Merge pull request #1119 from lammps/doc-clarify (e2293cc7) · Commits · 郑智淋 / lammps

doc/src/Howto_nemd.txt

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		@@ -24,6 +24,11 @@ by subtracting out the streaming velocity of the shearing atoms. The
		velocity profile or other properties of the fluid can be monitored via
		the "fix ave/chunk"_fix_ave_chunk.html command.

		NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-nemd
		discusses use of the SLLOD method and non-equilibrium MD (NEMD)
		thermostatting generally, for both simple and complex fluids,
		e.g. molecular systems. The latter can be tricky to do correctly.

		As discussed in the previous section on non-orthogonal simulation
		boxes, the amount of tilt or skew that can be applied is limited by
		LAMMPS for computational efficiency to be 1/2 of the parallel box
		@@ -46,3 +51,9 @@ An alternative method for calculating viscosities is provided via the
		NEMD simulations can also be used to measure transport properties of a fluid
		through a pore or channel. Simulations of steady-state flow can be performed
		using the "fix flow/gauss"_fix_flow_gauss.html command.

		:line

		:link(Daivis-nemd)
		[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
		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
		velocities but also rotational velocities for spherical and aspherical
		particles.

		NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-thermostat
		discusses use of the SLLOD method and non-equilibrium MD (NEMD)
		thermostatting generally, for both simple and complex fluids,
		e.g. molecular systems. The latter can be tricky to do correctly.

		DPD thermostatting alters pairwise interactions in a manner analogous
		to the per-particle thermostatting of "fix
		langevin"_fix_langevin.html.
		@@ -87,3 +92,9 @@ specify them explicitly via the "thermo_style
		custom"_thermo_style.html command. Or you can use the
		"thermo_modify"_thermo_modify.html command to re-define what
		temperature compute is used for default thermodynamic output.

		:line

		:link(Daivis-thermostat)
		[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
		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
		thermostat that modifies only the thermal (non-shearing) components of
		velocity to prevent the fluid from heating up.

		NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-viscosity
		discusses use of the SLLOD method and non-equilibrium MD (NEMD)
		thermostatting generally, for both simple and complex fluids,
		e.g. molecular systems. The latter can be tricky to do correctly.

		In both cases, the velocity profile setup in the fluid by this
		procedure can be monitored by the "fix ave/chunk"_fix_ave_chunk.html
		command, which determines grad(Vstream) in the equation above.
		@@ -131,3 +136,9 @@ mean-square-displacement formulation for self-diffusivity. The
		time-integrated momentum fluxes play the role of Cartesian
		coordinates, whose mean-square displacement increases linearly
		with time at sufficiently long times.

		:line

		:link(Daivis-viscosity)
		[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
		Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

+2 −2

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		@@ -221,8 +221,8 @@ This equation only applies when the box dimensions are equal to those
		of the reference dimensions. If this is not the case, then the
		converged stress tensor will not equal that specified by the user. We
		can resolve this problem by periodically resetting the reference
		dimensions. The keyword {nreset_ref} controls how often this is done.
		If this keyword is not used, or is given a value of zero, then the
		dimensions. The keyword {nreset} controls how often this is done. If
		this keyword is not used, or is given a value of zero, then the
		reference dimensions are set to those of the initial simulation domain
		and are never changed. A value of {nstep} means that every {nstep}
		minimization steps, the reference dimensions are set to those of the

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		@@ -63,6 +63,11 @@ implemented in LAMMPS, they are coupled to a Nose/Hoover chain
		thermostat in a velocity Verlet formulation, closely following the
		implementation used for the "fix nvt"_fix_nh.html command.

		NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-sllod
		discusses use of the SLLOD method and non-equilibrium MD (NEMD)
		thermostatting generally, for both simple and complex fluids,
		e.g. molecular systems. The latter can be tricky to do correctly.

		Additional parameters affecting the thermostat are specified by
		keywords and values documented with the "fix nvt"_fix_nh.html
		command. See, for example, discussion of the {temp} and {drag}
		@@ -177,3 +182,7 @@ Same as "fix nvt"_fix_nh.html, except tchain = 1.

		:link(Daivis)
		[(Daivis and Todd)] Daivis and Todd, J Chem Phys, 124, 194103 (2006).

		:link(Daivis-sllod)
		[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
		Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).