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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1361 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2008-01-09 21:57:06 +00:00
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doc/compute_stress_atom.html
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@ -18,7 +18,7 @@
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>stress/atom = style name of this compute command
<LI>zero or more keywords may be appended
<LI>keyword = <I>ke</I> or <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I>
<LI>keyword = <I>ke</I> or <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or <I>fix</I>
</UL>
<P><B>Examples:</B>
</P>
@ -51,14 +51,20 @@ second term is a pairwise energy contribution where <I>n</I> loops over the
atoms in the pairwise interaction, and <I>F1</I> and <I>F2</I> are the forces on
the 2 atoms resulting from the pairwise interaction. The third term
is a bond contribution of similar form for the <I>Nb</I> bonds which atom
<I>I</I> is part of. The remaining terms are for the <I>Na</I> angle, <I>Nd</I>
<I>I</I> is part of. There are similar terms for the <I>Na</I> angle, <I>Nd</I>
dihedral, and <I>Ni</I> improper interactions atom <I>I</I> is part of.
Finally, there is a term for the <I>Nf</I> <A HREF = "fix.html">fixes</A> that apply
internal constraint forces to atom <I>I</I>. Currently, only the <A HREF = "fix_shake.html">fix
shake</A> and <A HREF = "fix_rigid.html">fix rigid</A> commands
contribute to this term.
</P>
<P>As the coefficients in the formula imply, a virial contribution
produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
atoms in a Tersoff 3-body interaction) is assigned in equal portions
to each atom in the set. E.g. 1/4 of the dihedral virial to each of
the 4 atoms.
the 4 atoms, or 1/3 of the fix virial due to SHAKE constraints applied
to atoms in a a water molecule via the <A HREF = "fix_shake.html">fix shake</A>
command.
</P>
<P>If no extra keywords are listed, all of the terms in this formula are
included in the per-atom stress tensor. If any extra keywords are
@ -81,22 +87,20 @@ the system and the sum is divided by 3V, where V is the volume of the
system, the result should be -P, where P is the total pressure of the
system.
</P>
<P>These lines in an input script should yield that result (assuming
there is no fix or long-range contribution to the stress). I.e. the
<P>These lines in an input script should yield that result. I.e. the
last 2 columns of thermo output will be the same:
</P>
<PRE>compute peratom all stress/atom
compute p all sum peratom<B>1</B> peratom<B>2</B> peratom<B>3</B>
compute p all sum c_peratom<B>1</B> c_peratom<B>2</B> c_peratom<B>3</B>
variable press equal -(c_p<B>1</B>+c_p<B>2</B>+c_p<B>3</B>)/(3*vol)
thermo_style custom step temp etotal press v_press
</PRE>
<P>IMPORTANT NOTE: The per-atom stress does NOT include contributions due
to fixes (e.g. <A HREF = "fix_shake.html">SHAKE</A>) or long-range Coulombic
interactions (via the <A HREF = "kspace_style.html">kspace_style</A> command). The
former needs to be added to LAMMPS. We're not sure if the latter is
possible to compute. There are also a few pair styles for manybody
potentials that are not yet instrumented to yield per-atom stress.
See the Restrictions below.
to long-range Coulombic interactions (via the
<A HREF = "kspace_style.html">kspace_style</A> command). We're not sure this is
even possible to compute. There are also a few pair styles for
manybody potentials that are not yet instrumented to yield per-atom
stress. See the Restrictions below.
</P>
<P><B>Output info:</B>
</P>