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rLAMMPS lammps
compute_atom_molecule.html
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<HTML>
<CENTER><A
HREF =
"http://lammps.sandia.gov"
>
LAMMPS WWW Site
</A>
-
<A
HREF =
"Manual.html"
>
LAMMPS Documentation
</A>
-
<A
HREF =
"Section_commands.html#comm"
>
LAMMPS Commands
</A>
</CENTER>
<HR>
<H3>
compute atom/molecule command
</H3>
<P><B>
Syntax:
</B>
</P>
<PRE>
compute ID group-ID atom/molecule input1 input2 ...
</PRE>
<UL><LI>
ID, group-ID are documented in
<A
HREF =
"compute.html"
>
compute
</A>
command
<LI>
atom/molecule = style name of this compute command
<LI>
one or more inputs can be listed
<LI>
input = c_ID, c_ID[N], f_ID, f_ID[N], v_name
<PRE>
c_ID = per-atom vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID
f_ID[I] = Ith column of per-atom array calculated by a fix with ID
v_name = per-atom vector calculated by an atom-style variable with name
</PRE>
</UL>
<P><B>
Examples:
</B>
</P>
<PRE>
compute 1 all atom/molecule c_ke c_pe
compute 1 top atom/molecule v_myFormula c_stress
<B>
3
</B>
</PRE>
<P><B>
Description:
</B>
</P>
<P>
Define a calculation that sums per-atom values on a per-molecule
basis, one per listed input. The inputs can
<A
HREF =
"compute.html"
>
computes
</A>
,
<A
HREF =
"fix.html"
>
fixes
</A>
, or
<A
HREF =
"variable.html"
>
variables
</A>
that generate per-atom
quantities. Note that attributes stored by atoms, such as mass or
force, can also be summed on a per-molecule basis, by accessing these
quantities via the
<A
HREF =
"compute_property_atom.html"
>
compute property/atom
</A>
command.
</P>
<P>
Each listed input is operated on independently. Only atoms within the
specified group contribute to the per-molecule sum. Note that compute
or fix inputs define their own group which may affect the quantities
they return. For example, if a compute is used as an input which
generates a per-atom vector, it will generate values of 0.0 for atoms
that are not in the group specified for that compute.
</P>
<P>
The ordering of per-molecule quantities produced by this compute is
consistent with the ordering produced by other compute commands that
generate per-molecule datums. Conceptually, them molecule IDs will be
in ascending order for any molecule with one or more of its atoms in
the specified group.
</P>
<P>
If an input begins with "c_", a compute ID must follow which has been
previously defined in the input script and which generates per-atom
quantities. See the individual
<A
HREF =
"compute.html"
>
compute
</A>
doc page for
details. If no bracketed integer is appended, the vector calculated
by the compute is used. If a bracketed interger is appended, the Ith
column of the array calculated by the compute is used. Users can also
write code for their own compute styles and
<A
HREF =
"Section_modify.html"
>
add them to
LAMMPS
</A>
.
</P>
<P>
If an input begins with "f_", a fix ID must follow which has been
previously defined in the input script and which generates per-atom
quantities. See the individual
<A
HREF =
"fix.html"
>
fix
</A>
doc page for details.
Note that some fixes only produce their values on certain timesteps,
which must be compatible with when compute atom/molecule references
the values, else an error results. If no bracketed integer is
appended, the vector calculated by the fix is used. If a bracketed
integer is appended, the Ith column of the array calculated by the fix
is used. Users can also write code for their own fix style and
<A
HREF =
"Section_modify.html"
>
add
them to LAMMPS
</A>
.
</P>
<P>
If an input begins with "v_", a variable name must follow which has
been previously defined in the input script. It must be an
<A
HREF =
"variable.html"
>
atom-style variable
</A>
. Atom-style variables can
reference thermodynamic keywords and various per-atom attributes, or
invoke other computes, fixes, or variables when they are evaluated, so
this is a very general means of generating per-atom quantities to sum
on a per-molecule basis.
</P>
<HR>
<P><B>
Output info:
</B>
</P>
<P>
This compute calculates a global vector or global array depending on
the number of input values. The length of the vector or number of
rows in the array is the number of molecules. If a single input is
specified, a global vector is produced. If two or more inputs are
specified, a global array is produced where the number of columns =
the number of inputs. The vector or array can be accessed by any
command that uses global values from a compute as input. See
<A
HREF =
"Section_howto.html#4_15"
>
this
section
</A>
for an overview of LAMMPS output
options.
</P>
<P>
All the vector or array values calculated by this compute are
"extensive".
</P>
<P>
The vector or array values will be in whatever
<A
HREF =
"units.html"
>
units
</A>
the
input quantities are in.
</P>
<P><B>
Restrictions:
</B>
none
</P>
<P><B>
Related commands:
</B>
</P>
<P><A
HREF =
"compute.html"
>
compute
</A>
,
<A
HREF =
"fix.html"
>
fix
</A>
,
<A
HREF =
"variable.html"
>
variable
</A>
</P>
<P><B>
Default:
</B>
none
</P>
</HTML>
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