# compute viscosity/cos command¶

## Syntax¶

compute ID group-ID viscosity/cos

• ID, group-ID are documented in compute command

• viscosity/cos = style name of this compute command

## Examples¶

units    real
compute  cos all viscosity/cos
variable V equal c_cos
variable A equal 0.02E-5  # A/fs^2
variable density equal density
variable lz equal lz
variable reciprocalViscosity equal v_V/\${A}/v_density*39.4784/v_lz/v_lz*100  # 1/(Pa*s)


## Description¶

Define a computation that calculates the velocity amplitude of a group of atoms with an cosine-shaped velocity profile and the temperature of them after subtracting out the velocity profile before computing the kinetic energy. A compute of this style can be used by any command that computes a temperature, e.g. thermo_modify, fix npt, etc.

This command together with fix_accelerate/cos enables viscosity calculation with periodic perturbation method, as described by Hess. An acceleration along the x-direction is applied to the simulation system by using fix_accelerate/cos command. The acceleration is a periodic function along the z-direction:

$a_{x}(z) = A \cos \left(\frac{2 \pi z}{l_{z}}\right)$

where $$A$$ is the acceleration amplitude, $$l_z$$ is the z-length of the simulation box. At steady state, the acceleration generates a velocity profile:

$v_{x}(z) = V \cos \left(\frac{2 \pi z}{l_{z}}\right)$

The generated velocity amplitude $$V$$ is related to the shear viscosity $$\eta$$ by:

$V = \frac{A \rho}{\eta}\left(\frac{l_{z}}{2 \pi}\right)^{2}$

and it can be obtained from ensemble average of the velocity profile:

$V = \frac{\sum_i 2 m_{i} v_{i, x} \cos \left(\frac{2 \pi z_i}{l_{z}}\right)}{\sum_i m_{i}}$

where $$m_i$$, $$v_{i,x}$$ and $$z_i$$ are the mass, x-component velocity and z coordinate of a particle.

After the cosine-shaped collective velocity in $$x$$ direction has been subtracted for each atom, 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 the group, k = Boltzmann constant, and T = temperature.

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.

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. However, in order to get meaningful result, the group ID of this compute should be all.

The removal of the cosine-shaped velocity component by this command 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 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 7, which can be accessed by indices 1-7. The first 6 elements of the vector are the KE tensor, and the 7-th is the cosine-shaped velocity amplitude $$V$$, which can be used to calculate the reciprocal viscosity, as shown in the example. 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 first 6 elements of vector values are “extensive”, and the 7-th element of vector values is “intensive”.

The scalar value will be in temperature units. The first 6 elements of vector values will be in energy units. The 7-th element of vector value will be in velocity units.

## Restrictions¶

This command is only available when LAMMPS was built with the MISC package. Since this compute depends on fix accelerate/cos which can only work for 3d systems, it cannot be used for 2d systems.

## Default¶

none

(Hess) Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.