RNEMD¶

A nonequilibrium method for calculating the shear viscosity is presented. It reverses the cause-and-effect picture customarily used in nonequilibrium molecular dynamics: the effect, the momentum flux or stress, is imposed, whereas the cause, the velocity gradient or shear rate, is obtained from the simulation. Reference: F. Müller-Plathe, Phys. Rev. E 59, 4894, 1999.

Schematic view of the periodic simulation box

class RNEMD(all_info, np_per_swap, nslabs, filename)¶

The constructor of a RNEMD object to implement a shear field.

Parameters:

all_info (AllInfo) – The system information.
np_per_swap – The number of particles selected for velocity swap.
nslabs – The number of divided slabs of simulation box.

Filename:

The name of file for data output including velocity profile, momentum plus and viscosity.

setSwapPeriod(unsigned int swap_period)¶: specifies the period of particle velocity swap.

setProfVelPeriod(unsigned int profvel_period)¶: specifies the period of profiling velocity of slabs, the default value is 10.

setSwapGroup(ParticleSet group)¶: specifies the group of particles for velocity swap.

setVelProfile(bool vel_profile)¶: True or False for profiling velocity of slabs.

setPeriod(unsigned int period)¶: specifies the period of data output in which the velocity profile and momentum plus will be averaged.

Example:

rnemd = gala.RNEMD(all_info, 1, 30, 'velocity_profile.data')
rnemd.setSwapPeriod(50)
rnemd.setSwapGroup(group)
rnemd.setVelProfile(True)
rnemd.setPeriod(10000)
app.add(rnemd)