2007-02-10 05:40:32 +08:00
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<HTML>
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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 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 style args
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</PRE>
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<UL><LI>ID = user-assigned name for the computation
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<LI>group-ID = ID of the group of atoms to perform the computation on
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<LI>style = one of a list of possible style names (see below)
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<LI>args = arguments used by a particular style
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>compute 1 all temp
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compute newtemp flow temp/partial 1 1 0
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compute 3 all ke/atom
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</PRE>
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<P><B>Description:</B>
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</P>
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2009-12-10 05:20:59 +08:00
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<P>Define a computation that will be performed on a group of atoms.
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2008-01-03 03:25:15 +08:00
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Quantities calculated by a compute are instantaneous values, meaning
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they are calculated from information about atoms on the current
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2009-12-10 05:20:59 +08:00
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timestep or iteration, though a compute may internally store some
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2009-12-11 01:10:35 +08:00
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information about a previous state of the system. Defining a compute
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does not perform a computation. Instead computes are invoked by other
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LAMMPS commands as needed, e.g. to calculate a temperature needed for
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a thermostat fix or to generate thermodynamic or dump file output.
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See this <A HREF = "Section_howto.html#4_15">howto section</A> for a summary of
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various LAMMPS output options, many of which involve computes.
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2009-12-10 05:20:59 +08:00
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</P>
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<P>The ID of a compute can only contain alphanumeric characters and
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underscores.
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</P>
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<HR>
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<P>Computes calculate one of three styles of quantities: global,
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per-atom, or local. A global quantity is one or more system-wide
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values, e.g. the temperature of the system. A per-atom quantity is
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one or more values per atom, e.g. the kinetic energy of each atom.
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Per-atom values are set to 0.0 for atoms not in the specified compute
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group. Local quantities are calculated by each processor based on the
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atoms it owns, but there may be zero or more per atom, e.g. a list of
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bond distances. Computes that produce per-atom quantities have the
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word "atom" in their style, e.g. <I>ke/atom</I>. Computes that produce
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local quantities have the word "local" in their style,
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e.g. <I>bond/local</I>. Styles with neither "atom" or "local" in their
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style produce global quantities.
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</P>
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<P>Note that a single compute produces either global or per-atom or local
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quantities, but never more than one of these.
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</P>
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<P>Global, per-atom, and local quantities each come in three kinds: a
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single scalar value, a vector of values, or a 2d array of values. The
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doc page for each compute describes the style and kind of values it
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produces, e.g. a per-atom vector. Some computes produce more than one
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kind of a single style, e.g. a global scalar and a global vector.
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</P>
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<P>When a compute quantity is accessed, as in many of the output commands
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discussed below, it can be referenced via the following bracket
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notation, where ID is the ID of the compute:
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR><TD >c_ID </TD><TD > entire scalar, vector, or array</TD></TR>
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<TR><TD >c_ID[I] </TD><TD > one element of vector, one column of array</TD></TR>
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<TR><TD >c_ID[I][J] </TD><TD > one element of array
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</TD></TR></TABLE></DIV>
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<P>In other words, using one bracket reduces the dimension of the
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quantity once (vector -> scalar, array -> vector). Using two brackets
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reduces the dimension twice (array -> scalar). Thus a command that
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uses scalar compute values as input can also process elements of a
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vector or array.
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</P>
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<P>Note that commands and <A HREF = "variable.html">variables</A> which use compute
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quantities typically do not allow for all kinds, e.g. a command may
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require a vector of values, not a scalar. This means there is no
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ambiguity about referring to a compute quantity as c_ID even if it
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produces, for example, both a scalar and vector. The doc pages for
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various commands explain the details.
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</P>
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<HR>
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<P>In LAMMPS, the values generated by a compute can be used in several
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ways:
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</P>
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<UL><LI>The results of computes that calculate a global temperature or
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pressure can be used by fixes that do thermostatting or barostatting
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or when atom velocities are created.
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<LI>Global values can be output via the <A HREF = "thermo_style.html">thermo_style
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2007-09-28 07:25:52 +08:00
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custom</A> or <A HREF = "fix_ave_time.html">fix ave/time</A> command.
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2008-01-03 03:25:15 +08:00
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Or the values can be referenced in a <A HREF = "variable.html">variable equal</A> or
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2009-12-10 05:20:59 +08:00
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<A HREF = "variable.html">variable atom</A> command.
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<LI>Per-atom values can be output via the <A HREF = "dump.html">dump custom</A> command
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or the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command. Or they can be
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time-averaged via the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command or
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reduced by the <A HREF = "compute_reduce.html">compute reduce</A> command. Or the
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per-atom values can be referenced in an <A HREF = "variable.html">atom-style
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variable</A>.
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<LI>Local values can be reduced by the <A HREF = "compute_reduce.html">compute
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reduce</A> command, or histogrammed by the <A HREF = "fix_ave_histo.html">fix
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2009-12-18 01:28:42 +08:00
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ave/histo</A> command, or output by the <A HREF = "dump.html">dump
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local</A> command.
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2009-12-10 05:20:59 +08:00
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</UL>
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2008-01-03 03:25:15 +08:00
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<P>The results of computes that calculate global quantities can be either
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"intensive" or "extensive" values. Intensive means the value is
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independent of the number of atoms in the simulation,
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e.g. temperature. Extensive means the value scales with the number of
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atoms in the simulation, e.g. total rotational kinetic energy.
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<A HREF = "thermo_style.html">Thermodynamic output</A> will normalize extensive
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2010-03-03 05:51:16 +08:00
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values by the number of atoms in the system, depending on the
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"thermo_modify norm" setting. It will not normalize intensive values.
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If a compute value is accessed in another way, e.g. by a
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<A HREF = "variable.html">variable</A>, you may want to know whether it is an
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2008-01-03 03:25:15 +08:00
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intensive or extensive value. See the doc page for individual
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computes for further info.
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2007-10-10 02:24:42 +08:00
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</P>
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2009-12-10 05:20:59 +08:00
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<HR>
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<P>LAMMPS creates its own computes internally for thermodynamic output.
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2007-11-02 00:46:50 +08:00
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Three computes are always created, named "thermo_temp",
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2008-01-18 07:46:30 +08:00
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"thermo_press", and "thermo_pe", as if these commands had been invoked
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in the input script:
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2007-06-20 20:56:17 +08:00
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</P>
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<PRE>compute thermo_temp all temp
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2008-01-18 07:46:30 +08:00
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compute thermo_press all pressure thermo_temp
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2007-11-02 00:46:50 +08:00
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compute thermo_pe all pe
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2007-06-20 20:56:17 +08:00
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</PRE>
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2008-01-03 03:25:15 +08:00
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<P>Additional computes for other quantities are created if the thermo
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style requires it. See the documentation for the
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<A HREF = "thermo_style.html">thermo_style</A> command.
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2007-06-20 20:56:17 +08:00
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</P>
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2008-01-03 03:25:15 +08:00
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<P>Fixes that calculate temperature or pressure, i.e. for thermostatting
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or barostatting, may also create computes. These are discussed in the
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documentation for specific <A HREF = "fix.html">fix</A> commands.
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2007-02-10 05:40:32 +08:00
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</P>
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2009-12-10 05:20:59 +08:00
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<P>In all these cases, the default computes LAMMPS creates can be
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replaced by computes defined by the user in the input script, as
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described by the <A HREF = "thermo_modify.html">thermo_modify</A> and <A HREF = "fix_modify.html">fix
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modify</A> commands.
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2007-06-20 20:56:17 +08:00
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</P>
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2008-01-03 03:25:15 +08:00
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<P>Properties of either a default or user-defined compute can be modified
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2007-06-20 20:56:17 +08:00
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via the <A HREF = "compute_modify.html">compute_modify</A> command.
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2007-02-10 05:40:32 +08:00
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</P>
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2007-06-20 20:56:17 +08:00
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<P>Computes can be deleted with the <A HREF = "uncompute.html">uncompute</A> command.
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2007-02-10 05:40:32 +08:00
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</P>
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2007-06-20 20:56:17 +08:00
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<P>Code for new computes can be added to LAMMPS (see <A HREF = "Section_modify.html">this
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2008-02-20 05:47:37 +08:00
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section</A> of the manual) and the results of their
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2007-06-20 20:56:17 +08:00
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calculations accessed in the various ways described above.
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2007-02-10 05:40:32 +08:00
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</P>
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2009-12-10 05:20:59 +08:00
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<HR>
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2007-02-10 05:40:32 +08:00
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<P>Each compute style has its own doc page which describes its arguments
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and what it does. Here is an alphabetic list of compute styles
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2008-01-03 03:25:15 +08:00
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available in LAMMPS:
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2007-02-10 05:40:32 +08:00
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</P>
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2009-12-19 01:25:39 +08:00
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<UL><LI><A HREF = "compute_bond_local.html">angle/local</A> - theta and energy of each angle
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2010-10-19 01:42:05 +08:00
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<LI><A HREF = "compute_atom_molecule.html">atom/molecule</A> - sum per-atom properties for each molecule
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2009-12-19 01:25:39 +08:00
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<LI><A HREF = "compute_bond_local.html">bond/local</A> - distance and energy of each bond
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<LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
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2011-03-09 06:23:59 +08:00
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<LI><A HREF = "compute_cluster_atom.html">cluster/atom</A> - cluster ID for each atom
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2009-01-20 01:18:42 +08:00
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<LI><A HREF = "compute_cna_atom.html">cna/atom</A> - common neighbor analysis (CNA) for each atom
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2009-12-04 08:42:15 +08:00
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<LI><A HREF = "compute_com.html">com</A> - center-of-mass of group of atoms
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2009-12-22 01:27:08 +08:00
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<LI><A HREF = "compute_com_molecule.html">com/molecule</A> - center-of-mass for each molecule
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2007-06-20 21:09:50 +08:00
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<LI><A HREF = "compute_coord_atom.html">coord/atom</A> - coordination number for each atom
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2008-07-24 23:04:46 +08:00
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<LI><A HREF = "compute_damage_atom.html">damage/atom</A> - Peridynamic damage for each atom
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2009-12-19 05:24:44 +08:00
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<LI><A HREF = "compute_dihedral_local.html">dihedral/local</A> - angle of each dihedral
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2008-01-04 08:27:56 +08:00
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<LI><A HREF = "compute_displace_atom.html">displace/atom</A> - displacement of each atom
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2008-03-20 01:04:31 +08:00
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<LI><A HREF = "compute_erotate_asphere.html">erotate/asphere</A> - rotational energy of aspherical particles
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2008-03-18 08:23:39 +08:00
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<LI><A HREF = "compute_erotate_sphere.html">erotate/sphere</A> - rotational energy of spherical particles
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2009-10-30 06:41:53 +08:00
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<LI><A HREF = "compute_event_displace.html">event/displace</A> - detect event on atom displacement
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2008-02-15 07:24:11 +08:00
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<LI><A HREF = "compute_group_group.html">group/group</A> - energy/force between two groups of atoms
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2009-12-04 08:52:20 +08:00
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<LI><A HREF = "compute_gyration.html">gyration</A> - radius of gyration of group of atoms
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2009-12-22 01:27:08 +08:00
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<LI><A HREF = "compute_gyration_molecule.html">gyration/molecule</A> - radius of gyration for each molecule
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2009-07-03 00:38:31 +08:00
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<LI><A HREF = "compute_heat_flux.html">heat/flux</A> - heat flux through a group of atoms
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2009-12-19 05:24:44 +08:00
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<LI><A HREF = "compute_improper_local.html">improper/local</A> - angle of each improper
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2008-03-19 23:39:14 +08:00
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<LI><A HREF = "compute_ke.html">ke</A> - translational kinetic energy
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2007-02-10 05:40:32 +08:00
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<LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
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2009-12-04 07:58:11 +08:00
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<LI><A HREF = "compute_msd.html">msd</A> - mean-squared displacement of group of atoms
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2009-12-22 01:27:08 +08:00
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<LI><A HREF = "compute_msd_molecule.html">msd/molecule</A> - mean-squared displacement for each molecule
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2010-10-19 01:17:06 +08:00
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<LI><A HREF = "compute_pair.html">pair</A> - values computed by a pair style
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2009-12-22 07:01:36 +08:00
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<LI><A HREF = "compute_pair_local.html">pair/local</A> - distance/energy/force of each pairwise interaction
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2007-11-02 00:46:50 +08:00
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<LI><A HREF = "compute_pe.html">pe</A> - potential energy
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2008-01-03 03:25:15 +08:00
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<LI><A HREF = "compute_pe_atom.html">pe/atom</A> - potential energy for each atom
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2007-02-10 05:40:32 +08:00
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<LI><A HREF = "compute_pressure.html">pressure</A> - total pressure and pressure tensor
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2009-12-17 01:27:23 +08:00
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<LI><A HREF = "compute_property_atom.html">property/atom</A> - convert atom attributes to per-atom vectors/arrays
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2009-12-18 01:28:42 +08:00
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<LI><A HREF = "compute_property_local.html">property/local</A> - convert local attributes to localvectors/arrays
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2009-12-22 05:43:10 +08:00
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<LI><A HREF = "compute_property_molecule.html">property/molecule</A> - convert molecule attributes to localvectors/arrays
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2009-12-17 04:27:03 +08:00
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<LI><A HREF = "compute_rdf.html">rdf</A> - radial distribution function g(r) histogram of group of atoms
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2008-02-20 23:00:04 +08:00
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<LI><A HREF = "compute_reduce.html">reduce</A> - combine per-atom quantities into a single global value
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2009-04-28 22:56:27 +08:00
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<LI><A HREF = "compute_reduce.html">reduce/region</A> - same as compute reduce, within a region
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2007-02-10 05:40:32 +08:00
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<LI><A HREF = "compute_stress_atom.html">stress/atom</A> - stress tensor for each atom
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<LI><A HREF = "compute_temp.html">temp</A> - temperature of group of atoms
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2007-06-20 21:09:50 +08:00
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<LI><A HREF = "compute_temp_asphere.html">temp/asphere</A> - temperature of aspherical particles
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2008-03-12 00:37:01 +08:00
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<LI><A HREF = "compute_temp_com.html">temp/com</A> - temperature after subtracting center-of-mass velocity
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2007-06-20 21:09:50 +08:00
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<LI><A HREF = "compute_temp_deform.html">temp/deform</A> - temperature excluding box deformation velocity
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2007-02-10 05:40:32 +08:00
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<LI><A HREF = "compute_temp_partial.html">temp/partial</A> - temperature excluding one or more dimensions of velocity
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2009-04-30 00:54:14 +08:00
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<LI><A HREF = "compute_temp_profile.html">temp/profile</A> - temperature excluding a binned velocity profile
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2007-06-20 21:09:50 +08:00
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<LI><A HREF = "compute_temp_ramp.html">temp/ramp</A> - temperature excluding ramped velocity component
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2008-03-18 08:23:39 +08:00
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<LI><A HREF = "compute_temp_region.html">temp/region</A> - temperature of a region of atoms
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2010-10-23 05:24:33 +08:00
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<LI><A HREF = "compute_temp_sphere.html">temp/sphere</A> - temperature of spherical particles
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<LI><A HREF = "compute_ti.html">ti</A> - thermodyanmic integration free energy values
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2007-02-10 05:40:32 +08:00
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</UL>
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2007-10-03 06:56:45 +08:00
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<P>There are also additional compute styles submitted by users which are
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included in the LAMMPS distribution. The list of these with links to
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the individual styles are given in the compute section of <A HREF = "Section_commands.html#3_5">this
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page</A>.
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</P>
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2007-02-10 05:40:32 +08:00
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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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2007-10-27 04:42:35 +08:00
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<P><A HREF = "uncompute.html">uncompute</A>, <A HREF = "compute_modify.html">compute_modify</A>, <A HREF = "fix_ave_atom.html">fix
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ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>,
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2009-12-18 01:28:42 +08:00
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<A HREF = "fix_ave_time.html">fix ave/time</A>, <A HREF = "fix_ave_histo.html">fix ave/histo</A>
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2007-02-10 05:40:32 +08:00
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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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