git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9351 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/atom_style.html

@@ -18,8 +18,8 @@
 <UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>body</I> or <I>bond</I> or <I>charge</I> or <I>dipole</I> or         <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>line</I> or <I>meso</I> or 	<I>molecular</I> or <I>peri</I> or <I>sphere</I> or <I>tri</I> or <I>hybrid</I> 
 </UL>
 <PRE>  args = none for any style except <I>body</I> and <I>hybrid</I>
-  <I>body</I> args = Bstyle
+  <I>body</I> args = bstyle
-    Bstyle = style of body particles
+    bstyle = style of body particles
   <I>hybrid</I> args = list of one or more sub-styles, each with their args 
 </PRE>
 <P><B>Examples:</B>
@@ -27,9 +27,9 @@
 <PRE>atom_style atomic
 atom_style bond
 atom_style full
-atom_style body nparticle
+atom_style body nparticle 2 10
 atom_style hybrid charge bond
-atom_style hybrid charge body nparticle 
+atom_style hybrid charge body nparticle 2 5 
 </PRE>
 <P><B>Description:</B>
 </P>
@@ -122,21 +122,18 @@ points of the triangle).
 </P>
 <P>For the <I>body</I> style, the particles are arbitrary bodies with internal
 attributes defined by the "style" of the bodies, which is specified by
-the <I>Bstyle</I> argument.  Each body particle stores moments of inertia
+the <I>bstyle</I> argument.  This atom style enables LAMMPS to work with
-and a quaternion 4-vector, so that its orientation can be time
+particles that represent complex entities, such as surface meshes of
-integrated.  This atom style enables LAMMPS to work with particles
+discrete points, collections of sub-particles, deformable objects,
-that represent complex entities, such as surface meshes of discrete
+etc.  Of course, the interactions between pairs of bodies will need to
-points, collections of sub-particles, deformable objects, etc.  Of
+be encoded in an appropriate pair style.
-course, the interactions between pairs of bodies will need to be
-encoded in an appropriate pair style.
 </P>
-<P>These are the body styles that LAMMPS currently supports.  The name in
+<P>The <A HREF = "body.html">body</A> doc page descibes the body styles LAMMPS
-the first column is used as the <I>Bstyle</I> argument for atom_style body:
+currently supports, and provides more details as to the kind of body
+particles they represent.  For all styles, each body particle stores
+moments of inertia and a quaternion 4-vector, so that its orientation
+and position can be time integrated due to forces and torques.
 </P>
-<DIV ALIGN=center><TABLE  BORDER=1 >
-<TR><TD ><I>nparticle</I> </TD><TD > body with N sub-particles 
-</TD></TR></TABLE></DIV>
-
 <HR>
 
 <P>Typically, simulations require only a single (non-hybrid) atom style.
@@ -162,15 +159,16 @@ styles; see <A HREF = "Section_modify.html">this section</A>.
 <A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command.
 </P>
 <P>The <I>angle</I>, <I>bond</I>, <I>full</I>, and <I>molecular</I> styles are part of the
-MOLECULAR package.  The <I>line</I>, <I>tri</I>, and <I>body</I> styles are part of
+MOLECULAR package.  The <I>line</I> and <I>tri</I> styles are part of the
-the ASPHERE pacakge.  The <I>dipole</I> style is part of the DIPOLE
+ASPHERE pacakge.  The <I>body</I> style is part of the BODY package.  The
-package.  The <I>peri</I> style is part of the PERI package for
+<I>dipole</I> style is part of the DIPOLE package.  The <I>peri</I> style is
-Peridynamics.  The <I>electron</I> style is part of the USER-EFF package
+part of the PERI package for Peridynamics.  The <I>electron</I> style is
-for <A HREF = "pair_eff.html">electronic force fields</A>.  The <I>meso</I> style is part
+part of the USER-EFF package for <A HREF = "pair_eff.html">electronic force
-of the USER-SPH package for smoothed particle hydrodyanmics (SPH).
+fields</A>.  The <I>meso</I> style is part of the USER-SPH
-See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+package for smoothed particle hydrodyanmics (SPH).  See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF
-LAMMPS.  The <I>wavepacket</I> style is part of the USER-AWPMD package for
+guide</A> to using SPH in LAMMPS.  The
-the <A HREF = "pair_awpmd.html">antisymmetrized wave packet MD method</A>.  They are
+<I>wavepacket</I> style is part of the USER-AWPMD package for the
+<A HREF = "pair_awpmd.html">antisymmetrized wave packet MD method</A>.  They are
 only enabled if LAMMPS was built with that package.  See the <A HREF = "Section_start.html#start_3">Making
 LAMMPS</A> section for more info.
 </P>

doc/atom_style.txt

@@ -16,8 +16,8 @@ style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
         {electron} or {ellipsoid} or {full} or {line} or {meso} or \
 	{molecular} or {peri} or {sphere} or {tri} or {hybrid} :ul
   args = none for any style except {body} and {hybrid}
-  {body} args = Bstyle
+  {body} args = bstyle
-    Bstyle = style of body particles
+    bstyle = style of body particles
   {hybrid} args = list of one or more sub-styles, each with their args :pre
 
 [Examples:]
@@ -25,9 +25,9 @@ style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
 atom_style atomic
 atom_style bond
 atom_style full
-atom_style body nparticle
+atom_style body nparticle 2 10
 atom_style hybrid charge bond
-atom_style hybrid charge body nparticle :pre
+atom_style hybrid charge body nparticle 2 5 :pre
 
 [Description:]
 
@@ -118,18 +118,17 @@ points of the triangle).
 
 For the {body} style, the particles are arbitrary bodies with internal
 attributes defined by the "style" of the bodies, which is specified by
-the {Bstyle} argument.  Each body particle stores moments of inertia
+the {bstyle} argument.  This atom style enables LAMMPS to work with
-and a quaternion 4-vector, so that its orientation can be time
+particles that represent complex entities, such as surface meshes of
-integrated.  This atom style enables LAMMPS to work with particles
+discrete points, collections of sub-particles, deformable objects,
-that represent complex entities, such as surface meshes of discrete
+etc.  Of course, the interactions between pairs of bodies will need to
-points, collections of sub-particles, deformable objects, etc.  Of
+be encoded in an appropriate pair style.
-course, the interactions between pairs of bodies will need to be
-encoded in an appropriate pair style.
 
-These are the body styles that LAMMPS currently supports.  The name in
+The "body"_body.html doc page descibes the body styles LAMMPS
-the first column is used as the {Bstyle} argument for atom_style body:
+currently supports, and provides more details as to the kind of body
-
+particles they represent.  For all styles, each body particle stores
-{nparticle} | body with N sub-particles :tb(c=2,s=|)
+moments of inertia and a quaternion 4-vector, so that its orientation
+and position can be time integrated due to forces and torques.
 
 :line
 
@@ -156,15 +155,16 @@ This command cannot be used after the simulation box is defined by a
 "read_data"_read_data.html or "create_box"_create_box.html command.
 
 The {angle}, {bond}, {full}, and {molecular} styles are part of the
-MOLECULAR package.  The {line}, {tri}, and {body} styles are part of
+MOLECULAR package.  The {line} and {tri} styles are part of the
-the ASPHERE pacakge.  The {dipole} style is part of the DIPOLE
+ASPHERE pacakge.  The {body} style is part of the BODY package.  The
-package.  The {peri} style is part of the PERI package for
+{dipole} style is part of the DIPOLE package.  The {peri} style is
-Peridynamics.  The {electron} style is part of the USER-EFF package
+part of the PERI package for Peridynamics.  The {electron} style is
-for "electronic force fields"_pair_eff.html.  The {meso} style is part
+part of the USER-EFF package for "electronic force
-of the USER-SPH package for smoothed particle hydrodyanmics (SPH).
+fields"_pair_eff.html.  The {meso} style is part of the USER-SPH
-See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
+package for smoothed particle hydrodyanmics (SPH).  See "this PDF
-LAMMPS.  The {wavepacket} style is part of the USER-AWPMD package for
+guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS.  The
-the "antisymmetrized wave packet MD method"_pair_awpmd.html.  They are
+{wavepacket} style is part of the USER-AWPMD package for the
+"antisymmetrized wave packet MD method"_pair_awpmd.html.  They are
 only enabled if LAMMPS was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 

doc/read_data.html

@@ -379,12 +379,10 @@ It can be set to 0.0, which means that atom is a point particle.
 </P>
 <P>The ellipsoidflag, lineflag, triangleflag, and bodyflag determine
 whether the particle is a finite-size ellipsoid or line or triangle or
-body of finite size, or a point particle.  Additional attributes must
+body of finite size, or whether the particle is a point particle.
-be defined for each ellipsoid in the <I>Ellipsoids</I> section.  Additional
+Additional attributes must be defined for each ellipsoid, line,
-attributes must be defined for each line in the <I>Lines</I> section.
+triangle, or body in the corresponding <I>Ellipsoids</I>, <I>Lines</I>,
-Additional attributes must be defined for each triangle in the
+<I>Triangles</I>, or <I>Bodies</I> section.
-<I>Triangles</I> section.  Additional attributes must be defined for each
-body in the <I>Bodies</I> section.
 </P>
 <P>Some pair styles and fixes and computes that operate on finite-size
 particles allow for a mixture of finite-size and point particles.  See
@@ -395,10 +393,10 @@ particle volume to set the mass of each particle as mass = density *
 volume.  In this context, volume can be a 3d quantity (for spheres or
 ellipsoids), a 2d quantity (for triangles), or a 1d quantity (for line
 segments).  If the volume is 0.0, meaning a point particle, then the
-density value is used as the mass.  One exception is for the body
+density value is used as the mass.  One exception is for the body atom
 style, in which case the mass of each particle (body or point
 particle) is specified explicitly.  This is because the volume of the
-body is not known.
+body is unknown.
 </P>
 <P>For atom_style hybrid, following the 5 initial values (ID,type,x,y,z),
 specific values for each sub-style must be listed.  The order of the
@@ -475,14 +473,15 @@ script.
 
 </UL>
 <P>The <I>Bodies</I> section must appear if <A HREF = "atom_style.html">atom_style body</A>
-is used and any atoms are listed in the <I>Atoms</I> section with a
+is used and any atoms listed in the <I>Atoms</I> section have a bodyflag =
-bodyflag = 1.  The number of bodies should be specified in the header
+1.  The number of bodies should be specified in the header section via
-section via the "bodies" keyword.
+the "bodies" keyword.
 </P>
 <P>Each body can have a variable number of integer and/or floating-point
-values.  The number and meaning of the values is defined by the Body
+values.  The number and meaning of the values is defined by the body
-style which will process and store them for each body.  This style is
+style, as described in the <A HREF = "body.html">body</A> doc page.  The body style
-given as an argument to the <A HREF = "atom_style.html">atom_style body</A> command.
+is given as an argument to the <A HREF = "atom_style.html">atom_style body</A>
+command.
 </P>
 <P>The ninteger and ndouble values determine how many integer and
 floating-point values are specified for this particle.  Ninteger and

doc/read_data.txt

@@ -355,12 +355,10 @@ It can be set to 0.0, which means that atom is a point particle.
 
 The ellipsoidflag, lineflag, triangleflag, and bodyflag determine
 whether the particle is a finite-size ellipsoid or line or triangle or
-body of finite size, or a point particle.  Additional attributes must
+body of finite size, or whether the particle is a point particle.
-be defined for each ellipsoid in the {Ellipsoids} section.  Additional
+Additional attributes must be defined for each ellipsoid, line,
-attributes must be defined for each line in the {Lines} section.
+triangle, or body in the corresponding {Ellipsoids}, {Lines},
-Additional attributes must be defined for each triangle in the
+{Triangles}, or {Bodies} section.
-{Triangles} section.  Additional attributes must be defined for each
-body in the {Bodies} section.
 
 Some pair styles and fixes and computes that operate on finite-size
 particles allow for a mixture of finite-size and point particles.  See
@@ -371,10 +369,10 @@ particle volume to set the mass of each particle as mass = density *
 volume.  In this context, volume can be a 3d quantity (for spheres or
 ellipsoids), a 2d quantity (for triangles), or a 1d quantity (for line
 segments).  If the volume is 0.0, meaning a point particle, then the
-density value is used as the mass.  One exception is for the body
+density value is used as the mass.  One exception is for the body atom
 style, in which case the mass of each particle (body or point
 particle) is specified explicitly.  This is because the volume of the
-body is not known.
+body is unknown.
 
 For atom_style hybrid, following the 5 initial values (ID,type,x,y,z),
 specific values for each sub-style must be listed.  The order of the
@@ -442,14 +440,15 @@ example: :l
 :ule
 
 The {Bodies} section must appear if "atom_style body"_atom_style.html
-is used and any atoms are listed in the {Atoms} section with a
+is used and any atoms listed in the {Atoms} section have a bodyflag =
-bodyflag = 1.  The number of bodies should be specified in the header
+1.  The number of bodies should be specified in the header section via
-section via the "bodies" keyword.
+the "bodies" keyword.
 
 Each body can have a variable number of integer and/or floating-point
-values.  The number and meaning of the values is defined by the Body
+values.  The number and meaning of the values is defined by the body
-style which will process and store them for each body.  This style is
+style, as described in the "body"_body.html doc page.  The body style
-given as an argument to the "atom_style body"_atom_style.html command.
+is given as an argument to the "atom_style body"_atom_style.html
+command.
 
 The ninteger and ndouble values determine how many integer and
 floating-point values are specified for this particle.  Ninteger and