git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13369 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_property_atom.html

@@ -92,6 +92,15 @@ keyword with a value of <I>yes</I>.  This will invoke extra communication
 when ghost atoms are created (at every re-neighboring) to insure the
 new properties are also defined for the ghost atoms.
 </P>
+<P>IMPORTANT NOTE: If you use this command with the <I>mol</I> or <I>charge</I>
+vectors than you most likely want to set <I>ghost</I> yes, since these
+properties are stored with ghost atoms if you use an
+<A HREF = "atom_style.html">atom_style</A> that defines them, and many LAMMPS
+operations that use molecule IDs or charge, such as neighbor lists and
+pair styles, will expect ghost atoms to have these valuse.  LAMMPS
+will issue a warning it you define those vectors but do not set
+<I>ghost</I> yes.
+</P>
 <P>IMPORTANT NOTE: The properties for ghost atoms are not updated every
 timestep, but only once every few steps when neighbor lists are
 re-built.  Thus the <I>ghost</I> keyword is suitable for static properties,

doc/fix_property_atom.txt

@@ -82,6 +82,15 @@ keyword with a value of {yes}.  This will invoke extra communication
 when ghost atoms are created (at every re-neighboring) to insure the
 new properties are also defined for the ghost atoms.
 
+IMPORTANT NOTE: If you use this command with the {mol} or {charge}
+vectors than you most likely want to set {ghost} yes, since these
+properties are stored with ghost atoms if you use an
+"atom_style"_atom_style.html that defines them, and many LAMMPS
+operations that use molecule IDs or charge, such as neighbor lists and
+pair styles, will expect ghost atoms to have these valuse.  LAMMPS
+will issue a warning it you define those vectors but do not set
+{ghost} yes.
+
 IMPORTANT NOTE: The properties for ghost atoms are not updated every
 timestep, but only once every few steps when neighbor lists are
 re-built.  Thus the {ghost} keyword is suitable for static properties,

doc/fix_rigid.html

@@ -183,17 +183,23 @@ command), setting the force on them to 0.0 (via the <A HREF = "fix_setforce.html
 setforce</A> command), and integrating them as usual
 (e.g. via the <A HREF = "fix_nve.html">fix nve</A> command).
 </P>
-<P>NOTE: edit this
-</P>
 <P>IMPORTANT NOTE: The aggregate properties of each rigid body are
-calculated at the start of each simulation run.  These include its
-center of mass, moments of inertia, and net velocity and angular
-momentum.  This means that before or between runs, per-atom properties
-can be changed, e.g. via the <A HREF = "set.html">set</A> or
-<A HREF = "velocity.html">velocity</A> command, which will affect the bodies.  An
-exception is if the <I>infile</I> keyword is used, then all the body
-properties (except net velocity and angular momentum) are only
-calculated once so that values from the file are valid.
+calculated one time at the start of the first simulation run after
+this fix is specified.  The properties include the position and
+velocity of the center-of-mass of the body, its moments of inertia,
+and its angular momentum.  This is done using the properties of the
+constituent atoms of the body at that point in time (or see the
+<I>infile</I> keyword option).  Thereafter, changing properties of
+individual atoms in the body will have no effect on a rigid body's
+dynamics, unless they effect the <A HREF = "pair_style.html">pair_style</A>
+interactions that individual particles are part of.  For example, you
+might think you could displace the atoms in a body or add a large
+velocity to each atom in a body to make it move in a desired direction
+before a 2nd run is performed, using the <A HREF = "set.html">set</A> or
+<A HREF = "displace_atoms.html">displace_atoms</A> or <A HREF = "velocity.html">velocity</A>
+command.  But these commands will not affect the internal attributes
+of the body, and the position and velocity or individual atoms in the
+body will be reset when time integration starts.
 </P>
 <HR>
 
@@ -515,12 +521,10 @@ comment lines starting with "#" which are ignored.  The first
 non-blank, non-comment line should list N = the number of lines to
 follow.  The N successive lines contain the following information:
 </P>
-<P>NOTE: edit this
-</P>
-<PRE>ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
-ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
+<PRE>ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz
+ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz
 ...
-IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz 
+IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz 
 </PRE>
 <P>The rigid body IDs are all positive integers.  For the <I>single</I>
 bodystyle, only an ID of 1 can be used.  For the <I>group</I> bodystyle,
@@ -538,7 +542,10 @@ should be the values consistent with the current orientation of the
 rigid body around its center of mass.  The values are with respect to
 the simulation box XYZ axes, not with respect to the prinicpal axes of
 the rigid body itself.  LAMMPS performs the latter calculation
-internally.
+internally.  The (vxcm,vycm,vzcm) values are the velocity of the
+center of mass.  The (lx,ly,lz) values are the angular momentum of the
+body.  These last 6 values can simply be set to 0 if you wish the
+body to have no initial motion.
 </P>
 <P>IMPORTANT NOTE: If you use the <I>infile</I> or <I>mol</I> keywords and write
 restart files during a simulation, then each time a restart file is

doc/fix_rigid.txt

@@ -165,19 +165,23 @@ command), setting the force on them to 0.0 (via the "fix
 setforce"_fix_setforce.html command), and integrating them as usual
 (e.g. via the "fix nve"_fix_nve.html command).
 
-
-NOTE: edit this
-
-
 IMPORTANT NOTE: The aggregate properties of each rigid body are
-calculated at the start of each simulation run.  These include its
-center of mass, moments of inertia, and net velocity and angular
-momentum.  This means that before or between runs, per-atom properties
-can be changed, e.g. via the "set"_set.html or
-"velocity"_velocity.html command, which will affect the bodies.  An
-exception is if the {infile} keyword is used, then all the body
-properties (except net velocity and angular momentum) are only
-calculated once so that values from the file are valid.
+calculated one time at the start of the first simulation run after
+this fix is specified.  The properties include the position and
+velocity of the center-of-mass of the body, its moments of inertia,
+and its angular momentum.  This is done using the properties of the
+constituent atoms of the body at that point in time (or see the
+{infile} keyword option).  Thereafter, changing properties of
+individual atoms in the body will have no effect on a rigid body's
+dynamics, unless they effect the "pair_style"_pair_style.html
+interactions that individual particles are part of.  For example, you
+might think you could displace the atoms in a body or add a large
+velocity to each atom in a body to make it move in a desired direction
+before a 2nd run is performed, using the "set"_set.html or
+"displace_atoms"_displace_atoms.html or "velocity"_velocity.html
+command.  But these commands will not affect the internal attributes
+of the body, and the position and velocity or individual atoms in the
+body will be reset when time integration starts.
 
 :line
 
@@ -499,12 +503,10 @@ comment lines starting with "#" which are ignored.  The first
 non-blank, non-comment line should list N = the number of lines to
 follow.  The N successive lines contain the following information:
 
-NOTE: edit this
-
-ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
-ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
+ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz
+ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz
 ...
-IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz :pre
+IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz :pre
 
 The rigid body IDs are all positive integers.  For the {single}
 bodystyle, only an ID of 1 can be used.  For the {group} bodystyle,
@@ -522,7 +524,10 @@ should be the values consistent with the current orientation of the
 rigid body around its center of mass.  The values are with respect to
 the simulation box XYZ axes, not with respect to the prinicpal axes of
 the rigid body itself.  LAMMPS performs the latter calculation
-internally.
+internally.  The (vxcm,vycm,vzcm) values are the velocity of the
+center of mass.  The (lx,ly,lz) values are the angular momentum of the
+body.  These last 6 values can simply be set to 0 if you wish the
+body to have no initial motion.
 
 IMPORTANT NOTE: If you use the {infile} or {mol} keywords and write
 restart files during a simulation, then each time a restart file is

doc/molecule.html

@@ -97,9 +97,11 @@ appear if the value(s) are different than the default.
 </UL>
 <P>For <I>mass</I>, <I>com</I>, and <I>inertia</I>, the default is for LAMMPS to
 calculate this quantity itself if needed, assuming the molecules
-consists of a set of point particles.  You only need to specify these
-values for a rigid body consisting of finite-size particles,
-especially if they are overlapping.
+consists of a set of point particles or finite-size particles (with a
+non-zero diameter) that do not overlap.  If finite-size particles in
+the molecule do overlap, LAMMPS will not account for the overlap
+effects when calculating any of these 3 quantities, so you should
+pre-compute them yourself and list the values in the file.
 </P>
 <P>The mass and center-of-mass coordinates (Xc,Yc,Zc) are
 self-explanatory.  The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)

doc/molecule.txt

@@ -94,9 +94,11 @@ Ixx Iyy Izz Ixy Ixz Iyz {inertia} = 6 components of inertia tensor of molecule :
 
 For {mass}, {com}, and {inertia}, the default is for LAMMPS to
 calculate this quantity itself if needed, assuming the molecules
-consists of a set of point particles.  You only need to specify these
-values for a rigid body consisting of finite-size particles,
-especially if they are overlapping.
+consists of a set of point particles or finite-size particles (with a
+non-zero diameter) that do not overlap.  If finite-size particles in
+the molecule do overlap, LAMMPS will not account for the overlap
+effects when calculating any of these 3 quantities, so you should
+pre-compute them yourself and list the values in the file.
 
 The mass and center-of-mass coordinates (Xc,Yc,Zc) are
 self-explanatory.  The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)