Merge pull request #1119 from lammps/doc-clarify

doc page clarifications

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)"_#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).

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)"_#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).

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)"_#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).

doc/src/fix_box_relax.txt

@@ -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

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)"_#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).

doc/src/fix_shake.txt

@@ -214,8 +214,10 @@ which can lead to poor energy conservation.  You can test for this in
 your system by running a constant NVE simulation with a particular set
 of SHAKE parameters and monitoring the energy versus time.
 
-SHAKE or RATTLE should not be used to constrain an angle at 180 degrees
-(e.g. linear CO2 molecule).  This causes numeric difficulties.
+SHAKE or RATTLE should not be used to constrain an angle at 180
+degrees (e.g. linear CO2 molecule).  This causes numeric difficulties.
+You can use "fix rigid or fix rigid/small"_fix_rigid.html instead to
+make a linear molecule rigid.
 
 [Related commands:] none
 

doc/src/minimize.txt

@@ -216,10 +216,10 @@ The "fix box/relax"_fix_box_relax.html command can be used to apply an
 external pressure to the simulation box and allow it to shrink/expand
 during the minimization.
 
-Only a few other fixes (typically those that apply force constraints)
-are invoked during minimization.  See the doc pages for individual
-"fix"_fix.html commands to see which ones are relevant.  Current
-examples of fixes that can be used include:
+Only a few other fixes (typically those that add forces) are invoked
+during minimization.  See the doc pages for individual "fix"_fix.html
+commands to see which ones are relevant.  Current examples of fixes
+that can be used include:
 
 "fix addforce"_fix_addforce.html
 "fix addtorque"_fix_addtorque.html
@@ -242,6 +242,11 @@ you MUST enable the "fix_modify"_fix_modify.html {energy} option for
 that fix.  The doc pages for individual "fix"_fix.html commands
 specify if this should be done.
 
+NOTE: The minimizers in LAMMPS do not allow for bonds (or angles, etc)
+to be held fixed while atom coordinates are being relaxed, e.g. via
+"fix shake"_fix_shake.html or "fix rigid"_fix_rigid.html.  See more
+info in the Restrictions section below.
+
 :line
 
 [Restrictions:]