From 7f328d3f79bba1b3ce517084d556fccefc3e5bc4 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Tue, 11 Sep 2018 11:49:46 -0600
Subject: [PATCH] cite a good book on SLLOD thermostatting for molecular
systems
---
doc/src/Howto_nemd.txt | 11 +++++++++++
doc/src/Howto_thermostat.txt | 11 +++++++++++
doc/src/Howto_viscosity.txt | 11 +++++++++++
doc/src/fix_nvt_sllod.txt | 9 +++++++++
4 files changed, 42 insertions(+)
diff --git a/doc/src/Howto_nemd.txt b/doc/src/Howto_nemd.txt
index f787801c36..0a76859dcf 100644
--- a/doc/src/Howto_nemd.txt
+++ b/doc/src/Howto_nemd.txt
@@ -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)"_#Daivis2 discusses
+use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating
+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(Daivis2)
+[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
+Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
diff --git a/doc/src/Howto_thermostat.txt b/doc/src/Howto_thermostat.txt
index 0e2feb1869..6a0095e741 100644
--- a/doc/src/Howto_thermostat.txt
+++ b/doc/src/Howto_thermostat.txt
@@ -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)"_#Daivis2 discusses
+use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating
+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(Daivis2)
+[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
+Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
diff --git a/doc/src/Howto_viscosity.txt b/doc/src/Howto_viscosity.txt
index 8bcab6dd24..adfabf8279 100644
--- a/doc/src/Howto_viscosity.txt
+++ b/doc/src/Howto_viscosity.txt
@@ -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)"_#Daivis2 discusses
+use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating
+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(Daivis2)
+[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
+Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt
index 97a864a231..67c4d76417 100644
--- a/doc/src/fix_nvt_sllod.txt
+++ b/doc/src/fix_nvt_sllod.txt
@@ -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)"_#Daivis2 discusses
+use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating
+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(Daivis2)
+[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
+Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
--
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