git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2924 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_rigid.html

@@ -51,21 +51,52 @@ fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off
 </PRE>
 <P><B>Description:</B>
 </P>
-<P>Treat one or more sets of atoms as an independent rigid body.  This
+<P>Treat one or more sets of atoms as independent rigid bodies.  This
 means that each timestep the total force and torque on each rigid body
-is computed and the coordinates and velocities of the atoms in each
+is computed as the sum of the forces and torques on its constituent
-body are updated so that they move as a rigid body.  This can be
+particles and the coordinates, velocities, and orientations of the
-useful for freezing one or more portions of a large biomolecule, or
+atoms in each body are updated so that the body moves and rotates as a
-for simulating a system of colloidal particles.
+single entity.
 </P>
-<P>IMPORTANT NOTE: This fix is overkill if you just want to hold group of
+<P>Examples of large rigid bodies are a large colloidal particle, or
-atoms stationary of have them move with a constant velocity.  A
+portions of a large biomolecule such as a protein.
-simpler way to hold atoms stationary is to not include those atoms in
+</P>
-your time integration fix.  E.g. use "fix 1 mobile nve" instead of
+<P>Example of small rigid bodies are patchy nanoparticles, such as those
-"fix 1 all nve", where "mobile" is the group of atoms that you want to
+modeled by the <A HREF = "Glotzer">Glotzer group</A>, clumps of granular particles,
-move.  You can move atoms with a constant velocity by assigning them
+lipid molecules consiting of one or more point dipoles connected to
-an initial velocity (via the <A HREF = "velocity.html">velocity</A> command),
+other spheroids or ellipsoids, and coarse-grain models of nano or
-setting the force on them to 0.0 (via the <A HREF = "fix_setforce.html">fix
+colloidal particles consisting of a small number of constituent
+particles.  Note that the <A HREF = "fix_shake">fix shake</A> command can also be
+used to rigidify small molecules of 2, 3, or 4 atoms, e.g. water
+molecules.  That fix treats the constituent atoms as point masses.
+</P>
+<P>The constituent particles within a rigid body can be point particles
+(the default in LAMMPS) or finite-size particles, such as spheroids
+and ellipsoids.  See the <A HREF = "shape.html">shape</A> command and <A HREF = "atom_style.html">atom_style
+granular</A> for more details on these kinds of
+particles.  Finite-size particles contribute differently to the moment
+of inertia of a rigid body than do point particles.  Finite-size
+particles can also experience torque (e.g. due to <A HREF = "pair_gran.html">frictional granular
+interactions</A>) and have an orientation.  These
+contributions are accounted for by the fix.
+</P>
+<P>Forces between particles within a body do not contribute to the
+external force or torque on the body.  Thus for computational
+efficiency, you may wish to turn off pairwise and bond interactions
+between particles within each rigid body.  The <A HREF = "neigh_modify.html">neigh_modify
+exclude</A> and <A HREF = "delete_bonds.html">delete_bonds</A>
+commands are used to do this.  For finite-size particles this also
+means the particles can be highly overlapped when creating the rigid
+body.
+</P>
+<P>IMPORTANT NOTE: This fix is overkill if you simply want to hold a
+collection of atoms stationary or have them move with a constant
+velocity.  A simpler way to hold atoms stationary is to not include
+those atoms in your time integration fix.  E.g. use "fix 1 mobile nve"
+instead of "fix 1 all nve", where "mobile" is the group of atoms that
+you want to move.  You can move atoms with a constant velocity by
+assigning them an initial velocity (via the <A HREF = "velocity.html">velocity</A>
+command), setting the force on them to 0.0 (via the <A HREF = "fix_setforce.html">fix
 setforce</A> command), and integrating them as usual
 (e.g. via the <A HREF = "fix_nve.html">fix nve</A> command).
 </P>
@@ -73,6 +104,8 @@ setforce</A> command), and integrating them as usual
 rigid atoms with a constant-energy time integration, so you should not
 update the same atoms via other fixes (e.g. nve, nvt, npt).
 </P>
+<HR>
+
 <P>Each body must have two or more atoms.  An atom can belong to at most
 one rigid body.  Which atoms are in which bodies can be defined via
 several options.
@@ -214,4 +247,10 @@ exclude
 <P>The option defaults are force * on on on and torque * on on on meaning
 all rigid bodies are acted on by center-of-mass force and torque.
 </P>
+<HR>
+
+<A NAME = "Glotzer_group"></A>
+
+<P><B>(Zhang)</B> Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004).
+</P>
 </HTML>

doc/fix_rigid.txt

@@ -42,21 +42,52 @@ fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off :pre
 
 [Description:]
 
-Treat one or more sets of atoms as an independent rigid body.  This
+Treat one or more sets of atoms as independent rigid bodies.  This
 means that each timestep the total force and torque on each rigid body
-is computed and the coordinates and velocities of the atoms in each
+is computed as the sum of the forces and torques on its constituent
-body are updated so that they move as a rigid body.  This can be
+particles and the coordinates, velocities, and orientations of the
-useful for freezing one or more portions of a large biomolecule, or
+atoms in each body are updated so that the body moves and rotates as a
-for simulating a system of colloidal particles.
+single entity.
 
-IMPORTANT NOTE: This fix is overkill if you just want to hold group of
+Examples of large rigid bodies are a large colloidal particle, or
-atoms stationary of have them move with a constant velocity.  A
+portions of a large biomolecule such as a protein.
-simpler way to hold atoms stationary is to not include those atoms in
+
-your time integration fix.  E.g. use "fix 1 mobile nve" instead of
+Example of small rigid bodies are patchy nanoparticles, such as those
-"fix 1 all nve", where "mobile" is the group of atoms that you want to
+modeled by the "Glotzer group"_Glotzer, clumps of granular particles,
-move.  You can move atoms with a constant velocity by assigning them
+lipid molecules consiting of one or more point dipoles connected to
-an initial velocity (via the "velocity"_velocity.html command),
+other spheroids or ellipsoids, and coarse-grain models of nano or
-setting the force on them to 0.0 (via the "fix
+colloidal particles consisting of a small number of constituent
+particles.  Note that the "fix shake"_fix_shake command can also be
+used to rigidify small molecules of 2, 3, or 4 atoms, e.g. water
+molecules.  That fix treats the constituent atoms as point masses.
+
+The constituent particles within a rigid body can be point particles
+(the default in LAMMPS) or finite-size particles, such as spheroids
+and ellipsoids.  See the "shape"_shape.html command and "atom_style
+granular"_atom_style.html for more details on these kinds of
+particles.  Finite-size particles contribute differently to the moment
+of inertia of a rigid body than do point particles.  Finite-size
+particles can also experience torque (e.g. due to "frictional granular
+interactions"_pair_gran.html) and have an orientation.  These
+contributions are accounted for by the fix.
+
+Forces between particles within a body do not contribute to the
+external force or torque on the body.  Thus for computational
+efficiency, you may wish to turn off pairwise and bond interactions
+between particles within each rigid body.  The "neigh_modify
+exclude"_neigh_modify.html and "delete_bonds"_delete_bonds.html
+commands are used to do this.  For finite-size particles this also
+means the particles can be highly overlapped when creating the rigid
+body.
+
+IMPORTANT NOTE: This fix is overkill if you simply want to hold a
+collection of atoms stationary or have them move with a constant
+velocity.  A simpler way to hold atoms stationary is to not include
+those atoms in your time integration fix.  E.g. use "fix 1 mobile nve"
+instead of "fix 1 all nve", where "mobile" is the group of atoms that
+you want to move.  You can move atoms with a constant velocity by
+assigning them an initial velocity (via the "velocity"_velocity.html
+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).
 
@@ -64,6 +95,8 @@ IMPORTANT NOTE: This fix updates the positions and velocities of the
 rigid atoms with a constant-energy time integration, so you should not
 update the same atoms via other fixes (e.g. nve, nvt, npt).
 
+:line
+
 Each body must have two or more atoms.  An atom can belong to at most
 one rigid body.  Which atoms are in which bodies can be defined via
 several options.
@@ -205,3 +238,7 @@ exclude
 The option defaults are force * on on on and torque * on on on meaning
 all rigid bodies are acted on by center-of-mass force and torque.
 
+:line
+
+:link(Glotzer_group)
+[(Zhang)] Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004).

tools/pymol_asphere/src/asphere_vis.cpp

@@ -394,7 +394,7 @@ bool parse_to(const char * token,ifstream &in) {
     in.getline(iline,5000);
     if (in.eof() || !in)
       return false;
-    if (strcmp(token,iline)==0)
+    if (strncmp(token,iline,strlen(token))==0)
       return true;
   }
 }