git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@514 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/displace_atoms.html

@@ -63,11 +63,20 @@ spacings.  The <A HREF = "lattice.html">lattice</A> command must have been
 previously used to define the lattice spacing.
 </P>
 <P>Care should be taken not to move atoms on top of other atoms.  After
-the move, atoms are remapped to the periodic simulation box.  In
+the move, atoms are remapped into the periodic simulation box if
-parallel, atoms should not be moved so far that they cross more than
+needed.
-one processor's sub-domain, else they may be lost.  If this is a
+</P>
-problem, successive displace_atom commands can be used to move atoms a
+<P>Atoms can be moved arbitrarily long distances by this command.
-large distance.
+However if the box is non-periodic, this can change the shape of the
+simulation box.  This is not a problem, except that the mapping of
+processors to the simulation box is not changed from its initial 3d
+configuration by this command.  In other words, the number of
+processors assigned to each dimension of the simulation box so as to
+form a topological 3d grid of processors is not changed; see the
+<A HREF = "processors.html">processors</A> command.  Thus if the box shape changes
+dramatically, the simulation may not be as well load-balanced (atoms
+per processor) as the initial mapping tried to achieve.  This can be
+adjusted for by using the <A HREF = "processors.html">processors</A> command.
 </P>
 <P><B>Restrictions:</B>
 </P>

doc/displace_atoms.txt

@@ -55,11 +55,20 @@ spacings.  The "lattice"_lattice.html command must have been
 previously used to define the lattice spacing.
 
 Care should be taken not to move atoms on top of other atoms.  After
-the move, atoms are remapped to the periodic simulation box.  In
+the move, atoms are remapped into the periodic simulation box if
-parallel, atoms should not be moved so far that they cross more than
+needed.
-one processor's sub-domain, else they may be lost.  If this is a
+
-problem, successive displace_atom commands can be used to move atoms a
+Atoms can be moved arbitrarily long distances by this command.
-large distance.
+However if the box is non-periodic, this can change the shape of the
+simulation box.  This is not a problem, except that the mapping of
+processors to the simulation box is not changed from its initial 3d
+configuration by this command.  In other words, the number of
+processors assigned to each dimension of the simulation box so as to
+form a topological 3d grid of processors is not changed; see the
+"processors"_processors.html command.  Thus if the box shape changes
+dramatically, the simulation may not be as well load-balanced (atoms
+per processor) as the initial mapping tried to achieve.  This can be
+adjusted for by using the "processors"_processors.html command.
 
 [Restrictions:]
 

doc/fix_heat.html

@@ -27,20 +27,22 @@ fix 4 qout heat 1 -1.0
 </PRE>
 <P><B>Description:</B>
 </P>
-<P>Add non-translational kinetic energy (heat) to the a group of atoms
+<P>Add non-translational kinetic energy (heat) to a group of atoms such
-such that their aggregate momentum is conserved.  Two of these fixes
+that their aggregate momentum is conserved.  Two of these fixes can be
-can be used to establish a temperature gradient across a simulation
+used to establish a temperature gradient across a simulation domain by
-domain by adding heat to one group of atoms (hot reservoir) and
+adding heat to one group of atoms (hot reservoir) and subracting heat
-subracting heat from another (cold reservoir).  E.g. a simulation
+from another (cold reservoir).  E.g. a simulation sampling from the
-sampling from the McDLT ensemble.  Note that the fix is applied to a
+McDLT ensemble.  Note that the fix is applied to a group of atoms, not
-group of atoms, not a geometric region, so that the same set of atoms
+a geometric region, so that the same set of atoms is affected wherever
-is affected wherever they may move to.
+they may move to.
 </P>
 <P>Heat addition/subtraction is performed every N timesteps.  The <I>eflux</I>
 parameter determines the change in aggregate energy of the entire
-group of atoms.  If heat is subtracted from the system too
+group of atoms.  Since eflux is in units of energy/time, this means a
-aggressively so that the group's kinetic energy goes to zero, LAMMPS
+larger value of N will add/subract a larger amount of energy each
-halts with an error message.
+timestep the fix is invoked.  If heat is subtracted from the system
+too aggressively so that the group's kinetic energy goes to zero,
+LAMMPS halts with an error message.
 </P>
 <P>Fix heat is different from a thermostat such as <A HREF = "fix_nvt.html">fix nvt</A>
 or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A> in that energy is

doc/fix_heat.txt

@@ -24,20 +24,22 @@ fix 4 qout heat 1 -1.0 :pre
 
 [Description:]
 
-Add non-translational kinetic energy (heat) to the a group of atoms
+Add non-translational kinetic energy (heat) to a group of atoms such
-such that their aggregate momentum is conserved.  Two of these fixes
+that their aggregate momentum is conserved.  Two of these fixes can be
-can be used to establish a temperature gradient across a simulation
+used to establish a temperature gradient across a simulation domain by
-domain by adding heat to one group of atoms (hot reservoir) and
+adding heat to one group of atoms (hot reservoir) and subracting heat
-subracting heat from another (cold reservoir).  E.g. a simulation
+from another (cold reservoir).  E.g. a simulation sampling from the
-sampling from the McDLT ensemble.  Note that the fix is applied to a
+McDLT ensemble.  Note that the fix is applied to a group of atoms, not
-group of atoms, not a geometric region, so that the same set of atoms
+a geometric region, so that the same set of atoms is affected wherever
-is affected wherever they may move to.
+they may move to.
 
 Heat addition/subtraction is performed every N timesteps.  The {eflux}
 parameter determines the change in aggregate energy of the entire
-group of atoms.  If heat is subtracted from the system too
+group of atoms.  Since eflux is in units of energy/time, this means a
-aggressively so that the group's kinetic energy goes to zero, LAMMPS
+larger value of N will add/subract a larger amount of energy each
-halts with an error message.
+timestep the fix is invoked.  If heat is subtracted from the system
+too aggressively so that the group's kinetic energy goes to zero,
+LAMMPS halts with an error message.
 
 Fix heat is different from a thermostat such as "fix nvt"_fix_nvt.html
 or "fix temp/rescale"_fix_temp_rescale.html in that energy is