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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1273 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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doc/dump.html
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@ -53,11 +53,11 @@
mux,muy,muz = orientation of dipolar atom
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on aspherical particles
c_ID = scalar per-atom quantity calculated by a compute identified by its ID
c_ID[N] = Nth per-atom vector quantity calculated by a compute identified by its ID
f_ID = scalar per-atom quantity calculated by a fix identified by its ID
f_ID[N] = Nth per-atom vector quantity calculated by a fix identified by its ID
v_name = atom-style variable that calculates a per-atom quantity
c_ID = per-atom scalar value calculated by a compute with ID
c_ID[N] = Nth component of per-atom vector calculated by a compute with ID
f_ID = per-atom scalar value calculated by a fix with ID
f_ID[N] = Nth component of per-atom vector calculated by a fix with ID
v_name = per-atom value calculated by an atom-style variable with name
</PRE>
</UL>
@ -80,18 +80,19 @@ information for atoms in the specified group is dumped. The
included. Not all styles support all these options; see details
below.
</P>
<P>Note that because periodic boundary conditions are enforced only on
timesteps when neighbor lists are rebuilt, the coordinates of an atom
written to a dump file may be slightly outside the simulation box.
<P>IMPORTANT NOTE: Vecause periodic boundary conditions are enforced only
on timesteps when neighbor lists are rebuilt, the coordinates of an
atom written to a dump file may be slightly outside the simulation
box.
</P>
<P>Also note that when LAMMPS is running in parallel, the atom
information written to dump files (typically one line per atom) may be
written in an indeterminate order. This is because data for a single
snapshot is collected from multiple processors. This is always the
case for the <I>atom</I>, <I>bond</I>, and <I>custom</I> styles. It is also the case
for the <I>xyz</I> style if the dump group is not <I>all</I>. It is not the
case for the <I>dcd</I> and <I>xtc</I> styles which always write atoms in sorted
order. So does the <I>xyz</I> style if the dump group is <I>all</I>.
<P>When LAMMPS is running in parallel, the atom information written to
dump files (typically one line per atom) may be written in an
indeterminate order. This is because data for a single snapshot is
collected from multiple processors. This is always the case for the
<I>atom</I>, <I>bond</I>, and <I>custom</I> styles. It is also the case for the
<I>xyz</I> style if the dump group is not <I>all</I>. It is not the case for
the <I>dcd</I> and <I>xtc</I> styles which always write atoms in sorted order.
So does the <I>xyz</I> style if the dump group is <I>all</I>.
</P>
<HR>
@ -240,9 +241,9 @@ rotational torque on the particle.
quantities calculated by a <A HREF = "compute.html">compute</A> to be output. The
ID in the keyword should be replaced by the actual ID of the compute
that has been defined previously in the input script. See the
<A HREF = "compute.html">compute</A> command for details. There are computes for
calculating the energy, stress, centro-symmetry parameter, and
coordination number of individual atoms.
<A HREF = "compute.html">compute</A> command for details. There are per-atom
computes for calculating the energy, stress, centro-symmetry
parameter, and coordination number of individual atoms.
</P>
<P>Note that computes which calculate global scalar and vector
quantities, as opposed to per-atom quantities, cannot be output in a
@ -251,8 +252,8 @@ custom</A> command.
</P>
<P>If <I>c_ID</I> is used as a keyword, then the scalar per-atom quantity
calculated by the compute is printed. If <I>c_ID[N]</I> is used, then N
in the range from 1-M will print the Nth component of the M-length
per-atom vector calculated by the compute.
must be in the range from 1-M, which will print the Nth component of
the M-length per-atom vector calculated by the compute.
</P>
<P>The <I>f_ID</I> and <I>f_ID[N]</I> keywords allow scalar or vector per-atom
quantities calculated by a <A HREF = "fix.html">fix</A> to be output. The ID in the
@ -265,22 +266,22 @@ produced by any <A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</
be written to a dump file.
</P>
<P>If <I>f_ID</I> is used as a keyword, then the scalar per-atom quantity
calculated by the fix is printed. If <I>f_ID[N]</I> is used, then N
in the range from 1-M will print the Nth component of the M-length
per-atom vector calculated by the fix.
calculated by the fix is printed. If <I>f_ID[N]</I> is used, then N must
be in the range from 1-M, which will print the Nth component of the
M-length per-atom vector calculated by the fix.
</P>
<P>The <I>v_name</I> keyword allows per-atom quantities calculated by a
<A HREF = "variable.html">variable</A> to be output. The name in the keyword should
be replaced by the actual name of the variable that has been defined
previously in the input script. Only an atom-style variable can be
referenced, since it is the only one that generates per-atom values.
referenced, since it is the only style that generates per-atom values.
Variables of style <I>atom</I> can reference individual atom attributes,
per-atom atom attributes, thermodynamic keywords, or invoke other
computes, fixes, or variables when they are evaluated, so this is a
very general means of generating quantities to output to a dump file.
very general means of creating quantities to output to a dump file.
</P>
<P>See <A HREF = "Section_modify.html">this section</A> of the manual for information
on how to add new compute and fix styles to LAMMPS that calculate
on how to add new compute and fix styles to LAMMPS to calculate
per-atom quantities which could then be output into dump files.
</P>
<HR>