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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14140 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/doc2/Section_howto.html

@@ -2515,7 +2515,9 @@ the electrostatic environment inducing polarizability.
 <P>Technically, shells are attached to the cores by a spring force f =
 k*r where k is a parametrized spring constant and r is the distance
 between the core and the shell. The charges of the core and the shell
-add up to the ion charge, thus q(ion) = q(core) + q(shell). In a
+add up to the ion charge, thus q(ion) = q(core) + q(shell). This 
+setup introduces the ion polarizability (alpha) given by 
+alpha = q(shell)^2 / k. In a
 similar fashion the mass of the ion is distributed on the core and the
 shell with the core having the larger mass.
 </P>
@@ -2560,7 +2562,7 @@ for NaCl, as found in examples/coreshell, has this format:
 <P>Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only
 defined between the shells.  Coulombic interactions are defined
 between all cores and shells.  If desired, additional bonds can be
-specified between cores.
+specified between cores.  
 </P>
 <P>The <A HREF = "special_bonds.html">special_bonds</A> command should be used to
 turn-off the Coulombic interaction within core/shell pairs, since that
@@ -2577,7 +2579,7 @@ satellite particle if desired.
 </P>
 <P>Since the core/shell model permits distances of r = 0.0 between the
 core and shell, a pair style with a "cs" suffix needs to be used to
-implement a valid long-rangeCoulombic correction.  Several such pair
+implement a valid long-range Coulombic correction.  Several such pair
 styles are provided in the CORESHELL package.  See <A HREF = "pair_cs.html">this doc
 page</A> for details.  All of the core/shell enabled pair
 styles require the use of a long-range Coulombic solver, as specified
@@ -2600,8 +2602,9 @@ bond_coeff      2 25.724 0.0
 <P>When running dynamics with the adiabatic core/shell model, the
 following issues should be considered.  Since the relative motion of
 the core and shell particles corresponds to the polarization, typical
-thermostats can alter the polarization behaviour, meaining the shell
-will not react freely to its electrostatic environment.  Therefore
+thermostats can alter the polarization behaviour, meaning the shell
+will not react freely to its electrostatic environment.  This is
+critical during the equilibration of the system. Therefore
 it's typically desirable to decouple the relative motion of the
 core/shell pair, which is an imaginary degree of freedom, from the
 real physical system.  To do that, the <A HREF = "compute_temp_cs.html">compute
@@ -2620,9 +2623,9 @@ into account by the <I>group-ID</I> (2nd argument) of the compute.  The
 groups can be defined using the <A HREF = "group.html">group <I>type</I></A> command.
 Note that to perform thermostatting using this definition of
 temperature, the <A HREF = "fix_modify.html">fix modify temp</A> command should be
-used to assign the comptue to the thermostat fix.  Likewise the
+used to assign the compute to the thermostat fix.  Likewise the
 <A HREF = "thermo_modify.html">thermo_modify temp</A> command can be used to make
-this temperature be output for the overall system.
+this temperature be output for the overall system. 
 </P>
 <P>For the NaCl example, this can be done as follows:
 </P>
@@ -2634,6 +2637,15 @@ fix thermostatequ all nve                               # integrator as needed f
 fix_modify thermoberendsen temp CSequ
 thermo_modify temp CSequ                                # output of center-of-mass derived temperature 
 </PRE>
+<P>If <A HREF = "compute_temp_cs.html">compute temp/cs</A> is used, the decoupled 
+relative motion of the core and the shell should in theory be 
+stable.  However numerical fluctuation can introduce a small
+momentum to the system, which is noticable over long trajectories.
+Therefore it is recomendable to use the <A HREF = "fix_momentum.html">fix 
+momentum</A> command in combination with <A HREF = "compute_temp_cs.html">compute 
+temp/cs</A> when equilibrating the system to 
+prevent any drift.
+</P>
 <P>When intializing the velocities of a system with core/shell pairs, it
 is also desirable to not introduce energy into the relative motion of
 the core/shell particles, but only assign a center-of-mass velocity to
@@ -2653,12 +2665,19 @@ velocity. This allow the shells to effectively react instantaneously
 to the electrostatic environment.  This fast movement also limits the
 timestep size that can be used.
 </P>
-<P>Additionally, the mass mismatch of the core and shell particles means
-that only a small amount of energy is transfered to the decoupled
-imaginary degrees of freedom.  However, this transfer will typically
-lead to a a small drift in total energy over time.  This internal
-energy can be monitored using the <A HREF = "compute_chunk_atom.html">compute
-chunk/atom</A> and <A HREF = "compute_temp_chunk.html">compute
+<P>The primary literature of the adiabatic core/shell model suggests that
+the fast relative motion of the core/shell pairs only allows negligible 
+energy transfer to the environment. Therefore it is not intended to
+decouple the core/shell degree of freedom from the physical system
+during production runs. In other words, the <A HREF = "compute_temp_cs.html">compute
+temp/cs</A> command should not be used during
+production runs and is only required during equilibration. This way one 
+is consistent with literature (based on the code packages DL_POLY or 
+GULP for instance).
+</P>
+<P>The mentioned energy transfer will typically lead to a a small drift 
+in total energy over time.  This internal energy can be monitored 
+using the <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> and <A HREF = "compute_temp_chunk.html">compute
 temp/chunk</A> commands.  The internal kinetic
 energies of each core/shell pair can then be summed using the sum()
 special function of the <A HREF = "variable.html">variable</A> command.  Or they can

doc/doc2/compute_temp_cs.html

@@ -67,8 +67,8 @@ calculated by this compute for use in the computation of a pressure
 tensor.  The formula for the components of the tensor is the same as
 the above formula, except that v^2 is replaced by vx*vy for the xy
 component, etc.  The 6 components of the vector are ordered xx, yy,
-zz, xy, xz, yz.  Again, the velocity of each core or shell atom is its
-COM velocity.
+zz, xy, xz, yz.  In contrast to the temperature, the velocity of 
+each core or shell atom is taken individually.
 </P>
 <P>The change this fix makes to core/shell atom velocities is essentially
 computing the temperature after a "bias" has been removed from the

doc/doc2/genindex.html

@@ -926,6 +926,10 @@
   </dt>
 
       
+  <dt><a href="fix_ave_correlate_long.html#index-0">fix ave/correlate/long</a>
+  </dt>
+
+      
   <dt><a href="fix_ave_histo.html#index-0">fix ave/histo</a>
   </dt>