52 lines
2.5 KiB
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52 lines
2.5 KiB
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NEMD simulations
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================
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Non-equilibrium molecular dynamics or NEMD simulations are typically
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used to measure a fluid's rheological properties such as viscosity.
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In LAMMPS, such simulations can be performed by first setting up a
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non-orthogonal simulation box (see the preceding Howto section).
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A shear strain can be applied to the simulation box at a desired
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strain rate by using the :doc:`fix deform <fix_deform>` command. The
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:doc:`fix nvt/sllod <fix_nvt_sllod>` command can be used to thermostat
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the sheared fluid and integrate the SLLOD equations of motion for the
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system. Fix nvt/sllod uses :doc:`compute temp/deform <compute_temp_deform>` to compute a thermal temperature
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by subtracting out the streaming velocity of the shearing atoms. The
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velocity profile or other properties of the fluid can be monitored via
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the :doc:`fix ave/chunk <fix_ave_chunk>` command.
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.. note::
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A recent (2017) book by :ref:`(Daivis and Todd) <Daivis-nemd>`
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discusses use of the SLLOD method and non-equilibrium MD (NEMD)
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thermostatting generally, for both simple and complex fluids,
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e.g. molecular systems. The latter can be tricky to do correctly.
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As discussed in the previous section on non-orthogonal simulation
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boxes, the amount of tilt or skew that can be applied is limited by
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LAMMPS for computational efficiency to be 1/2 of the parallel box
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length. However, :doc:`fix deform <fix_deform>` can continuously strain
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a box by an arbitrary amount. As discussed in the :doc:`fix deform <fix_deform>` command, when the tilt value reaches a limit,
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the box is flipped to the opposite limit which is an equivalent tiling
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of periodic space. The strain rate can then continue to change as
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before. In a long NEMD simulation these box re-shaping events may
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occur many times.
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In a NEMD simulation, the "remap" option of :doc:`fix deform <fix_deform>` should be set to "remap v", since that is what
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:doc:`fix nvt/sllod <fix_nvt_sllod>` assumes to generate a velocity
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profile consistent with the applied shear strain rate.
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An alternative method for calculating viscosities is provided via the
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:doc:`fix viscosity <fix_viscosity>` command.
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NEMD simulations can also be used to measure transport properties of a fluid
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through a pore or channel. Simulations of steady-state flow can be performed
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using the :doc:`fix flow/gauss <fix_flow_gauss>` command.
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----------
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.. _Daivis-nemd:
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**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
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Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
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