform) has an option for remapping either atom
coordinates or velocities to the changing simulation box. When using
this compute in conjunction with a deforming box, fix deform should NOT
remap atom positions, but rather should let atoms respond to the
changing box by adjusting their own velocities (or let [fix
deform](fix_deform) remap the atom velocities; see its remap option). If
fix deform does remap atom positions, then they appear to move with the
box but their velocity is not changed, and thus they do NOT have the
streaming velocity assumed by this compute. LAMMPS will warn you if fix
deform is defined and its remap setting is not consistent with this
compute.
::::

After the streaming velocity has been subtracted from each atom, the
temperature is calculated by the formula

$$\text{KE} = \frac{\text{dim}}{2} N k_B T,$$

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 the group, $k_B$ is the Boltzmann
constant, and $T$ is the temperature. Note that $v$ in the kinetic
energy formula is the atom\'s velocity.

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](compute_modify) command if this is not the case.

The removal of the box deformation velocity component 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_nh), [fix
temp/rescale](fix_temp_rescale), [fix
temp/berendsen](fix_temp_berendsen), and [fix langevin](fix_langevin).

:::: note
::: title
Note
:::

The temperature calculated by this compute is only accurate if the atoms
are indeed moving with a stream velocity profile that matches the box
deformation. If not, then the compute will subtract off an incorrect
stream velocity, yielding a bogus thermal temperature. You should
**not** assume that your atoms are streaming at the same rate the box is
deforming. Rather, you should monitor their velocity profiles (e.g., via
the [fix ave/chunk](fix_ave_chunk) command). You can also compare the
results of this compute to [compute temp/profile](compute_temp_profile),
which actually calculates the stream profile before subtracting it. If
the two computes do not give roughly the same temperature, then your
atoms are not streaming consistent with the box deformation. See the
[fix deform](fix_deform) command for more details on ways to get atoms
to stream consistently with the box deformation.
::::

This compute subtracts out degrees-of-freedom due to fixes that
constrain molecular motion, such as [fix shake](fix_shake) and [fix
rigid](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](compute_modify) command.

See the [Howto thermostat](Howto_thermostat) page for a discussion of
different ways to compute temperature and perform thermostatting.

## Output info

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](Howto_output) page for an overview of LAMMPS output options.

The scalar value calculated by this compute is \"intensive\". The vector
values are \"extensive\".

The scalar value will be in temperature [units](units). The vector
values will be in energy [units](units).

## Restrictions

> none

## Related commands

[compute temp/ramp](compute_temp_ramp), [compute
temp/profile](compute_temp_profile), [fix deform](fix_deform), [fix
nvt/sllod](fix_nvt_sllod)

## Default

none