forked from lijiext/lammps
cite a good book on SLLOD thermostatting for molecular systems
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@ -24,6 +24,11 @@ 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 "fix ave/chunk"_fix_ave_chunk.html command.
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NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses
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use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating
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generally, for both simple and complex fluids, e.g. molecular systems.
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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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@ -46,3 +51,9 @@ An alternative method for calculating viscosities is provided via the
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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 "fix flow/gauss"_fix_flow_gauss.html command.
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:line
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:link(Daivis2)
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[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
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Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
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@ -43,6 +43,11 @@ nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
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velocities but also rotational velocities for spherical and aspherical
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particles.
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NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses
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use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating
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generally, for both simple and complex fluids, e.g. molecular systems.
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The latter can be tricky to do correctly.
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DPD thermostatting alters pairwise interactions in a manner analogous
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to the per-particle thermostatting of "fix
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langevin"_fix_langevin.html.
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@ -87,3 +92,9 @@ specify them explicitly via the "thermo_style
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custom"_thermo_style.html command. Or you can use the
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"thermo_modify"_thermo_modify.html command to re-define what
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temperature compute is used for default thermodynamic output.
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:line
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:link(Daivis2)
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[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
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Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
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@ -37,6 +37,11 @@ used to shear the fluid in between them, again with some kind of
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thermostat that modifies only the thermal (non-shearing) components of
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velocity to prevent the fluid from heating up.
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NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses
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use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating
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generally, for both simple and complex fluids, e.g. molecular systems.
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The latter can be tricky to do correctly.
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In both cases, the velocity profile setup in the fluid by this
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procedure can be monitored by the "fix ave/chunk"_fix_ave_chunk.html
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command, which determines grad(Vstream) in the equation above.
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@ -131,3 +136,9 @@ mean-square-displacement formulation for self-diffusivity. The
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time-integrated momentum fluxes play the role of Cartesian
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coordinates, whose mean-square displacement increases linearly
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with time at sufficiently long times.
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:line
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:link(Daivis2)
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[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
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Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
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@ -63,6 +63,11 @@ implemented in LAMMPS, they are coupled to a Nose/Hoover chain
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thermostat in a velocity Verlet formulation, closely following the
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implementation used for the "fix nvt"_fix_nh.html command.
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NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses
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use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating
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generally, for both simple and complex fluids, e.g. molecular systems.
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The latter can be tricky to do correctly.
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Additional parameters affecting the thermostat are specified by
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keywords and values documented with the "fix nvt"_fix_nh.html
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command. See, for example, discussion of the {temp} and {drag}
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@ -177,3 +182,7 @@ Same as "fix nvt"_fix_nh.html, except tchain = 1.
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:link(Daivis)
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[(Daivis and Todd)] Daivis and Todd, J Chem Phys, 124, 194103 (2006).
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:link(Daivis2)
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[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
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Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
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