diff --git a/doc/Manual.txt b/doc/Manual.txt
index 63b08660d4b17bf76422908d64265ed3fd02ced1..ff8bbab6b980e118ef319cb011a8dba13abced62 100644
--- a/doc/Manual.txt
+++ b/doc/Manual.txt
@@ -35,6 +35,10 @@ you find errors or omissions in this manual or have suggestions for
 useful information to add, please send an email to the developers so
 we can improve the LAMMPS documentation.
 
+Once you are familiar with LAMMPS, you may want to bookmark "this
+page"_Section_commands.html#comm at Section_commands.html#comm since
+it gives quick access to documentation for all LAMMPS commands.
+
 "PDF file"_Manual.pdf of the entire manual, generated by
 "htmldoc"_http://www.easysw.com/htmldoc
 
@@ -70,7 +74,10 @@ we can improve the LAMMPS documentation.
   4.8 "TIP4P water model"_4_8 :b
   4.9 "SPC water model"_4_9 :b
   4.10 "Coupling LAMMPS to other codes"_4_10 :b
-  4.11 "Visualizing LAMMPS snapshots"_4_11 :ule,b
+  4.11 "Visualizing LAMMPS snapshots"_4_11 :b
+  4.12 "Non-orthogonal simulation boxes"_4_12 :b
+  4.13 "NEMD simulations"_4_13 :b
+  4.14 "Aspherical particles"_4_14 :ule,b
 "Example problems"_Section_example.html :l
 "Performance & scalability"_Section_perf.html :l
 "Additional tools"_Section_tools.html :l
@@ -116,6 +123,9 @@ we can improve the LAMMPS documentation.
 :link(4_9,Section_howto.html#4_9)
 :link(4_10,Section_howto.html#4_10)
 :link(4_11,Section_howto.html#4_11)
+:link(4_12,Section_howto.html#4_12)
+:link(4_13,Section_howto.html#4_13)
+:link(4_14,Section_howto.html#4_14)
 
 :link(9_1,Section_errors.html#9_1)
 :link(9_2,Section_errors.html#9_2)
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index 4fe7875174bc8a8aca1d63484cb893e1b03306d6..5efd8e093ec1471320729fd3b57a479b323442a8 100644
--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -459,6 +459,7 @@ full description:
 
 "none"_pair_none.html,
 "hybrid"_pair_hybrid.html,
+"airebo"_pair_airebo.html,
 "buck"_pair_buck.html,
 "buck/coul/cut"_pair_buck.html,
 "buck/coul/long"_pair_buck.html,
diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt
index dd2d99d70695362fec154ef5765367696fa25062..5dd14d746cbddbdac9f21c9de61e2f691686ceee 100644
--- a/doc/Section_howto.txt
+++ b/doc/Section_howto.txt
@@ -21,7 +21,10 @@ certain kinds of LAMMPS simulations.
 4.8 "TIP4P water model"_#4_8
 4.9 "SPC water model"_#4_9
 4.10 "Coupling LAMMPS to other codes"_#4_10
-4.11 "Visualizing LAMMPS snapshots"_#4_11 :all(b)
+4.11 "Visualizing LAMMPS snapshots"_#4_11
+4.12 "Non-orthogonal simulation boxes"_#4_12
+4.13 "NEMD simulations"_#4_13
+4.14 "Aspherical particles"_#4_14 :all(b)
 
 The example input scripts included in the LAMMPS distribution and
 highlighted in "this section"_Section_example.html also show how to
@@ -642,6 +645,145 @@ See the "dump"_dump.html command for more information on XTC files.
 
 :line
 
+4.12 Non-orthogonal simulation boxes :link(4_12),h4
+
+By default, LAMMPS uses an orthogonal simulation box to encompass the
+particles.  The "boundary"_boundary.html command sets the boundary
+conditions of the box (periodic, non-periodic, etc).  If the box size
+is xprd by yprd by zprd then the 3 mutually orthogonal edge vectors of
+an orthogonal simulation box are a = (xprd,0,0), b = (0,yprd,0), and c
+= (0,0,zprd).
+
+LAMMPS also allows non-orthogonal simulation boxes (triclinic
+symmetry) to be defined with 3 additional "tilt" parameters which
+change the edge vectors of the simulation box to be a = (xprd,0,0), b
+= (xy,yprd,0), and c = (xz,yz,zprd).  The xy, xz, and yz parameters
+can be positive or negative.  The simulation box must be periodic in
+both dimensions associated with a tilt factor.  For example, if xz !=
+0.0, then the x and z dimensions must be periodic.
+
+To avoid extremely tilted boxes (which would be computationally
+inefficient), no tilt factor can skew the box more than half the
+distance of the parallel box length, which is the 1st dimension in the
+tilt factor (x for xz).  For example, if xlo = 2 and xhi = 12, then
+the x box length is 10 and the xy tilt factor must be between -5 and
+5.  Similarly, both xz and yz must be between -(xhi-xlo)/2 and
++(yhi-ylo)/2.  Note that this is not a limitation, since if the
+maximum tilt factor is 5 (as in this example), then configurations
+with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent.
+
+You tell LAMMPS to use a non-orthogonal box when the simulation box is
+defined.  This happens in one of 3 ways.  If the
+"create_box"_create_box.html command is used with a region of style
+{prism}, then a non-orthogonal domain is setup.  See the
+"region"_region.html command for details.  If the
+"read_data"_read_data.html command is used to define the simulation
+box, and the header of the data file contains a line with the "xy xz
+yz" keyword, then a non-orthogonal domain is setup.  See the
+"read_data"_read_data.html command for details.  Finally, if the
+"read_restart"_read_restart.html command reads a restart file which
+was written from a simulation using a triclinic box, then a
+non-orthogonal box will be enabled for the restarted simulation.
+
+Note that you can define a non-orthogonal box with all 3 tilt factors
+= 0.0, so that it is initially orthogonal.  This is necessary if the
+box will ever become non-orthogonal.
+
+One use of non-orthogonal boxes is to model solid-state crystals with
+triclinic symmetry.  The "lattice"_lattice.html command can be used
+with non-orthogonal basis vectors to define a lattice that will tile a
+non-orthogonal simulation box via the "create_atoms"_create_atoms.html
+command.  Note that while the box edge vectors a,b,c cannot be
+arbitrary vectors (e.g. a must be aligned with the x axis), it is
+possible to rotate any crystal's basis vectors so that they meet these
+restrictions.
+
+A second use of non-orthogonal boxes is to shear a bulk solid to study
+the response of the material.  The "fix deform"_fix_deform.html
+command can be used for this purpose.  It allows dynamic control of
+the xy, xz, and yz tilt factors as a simulation runs.
+
+Another use of non-orthogonal boxes is to perform non-equilibrium MD
+(NEMD) simulations, as discussed in the next section.
+
+:line
+
+4.13 NEMD simulations :link(4_13),h4
+
+Non-equilibrium molecular dynamics or NEMD simulations are typically
+used to measure a fluid's rheological properties such as viscosity.
+In LAMMPS, such simulations can be performed by first setting up a
+non-orthogonal simulation box (see the preceeding Howto section).
+
+A shear strain can be applied to the simualation box at a desired
+strain rate by using the "fix deform"_fix_deform.html command.  The
+"fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat
+the sheared fluid and integrate the SLLOD equations of motion for the
+system.  Fix nvt/sllod uses "compute
+temp/deform"_compute_temp_deform.html to compute a thermal temperature
+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/spatial"_fix_ave_spatial.html command.
+
+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 computation efficiency to be 1/2 of the paralell box
+length.  However, "fix deform"_fix_deform.html can be used to
+continuously strain a box by an arbitrary amount.  As discussed in the
+"fix deform"_fix_deform.html command, when the tilt reaches a limit,
+the box is re-shaped to the opposite limit which is an equivalent
+tiling of the periodic plane.  The strain rate can then continue to
+change as before.  In a long NEMD simulation these box re-shaping may
+occur any number of times.
+
+In a NEMD simulation, the "remap" option of "fix
+deform"_fix_deform.html should be set to "remap v", since that is what
+"fix nvt/sllod"_fix_nvt_sllod.html assumes to generate a velocity
+profile consistent with the applied shear strain rate.
+
+:line
+
+4.14 Aspherical particles :link(4_14),h4
+
+LAMMPS supports ellipsoidal particles via the "atom_style
+ellipsoid"_atom_style.html and "shape"_shape.html commands.  The
+latter defines the 3 axes (diamaters) of a general ellipsoid.  The
+"pair_style gayberne"_pair_gayberne.html command can be used to define
+a Gay-Berne (GB) potential for how such particles interact with each
+other and with spherical particles.  The GB potential is like a
+Lennard-Jones (LJ) potential generalized for ellipsoids interacting in
+an orientiation-dependent manner.
+
+The orientation of ellipsoidal particles is stored as a quaternion.
+See the "set"_set.html command for a brief explanation of quaternions
+and how the orientation of such particles can be initialized.  The
+data file read by the "read_data"_read_data.html command also contains
+quaternions for each atom in the Atoms section if "atom_style
+ellipsoid"_atom_style.html is being used.  The "compute
+temp/asphere"_compute_temp_asphere.html command can be used to
+calculate the temperature of a group of ellipsoidal particles, taking
+account of rotational degrees of freedom.  The motion of the particles
+can be integrated via the "fix nve/asphere"_fix_nve_asphere.html, "fix
+nvt/asphere"_fix_nvt_asphere.html, or "fix
+npt/asphere"_fix_npt_asphere.html commands.  All of these commands are
+part of the ASPHERE package in LAMMPS.
+
+Computationally, the cost for two ellipsoidal particles to interact is
+30x or more expensive than for 2 LJ particles.  Thus if you are
+modeling a system with many spherical particles (e.g. as the solvent),
+then you should insure sphere-sphere interactions are computed with
+the a cheaper potential than GB.  This can be done by setting the
+particle's 3 shape parameters to all be equal (a sphere).
+Additionally, the corresponding GB potential coefficients can be set
+so the GB potential will treat the pair of particles as LJ spheres.
+Details are given in the doc page for the "pair_style
+gayberne"_pair_gayberne.html.  Alternatively, the "pair_style
+hybrid"_pair_hybrid.html potential can be used, with the sphere-sphere
+interactions computed by another pair potential, such as "pair_style
+lj/cut"_pair_lj.html.
+
+:line
+
 :link(Cornell)
 [(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
 Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt
index ab35337250dafe071e6b55f440b306265e4fb79b..c9593a1b2d86218bead9014adc33b57be8aa3b96 100644
--- a/doc/Section_intro.txt
+++ b/doc/Section_intro.txt
@@ -129,7 +129,7 @@ commands)
     class 2 (COMPASS), OPLS
   improper potentials: harmonic, cvff, class 2 (COMPASS)
   hybrid potentials: multiple pair, bond, angle, dihedral, improper \
-    potentials can be used
+    potentials can be used in one simlulation
   polymer potentials: all-atom, united-atom, bead-spring, breakable
   water potentials: TIP3P, TIP4P, SPC
   long-range Coulombics: Ewald, PPPM (similar to particle-mesh Ewald)
diff --git a/doc/angle_charmm.txt b/doc/angle_charmm.txt
index 5e6dffb7935cfb22441e82fd54b3615301ed75d6..e1356cb061dc1fb01055dae52bdeb19e1beee582 100644
--- a/doc/angle_charmm.txt
+++ b/doc/angle_charmm.txt
@@ -43,7 +43,11 @@ r_ub (distance) :ul
 Theta0 is specified in degrees, but LAMMPS converts it to radians
 internally; hence the units of K are in energy/radian^2.
 
-[Restrictions:] none
+[Restrictions:]
+
+This angle style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/angle_class2.txt b/doc/angle_class2.txt
index b49abf0a2591bd30af709b5acafe74d7497b6510..6d343f324cc4786dc381cd7924e883638925f05e 100644
--- a/doc/angle_class2.txt
+++ b/doc/angle_class2.txt
@@ -29,8 +29,8 @@ the equilibrium bond lengths.
 
 See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
 
-For this style, only coefficients for the Ea formula can be specified
-in the input script.  These are the 4 coefficients:
+For this style, coefficients for the Ea formula can be specified in
+the input script or data file.  These are the 4 coefficients:
 
 theta0 (degrees)
 K2 (energy/radian^2)
@@ -40,7 +40,7 @@ K4 (energy/radian^2) :ul
 Theta0 is specified in degrees, but LAMMPS converts it to radians
 internally; hence the units of K are in energy/radian^2.
 
-Coefficients for the Ebb and Eba formulas must be specified in the
+Coefficients for the Ebb and Eba formulas can only be specified in the
 data file.
 
 For the Ebb formula, the coefficients are listed under a "BondBond
@@ -63,9 +63,9 @@ same value from the Ea formula.
 
 [Restrictions:]
 
-This angle style is part of the "class2" package.  It is only enabled
-if LAMMPS was built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
+This angle style can only be used if LAMMPS was built with the
+"class2" package.  See the "Making LAMMPS"_Section_start.html#2_3
+section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/angle_cosine.txt b/doc/angle_cosine.txt
index ba161cd9ffe2fc6321fb82ab1ba94f23d12b802b..4c6cef912f419df24ad47eb273069518c8a36871 100644
--- a/doc/angle_cosine.txt
+++ b/doc/angle_cosine.txt
@@ -32,7 +32,11 @@ or "read_restart"_read_restart.html commands:
 
 K (energy) :ul
 
-[Restrictions:] none
+[Restrictions:]
+
+This angle style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/angle_cosine_squared.txt b/doc/angle_cosine_squared.txt
index 79e7d946bda9f766758318745c789bb43f246dcd..d39623ed31ea8e21f2b4cc30a6857e5ea6e52b54 100644
--- a/doc/angle_cosine_squared.txt
+++ b/doc/angle_cosine_squared.txt
@@ -37,7 +37,11 @@ theta0 (degrees) :ul
 Theta0 is specified in degrees, but LAMMPS converts it to radians
 internally.
 
-[Restrictions:] none
+[Restrictions:]
+
+This angle style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/angle_harmonic.txt b/doc/angle_harmonic.txt
index 6ab256c57a3a510c55b0a3eee570dadda4aba8b7..dc98882ee9e776cfc87efc3de2611578bc9c1cb7 100644
--- a/doc/angle_harmonic.txt
+++ b/doc/angle_harmonic.txt
@@ -39,6 +39,10 @@ internally; hence the units of K are in energy/radian^2.
 
 [Restrictions:] none
 
+This angle style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
+
 [Related commands:]
 
 "angle_coeff"_angle_coeff.html
diff --git a/doc/angle_hybrid.txt b/doc/angle_hybrid.txt
index 33df13030be24680c6fa198bafaa42c1a5954cac..554fcf261bd3749d5ecf79792707539c3c90cb7a 100644
--- a/doc/angle_hybrid.txt
+++ b/doc/angle_hybrid.txt
@@ -49,7 +49,11 @@ An angle style of {none} can be specified as an argument to
 angle_style hybrid and the corresponding angle_coeff commands, if you
 desire to turn off certain angle types.
 
-[Restrictions:] none
+[Restrictions:]
+
+This angle style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/angle_style.txt b/doc/angle_style.txt
index 2d7ee8238b6d5181f3c0a51f9565d7dffb2c2a48..897ba5ccabf95130b2b43b634eece666eb0e54d4 100644
--- a/doc/angle_style.txt
+++ b/doc/angle_style.txt
@@ -35,14 +35,22 @@ potentials can be setup using the {hybrid} angle style.
 The coefficients associated with a angle style can be specified in a
 data or restart file or via the "angle_coeff"_angle_coeff.html command.
 
+All angle potentials store their coefficient data in binary restart
+files which means angle_style and "angle_coeff"_angle_coeff.html
+commands do not need to be re-specified in an input script that
+restarts a simulation.  See the "read_restart"_read_restart.html
+command for details on how to do this.  The one exception is that
+angle_style {hybrid} only stores the list of sub-styles in the restart
+file; angle coefficients need to be re-specified.
+
+IMPORTANT NOTE: When both an angle and pair style is defined, the
+"special_bonds"_special_bonds.html command often needs to be used to
+turn off (or weight) the pairwise interaction that would otherwise
+exist between 3 bonded atoms.
+
 In the formulas listed for each angle style, {theta} is the angle
 between the 3 atoms in the angle.
 
-Note that when both an angle and pair style is defined, the
-"special_bond"_special_bond.html command often needs to be used to
-turn off (or weight) the pairwise interactions that would otherwise
-exist between the 3 bonded atoms.
-
 :line
 
 Here is an alphabetic list of angle styles defined in LAMMPS.  Click on
@@ -65,10 +73,11 @@ specified by the associated "angle_coeff"_angle_coeff.html command:
 Angle styles can only be set for atom_styles that allow angles to be
 defined.
 
-Angle styles are part of the "molecular" package or other packages as
-noted in their documentation.  They are only enabled if LAMMPS was
-built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
+Most angle styles are part of the "molecular" package.  They are only
+enabled if LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.  The
+doc pages for individual bond potentials tell if it is part of a
+package.
 
 [Related commands:]
 
diff --git a/doc/bond_class2.txt b/doc/bond_class2.txt
index 9f1befe12db94307cbb51ab266a7d7efa4f5adc2..7fb7b83af9daabdaf4de313a078c5b7dd1b28b60 100644
--- a/doc/bond_class2.txt
+++ b/doc/bond_class2.txt
@@ -39,9 +39,9 @@ K4 (energy/distance^2) :ul
 
 [Restrictions:]
 
-This bond style is part of the "class2" package.  It is only enabled
-if LAMMPS was built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
+This bond style can only be used if LAMMPS was built with the "class2"
+package.  See the "Making LAMMPS"_Section_start.html#2_3 section for
+more info on packages.
 
 [Related commands:]
 
diff --git a/doc/bond_fene.txt b/doc/bond_fene.txt
index 0e938d3ff36b521d2a2ef87902faba9fedbfda10..6b2b2d2a4a89f68c7d75d918e10d95387dd2c16b 100644
--- a/doc/bond_fene.txt
+++ b/doc/bond_fene.txt
@@ -39,7 +39,11 @@ R0 (distance)
 epsilon (energy)
 sigma (distance) :ul
 
-[Restrictions:] none
+[Restrictions:]
+
+This bond style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/bond_fene_expand.txt b/doc/bond_fene_expand.txt
index aa165a02719f21b63b58162ee1eafbfb4b6aed9c..e84623fba4e9d2fe6ee75be73b978b1d6f7ca197 100644
--- a/doc/bond_fene_expand.txt
+++ b/doc/bond_fene_expand.txt
@@ -44,7 +44,11 @@ epsilon (energy)
 sigma (distance)
 delta (distance) :ul
 
-[Restrictions:] none
+[Restrictions:]
+
+This bond style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/bond_harmonic.txt b/doc/bond_harmonic.txt
index 3fea41d64159104db3a131be58d5037b11e8929b..1ccbbd4f45f859cf4e777c46a2e4d7e4f45c946e 100644
--- a/doc/bond_harmonic.txt
+++ b/doc/bond_harmonic.txt
@@ -34,7 +34,11 @@ or "read_restart"_read_restart.html commands:
 K (energy/distance^2)
 r0 (distance) :ul
 
-[Restrictions:] none
+[Restrictions:]
+
+This bond style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/bond_hybrid.txt b/doc/bond_hybrid.txt
index 37cd829ddc08ebb50241ae7ee14b926be4da83da..bf21d39bad97d33ece1a0f6a955d157c1ff0da0c 100644
--- a/doc/bond_hybrid.txt
+++ b/doc/bond_hybrid.txt
@@ -42,7 +42,11 @@ A bond style of {none} can be specified as an argument to bond_style
 hybrid and the corresponding bond_coeff commands, if you desire to
 turn off certain bond types.
 
-[Restrictions:] none
+[Restrictions:]
+
+This bond style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/bond_morse.txt b/doc/bond_morse.txt
index 17ac84155457c40fd9b5b01578773ed5010fd781..fd67478ef473064e68b12a61b1c6b6c20ec518d3 100644
--- a/doc/bond_morse.txt
+++ b/doc/bond_morse.txt
@@ -35,7 +35,11 @@ D (energy)
 alpha (inverse distance)
 r0 (distance) :ul
 
-[Restrictions:] none
+[Restrictions:]
+
+This bond style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/bond_nonlinear.txt b/doc/bond_nonlinear.txt
index 7a3be2214c679fbdadb326b54ec5f71609cb74cb..480109ff48c849ab5dbbc6a04be08b8c5af4d8c4 100644
--- a/doc/bond_nonlinear.txt
+++ b/doc/bond_nonlinear.txt
@@ -35,7 +35,11 @@ epsilon (energy)
 r0 (distance)
 lamda (distance) :ul
 
-[Restrictions:] none
+[Restrictions:]
+
+This bond style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/bond_quartic.txt b/doc/bond_quartic.txt
index 20baf5d152f43d2d22c152210c9693e8e3413055..fc7afa2b9e52e101fd4ebdfac589ab28d44798fb 100644
--- a/doc/bond_quartic.txt
+++ b/doc/bond_quartic.txt
@@ -72,6 +72,10 @@ delete_bonds all bond 0 remove :pre
 
 [Restrictions:]
 
+This bond style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
+
 The {quartic} style requires that "special_bonds"_special_bonds.html
 parameters be set to 1,1,1.  Three- and four-body interactions (angle,
 dihedral, etc) cannot be used with {quartic} bonds.
diff --git a/doc/bond_style.txt b/doc/bond_style.txt
index 962650dccfded9113da1fc49471f0e45a03c6188..cf2b7ec520a9e9d91bc63281e4af310af4acf0cb 100644
--- a/doc/bond_style.txt
+++ b/doc/bond_style.txt
@@ -33,9 +33,9 @@ remain in force for the duration of the simulation (unless the bond
 breaks which is possible in some bond potentials).  The list of bonded
 atoms is read in by a "read_data"_read_data.html or
 "read_restart"_read_restart.html command from a data or restart file.
-By contrast, pair potentials are defined between pairs of atoms that
-are within a cutoff distance and the set of active interactions
-typically changes over time.
+By contrast, pair potentials are typically defined between all pairs
+of atoms within a cutoff distance and the set of active interactions
+changes over time.
 
 Hybrid models where bonds are computed using different bond potentials
 can be setup using the {hybrid} bond style.
@@ -43,14 +43,22 @@ can be setup using the {hybrid} bond style.
 The coefficients associated with a bond style can be specified in a
 data or restart file or via the "bond_coeff"_bond_coeff.html command.
 
-In the formulas listed for each bond style, {r} is the distance
-between the 2 atoms in the bond.
+All bond potentials store their coefficient data in binary restart
+files which means bond_style and "bond_coeff"_bond_coeff.html commands
+do not need to be re-specified in an input script that restarts a
+simulation.  See the "read_restart"_read_restart.html command for
+details on how to do this.  The one exception is that bond_style
+{hybrid} only stores the list of sub-styles in the restart file; bond
+coefficients need to be re-specified.
 
-Note that when both a bond and pair style is defined, the
+IMPORTANT NOTE: When both a bond and pair style is defined, the
 "special_bonds"_special_bonds.html command often needs to be used to
 turn off (or weight) the pairwise interaction that would otherwise
 exist between 2 bonded atoms.
 
+In the formulas listed for each bond style, {r} is the distance
+between the 2 atoms in the bond.
+
 :line
 
 Here is an alphabetic list of bond styles defined in LAMMPS.  Click on
@@ -75,10 +83,11 @@ specified by the associated "bond_coeff"_bond_coeff.html command:
 Bond styles can only be set for atom styles that allow bonds to be
 defined.
 
-Bond styles are part of the "molecular" package or other packages as
-noted in their documentation.  They are only enabled if LAMMPS was
-built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
+Most bond styles are part of the "molecular" package.  They are only
+enabled if LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.  The
+doc pages for individual bond potentials tell if it is part of a
+package.
 
 [Related commands:]
 
diff --git a/doc/dihedral_charmm.txt b/doc/dihedral_charmm.txt
index 62e6c24e4f85753f95fd6435bc03ecffe222e253..c9aefa7266d8a0e231145914894648e7b196ea7c 100644
--- a/doc/dihedral_charmm.txt
+++ b/doc/dihedral_charmm.txt
@@ -62,7 +62,11 @@ weighting factors (4th coeff above) should be set to 0.0.  In this
 case, you can use any pair style you wish, since the dihedral does not
 need any 1-4 information.
 
-[Restrictions:] none
+[Restrictions:]
+
+This dihedral style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/dihedral_class2.txt b/doc/dihedral_class2.txt
index a638f976ece498889465feafc2449290420e64fb..002896a3bd055fd874116e6d16f208cdf46993d0 100644
--- a/doc/dihedral_class2.txt
+++ b/doc/dihedral_class2.txt
@@ -32,8 +32,8 @@ bond lengths.
 
 See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
 
-For this style, only coefficients for the Ed formula can be specified
-in the input script.  These are the 6 coefficients:
+For this style, coefficients for the Ed formula can be specified in
+either the input script or data file.  These are the 6 coefficients:
 
 K1 (energy)
 phi1 (degrees)
@@ -42,8 +42,8 @@ phi2 (degrees)
 K3 (energy)
 phi3 (degrees) :ul
 
-Coefficients for all the other formulas must be specified in the data
-file.
+Coefficients for all the other formulas can only be specified in the
+data file.
 
 For the Embt formula, the coefficients are listed under a
 "MiddleBondTorsion Coeffs" heading and each line lists 4 coefficients:
@@ -100,9 +100,9 @@ r3 (distance) :ul
 
 [Restrictions:]
 
-This dihedral style is part of the "class2" package.  It is only
-enabled if LAMMPS was built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
+This dihedral style can only be used if LAMMPS was built with the
+"class2" package.  See the "Making LAMMPS"_Section_start.html#2_3
+section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/dihedral_harmonic.txt b/doc/dihedral_harmonic.txt
index ecae8a1113111504770bef83feccaa302970860c..6e9c5dee066eec3d8245434f389b4db18ffa38a6 100644
--- a/doc/dihedral_harmonic.txt
+++ b/doc/dihedral_harmonic.txt
@@ -32,7 +32,11 @@ K (energy)
 d (+1 or -1)
 n (integer >= 0) :ul
 
-[Restrictions:] none
+[Restrictions:]
+
+This dihedral style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/dihedral_helix.txt b/doc/dihedral_helix.txt
index 7827c65c006482d966558b6ae8418123ed6240b4..f68d66e6f824cd934e44dced8baef2e35a0aaef5 100644
--- a/doc/dihedral_helix.txt
+++ b/doc/dihedral_helix.txt
@@ -40,7 +40,11 @@ A (energy)
 B (energy)
 C (energy) :ul
 
-[Restrictions:] none
+[Restrictions:]
+
+This dihedral style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/dihedral_hybrid.txt b/doc/dihedral_hybrid.txt
index 87e316a12dda9e0377b1a2197074e6a6ad2f3be3..d7eda64a3e3355bb34eb1aab007fd838b46e638c 100644
--- a/doc/dihedral_hybrid.txt
+++ b/doc/dihedral_hybrid.txt
@@ -51,7 +51,11 @@ A dihedral style of {none} can be specified as an argument to
 dihedral_style hybrid and the corresponding dihedral_coeff commands,
 if you desire to turn off certain dihedral types.
 
-[Restrictions:] none
+[Restrictions:]
+
+This dihedral style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/dihedral_multi_harmonic.txt b/doc/dihedral_multi_harmonic.txt
index 53fffc0bfd86a7313ee48409e249d4049e271554..4c71dbc3ca6778ffe2c5ce147ecee9724c12a505 100644
--- a/doc/dihedral_multi_harmonic.txt
+++ b/doc/dihedral_multi_harmonic.txt
@@ -34,7 +34,11 @@ A3 (energy)
 A4 (energy)
 A5 (energy) :ul
 
-[Restrictions:] none
+[Restrictions:]
+
+This dihedral style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/dihedral_opls.txt b/doc/dihedral_opls.txt
index 639e3a3f30900a2e0f0f768f1543765af3362e8a..67c08e65435d8400db6de58b35de33d9a4b3efc4 100644
--- a/doc/dihedral_opls.txt
+++ b/doc/dihedral_opls.txt
@@ -38,7 +38,11 @@ K2 (energy)
 K3 (energy)
 K4 (energy) :ul
 
-[Restrictions:] none
+[Restrictions:]
+
+This dihedral style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/dihedral_style.txt b/doc/dihedral_style.txt
index ea01bc7205103f197c91cde5f905e6da6c862164..e540c5540e469f01419e85b155bb1c28ab593628 100644
--- a/doc/dihedral_style.txt
+++ b/doc/dihedral_style.txt
@@ -32,17 +32,27 @@ from a data or restart file.
 Hybrid models where dihedrals are computed using different dihedral
 potentials can be setup using the {hybrid} dihedral style.
 
-The coefficients associated with a dihedral style can be specified in a
-data or restart file or via the "dihedral_coeff"_dihedral_coeff.html command.
+The coefficients associated with a dihedral style can be specified in
+a data or restart file or via the "dihedral_coeff"_dihedral_coeff.html
+command.
+
+All dihedral potentials store their coefficient data in binary restart
+files which means dihedral_style and
+"dihedral_coeff"_dihedral_coeff.html commands do not need to be
+re-specified in an input script that restarts a simulation.  See the
+"read_restart"_read_restart.html command for details on how to do
+this.  The one exception is that dihedral_style {hybrid} only stores
+the list of sub-styles in the restart file; dihedral coefficients need
+to be re-specified.
+
+IMPORTANT NOTE: When both a dihedral and pair style is defined, the
+"special_bonds"_special_bonds.html command often needs to be used to
+turn off (or weight) the pairwise interaction that would otherwise
+exist between 4 bonded atoms.
 
 In the formulas listed for each dihedral style, {phi} is the torsional
 angle defined by the quadruplet of atoms.
 
-Note that when both a dihedral and pair style is defined, the
-"special_bond"_special_bond.html command often needs to be used to
-turn off (or weight) the pairwise interactions that would otherwise
-exist between the 4 bonded atoms.
-
 Here are some important points to take note of when defining the
 LAMMPS dihedral coefficients in the formulas that follow so that they
 are compatible with other force fields:
@@ -81,10 +91,11 @@ specified by the associated "dihedral_coeff"_dihedral_coeff.html command:
 Dihedral styles can only be set for atom styles that allow dihedrals
 to be defined.
 
-Dihedral styles are part of the "molecular" package or other packages
-as noted in their documentation.  They are only enabled if LAMMPS was
-built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
+Most dihedral styles are part of the "molecular" package.  They are
+only enabled if LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.  The
+doc pages for individual dihedral potentials tell if it is part of a
+package.
 
 [Related commands:]
 
diff --git a/doc/dump.txt b/doc/dump.txt
index e7953c5f09c147bcaf340a5855c97e218ee8a0ac..965d7453f5c6af1e9f19477581bd7b0e248a7514 100644
--- a/doc/dump.txt
+++ b/doc/dump.txt
@@ -291,11 +291,11 @@ documentation.
 
 The {bond} style is part of the "molecular" package.  It is only
 enabled if LAMMPS was built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
+LAMMPS"_Section_start.html#2_3 section for more info.
 
 The {xtc} style is part of the "xtc" package.  It is only enabled if
 LAMMPS was built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.  This is because
+LAMMPS"_Section_start.html#2_3 section for more info.  This is because
 some machines may not support the lo-level XDR data format that XTC
 files are written with, which will result in a compile-time error when
 a lo-level include file is not found.  Putting this style in a package
diff --git a/doc/fix.txt b/doc/fix.txt
index 8a6ffe576360127c9f1604112a0dca722db320f4..05ad174eceecd43455b767958c46fbfe16e9f2c1 100644
--- a/doc/fix.txt
+++ b/doc/fix.txt
@@ -35,8 +35,7 @@ defined in LAMMPS and new ones can be added - see "this
 section"_Section_modify.html for a discussion.
 
 Each fix style has its own documentation page which describes its
-arguments and what it does.  For example, see the "fix
-setforce"_fix_setforce.html page for information on style {setforce}.
+arguments and what it does, as listed below.
 
 Fixes perform their operations at different stages of the timestep.
 If 2 or more fixes both operate at the same stage of the timestep,
@@ -45,10 +44,10 @@ they are invoked in the order they were specified in the input script.
 Fixes can be deleted with the "unfix"_unfix.html command.  Note that
 this is the only way to turn off a fix; simply specifying a new fix
 with a similar style will not turn off the first one.  For example,
-using a "fix nve" command for a second run after using a "fix nvt"
-command for the first run, will not cancel out the NVT time
-integration invoked by the "fix nvt" command.  Thus two time
-integrators would be in place!
+using a "fix nve"_fix_nve.html command for a second run after using a
+"fix nvt"_fix_nvt.html command for the first run, will not cancel out
+the NVT time integration invoked by the "fix nvt" command.  Thus two
+time integrators would be in place!
 
 If you specify a new fix with the same ID and style as an existing
 fix, the old fix is deleted and the new one is created (presumably
@@ -58,7 +57,18 @@ same order relative to the existing fixes as the old one originally
 was.  Note that this operation also wipes out any additional changes
 made to the old fix via the "fix_modify"_fix_modify.html command.
 
-Here is an alphabetic list of fix styles defined in LAMMPS:
+The "fix modify"_fix_modify.html command allows settings for some
+fixes to be reset.  See the doc page for individual fixes for details.
+
+Some fixes store an internal "state" which is written to binary
+restart files via the "restart"_restart.html or
+"write_restart"_write_restart.html commands.  This allows the fix to
+continue on with its calculations in a restarted simulation.  See the
+"read_restart"_read_restart.html command for info on how to re-specify
+a fix in an input script that reads a restart file.  See the doc pages
+for individual fixes for info on which ones can be restarted.
+
+Here is an alphabetic list of fix styles available in LAMMPS:
 
 "fix addforce"_fix_addforce.html - add a force to each atom
 "fix aveforce"_fix_aveforce.html - add an averaged force to each atom
@@ -124,12 +134,8 @@ Here is an alphabetic list of fix styles defined in LAMMPS:
 
 Some fix styles are part of specific packages.  They are only enabled
 if LAMMPS was built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
-
-The {freeze}, {gran/diag}, {gravity}, {nve/gran}, {pour}, and
-{wall/gran} styles are part of the "granular" package.
-
-The {poems} style is part of the "poems" package.
+LAMMPS"_Section_start.html#2_3 section for more info on packages.  The
+doc pages for individual fixes tell if it is part of a package.
 
 [Related commands:]
 
diff --git a/doc/fix_addforce.html b/doc/fix_addforce.html
index 3a0039508e70d3e7d8d3114cfa2a29fffb4d00f4..6aeb7608e2e2ad3912f4de82042280999bb9bde4 100644
--- a/doc/fix_addforce.html
+++ b/doc/fix_addforce.html
@@ -30,8 +30,17 @@ the group.  This command can be used to give an additional push to
 atoms in a simulation, such as for a simulation of Poiseuille flow in
 a channel.
 </P>
-<P>The forces due to this fix are also imposed during an energy
-minimization, invoked by the <A HREF = "minimize.html">minimize</A> command.
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.
 </P>
 <P><B>Restrictions:</B> none
 </P>
diff --git a/doc/fix_addforce.txt b/doc/fix_addforce.txt
index 85dc07926fe694fb82b69d6a39010e3ca1a795af..dde46e4e72a20a317e4b1777b2195a4d0943bdd3 100644
--- a/doc/fix_addforce.txt
+++ b/doc/fix_addforce.txt
@@ -27,8 +27,17 @@ the group.  This command can be used to give an additional push to
 atoms in a simulation, such as for a simulation of Poiseuille flow in
 a channel.
 
-The forces due to this fix are also imposed during an energy
-minimization, invoked by the "minimize"_minimize.html command.
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the "minimize"_minimize.html command.
 
 [Restrictions:] none
 
diff --git a/doc/fix_ave_spatial.html b/doc/fix_ave_spatial.html
index a37b08c3a1bd695a3ecf9d373bea05e43a8a30b1..f34f1bec0f1ecdffe1e5ed18cdae2492cd455f6e 100644
--- a/doc/fix_ave_spatial.html
+++ b/doc/fix_ave_spatial.html
@@ -143,6 +143,16 @@ the fix group and compute group do not match.
 or creation of neighbor lists.  If the compute is invoked too often by
 fix ave/spatial, it can slow down a simulation.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
diff --git a/doc/fix_ave_spatial.txt b/doc/fix_ave_spatial.txt
index ddaba0fe4116d4091f93306808e127df44f58b01..9b15930a0df831b47b37eeb6b7ace4a38952660f 100644
--- a/doc/fix_ave_spatial.txt
+++ b/doc/fix_ave_spatial.txt
@@ -130,6 +130,16 @@ Note that some computes perform costly calculations, involving use of
 or creation of neighbor lists.  If the compute is invoked too often by
 fix ave/spatial, it can slow down a simulation.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] none
 
 [Related commands:]
diff --git a/doc/fix_ave_time.html b/doc/fix_ave_time.html
index f7eef1964407701d0d991e1fa507bb9d52db3b0e..35cdba8f4d0a902435f70f3ce1bb20c0be6e9154 100644
--- a/doc/fix_ave_time.html
+++ b/doc/fix_ave_time.html
@@ -74,6 +74,16 @@ if a constant pressure simulation is being run (<A HREF = "fix_npt.html">fix npt
 or <A HREF = "fix_nph.html">fix nph</A>), LAMMPS is already calculating virial terms
 for the pressure every timestep.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
diff --git a/doc/fix_ave_time.txt b/doc/fix_ave_time.txt
index 3a716ab0a8fc8e3a242b4f897a126182f4d611e6..f951d804e1901a6e9a96fca0e75d3810e2015b7d 100644
--- a/doc/fix_ave_time.txt
+++ b/doc/fix_ave_time.txt
@@ -71,6 +71,16 @@ if a constant pressure simulation is being run ("fix npt"_fix_npt.html
 or "fix nph"_fix_nph.html), LAMMPS is already calculating virial terms
 for the pressure every timestep.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] none
 
 [Related commands:]
diff --git a/doc/fix_aveforce.html b/doc/fix_aveforce.html
index 84efd0c528acfd1289f96e308ee2dc8921399444..29f57680b8244fded87da05cbd86596c20c4516d 100644
--- a/doc/fix_aveforce.html
+++ b/doc/fix_aveforce.html
@@ -41,8 +41,17 @@ dimension are not changed.  Note that this is not the same as
 specifying a 0.0 value, since that sets all forces to the same average
 value without adding in any additional force.
 </P>
-<P>The forces due to this fix are also imposed during an energy
-minimization, invoked by the <A HREF = "minimize.html">minimize</A> command.
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.
 </P>
 <P><B>Restrictions:</B> none
 </P>
diff --git a/doc/fix_aveforce.txt b/doc/fix_aveforce.txt
index 4968bb0c66fc72136001834a5f304b3a553520f2..4d6a3ae0bc8ca14634957a2d8650f7297772c3d6 100644
--- a/doc/fix_aveforce.txt
+++ b/doc/fix_aveforce.txt
@@ -38,8 +38,17 @@ dimension are not changed.  Note that this is not the same as
 specifying a 0.0 value, since that sets all forces to the same average
 value without adding in any additional force.
 
-The forces due to this fix are also imposed during an energy
-minimization, invoked by the "minimize"_minimize.html command.
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the "minimize"_minimize.html command.
 
 [Restrictions:] none
 
diff --git a/doc/fix_com.html b/doc/fix_com.html
index ede1fefe45f433b90a511c5eecb0a7ea733d0e77..e44fc277a845f786c9a1dcbde84e47368f8ad548 100644
--- a/doc/fix_com.html
+++ b/doc/fix_com.html
@@ -30,6 +30,16 @@
 including all effects due to atoms passing thru periodic boundaries.
 Write the results to the specified file.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B> none
diff --git a/doc/fix_com.txt b/doc/fix_com.txt
index c5b5a71f8beb1d78a5c49b7b35e62db15e6e5b22..7d4305bcf1c06d7c8aa431b13980962d12abfccc 100644
--- a/doc/fix_com.txt
+++ b/doc/fix_com.txt
@@ -27,6 +27,16 @@ Compute the center-of-mass of the group of atoms every N steps,
 including all effects due to atoms passing thru periodic boundaries.
 Write the results to the specified file.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] none
 
 [Related commands:] none
diff --git a/doc/fix_deform.html b/doc/fix_deform.html
index daf8ee6db793078472e968dd012d4a3b93089f43..fa827892f44b118280e7704e15514e61ee6e0987 100644
--- a/doc/fix_deform.html
+++ b/doc/fix_deform.html
@@ -111,8 +111,7 @@ triclinic, even if its initial tilt factors are 0.0.
 end of the run are determined by the parameters of the fix deform
 command.  Every Nth timestep during the run, the simulation box is
 expanded, contracted, or tilted to ramped values between the initial
-and final values.  The <A HREF = "run.html">run</A> command documents how to make
-the ramping take place across multiple runs.
+and final values.
 </P>
 <HR>
 
@@ -352,8 +351,19 @@ been previously used to define the lattice spacing.  Note that the
 units choice also affects the <I>vel</I> style parameters since it is
 defined in terms of distance/time.
 </P>
-<HR>
-
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.
+</P>
+<P>This fix can perform deformation over multiple runs, using the <I>start</I>
+and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command.  See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
 <P><B>Restrictions:</B>
 </P>
 <P>Any box dimension varied by this fix must be periodic.
diff --git a/doc/fix_deform.txt b/doc/fix_deform.txt
index ba195a261d3b29c5bae0df75cf82700da444ab6a..7b3d1f8ea7356d7343f4162b54700390c1a2b55c 100644
--- a/doc/fix_deform.txt
+++ b/doc/fix_deform.txt
@@ -50,7 +50,7 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
 zero or more keyword/value pairs may be appended to the args :l
 keyword = {remap} or {units} :l
   {remap} value = {x} or {v} or {none}
-    x = remap coords of atoms in group into deforming box (affine deformation)
+    x = remap coords of atoms in group into deforming box
     v = remap velocities of all atoms when they cross periodic boundaries
     none = no remapping of x or v
   {units} value = {lattice} or {box}
@@ -100,8 +100,7 @@ As described below, the desired simulation box size and shape at the
 end of the run are determined by the parameters of the fix deform
 command.  Every Nth timestep during the run, the simulation box is
 expanded, contracted, or tilted to ramped values between the initial
-and final values.  The "run"_run.html command documents how to make
-the ramping take place across multiple runs.
+and final values.
 
 :line
 
@@ -313,18 +312,13 @@ remapped into the new box in the appropriate manner.
 Each time the box size or shape is changed, the {remap} keyword
 determines whether atom positions are re-mapped to the new box.  If
 {remap} is set to {x} (the default), atoms in the fix group are
-re-mapped; otherwise they are not.  If all atoms are remapped, this is
-effectively an "affine" deformation.
-
-If {remap} is set to {v}, then any atom in the fix group that crosses
-a periodic boundary will have a delta added to its velocity equal to
-the difference in velocities between the lo and hi boundaries.  Note
-that this velocity difference can include tilt components, e.g. a
-delta in the x velocity when an atom crosses the y periodic boundary.
-If {remap} is set to {none}, then neither of these remappings take
-place.  Note that unlike remap x which changes atom coords
-continuously as the box deforms, this remapping of v is done ONLY when
-an atom crosses a periodic boundary.
+re-mapped; otherwise they are not.  If {remap} is set to {v}, then any
+atom in the fix group that crosses a periodic boundary will have a
+delta added to its velocity equal to the difference in velocities
+between the lo and hi boundaries.  Note that this velocity difference
+can include tilt components, e.g. a delta in the x velocity when an
+atom crosses the y periodic boundary.  If {remap} is set to {none},
+then neither of these remappings take place.
 
 IMPORTANT NOTE: When non-equilibrium MD (NEMD) simulations are
 performed using this fix, the option "remap v" should normally be
@@ -346,13 +340,26 @@ been previously used to define the lattice spacing.  Note that the
 units choice also affects the {vel} style parameters since it is
 defined in terms of distance/time.
 
-:line
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.
+
+This fix can perform deformation over multiple runs, using the {start}
+and {stop} keywords of the "run"_run.html command.  See the
+"run"_run.html command for details of how to do this.
+
+This fix is not invoked during "energy minimization"_minimize.html.
 
 [Restrictions:]
 
 Any box dimension varied by this fix must be periodic.
 
-[Related commands:] none
+[Related commands:]
+
+"displace_box"_displace_box.html
 
 [Default:]
 
diff --git a/doc/fix_deposit.html b/doc/fix_deposit.html
index aa445895640b6a33b253c68287ba8f156cb7e5e5..d305f68097297bc39767384a24480feba78cd555 100644
--- a/doc/fix_deposit.html
+++ b/doc/fix_deposit.html
@@ -131,6 +131,30 @@ command must have been previously used to define the lattice spacing.
 Note that the units choice affects all the keyword values that have
 units of distance or velocity.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  This means you must be careful when restarting a
+deposition simulation, when the restart file was written in the middle
+of the deposition operation.  Specifically, you should use a new fix
+deposit command in the input script for the restarted simulation that
+continues the operation.  You will need to adjust the arguments of the
+original fix deposit command to do this.
+</P>
+<P>Also note that because the state of the random number generator is not
+saved in restart files, you cannot do "exact" restarts with this fix,
+where the simulation continues on the same as if no restart had taken
+place.  However, in a statistical sense, a restarted simulation should
+produce the same behavior if you adjust the fix deposit parameters
+appropriately.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix.  No quantities calculated by this fix can be output by the
+<A HREF = "thermo_style.html">thermo_style custom</A> command.  No parameter of this
+fix can be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A>
+command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
diff --git a/doc/fix_deposit.txt b/doc/fix_deposit.txt
index ae2bf0f75b7d85994346cba5fea8c1e65a7e4f88..524f147ea95e7e0012fea11c81ad937c89583256 100644
--- a/doc/fix_deposit.txt
+++ b/doc/fix_deposit.txt
@@ -119,6 +119,30 @@ command must have been previously used to define the lattice spacing.
 Note that the units choice affects all the keyword values that have
 units of distance or velocity.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  This means you must be careful when restarting a
+deposition simulation, when the restart file was written in the middle
+of the deposition operation.  Specifically, you should use a new fix
+deposit command in the input script for the restarted simulation that
+continues the operation.  You will need to adjust the arguments of the
+original fix deposit command to do this.
+
+Also note that because the state of the random number generator is not
+saved in restart files, you cannot do "exact" restarts with this fix,
+where the simulation continues on the same as if no restart had taken
+place.  However, in a statistical sense, a restarted simulation should
+produce the same behavior if you adjust the fix deposit parameters
+appropriately.
+
+None of the "fix_modify"_fix_modify.html options are relevant to this
+fix.  No quantities calculated by this fix can be output by the
+"thermo_style custom"_thermo_style.html command.  No parameter of this
+fix can be used with the {start/stop} keywords of the "run"_run.html
+command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] none
 
 [Related commands:]
diff --git a/doc/fix_drag.html b/doc/fix_drag.html
index 48eebee2d86fd2c1c8fea051358acafd5c620d90..aac8731c8816f1a6e8b9b5dfaa6e8c2677bd3c04 100644
--- a/doc/fix_drag.html
+++ b/doc/fix_drag.html
@@ -39,6 +39,16 @@ application.
 <P>This command can be used to steer one or more atoms to a new location
 in the simulation.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B> 
diff --git a/doc/fix_drag.txt b/doc/fix_drag.txt
index 45eabd6695e8551500f0563a22f85223956147ab..f360fb719ac647d6922bb23cfa6b69b9d6d22b4b 100644
--- a/doc/fix_drag.txt
+++ b/doc/fix_drag.txt
@@ -37,6 +37,16 @@ application.
 This command can be used to steer one or more atoms to a new location
 in the simulation.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] none
 
 [Related commands:] 
diff --git a/doc/fix_efield.html b/doc/fix_efield.html
index a74e9252ae573a32af06121a18ba679f7d14a310..20f5204af572a379213040de2a88398dd34fa248 100644
--- a/doc/fix_efield.html
+++ b/doc/fix_efield.html
@@ -28,6 +28,16 @@
 <P>Add a force F = qE to each charged atom in the group due to an
 external electric field being applied to the system.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
diff --git a/doc/fix_efield.txt b/doc/fix_efield.txt
index f2c3b7fd2b4e5e2cd50d2a415c4ba74fc3ac87b1..20aff825e29316bd3237b76d57afdf7cc4b3f883 100644
--- a/doc/fix_efield.txt
+++ b/doc/fix_efield.txt
@@ -25,6 +25,16 @@ fix kick external-field efield 1.0 0.0 0.0 :pre
 Add a force F = qE to each charged atom in the group due to an
 external electric field being applied to the system.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] none
 
 [Related commands:]
diff --git a/doc/fix_enforce2d.html b/doc/fix_enforce2d.html
index e209a917948a1bb056fdb0f3abaf25e574966b0d..5d2bd8636244cbab1492e4c108d791d6475c983c 100644
--- a/doc/fix_enforce2d.html
+++ b/doc/fix_enforce2d.html
@@ -28,8 +28,17 @@
 This is useful when running a 2d simulation to insure that atoms do
 not move from their initial z coordinate.
 </P>
-<P>The forces due to this fix are also imposed during an energy
-minimization, invoked by the <A HREF = "minimize.html">minimize</A> command.
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.
 </P>
 <P><B>Restrictions:</B> none
 </P>
diff --git a/doc/fix_enforce2d.txt b/doc/fix_enforce2d.txt
index 070cc627cb93a337d0711504f1a52708355350aa..29db81fb748bfc8fd313d58e6f538e2fbf223d00 100644
--- a/doc/fix_enforce2d.txt
+++ b/doc/fix_enforce2d.txt
@@ -25,8 +25,17 @@ Zero out the z-dimension velocity and force on each atom in the group.
 This is useful when running a 2d simulation to insure that atoms do
 not move from their initial z coordinate.
 
-The forces due to this fix are also imposed during an energy
-minimization, invoked by the "minimize"_minimize.html command.
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the "minimize"_minimize.html command.
 
 [Restrictions:] none
 
diff --git a/doc/fix_freeze.html b/doc/fix_freeze.html
index c8e43efd9db086af2592bca29286149accb1d2b2..5ef6820fa3f143277d26e36e09072beae735cc54 100644
--- a/doc/fix_freeze.html
+++ b/doc/fix_freeze.html
@@ -27,9 +27,21 @@
 <P>Zero out the force and torque on a granular particle.  This is useful
 for preventing certain particles from moving in a simulation.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B>
 </P>
-<P>Can only be used if LAMMPS was built with the "granular" package.
+<P>This fix is part of the "granular" package.  It is only enabled if
+LAMMPS was built with that package.  See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS</A> section for more info.
 </P>
 <P>There can only be a single freeze fix defined.  This is because other
 parts of the code (pair potentials, thermodynamics, etc) treat frozen
diff --git a/doc/fix_freeze.txt b/doc/fix_freeze.txt
index c332647a068814e05ce287acbe0288f2d26482f6..46f9625b5797bc0c79e74ff4b798e78d04118ad6 100644
--- a/doc/fix_freeze.txt
+++ b/doc/fix_freeze.txt
@@ -24,9 +24,21 @@ fix 2 bottom freeze :pre
 Zero out the force and torque on a granular particle.  This is useful
 for preventing certain particles from moving in a simulation.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:]
 
-Can only be used if LAMMPS was built with the "granular" package.
+This fix is part of the "granular" package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
 
 There can only be a single freeze fix defined.  This is because other
 parts of the code (pair potentials, thermodynamics, etc) treat frozen
diff --git a/doc/fix_gran_diag.html b/doc/fix_gran_diag.html
index ec1f9f804fb9ef8df61258dba55daa90ec8169e7..d5df6ab372848dcf1ee9779a59608aa70376df30 100644
--- a/doc/fix_gran_diag.html
+++ b/doc/fix_gran_diag.html
@@ -34,9 +34,21 @@ and file.str.  The z bins begin at the bottom of the system and extend
 upward with a thickness of <I>zlayer</I> for each bin.  The quantities
 written to the file are averaged over all atoms in the bin.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B>
 </P>
-<P>Can only be used if LAMMPS was built with the "granular" package.
+<P>This fix is part of the "granular" package.  It is only enabled if
+LAMMPS was built with that package.  See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS</A> section for more info.
 </P>
 <P><B>Related commands:</B>
 </P>
diff --git a/doc/fix_gran_diag.txt b/doc/fix_gran_diag.txt
index 6818538098fb1a93d0aee6f74560fc0edf8e15ac..e3f43133e25c39cded61b20ce14279db6fa744fc 100644
--- a/doc/fix_gran_diag.txt
+++ b/doc/fix_gran_diag.txt
@@ -31,9 +31,21 @@ and file.str.  The z bins begin at the bottom of the system and extend
 upward with a thickness of {zlayer} for each bin.  The quantities
 written to the file are averaged over all atoms in the bin.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:]
 
-Can only be used if LAMMPS was built with the "granular" package.
+This fix is part of the "granular" package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
 
 [Related commands:]
 
diff --git a/doc/fix_gravity.html b/doc/fix_gravity.html
index b5d9783263b60bba131328121688c207a608cb28..538bad27bd9f7c65d9f9c9944dd3d0e4f6541e45 100644
--- a/doc/fix_gravity.html
+++ b/doc/fix_gravity.html
@@ -80,6 +80,16 @@ vector direction given by (x,y,z).
 <P>The strength of the acceleration due to gravity is 1.0 in LJ units,
 which are the only allowed units for granular systems.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B>
 </P>
 <P>Styles <I>chute</I>, <I>spherical</I>, and <I>gradient</I> can only be used with
diff --git a/doc/fix_gravity.txt b/doc/fix_gravity.txt
index 70cc50e172dc2962efbf5c324306b04b8c1daffa..06b772a8593aed97d98713fdc733773ce0051583 100644
--- a/doc/fix_gravity.txt
+++ b/doc/fix_gravity.txt
@@ -73,6 +73,16 @@ vector direction given by (x,y,z).
 The strength of the acceleration due to gravity is 1.0 in LJ units,
 which are the only allowed units for granular systems.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:]
 
 Styles {chute}, {spherical}, and {gradient} can only be used with
diff --git a/doc/fix_gyration.html b/doc/fix_gyration.html
index 1110a353682be80343e44bf6552024998b8f6b84..f2c498ddfdab8b90d914b57a0c4d46268898bfbd 100644
--- a/doc/fix_gyration.html
+++ b/doc/fix_gyration.html
@@ -38,6 +38,16 @@ this formula
 <P>where M is the total mass of the group and Rcm is the center-of-mass
 position of the group.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B> none
diff --git a/doc/fix_gyration.txt b/doc/fix_gyration.txt
index 6f285842fe9081061df9999c674ab32c0b12c113..911526a57e4928b10cbc1323fac4d52888015648 100644
--- a/doc/fix_gyration.txt
+++ b/doc/fix_gyration.txt
@@ -35,6 +35,16 @@ this formula
 where M is the total mass of the group and Rcm is the center-of-mass
 position of the group.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] none
 
 [Related commands:] none
diff --git a/doc/fix_heat.html b/doc/fix_heat.html
index e1028c33606bc5bb695be8ff532f9e50eea3e083..93099a72c8c5f42973396f17b8eae8d51db9cf1a 100644
--- a/doc/fix_heat.html
+++ b/doc/fix_heat.html
@@ -59,6 +59,16 @@ not normally be used on atoms that have their temperature controlled
 by another fix - e.g. <A HREF = "fix_nvt.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
 langevin</A> fix.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
diff --git a/doc/fix_heat.txt b/doc/fix_heat.txt
index 03fb62a2876d99a8a9f9970992ba28624f4e1b84..c0839e9370c67fbcdfe2ebf110afa4021696f3d8 100644
--- a/doc/fix_heat.txt
+++ b/doc/fix_heat.txt
@@ -56,6 +56,16 @@ not normally be used on atoms that have their temperature controlled
 by another fix - e.g. "fix nvt"_fix_nvt.html or "fix
 langevin"_fix_langevin.html fix.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] none
 
 [Related commands:]
diff --git a/doc/fix_indent.html b/doc/fix_indent.html
index 37f96f8f63784a5c92d81398c3121c80beea9eaa..d66cd11c6a0dc2af94349e78b3184d5527429fc7 100644
--- a/doc/fix_indent.html
+++ b/doc/fix_indent.html
@@ -80,15 +80,9 @@ specified velocity.
 <P>If the <I>rstart</I> keyword is specified, then the radius of the indenter
 is a time-dependent quantity.  R0 is the value assigned at the start
 of the run; R is the value at the end.  At intermediate times, the
-radius is linearly interpolated between these two values.  The
-<A HREF = "run.html">run</A> command documents how to make the interpolation take
-place across multiple runs.  This option can be used, for example, to
-grow/shrink a void within the simulation box.  This option is not
-relevant during an energy minimization; the indenter always has radius
-R in that case.  Note that if you do multiple runs, you may need to
-re-specify the fix so that the indenter radius has the appropriate
-value.  If you do nothing, it will be reset to R0 at the beginning of
-each run.
+radius is linearly interpolated between these two values.  This option
+can be used, for example, to grow/shrink a void within the simulation
+box.
 </P>
 <P>The <I>units</I> keyword determines the meaning of the distance units used
 to define the indenter.  A <I>box</I> value selects standard distance units
@@ -100,18 +94,36 @@ choice affects not only the indenter's physical geometry, but also its
 velocity and force constant since they are defined in terms of
 distance as well.
 </P>
-<P>This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the <A HREF = "fix_modify.html">fix_modify energy</A> option.  The energy of each
-particle interacting with the indenter is K/3 (r - R)^3.  The
-contribution can also be printed by itself via the keyword <I>f_fix-ID</I>
-in the <A HREF = "thermo_style.html">thermo_style custom</A> command.
-</P>
-<P>The forces due to this fix are also imposed during an energy
-minimization, invoked by the <A HREF = "minimize.html">minimize</A> command.  If you
-want that energy to be included in the total potential energy of the
-system (the quantity being minimized), you must enable the
-<A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for this fix.
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy of interaction between atoms and the indenter to
+the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.  The energy of each particle interacting
+with the indenter is K/3 (r - R)^3.
+</P>
+<P>The atom/indenter interaction energy can be printed as part of
+thermodynamic output via the keyword f_ID, where ID is the fix-ID of
+this fix.  See the <A HREF = "thermo_style.html">thermo_style custom</A> command for
+details.
+</P>
+<P>This fix can adjust the indenter position and radius over multiple
+runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
+command.  See the <A HREF = "run.html">run</A> command for details of how to do
+this.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.  The <I>rstart</I> keyword
+does not change the indenter radius during an energy minimization; the
+indenter always has a radius of its final value R in that case.
+</P>
+<P>IMPORTANT NOTE: If you want the atom/indenter interaction energy to be
+included in the total potential energy of the system (the quantity
+being minimized), you MUST enable the <A HREF = "fix_modify.html">fix_modify</A>
+<I>energy</I> option for this fix.
 </P>
 <P><B>Restrictions:</B> none
 </P>
diff --git a/doc/fix_indent.txt b/doc/fix_indent.txt
index ff045b9236addf212757724920e24b5f57afd67b..50947370e70941c6db4471bc9a58dd9ef501dd80 100644
--- a/doc/fix_indent.txt
+++ b/doc/fix_indent.txt
@@ -71,15 +71,9 @@ specified velocity.
 If the {rstart} keyword is specified, then the radius of the indenter
 is a time-dependent quantity.  R0 is the value assigned at the start
 of the run; R is the value at the end.  At intermediate times, the
-radius is linearly interpolated between these two values.  The
-"run"_run.html command documents how to make the interpolation take
-place across multiple runs.  This option can be used, for example, to
-grow/shrink a void within the simulation box.  This option is not
-relevant during an energy minimization; the indenter always has radius
-R in that case.  Note that if you do multiple runs, you may need to
-re-specify the fix so that the indenter radius has the appropriate
-value.  If you do nothing, it will be reset to R0 at the beginning of
-each run.
+radius is linearly interpolated between these two values.  This option
+can be used, for example, to grow/shrink a void within the simulation
+box.
 
 The {units} keyword determines the meaning of the distance units used
 to define the indenter.  A {box} value selects standard distance units
@@ -91,18 +85,36 @@ choice affects not only the indenter's physical geometry, but also its
 velocity and force constant since they are defined in terms of
 distance as well.
 
-This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the "fix_modify energy"_fix_modify.html option.  The energy of each
-particle interacting with the indenter is K/3 (r - R)^3.  The
-contribution can also be printed by itself via the keyword {f_fix-ID}
-in the "thermo_style custom"_thermo_style.html command.
-
-The forces due to this fix are also imposed during an energy
-minimization, invoked by the "minimize"_minimize.html command.  If you
-want that energy to be included in the total potential energy of the
-system (the quantity being minimized), you must enable the
-"fix_modify"_fix_modify.html {energy} option for this fix.
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the energy of interaction between atoms and the indenter to
+the system's potential energy as part of "thermodynamic
+output"_thermo_style.html.  The energy of each particle interacting
+with the indenter is K/3 (r - R)^3.
+
+The atom/indenter interaction energy can be printed as part of
+thermodynamic output via the keyword f_ID, where ID is the fix-ID of
+this fix.  See the "thermo_style custom"_thermo_style.html command for
+details.
+
+This fix can adjust the indenter position and radius over multiple
+runs, using the {start} and {stop} keywords of the "run"_run.html
+command.  See the "run"_run.html command for details of how to do
+this.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the "minimize"_minimize.html command.  The {rstart} keyword
+does not change the indenter radius during an energy minimization; the
+indenter always has a radius of its final value R in that case.
+
+IMPORTANT NOTE: If you want the atom/indenter interaction energy to be
+included in the total potential energy of the system (the quantity
+being minimized), you MUST enable the "fix_modify"_fix_modify.html
+{energy} option for this fix.
 
 [Restrictions:] none
 
diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html
index 944d69b6ad474ada867f4af85cf4036cd9fa68f9..ba0ccdf5defd4d9762b051c7e32d001a532204ce 100644
--- a/doc/fix_langevin.html
+++ b/doc/fix_langevin.html
@@ -71,8 +71,7 @@ timestep size, and damp is the damping factor.  Random numbers are
 used to randomize the direction and magnitude of this force.
 </P>
 <P>The desired temperature at each timestep is a ramped value during the
-run from <I>Tstart</I> to <I>Tstop</I>.  The <A HREF = "run.html">run</A> command documents
-how to make the ramping take place across multiple runs.
+run from <I>Tstart</I> to <I>Tstop</I>.
 </P>
 <P>The <I>damp</I> parameter is specified in time units and determines how
 rapidly the temperature is relaxed.  For example, a value of 100.0
@@ -88,10 +87,7 @@ viscous</A> command for more details.
 A Marsaglia random number generator is used.  Each processor uses the
 input seed to generate its own unique seed and its own stream of
 random numbers.  Thus the dynamics of the system will not be identical
-on two runs on different numbers of processors.  Also, the state of
-the random number generator is not saved in a restart file.  This
-means you cannot do exact restarts when a fix <I>langevin</I> command is
-used.
+on two runs on different numbers of processors. 
 </P>
 <P>The keyword <I>axes</I> can be used to specify which dimensions to add Ff
 and Fr to.  A flag of 0 means skip that dimension; a flag of 1 means
@@ -121,6 +117,25 @@ should not normally be used on atoms that also have their temperature
 controlled by another fix - e.g. a <A HREF = "fix_nvt.html">nvt</A> or
 <A HREF = "fix_temp_rescale.html">temp/rescale</A> fix.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  Because the state of the random number generator
+is not saved in restart files, this means you cannot do "exact"
+restarts with this fix, where the simulation continues on the same as
+if no restart had taken place.  However, in a statistical sense, a
+restarted simulation should produce the same behavior.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.
+</P>
+<P>This fix can ramp its target temperature over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command.  See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
diff --git a/doc/fix_langevin.txt b/doc/fix_langevin.txt
index 8d9bd8c68365497bed0e13b10f09325f7aa37258..869649c60926f3949136d8523da479f5af97e9f2 100644
--- a/doc/fix_langevin.txt
+++ b/doc/fix_langevin.txt
@@ -61,8 +61,7 @@ timestep size, and damp is the damping factor.  Random numbers are
 used to randomize the direction and magnitude of this force.
 
 The desired temperature at each timestep is a ramped value during the
-run from {Tstart} to {Tstop}.  The "run"_run.html command documents
-how to make the ramping take place across multiple runs.
+run from {Tstart} to {Tstop}.
 
 The {damp} parameter is specified in time units and determines how
 rapidly the temperature is relaxed.  For example, a value of 100.0
@@ -78,10 +77,7 @@ The random # {seed} should be a non-zero integer with 1 to 8 digits.
 A Marsaglia random number generator is used.  Each processor uses the
 input seed to generate its own unique seed and its own stream of
 random numbers.  Thus the dynamics of the system will not be identical
-on two runs on different numbers of processors.  Also, the state of
-the random number generator is not saved in a restart file.  This
-means you cannot do exact restarts when a fix {langevin} command is
-used.
+on two runs on different numbers of processors. 
 
 The keyword {axes} can be used to specify which dimensions to add Ff
 and Fr to.  A flag of 0 means skip that dimension; a flag of 1 means
@@ -111,6 +107,25 @@ should not normally be used on atoms that also have their temperature
 controlled by another fix - e.g. a "nvt"_fix_nvt.html or
 "temp/rescale"_fix_temp_rescale.html fix.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  Because the state of the random number generator
+is not saved in restart files, this means you cannot do "exact"
+restarts with this fix, where the simulation continues on the same as
+if no restart had taken place.  However, in a statistical sense, a
+restarted simulation should produce the same behavior.
+
+None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.
+
+This fix can ramp its target temperature over multiple runs, using the
+{start} and {stop} keywords of the "run"_run.html command.  See the
+"run"_run.html command for details of how to do this.
+
+This fix is not invoked during "energy minimization"_minimize.html.
+
 [Restrictions:] none
 
 [Related commands:]
diff --git a/doc/fix_lineforce.html b/doc/fix_lineforce.html
index 930dd668363caa0e2a9814cb8f722334a002bbf6..208351bd767976fd8c60d61fb7181b7fdd1067a0 100644
--- a/doc/fix_lineforce.html
+++ b/doc/fix_lineforce.html
@@ -33,8 +33,17 @@ line.
 <P>If the initial velocity of the atom is 0.0 (or along the line), then
 it should continue to move along the line thereafter.
 </P>
-<P>The forces due to this fix are also imposed during an energy
-minimization, invoked by the <A HREF = "minimize.html">minimize</A> command.
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.
 </P>
 <P><B>Restrictions:</B> none
 </P>
diff --git a/doc/fix_lineforce.txt b/doc/fix_lineforce.txt
index c053f00855f7f196b52ba75e3d918da44bc32b02..151f0b70dd20c914ae517e1465969dfef07af504 100644
--- a/doc/fix_lineforce.txt
+++ b/doc/fix_lineforce.txt
@@ -30,8 +30,17 @@ line.
 If the initial velocity of the atom is 0.0 (or along the line), then
 it should continue to move along the line thereafter.
 
-The forces due to this fix are also imposed during an energy
-minimization, invoked by the "minimize"_minimize.html command.
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the "minimize"_minimize.html command.
 
 [Restrictions:] none
 
diff --git a/doc/fix_modify.html b/doc/fix_modify.html
index 806948504272f6fcb3b0bcbf360fc27765b5af3d..362942c298e2bc2191e9a6780116c4ab04845304 100644
--- a/doc/fix_modify.html
+++ b/doc/fix_modify.html
@@ -58,10 +58,10 @@ default method for computing P.
 <P>For fixes that calculate a contribution to the potential energy of the
 system, the <I>energy</I> keyword will include that contribution in
 thermodyanmic output of potential energy.  See the
-<A HREF = "thermo_style.html">thermo_style</A> command for info on how to output
-potential energy is printed.  The contribution itself can also be
-printed by using the keyword f_ID in the thermo_style custom command,
-where ID is the fix-ID of the appropriate fix.
+<A HREF = "thermo_style.html">thermo_style</A> command for info on how potential
+energy is output.  The contribution by itself can be printed by using
+the keyword f_ID in the thermo_style custom command, where ID is the
+fix-ID of the appropriate fix.
 </P>
 <P><B>Restrictions:</B> none
 </P>
diff --git a/doc/fix_modify.txt b/doc/fix_modify.txt
index 19812f4cacdf930de7ffee3649244e78b9b84961..a4699187a1c0262b571b488f818b94a9848f0e46 100644
--- a/doc/fix_modify.txt
+++ b/doc/fix_modify.txt
@@ -27,33 +27,34 @@ fix_modify 1 energy yes :pre
 
 [Description:]
 
-Modify one or more parameters of a previously defined fix.  Not all
-fix styles support all parameters.
+Modify one or more parameters of a previously defined fix.  Only
+specific fix styles support specific parameters.  See the doc pages
+for individual fix commands for info on which ones support which
+fix_modify parameters.
 
 The {temp} keyword is used to determine how a fix computes
 temperature.  The specified compute ID must have been previously
 defined by the user via the "compute"_compute.html command and it must
 be a style of compute that calculates a temperature.  All fixes that
-compute temperatures defined their own compute by default, as
-described in their documentation.  Thus this option allows the user to
-override the default method for computing T.
+compute temperatures define their own compute by default, as described
+in their documentation.  Thus this option allows the user to override
+the default method for computing T.
 
 The {press} keyword is used to determine how a fix computes pressure.
 The specified compute ID must have been previously defined by the user
 via the "compute"_compute.html command and it must be a style of
 compute that calculates a pressure.  All fixes that compute pressures
-defined their own compute by default, as described in their
+define their own compute by default, as described in their
 documentation.  Thus this option allows the user to override the
 default method for computing P.
 
-For fixes that calculates a contribution to the potential energy of
-the system, the {energy} keyword will include that contribution in
-thermodyanmic output of the potential energy, as invoked by the
-"thermo_style"_thermo_style.html command.  The value of the
-contribution can also be printed by itself using the "thermo_style
-custom"_thermo_style.html keywords.  The documentation for individual
-fix commands specifies whether they make a contribution to the
-potential energy.
+For fixes that calculate a contribution to the potential energy of the
+system, the {energy} keyword will include that contribution in
+thermodyanmic output of potential energy.  See the
+"thermo_style"_thermo_style.html command for info on how potential
+energy is output.  The contribution by itself can be printed by using
+the keyword f_ID in the thermo_style custom command, where ID is the
+fix-ID of the appropriate fix.
 
 [Restrictions:] none
 
diff --git a/doc/fix_momentum.html b/doc/fix_momentum.html
index c18b2d35472b511641f7694d40fb0ac215a64227..89d7eb6f8afadbc9358217eab7e29c4682d59887 100644
--- a/doc/fix_momentum.html
+++ b/doc/fix_momentum.html
@@ -58,6 +58,16 @@ thermostatting).
 <P>Note that the <A HREF = "velocity.html">velocity</A> command can be used to create
 initial velocities with zero aggregate linear and/or angular momentum.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
diff --git a/doc/fix_momentum.txt b/doc/fix_momentum.txt
index 8e55236025b1e7522d5259b986ebefc822de68a6..8a1c3ed98361d483c932d21b461ede0a5fc9fc1b 100644
--- a/doc/fix_momentum.txt
+++ b/doc/fix_momentum.txt
@@ -50,6 +50,16 @@ thermostatting).
 Note that the "velocity"_velocity.html command can be used to create
 initial velocities with zero aggregate linear and/or angular momentum.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] none
 
 [Related commands:]
diff --git a/doc/fix_msd.html b/doc/fix_msd.html
index f69594039923ec8817fb82497561b2e1fa8662a7..94ff529e7c02defe1470a9ca501a4338479f2947 100644
--- a/doc/fix_msd.html
+++ b/doc/fix_msd.html
@@ -33,6 +33,22 @@ proportional to the diffusion coefficient of the diffusing atoms.  The
 "origin" of the displacement for each atom is its position at the time
 the fix command was issued.  Write the results to the specified file.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the original coordinates of diffusing atoms to <A HREF = "restart.html">binary
+restart files</A>, so that the mean-squared displacement
+will be accurate in a restarted simulation.  See the
+<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix.  No quantities calculated by this fix can be output by the
+<A HREF = "thermo_style.html">thermo_style custom</A> command.  No parameter of this
+fix can be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A>
+command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B> none
diff --git a/doc/fix_msd.txt b/doc/fix_msd.txt
index f808f14901b4886b2ba64eba159b425a35b14324..29657cfecf37b634963ea17b0a1238d5d7a0ffa7 100644
--- a/doc/fix_msd.txt
+++ b/doc/fix_msd.txt
@@ -30,6 +30,22 @@ proportional to the diffusion coefficient of the diffusing atoms.  The
 "origin" of the displacement for each atom is its position at the time
 the fix command was issued.  Write the results to the specified file.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+This fix writes the original coordinates of diffusing atoms to "binary
+restart files"_restart.html, so that the mean-squared displacement
+will be accurate in a restarted simulation.  See the
+"read_restart"_read_restart.html command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+
+None of the "fix_modify"_fix_modify.html options are relevant to this
+fix.  No quantities calculated by this fix can be output by the
+"thermo_style custom"_thermo_style.html command.  No parameter of this
+fix can be used with the {start/stop} keywords of the "run"_run.html
+command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] none
 
 [Related commands:] none
diff --git a/doc/fix_nph.html b/doc/fix_nph.html
index a2b625fa04759221b6da5f73fbba5e10fc2889f5..4cb1ebbfa621144672da1106ad943272635c4b13 100644
--- a/doc/fix_nph.html
+++ b/doc/fix_nph.html
@@ -76,8 +76,7 @@ unchanged and controlling the pressure of a surrounding fluid.
 <P>The pressure can be controlled in one of several styles, as specified
 by the <I>p-style</I> argument.  In each case, the desired pressure at each
 timestep is a ramped value during the run from the starting value to
-the end value.  The <A HREF = "run.html">run</A> command documents how to make the
-ramping take place across multiple runs.
+the end value.
 </P>
 <P>Style <I>xyz</I> means couple all 3 dimensions together when pressure is
 computed (isotropic pressure), and dilate/contract the 3 dimensions
@@ -142,19 +141,39 @@ this fix's temperature or pressure via the
 or pressure during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
 custom</A> command using the appropriate compute-ID.
 It also means that changing attributes of <I>thermo_temp</I> or
-<I>thermo_pressure</I> will have no effect on this fix.  Alternatively, you
-can directly assign a new compute (for calculating temeperature or
-pressure) that you have defined to this fix via the
-<A HREF = "fix_modify.html">fix_modify</A> command.  If you do this, note that the
-kinetic energy derived from T should be consistent with the virial
-term computed using all atoms.  LAMMPS will warn you if you choose to
-compute temperature on a subset of atoms.
-</P>
-<P>This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the <A HREF = "fix_modify.html">fix_modify energy</A> option.  The contribution can
-also be printed by itself via the keyword <I>f_fix-ID</I> in the
-<A HREF = "thermo_style.html">thermo_style custom</A> command.
+<I>thermo_pressure</I> will have no effect on this fix.
+</P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the state of the Nose/Hoover barostat to <A HREF = "restart.html">binary
+restart files</A>.  See the <A HREF = "read_restart.html">read_restart</A>
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
+supported by this fix.  You can use them to assign a
+<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
+in its thermostatting or barostatting procedure.  If you do this, note
+that the kinetic energy derived from the compute temperature should be
+consistent with the virial term computed using all atoms for the
+pressure.  LAMMPS will warn you if you choose to compute temperature
+on a subset of atoms.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change induced by Nose/Hoover barostatting to
+the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>The energy change can be printed as part of thermodynamic output via
+the keyword f_ID, where ID is the fix-ID of this fix.  See the
+<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
+</P>
+<P>This fix can ramp its target pressure over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command.  See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
 </P>
 <P><B>Restrictions:</B>
 </P>
diff --git a/doc/fix_nph.txt b/doc/fix_nph.txt
index be0939bec92fbffa78b815d82788ba44734bf412..01a34c7fb2d9264672b9ff6a3dc341e2b58de115 100644
--- a/doc/fix_nph.txt
+++ b/doc/fix_nph.txt
@@ -67,8 +67,7 @@ unchanged and controlling the pressure of a surrounding fluid.
 The pressure can be controlled in one of several styles, as specified
 by the {p-style} argument.  In each case, the desired pressure at each
 timestep is a ramped value during the run from the starting value to
-the end value.  The "run"_run.html command documents how to make the
-ramping take place across multiple runs.
+the end value.
 
 Style {xyz} means couple all 3 dimensions together when pressure is
 computed (isotropic pressure), and dilate/contract the 3 dimensions
@@ -132,19 +131,39 @@ this fix's temperature or pressure via the
 or pressure during thermodyanmic output via the "thermo_style
 custom"_thermo_style.html command using the appropriate compute-ID.
 It also means that changing attributes of {thermo_temp} or
-{thermo_pressure} will have no effect on this fix.  Alternatively, you
-can directly assign a new compute (for calculating temeperature or
-pressure) that you have defined to this fix via the
-"fix_modify"_fix_modify.html command.  If you do this, note that the
-kinetic energy derived from T should be consistent with the virial
-term computed using all atoms.  LAMMPS will warn you if you choose to
-compute temperature on a subset of atoms.
-
-This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the "fix_modify energy"_fix_modify.html option.  The contribution can
-also be printed by itself via the keyword {f_fix-ID} in the
-"thermo_style custom"_thermo_style.html command.
+{thermo_pressure} will have no effect on this fix.
+
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+This fix writes the state of the Nose/Hoover barostat to "binary
+restart files"_restart.html.  See the "read_restart"_read_restart.html
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+The "fix_modify"_fix_modify.html {temp} and {press} options are
+supported by this fix.  You can use them to assign a
+"compute"_compute.html you have defined to this fix which will be used
+in its thermostatting or barostatting procedure.  If you do this, note
+that the kinetic energy derived from the compute temperature should be
+consistent with the virial term computed using all atoms for the
+pressure.  LAMMPS will warn you if you choose to compute temperature
+on a subset of atoms.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the energy change induced by Nose/Hoover barostatting to
+the system's potential energy as part of "thermodynamic
+output"_thermo_style.html.
+
+The energy change can be printed as part of thermodynamic output via
+the keyword f_ID, where ID is the fix-ID of this fix.  See the
+"thermo_style custom"_thermo_style.html command for details.
+
+This fix can ramp its target pressure over multiple runs, using the
+{start} and {stop} keywords of the "run"_run.html command.  See the
+"run"_run.html command for details of how to do this.
+
+This fix is not invoked during "energy minimization"_minimize.html.
 
 [Restrictions:]
 
diff --git a/doc/fix_npt.html b/doc/fix_npt.html
index f4b7f5583664eba30b25d8efe5fb90642525935f..f765d33167280de91d812227341135242eccc85c 100644
--- a/doc/fix_npt.html
+++ b/doc/fix_npt.html
@@ -57,12 +57,11 @@ temperature.  This creates a system trajectory consistent with the
 isothermal-isobaric ensemble.
 </P>
 <P>The desired temperature at each timestep is a ramped value during the
-run from <I>Tstart</I> to <I>Tstop</I>.  The <A HREF = "run.html">run</A> command documents
-how to make the ramping take place across multiple runs.  The <I>Tdamp</I>
-parameter is specified in time units and determines how rapidly the
-temperature is relaxed.  For example, a value of 100.0 means to relax
-the temperature in a timespan of (roughly) 100 time units (tau or
-fmsec or psec - see the <A HREF = "units.html">units</A> command).
+run from <I>Tstart</I> to <I>Tstop</I>.  The <I>Tdamp</I> parameter is specified in
+time units and determines how rapidly the temperature is relaxed.  For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+<A HREF = "units.html">units</A> command).
 </P>
 <P>The atoms in the fix group are the only ones whose velocities and
 positions are updated by the velocity/position update portion of the
@@ -81,8 +80,7 @@ unchanged and controlling the pressure of a surrounding fluid.
 <P>The pressure can be controlled in one of several styles, as specified
 by the <I>p-style</I> argument.  In each case, the desired pressure at each
 timestep is a ramped value during the run from the starting value to
-the end value.  The <A HREF = "run.html">run</A> command documents how to make the
-ramping take place across multiple runs.
+the end value.
 </P>
 <P>Style <I>xyz</I> means couple all 3 dimensions together when pressure is
 computed (isotropic pressure), and dilate/contract the 3 dimensions
@@ -146,19 +144,40 @@ this fix's temperature or pressure via the
 or pressure during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
 custom</A> command using the appropriate compute-ID.
 It also means that changing attributes of <I>thermo_temp</I> or
-<I>thermo_pressure</I> will have no effect on this fix.  Alternatively, you
-can directly assign a new compute (for calculating temeperature or
-pressure) that you have defined to this fix via the
-<A HREF = "fix_modify.html">fix_modify</A> command.  If you do this, note that the
-kinetic energy derived from T should be consistent with the virial
-term computed using all atoms.  LAMMPS will warn you if you choose to
-compute temperature on a subset of atoms.
-</P>
-<P>This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the <A HREF = "fix_modify.html">fix_modify energy</A> option.  The contribution can
-also be printed by itself via the keyword <I>f_fix-ID</I> in the
-<A HREF = "thermo_style.html">thermo_style custom</A> command.
+<I>thermo_pressure</I> will have no effect on this fix.
+</P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the state of the Nose/Hoover thermostat and barostat
+to <A HREF = "restart.html">binary restart files</A>.  See the
+<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
+supported by this fix.  You can use them to assign a
+<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
+in its thermostatting or barostatting procedure.  If you do this, note
+that the kinetic energy derived from the compute temperature should be
+consistent with the virial term computed using all atoms for the
+pressure.  LAMMPS will warn you if you choose to compute temperature
+on a subset of atoms.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting and
+barostatting to the system's potential energy as part of
+<A HREF = "thermo_style.html">thermodynamic output</A>.
+</P>
+<P>The energy change can be printed as part of thermodynamic output via
+the keyword f_ID, where ID is the fix-ID of this fix.  See the
+<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
+</P>
+<P>This fix can ramp its target temperature and pressure over multiple
+runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
+command.  See the <A HREF = "run.html">run</A> command for details of how to do
+this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
 </P>
 <P><B>Restrictions:</B>
 </P>
diff --git a/doc/fix_npt.txt b/doc/fix_npt.txt
index 793b190a93cfe0a07f5ab2346e905a0395bcae6c..00e4aa87b1e48c1be254c59cff18c87b81e82fb6 100644
--- a/doc/fix_npt.txt
+++ b/doc/fix_npt.txt
@@ -46,12 +46,11 @@ temperature.  This creates a system trajectory consistent with the
 isothermal-isobaric ensemble.
 
 The desired temperature at each timestep is a ramped value during the
-run from {Tstart} to {Tstop}.  The "run"_run.html command documents
-how to make the ramping take place across multiple runs.  The {Tdamp}
-parameter is specified in time units and determines how rapidly the
-temperature is relaxed.  For example, a value of 100.0 means to relax
-the temperature in a timespan of (roughly) 100 time units (tau or
-fmsec or psec - see the "units"_units.html command).
+run from {Tstart} to {Tstop}.  The {Tdamp} parameter is specified in
+time units and determines how rapidly the temperature is relaxed.  For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+"units"_units.html command).
 
 The atoms in the fix group are the only ones whose velocities and
 positions are updated by the velocity/position update portion of the
@@ -70,8 +69,7 @@ unchanged and controlling the pressure of a surrounding fluid.
 The pressure can be controlled in one of several styles, as specified
 by the {p-style} argument.  In each case, the desired pressure at each
 timestep is a ramped value during the run from the starting value to
-the end value.  The "run"_run.html command documents how to make the
-ramping take place across multiple runs.
+the end value.
 
 Style {xyz} means couple all 3 dimensions together when pressure is
 computed (isotropic pressure), and dilate/contract the 3 dimensions
@@ -135,19 +133,40 @@ this fix's temperature or pressure via the
 or pressure during thermodyanmic output via the "thermo_style
 custom"_thermo_style.html command using the appropriate compute-ID.
 It also means that changing attributes of {thermo_temp} or
-{thermo_pressure} will have no effect on this fix.  Alternatively, you
-can directly assign a new compute (for calculating temeperature or
-pressure) that you have defined to this fix via the
-"fix_modify"_fix_modify.html command.  If you do this, note that the
-kinetic energy derived from T should be consistent with the virial
-term computed using all atoms.  LAMMPS will warn you if you choose to
-compute temperature on a subset of atoms.
-
-This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the "fix_modify energy"_fix_modify.html option.  The contribution can
-also be printed by itself via the keyword {f_fix-ID} in the
-"thermo_style custom"_thermo_style.html command.
+{thermo_pressure} will have no effect on this fix.
+
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+This fix writes the state of the Nose/Hoover thermostat and barostat
+to "binary restart files"_restart.html.  See the
+"read_restart"_read_restart.html command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+
+The "fix_modify"_fix_modify.html {temp} and {press} options are
+supported by this fix.  You can use them to assign a
+"compute"_compute.html you have defined to this fix which will be used
+in its thermostatting or barostatting procedure.  If you do this, note
+that the kinetic energy derived from the compute temperature should be
+consistent with the virial term computed using all atoms for the
+pressure.  LAMMPS will warn you if you choose to compute temperature
+on a subset of atoms.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting and
+barostatting to the system's potential energy as part of
+"thermodynamic output"_thermo_style.html.
+
+The energy change can be printed as part of thermodynamic output via
+the keyword f_ID, where ID is the fix-ID of this fix.  See the
+"thermo_style custom"_thermo_style.html command for details.
+
+This fix can ramp its target temperature and pressure over multiple
+runs, using the {start} and {stop} keywords of the "run"_run.html
+command.  See the "run"_run.html command for details of how to do
+this.
+
+This fix is not invoked during "energy minimization"_minimize.html.
 
 [Restrictions:]
 
diff --git a/doc/fix_npt_asphere.html b/doc/fix_npt_asphere.html
index 8f0c15cb76b39ccaf7a261f1a2cdac1fa34a64c5..d91d02aa87b3f1c7671036efff7e4a1d7e1d672e 100644
--- a/doc/fix_npt_asphere.html
+++ b/doc/fix_npt_asphere.html
@@ -58,12 +58,11 @@ temperature.  This creates a system trajectory consistent with the
 isothermal-isobaric ensemble.
 </P>
 <P>The desired temperature at each timestep is a ramped value during the
-run from <I>Tstart</I> to <I>Tstop</I>.  The <A HREF = "run.html">run</A> command documents
-how to make the ramping take place across multiple runs.  The <I>Tdamp</I>
-parameter is specified in time units and determines how rapidly the
-temperature is relaxed.  For example, a value of 100.0 means to relax
-the temperature in a timespan of (roughly) 100 time units (tau or
-fmsec or psec - see the <A HREF = "units.html">units</A> command).
+run from <I>Tstart</I> to <I>Tstop</I>.  The <I>Tdamp</I> parameter is specified in
+time units and determines how rapidly the temperature is relaxed.  For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+<A HREF = "units.html">units</A> command).
 </P>
 <P>The particles in the fix group are the only ones whose velocities and
 positions are updated by the velocity/position update portion of the
@@ -82,8 +81,7 @@ unchanged and controlling the pressure of a surrounding fluid.
 <P>The pressure can be controlled in one of several styles, as specified
 by the <I>p-style</I> argument.  In each case, the desired pressure at each
 timestep is a ramped value during the run from the starting value to
-the end value.  The <A HREF = "run.html">run</A> command documents how to make the
-ramping take place across multiple runs.
+the end value.
 </P>
 <P>Style <I>xyz</I> means couple all 3 dimensions together when pressure is
 computed (isotropic pressure), and dilate/contract the 3 dimensions
@@ -115,7 +113,7 @@ is working.  Typically a value between 0.2 to 2.0 is sufficient to
 damp oscillations after a few periods.
 </P>
 <P>For all pressure styles, the simulation box stays rectangular in
-shape.  Parinello-Rahman boundary conditions (tilted box) are not
+shape.  Parinello-Rahman boundary conditions (tilted box) are not yet
 implemented in LAMMPS.
 </P>
 <P>For all styles, the <I>Pdamp</I> parameter operates like the <I>Tdamp</I>
@@ -147,23 +145,46 @@ fix's temperature or pressure via the
 or pressure during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
 custom</A> command using the appropriate compute-ID.
 It also means that changing attributes of <I>thermo_temp</I> or
-<I>thermo_press</I> will have no effect on this fix.  Alternatively, you
-can directly assign a new compute (for calculating temeperature or
-pressure) that you have defined to this fix via the
-<A HREF = "fix_modify.html">fix_modify</A> command.  If you do this, note that the
-kinetic energy derived from T should be consistent with the virial
-term computed using all particles.  LAMMPS will warn you if you choose 
-to compute temperature on a subset of particles.
-</P>
-<P>This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the <A HREF = "fix_modify.html">fix_modify energy</A> option.  The contribution can
-also be printed by itself via the keyword <I>f_fix-ID</I> in the
-<A HREF = "thermo_style.html">thermo_style custom</A> command.
+<I>thermo_press</I> will have no effect on this fix. 
+</P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the state of the Nose/Hoover thermostat and barostat
+to <A HREF = "restart.html">binary restart files</A>.  See the
+<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
+supported by this fix.  You can use them to assign a
+<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
+in its thermostatting or barostatting procedure.  If you do this, note
+that the kinetic energy derived from the compute temperature should be
+consistent with the virial term computed using all atoms for the
+pressure.  LAMMPS will warn you if you choose to compute temperature
+on a subset of atoms.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting and
+barostatting to the system's potential energy as part of
+<A HREF = "thermo_style.html">thermodynamic output</A>.
+</P>
+<P>The energy change can be printed as part of thermodynamic output via
+the keyword f_ID, where ID is the fix-ID of this fix.  See the
+<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
+</P>
+<P>This fix can ramp its target temperature and pressure over multiple
+runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
+command.  See the <A HREF = "run.html">run</A> command for details of how to do
+this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
 </P>
 <P><B>Restrictions:</B>
 </P>
-<P>Can only be used if LAMMPS was built with the "asphere" package.
+<P>This fix is part of the "asphere" package.  It is only enabled if
+LAMMPS was built with that package.  See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS</A> section for more info.
 </P>
 <P>Any dimension being adjusted by this fix must be periodic.  A
 dimension whose target pressures are specified as NULL can be
diff --git a/doc/fix_npt_asphere.txt b/doc/fix_npt_asphere.txt
index 654d3de6628183a6dc2116f4c30f0279477304f5..0661677692ac55e6fa63a0b2815c23d92596b0cb 100755
--- a/doc/fix_npt_asphere.txt
+++ b/doc/fix_npt_asphere.txt
@@ -47,12 +47,11 @@ temperature.  This creates a system trajectory consistent with the
 isothermal-isobaric ensemble.
 
 The desired temperature at each timestep is a ramped value during the
-run from {Tstart} to {Tstop}.  The "run"_run.html command documents
-how to make the ramping take place across multiple runs.  The {Tdamp}
-parameter is specified in time units and determines how rapidly the
-temperature is relaxed.  For example, a value of 100.0 means to relax
-the temperature in a timespan of (roughly) 100 time units (tau or
-fmsec or psec - see the "units"_units.html command).
+run from {Tstart} to {Tstop}.  The {Tdamp} parameter is specified in
+time units and determines how rapidly the temperature is relaxed.  For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+"units"_units.html command).
 
 The particles in the fix group are the only ones whose velocities and
 positions are updated by the velocity/position update portion of the
@@ -71,8 +70,7 @@ unchanged and controlling the pressure of a surrounding fluid.
 The pressure can be controlled in one of several styles, as specified
 by the {p-style} argument.  In each case, the desired pressure at each
 timestep is a ramped value during the run from the starting value to
-the end value.  The "run"_run.html command documents how to make the
-ramping take place across multiple runs.
+the end value.
 
 Style {xyz} means couple all 3 dimensions together when pressure is
 computed (isotropic pressure), and dilate/contract the 3 dimensions
@@ -104,7 +102,7 @@ is working.  Typically a value between 0.2 to 2.0 is sufficient to
 damp oscillations after a few periods.
 
 For all pressure styles, the simulation box stays rectangular in
-shape.  Parinello-Rahman boundary conditions (tilted box) are not
+shape.  Parinello-Rahman boundary conditions (tilted box) are not yet
 implemented in LAMMPS.
 
 For all styles, the {Pdamp} parameter operates like the {Tdamp}
@@ -136,23 +134,46 @@ fix's temperature or pressure via the
 or pressure during thermodyanmic output via the "thermo_style
 custom"_thermo_style.html command using the appropriate compute-ID.
 It also means that changing attributes of {thermo_temp} or
-{thermo_press} will have no effect on this fix.  Alternatively, you
-can directly assign a new compute (for calculating temeperature or
-pressure) that you have defined to this fix via the
-"fix_modify"_fix_modify.html command.  If you do this, note that the
-kinetic energy derived from T should be consistent with the virial
-term computed using all particles.  LAMMPS will warn you if you choose 
-to compute temperature on a subset of particles.
-
-This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the "fix_modify energy"_fix_modify.html option.  The contribution can
-also be printed by itself via the keyword {f_fix-ID} in the
-"thermo_style custom"_thermo_style.html command.
+{thermo_press} will have no effect on this fix. 
+
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+This fix writes the state of the Nose/Hoover thermostat and barostat
+to "binary restart files"_restart.html.  See the
+"read_restart"_read_restart.html command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+
+The "fix_modify"_fix_modify.html {temp} and {press} options are
+supported by this fix.  You can use them to assign a
+"compute"_compute.html you have defined to this fix which will be used
+in its thermostatting or barostatting procedure.  If you do this, note
+that the kinetic energy derived from the compute temperature should be
+consistent with the virial term computed using all atoms for the
+pressure.  LAMMPS will warn you if you choose to compute temperature
+on a subset of atoms.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting and
+barostatting to the system's potential energy as part of
+"thermodynamic output"_thermo_style.html.
+
+The energy change can be printed as part of thermodynamic output via
+the keyword f_ID, where ID is the fix-ID of this fix.  See the
+"thermo_style custom"_thermo_style.html command for details.
+
+This fix can ramp its target temperature and pressure over multiple
+runs, using the {start} and {stop} keywords of the "run"_run.html
+command.  See the "run"_run.html command for details of how to do
+this.
+
+This fix is not invoked during "energy minimization"_minimize.html.
 
 [Restrictions:]
 
-Can only be used if LAMMPS was built with the "asphere" package.
+This fix is part of the "asphere" package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
 
 Any dimension being adjusted by this fix must be periodic.  A
 dimension whose target pressures are specified as NULL can be
diff --git a/doc/fix_nve.html b/doc/fix_nve.html
index 61b962a03266868f14f593706d32b0ab688783c4..ab4259178849804ace497127f3af1850b6661849 100644
--- a/doc/fix_nve.html
+++ b/doc/fix_nve.html
@@ -28,6 +28,16 @@
 group each timestep.  V is volume; E is energy.  This creates a system
 trajectory consistent with the microcanonical ensemble.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
diff --git a/doc/fix_nve.txt b/doc/fix_nve.txt
index cd3f90937bc58e864b2ff5dd781fa350ef028190..2ff28977e4b31bd9e74ded3172ae4e69c8684e58 100644
--- a/doc/fix_nve.txt
+++ b/doc/fix_nve.txt
@@ -25,6 +25,16 @@ Perform constant NVE updates of position and velocity for atoms in the
 group each timestep.  V is volume; E is energy.  This creates a system
 trajectory consistent with the microcanonical ensemble.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] none
 
 [Related commands:]
diff --git a/doc/fix_nve_asphere.html b/doc/fix_nve_asphere.html
index 054b2c63c2b41dc7a46ff61305ebd26b641d6b69..3f670bf0e562f4bf17aa1b7873e6d59f217b8ee7 100644
--- a/doc/fix_nve_asphere.html
+++ b/doc/fix_nve_asphere.html
@@ -29,9 +29,21 @@ angular velocity for aspherical or ellipsoidal particles in the group
 each timestep.  V is volume; E is energy.  This creates a system
 trajectory consistent with the microcanonical ensemble.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> 
 </P>
-<P>Can only be used if LAMMPS was built with the "asphere" package.
+<P>This fix is part of the "asphere" package.  It is only enabled if
+LAMMPS was built with that package.  See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS</A> section for more info.
 </P>
 <P><B>Related commands:</B>
 </P>
diff --git a/doc/fix_nve_asphere.txt b/doc/fix_nve_asphere.txt
index 90f4ace9fc9345befed61fc1e94a0d5b4b8cb279..b40be7224fff15e6293ba9ce5478355cf548d16b 100755
--- a/doc/fix_nve_asphere.txt
+++ b/doc/fix_nve_asphere.txt
@@ -26,9 +26,21 @@ angular velocity for aspherical or ellipsoidal particles in the group
 each timestep.  V is volume; E is energy.  This creates a system
 trajectory consistent with the microcanonical ensemble.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] 
 
-Can only be used if LAMMPS was built with the "asphere" package.
+This fix is part of the "asphere" package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
 
 [Related commands:]
 
diff --git a/doc/fix_nve_dipole.html b/doc/fix_nve_dipole.html
index aa1fa9d9d2d6ebd411b47085cf954ec1e5943b7e..4c90f1e6138b5eeaf5ffc6f7f153b38e6fd42304 100644
--- a/doc/fix_nve_dipole.html
+++ b/doc/fix_nve_dipole.html
@@ -29,9 +29,21 @@ angular velocity for particles with point dipole moments in the group
 each timestep.  V is volume; E is energy.  This creates a system
 trajectory consistent with the microcanonical ensemble.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> 
 </P>
-<P>Can only be used if LAMMPS was built with the "dipole" package.
+<P>This fix is part of the "dipole" package.  It is only enabled if
+LAMMPS was built with that package.  See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS</A> section for more info.
 </P>
 <P><B>Related commands:</B>
 </P>
diff --git a/doc/fix_nve_dipole.txt b/doc/fix_nve_dipole.txt
index b78f4c2383395b4c3b24895f1570ef5e637eebe9..ce54074c839db8273a9c73e8bd486ae93d3079c3 100755
--- a/doc/fix_nve_dipole.txt
+++ b/doc/fix_nve_dipole.txt
@@ -26,9 +26,21 @@ angular velocity for particles with point dipole moments in the group
 each timestep.  V is volume; E is energy.  This creates a system
 trajectory consistent with the microcanonical ensemble.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] 
 
-Can only be used if LAMMPS was built with the "dipole" package.
+This fix is part of the "dipole" package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
 
 [Related commands:]
 
diff --git a/doc/fix_nve_gran.html b/doc/fix_nve_gran.html
index 21d9c1ec2493b563798f607fd3250b69228dde0e..1fae9ed3cc4d858e6fc857bc47a9cbfd8e869a08 100644
--- a/doc/fix_nve_gran.html
+++ b/doc/fix_nve_gran.html
@@ -30,9 +30,21 @@ rotational information as well as position and velocity, so this
 integrator updates translational and rotational degrees of freedom due
 to forces and torques.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
-<P>Can only be used if LAMMPS was built with the "granular" package.
+<P>This fix is part of the "granular" package.  It is only enabled if
+LAMMPS was built with that package.  See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS</A> section for more info.
 </P>
 <P><B>Related commands:</B>
 </P>
diff --git a/doc/fix_nve_gran.txt b/doc/fix_nve_gran.txt
index 22caaf49ea3e2e6a13caebc16a37b59017bc3aff..4423733b909b9300813a43470eaf5202b1e6f989 100644
--- a/doc/fix_nve_gran.txt
+++ b/doc/fix_nve_gran.txt
@@ -27,9 +27,21 @@ rotational information as well as position and velocity, so this
 integrator updates translational and rotational degrees of freedom due
 to forces and torques.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] none
 
-Can only be used if LAMMPS was built with the "granular" package.
+This fix is part of the "granular" package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
 
 [Related commands:]
 
diff --git a/doc/fix_nve_noforce.html b/doc/fix_nve_noforce.html
index c6dab7199fe94a5c253619ad3f0dfbbdeb2112ca..bac32dc510336792c3d998300050a90f11a00dd1 100644
--- a/doc/fix_nve_noforce.html
+++ b/doc/fix_nve_noforce.html
@@ -38,6 +38,16 @@ unchanged, and can thus be printed by the <A HREF = "dump.html">dump</A> command
 queried with an equal-style <A HREF = "variable.html">variable</A> that uses the
 fcm() group function to compute the total force on the group of atoms.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
diff --git a/doc/fix_nve_noforce.txt b/doc/fix_nve_noforce.txt
index 627dc686f9162783d80d6cffd615550631d654af..12716b6be497e8d9371a32b7f2b1acc23bd94059 100644
--- a/doc/fix_nve_noforce.txt
+++ b/doc/fix_nve_noforce.txt
@@ -35,6 +35,16 @@ unchanged, and can thus be printed by the "dump"_dump.html command or
 queried with an equal-style "variable"_variable.html that uses the
 fcm() group function to compute the total force on the group of atoms.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] none
 
 [Related commands:]
diff --git a/doc/fix_nvt.html b/doc/fix_nvt.html
index 0f89ae6c6194edcc747304f80fccd1fdc32ce54d..a1939a03d71b4d13d539bd74334ed83ed711e655 100644
--- a/doc/fix_nvt.html
+++ b/doc/fix_nvt.html
@@ -44,12 +44,11 @@ thermostat.  V is volume; T is temperature.  This creates a system
 trajectory consistent with the canonical ensemble.
 </P>
 <P>The desired temperature at each timestep is a ramped value during the
-run from <I>Tstart</I> to <I>Tstop</I>.  The <A HREF = "run.html">run</A> command documents
-how to make the ramping take place across multiple runs.  The <I>Tdamp</I>
-parameter is specified in time units and determines how rapidly the
-temperature is relaxed.  For example, a value of 100.0 means to relax
-the temperature in a timespan of (roughly) 100 time units (tau or
-fmsec or psec - see the <A HREF = "units.html">units</A> command).
+run from <I>Tstart</I> to <I>Tstop</I>.  The <I>Tdamp</I> parameter is specified in
+time units and determines how rapidly the temperature is relaxed.  For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+<A HREF = "units.html">units</A> command).
 </P>
 <P>In some cases (e.g. for solids) the temperature of the system can
 oscillate undesirably when a Nose/Hoover thermostat is applied.  The
@@ -80,15 +79,35 @@ This means you can change the attributes of this fix's temperature
 during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
 custom</A> command using the appropriate compute-ID.
 It also means that changing attributes of <I>thermo_temp</I> will have no
-effect on this fix.  Alternatively, you can directly assign a new
-compute (for calculating temeperature) that you have defined to this
-fix via the <A HREF = "fix_modify.html">fix_modify</A> command.
-</P>
-<P>This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the <A HREF = "fix_modify.html">fix_modify energy</A> option.  The contribution can
-also be printed by itself via the keyword <I>f_fix-ID</I> in the
-<A HREF = "thermo_style.html">thermo_style custom</A> command.
+effect on this fix.
+</P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary
+restart files</A>.  See the <A HREF = "read_restart.html">read_restart</A>
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
+fix.  You can use it to assign a <A HREF = "compute.html">compute</A> you have
+defined to this fix which will be used in its thermostatting
+procedure.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting to
+the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>The energy change can be printed as part of thermodynamic output via
+the keyword f_ID, where ID is the fix-ID of this fix.  See the
+<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
+</P>
+<P>This fix can ramp its target temperature over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command.  See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
 </P>
 <P><B>Restrictions:</B>
 </P>
diff --git a/doc/fix_nvt.txt b/doc/fix_nvt.txt
index 58e8a3da034f06cfb53b81f3af16addd398fa4d0..b50df05e0cf077c62045a42daef576ec87cbe677 100644
--- a/doc/fix_nvt.txt
+++ b/doc/fix_nvt.txt
@@ -35,12 +35,11 @@ thermostat.  V is volume; T is temperature.  This creates a system
 trajectory consistent with the canonical ensemble.
 
 The desired temperature at each timestep is a ramped value during the
-run from {Tstart} to {Tstop}.  The "run"_run.html command documents
-how to make the ramping take place across multiple runs.  The {Tdamp}
-parameter is specified in time units and determines how rapidly the
-temperature is relaxed.  For example, a value of 100.0 means to relax
-the temperature in a timespan of (roughly) 100 time units (tau or
-fmsec or psec - see the "units"_units.html command).
+run from {Tstart} to {Tstop}.  The {Tdamp} parameter is specified in
+time units and determines how rapidly the temperature is relaxed.  For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+"units"_units.html command).
 
 In some cases (e.g. for solids) the temperature of the system can
 oscillate undesirably when a Nose/Hoover thermostat is applied.  The
@@ -71,15 +70,35 @@ This means you can change the attributes of this fix's temperature
 during thermodyanmic output via the "thermo_style
 custom"_thermo_style.html command using the appropriate compute-ID.
 It also means that changing attributes of {thermo_temp} will have no
-effect on this fix.  Alternatively, you can directly assign a new
-compute (for calculating temeperature) that you have defined to this
-fix via the "fix_modify"_fix_modify.html command.
-
-This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the "fix_modify energy"_fix_modify.html option.  The contribution can
-also be printed by itself via the keyword {f_fix-ID} in the
-"thermo_style custom"_thermo_style.html command.
+effect on this fix.
+
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+This fix writes the state of the Nose/Hoover thermostat to "binary
+restart files"_restart.html.  See the "read_restart"_read_restart.html
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+The "fix_modify"_fix_modify.html {temp} option is supported by this
+fix.  You can use it to assign a "compute"_compute.html you have
+defined to this fix which will be used in its thermostatting
+procedure.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting to
+the system's potential energy as part of "thermodynamic
+output"_thermo_style.html.
+
+The energy change can be printed as part of thermodynamic output via
+the keyword f_ID, where ID is the fix-ID of this fix.  See the
+"thermo_style custom"_thermo_style.html command for details.
+
+This fix can ramp its target temperature over multiple runs, using the
+{start} and {stop} keywords of the "run"_run.html command.  See the
+"run"_run.html command for details of how to do this.
+
+This fix is not invoked during "energy minimization"_minimize.html.
 
 [Restrictions:]
 
diff --git a/doc/fix_nvt_asphere.html b/doc/fix_nvt_asphere.html
index c8bbee14b26537b26953cfc4689494d6c2fa9ee6..cdffdedb76d9be578999253a4252f98f3e4028c0 100644
--- a/doc/fix_nvt_asphere.html
+++ b/doc/fix_nvt_asphere.html
@@ -45,12 +45,11 @@ V is volume; T is temperature.  This creates a system trajectory
 consistent with the canonical ensemble.
 </P>
 <P>The desired temperature at each timestep is a ramped value during the
-run from <I>Tstart</I> to <I>Tstop</I>.  The <A HREF = "run.html">run</A> command documents
-how to make the ramping take place across multiple runs.  The <I>Tdamp</I>
-parameter is specified in time units and determines how rapidly the
-temperature is relaxed.  For example, a value of 100.0 means to relax
-the temperature in a timespan of (roughly) 100 time units (tau or
-fmsec or psec - see the <A HREF = "units.html">units</A> command).
+run from <I>Tstart</I> to <I>Tstop</I>.  The <I>Tdamp</I> parameter is specified in
+time units and determines how rapidly the temperature is relaxed.  For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+<A HREF = "units.html">units</A> command).
 </P>
 <P>In some cases (e.g. for solids) the temperature of the system can
 oscillate undesirably when a Nose/Hoover thermostat is applied.  The
@@ -81,19 +80,41 @@ This means you can change the attributes of this fix's temperature
 during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
 custom</A> command using the appropriate compute-ID.
 It also means that changing attributes of <I>thermo_temp</I> will have no
-effect on this fix.  Alternatively, you can directly assign a new
-compute (for calculating temeperature) that you have defined to this
-fix via the <A HREF = "fix_modify.html">fix_modify</A> command.
+effect on this fix.
 </P>
-<P>This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the <A HREF = "fix_modify.html">fix_modify energy</A> option.  The contribution can
-also be printed by itself via the keyword <I>f_fix-ID</I> in the
-<A HREF = "thermo_style.html">thermo_style custom</A> command.
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary
+restart files</A>.  See the <A HREF = "read_restart.html">read_restart</A>
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
+fix.  You can use it to assign a <A HREF = "compute.html">compute</A> you have
+defined to this fix which will be used in its thermostatting
+procedure.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting to
+the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>The energy change can be printed as part of thermodynamic output via
+the keyword f_ID, where ID is the fix-ID of this fix.  See the
+<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
+</P>
+<P>This fix can ramp its target temperature over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command.  See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
 </P>
 <P><B>Restrictions:</B>
 </P>
-<P>Can only be used if LAMMPS was built with the "asphere" package.
+<P>This fix is part of the "asphere" package.  It is only enabled if
+LAMMPS was built with that package.  See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS</A> section for more info.
 </P>
 <P>The final Tstop cannot be 0.0 since it would make the target T = 0.0
 at some timestep during the simulation which is not allowed in 
diff --git a/doc/fix_nvt_asphere.txt b/doc/fix_nvt_asphere.txt
index 7909fee987ad53ec498dfc15c7a1c4d2d17483b6..e38b3ba71778c1a723b6fe1d6cd9419e458c3e1f 100755
--- a/doc/fix_nvt_asphere.txt
+++ b/doc/fix_nvt_asphere.txt
@@ -36,12 +36,11 @@ V is volume; T is temperature.  This creates a system trajectory
 consistent with the canonical ensemble.
 
 The desired temperature at each timestep is a ramped value during the
-run from {Tstart} to {Tstop}.  The "run"_run.html command documents
-how to make the ramping take place across multiple runs.  The {Tdamp}
-parameter is specified in time units and determines how rapidly the
-temperature is relaxed.  For example, a value of 100.0 means to relax
-the temperature in a timespan of (roughly) 100 time units (tau or
-fmsec or psec - see the "units"_units.html command).
+run from {Tstart} to {Tstop}.  The {Tdamp} parameter is specified in
+time units and determines how rapidly the temperature is relaxed.  For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+"units"_units.html command).
 
 In some cases (e.g. for solids) the temperature of the system can
 oscillate undesirably when a Nose/Hoover thermostat is applied.  The
@@ -72,19 +71,41 @@ This means you can change the attributes of this fix's temperature
 during thermodyanmic output via the "thermo_style
 custom"_thermo_style.html command using the appropriate compute-ID.
 It also means that changing attributes of {thermo_temp} will have no
-effect on this fix.  Alternatively, you can directly assign a new
-compute (for calculating temeperature) that you have defined to this
-fix via the "fix_modify"_fix_modify.html command.
+effect on this fix.
 
-This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the "fix_modify energy"_fix_modify.html option.  The contribution can
-also be printed by itself via the keyword {f_fix-ID} in the
-"thermo_style custom"_thermo_style.html command.
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+This fix writes the state of the Nose/Hoover thermostat to "binary
+restart files"_restart.html.  See the "read_restart"_read_restart.html
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+The "fix_modify"_fix_modify.html {temp} option is supported by this
+fix.  You can use it to assign a "compute"_compute.html you have
+defined to this fix which will be used in its thermostatting
+procedure.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting to
+the system's potential energy as part of "thermodynamic
+output"_thermo_style.html.
+
+The energy change can be printed as part of thermodynamic output via
+the keyword f_ID, where ID is the fix-ID of this fix.  See the
+"thermo_style custom"_thermo_style.html command for details.
+
+This fix can ramp its target temperature over multiple runs, using the
+{start} and {stop} keywords of the "run"_run.html command.  See the
+"run"_run.html command for details of how to do this.
+
+This fix is not invoked during "energy minimization"_minimize.html.
 
 [Restrictions:]
 
-Can only be used if LAMMPS was built with the "asphere" package.
+This fix is part of the "asphere" package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
 
 The final Tstop cannot be 0.0 since it would make the target T = 0.0
 at some timestep during the simulation which is not allowed in 
diff --git a/doc/fix_nvt_sllod.html b/doc/fix_nvt_sllod.html
index 61dc955787fdafa38cb063466104bbaaf9c7915c..1ee4502548aa9fc77fa8d0f267ec8d9f2aa0777b 100644
--- a/doc/fix_nvt_sllod.html
+++ b/doc/fix_nvt_sllod.html
@@ -71,12 +71,11 @@ discussed in <A HREF = "#Tuckerman">(Tuckerman)</A> (eqs 4 and 5), which is what
 implemented in LAMMPS in a velocity Verlet formulation.
 </P>
 <P>The desired temperature at each timestep is a ramped value during the
-run from <I>Tstart</I> to <I>Tstop</I>.  The <A HREF = "run.html">run</A> command documents
-how to make the ramping take place across multiple runs.  The <I>Tdamp</I>
-parameter is specified in time units and determines how rapidly the
-temperature is relaxed.  For example, a value of 100.0 means to relax
-the temperature in a timespan of (roughly) 100 time units (tau or
-fmsec or psec - see the <A HREF = "units.html">units</A> command).
+run from <I>Tstart</I> to <I>Tstop</I>.  The <I>Tdamp</I> parameter is specified in
+time units and determines how rapidly the temperature is relaxed.  For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+<A HREF = "units.html">units</A> command).
 </P>
 <P>In some cases (e.g. for solids) the temperature of the system can
 oscillate undesirably when a Nose/Hoover thermostat is applied.  The
@@ -107,15 +106,35 @@ This means you can change the attributes of this fix's temperature
 during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
 custom</A> command using the appropriate compute-ID.
 It also means that changing attributes of <I>thermo_temp</I> will have no
-effect on this fix.  Alternatively, you can directly assign a new
-compute (for calculating temeperature) that you have defined to this
-fix via the <A HREF = "fix_modify.html">fix_modify</A> command.
-</P>
-<P>This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the <A HREF = "fix_modify.html">fix_modify energy</A> option.  The contribution can
-also be printed by itself via the keyword <I>f_fix-ID</I> in the
-<A HREF = "thermo_style.html">thermo_style custom</A> command.
+effect on this fix.
+</P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary
+restart files</A>.  See the <A HREF = "read_restart.html">read_restart</A>
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
+fix.  You can use it to assign a <A HREF = "compute.html">compute</A> you have
+defined to this fix which will be used in its thermostatting
+procedure.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting to
+the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>The energy change can be printed as part of thermodynamic output via
+the keyword f_ID, where ID is the fix-ID of this fix.  See the
+<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
+</P>
+<P>This fix can ramp its target temperature over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command.  See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
 </P>
 <P><B>Restrictions:</B>
 </P>
diff --git a/doc/fix_nvt_sllod.txt b/doc/fix_nvt_sllod.txt
index d4896d95370e6cbb090f515f271dfd7c506cf173..f951f8c112dcedd0c90e0b99b6af24fe8818f79e 100644
--- a/doc/fix_nvt_sllod.txt
+++ b/doc/fix_nvt_sllod.txt
@@ -62,12 +62,11 @@ discussed in "(Tuckerman)"_#Tuckerman (eqs 4 and 5), which is what is
 implemented in LAMMPS in a velocity Verlet formulation.
 
 The desired temperature at each timestep is a ramped value during the
-run from {Tstart} to {Tstop}.  The "run"_run.html command documents
-how to make the ramping take place across multiple runs.  The {Tdamp}
-parameter is specified in time units and determines how rapidly the
-temperature is relaxed.  For example, a value of 100.0 means to relax
-the temperature in a timespan of (roughly) 100 time units (tau or
-fmsec or psec - see the "units"_units.html command).
+run from {Tstart} to {Tstop}.  The {Tdamp} parameter is specified in
+time units and determines how rapidly the temperature is relaxed.  For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+"units"_units.html command).
 
 In some cases (e.g. for solids) the temperature of the system can
 oscillate undesirably when a Nose/Hoover thermostat is applied.  The
@@ -98,15 +97,35 @@ This means you can change the attributes of this fix's temperature
 during thermodyanmic output via the "thermo_style
 custom"_thermo_style.html command using the appropriate compute-ID.
 It also means that changing attributes of {thermo_temp} will have no
-effect on this fix.  Alternatively, you can directly assign a new
-compute (for calculating temeperature) that you have defined to this
-fix via the "fix_modify"_fix_modify.html command.
-
-This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the "fix_modify energy"_fix_modify.html option.  The contribution can
-also be printed by itself via the keyword {f_fix-ID} in the
-"thermo_style custom"_thermo_style.html command.
+effect on this fix.
+
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+This fix writes the state of the Nose/Hoover thermostat to "binary
+restart files"_restart.html.  See the "read_restart"_read_restart.html
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+The "fix_modify"_fix_modify.html {temp} option is supported by this
+fix.  You can use it to assign a "compute"_compute.html you have
+defined to this fix which will be used in its thermostatting
+procedure.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the energy change induced by Nose/Hoover thermostatting to
+the system's potential energy as part of "thermodynamic
+output"_thermo_style.html.
+
+The energy change can be printed as part of thermodynamic output via
+the keyword f_ID, where ID is the fix-ID of this fix.  See the
+"thermo_style custom"_thermo_style.html command for details.
+
+This fix can ramp its target temperature over multiple runs, using the
+{start} and {stop} keywords of the "run"_run.html command.  See the
+"run"_run.html command for details of how to do this.
+
+This fix is not invoked during "energy minimization"_minimize.html.
 
 [Restrictions:]
 
diff --git a/doc/fix_orient_fcc.html b/doc/fix_orient_fcc.html
index 36ed72e7ac204ae60c1c3731d8b30ce8f57b5452..66fc8f7856756b4d8185b406b55edc9e61e5e491 100644
--- a/doc/fix_orient_fcc.html
+++ b/doc/fix_orient_fcc.html
@@ -116,11 +116,24 @@ symmetry, so the list must include one from each pair of
 equal-and-opposite neighbors.  A pair of orientation files for a
 Sigma=5 tilt boundary are show below.
 </P>
-<P>This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the <A HREF = "fix_modify.html">fix_modify energy</A> option.  The contribution can
-also be printed by itself via the keyword <I>f_fix-ID</I> in the
-<A HREF = "thermo_style.html">thermo_style custom</A> command.
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the potential energy of atom interactions with the grain
+boundary driving force to the system's potential energy as part of
+<A HREF = "thermo_style.html">thermodynamic output</A>.
+</P>
+<P>The atom/grain-boundary interaction energy can be printed as part of
+thermodynamic output via the keyword f_ID, where ID is the fix-ID of
+this fix.  See the <A HREF = "thermo_style.html">thermo_style custom</A> command for
+details.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
 </P>
 <P><B>Restrictions:</B>
 </P>
diff --git a/doc/fix_orient_fcc.txt b/doc/fix_orient_fcc.txt
index 44cfd3045a79be082744357b4372d0aaccb472c8..2f586125c5583cab6f455ebc898d560814c3b5ba 100644
--- a/doc/fix_orient_fcc.txt
+++ b/doc/fix_orient_fcc.txt
@@ -113,11 +113,24 @@ symmetry, so the list must include one from each pair of
 equal-and-opposite neighbors.  A pair of orientation files for a
 Sigma=5 tilt boundary are show below.
 
-This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the "fix_modify energy"_fix_modify.html option.  The contribution can
-also be printed by itself via the keyword {f_fix-ID} in the
-"thermo_style custom"_thermo_style.html command.
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the potential energy of atom interactions with the grain
+boundary driving force to the system's potential energy as part of
+"thermodynamic output"_thermo_style.html.
+
+The atom/grain-boundary interaction energy can be printed as part of
+thermodynamic output via the keyword f_ID, where ID is the fix-ID of
+this fix.  See the "thermo_style custom"_thermo_style.html command for
+details.
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
 
 [Restrictions:]
 
diff --git a/doc/fix_planeforce.html b/doc/fix_planeforce.html
index 438f75572f812ac59552cfd0ed656409bc8c2bb2..6560681e1a090e5102de26addb515e90695327bb 100644
--- a/doc/fix_planeforce.html
+++ b/doc/fix_planeforce.html
@@ -32,8 +32,17 @@ by subtracting out components of force perpendicular to the plane.
 <P>If the initial velocity of the atom is 0.0 (or in the plane), then it
 should continue to move in the plane thereafter.
 </P>
-<P>The forces due to this fix are also imposed during an energy
-minimization, invoked by the <A HREF = "minimize.html">minimize</A> command.
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.
 </P>
 <P><B>Restrictions:</B> none
 </P>
diff --git a/doc/fix_planeforce.txt b/doc/fix_planeforce.txt
index e584faec5240e89569c6418729d3ff8e5858ca60..134d3c6d50c5cc3b49f44505fa522bca77caf539 100644
--- a/doc/fix_planeforce.txt
+++ b/doc/fix_planeforce.txt
@@ -29,8 +29,17 @@ by subtracting out components of force perpendicular to the plane.
 If the initial velocity of the atom is 0.0 (or in the plane), then it
 should continue to move in the plane thereafter.
 
-The forces due to this fix are also imposed during an energy
-minimization, invoked by the "minimize"_minimize.html command.
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the "minimize"_minimize.html command.
 
 [Restrictions:] none
 
diff --git a/doc/fix_poems.html b/doc/fix_poems.html
index c6bc5521089baff9c11140c89a664c86d0998649..b1e7c5217386f122c73ddd7977599e2c6044fc11 100644
--- a/doc/fix_poems.html
+++ b/doc/fix_poems.html
@@ -110,9 +110,22 @@ body contribution to the pressure virial is also accounted for.  The
 latter is only correct if forces within the bodies have been turned
 off, and there is only a single fix poems defined.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B>
 </P>
-<P>Can only be used if LAMMPS was built with the "poems" package.
+<P>This fix is part of the "poems" package.  It is only enabled if LAMMPS
+was built with that package, which also requires the POEMS library be
+built and linked with LAMMPS.  See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS</A> section for more info.
 </P>
 <P><B>Related commands:</B>
 </P>
diff --git a/doc/fix_poems.txt b/doc/fix_poems.txt
index a814985d1e3ba6f190bb05fef59d22b6e8746391..3b0634dc52afaf9a1ab80a9c7d60a810eb5b19dd 100644
--- a/doc/fix_poems.txt
+++ b/doc/fix_poems.txt
@@ -103,9 +103,22 @@ body contribution to the pressure virial is also accounted for.  The
 latter is only correct if forces within the bodies have been turned
 off, and there is only a single fix poems defined.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:]
 
-Can only be used if LAMMPS was built with the "poems" package.
+This fix is part of the "poems" package.  It is only enabled if LAMMPS
+was built with that package, which also requires the POEMS library be
+built and linked with LAMMPS.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
 
 [Related commands:]
 
diff --git a/doc/fix_pour.html b/doc/fix_pour.html
index 422a340b081af00c7b2c2b4fe8946b1c51a474f3..55bf5442456b366a3dabf7a778b5b9eac1b27d05 100644
--- a/doc/fix_pour.html
+++ b/doc/fix_pour.html
@@ -101,9 +101,35 @@ completing all insertions, it prints a warning.
 or y direction (2d).  This enables pouring particles from a
 successively higher height over time.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  This means you must be careful when restarting a
+pouring simulation, when the restart file was written in the middle of
+the pouring operation.  Specifically, you should use a new fix pour
+command in the input script for the restarted simulation that
+continues the operation.  You will need to adjust the arguments of the
+original fix pour command to do this.
+</P>
+<P>Also note that because the state of the random number generator is not
+saved in restart files, you cannot do "exact" restarts with this fix,
+where the simulation continues on the same as if no restart had taken
+place.  However, in a statistical sense, a restarted simulation should
+produce the same behavior if you adjust the fix pour parameters
+appropriately.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix.  No quantities calculated by this fix can be output by the
+<A HREF = "thermo_style.html">thermo_style custom</A> command.  No parameter of this
+fix can be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A>
+command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B>
 </P>
-<P>Can only be used if LAMMPS was built with the "granular" package.
+<P>This fix is part of the "granular" package.  It is only enabled if
+LAMMPS was built with that package.  See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS</A> section for more info.
 </P>
 <P>For 3d simulations, a gravity fix in the -z direction must be defined
 for use in conjunction with this fix.  For 2d simulations, gravity
diff --git a/doc/fix_pour.txt b/doc/fix_pour.txt
index 499ba8aa4c80a8ff44544701fd5ccf8233e19a82..fd1044fbd484fc694ded6d4875a54f14384217f4 100644
--- a/doc/fix_pour.txt
+++ b/doc/fix_pour.txt
@@ -90,9 +90,35 @@ The {rate} option moves the insertion volume in the z direction (3d)
 or y direction (2d).  This enables pouring particles from a
 successively higher height over time.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  This means you must be careful when restarting a
+pouring simulation, when the restart file was written in the middle of
+the pouring operation.  Specifically, you should use a new fix pour
+command in the input script for the restarted simulation that
+continues the operation.  You will need to adjust the arguments of the
+original fix pour command to do this.
+
+Also note that because the state of the random number generator is not
+saved in restart files, you cannot do "exact" restarts with this fix,
+where the simulation continues on the same as if no restart had taken
+place.  However, in a statistical sense, a restarted simulation should
+produce the same behavior if you adjust the fix pour parameters
+appropriately.
+
+None of the "fix_modify"_fix_modify.html options are relevant to this
+fix.  No quantities calculated by this fix can be output by the
+"thermo_style custom"_thermo_style.html command.  No parameter of this
+fix can be used with the {start/stop} keywords of the "run"_run.html
+command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:]
 
-Can only be used if LAMMPS was built with the "granular" package.
+This fix is part of the "granular" package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
 
 For 3d simulations, a gravity fix in the -z direction must be defined
 for use in conjunction with this fix.  For 2d simulations, gravity
diff --git a/doc/fix_print.html b/doc/fix_print.html
index 6376baae681b3e6ac06b77837f68f25f71bf28e5..faec35aa710a8f0d6fdafc05ad0ad2da5c27430d 100644
--- a/doc/fix_print.html
+++ b/doc/fix_print.html
@@ -42,6 +42,16 @@ fix print line is output.  Equal-style variables can calculate complex
 formulas involving atom and group properties, mathematical operations,
 other variables, etc.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B>
 </P>
 <P>If <I>equal</I>-style variables are used which contain
diff --git a/doc/fix_print.txt b/doc/fix_print.txt
index f6bcfe1bb09ad4c8e20eeb458f213dd1c4ac72b7..d9f5f5e39ba0c472a2b987d8856eeea87603fb5d 100644
--- a/doc/fix_print.txt
+++ b/doc/fix_print.txt
@@ -39,6 +39,16 @@ fix print line is output.  Equal-style variables can calculate complex
 formulas involving atom and group properties, mathematical operations,
 other variables, etc.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:]
 
 If {equal}-style variables are used which contain
diff --git a/doc/fix_rdf.html b/doc/fix_rdf.html
index 53897154f5714b45faea25c86c292612353b6dfd..71c25a42688e801ad8d8a9940ab588a06edc4305 100644
--- a/doc/fix_rdf.html
+++ b/doc/fix_rdf.html
@@ -48,6 +48,16 @@ factor is set by the <A HREF = "special_bonds.html">special_bonds</A> command.
 <P>The RDF statistics for each timestep are written to the specified
 file, as are the RDF values averaged over all timesteps.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B>
 </P>
 <P>The RDF is not computed for distances longer than the force cutoff,
diff --git a/doc/fix_rdf.txt b/doc/fix_rdf.txt
index 9716efadad4a43f6b2b44355363ac03dd4450a9e..e4b52a59baa27dfd7c87f9efee2872b3f89d44bd 100644
--- a/doc/fix_rdf.txt
+++ b/doc/fix_rdf.txt
@@ -45,6 +45,16 @@ factor is set by the "special_bonds"_special_bonds.html command.
 The RDF statistics for each timestep are written to the specified
 file, as are the RDF values averaged over all timesteps.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:]
 
 The RDF is not computed for distances longer than the force cutoff,
diff --git a/doc/fix_recenter.html b/doc/fix_recenter.html
index f6b1a05df55340a1a13a04a2490a858401d51bbd..c467b2920702afac31acb1a6821d5ddf86722cb0 100644
--- a/doc/fix_recenter.html
+++ b/doc/fix_recenter.html
@@ -82,6 +82,16 @@ the input script, since the adjustments it makes to atom coordinates
 should come after the changes made by time integration.  LAMMPS will
 warn you if your fixes are not ordered this way.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B>
 </P>
 <P>This fix should not be used with an x,y,z setting that causes a large
diff --git a/doc/fix_recenter.txt b/doc/fix_recenter.txt
index cc8bdf7a2edbf99c5620fd472f8f0c9214a0c3bf..a9d7809208c5978dfec495e1a54e58f523fca7a7 100644
--- a/doc/fix_recenter.txt
+++ b/doc/fix_recenter.txt
@@ -74,6 +74,16 @@ the input script, since the adjustments it makes to atom coordinates
 should come after the changes made by time integration.  LAMMPS will
 warn you if your fixes are not ordered this way.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:]
 
 This fix should not be used with an x,y,z setting that causes a large
diff --git a/doc/fix_rigid.html b/doc/fix_rigid.html
index 8f9de65346f69493670f13cb8238ff6ded1dbd5a..e6a4d232a47a8387baa7674e29dcb01d77f762b1 100644
--- a/doc/fix_rigid.html
+++ b/doc/fix_rigid.html
@@ -87,6 +87,16 @@ effectively immersed in an implicit solvent, i.e. a Brownian dynamics
 model.  Or you can thermostat additional atoms of an explicit solvent
 directly.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B>
 </P>
 <P>This fix performs an MPI_Allreduce each timestep that is proportional
diff --git a/doc/fix_rigid.txt b/doc/fix_rigid.txt
index 34a7fba925b51369d96cc74d50fc91676bbbb7cd..468114d81f268b9cfed099d9676ffa18106c6fe6 100644
--- a/doc/fix_rigid.txt
+++ b/doc/fix_rigid.txt
@@ -80,6 +80,16 @@ effectively immersed in an implicit solvent, i.e. a Brownian dynamics
 model.  Or you can thermostat additional atoms of an explicit solvent
 directly.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:]
 
 This fix performs an MPI_Allreduce each timestep that is proportional
diff --git a/doc/fix_setforce.html b/doc/fix_setforce.html
index 77083a54a9a0752cc1a1b8b21d1954d6457ca570..1d68b32c0e9154adc39bbc56f91abc128fe23bdb 100644
--- a/doc/fix_setforce.html
+++ b/doc/fix_setforce.html
@@ -35,17 +35,27 @@ force, assuming their initial velocity zero.
 <P>Any of the fx,fy,fz values can be specified as NULL which means do not
 alter the force component in that dimension.
 </P>
-<P>The forces due to this fix are also imposed during an energy
-minimization, invoked by the <A HREF = "minimize.html">minimize</A> command.
-</P>
-<P>The total force on the group of atoms before it is reset is stored by
-the fix and its components can be accessed during thermodynamic
-print-out by using f_ID[N] where ID = he fix-ID and N = 1,2,3.  See
-the <A HREF = "thermo_style.html">thermo_style custom</A> command for details.  Note
-that the fix stores the total force on the group of atoms, but the
-printed value may be normalized by the total number of atoms in the
-simulation depending on the <A HREF = "thermo_modify.html">thermo_modify norm</A>
-option you are using.
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>The total vector force on the group of atoms before it is reset is
+stored by the fix and its components can be printed as part of
+thermodynamic output via the keywords f_ID[N] where ID is the fix-ID
+of this fix and N = 1,2,3.  See the <A HREF = "thermo_style.html">thermo_style
+custom</A> command for details.  Note that the fix
+stores the total force on the group of atoms, but the printed value
+may be normalized by the total number of atoms in the simulation
+depending on the <A HREF = "thermo_modify.html">thermo_modify norm</A> option being
+used.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.
 </P>
 <P><B>Restrictions:</B> none
 </P>
diff --git a/doc/fix_setforce.txt b/doc/fix_setforce.txt
index 5cef6a4cebd9c531db01293fed0d0560bf7aed11..6c2180792a2292484f18ca37a39365fef7974b51 100644
--- a/doc/fix_setforce.txt
+++ b/doc/fix_setforce.txt
@@ -32,17 +32,27 @@ force, assuming their initial velocity zero.
 Any of the fx,fy,fz values can be specified as NULL which means do not
 alter the force component in that dimension.
 
-The forces due to this fix are also imposed during an energy
-minimization, invoked by the "minimize"_minimize.html command.
-
-The total force on the group of atoms before it is reset is stored by
-the fix and its components can be accessed during thermodynamic
-print-out by using f_ID\[N\] where ID = he fix-ID and N = 1,2,3.  See
-the "thermo_style custom"_thermo_style.html command for details.  Note
-that the fix stores the total force on the group of atoms, but the
-printed value may be normalized by the total number of atoms in the
-simulation depending on the "thermo_modify norm"_thermo_modify.html
-option you are using.
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.
+
+The total vector force on the group of atoms before it is reset is
+stored by the fix and its components can be printed as part of
+thermodynamic output via the keywords f_ID\[N\] where ID is the fix-ID
+of this fix and N = 1,2,3.  See the "thermo_style
+custom"_thermo_style.html command for details.  Note that the fix
+stores the total force on the group of atoms, but the printed value
+may be normalized by the total number of atoms in the simulation
+depending on the "thermo_modify norm"_thermo_modify.html option being
+used.
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the "minimize"_minimize.html command.
 
 [Restrictions:] none
 
diff --git a/doc/fix_shake.html b/doc/fix_shake.html
index 1315ddbc554dc36a9391c9df15645d7dc65b9890..c1e8870d4183cf1b15dacdd8ee0ef92c66bfd92f 100644
--- a/doc/fix_shake.html
+++ b/doc/fix_shake.html
@@ -85,6 +85,16 @@ in the bond are in the group specified with the SHAKE fix.
 for in temperature and pressure computations.  Similarly, the SHAKE
 contribution to the pressure virial is also accounted for.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B>
 </P>
 <P>For computational efficiency, there can only be one shake fix defined
diff --git a/doc/fix_shake.txt b/doc/fix_shake.txt
index 86f32d1588fb778c6373b731a1c402fe344174e6..3ce8e1f8b2e52d536e723e0ca40c5995d7af62fc 100644
--- a/doc/fix_shake.txt
+++ b/doc/fix_shake.txt
@@ -74,6 +74,16 @@ The degrees-of-freedom removed by SHAKE bonds and angles are accounted
 for in temperature and pressure computations.  Similarly, the SHAKE
 contribution to the pressure virial is also accounted for.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:]
 
 For computational efficiency, there can only be one shake fix defined
diff --git a/doc/fix_spring.html b/doc/fix_spring.html
index 1016420171af3bd14af5a31bb357ec26a1dc5186..689ead3fcaa072e2208a862005305227f8bcdedd 100644
--- a/doc/fix_spring.html
+++ b/doc/fix_spring.html
@@ -91,6 +91,16 @@ below the z = 0 center plane of the pore (umbrella sampling).  The
 last example holds the ion a distance 5 away from the pore axis
 (assuming the center-of-mass of the pore in x,y is the pore axis).
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
diff --git a/doc/fix_spring.txt b/doc/fix_spring.txt
index e05af0e1fdd976662bbbd7cbeae140a43f0ec33f..cfe2c6c00cbce9434db699a040df9f06e7417bf9 100644
--- a/doc/fix_spring.txt
+++ b/doc/fix_spring.txt
@@ -84,6 +84,16 @@ below the z = 0 center plane of the pore (umbrella sampling).  The
 last example holds the ion a distance 5 away from the pore axis
 (assuming the center-of-mass of the pore in x,y is the pore axis).
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] none
 
 [Related commands:]
diff --git a/doc/fix_spring_rg.html b/doc/fix_spring_rg.html
index 13f51832d306f24267f8cf975f5b5209159f9af9..d42648e5e2255cebb3c15e672250dfbc60f06f14 100644
--- a/doc/fix_spring_rg.html
+++ b/doc/fix_spring_rg.html
@@ -50,6 +50,16 @@ for the aggregate force on the group of atoms, not a per-atom force.
 <P>If RG0 is specified as NULL, then the RG of the group is computed at
 the time the fix is specified, and that value is used as the target.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
diff --git a/doc/fix_spring_rg.txt b/doc/fix_spring_rg.txt
index e8561b260c2e70b161a1aa41784de1286302ccbc..5dafee6f980367d025488d99d5bcfd0874a25622 100644
--- a/doc/fix_spring_rg.txt
+++ b/doc/fix_spring_rg.txt
@@ -46,6 +46,16 @@ for the aggregate force on the group of atoms, not a per-atom force.
 If RG0 is specified as NULL, then the RG of the group is computed at
 the time the fix is specified, and that value is used as the target.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] none
 
 [Related commands:]
diff --git a/doc/fix_spring_self.html b/doc/fix_spring_self.html
index 1028781c825c34a238363a9d4fec291cc1924c1f..9f0c1d4f4c51cc379e5ae187420376766052033c 100644
--- a/doc/fix_spring_self.html
+++ b/doc/fix_spring_self.html
@@ -32,6 +32,22 @@ the magnitude of the force on each atom is -Kr, where r is the
 displacement of the atom from its current position to its initial
 position.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the original coordinates of tethered atoms to <A HREF = "restart.html">binary
+restart files</A>, so that the spring effect will be the
+same in a restarted simulation.  See the
+<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix.  No quantities calculated by this fix can be output by the
+<A HREF = "thermo_style.html">thermo_style custom</A> command.  No parameter of this
+fix can be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A>
+command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
diff --git a/doc/fix_spring_self.txt b/doc/fix_spring_self.txt
index b221e7f81bddf926b552e45cf487dbd2ea7d4b14..466525d5ed8eb88fe2e6f4ca60cbc29996d39c9f 100644
--- a/doc/fix_spring_self.txt
+++ b/doc/fix_spring_self.txt
@@ -29,6 +29,22 @@ the magnitude of the force on each atom is -Kr, where r is the
 displacement of the atom from its current position to its initial
 position.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+This fix writes the original coordinates of tethered atoms to "binary
+restart files"_restart.html, so that the spring effect will be the
+same in a restarted simulation.  See the
+"read_restart"_read_restart.html command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+
+None of the "fix_modify"_fix_modify.html options are relevant to this
+fix.  No quantities calculated by this fix can be output by the
+"thermo_style custom"_thermo_style.html command.  No parameter of this
+fix can be used with the {start/stop} keywords of the "run"_run.html
+command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] none
 
 [Related commands:]
diff --git a/doc/fix_temp_rescale.html b/doc/fix_temp_rescale.html
index d5531cfb12d987cf34edb3db443f43c283bbffaf..7f84d702fe62ce92a5d8041ffb10a01ac10d45db 100644
--- a/doc/fix_temp_rescale.html
+++ b/doc/fix_temp_rescale.html
@@ -38,8 +38,7 @@ their velocities.
 </P>
 <P>Rescaling is performed every N timesteps.  The target temperature is a
 ramped value between the <I>Tstart</I> and <I>Tstop</I> temperatures at the
-beginning and end of the run.  The <A HREF = "run.html">run</A> command documents
-how to make the ramping take place across multiple runs.
+beginning and end of the run.
 </P>
 <P>Rescaling is only performed if the difference between the current and
 desired temperatures is greater than the <I>window</I> value.  The amount
@@ -80,20 +79,37 @@ This means you can change the attributes of this fix's temperature
 during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
 custom</A> command using the appropriate compute-ID.
 It also means that changing attributes of <I>thermo_temp</I> will have no
-effect on this fix.  Alternatively, you can directly assign a new
-compute (for calculating temeperature) that you have defined to this
-fix via the <A HREF = "fix_modify.html">fix_modify</A> command.  For consistency, if
-using the keyword <I>region</I>, the compute you assign should also be of
-style <I>temp/region</I>.
-</P>
-<P>This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the <A HREF = "fix_modify.html">fix_modify energy</A> option.  The contribution can
-also be printed by itself via the keyword <I>f_fix-ID</I> in the
-<A HREF = "thermo_style.html">thermo_style custom</A> command.  Note that because
-this fix is invoked every N steps and thermodynamic info may be
-printed every M steps, that unless M is a multiple of N, the energy
-info accessed will not be for the current timestep.
+effect on this fix.
+</P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
+fix.  You can use it to assign a <A HREF = "compute.html">compute</A> you have
+defined to this fix which will be used in its thermostatting
+procedure.  For consistency, if using the keyword <I>region</I>, the
+compute you assign should also be of style
+<A HREF = "compute_temp_region.html">temp/region</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy change implied by a velocity rescaling to the
+system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.  Note that because this fix is invoked
+every N steps and thermodynamic info is printed every M steps, that
+unless M is a multiple of N, the energy contribution will not be for
+the current timestep.
+</P>
+<P>The energy change can be printed as part of thermodynamic output via
+the keyword f_ID, where ID is the fix-ID of this fix.  See the
+<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
+</P>
+<P>This fix can ramp its target temperature over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command.  See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
 </P>
 <P><B>Restrictions:</B> none
 </P>
diff --git a/doc/fix_temp_rescale.txt b/doc/fix_temp_rescale.txt
index 871ad50ceee581168d295aacf6c06048be91c902..9ae3d08d628bdfcbda8c6979043c4d742e900a7a 100644
--- a/doc/fix_temp_rescale.txt
+++ b/doc/fix_temp_rescale.txt
@@ -34,8 +34,7 @@ their velocities.
 
 Rescaling is performed every N timesteps.  The target temperature is a
 ramped value between the {Tstart} and {Tstop} temperatures at the
-beginning and end of the run.  The "run"_run.html command documents
-how to make the ramping take place across multiple runs.
+beginning and end of the run.
 
 Rescaling is only performed if the difference between the current and
 desired temperatures is greater than the {window} value.  The amount
@@ -76,20 +75,37 @@ This means you can change the attributes of this fix's temperature
 during thermodyanmic output via the "thermo_style
 custom"_thermo_style.html command using the appropriate compute-ID.
 It also means that changing attributes of {thermo_temp} will have no
-effect on this fix.  Alternatively, you can directly assign a new
-compute (for calculating temeperature) that you have defined to this
-fix via the "fix_modify"_fix_modify.html command.  For consistency, if
-using the keyword {region}, the compute you assign should also be of
-style {temp/region}.
-
-This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the "fix_modify energy"_fix_modify.html option.  The contribution can
-also be printed by itself via the keyword {f_fix-ID} in the
-"thermo_style custom"_thermo_style.html command.  Note that because
-this fix is invoked every N steps and thermodynamic info may be
-printed every M steps, that unless M is a multiple of N, the energy
-info accessed will not be for the current timestep.
+effect on this fix.
+
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html {temp} option is supported by this
+fix.  You can use it to assign a "compute"_compute.html you have
+defined to this fix which will be used in its thermostatting
+procedure.  For consistency, if using the keyword {region}, the
+compute you assign should also be of style
+"temp/region"_compute_temp_region.html.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the energy change implied by a velocity rescaling to the
+system's potential energy as part of "thermodynamic
+output"_thermo_style.html.  Note that because this fix is invoked
+every N steps and thermodynamic info is printed every M steps, that
+unless M is a multiple of N, the energy contribution will not be for
+the current timestep.
+
+The energy change can be printed as part of thermodynamic output via
+the keyword f_ID, where ID is the fix-ID of this fix.  See the
+"thermo_style custom"_thermo_style.html command for details.
+
+This fix can ramp its target temperature over multiple runs, using the
+{start} and {stop} keywords of the "run"_run.html command.  See the
+"run"_run.html command for details of how to do this.
+
+This fix is not invoked during "energy minimization"_minimize.html.
 
 [Restrictions:] none
 
diff --git a/doc/fix_tmd.html b/doc/fix_tmd.html
index 7df6e41b6f6f8e2cd22e02586abbc6aa3ca408f6..c5ddf6755dd4db962fef125c696e4e68f3b8fe13 100644
--- a/doc/fix_tmd.html
+++ b/doc/fix_tmd.html
@@ -33,8 +33,7 @@ fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file
 holonomic constraint is used to force the atoms to move towards (or
 away from) the target configuration.  The parameter "rho" is
 monotonically decreased (or increased) from its initial value to
-rho_final at the end of the run.  The <A HREF = "run.html">run</A> command documents
-how to make the ramping take place across multiple runs.
+rho_final at the end of the run.
 </P>
 <P>Rho has distance units and is a measure of the root-mean-squared
 distance (RMSD) between the current configuration of the atoms in the
@@ -88,6 +87,19 @@ to prevent it being overwritten.
 <P>For more information about TMD, see <A HREF = "#Schlitter1">(Schlitter1)</A> and
 <A HREF = "#Schlitter2">(Schlitter2)</A>.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.
+</P>
+<P>This fix can ramp its rho parameter over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command.  See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
 <P><B>Restrictions:</B>
 </P>
 <P>All TMD fixes must be listed in the input script after all integrator
diff --git a/doc/fix_tmd.txt b/doc/fix_tmd.txt
index 6f51d792dcb76e45b050ba6194b6a0a922cfccf3..bd7096f5064e10db2f3143bf4bdc36e8937e3e3f 100644
--- a/doc/fix_tmd.txt
+++ b/doc/fix_tmd.txt
@@ -30,8 +30,7 @@ Perform targeted molecular dynamics (TMD) on a group of atoms.  A
 holonomic constraint is used to force the atoms to move towards (or
 away from) the target configuration.  The parameter "rho" is
 monotonically decreased (or increased) from its initial value to
-rho_final at the end of the run.  The "run"_run.html command documents
-how to make the ramping take place across multiple runs.
+rho_final at the end of the run.
 
 Rho has distance units and is a measure of the root-mean-squared
 distance (RMSD) between the current configuration of the atoms in the
@@ -85,6 +84,19 @@ to prevent it being overwritten.
 For more information about TMD, see "(Schlitter1)"_#Schlitter1 and
 "(Schlitter2)"_#Schlitter2.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.
+
+This fix can ramp its rho parameter over multiple runs, using the
+{start} and {stop} keywords of the "run"_run.html command.  See the
+"run"_run.html command for details of how to do this.
+
+This fix is not invoked during "energy minimization"_minimize.html.
+
 [Restrictions:]
 
 All TMD fixes must be listed in the input script after all integrator
diff --git a/doc/fix_viscous.html b/doc/fix_viscous.html
index 81efb9797d63b4b66bf544ad214ebe8520e6b414..c536a974e90b1b4792a5f37fb063190e52c4d3c6 100644
--- a/doc/fix_viscous.html
+++ b/doc/fix_viscous.html
@@ -75,6 +75,16 @@ langevin</A> command adds both a viscous damping term
 and this random force to each atom; hence if using fix <I>langevin</I> you
 do not typically need to use fix <I>viscous</I>.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
diff --git a/doc/fix_viscous.txt b/doc/fix_viscous.txt
index f9b96826cd0e3479cd84e4964c02c44d70beac0c..bec27a7054466a31a05620a520dbd4fa20b58483 100644
--- a/doc/fix_viscous.txt
+++ b/doc/fix_viscous.txt
@@ -65,6 +65,16 @@ langevin"_fix_langevin.html command adds both a viscous damping term
 and this random force to each atom; hence if using fix {langevin} you
 do not typically need to use fix {viscous}.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] none
 
 [Related commands:]
diff --git a/doc/fix_wall_gran.html b/doc/fix_wall_gran.html
index 482e1639069aa562805f7f667425db1a54fb55c9..a57b6e4c2a601742e951cbf41fea02f88503f666 100644
--- a/doc/fix_wall_gran.html
+++ b/doc/fix_wall_gran.html
@@ -77,13 +77,32 @@ the <I>amplitude</I>, <I>omega</I> is 2 PI / <I>period</I>, and <I>delta</I> is
 elapsed time since the fix was specified.  The velocity of the wall is
 also set to the derivative of this expression.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>This fix writes the shear friction state of atoms interacting with the
+wall to <A HREF = "restart.html">binary restart files</A>, so that a simulation can
+continue correctly if granular potentials with shear "history" effects
+are being used.  See the <A HREF = "read_restart.html">read_restart</A> command for
+info on how to re-specify a fix in an input script that reads a
+restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+</P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix.  No quantities calculated by this fix can be output by the
+<A HREF = "thermo_style.html">thermo_style custom</A> command.  No parameter of this
+fix can be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A>
+command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B>
 </P>
+<P>This fix is part of the "granular" package.  It is only enabled if
+LAMMPS was built with that package.  See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS</A> section for more info.
+</P>
 <P>Any dimension (xyz) that has a granular wall must be non-periodic.
 </P>
-<P>This fix can only be used if LAMMPS was built with the "granular"
-package and with atom_style granular.  A zcylinder wall can only be
-oscillated in the z dimension.
+<P>A zcylinder wall can only be oscillated in the z dimension.
 </P>
 <P><B>Related commands:</B>
 </P>
diff --git a/doc/fix_wall_gran.txt b/doc/fix_wall_gran.txt
index c5b36bd8b3230933d8ea2f8cc2155307482f720b..2f6c31ff141bed07da53c596b1664ef98d8cc301 100644
--- a/doc/fix_wall_gran.txt
+++ b/doc/fix_wall_gran.txt
@@ -67,13 +67,32 @@ the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the
 elapsed time since the fix was specified.  The velocity of the wall is
 also set to the derivative of this expression.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+This fix writes the shear friction state of atoms interacting with the
+wall to "binary restart files"_restart.html, so that a simulation can
+continue correctly if granular potentials with shear "history" effects
+are being used.  See the "read_restart"_read_restart.html command for
+info on how to re-specify a fix in an input script that reads a
+restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+None of the "fix_modify"_fix_modify.html options are relevant to this
+fix.  No quantities calculated by this fix can be output by the
+"thermo_style custom"_thermo_style.html command.  No parameter of this
+fix can be used with the {start/stop} keywords of the "run"_run.html
+command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:]
 
+This fix is part of the "granular" package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
+
 Any dimension (xyz) that has a granular wall must be non-periodic.
 
-This fix can only be used if LAMMPS was built with the "granular"
-package and with atom_style granular.  A zcylinder wall can only be
-oscillated in the z dimension.
+A zcylinder wall can only be oscillated in the z dimension.
 
 [Related commands:]
 
diff --git a/doc/fix_wall_lj126.html b/doc/fix_wall_lj126.html
index 512552fc0c10d2232dedf1fe72a1dbc1773ddc84..46dae8478f7222f70250badc3e9e9450ab004d04 100644
--- a/doc/fix_wall_lj126.html
+++ b/doc/fix_wall_lj126.html
@@ -44,17 +44,31 @@ provided by the <A HREF = "fix_wall_lj93.html">fix wall/lj93</A> command.
 <P>The wall potential is shifted so that the energy of a wall-particle
 interaction is 0.0 at the cutoff distance.
 </P>
-<P>This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the <A HREF = "fix_modify.html">fix_modify energy</A> option.  The contribution can
-also be printed by itself via the keyword <I>f_fix-ID</I> in the
-<A HREF = "thermo_style.html">thermo_style custom</A> command.
-</P>
-<P>The forces due to this fix are also imposed during an energy
-minimization, invoked by the <A HREF = "minimize.html">minimize</A> command.  If you
-want that energy to be included in the total potential energy of the
-system (the quantity being minimized), you must enable the
-<A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for this fix.
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy of interaction between atoms and the wall to the
+system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>The atom/wall interaction energy can be printed as part of
+thermodynamic output via the keyword f_ID, where ID is the fix-ID of
+this fix.  See the <A HREF = "thermo_style.html">thermo_style custom</A> command for
+details.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.
+</P>
+<P>IMPORTANT NOTE: If you want the atom/wall interaction energy to be
+included in the total potential energy of the system (the quantity
+being minimized), you MUST enable the <A HREF = "fix_modify.html">fix_modify</A>
+<I>energy</I> option for this fix.
 </P>
 <P><B>Restrictions:</B>
 </P>
diff --git a/doc/fix_wall_lj126.txt b/doc/fix_wall_lj126.txt
index 23a269298be2cefac3b5974df86f15aef20db3e7..3bb4f103370ba33e672510ccfbd74dccfeb35261 100644
--- a/doc/fix_wall_lj126.txt
+++ b/doc/fix_wall_lj126.txt
@@ -41,17 +41,31 @@ provided by the "fix wall/lj93"_fix_wall_lj93.html command.
 The wall potential is shifted so that the energy of a wall-particle
 interaction is 0.0 at the cutoff distance.
 
-This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the "fix_modify energy"_fix_modify.html option.  The contribution can
-also be printed by itself via the keyword {f_fix-ID} in the
-"thermo_style custom"_thermo_style.html command.
-
-The forces due to this fix are also imposed during an energy
-minimization, invoked by the "minimize"_minimize.html command.  If you
-want that energy to be included in the total potential energy of the
-system (the quantity being minimized), you must enable the
-"fix_modify"_fix_modify.html {energy} option for this fix.
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the energy of interaction between atoms and the wall to the
+system's potential energy as part of "thermodynamic
+output"_thermo_style.html.
+
+The atom/wall interaction energy can be printed as part of
+thermodynamic output via the keyword f_ID, where ID is the fix-ID of
+this fix.  See the "thermo_style custom"_thermo_style.html command for
+details.
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the "minimize"_minimize.html command.
+
+IMPORTANT NOTE: If you want the atom/wall interaction energy to be
+included in the total potential energy of the system (the quantity
+being minimized), you MUST enable the "fix_modify"_fix_modify.html
+{energy} option for this fix.
 
 [Restrictions:]
 
diff --git a/doc/fix_wall_lj93.html b/doc/fix_wall_lj93.html
index d60ecc30bc02b89880993d6ff53c5c69c3d0f978..116fa5ddeff88f22b9b5c930d6dcef4b4ac4d992 100644
--- a/doc/fix_wall_lj93.html
+++ b/doc/fix_wall_lj93.html
@@ -45,17 +45,31 @@ wall/lj126</A> command.
 <P>The wall potential is shifted so that the energy of a wall-particle
 interaction is 0.0 at the cutoff distance.
 </P>
-<P>This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the <A HREF = "fix_modify.html">fix_modify energy</A> option.  The contribution can
-also be printed by itself via the keyword <I>f_fix-ID</I> in the
-<A HREF = "thermo_style.html">thermo_style custom</A> command.
-</P>
-<P>The forces due to this fix are also imposed during an energy
-minimization, invoked by the <A HREF = "minimize.html">minimize</A> command.  If you
-want that energy to be included in the total potential energy of the
-system (the quantity being minimized), you must enable the
-<A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for this fix.
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the energy of interaction between atoms and the wall to the
+system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>The atom/wall interaction energy can be printed as part of
+thermodynamic output via the keyword f_ID, where ID is the fix-ID of
+this fix.  See the <A HREF = "thermo_style.html">thermo_style custom</A> command for
+details.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+invoked by the <A HREF = "minimize.html">minimize</A> command.
+</P>
+<P>IMPORTANT NOTE: If you want the atom/wall interaction energy to be
+included in the total potential energy of the system (the quantity
+being minimized), you MUST enable the <A HREF = "fix_modify.html">fix_modify</A>
+<I>energy</I> option for this fix.
 </P>
 <P><B>Restrictions:</B>
 </P>
diff --git a/doc/fix_wall_lj93.txt b/doc/fix_wall_lj93.txt
index a859c8668894244c2abd26ab6d204ad3e6c23678..49fb34872ab56110ee8e319ee4e5a40947faaf9d 100644
--- a/doc/fix_wall_lj93.txt
+++ b/doc/fix_wall_lj93.txt
@@ -42,17 +42,31 @@ wall/lj126"_fix_wall_lj126.html command.
 The wall potential is shifted so that the energy of a wall-particle
 interaction is 0.0 at the cutoff distance.
 
-This fix makes a contribution to the potential energy of the system
-that can be included in thermodynamic output of potential energy using
-the "fix_modify energy"_fix_modify.html option.  The contribution can
-also be printed by itself via the keyword {f_fix-ID} in the
-"thermo_style custom"_thermo_style.html command.
-
-The forces due to this fix are also imposed during an energy
-minimization, invoked by the "minimize"_minimize.html command.  If you
-want that energy to be included in the total potential energy of the
-system (the quantity being minimized), you must enable the
-"fix_modify"_fix_modify.html {energy} option for this fix.
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the energy of interaction between atoms and the wall to the
+system's potential energy as part of "thermodynamic
+output"_thermo_style.html.
+
+The atom/wall interaction energy can be printed as part of
+thermodynamic output via the keyword f_ID, where ID is the fix-ID of
+this fix.  See the "thermo_style custom"_thermo_style.html command for
+details.
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the "minimize"_minimize.html command.
+
+IMPORTANT NOTE: If you want the atom/wall interaction energy to be
+included in the total potential energy of the system (the quantity
+being minimized), you MUST enable the "fix_modify"_fix_modify.html
+{energy} option for this fix.
 
 [Restrictions:]
 
diff --git a/doc/fix_wall_reflect.html b/doc/fix_wall_reflect.html
index d592c7691a886e93407912fddd9fbca250574140..85c644b02c2594fd6a5d434ca46b3d2b4f686c66 100644
--- a/doc/fix_wall_reflect.html
+++ b/doc/fix_wall_reflect.html
@@ -43,6 +43,16 @@ in the input script, since the adjustments it makes to atom
 coordinates should come after the changes made by time integration.
 LAMMPS will warn you if your fixes are not ordered this way.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B>
 </P>
 <P>Any dimension (xyz) that has a reflecting wall must be non-periodic.
diff --git a/doc/fix_wall_reflect.txt b/doc/fix_wall_reflect.txt
index 330b172f67cd9dd5e373288c41474ad16b07653c..334a3229eac0bdeebd205107bf4e1e96339e740b 100644
--- a/doc/fix_wall_reflect.txt
+++ b/doc/fix_wall_reflect.txt
@@ -40,6 +40,16 @@ in the input script, since the adjustments it makes to atom
 coordinates should come after the changes made by time integration.
 LAMMPS will warn you if your fixes are not ordered this way.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:]
 
 Any dimension (xyz) that has a reflecting wall must be non-periodic.
diff --git a/doc/fix_wiggle.html b/doc/fix_wiggle.html
index aefff2ec10eed2f15411226d2a5b7823f2292b2c..422b63a3cd771c708ff1e37f2475ad00975e2a5b 100644
--- a/doc/fix_wiggle.html
+++ b/doc/fix_wiggle.html
@@ -40,6 +40,16 @@ the <I>dim</I> coordinate of each atom is set to
 elapsed time since the fix was specified.  The velocity of the atom is
 set to the derivative of this expression.
 </P>
+<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.  No
+parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B> none
diff --git a/doc/fix_wiggle.txt b/doc/fix_wiggle.txt
index 6f82cd7b2215c9a121777b01d343d30e0e570ea6..a4f9dcdd5d27a97c83c9380c4efcceaa2f74da57 100644
--- a/doc/fix_wiggle.txt
+++ b/doc/fix_wiggle.txt
@@ -37,6 +37,16 @@ where {coord0} is the coordinate at the time the fix was specified,
 elapsed time since the fix was specified.  The velocity of the atom is
 set to the derivative of this expression.
 
+[Restart, fix_modify, thermo output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No quantities calculated by this fix can be
+output by the "thermo_style custom"_thermo_style.html command.  No
+parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
 [Restrictions:] none
 
 [Related commands:] none
diff --git a/doc/improper_class2.txt b/doc/improper_class2.txt
index f5390e56a28bbc8be5847a4ea701096a3dd37bcd..5e27bb6aa2c1646aeef6f74ed66e898303e882dd 100644
--- a/doc/improper_class2.txt
+++ b/doc/improper_class2.txt
@@ -36,8 +36,8 @@ The following coefficients must be defined for each improper type via the
 the data file or restart files read by the "read_data"_read_data.html
 or "read_restart"_read_restart.html commands:
 
-For this style, only coefficients for the Ei formula can be specified
-in the input script.  These are the 2 coefficients:
+For this style, coefficients for the Ei formula can be specified in
+eiher the input script or data file.  These are the 2 coefficients:
 
 K (energy/radian^2)
 X0 (degrees) :ul
@@ -45,8 +45,8 @@ X0 (degrees) :ul
 X0 is specified in degrees, but LAMMPS converts it to radians
 internally; hence the units of K are in energy/radian^2.
 
-Coefficients for the Eaa formula must be specified in the data file.
-For the Eaa formula, the coefficients are listed under a
+Coefficients for the Eaa formula can only be specified in the data
+file.  For the Eaa formula, the coefficients are listed under a
 "AngleAngle Coeffs" heading and each line lists 6 coefficients:
 
 M1 (energy/distance)
@@ -61,9 +61,9 @@ radians internally; hence the units of M are in energy/radian^2.
 
 [Restrictions:]
 
-This improper style is part of the "class2" package.  It is only
-enabled if LAMMPS was built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
+This improper style can only be used if LAMMPS was built with the
+"class2" package.  See the "Making LAMMPS"_Section_start.html#2_3
+section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/improper_cvff.txt b/doc/improper_cvff.txt
index d47660d79fa09e952f08c44187a6233dba1c160e..ddec5bcfe70f55c9378418769b868663b42a739e 100644
--- a/doc/improper_cvff.txt
+++ b/doc/improper_cvff.txt
@@ -34,7 +34,11 @@ K (energy)
 d (+1 or -1)
 n (0,1,2,3,4,6) :ul
 
-[Restrictions:] none
+[Restrictions:]
+
+This improper style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/improper_harmonic.txt b/doc/improper_harmonic.txt
index a5567428e1c4667ae41f1da84e46b1a880dde759..9b66c35ec716e9e286cf138f6850aebe553ae25c 100644
--- a/doc/improper_harmonic.txt
+++ b/doc/improper_harmonic.txt
@@ -37,7 +37,11 @@ X0 (degrees) :ul
 X0 is specified in degrees, but LAMMPS converts it to radians
 internally; hence the units of K are in energy/radian^2.
 
-[Restrictions:] none
+[Restrictions:]
+
+This improper style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/improper_hybrid.txt b/doc/improper_hybrid.txt
index 3bed0c6c34aa597de8040d287602ab8b981d17b7..b6f2e92a9321ef5e09267070f808448ee4058187 100644
--- a/doc/improper_hybrid.txt
+++ b/doc/improper_hybrid.txt
@@ -50,7 +50,11 @@ An improper style of {none} can be specified as an argument to
 improper_style hybrid and the corresponding improper_coeff commands,
 if you desire to turn off certain improper types.
 
-[Restrictions:] none
+[Restrictions:]
+
+This improper style can only be used if LAMMPS was built with the
+"molecular" package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
 [Related commands:]
 
diff --git a/doc/improper_style.txt b/doc/improper_style.txt
index 85fbc6918306ee4e05558af32ba99b5d902bef20..420bbc0e75d6bc0caeea090811846843bde4726a 100644
--- a/doc/improper_style.txt
+++ b/doc/improper_style.txt
@@ -31,13 +31,23 @@ from a data or restart file.
 Hybrid models where impropers are computed using different improper
 potentials can be setup using the {hybrid} improper style.
 
-The coefficients associated with an improper style can be specified in a
-data or restart file or via the "improper_coeff"_improper_coeff.html command.
-
-Note that when both an improper and pair style is defined, the
-"special_bond"_special_bond.html command often needs to be used to
-turn off (or weight) the pairwise interactions that would otherwise
-exist between the 4 bonded atoms.
+The coefficients associated with an improper style can be specified in
+a data or restart file or via the "improper_coeff"_improper_coeff.html
+command.
+
+All improper potentials store their coefficient data in binary restart
+files which means improper_style and
+"improper_coeff"_improper_coeff.html commands do not need to be
+re-specified in an input script that restarts a simulation.  See the
+"read_restart"_read_restart.html command for details on how to do
+this.  The one exception is that improper_style {hybrid} only stores
+the list of sub-styles in the restart file; improper coefficients need
+to be re-specified.
+
+IMPORTANT NOTE: When both an improper and pair style is defined, the
+"special_bonds"_special_bonds.html command often needs to be used to
+turn off (or weight) the pairwise interaction that would otherwise
+exist between 4 bonded atoms.
 
 :line
 
@@ -59,10 +69,11 @@ specified by the associated "improper_coeff"_improper_coeff.html command:
 Improper styles can only be set for atom_style choices that allow
 impropers to be defined.
 
-Improper styles are part of the "molecular" package or other packages
-as noted in their documentation.  They are only enabled if LAMMPS was
-built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
+Most improper styles are part of the "molecular" package.  They are
+only enabled if LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info on packages.  The
+doc pages for individual improper potentials tell if it is part of a
+package.
 
 [Related commands:]
 
diff --git a/doc/kspace_style.txt b/doc/kspace_style.txt
index 3a8bd6d8cd83cbf5208ca39f30b18b8c754e9ed3..e7e5e244798a4a77bc73f7cdb0fdb1d40831e420 100644
--- a/doc/kspace_style.txt
+++ b/doc/kspace_style.txt
@@ -73,7 +73,7 @@ must be periodic and the z dimension must be non-periodic.
 
 Kspace styles are part of the "kspace" package.  They are only enabled
 if LAMMPS was built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
+LAMMPS"_Section_start.html#2_3 section for more info.
 
 When using a long-range pairwise TIP4P potential, you must use kspace
 style {pppm/tip4p} and vice versa.
diff --git a/doc/minimize.html b/doc/minimize.html
index 64c251b2bd5a7b8b79f283b4b7ef8a84a2fee707..7f1550b278fabe9636bc83cf5c4ac433bc7baabd 100644
--- a/doc/minimize.html
+++ b/doc/minimize.html
@@ -34,6 +34,9 @@ fashion that should allow for systems with highly overlapped atoms
 (large energies and forces) to still be minimized by pushing the atoms
 off of each other.
 </P>
+<P>Following the minimization a statistical summary is printed that
+includes the energy change and convergence criteria information.
+</P>
 <P>A minimization involves an outer iteration loop which sets the search
 direction along which coordinates are changed.  An inner iteration is
 then performed using a line search algorithm.  The line search
@@ -61,21 +64,20 @@ include <I>pair/lj/charmm/coul/charmm</I> and <I>pair/lj/charmm/coul/long</I>.
 If a <I>soft</I> potential is used the Astop value is used for the
 prefactor (no time dependence).
 </P>
-<P>Only fixes that apply force constraints are invoked during
-minimization.  The list of the currently implemented ones include fix
-<I>addforce</I>, <I>aveforce</I>, <I>enforce2d</I>, <I>indent</I>, <I>lineforce</I>,
-<I>planeforce</I>, <I>setforce</I>, and <I>wall/lj93</I>.  Note that <I>indent</I>,
-<I>wall/lj93</I> have an associated potential energy.  If you want that
-energy to be included in the total potential energy of the system (the
-quantity being minimized), you must enable the
-<A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for that fix.
+<P>Only some fixes (typically those that apply force constraints) are
+invoked during minimization.  See the doc pages for individual
+<A HREF = "fix.html">fix</A> commands to see which ones are relevant.
 </P>
-<P>Following the minimization a statistical summary is printed that
-includes the energy change and convergence criteria information.
+<P>IMPORTANT NOTE: Some fixes which are invoked during minimization have
+an associated potential energy.  For that energy to be included in the
+total potential energy of the system (the quantity being minimized),
+you MUST enable the <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for
+that fix.  The doc pages for individual <A HREF = "fix.html">fix</A> commands
+specify if this should be done.
 </P>
 <P><B>Restrictions:</B>
 </P>
-<P>Features that are not yet implemented listed here, in case someone
+<P>Features that are not yet implemented are listed here, in case someone
 knows how they could be coded:
 </P>
 <P>It is an error to use <A HREF = "fix_shake.html">fix shake</A> with minimization
diff --git a/doc/minimize.txt b/doc/minimize.txt
index 0b3459a076361f8fef6d59eeacedeab90d502880..30a7609a5862fed5073561bfc0e0d2893a1fc620 100644
--- a/doc/minimize.txt
+++ b/doc/minimize.txt
@@ -31,6 +31,9 @@ fashion that should allow for systems with highly overlapped atoms
 (large energies and forces) to still be minimized by pushing the atoms
 off of each other.
 
+Following the minimization a statistical summary is printed that
+includes the energy change and convergence criteria information.
+
 A minimization involves an outer iteration loop which sets the search
 direction along which coordinates are changed.  An inner iteration is
 then performed using a line search algorithm.  The line search
@@ -58,21 +61,20 @@ include {pair/lj/charmm/coul/charmm} and {pair/lj/charmm/coul/long}.
 If a {soft} potential is used the Astop value is used for the
 prefactor (no time dependence).
 
-Only fixes that apply force constraints are invoked during
-minimization.  The list of the currently implemented ones include fix
-{addforce}, {aveforce}, {enforce2d}, {indent}, {lineforce},
-{planeforce}, {setforce}, and {wall/lj93}.  Note that {indent},
-{wall/lj93} have an associated potential energy.  If you want that
-energy to be included in the total potential energy of the system (the
-quantity being minimized), you must enable the
-"fix_modify"_fix_modify.html {energy} option for that fix.
+Only some 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.
 
-Following the minimization a statistical summary is printed that
-includes the energy change and convergence criteria information.
+IMPORTANT NOTE: Some fixes which are invoked during minimization have
+an associated potential energy.  For that energy to be included in the
+total potential energy of the system (the quantity being minimized),
+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.
 
 [Restrictions:]
 
-Features that are not yet implemented listed here, in case someone
+Features that are not yet implemented are listed here, in case someone
 knows how they could be coded:
 
 It is an error to use "fix shake"_fix_shake.html with minimization
diff --git a/doc/pair_buck.txt b/doc/pair_buck.txt
index 9d23621c2af691fe1eb197bf0db71cd32a23db9c..e485597434fd00918d8984352f783c7a34786194 100644
--- a/doc/pair_buck.txt
+++ b/doc/pair_buck.txt
@@ -80,20 +80,41 @@ Coulombic cutoff cannot be specified for an individual I,J type pair.
 All type pairs use the same global Coulombic cutoff specified in the
 pair_style command.
 
-[Restrictions:]
+:line
 
-The {buck} potentials do not support the
-"pair_modify"_pair_modify.hmtl {mix} option.  Coefficients for all i,j
-pairs must be specified explicitly.
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
 
-The {buck/coul/long} style is part of the "kspace" package.  It is
-only enabled if LAMMPS was built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
+None of the Buckingham pair styles support mixing.  Thus, coefficients
+for all I,J pairs must be specified explicitly.
+
+All of the Buckingham pair styles support the
+"pair_modify"_pair_modify.html shift option for the energy of the
+exp() and 1/r^6 portion of the pair interaction.
+
+The {buck/coul/long} pair style does not support the
+"pair_modify"_pair_modify.html table option since a tabulation
+capability has not yet been added to this potential.
+
+None of the Buckingham pair styles support the
+"pair_modify"_pair_modify.html tail option for adding long-range tail
+corrections to energy and pressure.
 
-On some 64-bit machines, compiling with -O3 appears to break the
-Coulombic tabling option used by the {buck/coul/long} style.  See
-the "Additional build tips" section of the Making LAMMPS documentation
-pages for workarounds on this issue.
+All of the Buckinham pair styles can calculate per-atom energy and
+stress, as used by the "compute epair/atom"_compute_epair_atom.html,
+"compute stress/atom"_compute_stress_atom.html, and "dump
+custom"_dump.html commands.
+
+All of the Buckinham pair styles write their information to "binary
+restart files"_restart.html, so pair_style and pair_coeff commands do
+not need to be specified in an input script that reads a restart file.
+
+[Restrictions:]
+
+The {buck/coul/long} style is part of the "kspace" package.  It is
+only enabled if LAMMPS was built with that package (which it is by
+default).  See the "Making LAMMPS"_Section_start.html#2_3 section for
+more info.
 
 [Related commands:]
 
diff --git a/doc/pair_charmm.txt b/doc/pair_charmm.txt
index abc291acae557c998654d8a05ae9591eb20d70cf..312ac09deb0694029d11f8ed8ec6d9267365e93f 100644
--- a/doc/pair_charmm.txt
+++ b/doc/pair_charmm.txt
@@ -88,7 +88,7 @@ The following coefficients must be defined for each pair of atoms
 types via the "pair_coeff"_pair_coeff.html command as in the examples
 above, or in the data file or restart files read by the
 "read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
+commands, or by mixing as described below:
 
 epsilon (energy units)
 sigma (distance units)
@@ -106,11 +106,40 @@ because this CHARMM force field does not allow varying cutoffs for
 individual atom pairs; all pairs use the global cutoff(s) specified in
 the pair_style command.
 
-If the pair_coeff command is not used to define coefficients for a
-particular I != J type pair, the mixing rule for epsilon and sigma for
-all CHARMM potentials is to use the {arithmetic} formulas documented
-by the "pair_modify"_pair_modify.html command.  The "pair_modify
-mix"_pair_modify.html setting is thus ignored for CHARMM potentials.
+:line
+
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14,
+and sigma_14 coefficients for all of the lj/charmm pair styles can be
+mixed.  They are always mixed with the value {arithmetic}.  See the
+"pair_modify" command for details.
+
+None of the lj/charmm pair styles support the
+"pair_modify"_pair_modify.html shift option, since the Lennard-Jones
+portion of the pair interaction is smoothed to 0.0 at the cutoff.
+
+The {lj/charmm/coul/long} and {lj/charmm/coul/long/opt} pair styles
+support the "pair_modify"_pair_modify.html table option since they can
+tabulate the short-range portion of the long-range Coulombic
+interaction.
+
+None of the lj/charmm pair styles support the
+"pair_modify"_pair_modify.html tail option for adding long-range tail
+corrections to energy and pressure, since the Lennard-Jones portion of
+the pair interaction is smoothed to 0.0 at the cutoff.
+
+All of the lj/charmm pair styles can calculate per-atom energy and
+stress, as used by the "compute epair/atom"_compute_epair_atom.html,
+"compute stress/atom"_compute_stress_atom.html, and "dump
+custom"_dump.html commands.
+
+All of the lj/charmm pair styles write their information to "binary
+restart files"_restart.html, so pair_style and pair_coeff commands do
+not need to be specified in an input script that reads a restart file.
+
+:line
 
 [Restrictions:]
 
@@ -119,8 +148,8 @@ styles are part of the "molecule" package.  The {lj/charmm/coul/long}
 style is part of the "kspace" package.  The {lj/charmm/coul/long/opt}
 style is part of the "opt" package and also requires the "kspace"
 package.  They are only enabled if LAMMPS was built with those
-package(s).  See the "Making LAMMPS"_Section_start.html#2_3 section
-for more info.
+package(s) (molecule and kspace are by default).  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
 
 On some 64-bit machines, compiling with -O3 appears to break the
 Coulombic tabling option used by the {lj/charmm/coul/long} style.  See
diff --git a/doc/pair_class2.txt b/doc/pair_class2.txt
index 10deb96488f7fdfc6adef1dd4a6ab9a73f056701..ed29ceaff31d921653855877cda83ad8c518afcc 100644
--- a/doc/pair_class2.txt
+++ b/doc/pair_class2.txt
@@ -60,7 +60,7 @@ The following coefficients must be defined for each pair of atoms
 types via the "pair_coeff"_pair_coeff.html command as in the examples
 above, or in the data file or restart files read by the
 "read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
+commands, or by mixing as described below:
 
 epsilon (energy units)
 sigma (distance units)
@@ -80,6 +80,8 @@ since a Coulombic cutoff cannot be specified for an individual I,J
 type pair.  All type pairs use the same global Coulombic cutoff
 specified in the pair_style command.
 
+: line
+
 If the pair_coeff command is not used to define coefficients for a
 particular I != J type pair, the mixing rule for epsilon and sigma for
 all class2 potentials is to use the {sixthpower} formulas documented
@@ -88,16 +90,43 @@ mix"_pair_modify.html setting is thus ignored for class2 potentials
 for epsilon and sigma.  However it is still followed for mixing the
 cutoff distance.
 
-[Restrictions:]
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/class2 pair styles can be mixed.
+Epsilon and sigma are always mixed with the value {sixthpower}.  The
+cutoff distance is mixed by whatever option is set by the pair_modify
+command (default = geometric).  See the "pair_modify" command for
+details.
+
+All of the lj/class2 pair styles support the
+"pair_modify"_pair_modify.html shift option for the energy of the
+Lennard-Jones portion of the pair interaction.
+
+The {lj/class2/coul/long} pair style does not support the
+"pair_modify"_pair_modify.html table option since a tabulation
+capability has not yet been added to this potential.
 
-These styles are part of the "class2" package.  They are only enabled
-if LAMMPS was built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
+All of the lj/class2 pair styles support the
+"pair_modify"_pair_modify.html tail option for adding a long-range
+tail correction to the energy and pressure of the Lennard-Jones
+portion of the pair interaction.
+
+All of the lj/class2 pair styles can calculate per-atom energy and
+stress, as used by the "compute epair/atom"_compute_epair_atom.html,
+"compute stress/atom"_compute_stress_atom.html, and "dump
+custom"_dump.html commands.
+
+All of the lj/class2 pair styles write their information to "binary
+restart files"_restart.html, so pair_style and pair_coeff commands do
+not need to be specified in an input script that reads a restart file.
+
+[Restrictions:]
 
-On some 64-bit machines, compiling with -O3 appears to break the
-Coulombic tabling option used by the {lj/class2/coul/long} style.  See
-the "Additional build tips" section of the Making LAMMPS documentation
-pages for workarounds on this issue.
+All of these pair styles are part of the "class2" package.  They are
+only enabled if LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
 
 [Related commands:]
 
diff --git a/doc/pair_coeff.txt b/doc/pair_coeff.txt
index 040236aa0bd682d39d9fb7a0fe95f521435b51b5..acaeafab1cf40c443ec12176159134204a2d4b69 100644
--- a/doc/pair_coeff.txt
+++ b/doc/pair_coeff.txt
@@ -37,7 +37,7 @@ can be used for each, as in the 1st example above.  I <= J is
 required.  LAMMPS sets the coefficients for the symmetric J,I
 interaction to the same values.
 
-A wild-card asterik can be used in place of in conjunction with the
+A wild-card asterik can be used in place of or in conjunction with the
 I,J arguments to set the coefficients for multiple pairs of atom
 types.  This takes the form "*" or "*n" or "n*" or "m*n".  If N = the
 number of atom types, then an asterik with no numeric values means all
@@ -70,8 +70,9 @@ as
 For many potentials, if coefficients for type pairs with I != J are
 not set explicity by a pair_coeff command, the values are inferred
 from the I,I and J,J settings by mixing rules; see the
-"pair_modify"_pair_modify.html command for a discussion.  Exceptions
-to the mixing rules are discussed with the individual pair styles.
+"pair_modify"_pair_modify.html command for a discussion.  Details on
+this option as it pertains to individual potentials are described on
+the doc page for the potential.
 
 :line
 
@@ -80,20 +81,15 @@ the style to display the formula it computes, arguments specified in
 the pair_style command, and coefficients specified by the associated
 "pair_coeff"_pair_coeff.html command:
 
-"pair_style none"_pair_none.html - turn off pairwise interactions
-"pair_style hybrid"_pair_hybrid.html - define multiple styles of pairwise interactions :ul
+"pair_style airebo"_pair_airebo.html - AI-REBO potential
 "pair_style buck"_pair_buck.html - Buckingham potential
 "pair_style buck/coul/cut"_pair_buck.html - Buckinhham with cutoff Coulomb
 "pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulomb
 "pair_style colloid"_pair_colloid.html - integrated colloidal potential
-"pair_style dipole/cut"_pair_dpd.html - point dipole potential
 "pair_style dpd"_pair_dpd.html - dissipative particle dynamics (DPD)
 "pair_style eam"_pair_eam.html - embedded atom method (EAM)
-"pair_style eam/opt"_pair_eam.html - optimized embedded atom method (EAM)
 "pair_style eam/alloy"_pair_eam.html - alloy EAM
-"pair_style eam/alloy/opt"_pair_eam.html - optimized alloy EAM
 "pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
-"pair_style eam/fs/opt"_pair_eam.html - optimized Finnis-Sinclair EAM
 "pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
 "pair_style gran/hertzian"_pair_gran.html - granular potential with Hertizain interactions
 "pair_style gran/history"_pair_gran.html - granular potential with history effects
@@ -101,12 +97,10 @@ the pair_style command, and coefficients specified by the associated
 "pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
 "pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
 "pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
-"pair_style lj/charmm/coul/long/opt"_pair_charmm.html - optimized CHARMM with long-range Coulomb
 "pair_style lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb
 "pair_style lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb
 "pair_style lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb
 "pair_style lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb
-"pair_style lj/cut/opt"_pair_lj.html - optimized cutoff Lennard-Jones potential with no Coulomb
 "pair_style lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb
 "pair_style lj/cut/coul/debye"_pair_lj.html - LJ with Debye damping added to Coulomb
 "pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulomb
@@ -115,7 +109,6 @@ the pair_style command, and coefficients specified by the associated
 "pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
 "pair_style meam"_pair_meam.html - modified embedded atom method (MEAM)
 "pair_style morse"_pair_morse.html - Morse potential
-"pair_style morse/opt"_pair_morse.html - optimized Morse potential
 "pair_style soft"_pair_soft.html - Soft (cosine) potential
 "pair_style sw"_pair_sw.html - Stillinger-Weber 3-body potential
 "pair_style table"_pair_table.html - tabulated pair potential
diff --git a/doc/pair_colloid.txt b/doc/pair_colloid.txt
index d7a263069a904c1cea7c689e7fdde37533d9558d..72832c66468bf82cae0b890a1084ce1b6327a123 100644
--- a/doc/pair_colloid.txt
+++ b/doc/pair_colloid.txt
@@ -59,7 +59,7 @@ The following coefficients must be defined for each pair of atoms
 types via the "pair_coeff"_pair_coeff.html command as in the examples
 above, or in the data file or restart files read by the
 "read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
+commands, or by mixing as described below:
 
 A (energy units)
 sigma (distance units)
@@ -107,16 +107,42 @@ rule-of-thumb is to use a colloid-solvent cutoff that is half the big
 diamter + 4 times the small diamter.  I.e. 9 = 5 + 4 for the
 colloid-solvent cutoff in this case.
 
-If a pair_coeff command is not specified for I != J, then the
-coefficients are mixed according the mixing rules defined by the
-"pair_modify"_pair_modify.html command.  The prefactor A is mixed like
-the Lennard-Jones epsilon; sigma,d1,d2 are all mixed like the
-Lennard-Jones sigma.
+:line
+
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+For atom type pairs I,J and I != J, the A, sigma, d1, and d2
+coefficients and cutoff distance for this pair style can be mixed.  A
+is an energy value mixed like a LJ epsilon.  D1 and d2 are distance
+values and are mixed like sigma.  The default mix value is
+{geometric}.  See the "pair_modify" command for details.
+
+This pair style supports the "pair_modify"_pair_modify.html shift
+option for the energy of the pair interaction.
+
+The "pair_modify"_pair_modify.html table option is not relevant
+for this pair style.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style can calculate per-atom energy and stress, as used by
+the "compute epair/atom"_compute_epair_atom.html, "compute
+stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
+commands.
+
+This pair style writes its information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+:line
 
 [Restrictions:]
 
-The {colloid} style is part of the "colloid" package.  It is only
-enabled if LAMMPS was built with that package.  See the "Making
+This style is part of the "colloid" package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
 LAMMPS"_Section_start.html#2_3 section for more info.
 
 [Related commands:]
diff --git a/doc/pair_dipole.txt b/doc/pair_dipole.txt
index 5d6662902c53b1b96ba6205347f5d195adf396d8..cea8a63e826dc4114f75acb3fafb48916760b65c 100755
--- a/doc/pair_dipole.txt
+++ b/doc/pair_dipole.txt
@@ -59,7 +59,7 @@ The following coefficients must be defined for each pair of atoms
 types via the "pair_coeff"_pair_coeff.html command as in the examples
 above, or in the data file or restart files read by the
 "read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
+commands, or by mixing as described below:
 
 epsilon (energy units)
 sigma (distance units)
@@ -73,12 +73,46 @@ and Coulombic interactions for this type pair.  If both coefficients
 are specified, they are used as the LJ and Coulombic cutoffs for this
 type pair.
 
-[Restrictions:]
+:line
+
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distances for this pair style can be mixed.  The default
+mix value is {geometric}.  See the "pair_modify" command for details.
+
+For atom type pairs I,J and I != J, the A, sigma, d1, and d2
+coefficients and cutoff distance for this pair style can be mixed.  A
+is an energy value mixed like a LJ epsilon.  D1 and d2 are distance
+values and are mixed like sigma.  The default mix value is
+{geometric}.  See the "pair_modify" command for details.
+
+This pair style supports the "pair_modify"_pair_modify.html shift
+option for the energy of the Lennard-Jones portion of the pair
+interaction.
 
-Can only be used if LAMMPS was built with the "dipole" package.
+The "pair_modify"_pair_modify.html table option is not relevant
+for this pair style.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style can calculate per-atom energy and stress, as used by
+the "compute epair/atom"_compute_epair_atom.html, "compute
+stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
+commands.
+
+This pair style writes its information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+[Restrictions:]
 
-The use of this potential requires additional fixes as described
-above.
+This style is part of the "dipole" package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
 
 [Related commands:]
 
diff --git a/doc/pair_dpd.txt b/doc/pair_dpd.txt
index cfd8c5f565ecf5f878978a7ea6d766b37bc6da2f..95dc12146a14b782ee2ca0b0fb332e6c2a056b53 100644
--- a/doc/pair_dpd.txt
+++ b/doc/pair_dpd.txt
@@ -53,15 +53,48 @@ cutoff is used.  Note that sigma is set equal to sqrt(2 T gamma),
 where T is the temperature set by the "pair_style"_pair_style.html
 command so it does not need to be specified.
 
-[Restrictions:] none
+:line
+
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+Thsi pair style does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift option for the energy of the pair interaction.
+
+The "pair_modify"_pair_modify.html table option is not relevant
+for this pair style.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style can calculate per-atom energy and stress, as used by
+the "compute epair/atom"_compute_epair_atom.html, "compute
+stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
+commands.  However, only the first term with the A coefficienct
+(conservative force) is used for these computations.  The drag force
+and random force terms are not.
+
+This pair style writes its information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.  Note
+that the user-specifice random number seed is stored in the restart
+file, so when a simulation is restarted, each processor will
+re-initialize its random number generator the same way it did
+intially.  This means the random forces will be random, but will not
+be the same as they would have been if the original simulation had
+continued past the restart time.
+
+:line
 
-This style is part of the "dpd" package.  It is only enabled if LAMMPS
-was built with those package.  See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
+[Restrictions:]
 
-The {dpd} potential does not support the
-"pair_modify"_pair_modify.hmtl {mix} option.  Coefficients for all i,j
-pairs must be specified explicitly.
+This style is part of the "dpd" package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
 
 The default frequency for rebuilding neighbor lists is every 10 steps
 (see the "neigh_modify"_neigh_modify.html command). This may be too
diff --git a/doc/pair_eam.html b/doc/pair_eam.html
index 5b07c4cc6fc052911931c170b505fc400f1463f7..826d478ba324af08c1de2afc787fffe647ec9fca 100644
--- a/doc/pair_eam.html
+++ b/doc/pair_eam.html
@@ -325,21 +325,13 @@ are listed.
 <P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
 restart info</B>:
 </P>
-<P>For atom type pairs I,J and I != J, mixing is performed by LAMMPS as
+<P>For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
 described above with the individual styles.  You never need to specify
 a pair_coeff command with I != J arguments for the eam styles.
 </P>
 <P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
-shift option for the energy of the pair interaction.
-</P>
-<P>The <A HREF = "pair_modify.html">pair_modify</A> shift option is not relevant
-for this pair style.
-</P>
-<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
-for this pair style.
-</P>
-<P>The <A HREF = "pair_modify.html">pair_modify</A> tail option is not relevant
-for this pair style.
+shift, table, and tail options.
 </P>
 <P>All of the eam pair styles can calculate per-atom energy and stress,
 as used by the <A HREF = "compute_epair_atom.html">compute epair/atom</A>, <A HREF = "compute_stress_atom.html">compute
@@ -347,10 +339,10 @@ stress/atom</A>, and <A HREF = "dump.html">dump custom</A>
 commands.  These quantities include the contribution from the
 embedding term in the EAM formulas.
 </P>
-<P>None of the eam pair styles write their information to <A HREF = "restart.html">binary restart
-files</A>, since the info is tabulated in potential files.
-Thus, you need to re-specify the pair style and coefficient commands
-in an input script that reads a restart file.
+<P>The eam pair styles do not write their information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
 </P>
 <HR>
 
diff --git a/doc/pair_eam.txt b/doc/pair_eam.txt
index 3c2fba83a7b9b10364b38a2593c39348f76f9477..a9d9652e5a5c8b1a10ef93873e4d74bc5cea5439 100644
--- a/doc/pair_eam.txt
+++ b/doc/pair_eam.txt
@@ -314,11 +314,38 @@ are listed.
 
 :line
 
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above with the individual styles.  You never need to specify
+a pair_coeff command with I != J arguments for the eam styles.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+All of the eam pair styles can calculate per-atom energy and stress,
+as used by the "compute epair/atom"_compute_epair_atom.html, "compute
+stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
+commands.  These quantities include the contribution from the
+embedding term in the EAM formulas.
+
+The eam pair styles do not write their information to "binary restart
+files"_restart.html, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+
+:line
+
 [Restrictions:]
 
-The {opt} styles are part of the "opt" package.  They are only enabled
-if LAMMPS was built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_3 section for more info.
+All of these styles except those ending in {opt} are part of the
+"manybody" package.  They are only enabled if LAMMPS was built with
+that package (which it is by default).  The styles ending in {opt} are
+part of the "opt" package and also require the "manybody" package.
+They are only enabled if LAMMPS was built with those packages.  See
+the "Making LAMMPS"_Section_start.html#2_3 section for more info.
 
 [Related commands:]
 
diff --git a/doc/pair_gayberne.html b/doc/pair_gayberne.html
index bd6a7a0f6988ae23457a127a5411d9f271d627eb..912913129cfb825eac1bd2388480c506b3e02a50 100644
--- a/doc/pair_gayberne.html
+++ b/doc/pair_gayberne.html
@@ -67,7 +67,7 @@ listed below and in <A HREF = "Eqs/pair_gayberne_extra.pdf">this document</A>.
 types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
 above, or in the data file or restart files read by the
 <A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
-commands:
+commands, or by mixing as described below:
 </P>
 <UL><LI>epsilon = well depth (energy units)
 <LI>sigma = minimum effective particle radii (distance units)
diff --git a/doc/pair_gayberne.txt b/doc/pair_gayberne.txt
index 11ef63cfc1d48bdbdec568bc2697c6ea729ee9de..7c54b974f4db83a56357aa17f1aee2f9352fdb02 100755
--- a/doc/pair_gayberne.txt
+++ b/doc/pair_gayberne.txt
@@ -64,7 +64,7 @@ The following coefficients must be defined for each pair of atoms
 types via the "pair_coeff"_pair_coeff.html command as in the examples
 above, or in the data file or restart files read by the
 "read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
+commands, or by mixing as described below:
 
 epsilon = well depth (energy units)
 sigma = minimum effective particle radii (distance units)
@@ -79,10 +79,6 @@ cutoff (distance units) :ul
 The last coefficient is optional.  If not specified, the global
 cutoff specified in the pair_style command is used.
 
-The epsilon and sigma parameters are mixed for I != J atom pairings
-the same as Lennard-Jones parameters; see the "pair_modify
-mix"_pair_modify.html documentation for details. 
-
 The epsilon_i and epsilon_j coefficients are actually defined for atom
 types, not for pairs of atom types.  Thus, in a series of pair_coeff
 commands, they only need to be specified once for each atom type.
@@ -116,17 +112,49 @@ than the full Gay-Berne formula.  Thus you should insure epsilon a,b,c
 are set to 1.0 for spherical particle types and use epsilon and sigma
 to specify its interaction with other spherical particles.
 
+:line
+
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for this pair style can be mixed.  The default mix
+value is {geometric}.  See the "pair_modify" command for details.
+
+This pair styles supports the "pair_modify"_pair_modify.html shift
+option for the energy of the Lennard-Jones portion of the pair
+interaction, but only for sphere-sphere interactions.  There is no
+shifting performed for ellipsoidal interactions due to the anisotropic
+dependence of the interaction.
+
+The "pair_modify"_pair_modify.html table option is not relevant
+for this pair style.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style does not calculate per-atom energy and stress, as used
+by the "compute epair/atom"_compute_epair_atom.html, "compute
+stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
+commands.
+
+This pair style writes its information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+:line
+
 [Restrictions:]
 
-Can only be used if LAMMPS was built with the "asphere" package.
+This style is part of the "asphere" package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
 
-The "shift yes" option in "pair_modify"_pair_modify.html only applies
-to sphere-sphere interactions for this potential; there is no shifting
-performed for ellipsoidal interactions due to the anisotropic
-dependence of the interaction.  The Gay-Berne potential does not
-become isotropic as r increases "(Everaers)"_#Everaers.  The
-distance-of-closest-approach approximation used by LAMMPS becomes less
-accurate when high-aspect ratio ellipsoids are used.
+The Gay-Berne potential does not become isotropic as r increases
+"(Everaers)"_#Everaers.  The distance-of-closest-approach
+approximation used by LAMMPS becomes less accurate when high-aspect
+ratio ellipsoids are used.
 
 [Related commands:]
 
diff --git a/doc/pair_gran.html b/doc/pair_gran.html
index cc6559c6ece25c601a2254e1241deb7fc1055639..3610997cb00da4768e8ed528cc0a89b383cc3692 100644
--- a/doc/pair_gran.html
+++ b/doc/pair_gran.html
@@ -67,19 +67,35 @@ spring and dash-pot model until Ft/Fn = xmu and then is held at Ft =
 Fn*xmu until the particles lose contact.
 </P>
 <P>For granular styles there are no individual atom type coefficients
-that can be set.  All global settings are made via the pair_style
-command.
+that can be set via the <A HREF = "pair_coeff.html">pair_coeff</A> command.  All
+global settings are made via the pair_style command.
 </P>
-<P>See the citation for more discussion of the granular potentials.
+<P>See the citation below for more discussion of granular potentials.
 </P>
-<P><B>Restrictions:</B> none
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info</B>:
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> mix, shift, table, and tail options
+are not relevant for granular pair styles.
+</P>
+<P>This pair style does not calculate per-atom energy and stress, as used
+by the <A HREF = "compute_epair_atom.html">compute epair/atom</A>, <A HREF = "compute_stress_atom.html">compute
+stress/atom</A>, and <A HREF = "dump.html">dump custom</A>
+commands.
 </P>
-<P>All of these styles are part of the "granular" package.  It is only
-enabled if LAMMPS was built with that package.  See the <A HREF = "Section_start.html#2_3">Making
-LAMMPS</A> section for more info.
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so a pair_style commands does not need to be
+specified in an input script that reads a restart file.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
 </P>
-<P>You must use <A HREF = "atom_style.html">atom style</A> <I>granular</I> with these pair
-styles.
+<P>All the granular pair styles are part of the "granular" package.  It
+is only enabled if LAMMPS was built with that package.  See the
+<A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for more info.
 </P>
 <P><B>Related commands:</B>
 </P>
diff --git a/doc/pair_gran.txt b/doc/pair_gran.txt
index 15d2ca24ea67cb33c6060f4472765f7f1548d308..43fee9582b7807ddf69d897ba9ba17e338901166 100644
--- a/doc/pair_gran.txt
+++ b/doc/pair_gran.txt
@@ -58,19 +58,35 @@ spring and dash-pot model until Ft/Fn = xmu and then is held at Ft =
 Fn*xmu until the particles lose contact.
 
 For granular styles there are no individual atom type coefficients
-that can be set.  All global settings are made via the pair_style
-command.
+that can be set via the "pair_coeff"_pair_coeff.html command.  All
+global settings are made via the pair_style command.
 
-See the citation for more discussion of the granular potentials.
+See the citation below for more discussion of granular potentials.
 
-[Restrictions:] none
+:line
+
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+The "pair_modify"_pair_modify.html mix, shift, table, and tail options
+are not relevant for granular pair styles.
+
+This pair style does not calculate per-atom energy and stress, as used
+by the "compute epair/atom"_compute_epair_atom.html, "compute
+stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
+commands.
 
-All of these styles are part of the "granular" package.  It is only
-enabled if LAMMPS was built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
+This pair style writes its information to "binary restart
+files"_restart.html, so a pair_style commands does not need to be
+specified in an input script that reads a restart file.
+
+:line
+
+[Restrictions:] none
 
-You must use "atom style"_atom_style.html {granular} with these pair
-styles.
+All the granular pair styles are part of the "granular" package.  It
+is only enabled if LAMMPS was built with that package.  See the
+"Making LAMMPS"_Section_start.html#2_3 section for more info.
 
 [Related commands:]
 
diff --git a/doc/pair_hybrid.html b/doc/pair_hybrid.html
index 05f66c2ed5cbc94c6be6b3099ea97f6bb912f42b..3a389128fa0f2b9748a377a51e29f4705be04dc8 100644
--- a/doc/pair_hybrid.html
+++ b/doc/pair_hybrid.html
@@ -50,14 +50,6 @@ pair_coeff * * eam/alloy nialhjea 1 1 0
 pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
 pair_coeff 1*2 3 lj/cut 0.8 1.1 
 </PRE>
-<P>Note that as with any pair_style, coeffs must be defined for all I,J
-interactions.  If the sub-style allows for mixing (see the
-<A HREF = "pair_modify.html">pair_modify</A> command), then I,J interactions between
-atom types which both are assigned to that sub-style do not need to be
-specified.  I.e. if atom types 1 and 2 are both computed with <I>lj/cut</I>
-and coeffs for 1,1 and 2,2 interactions are specified, then coeffs for
-1,2 interactions will be generated automatically via mixing.
-</P>
 <P>If the pair_coeff command for a sub-style requires the use of * * as
 atom type arguments (e.g. the <I>eam/alloy</I> example above), then it will
 also include trailing arguments which map atom types to elements in
@@ -69,8 +61,43 @@ hybrid command in your input script, if atoms in the simulation will
 have attributes from several atom styles, due to using multiple pair
 potentials.
 </P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info</B>:
+</P>
+<P>Any pair potential settings made via the
+<A HREF = "pair_modify.html">pair_modify</A> command are passed along to all
+sub-styles of the hybrid potential.
+</P>
+<P>For atom type pairs I,J and I != J, if the sub-style assigned to I,I
+and J,J is the same, and if the sub-style allows for mixing, then the
+coefficients for I,J can be mixed.  The default mix value is
+<I>geometric</I>.  See the "pair_modify" command for details.  See the
+See the doc page for the sub-style to see if allows for mixing.
+</P>
+<P>The hybrid pair style supports the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options for an I,J pair interaction, if the
+associated sub-style supports it.
+</P>
+<P>The hybrid pair style can calculate per-atom energy and stress, as
+used by the <A HREF = "compute_epair_atom.html">compute epair/atom</A>, <A HREF = "compute_stress_atom.html">compute
+stress/atom</A>, and <A HREF = "dump.html">dump custom</A>
+commands, if all its sub-styles can perform per-atom calculations.
+</P>
+<P>For the hybrid pair style, the list of sub-styles and their respective
+settings are written to <A HREF = "restart.html">binary restart files</A>, so a
+pair_style command does not need to specified in an input script that
+reads a restart file.  However, the coefficient information is not
+stored in the restart file.  Thus, pair_coeff commands do need to be
+specified in the restart input script.
+</P>
 <P><B>Restrictions:</B>
 </P>
+<P>A pair style of <I>none</I> can be specified as an argument to pair_style
+hybrid and the corresponding pair_coeff commands, if you desire to
+turn off pairwise interactions between certain pairs of atom types.
+</P>
 <P>When using a long-range Coulomic solver (via the
 <A HREF = "kspace_style">kspace_style</A> command) with pair_style hybrid, one or
 more sub-styles will be of the "long" variety.
@@ -79,17 +106,6 @@ than one sub-style with a "long" component, but you must insure that
 the short-range Coulombic cutoff used by each of these pair styles is
 consistent.  Else the long-range Coulombic solve will be inconsistent.
 </P>
-<P>A pair style of <I>none</I> can be specified as an argument to pair_style
-hybrid and the corresponding pair_coeff commands, if you desire to
-turn off pairwise interactions between certain pairs of atom types.
-</P>
-<P>The hybrid style cannot include any of the <I>granular</I> styles in its
-list of styles to use.
-</P>
-<P>If you use multiple <I>coul/long</I> pair styles along with a <A HREF = "kspace_style.html">kspace
-style</A>, then you should make sure the pairwise
-Coulombic cutoff is the same for all the pair styles.
-</P>
 <P><B>Related commands:</B>
 </P>
 <P><A HREF = "pair_coeff.html">pair_coeff</A>
diff --git a/doc/pair_hybrid.txt b/doc/pair_hybrid.txt
index 37ad495cd5d955f581589310922c91b756616f6b..ff27251384328269c5008ff1fab4417950f1d59b 100644
--- a/doc/pair_hybrid.txt
+++ b/doc/pair_hybrid.txt
@@ -47,14 +47,6 @@ pair_coeff * * eam/alloy nialhjea 1 1 0
 pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
 pair_coeff 1*2 3 lj/cut 0.8 1.1 :pre
 
-Note that as with any pair_style, coeffs must be defined for all I,J
-interactions.  If the sub-style allows for mixing (see the
-"pair_modify"_pair_modify.html command), then I,J interactions between
-atom types which both are assigned to that sub-style do not need to be
-specified.  I.e. if atom types 1 and 2 are both computed with {lj/cut}
-and coeffs for 1,1 and 2,2 interactions are specified, then coeffs for
-1,2 interactions will be generated automatically via mixing.
-
 If the pair_coeff command for a sub-style requires the use of * * as
 atom type arguments (e.g. the {eam/alloy} example above), then it will
 also include trailing arguments which map atom types to elements in
@@ -66,8 +58,43 @@ hybrid command in your input script, if atoms in the simulation will
 have attributes from several atom styles, due to using multiple pair
 potentials.
 
+:line
+
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+Any pair potential settings made via the
+"pair_modify"_pair_modify.html command are passed along to all
+sub-styles of the hybrid potential.
+
+For atom type pairs I,J and I != J, if the sub-style assigned to I,I
+and J,J is the same, and if the sub-style allows for mixing, then the
+coefficients for I,J can be mixed.  The default mix value is
+{geometric}.  See the "pair_modify" command for details.  See the
+See the doc page for the sub-style to see if allows for mixing.
+
+The hybrid pair style supports the "pair_modify"_pair_modify.html
+shift, table, and tail options for an I,J pair interaction, if the
+associated sub-style supports it.
+
+The hybrid pair style can calculate per-atom energy and stress, as
+used by the "compute epair/atom"_compute_epair_atom.html, "compute
+stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
+commands, if all its sub-styles can perform per-atom calculations.
+
+For the hybrid pair style, the list of sub-styles and their respective
+settings are written to "binary restart files"_restart.html, so a
+pair_style command does not need to specified in an input script that
+reads a restart file.  However, the coefficient information is not
+stored in the restart file.  Thus, pair_coeff commands do need to be
+specified in the restart input script.
+
 [Restrictions:]
 
+A pair style of {none} can be specified as an argument to pair_style
+hybrid and the corresponding pair_coeff commands, if you desire to
+turn off pairwise interactions between certain pairs of atom types.
+
 When using a long-range Coulomic solver (via the
 "kspace_style"_kspace_style command) with pair_style hybrid, one or
 more sub-styles will be of the "long" variety.
@@ -76,17 +103,6 @@ than one sub-style with a "long" component, but you must insure that
 the short-range Coulombic cutoff used by each of these pair styles is
 consistent.  Else the long-range Coulombic solve will be inconsistent.
 
-A pair style of {none} can be specified as an argument to pair_style
-hybrid and the corresponding pair_coeff commands, if you desire to
-turn off pairwise interactions between certain pairs of atom types.
-
-The hybrid style cannot include any of the {granular} styles in its
-list of styles to use.
-
-If you use multiple {coul/long} pair styles along with a "kspace
-style"_kspace_style.html, then you should make sure the pairwise
-Coulombic cutoff is the same for all the pair styles.
-
 [Related commands:]
 
 "pair_coeff"_pair_coeff.html
diff --git a/doc/pair_lj.txt b/doc/pair_lj.txt
index 5730d0a91cc0be0a2df24a9c6fa5fee0885f5713..154045a7226cc4934d7f8a0c413349c79cc7acf5 100644
--- a/doc/pair_lj.txt
+++ b/doc/pair_lj.txt
@@ -131,7 +131,7 @@ The following coefficients must be defined for each pair of atoms
 types via the "pair_coeff"_pair_coeff.html command as in the examples
 above, or in the data file or restart files read by the
 "read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
+commands, or by mixing as described below:
 
 epsilon (energy units)
 sigma (distance units)
@@ -155,13 +155,49 @@ can be specified since a Coulombic cutoff cannot be specified for an
 individual I,J type pair.  All type pairs use the same global
 Coulombic cutoff specified in the pair_style command.
 
+:line
+
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/cut pair styles can be mixed.
+The default mix value is {geometric}.  See the "pair_modify" command
+for details.
+
+All of the lj/cut pair styles support the
+"pair_modify"_pair_modify.html shift option for the energy of the
+Lennard-Jones portion of the pair interaction.
+
+The {lj/cut/coul/long} and {lj/cut/coul/long/tip4p} pair styles
+support the "pair_modify"_pair_modify.html table option since they can
+tabulate the short-range portion of the long-range Coulombic
+interaction.
+
+All of the lj/cut pair styles support the
+"pair_modify"_pair_modify.html tail option for adding a long-range
+tail correction to the energy and pressure of the Lennard-Jones
+portion of the pair interaction.
+
+All of the lj/cut pair styles can calculate per-atom energy and
+stress, as used by the "compute epair/atom"_compute_epair_atom.html,
+"compute stress/atom"_compute_stress_atom.html, and "dump
+custom"_dump.html commands.
+
+All of the lj/cut pair styles write their information to "binary
+restart files"_restart.html, so pair_style and pair_coeff commands do
+not need to be specified in an input script that reads a restart file.
+
+:line
+
 [Restrictions:]
 
-The {lj/cut/coul/long} style is part of the "kspace" package.  It is
-only enabled if LAMMPS was built with that package.  The {lj/cut/opt}
-style is part of the "opt" package.  It is only enabled if LAMMPS was
-built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_3 section for more info.
+The {lj/cut/coul/long} and {lj/cut/coul/long/tip4p} styles are part of
+the "kspace" package.  They are only enabled if LAMMPS was built with
+that package (which it is by default).  The {lj/cut/opt} style is part
+of the "opt" package.  It is only enabled if LAMMPS was built with
+that package.  See the "Making LAMMPS"_Section_start.html#2_3 section
+for more info.
 
 On some 64-bit machines, compiling with -O3 appears to break the
 Coulombic tabling option used by the {lj/cut/coul/long} style.  See
diff --git a/doc/pair_lj_expand.html b/doc/pair_lj_expand.html
index 89604c17de9d9e8c1ae95b0d234e071186d36b0b..09082f4ff7e396df6b359a92989f6c2232af3c0a 100644
--- a/doc/pair_lj_expand.html
+++ b/doc/pair_lj_expand.html
@@ -39,7 +39,7 @@ actual force cutoff is the sum of cutoff + delta.
 types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
 above, or in the data file or restart files read by the
 <A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
-commands:
+commands, or by mixing as described below:
 </P>
 <UL><LI>epsilon (energy units)
 <LI>sigma (distance units)
@@ -49,13 +49,39 @@ commands:
 <P>The delta values can be positive or negative.  The last coefficient is
 optional.  If not specified, the global LJ cutoff is used.
 </P>
-<P>If the pair_coeff command is not used to define coefficients for a
-particular I != J type pair, the mixing rule is set by the
-<A HREF = "pair_modify.html">pair_modify</A> command.  Additionally, the delta
-coefficient is always mixed by the rule
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info</B>:
 </P>
-<PRE>delta_ij = (delta_i + delta_j) / 2 
-</PRE>
+<P>For atom type pairs I,J and I != J, the epsilon, sigma, and shift
+coefficients and cutoff distance for this pair style can be mixed.
+Shift is always mixed via an <I>arithmetic</I> rule.  The other
+coefficients are mixed according to the pair_modify mix value.  The
+default mix value is <I>geometric</I>.  See the "pair_modify" command for
+details.
+</P>
+<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the pair interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> tail
+option for adding a long-range tail correction to the energy and
+pressure of the pair interaction.
+</P>
+<P>This pair style can calculate per-atom energy and stress, as used by
+the <A HREF = "compute_epair_atom.html">compute epair/atom</A>, <A HREF = "compute_stress_atom.html">compute
+stress/atom</A>, and <A HREF = "dump.html">dump custom</A>
+commands.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<HR>
+
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
diff --git a/doc/pair_lj_expand.txt b/doc/pair_lj_expand.txt
index ed8885294ad1398dbd0f481584bd0b01bd5b8172..221f8e0baeb9fcbaaa2d755002974d2f2e37df07 100644
--- a/doc/pair_lj_expand.txt
+++ b/doc/pair_lj_expand.txt
@@ -36,7 +36,7 @@ The following coefficients must be defined for each pair of atoms
 types via the "pair_coeff"_pair_coeff.html command as in the examples
 above, or in the data file or restart files read by the
 "read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
+commands, or by mixing as described below:
 
 epsilon (energy units)
 sigma (distance units)
@@ -46,12 +46,38 @@ cutoff (distance units) :ul
 The delta values can be positive or negative.  The last coefficient is
 optional.  If not specified, the global LJ cutoff is used.
 
-If the pair_coeff command is not used to define coefficients for a
-particular I != J type pair, the mixing rule is set by the
-"pair_modify"_pair_modify.html command.  Additionally, the delta
-coefficient is always mixed by the rule
+:line
+
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+For atom type pairs I,J and I != J, the epsilon, sigma, and shift
+coefficients and cutoff distance for this pair style can be mixed.
+Shift is always mixed via an {arithmetic} rule.  The other
+coefficients are mixed according to the pair_modify mix value.  The
+default mix value is {geometric}.  See the "pair_modify" command for
+details.
+
+This pair style supports the "pair_modify"_pair_modify.html shift
+option for the energy of the pair interaction.
+
+The "pair_modify"_pair_modify.html table option is not relevant
+for this pair style.
 
-delta_ij = (delta_i + delta_j) / 2 :pre
+This pair style supports the "pair_modify"_pair_modify.html tail
+option for adding a long-range tail correction to the energy and
+pressure of the pair interaction.
+
+This pair style can calculate per-atom energy and stress, as used by
+the "compute epair/atom"_compute_epair_atom.html, "compute
+stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
+commands.
+
+This pair style writes its information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+:line
 
 [Restrictions:] none
 
diff --git a/doc/pair_lj_smooth.html b/doc/pair_lj_smooth.html
index 085ae8fd20a324e8c1fd9c18bc0f247ce938b2f2..544cc11bd728c3e82166f09208a65429b1b40939 100644
--- a/doc/pair_lj_smooth.html
+++ b/doc/pair_lj_smooth.html
@@ -46,7 +46,7 @@ Plot the energy and force resulting from this formula via the
 types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
 above, or in the data file or restart files read by the
 <A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
-commands:
+commands, or by mixing as described below:
 </P>
 <UL><LI>epsilon (energy units)
 <LI>sigma (distance units)
@@ -58,6 +58,40 @@ Rin and cutoff are used.  Rin cannot be 0.0.  If Rin = cutoff, then no
 force smoothing is performed for this type pair; the standard LJ
 formula is used.
 </P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the epsilon, sigma, Rin
+coefficients and the cutoff distance for this pair style can be mixed.
+Rin is a cutoff value and is mixed like the cutoff.  The other
+coefficients are mixed according to the pair_modify mix option.  The
+default mix value is <I>geometric</I>.  See the "pair_modify" command for
+details.
+</P>
+<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the pair interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure, since the energy of the pair interaction is smoothed to 0.0
+at the cutoff.
+</P>
+<P>This pair style can calculate per-atom energy and stress, as used by
+the <A HREF = "compute_epair_atom.html">compute epair/atom</A>, <A HREF = "compute_stress_atom.html">compute
+stress/atom</A>, and <A HREF = "dump.html">dump custom</A>
+commands.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<HR>
+
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
diff --git a/doc/pair_lj_smooth.txt b/doc/pair_lj_smooth.txt
index 3e678f4567e64c27b78fc2c595f7074f7b2f8bc8..db6fa7cc148bad1b020a7c6e0d23f72776e582e1 100644
--- a/doc/pair_lj_smooth.txt
+++ b/doc/pair_lj_smooth.txt
@@ -43,7 +43,7 @@ The following coefficients must be defined for each pair of atoms
 types via the "pair_coeff"_pair_coeff.html command as in the examples
 above, or in the data file or restart files read by the
 "read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
+commands, or by mixing as described below:
 
 epsilon (energy units)
 sigma (distance units)
@@ -55,6 +55,41 @@ Rin and cutoff are used.  Rin cannot be 0.0.  If Rin = cutoff, then no
 force smoothing is performed for this type pair; the standard LJ
 formula is used.
 
+:line
+
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+For atom type pairs I,J and I != J, the epsilon, sigma, Rin
+coefficients and the cutoff distance for this pair style can be mixed.
+Rin is a cutoff value and is mixed like the cutoff.  The other
+coefficients are mixed according to the pair_modify mix option.  The
+default mix value is {geometric}.  See the "pair_modify" command for
+details.
+
+This pair style supports the "pair_modify"_pair_modify.html shift
+option for the energy of the pair interaction.
+
+The "pair_modify"_pair_modify.html table option is not relevant
+for this pair style.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+tail option for adding long-range tail corrections to energy and
+pressure, since the energy of the pair interaction is smoothed to 0.0
+at the cutoff.
+
+This pair style can calculate per-atom energy and stress, as used by
+the "compute epair/atom"_compute_epair_atom.html, "compute
+stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
+commands.
+
+This pair style writes its information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+:line
+
+
 [Restrictions:] none
 
 [Related commands:]
diff --git a/doc/pair_meam.html b/doc/pair_meam.html
index c04ad14c4202085bcdf08c50b9b396e638f36bc0..103f2000935720acfb993956bbbc67540ed24e30 100644
--- a/doc/pair_meam.html
+++ b/doc/pair_meam.html
@@ -187,7 +187,35 @@ alloy interaction between elements 1 and 2 to 4.37.
 </P>
 <HR>
 
-<P><B>Restrictions:</B> none
+<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS with
+user-specifiable parameters as described above.  You never need to
+specify a pair_coeff command with I != J arguments for this style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This pair style does not calculate per-atom energy and stress, as used
+by the <A HREF = "compute_epair_atom.html">compute epair/atom</A>, <A HREF = "compute_stress_atom.html">compute
+stress/atom</A>, and <A HREF = "dump.html">dump custom</A>
+commands.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This style is part of the "meam" package.  It is only enabled if
+LAMMPS was built with that package, which also requires the MEAM
+library be built and linked with LAMMPS.  See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS</A> section for more info.
 </P>
 <P><B>Related commands:</B>
 </P>
diff --git a/doc/pair_meam.txt b/doc/pair_meam.txt
index 49bed99bac3c8bda9fea7e45754ddcaf6e3e2ffa..af15b3e8600919ec8fe171e25dc96cf65b745a76 100644
--- a/doc/pair_meam.txt
+++ b/doc/pair_meam.txt
@@ -184,7 +184,35 @@ alloy interaction between elements 1 and 2 to 4.37.
 
 :line
 
-[Restrictions:] none
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS with
+user-specifiable parameters as described above.  You never need to
+specify a pair_coeff command with I != J arguments for this style.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This pair style does not calculate per-atom energy and stress, as used
+by the "compute epair/atom"_compute_epair_atom.html, "compute
+stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
+commands.
+
+This pair style does not write its information to "binary restart
+files"_restart.html, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+
+:line
+
+[Restrictions:]
+
+This style is part of the "meam" package.  It is only enabled if
+LAMMPS was built with that package, which also requires the MEAM
+library be built and linked with LAMMPS.  See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
 
 [Related commands:]
 
diff --git a/doc/pair_modify.txt b/doc/pair_modify.txt
index 71ad1a48341555e122b10024a46bef1049af60f1..ddde445e8e46777d445d933ce9bb6c9e18cce74f 100644
--- a/doc/pair_modify.txt
+++ b/doc/pair_modify.txt
@@ -14,8 +14,8 @@ pair_modify keyword value ... :pre
 
 one or more keyword/value pairs may be listed :ulb,l
 keyword = {shift} or {mix} or {table} or {tabinner} or {tail} :l
-  {shift} value = {yes} or {no}
   {mix} value = {geometric} or {arithmetic} or {sixthpower}
+  {shift} value = {yes} or {no}
   {table} value = N
     2^N = # of values in table
   {tabinner} value = cutoff
@@ -34,51 +34,56 @@ pair_modify table 12 :pre
 Modify the parameters of the currently defined pair style.  Not all
 parameters are relevant to all pair styles.
 
-The {shift} keyword determines whether the Lennard-Jones potential is
-shifted at its cutoff to 0.0.  If so, this adds an energy term to each
-pairwise interaction which will be printed in the thermodynamic
-output, but does not affect atom dynamics (forces).  Pair styles that
-are already 0.0 at their cutoff such as {lj/charmm/coul/charmm} are
-not affected by this setting.
-
-The {mix} keyword affects how Lennard-Jones coefficients for epsilon,
-sigma, and the cutoff are generated for interactions between atoms of
-type I and J, when I != J.  Coefficients for I = J are set explicitly
-in the data file or input script.  The "pair_coeff"_pair_coeff.html
-command can be used in the input script to specify epilon/sigma for a
-specific I != J pairing, which overrides the setting of the {mix}
-keyword.
-
-These are the formulas used by the 3 {mix} options.  In each case, the
-LJ cutoff is mixed the same way as sigma.  Note that some of these
-options are not available for certain pair styles.  See the doc page
-for individual pair styles for those restrictions.
-
-{geometric}
+The {mix} keyword affects pair coefficients for interactions between
+atoms of type I and J, when I != J and the coefficients are not
+explicity set in the input script.  Note that coefficients for I = J
+must be set explicitly, either in the input script via the
+"pair_coeff" command or in the "Pair Coeffs" section of the "data
+file"_read_data.html.  For some pair styles is is not necessary to
+specify coefficients when I != J, since a "mixing" rule will create
+them from the I,I and J,J settings.  The pair_modify {mix} value
+determines what formulas are used to compute the mixed coefficients.
+In each case, the cutoff distance is mixed the same way as sigma.
+
+Note that not all pair styles support mixing.  Also, some mix options
+are not available for certain pair styles.  See the doc page for
+individual pair styles for those restrictions.  Note also that the
+"pair_coeff"_pair_coeff.html command also can be to directly set
+coefficients for a specific I != J pairing, in which case no mixing is
+performed.
+
+mix {geometric}
 
 epsilon_ij = sqrt(epsilon_i * epsilon_j)
 sigma_ij = sqrt(sigma_i * sigma_j) :pre
 
-{arithmetic}
+mix {arithmetic}
 
 epsilon_ij = sqrt(epsilon_i * epsilon_j)
 sigma_ij = (sigma_i + sigma_j) / 2 :pre
 
-{sixthpower}
+mix {sixthpower}
 
 epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
              (sigma_i^6 + sigma_j^6)
 sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6) :pre
 
+The {shift} keyword determines whether a Lennard-Jones potential is
+shifted at its cutoff to 0.0.  If so, this adds an energy term to each
+pairwise interaction which will be included in the thermodynamic
+output, but does not affect pair forces or atom trajectories.  See the
+doc page for individual pair styles to see which ones support this
+option.
+
 The {table} keyword applies to pair styles with a long-range Coulombic
-term (lj/cut/coul/long and lj/charmm/coul/long).  If N is non-zero, a
-table of length 2^N is pre-computed for forces and energies, which can
-shrink their computational cost by up to a factor of 2.  The table is
-indexed via a bit-mapping technique "(Wolff)"_#Wolff and a linear
-interpolation is performed between adjacent table values.  In our
-experiments with different table styles (lookup, linear, spline), this
-method typically gave the best performance in terms of speed and
-accuracy.
+term; see the doc page for individual styles to see which potentials
+support this option.  If N is non-zero, a table of length 2^N is
+pre-computed for forces and energies, which can shrink their
+computational cost by up to a factor of 2.  The table is indexed via a
+bit-mapping technique "(Wolff)"_#Wolff and a linear interpolation is
+performed between adjacent table values.  In our experiments with
+different table styles (lookup, linear, spline), this method typically
+gave the best performance in terms of speed and accuracy.
 
 The choice of table length is a tradeoff in accuracy versus speed.  A
 larger N yields more accurate force computations, but requires more
@@ -100,19 +105,16 @@ nearly all pairwise interactions are computed via table lookup for
 simulations with "real" units, but some close pairs may be computed
 directly (non-table) for simulations with "lj" units.
 
-When the {tail} keyword is set to {yes}, long-range VanderWaals tail
-"corrections" are added to the energy and pressure.  These are
-included in the calculation and printing of thermodynamic quantities
-(see the "thermo_style"_thermo_style.html command).  Their effect will
-also be included in constant NPT or NPH simulations where the pressure
-influences the simulation box dimensions (see the "fix
-npt"_fix_npt.html and "fix nph"_fix_nph.html commands).
-
-The {tail} keyword is only supported by "pair_style"_pair_style.html
-pairwise potentials which include Lennard-Jones interactions which are
-cutoff at a non-zero energy.  This does not include the LJ CHARMM
-potentials or {lj/smooth} since they go to zero at the cutoff.  The
-formulas used for the long-range corrections come from equation 5 of
+When the {tail} keyword is set to {yes}, certain pair styles will add
+a long-range VanderWaals tail "correction" to the energy and pressure.
+See the doc page for individual styles to see which support this
+option.  These corrections are included in the calculation and
+printing of thermodynamic quantities (see the
+"thermo_style"_thermo_style.html command).  Their effect will also be
+included in constant NPT or NPH simulations where the pressure
+influences the simulation box dimensions (e.g. the "fix
+npt"_fix_npt.html and "fix nph"_fix_nph.html commands).  The formulas
+used for the long-range corrections come from equation 5 of
 "(Sun)"_#Sun.
 
 Several assumptions are inherent in using tail corrections, including
@@ -138,13 +140,8 @@ those interactions. :l,ule
 
 [Restrictions:] none
 
-Not all pair styles support mixing.  See the doc page for individual
-pair styles for details.
-
 You cannot use {shift} yes with {tail} yes, since those are
-conflicting options.
-
-You cannot use {tail} yes with 2d simulations.
+conflicting options.  You cannot use {tail} yes with 2d simulations.
 
 [Related commands:]
 
@@ -153,9 +150,11 @@ You cannot use {tail} yes with 2d simulations.
 
 [Default:]
 
-The option defaults are shift = no, mix = arithmetic (for lj/charmm
-pair styles), mix = geometric (for other pair styles), table = 12,
-and tabinner = sqrt(2.0), tail = no.
+The option defaults are mix = geometric, shift = no, table = 12,
+tabinner = sqrt(2.0), tail = no.
+
+Note that some pair styles perform mixing, but only a certain style of
+mixing.  See the doc pages for individual pair styles for details.
 
 :line
 
diff --git a/doc/pair_morse.html b/doc/pair_morse.html
index a489fae1e80447996cdcdff3222497e383edae97..0bc9956c01b5494d705e463f414c7afc7eaeed20 100644
--- a/doc/pair_morse.html
+++ b/doc/pair_morse.html
@@ -53,11 +53,37 @@ give identical answers.  Depending on system size and the processor
 you are running on, it may be 5-25% faster (for the pairwise portion
 of the run time).
 </P>
-<P><B>Restrictions:</B>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info</B>:
+</P>
+<P>None of the Morse pair styles support mixing.  Thus, coefficients for
+all I,J pairs must be specified explicitly.
+</P>
+<P>All of the Morse pair styles support the
+<A HREF = "pair_modify.html">pair_modify</A> shift option for the energy of the pair
+interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table options is not relevant for
+the Morse pair styles.
 </P>
-<P>The <I>morse</I> potential does not support the
-<A HREF = "pair_modify.hmtl">pair_modify</A> <I>mix</I> option.  Coefficients for all i,j
-pairs must be specified explicitly.
+<P>None of the Morse pair styles support the
+<A HREF = "pair_modify.html">pair_modify</A> tail option for adding long-range tail
+corrections to energy and pressure.
+</P>
+<P>All of the Morse pair styles can calculate per-atom energy and
+stress, as used by the <A HREF = "compute_epair_atom.html">compute epair/atom</A>,
+<A HREF = "compute_stress_atom.html">compute stress/atom</A>, and <A HREF = "dump.html">dump
+custom</A> commands.
+</P>
+<P>All of the Morse pair styles write their information to <A HREF = "restart.html">binary
+restart files</A>, so pair_style and pair_coeff commands do
+not need to be specified in an input script that reads a restart file.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
 </P>
 <P>The <I>morse/opt</I> style is part of the "opt" package.  It is only
 enabled if LAMMPS was built with that package.  See the <A HREF = "Section_start.html#2_3">Making
diff --git a/doc/pair_morse.txt b/doc/pair_morse.txt
index f673db8a9fa57ffb52aa89d5f21b6c649d9d9550..4849968d889e4370b5b8588b8c2b73b2c9c2e472 100644
--- a/doc/pair_morse.txt
+++ b/doc/pair_morse.txt
@@ -49,11 +49,37 @@ give identical answers.  Depending on system size and the processor
 you are running on, it may be 5-25% faster (for the pairwise portion
 of the run time).
 
-[Restrictions:]
+:line
+
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+None of the Morse pair styles support mixing.  Thus, coefficients for
+all I,J pairs must be specified explicitly.
+
+All of the Morse pair styles support the
+"pair_modify"_pair_modify.html shift option for the energy of the pair
+interaction.
+
+The "pair_modify"_pair_modify.html table options is not relevant for
+the Morse pair styles.
 
-The {morse} potential does not support the
-"pair_modify"_pair_modify.hmtl {mix} option.  Coefficients for all i,j
-pairs must be specified explicitly.
+None of the Morse pair styles support the
+"pair_modify"_pair_modify.html tail option for adding long-range tail
+corrections to energy and pressure.
+
+All of the Morse pair styles can calculate per-atom energy and
+stress, as used by the "compute epair/atom"_compute_epair_atom.html,
+"compute stress/atom"_compute_stress_atom.html, and "dump
+custom"_dump.html commands.
+
+All of the Morse pair styles write their information to "binary
+restart files"_restart.html, so pair_style and pair_coeff commands do
+not need to be specified in an input script that reads a restart file.
+
+:line
+
+[Restrictions:]
 
 The {morse/opt} style is part of the "opt" package.  It is only
 enabled if LAMMPS was built with that package.  See the "Making
diff --git a/doc/pair_soft.html b/doc/pair_soft.html
index 92a970717e0dc44fc45484fb7fb9a1dbe9939371..098d2de85b2b979374896f054cf6fc27f0f49519 100644
--- a/doc/pair_soft.html
+++ b/doc/pair_soft.html
@@ -39,7 +39,7 @@ cutoff.
 types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
 above, or in the data file or restart files read by the
 <A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
-commands:
+commands, or by mixing as described below:
 </P>
 <UL><LI>Astart (energy units)
 <LI>Astop (energy units)
@@ -54,12 +54,34 @@ or switch to a new pair style.
 <P>The last coefficient is optional.  If not specified, the global soft
 cutoff is used.
 </P>
-<P>If the pair_coeff command is not used to define coefficients for a
-particular I != J type pair, the mixing rule for Astart and Astop is
-as follows:
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info</B>:
 </P>
-<PRE>A_ij = sqrt(A_i * A_j) 
-</PRE>
+<P>For atom type pairs I,J and I != J, the Astart, Astop coefficients and
+cutoff distance for this pair style can be mixed.  Astart and Atop are
+always mixed via a <I>geometric</I> rule.  The cutoff is mixed according to
+the pair_modify mix value.  The default mix value is <I>geometric</I>.  See
+the "pair_modify" command for details.
+</P>
+<P>This pair styles does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift option, since the pair interaction is goes to 0.0 at the cutoff.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table and tail options are not
+relevant for this pair style.
+</P>
+<P>This pair style can calculate per-atom energy and stress, as used by
+the <A HREF = "compute_epair_atom.html">compute epair/atom</A>, <A HREF = "compute_stress_atom.html">compute
+stress/atom</A>, and <A HREF = "dump.html">dump custom</A>
+commands.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<HR>
+
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
diff --git a/doc/pair_soft.txt b/doc/pair_soft.txt
index 5f1f21b895dc8030d0d12fe807e07c2c2d7e8b5d..6894ced294086eda9875d485d4fc64d59475539e 100644
--- a/doc/pair_soft.txt
+++ b/doc/pair_soft.txt
@@ -36,7 +36,7 @@ The following coefficients must be defined for each pair of atoms
 types via the "pair_coeff"_pair_coeff.html command as in the examples
 above, or in the data file or restart files read by the
 "read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
+commands, or by mixing as described below:
 
 Astart (energy units)
 Astop (energy units)
@@ -51,11 +51,33 @@ or switch to a new pair style.
 The last coefficient is optional.  If not specified, the global soft
 cutoff is used.
 
-If the pair_coeff command is not used to define coefficients for a
-particular I != J type pair, the mixing rule for Astart and Astop is
-as follows:
+:line
+
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+For atom type pairs I,J and I != J, the Astart, Astop coefficients and
+cutoff distance for this pair style can be mixed.  Astart and Atop are
+always mixed via a {geometric} rule.  The cutoff is mixed according to
+the pair_modify mix value.  The default mix value is {geometric}.  See
+the "pair_modify" command for details.
+
+This pair styles does not support the "pair_modify"_pair_modify.html
+shift option, since the pair interaction is goes to 0.0 at the cutoff.
 
-A_ij = sqrt(A_i * A_j) :pre
+The "pair_modify"_pair_modify.html table and tail options are not
+relevant for this pair style.
+
+This pair style can calculate per-atom energy and stress, as used by
+the "compute epair/atom"_compute_epair_atom.html, "compute
+stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
+commands.
+
+This pair style writes its information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+:line
 
 [Restrictions:] none
 
diff --git a/doc/pair_style.txt b/doc/pair_style.txt
index d5465744151010b7268e5a931e310bda09a470f2..9a6384a8a101bb4af1a47cf429e92a6b8de19890 100644
--- a/doc/pair_style.txt
+++ b/doc/pair_style.txt
@@ -14,17 +14,14 @@ pair_style style args :pre
 
 style = one of the following :ulb,l
 
-{none}, {hybrid}, {buck}, {buck/coul/cut}, {buck/coul/long},
-{colloid}, {dipole/cut}, {dpd}, {eam}, {eam/opt}, {eam/alloy},
-{eam/alloy/opt}, {eam/fs}, {eam/fs/opt}, {gayberne},
-{gran/hertzian}, {gran/history}, {gran/no_history},
-{lj/charmm/coul/charmm}, {lj/charmm/coul/charmm/opt},
-{lj/charmm/coul/charmm/implicit}, {lj/charmm/coul/long},
-{lj/class2}, {lj/class2/coul/cut}, {lj/class2/coul/long},
-{lj/cut}, {lj/cut/opt}, {lj/cut/coul/cut},
-{lj/cut/coul/debye}, {lj/cut/coul/long}, {lj/cut/coul/long/tip4p},
-{lj/expand}, {lj/smooth}, {meam}, {morse}, {morse/opt}, {soft}, {sw}, {table},
-{tersoff}, {yukawa} :ul
+{none}, {hybrid}, {airebo}, {buck}, {buck/coul/cut}, {buck/coul/long},
+{dpd}, {eam}, {eam/alloy} or {eam/fs}, {gran/hertzian},
+{gran/history}, {gran/no_history}, {lj/charmm/coul/charmm},
+{lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long},
+{lj/class2}, {lj/class2/coul/cut} or {lj/class2/coul/long}, {lj/cut},
+{lj/cut/coul/cut} or {lj/cut/coul/debye}, {lj/cut/coul/long},
+{lj/cut/coul/long/tip4p}, {lj/expand}, {lj/smooth}, {meam}, {morse},
+{soft}, {sw}, {table}, {tersoff}, {yukawa} :ul
 
 args = arguments used by a particular style :l,ule
 
@@ -49,7 +46,7 @@ In LAMMPS, pairwise force fields encompass a variety of interactions,
 some of which include many-body effects, e.g. EAM, Stillinger-Weber,
 Tersoff, REBO potentials.  They are still classified as "pairwise"
 potentials because the set of interacting atoms changes with time
-(unlike a bonded system) and thus a neighbor list is used to find
+(unlike molecular bonds) and thus a neighbor list is used to find
 nearby interacting atoms.
 
 Hybrid models where specified pairs of atom types interact via
@@ -59,9 +56,18 @@ The coefficients associated with a pair style are typically set for
 each pair of atom types, and are specified by the
 "pair_coeff"_pair_coeff.html command or read from a file by the
 "read_data"_read_data.html or "read_restart"_read_restart.html
-commands.  Mixing, shifting, and tail corrections for the potentials
-is discussed is the documentation for the
-"pair_modify"_pair_modify.html command.
+commands.
+
+The "pair_modify"_pair_modify.html command sets options for mixing of
+type I-J interaction coefficients and adding energy offsets or tail
+corrections to Lennard-Jones potentials.  Details on these options as
+they pertain to individual potentials are described on the doc page
+for the potential.  Likewise, info on whether the potential
+information is stored in a "restart file"_write_restart.html or
+whether the potential supports calculation of per-atom energy and
+stress by the "compute epair/atom"_compute_epair_atom.html and
+"compute stress/atom"_compute_stress_atom.html commands is given on
+the potential doc page.
 
 In the formulas listed for each pair style, {E} is the energy of a
 pairwise interaction between two atoms separated by a distance {r}.
@@ -92,18 +98,15 @@ the pair_style command, and coefficients specified by the associated
 "pair_style none"_pair_none.html - turn off pairwise interactions
 "pair_style hybrid"_pair_hybrid.html - define multiple styles of pairwise interactions :ul
 
+"pair_style airebo"_pair_airebo.html - AI-REBO potential
 "pair_style buck"_pair_buck.html - Buckingham potential
 "pair_style buck/coul/cut"_pair_buck.html - Buckinhham with cutoff Coulomb
 "pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulomb
 "pair_style colloid"_pair_colloid.html - integrated colloidal potential
-"pair_style dipole/cut"_pair_dpd.html - point dipole potential
 "pair_style dpd"_pair_dpd.html - dissipative particle dynamics (DPD)
 "pair_style eam"_pair_eam.html - embedded atom method (EAM)
-"pair_style eam/opt"_pair_eam.html - optimized embedded atom method (EAM)
 "pair_style eam/alloy"_pair_eam.html - alloy EAM
-"pair_style eam/alloy/opt"_pair_eam.html - optimized alloy EAM
 "pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
-"pair_style eam/fs/opt"_pair_eam.html - optimized Finnis-Sinclair EAM
 "pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
 "pair_style gran/hertzian"_pair_gran.html - granular potential with Hertizain interactions
 "pair_style gran/history"_pair_gran.html - granular potential with history effects
@@ -111,12 +114,10 @@ the pair_style command, and coefficients specified by the associated
 "pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
 "pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
 "pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
-"pair_style lj/charmm/coul/long/opt"_pair_charmm.html - optimized CHARMM with long-range Coulomb
 "pair_style lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb
 "pair_style lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb
 "pair_style lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb
 "pair_style lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb
-"pair_style lj/cut/opt"_pair_lj.html - optimized cutoff Lennard-Jones potential with no Coulomb
 "pair_style lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb
 "pair_style lj/cut/coul/debye"_pair_lj.html - LJ with Debye damping added to Coulomb
 "pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulomb
@@ -125,7 +126,6 @@ the pair_style command, and coefficients specified by the associated
 "pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
 "pair_style meam"_pair_meam.html - modified embedded atom method (MEAM)
 "pair_style morse"_pair_morse.html - Morse potential
-"pair_style morse/opt"_pair_morse.html - optimized Morse potential
 "pair_style soft"_pair_soft.html - Soft (cosine) potential
 "pair_style sw"_pair_sw.html - Stillinger-Weber 3-body potential
 "pair_style table"_pair_table.html - tabulated pair potential
@@ -142,7 +142,9 @@ This command must be used before any coefficients are set by the
 
 Some pair styles are part of specific packages.  They are only enabled
 if LAMMPS was built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
+LAMMPS"_Section_start.html#2_3 section for more info on packages.  The
+doc pages for individual pair potentials tell if it is part of a
+package.
 
 [Related commands:]
 
diff --git a/doc/pair_sw.html b/doc/pair_sw.html
index 9f3bad4b1b2564ccc6ca8c46766cfb3279c15a20..b33623832bd335c02f7aa0952deec844dd06d33f 100644
--- a/doc/pair_sw.html
+++ b/doc/pair_sw.html
@@ -110,16 +110,44 @@ The parameters used only for two-body interactions (A, B, p, and q)
 in entries whose 2nd and 3rd element are different (e.g. SiCSi) 
 are not used for anything and can be set to 0.0 if desired.
 </P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above from values in the potential file.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This pair style does not calculate per-atom energy and stress, as used
+by the <A HREF = "compute_epair_atom.html">compute epair/atom</A>, <A HREF = "compute_stress_atom.html">compute
+stress/atom</A>, and <A HREF = "dump.html">dump custom</A>
+commands.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<HR>
+
 <P><B>Restrictions:</B>
 </P>
-<P>This pair potential requires the <A HREF = "newton.html">newton</A> setting to be
-"on" for pair interactions.
+<P>This pair style is part of the "manybody" package.  It is only enabled
+if LAMMPS was built with that package (which it is by default).  See
+the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for more info.
+</P>
+<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
+for pair interactions.
 </P>
 <P>The Stillinger-Weber potential files provided with LAMMPS (see the
 potentials directory) are parameterized for metal <A HREF = "units.html">units</A>.
-You can use the SW potential with any LAMMPS units, but you need to
-create your own SW potential file if your simulation doesn't use
-"metal" units.
+You can use the SW potential with any LAMMPS units, but you would need
+to create your own SW potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
 </P>
 <P><B>Related commands:</B>
 </P>
diff --git a/doc/pair_sw.txt b/doc/pair_sw.txt
index d2f7c4625c5814792c9c52b8d7cd266ec0c9ba7e..3797815995f050fd1b82b175854a6a367e766d44 100644
--- a/doc/pair_sw.txt
+++ b/doc/pair_sw.txt
@@ -107,16 +107,44 @@ The parameters used only for two-body interactions (A, B, p, and q)
 in entries whose 2nd and 3rd element are different (e.g. SiCSi) 
 are not used for anything and can be set to 0.0 if desired.
 
+:line
+
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above from values in the potential file.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This pair style does not calculate per-atom energy and stress, as used
+by the "compute epair/atom"_compute_epair_atom.html, "compute
+stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
+commands.
+
+This pair style does not write its information to "binary restart
+files"_restart.html, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+
+:line
+
 [Restrictions:]
 
-This pair potential requires the "newton"_newton.html setting to be
-"on" for pair interactions.
+This pair style is part of the "manybody" package.  It is only enabled
+if LAMMPS was built with that package (which it is by default).  See
+the "Making LAMMPS"_Section_start.html#2_3 section for more info.
+
+This pair style requires the "newton"_newton.html setting to be "on"
+for pair interactions.
 
 The Stillinger-Weber potential files provided with LAMMPS (see the
 potentials directory) are parameterized for metal "units"_units.html.
-You can use the SW potential with any LAMMPS units, but you need to
-create your own SW potential file if your simulation doesn't use
-"metal" units.
+You can use the SW potential with any LAMMPS units, but you would need
+to create your own SW potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
 
 [Related commands:]
 
diff --git a/doc/pair_table.html b/doc/pair_table.html
index 34c78e993f5794f3c60defe169fb0a2093c57b14..db24c18de0521984affc4515076cd6e6516800cc 100644
--- a/doc/pair_table.html
+++ b/doc/pair_table.html
@@ -140,11 +140,32 @@ from one line to the next (unless the BITMAP parameter is specified).
 potential.  LAMMPS reads the file section by section until it finds
 one that matches the specified keyword.
 </P>
-<P><B>Restrictions:</B>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info</B>:
+</P>
+<P>This pair style does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> shift, table, and tail options are
+not relevant for this pair style.
 </P>
-<P>The <I>table</I> potential does not support the
-<A HREF = "pair_modify.hmtl">pair_modify</A> <I>mix</I> option.  Coefficients for all i,j
-pairs must be specified explicitly.
+<P>This pair style can calculate per-atom energy and stress, as used by
+the <A HREF = "compute_epair_atom.html">compute epair/atom</A>, <A HREF = "compute_stress_atom.html">compute
+stress/atom</A>, and <A HREF = "dump.html">dump custom</A>
+commands.
+</P>
+<P>This pair style writes the settings for the "pair_style table" command
+to <A HREF = "restart.html">binary restart files</A>, so a pair_style command does
+not need to specified in an input script that reads a restart file.
+However, the coefficient information is not stored in the restart
+file, since it is tabulated in the potential files.  Thus, pair_coeff
+commands do need to be specified in the restart input script.
+</P>
+<HR>
+
+<P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
 </P>
diff --git a/doc/pair_table.txt b/doc/pair_table.txt
index d362690a4b8b97edd543ad14d96f0be8cf2de68e..96c7c15cd2b43b5ebf17e46f2a2c9b5cd87e2880 100644
--- a/doc/pair_table.txt
+++ b/doc/pair_table.txt
@@ -137,11 +137,32 @@ Note that one file can contain many sections, each with a tabulated
 potential.  LAMMPS reads the file section by section until it finds
 one that matches the specified keyword.
 
-[Restrictions:]
+:line
+
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+This pair style does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+The "pair_modify"_pair_modify.html shift, table, and tail options are
+not relevant for this pair style.
+
+This pair style can calculate per-atom energy and stress, as used by
+the "compute epair/atom"_compute_epair_atom.html, "compute
+stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
+commands.
+
+This pair style writes the settings for the "pair_style table" command
+to "binary restart files"_restart.html, so a pair_style command does
+not need to specified in an input script that reads a restart file.
+However, the coefficient information is not stored in the restart
+file, since it is tabulated in the potential files.  Thus, pair_coeff
+commands do need to be specified in the restart input script.
+
+:line
 
-The {table} potential does not support the
-"pair_modify"_pair_modify.hmtl {mix} option.  Coefficients for all i,j
-pairs must be specified explicitly.
+[Restrictions:] none
 
 [Related commands:]
 
diff --git a/doc/pair_tersoff.html b/doc/pair_tersoff.html
index b60f3594477b3fb412f0651c0f6a766a88f63c5f..4a8bf839b342438784b5f2e1a8877a815ddb8f66 100644
--- a/doc/pair_tersoff.html
+++ b/doc/pair_tersoff.html
@@ -113,16 +113,44 @@ The parameters used only for two-body interactions
 in entries whose 2nd and 3rd element are different (e.g. SiCSi) 
 are not used for anything and can be set to 0.0 if desired.
 </P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above from values in the potential file.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This pair style does not calculate per-atom energy and stress, as used
+by the <A HREF = "compute_epair_atom.html">compute epair/atom</A>, <A HREF = "compute_stress_atom.html">compute
+stress/atom</A>, and <A HREF = "dump.html">dump custom</A>
+commands.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+</P>
+<HR>
+
 <P><B>Restrictions:</B>
 </P>
-<P>This pair potential requires the <A HREF = "newton.html">newton</A> setting to be
-"on" for pair interactions.
+<P>This pair style is part of the "manybody" package.  It is only enabled
+if LAMMPS was built with that package (which it is by default).  See
+the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for more info.
+</P>
+<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
+for pair interactions.
 </P>
 <P>The Tersoff potential files provided with LAMMPS (see the potentials
 directory) are parameterized for metal <A HREF = "units.html">units</A>.  You can
-use the Tersoff potential with any LAMMPS units, but you need to
-create your own Tersoff potential file if your simulation doesn't use
-"metal" units.
+use the Tersoff potential with any LAMMPS units, but you would need to
+create your own Tersoff potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
 </P>
 <P><B>Related commands:</B>
 </P>
diff --git a/doc/pair_tersoff.txt b/doc/pair_tersoff.txt
index ad6328498adea2a5b26ae71a3c598474c62bfb0b..6542bf30ed780021072722a5324d2a28dd6b7f52 100644
--- a/doc/pair_tersoff.txt
+++ b/doc/pair_tersoff.txt
@@ -110,16 +110,44 @@ The parameters used only for two-body interactions
 in entries whose 2nd and 3rd element are different (e.g. SiCSi) 
 are not used for anything and can be set to 0.0 if desired.
 
+:line
+
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above from values in the potential file.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This pair style does not calculate per-atom energy and stress, as used
+by the "compute epair/atom"_compute_epair_atom.html, "compute
+stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
+commands.
+
+This pair style does not write its information to "binary restart
+files"_restart.html, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+
+:line
+
 [Restrictions:]
 
-This pair potential requires the "newton"_newton.html setting to be
-"on" for pair interactions.
+This pair style is part of the "manybody" package.  It is only enabled
+if LAMMPS was built with that package (which it is by default).  See
+the "Making LAMMPS"_Section_start.html#2_3 section for more info.
+
+This pair style requires the "newton"_newton.html setting to be "on"
+for pair interactions.
 
 The Tersoff potential files provided with LAMMPS (see the potentials
 directory) are parameterized for metal "units"_units.html.  You can
-use the Tersoff potential with any LAMMPS units, but you need to
-create your own Tersoff potential file if your simulation doesn't use
-"metal" units.
+use the Tersoff potential with any LAMMPS units, but you would need to
+create your own Tersoff potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
 
 [Related commands:]
 
diff --git a/doc/pair_yukawa.html b/doc/pair_yukawa.html
index fec92cab2222fb4c7b027b166fa36029f1748d93..9f00f8495143968f3bc96aa91e7104de61e6024e 100644
--- a/doc/pair_yukawa.html
+++ b/doc/pair_yukawa.html
@@ -36,7 +36,7 @@ pair_coeff * * 100.0
 types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
 above, or in the data file or restart files read by the
 <A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
-commands:
+commands, or by mixing as described below:
 </P>
 <UL><LI>A (energy units)
 <LI>cutoff (distance units) 
@@ -44,6 +44,37 @@ commands:
 <P>The last coefficient is optional.  If not specified, the global yukawa
 cutoff is used.
 </P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info</B>:
+</P>
+<P>For atom type pairs I,J and I != J, the A coefficient and cutoff
+distance for this pair style can be mixed.  A is an energy value mixed
+like a LJ epsilon.  The default mix value is <I>geometric</I>.  See the
+"pair_modify" command for details.
+</P>
+<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
+option for the energy of the pair interaction.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
+for this pair style.
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+tail option for adding long-range tail corrections to energy and
+pressure.
+</P>
+<P>This pair style can calculate per-atom energy and stress, as used by
+the <A HREF = "compute_epair_atom.html">compute epair/atom</A>, <A HREF = "compute_stress_atom.html">compute
+stress/atom</A>, and <A HREF = "dump.html">dump custom</A>
+commands.
+</P>
+<P>This pair style writes its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+</P>
+<HR>
+
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
diff --git a/doc/pair_yukawa.txt b/doc/pair_yukawa.txt
index 1e692b1cb3d9efe5c6a104be2ced6003b19b40fc..7c72ccbb5d00e19780d618b8c9add738aae00829 100644
--- a/doc/pair_yukawa.txt
+++ b/doc/pair_yukawa.txt
@@ -33,7 +33,7 @@ The following coefficients must be defined for each pair of atoms
 types via the "pair_coeff"_pair_coeff.html command as in the examples
 above, or in the data file or restart files read by the
 "read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
+commands, or by mixing as described below:
 
 A (energy units)
 cutoff (distance units) :ul
@@ -41,6 +41,37 @@ cutoff (distance units) :ul
 The last coefficient is optional.  If not specified, the global yukawa
 cutoff is used.
 
+:line
+
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+For atom type pairs I,J and I != J, the A coefficient and cutoff
+distance for this pair style can be mixed.  A is an energy value mixed
+like a LJ epsilon.  The default mix value is {geometric}.  See the
+"pair_modify" command for details.
+
+This pair style supports the "pair_modify"_pair_modify.html shift
+option for the energy of the pair interaction.
+
+The "pair_modify"_pair_modify.html table option is not relevant
+for this pair style.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style can calculate per-atom energy and stress, as used by
+the "compute epair/atom"_compute_epair_atom.html, "compute
+stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
+commands.
+
+This pair style writes its information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+:line
+
 [Restrictions:] none
 
 [Related commands:]
diff --git a/doc/read_restart.txt b/doc/read_restart.txt
index 48a94a695032eded43ef5e84c51cd077d38b7875..04a4e8d795cc68e724455bb0c097137454bc8e49 100644
--- a/doc/read_restart.txt
+++ b/doc/read_restart.txt
@@ -24,8 +24,9 @@ read_restart poly.*.% :pre
 
 [Description:]
 
-Read in a previously saved problem from a restart file.  This allows
-continuation of a previous run.
+Read in a previously saved simulation from a restart file.  This
+allows continuation of a previous run.  Information about what is
+stored in a restart file is given below.
 
 Restart files are saved in binary format to enable exact restarts,
 meaning that the trajectories of a restarted run will precisely match
@@ -36,11 +37,11 @@ include running on a different number of processors or changing
 certain settings such as those set by the "newton"_newton.html or
 "processors"_processors.html commands.  LAMMPS will issue a WARNING in
 these cases.  Certain fixes will also not restart exactly, though they
-should provide statistically similar results.  These include the shake
-and langevin styles.  If a restarted run is immediately different than
-the run which produced the restart file, it could be a LAMMPS bug, so
-consider "reporting it"_Section_errors.html#9_2 if you think the
-behavior is wrong.
+should provide statistically similar results.  These include "fix
+shake"_fix_shake.html and "fix langevin"_fix_langevin.html.  If a
+restarted run is immediately different than the run which produced the
+restart file, it could be a LAMMPS bug, so consider "reporting
+it"_Section_errors.html#9_2 if you think the behavior is wrong.
 
 Because restart files are binary, they may not be portable to other
 machines.  They can be converted to ASCII data files using the
@@ -74,36 +75,39 @@ current LAMMPS simulation.
 
 :line
 
-A restart file stores the units and atom style, simulation box
-attibutes (including whether it is an orthogonal box or a
-non-orthogonal parallelepiped with triclinic symmetry), individual
-atoms and their attributes including molecular topology, force field
-styles and coefficients, "special_bonds"_special_bonds.html settings,
-and atom group definitions.  This means that commands for these
-quantities do not need to be specified in your input script that reads
-the restart file.  The exceptions to this are listed below in the
-Restrictions section.
-
-Information about the "kspace_style"_kspace_style.html settings are
-not stored in the restart file.  Hence if you wish to invoke an Ewald
-or PPPM solver, this command must be re-issued after the restart file
-is read.
-
-The restart file also stores values for any fixes that require state
-information to enable restarting where they left off.  These include
-the {nvt} and {npt} styles that have a global state, as well as the
-{msd} and {wall/gran} styles that store information about each atom.
-
-"Fix"_fix.html commands are not stored in the restart file which means
-they must be specified in the input script that reads the restart
-file.  To re-enable a fix whose state was stored in the restart file,
-the fix command in the new input script must use the same fix-ID and
-group-ID as the input script that wrote the restart file.  LAMMPS will
-print a message indicating that the fix is being re-enabled.
-
-Note that no other information is stored in the restart file.  This
-means that your new input script should specify settings for
-quantities like timestep size, thermodynamic and dump output, etc.
+A restart file stores the following information about a simulation:
+units and atom style, simulation box size and shape and boundary
+settings, group definitions, atom type settings such as mass and
+particle shape, individual atoms and their group assignments and
+molecular topology attributes, force field styles and coefficients,
+and "special_bonds"_special_bonds.html settings.  This means that
+commands for these quantities do not need to be re-specified in the
+input script that reads the restart file, though you can redefine
+settings after the restart file is read.
+
+One exception is that some pair styles do not store their info in
+restart files.  The doc pages for individual pair styles note if this
+is the case.  This is also true of bond_style hybrid (and angle_style,
+dihedral_style, improper_style hybrid).
+
+Information about "kspace_style"_kspace_style.html settings are not
+stored in the restart file.  Hence if you wish to use an Ewald or PPPM
+solver, these commands must be re-issued after the restart file is
+read.
+
+The list of "fixes"_fix.html used for a simulation is not stored in
+the restart file.  This means the new input script should specify all
+fixes it will use.  Note that some fixes store an internal "state"
+which is written to the restart file.  This allows the fix to continue
+on with its calculations in a restarted simulation.  To re-enable such
+a fix, the fix command in the new input script must use the same
+fix-ID and group-ID as was used in the input script that wrote the
+restart file.  If a match is found, LAMMPS prints a message indicating
+that the fix is being re-enabled.  If no match is found before the
+first run or minimization is performed by the new script, the "state"
+information for the saved fix is discarded.  See the doc pages for
+individual fixes for info on which ones can be restarted in this
+manner.
 
 Bond interactions (angle, etc) that have been turned off by the "fix
 shake"_fix_shake.html or "delete_bonds"_delete_bonds.html command will
@@ -115,15 +119,13 @@ Bonds that are broken (e.g. by a bond-breaking potential) are written
 to the restart file as broken bonds with a type of 0.  Thus these
 bonds will still be broken when the restart file is read.
 
-[Restrictions:]
+IMPORTANT NOTE: No other information is stored in the restart file.
+This means that an input script that reads a restart file should
+specify settings for quantities like "timestep size"_timestep.html,
+"thermodynamic"_thermo_style.html and "dump"_dump.html output,
+"geometric regions"_region.html, etc.
 
-The "pair_style"_pair_style.html {eam}, {table}, and {hybrid} styles
-do not store coefficient data for individual atom type pairs in the
-restart file.  Nor does the "bond_style hybrid"_bond_style.html style
-(angle, dihedral hybrid, etc).  Thus for these styles you must use new
-"pair_coeff"_pair_coeff.html and "bond_coeff"_bond_coeff.html (angle,
-dihedral, etc) commands to read the appropriate tabulated files or
-reset the coefficients after the restart file is read.
+[Restrictions:] none
 
 [Related commands:]
 
diff --git a/doc/run.html b/doc/run.html
index 202b0dafde63a955003eccf39d43163d36a96198..1d48c2996243fdb6daeaa596d811b27280b68fc4 100644
--- a/doc/run.html
+++ b/doc/run.html
@@ -65,14 +65,12 @@ script with the same run command until the simulation finally
 completes.
 </P>
 <P>The <I>start</I> or <I>stop</I> keywords can be used if multiple runs are being
-performed and you want a <A HREF = "fix.html">fix</A> command that ramps some value
-(e.g. a temperature) over time to do its ramping across the entire set
-of runs and not just a single run.  Fixes in this category include
-<A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_npt.html">fix npt</A>, <A HREF = "fix_langevin.html">fix
-langevin</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>,
-<A HREF = "fix_deform.html">fix deform</A>, and <A HREF = "fix_indent.html">fix indent</A>.  The
-<A HREF = "pair_style.html">pair_style soft</A> potential also ramps its
-coefficients in a similar way.
+performed and you want a <A HREF = "fix.html">fix</A> command that changes some
+value over time (e.g. temperature) to make the change across the
+entire set of runs and not just a single run.  See the doc page for
+individual fixes to see which ones can be used with the <I>start/stop</I>
+keywords.  The <A HREF = "pair_style.html">pair_style soft</A> potential also
+changes its pair potential coefficients in this manner.
 </P>
 <P>For example, consider this fix followed by 10 run commands:
 </P>
diff --git a/doc/run.txt b/doc/run.txt
index 8568ad401dc8dfd2303533aecc950fe1de0fe952..a53cdc34d3cdcb448556a3255f79be9438f4ee10 100644
--- a/doc/run.txt
+++ b/doc/run.txt
@@ -58,14 +58,12 @@ script with the same run command until the simulation finally
 completes.
 
 The {start} or {stop} keywords can be used if multiple runs are being
-performed and you want a "fix"_fix.html command that ramps some value
-(e.g. a temperature) over time to do its ramping across the entire set
-of runs and not just a single run.  Fixes in this category include
-"fix nvt"_fix_nvt.html, "fix npt"_fix_npt.html, "fix
-langevin"_fix_langevin.html, "fix temp/rescale"_fix_temp_rescale.html,
-"fix deform"_fix_deform.html, and "fix indent"_fix_indent.html.  The
-"pair_style soft"_pair_style.html potential also ramps its
-coefficients in a similar way.
+performed and you want a "fix"_fix.html command that changes some
+value over time (e.g. temperature) to make the change across the
+entire set of runs and not just a single run.  See the doc page for
+individual fixes to see which ones can be used with the {start/stop}
+keywords.  The "pair_style soft"_pair_style.html potential also
+changes its pair potential coefficients in this manner.
 
 For example, consider this fix followed by 10 run commands:
 
diff --git a/doc/thermo_modify.txt b/doc/thermo_modify.txt
index 67e60be88e53f2e1c49ba3e85f5fbb5540d8eacc..432b3a413710f83b3e43044ea0663746ccef2d7e 100644
--- a/doc/thermo_modify.txt
+++ b/doc/thermo_modify.txt
@@ -41,11 +41,11 @@ Set options for how thermodynamic information is computed and printed
 by LAMMPS.
 
 IMPORTANT NOTE: These options apply to the currently defined thermo
-style (thermo_style {one} by default).  When you specify a
-"thermo_style"_thermo_style.html command, all thermodynamic settings
-are restored to their default values.  Thus a thermo_style command
-will wipe out any options previously specified by the
-"thermo_modify"_thermo_modify.html command.
+style.  When you specify a "thermo_style"_thermo_style.html command,
+all thermodynamic settings are restored to their default values,
+including those previously set by a thermo_modify command.  Thus if
+your input script specifies a thermo_style command, you should use the
+thermo_modify command after it.
 
 The {lost} keyword determines whether LAMMPS checks for lost atoms
 each time it computes thermodynamics and what it does if atoms are
diff --git a/doc/thermo_style.txt b/doc/thermo_style.txt
index b309594c4ff315f963665e0955fbaea5ab65d344..8a5c4efc2f60c74a0c70065a6667f12e5e362195 100644
--- a/doc/thermo_style.txt
+++ b/doc/thermo_style.txt
@@ -102,11 +102,11 @@ be used to set the one- or multi-line format of the print-out, the
 normalization of energy quantities (total or per-atom), and the
 numeric precision of each printed value.
 
-IMPORTANT NOTE: When you specify a "thermo_style"_thermo_style.html
-command, all thermodynamic settings are restored to their default
-values.  Thus a thermo_style command will wipe out any options
-previously specified by the "thermo_modify"_thermo_modify.html
-command.
+IMPORTANT NOTE: When you specify a "thermo_style" command, all
+thermodynamic settings are restored to their default values, including
+those previously set by a :thermo_modify"_thermo_modify.html command.
+Thus if your input script specifies a thermo_style command, you should
+use the thermo_modify command after it.
 
 :line
 
@@ -198,24 +198,29 @@ The {c_ID} and {c_ID\[N\]} keywords allow scalar or vector quantities
 calculated by a compute to be output.  The ID in the keyword should be
 replaced by the actual ID of the compute that has been defined
 elsewhere in the input script.  See the "compute"_compute.html command
-for details.  Note that per-atom quantities calcalated by a compute
-cannot be output as part of thermodynamics.  Rather, these quantities
-are output by the "dump custom"_dump.html command.
+for details.  Note that only global scalar or vector quantites
+calculated by a compute can be output as thermodynamic data; per-atom
+quantities calcalated by a compute are output by the "dump
+custom"_dump.html command.
 
 If {c_ID} is used as a keyword, then the scalar quantity calculated by
 the compute is printed.  If {c_ID\[N\]} is used, then N in the range
 from 1-M will print the Nth component of the M-length vector
-calculated by the compute.
+calculated by the compute.  See the doc pages for individual compute
+styles for info on what these quantities are.
 
 The {f_ID} and {f_ID\[N\]} keywords allow scalar or vector quantities
 calculated by a fix to be output.  The ID in the keyword should be
 replaced by the actual ID of the fix that has been defined elsewhere
-in the input script.  See the "fix"_fix.html command for details.
+in the input script.
 
 If {f_ID} is used as a keyword, then the scalar quantity calculated by
 the fix is printed.  If {f_ID\[N\]} is used, then N in the range from
 1-M will print the Nth component of the M-length vector calculated by
-the fix.
+the fix.  See the doc pages for individual fix styles for info on what
+these quantities are.  For fixes that compute a contribution to the
+potential energy of the system, the scalar quantity f_ID is typically
+that quantity.
 
 The {v_name} keyword allow the current value of a variable to be
 output.  The name in the keyword should be replaced by the actual namd
@@ -228,7 +233,8 @@ periodically during a simulation.
 
 See "this section"_Section_modify.html for information on how to add
 new compute and fix styles as well as variable options to LAMMPS that
-calculate quantities that could then be output with these keywords.
+calculate quantities that could then be output with these keywords as
+part of thermodyanmic information.
 
 :line