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This is the first step for moving the documentation format from *.txt to the *.rst format. In the last years we've been automatically converting txt files from Steve's markup into RST to generate the documentation pages via Sphinx. The decision has now been made to fully migrate to RST and avoid the conversion in the future. This will enable us to fully use RST and Sphinx to improve the documentation. For the intermediate period, while there are still pending PRs with documentation changes, we will keep both source files and update the RST files accordingly.
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61 lines
2.6 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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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Commands_all.html
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