2010-10-19 02:33:18 +08:00
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<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>
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<HR>
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<H3>compute atom/molecule command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID atom/molecule input1 input2 ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>atom/molecule = style name of this compute command
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<LI>one or more inputs can be listed
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<LI>input = c_ID, c_ID[N], f_ID, f_ID[N], v_name
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<PRE> c_ID = per-atom vector calculated by a compute with ID
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c_ID[I] = Ith column of per-atom array calculated by a compute with ID
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f_ID = per-atom vector calculated by a fix with ID
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f_ID[I] = Ith column of per-atom array calculated by a fix with ID
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v_name = per-atom vector calculated by an atom-style variable with name
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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2010-10-19 04:01:49 +08:00
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<PRE>compute 1 all atom/molecule c_ke c_pe
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2014-02-06 02:09:51 +08:00
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compute 1 top atom/molecule v_myFormula c_stress[3]
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2010-10-19 03:56:48 +08:00
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</PRE>
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2010-10-19 02:33:18 +08:00
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<P><B>Description:</B>
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</P>
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2010-10-19 03:56:48 +08:00
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<P>Define a calculation that sums per-atom values on a per-molecule
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basis, one per listed input. The inputs can <A HREF = "compute.html">computes</A>,
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<A HREF = "fix.html">fixes</A>, or <A HREF = "variable.html">variables</A> that generate per-atom
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quantities. Note that attributes stored by atoms, such as mass or
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force, can also be summed on a per-molecule basis, by accessing these
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quantities via the <A HREF = "compute_property_atom.html">compute property/atom</A>
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command.
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</P>
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<P>Each listed input is operated on independently. Only atoms within the
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specified group contribute to the per-molecule sum. Note that compute
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or fix inputs define their own group which may affect the quantities
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they return. For example, if a compute is used as an input which
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generates a per-atom vector, it will generate values of 0.0 for atoms
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that are not in the group specified for that compute.
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</P>
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2010-10-19 04:01:49 +08:00
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<P>The ordering of per-molecule quantities produced by this compute is
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2010-10-19 03:56:48 +08:00
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consistent with the ordering produced by other compute commands that
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2010-10-19 04:01:49 +08:00
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generate per-molecule datums. Conceptually, them molecule IDs will be
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in ascending order for any molecule with one or more of its atoms in
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the specified group.
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2010-10-19 03:56:48 +08:00
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</P>
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<P>If an input begins with "c_", a compute ID must follow which has been
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previously defined in the input script and which generates per-atom
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quantities. See the individual <A HREF = "compute.html">compute</A> doc page for
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details. If no bracketed integer is appended, the vector calculated
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2012-05-18 06:29:43 +08:00
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by the compute is used. If a bracketed integer is appended, the Ith
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2010-10-19 03:56:48 +08:00
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column of the array calculated by the compute is used. Users can also
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write code for their own compute styles and <A HREF = "Section_modify.html">add them to
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LAMMPS</A>.
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</P>
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<P>If an input begins with "f_", a fix ID must follow which has been
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previously defined in the input script and which generates per-atom
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quantities. See the individual <A HREF = "fix.html">fix</A> doc page for details.
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Note that some fixes only produce their values on certain timesteps,
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which must be compatible with when compute atom/molecule references
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the values, else an error results. If no bracketed integer is
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appended, the vector calculated by the fix is used. If a bracketed
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2010-10-19 02:33:18 +08:00
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integer is appended, the Ith column of the array calculated by the fix
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is used. Users can also write code for their own fix style and <A HREF = "Section_modify.html">add
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them to LAMMPS</A>.
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</P>
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2010-10-19 03:56:48 +08:00
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<P>If an input begins with "v_", a variable name must follow which has
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2010-10-19 02:33:18 +08:00
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been previously defined in the input script. It must be an
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<A HREF = "variable.html">atom-style variable</A>. Atom-style variables can
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reference thermodynamic keywords and various per-atom attributes, or
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invoke other computes, fixes, or variables when they are evaluated, so
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2010-10-19 03:56:48 +08:00
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this is a very general means of generating per-atom quantities to sum
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on a per-molecule basis.
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2010-10-19 02:33:18 +08:00
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</P>
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<HR>
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<P><B>Output info:</B>
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</P>
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2010-10-19 03:56:48 +08:00
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<P>This compute calculates a global vector or global array depending on
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the number of input values. The length of the vector or number of
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rows in the array is the number of molecules. If a single input is
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specified, a global vector is produced. If two or more inputs are
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specified, a global array is produced where the number of columns =
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the number of inputs. The vector or array can be accessed by any
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2011-08-26 01:01:01 +08:00
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command that uses global values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
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2010-10-19 03:56:48 +08:00
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section</A> for an overview of LAMMPS output
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options.
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</P>
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<P>All the vector or array values calculated by this compute are
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"extensive".
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</P>
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<P>The vector or array values will be in whatever <A HREF = "units.html">units</A> the
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input quantities are in.
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2010-10-19 02:33:18 +08:00
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</P>
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, <A HREF = "variable.html">variable</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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