git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14509 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/angle_charmm.html

@@ -155,7 +155,7 @@ angle_coeff 1 300.0 107.0 50.0 3.0
 <p>with an additional Urey_Bradley term based on the distance <em>r</em> between
 the 1st and 3rd atoms in the angle.  K, theta0, Kub, and Rub are
 coefficients defined for each angle type.</p>
-<p>See <a class="reference internal" href="dihedral_charmm.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
+<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
 field.</p>
 <p>The following coefficients must be defined for each angle type via the
 <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in

doc/dihedral_charmm.html

@@ -152,9 +152,9 @@ dihedral_coeff 1 120.0 1 60 0.5
 <h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
 <p>The <em>charmm</em> dihedral style uses the potential</p>
 <img alt="_images/dihedral_charmm.jpg" class="align-center" src="_images/dihedral_charmm.jpg" />
-<p>See <a class="reference internal" href="#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
+<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
 field.  This dihedral style can also be used for the AMBER force field
-(see comment on weighting factors below).  See <a class="reference internal" href="#cornell"><span>(Cornell)</span></a>
+(see comment on weighting factors below).  See <a class="reference internal" href="special_bonds.html#cornell"><span>(Cornell)</span></a>
 for a description of the AMBER force field.</p>
 <p>The following coefficients must be defined for each dihedral type via the
 <a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a> command as in the example above, or in

doc/dump_image.html

@@ -155,8 +155,10 @@
 <em>line</em> = color width
   color = <em>type</em>
   width = numeric value for line width (distance units)
-<em>tri</em> = color
+<em>tri</em> = color tflag width
   color = <em>type</em>
+  tflag = 1 for just triangle, 2 for just tri edges, 3 for both
+  width = numeric value for tringle edge width (distance units)
 <em>body</em> = color bflag1 bflag2
   color = <em>type</em>
   bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn
@@ -421,12 +423,14 @@ lines will be drawn as cylinders with that diameter, e.g. 1.0, which
 is in whatever distance <a class="reference internal" href="units.html"><em>units</em></a> the input script defines,
 e.g. Angstroms.</p>
 <p>The <em>tri</em> keyword can be used when <a class="reference internal" href="atom_style.html"><em>atom_style tri</em></a> is
-used to define particles as triangles, and will draw them as
+used to define particles as triangles, and will draw them as triangles
-triangles.  If this keyword is not used, such particles will be drawn
+or edges (3 lines) or both, depending on the setting for <em>tflag</em>.  If
-as spheres, the same as if they were regular atoms.  The only setting
+edges are drawn, the <em>width</em> setting determines the diameters of the
-currently allowed for the <em>color</em> value is <em>type</em>, which will color
+line segments.  If this keyword is not used, triangle particles will
-the triangles according to the atom type of the particle.  By default
+be drawn as spheres, the same as if they were regular atoms.  The only
-the mapping of types to colors is as follows:</p>
+setting currently allowed for the <em>color</em> value is <em>type</em>, which will
+color the triangles according to the atom type of the particle.  By
+default the mapping of types to colors is as follows:</p>
 <ul class="simple">
 <li>type 1 = red</li>
 <li>type 2 = green</li>

doc/dump_image.txt

@@ -31,8 +31,10 @@ keyword = {atom} or {adiam} or {bond} or {line} or {tri} or {body} or {size} or
   {line} = color width
     color = {type}
     width = numeric value for line width (distance units)
-  {tri} = color
+  {tri} = color tflag width
     color = {type}
+    tflag = 1 for just triangle, 2 for just tri edges, 3 for both
+    width = numeric value for tringle edge width (distance units)
   {body} = color bflag1 bflag2
     color = {type}
     bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn
@@ -317,12 +319,14 @@ is in whatever distance "units"_units.html the input script defines,
 e.g. Angstroms.
 
 The {tri} keyword can be used when "atom_style tri"_atom_style.html is
-used to define particles as triangles, and will draw them as
+used to define particles as triangles, and will draw them as triangles
-triangles.  If this keyword is not used, such particles will be drawn
+or edges (3 lines) or both, depending on the setting for {tflag}.  If
-as spheres, the same as if they were regular atoms.  The only setting
+edges are drawn, the {width} setting determines the diameters of the
-currently allowed for the {color} value is {type}, which will color
+line segments.  If this keyword is not used, triangle particles will
-the triangles according to the atom type of the particle.  By default
+be drawn as spheres, the same as if they were regular atoms.  The only
-the mapping of types to colors is as follows:
+setting currently allowed for the {color} value is {type}, which will
+color the triangles according to the atom type of the particle.  By
+default the mapping of types to colors is as follows:
 
 type 1 = red
 type 2 = green

doc/fix_pour.html

@@ -134,11 +134,11 @@
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
 <li>pour = style name of this fix command</li>
-<li>N = # of atoms to insert</li>
+<li>N = # of particles to insert</li>
-<li>type = atom type to assign to inserted atoms (offset for molecule insertion)</li>
+<li>type = atom type to assign to inserted particles (offset for molecule insertion)</li>
 <li>seed = random # seed (positive integer)</li>
 <li>one or more keyword/value pairs may be appended to args</li>
-<li>keyword = <em>region</em> or <em>diam</em> or <em>dens</em> or <em>vol</em> or <em>rate</em> or <em>vel</em> or <em>mol</em> or <em>rigid</em> or <em>shake</em></li>
+<li>keyword = <em>region</em> or <em>diam</em> or <em>vol</em> or <em>rate</em> or <em>dens</em> or <em>vel</em> or <em>mol</em> or <em>rigid</em> or <em>shake</em> or <em>ignore</em></li>
 </ul>
 <pre class="literal-block">
 <em>region</em> value = region-ID
@@ -153,12 +153,16 @@
       Npoly = # of (D,P) pairs
       D1,D2,... = diameter for subset of inserted particles (distance units)
       P1,P2,... = percentage of inserted particles with this diameter (0-1)
+<em>id</em> values = idflag
+  idflag = <em>max</em> or <em>next</em> = how to choose IDs for inserted particles and molecules
 <em>vol</em> values = fraction Nattempt
   fraction = desired volume fraction for filling insertion volume
-  Nattempt = max # of insertion attempts per atom
+  Nattempt = max # of insertion attempts per particle
 <em>rate</em> value = V
   V = z velocity (3d) or y velocity (2d) at which
       insertion volume moves (velocity units)
+<em>dens</em> values = Rholo Rhohi
+  Rholo,Rhohi = range of densities for inserted particles (mass/volume units)
 <em>vel</em> values (3d) = vxlo vxhi vylo vyhi vz
 <em>vel</em> values (2d) = vxlo vxhi vy
   vxlo,vxhi = range of x velocities for inserted particles (velocity units)
@@ -173,6 +177,9 @@
   fix-ID = ID of <a class="reference internal" href="fix_rigid.html"><em>fix rigid/small</em></a> command
 <em>shake</em> value = fix-ID
   fix-ID = ID of <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command
+<em>ignore</em> value = none
+  skip any line or triangle particles when detecting possible
+    overlaps with inserted particles
 </pre>
 </div>
 <div class="section" id="examples">
@@ -242,6 +249,14 @@ timestep.  Particles are inserted again after enough time has elapsed
 that the previously inserted particles fall out of the insertion
 volume under the influence of gravity.  Insertions continue every so
 many timesteps until the desired # of particles has been inserted.</p>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">If you are monitoring the temperature of a system where the
+particle count is changing due to adding particles, you typically
+should use the <a class="reference internal" href="compute_modify.html"><em>compute_modify dynamic yes</em></a>
+command for the temperature compute you are using.</p>
+</div>
+<hr class="docutils" />
 <p>All other keywords are optional with defaults as shown below.</p>
 <p>The <em>diam</em> option is only used when inserting atoms and specifes the
 diameters of inserted particles.  There are 3 styles: <em>one</em>, <em>range</em>,
@@ -257,11 +272,17 @@ or 1.5.  40% of the particles will be small; 60% will be large.</p>
 the molecule can be specified in the file read by the
 <a class="reference internal" href="molecule.html"><em>molecule</em></a> command.  If not specified, the diameter of
 each atom in the molecule has a default diameter of 1.0.</p>
-<p>The <em>dens</em> and <em>vel</em> options enable inserted particles to have a range
+<p>The <em>id</em> option has two settings which are used to determine the atom
-of densities or xy velocities.  The specific values for a particular
+or molecule IDs to assign to inserted particles/molecules.  In both
-inserted particle will be chosen randomly and uniformly between the
+cases a check is done of the current system to find the maximum
-specified bounds.  The <em>vz</em> or <em>vy</em> value for option <em>vel</em> assigns a
+current atom and molecule ID of any existing particle.  Newly inserted
-z-velocity (3d) or y-velocity (2d) to each inserted particle.</p>
+particles and molecules are assigned IDs that increment those max
+values.  For the <em>max</em> setting, which is the default, this check is
+done at every insertion step, which allows for particles to leave the
+system, and their IDs to potentially be re-used.  For the <em>next</em>
+setting this check is done only once when the fix is specified, which
+can be more efficient if you are sure particles will not be added in
+some other way.</p>
 <p>The <em>vol</em> option specifies what volume fraction of the insertion
 volume will be filled with particles.  For particles with a size
 specified by the <em>diam range</em> keyword, they are assumed to all be of
@@ -274,16 +295,27 @@ particles are inserted, LAMMPS will make up to a total of M tries to
 insert the new particles without overlaps, where M = # of inserted
 particles * Nattempt.  If LAMMPS is unsuccessful at completing all
 insertions, it prints a warning.</p>
+<p>The <em>dens</em> and <em>vel</em> options enable inserted particles to have a range
+of densities or xy velocities.  The specific values for a particular
+inserted particle will be chosen randomly and uniformly between the
+specified bounds.  Internally, the density value for a particle is
+converted to a mass, based on the radius (volume) of the particle.
+The <em>vz</em> or <em>vy</em> value for option <em>vel</em> assigns a z-velocity (3d) or
+y-velocity (2d) to each inserted particle.</p>
 <p>The <em>rate</em> 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.</p>
-<div class="admonition note">
+<p>The <em>ignore</em> option is useful when running a simulation that used line
-<p class="first admonition-title">Note</p>
+segment (2d) or triangle (3d) particles, typically to define
-<p class="last">If you are monitoring the temperature of a system where the
+boundaries for spherical granular particles to interact with.  See the
-particle count is changing due to adding particles, you typically
+<a class="reference internal" href="atom_style.html"><em>atom_style line or tri</em></a> command for details.  Lines
-should use the <a class="reference internal" href="compute_modify.html"><em>compute_modify dynamic yes</em></a>
+and triangles store their size, and if the size is large it may
-command for the temperature compute you are using.</p>
+overlap (in a spherical sense) with the insertion region, even if the
-</div>
+line/triangle is oriented such that there is no actual overlap.  This
+can prevent particles from being inserted.  The <em>ignore</em> keyword
+causes the overlap check to skip any line or triangle particles.
+Obviously you should only use it if there is in fact no overlap of the
+line or triangle particles with the insertion region.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
@@ -327,7 +359,8 @@ defined by the <a class="reference internal" href="region.html"><em>region</em><
 setting is defined.  If the <em>mol</em> keyword is used, the default for
 <em>molfrac</em> is an equal probabilities for all molecules in the template.
 Additional option defaults are diam = one 1.0, dens = 1.0 1.0, vol =
-0.25 50, rate = 0.0, vel = 0.0 0.0 0.0 0.0 0.0.</p>
+0.25 50, rate = 0.0, vel = 0.0 0.0 0.0 0.0 0.0 (for 3d), vel = 0.0 0.0 0.0
+(for 2d), and id = max.</p>
 </div>
 </div>
 

doc/fix_pour.txt

@@ -14,11 +14,11 @@ fix ID group-ID pour N type seed keyword values ... :pre
 
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 pour = style name of this fix command :l
-N = # of atoms to insert :l
+N = # of particles to insert :l
-type = atom type to assign to inserted atoms (offset for molecule insertion) :l
+type = atom type to assign to inserted particles (offset for molecule insertion) :l
 seed = random # seed (positive integer) :l
 one or more keyword/value pairs may be appended to args :l
-keyword = {region} or {diam} or {dens} or {vol} or {rate} or {vel} or {mol} or {rigid} or {shake} :l
+keyword = {region} or {diam} or {vol} or {rate} or {dens} or {vel} or {mol} or {rigid} or {shake} or {ignore} :l
   {region} value = region-ID
     region-ID = ID of region to use as insertion volume
   {diam} values = dstyle args
@@ -31,12 +31,16 @@ keyword = {region} or {diam} or {dens} or {vol} or {rate} or {vel} or {mol} or {
         Npoly = # of (D,P) pairs
         D1,D2,... = diameter for subset of inserted particles (distance units)
         P1,P2,... = percentage of inserted particles with this diameter (0-1)
+  {id} values = idflag
+    idflag = {max} or {next} = how to choose IDs for inserted particles and molecules
   {vol} values = fraction Nattempt
     fraction = desired volume fraction for filling insertion volume
-    Nattempt = max # of insertion attempts per atom
+    Nattempt = max # of insertion attempts per particle
   {rate} value = V
     V = z velocity (3d) or y velocity (2d) at which
         insertion volume moves (velocity units)
+  {dens} values = Rholo Rhohi
+    Rholo,Rhohi = range of densities for inserted particles (mass/volume units)
   {vel} values (3d) = vxlo vxhi vylo vyhi vz
   {vel} values (2d) = vxlo vxhi vy
     vxlo,vxhi = range of x velocities for inserted particles (velocity units)
@@ -50,7 +54,10 @@ keyword = {region} or {diam} or {dens} or {vol} or {rate} or {vel} or {mol} or {
   {rigid} value = fix-ID
     fix-ID = ID of "fix rigid/small"_fix_rigid.html command
   {shake} value = fix-ID
-    fix-ID = ID of "fix shake"_fix_shake.html command :pre
+    fix-ID = ID of "fix shake"_fix_shake.html command
+  {ignore} value = none
+    skip any line or triangle particles when detecting possible
+      overlaps with inserted particles :pre
 :ule
 
 [Examples:]
@@ -128,6 +135,13 @@ that the previously inserted particles fall out of the insertion
 volume under the influence of gravity.  Insertions continue every so
 many timesteps until the desired # of particles has been inserted.
 
+NOTE: If you are monitoring the temperature of a system where the
+particle count is changing due to adding particles, you typically
+should use the "compute_modify dynamic yes"_compute_modify.html
+command for the temperature compute you are using.
+
+:line
+
 All other keywords are optional with defaults as shown below.
 
 The {diam} option is only used when inserting atoms and specifes the
@@ -146,11 +160,17 @@ the molecule can be specified in the file read by the
 "molecule"_molecule.html command.  If not specified, the diameter of
 each atom in the molecule has a default diameter of 1.0.
 
-The {dens} and {vel} options enable inserted particles to have a range
+The {id} option has two settings which are used to determine the atom
-of densities or xy velocities.  The specific values for a particular
+or molecule IDs to assign to inserted particles/molecules.  In both
-inserted particle will be chosen randomly and uniformly between the
+cases a check is done of the current system to find the maximum
-specified bounds.  The {vz} or {vy} value for option {vel} assigns a
+current atom and molecule ID of any existing particle.  Newly inserted
-z-velocity (3d) or y-velocity (2d) to each inserted particle.
+particles and molecules are assigned IDs that increment those max
+values.  For the {max} setting, which is the default, this check is
+done at every insertion step, which allows for particles to leave the
+system, and their IDs to potentially be re-used.  For the {next}
+setting this check is done only once when the fix is specified, which
+can be more efficient if you are sure particles will not be added in
+some other way.
 
 The {vol} option specifies what volume fraction of the insertion
 volume will be filled with particles.  For particles with a size
@@ -166,14 +186,29 @@ insert the new particles without overlaps, where M = # of inserted
 particles * Nattempt.  If LAMMPS is unsuccessful at completing all
 insertions, it prints a warning.
 
+The {dens} and {vel} options enable inserted particles to have a range
+of densities or xy velocities.  The specific values for a particular
+inserted particle will be chosen randomly and uniformly between the
+specified bounds.  Internally, the density value for a particle is
+converted to a mass, based on the radius (volume) of the particle.
+The {vz} or {vy} value for option {vel} assigns a z-velocity (3d) or
+y-velocity (2d) to each inserted particle.
+
 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.
 
-NOTE: If you are monitoring the temperature of a system where the
+The {ignore} option is useful when running a simulation that used line
-particle count is changing due to adding particles, you typically
+segment (2d) or triangle (3d) particles, typically to define
-should use the "compute_modify dynamic yes"_compute_modify.html
+boundaries for spherical granular particles to interact with.  See the
-command for the temperature compute you are using.
+"atom_style line or tri"_atom_style.html command for details.  Lines
+and triangles store their size, and if the size is large it may
+overlap (in a spherical sense) with the insertion region, even if the
+line/triangle is oriented such that there is no actual overlap.  This
+can prevent particles from being inserted.  The {ignore} keyword
+causes the overlap check to skip any line or triangle particles.
+Obviously you should only use it if there is in fact no overlap of the
+line or triangle particles with the insertion region.
 
 :line
 
@@ -225,4 +260,5 @@ Insertions are performed for individual particles, i.e. no {mol}
 setting is defined.  If the {mol} keyword is used, the default for
 {molfrac} is an equal probabilities for all molecules in the template.
 Additional option defaults are diam = one 1.0, dens = 1.0 1.0, vol =
-0.25 50, rate = 0.0, vel = 0.0 0.0 0.0 0.0 0.0.
+0.25 50, rate = 0.0, vel = 0.0 0.0 0.0 0.0 0.0 (for 3d), vel = 0.0 0.0 0.0
+(for 2d), and id = max.

doc/set.html

@@ -135,7 +135,7 @@
 <li>style = <em>atom</em> or <em>type</em> or <em>mol</em> or <em>group</em> or <em>region</em></li>
 <li>ID = atom ID range or type range or mol ID range or group ID or region ID</li>
 <li>one or more keyword/value pairs may be appended</li>
-<li>keyword = <em>type</em> or <em>type/fraction</em> or <em>mol</em> or <em>x</em> or <em>y</em> or <em>z</em> or           <em>charge</em> or <em>dipole</em> or <em>dipole/random</em> or <em>quat</em> or     <em>quat/random</em> or <em>diameter</em> or <em>shape</em> or       <em>length</em> or <em>tri</em> or <em>theta</em> or <em>theta/random</em> or           <em>angmom</em> or <em>omega</em> or      <em>mass</em> or <em>density</em> or <em>volume</em> or <em>image</em> or           <em>bond</em> or <em>angle</em> or <em>dihedral</em> or <em>improper</em> or        <em>meso_e</em> or <em>meso_cv</em> or <em>meso_rho</em> or          <em>smd_contact_radius</em> or <em>smd_mass_density</em> or           <em>i_name</em> or <em>d_name</em></li>
+<li>keyword = <em>type</em> or <em>type/fraction</em> or <em>mol</em> or <em>x</em> or <em>y</em> or <em>z</em> or           <em>charge</em> or <em>dipole</em> or <em>dipole/random</em> or <em>quat</em> or     <em>quat/random</em> or <em>diameter</em> or <em>shape</em> or       <em>length</em> or <em>tri</em> or <em>theta</em> or <em>theta/random</em> or           <em>angmom</em> or <em>omega</em> or      <em>mass</em> or <em>density</em> or <em>volume</em> or <em>image</em> or           <em>bond</em> or <em>angle</em> or <em>dihedral</em> or <em>improper</em> or        <em>meso/e</em> or <em>meso/cv</em> or <em>meso/rho</em> or          <em>smd/contact/radius</em> or <em>smd/mass/density</em> or           <em>i_name</em> or <em>d_name</em></li>
 </ul>
 <pre class="literal-block">
 <em>type</em> value = atom type
@@ -195,15 +195,15 @@
 <em>angle</em> value = angle type for all angles between selected atoms
 <em>dihedral</em> value = dihedral type for all dihedrals between selected atoms
 <em>improper</em> value = improper type for all impropers between selected atoms
-<em>meso_e</em> value = energy of SPH particles (need units)
+<em>meso/e</em> value = energy of SPH particles (need units)
   value can be an atom-style variable (see below)
-<em>meso_cv</em> value = heat capacity of SPH particles (need units)
+<em>meso/cv</em> value = heat capacity of SPH particles (need units)
   value can be an atom-style variable (see below)
-<em>meso_rho</em> value = density of SPH particles (need units)
+<em>meso/rho</em> value = density of SPH particles (need units)
   value can be an atom-style variable (see below)
-<em>smd_contact_radius</em> = radius for short range interactions, i.e. contact and friction
+<em>smd/contact/radius</em> = radius for short range interactions, i.e. contact and friction
   value can be an atom-style variable (see below)
-<em>smd_mass_density</em> = set particle mass based on volume by providing a mass density
+<em>smd/mass/density</em> = set particle mass based on volume by providing a mass density
   value can be an atom-style variable (see below)
 <em>i_name</em> value = value for custom integer vector with name
 <em>d_name</em> value = value for custom floating-point vector with name
@@ -413,18 +413,6 @@ mass is set from the density and triangle area (the input density is
 assumed to be in mass/distance^2 units).  If none of these cases are
 valid, then the mass is set to the density value directly (the input
 density is assumed to be in mass units).</p>
-<p>Keyword <em>smd_mass_density</em> also sets the mass of all selected
-particles, but it is only applicable to the Smooth Mach Dynamics
-package USER-SMD.  This command assumes that the particle volume has
-already been correctly set and calculates particle mass from the
-provided mass density value.</p>
-<p>Keyword <em>smd_contact_radius</em> only applies to simulations with the
-Smooth Mach Dynamics package USER-SMD. This command sets an
-interaction radius for computing short-range interactions,
-e.g. repulsive forces to prevent different individual physical bodies
-from penetrating each other. Note that the SPH smoothing kernel
-diameter used for computing long range, nonlocal interactions, is set
-using the <em>diameter</em> keyword.</p>
 <p>Keyword <em>volume</em> sets the volume of all selected particles.
 Currently, only the <a class="reference internal" href="atom_style.html"><em>atom_style peri</em></a> command defines
 particles with a volume attribute.  Note that this command does not
@@ -458,10 +446,22 @@ order for the change to be made.  The value of nbondtype (nangletypes,
 etc) was set by the <em>bond types</em> (<em>angle types</em>, etc) field in the
 header of the data file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
 command.  These keywords do not allow use of an atom-style variable.</p>
-<p>Keywords <em>meso_e</em>, <em>meso_cv</em>, and <em>meso_rho</em> set the energy, heat
+<p>Keywords <em>meso/e</em>, <em>meso/cv</em>, and <em>meso/rho</em> set the energy, heat
 capacity, and density of smmothed particle hydrodynamics (SPH)
 particles.  See <a class="reference external" href="USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</a> to
 using SPH in LAMMPS.</p>
+<p>Keyword <em>smd/mass/density</em> sets the mass of all selected particles,
+but it is only applicable to the Smooth Mach Dynamics package
+USER-SMD.  It assumes that the particle volume has already been
+correctly set and calculates particle mass from the provided mass
+density value.</p>
+<p>Keyword <em>smd/contact/radius</em> only applies to simulations with the
+Smooth Mach Dynamics package USER-SMD.  Itsets an interaction radius
+for computing short-range interactions, e.g. repulsive forces to
+prevent different individual physical bodies from penetrating each
+other. Note that the SPH smoothing kernel diameter used for computing
+long range, nonlocal interactions, is set using the <em>diameter</em>
+keyword.</p>
 <p>Keywords <em>i_name</em> and <em>d_name</em> refer to custom integer and
 floating-point properties that have been added to each atom via the
 <a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> command.  When that command

doc/set.txt

@@ -22,8 +22,8 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
           {angmom} or {omega} or \
 	  {mass} or {density} or {volume} or {image} or \
 	  {bond} or {angle} or {dihedral} or {improper} or \
-	  {meso_e} or {meso_cv} or {meso_rho} or \
+	  {meso/e} or {meso/cv} or {meso/rho} or \
-	  {smd_contact_radius} or {smd_mass_density} or \
+	  {smd/contact/radius} or {smd/mass/density} or \
           {i_name} or {d_name} :l
   {type} value = atom type
     value can be an atom-style variable (see below)
@@ -82,15 +82,15 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
   {angle} value = angle type for all angles between selected atoms
   {dihedral} value = dihedral type for all dihedrals between selected atoms
   {improper} value = improper type for all impropers between selected atoms
-  {meso_e} value = energy of SPH particles (need units)
+  {meso/e} value = energy of SPH particles (need units)
     value can be an atom-style variable (see below)
-  {meso_cv} value = heat capacity of SPH particles (need units)
+  {meso/cv} value = heat capacity of SPH particles (need units)
     value can be an atom-style variable (see below)
-  {meso_rho} value = density of SPH particles (need units)
+  {meso/rho} value = density of SPH particles (need units)
     value can be an atom-style variable (see below)
-  {smd_contact_radius} = radius for short range interactions, i.e. contact and friction
+  {smd/contact/radius} = radius for short range interactions, i.e. contact and friction
     value can be an atom-style variable (see below) 
-  {smd_mass_density} = set particle mass based on volume by providing a mass density
+  {smd/mass/density} = set particle mass based on volume by providing a mass density
     value can be an atom-style variable (see below)
   {i_name} value = value for custom integer vector with name
   {d_name} value = value for custom floating-point vector with name :pre
@@ -333,20 +333,6 @@ assumed to be in mass/distance^2 units).  If none of these cases are
 valid, then the mass is set to the density value directly (the input
 density is assumed to be in mass units).
 
-Keyword {smd_mass_density} also sets the mass of all selected
-particles, but it is only applicable to the Smooth Mach Dynamics
-package USER-SMD.  This command assumes that the particle volume has
-already been correctly set and calculates particle mass from the
-provided mass density value.
-
-Keyword {smd_contact_radius} only applies to simulations with the
-Smooth Mach Dynamics package USER-SMD. This command sets an
-interaction radius for computing short-range interactions,
-e.g. repulsive forces to prevent different individual physical bodies
-from penetrating each other. Note that the SPH smoothing kernel
-diameter used for computing long range, nonlocal interactions, is set
-using the {diameter} keyword.
-
 Keyword {volume} sets the volume of all selected particles.
 Currently, only the "atom_style peri"_atom_style.html command defines
 particles with a volume attribute.  Note that this command does not
@@ -384,11 +370,25 @@ etc) was set by the {bond types} ({angle types}, etc) field in the
 header of the data file read by the "read_data"_read_data.html
 command.  These keywords do not allow use of an atom-style variable.
 
-Keywords {meso_e}, {meso_cv}, and {meso_rho} set the energy, heat
+Keywords {meso/e}, {meso/cv}, and {meso/rho} set the energy, heat
 capacity, and density of smmothed particle hydrodynamics (SPH)
 particles.  See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to
 using SPH in LAMMPS.
 
+Keyword {smd/mass/density} sets the mass of all selected particles,
+but it is only applicable to the Smooth Mach Dynamics package
+USER-SMD.  It assumes that the particle volume has already been
+correctly set and calculates particle mass from the provided mass
+density value.
+
+Keyword {smd/contact/radius} only applies to simulations with the
+Smooth Mach Dynamics package USER-SMD.  Itsets an interaction radius
+for computing short-range interactions, e.g. repulsive forces to
+prevent different individual physical bodies from penetrating each
+other. Note that the SPH smoothing kernel diameter used for computing
+long range, nonlocal interactions, is set using the {diameter}
+keyword.
+
 Keywords {i_name} and {d_name} refer to custom integer and
 floating-point properties that have been added to each atom via the
 "fix property/atom"_fix_property_atom.html command.  When that command