diff --git a/doc/angle_charmm.html b/doc/angle_charmm.html index 1afd5a5507..28329239e9 100644 --- a/doc/angle_charmm.html +++ b/doc/angle_charmm.html @@ -155,7 +155,7 @@ angle_coeff 1 300.0 107.0 50.0 3.0

with an additional Urey_Bradley term based on the distance r between the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are coefficients defined for each angle type.

-

See (MacKerell) for a description of the CHARMM force +

See (MacKerell) for a description of the CHARMM force field.

The following coefficients must be defined for each angle type via the angle_coeff command as in the example above, or in diff --git a/doc/dihedral_charmm.html b/doc/dihedral_charmm.html index 241c1dfefd..323219468a 100644 --- a/doc/dihedral_charmm.html +++ b/doc/dihedral_charmm.html @@ -152,9 +152,9 @@ dihedral_coeff 1 120.0 1 60 0.5

DescriptionΒΆ

The charmm dihedral style uses the potential

_images/dihedral_charmm.jpg -

See (MacKerell) for a description of the CHARMM force +

See (MacKerell) 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 (Cornell) +(see comment on weighting factors below). See (Cornell) for a description of the AMBER force field.

The following coefficients must be defined for each dihedral type via the dihedral_coeff command as in the example above, or in diff --git a/doc/dump_image.html b/doc/dump_image.html index 05e17d0ac4..ccf6bd74ee 100644 --- a/doc/dump_image.html +++ b/doc/dump_image.html @@ -155,8 +155,10 @@ 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 @@ -421,12 +423,14 @@ lines will be drawn as cylinders with that diameter, e.g. 1.0, which is in whatever distance units the input script defines, e.g. Angstroms.

The tri keyword can be used when atom_style tri is -used to define particles as triangles, and will draw them as -triangles. If this keyword is not used, such particles will be drawn -as spheres, the same as if they were regular atoms. The only 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:

+used to define particles as triangles, and will draw them as triangles +or edges (3 lines) or both, depending on the setting for tflag. If +edges are drawn, the width setting determines the diameters of the +line segments. If this keyword is not used, triangle particles will +be drawn as spheres, the same as if they were regular atoms. The only +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 value = atom type
@@ -195,15 +195,15 @@
 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
@@ -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).

-
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 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 bond types (angle types, etc) field in the
 header of the data file read by the read_data
 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 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 command.  When that command
diff --git a/doc/set.txt b/doc/set.txt
index 7dfa8bf129..d5d0d973c1 100644
--- a/doc/set.txt
+++ b/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 \
-	  {smd_contact_radius} or {smd_mass_density} or \
+	  {meso/e} or {meso/cv} or {meso/rho} 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