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compute temp/deform command
Accelerator Variants: temp/deform/kk
Syntax
compute ID group-ID temp/deform
ID, group-ID are documented in compute command
temp/deform = style name of this compute command
Examples
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 command. A compute of this style is created by the 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, fix temp/rescale, fix npt).
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
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 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
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 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 temp/rescale, fix temp/berendsen, and fix langevin.
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 command). You can also compare the results of this compute to 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 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 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 the 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 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. The vector values will be in energy units.
Restrictions
none
Default
none