git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13025 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/compute_pressure.html

@@ -59,13 +59,17 @@ second term uses components of the virial tensor:
 <CENTER><IMG SRC = "Eqs/pressure_tensor.jpg">
 </CENTER>
 <P>If no extra keywords are listed, the entire equations above are
-calculated which include a kinetic energy (temperature) term and the
+calculated.  This includes a kinetic energy (temperature) term and the
 virial as the sum of pair, bond, angle, dihedral, improper, kspace
 (long-range), and fix contributions to the force on each atom.  If any
 extra keywords are listed, then only those components are summed to
 compute temperature or ke and/or the virial.  The <I>virial</I> keyword
 means include all terms except the kinetic energy <I>ke</I>.
 </P>
+<P>Details of how LAMMPS computes the virial efficiently for the entire
+system, including the effects of periodic boundary conditions is
+discussed in <A HREF = "#Thompson">(Thompson)</A>.
+</P>
 <P>The temperature and kinetic energy tensor is not calculated by this
 compute, but rather by the temperature compute specified with the
 command.  If the kinetic energy is not included in the pressure, than
@@ -140,4 +144,10 @@ stress/atom</A>,
 </P>
 <P><B>Default:</B> none
 </P>
+<HR>
+
+<A NAME = "Thompson"></A>
+
+<P><B>(Thompson)</B> Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).
+</P>
 </HTML>

doc/compute_pressure.txt

@@ -55,13 +55,17 @@ second term uses components of the virial tensor:
 :c,image(Eqs/pressure_tensor.jpg)
 
 If no extra keywords are listed, the entire equations above are
-calculated which include a kinetic energy (temperature) term and the
+calculated.  This includes a kinetic energy (temperature) term and the
 virial as the sum of pair, bond, angle, dihedral, improper, kspace
 (long-range), and fix contributions to the force on each atom.  If any
 extra keywords are listed, then only those components are summed to
 compute temperature or ke and/or the virial.  The {virial} keyword
 means include all terms except the kinetic energy {ke}.
 
+Details of how LAMMPS computes the virial efficiently for the entire
+system, including the effects of periodic boundary conditions is
+discussed in "(Thompson)"_#Thompson.
+
 The temperature and kinetic energy tensor is not calculated by this
 compute, but rather by the temperature compute specified with the
 command.  If the kinetic energy is not included in the pressure, than
@@ -135,3 +139,8 @@ stress/atom"_compute_stress_atom.html,
 "thermo_style"_thermo_style.html,
 
 [Default:] none
+
+:line
+
+:link(Thompson)
+[(Thompson)] Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).

doc/compute_stress_atom.html

@@ -75,6 +75,18 @@ listed, only those terms are summed to compute the tensor.  The
 <P>Note that the stress for each atom is due to its interaction with all
 other atoms in the simulation, not just with other atoms in the group.
 </P>
+<P>Details of how LAMMPS computes the virial for individual atoms for
+either pairwise or manybody potentials, and including the effects of
+periodic boundary conditions is discussed in <A HREF = "#Thompson">(Thompson)</A>.
+The basic idea for manybody potentials is to treat each component of
+the force computation between a small cluster of atoms in the same
+manner as in the formula above for bond, angle, dihedral, etc
+interactions.  Namely the quantity R dot F is summed over the atoms in
+the interaction, with the R vectors unwrapped by periodic boundaries
+so that the cluster of atoms is close together.  The total
+contribution for the cluster interaction is divided evenly among those
+atoms.
+</P>
 <P>The <A HREF = "dihedral_charmm.html">dihedral_style charmm</A> style calculates
 pairwise interactions between 1-4 atoms.  The virial contribution of
 these terms is included in the pair virial, not the dihedral virial.
@@ -153,4 +165,8 @@ options.
 
 <P><B>(Sirk)</B> Sirk, Moore, Brown, J Chem Phys, 138, 064505 (2013).
 </P>
+<A NAME = "Thompson"></A>
+
+<P><B>(Thompson)</B> Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).
+</P>
 </HTML>

doc/compute_stress_atom.txt

@@ -72,6 +72,18 @@ listed, only those terms are summed to compute the tensor.  The
 Note that the stress for each atom is due to its interaction with all
 other atoms in the simulation, not just with other atoms in the group.
 
+Details of how LAMMPS computes the virial for individual atoms for
+either pairwise or manybody potentials, and including the effects of
+periodic boundary conditions is discussed in "(Thompson)"_#Thompson.
+The basic idea for manybody potentials is to treat each component of
+the force computation between a small cluster of atoms in the same
+manner as in the formula above for bond, angle, dihedral, etc
+interactions.  Namely the quantity R dot F is summed over the atoms in
+the interaction, with the R vectors unwrapped by periodic boundaries
+so that the cluster of atoms is close together.  The total
+contribution for the cluster interaction is divided evenly among those
+atoms.
+
 The "dihedral_style charmm"_dihedral_charmm.html style calculates
 pairwise interactions between 1-4 atoms.  The virial contribution of
 these terms is included in the pair virial, not the dihedral virial.
@@ -147,3 +159,6 @@ The per-atom array values will be in pressure*volume
 
 :link(Sirk)
 [(Sirk)] Sirk, Moore, Brown, J Chem Phys, 138, 064505 (2013).
+
+:link(Thompson)
+[(Thompson)] Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).