2009-12-18 01:28:50 +08:00
|
|
|
<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 property/local command
|
|
|
|
|
</H3>
|
|
|
|
|
<P><B>Syntax:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>compute ID group-ID property/local input1 input2 ...
|
|
|
|
|
</PRE>
|
|
|
|
|
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
|
|
|
|
|
|
|
|
|
<LI>property/local = style name of this compute command
|
|
|
|
|
|
|
|
|
|
<LI>input = one or more attributes
|
|
|
|
|
|
2012-08-10 23:08:25 +08:00
|
|
|
<PRE> possible attributes = natom1 natom2 ntype1 ntype2
|
|
|
|
|
patom1 patom2 ptype1 ptype2
|
2009-12-22 07:01:36 +08:00
|
|
|
batom1 batom2 btype
|
2009-12-18 01:28:50 +08:00
|
|
|
aatom1 aatom2 aatom3 atype
|
|
|
|
|
datom1 datom2 datom3 dtype
|
|
|
|
|
iatom1 iatom2 iatom3 itype
|
|
|
|
|
</PRE>
|
2010-06-19 02:58:59 +08:00
|
|
|
<PRE> natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff)
|
2012-08-10 23:08:25 +08:00
|
|
|
ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff)
|
2010-06-19 02:58:59 +08:00
|
|
|
patom1, patom2 = IDs of 2 atoms in each pair (within force cutoff)
|
2012-08-10 23:08:25 +08:00
|
|
|
ptype1, ptype2 = type of 2 atoms in each pair (within force cutoff)
|
2009-12-22 07:01:36 +08:00
|
|
|
batom1, batom2 = IDs of 2 atoms in each bond
|
2009-12-18 01:28:50 +08:00
|
|
|
btype = bond type of each bond
|
|
|
|
|
aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle
|
|
|
|
|
atype = angle type of each angle
|
|
|
|
|
datom1, datom2, datom3, datom4 = IDs of 4 atoms in each dihedral
|
|
|
|
|
dtype = dihedral type of each dihedral
|
|
|
|
|
iatom1, iatom2, iatom3, iatom4 = IDs of 4 atoms in each improper
|
|
|
|
|
itype = improper type of each improper
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P><B>Examples:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>compute 1 all property/local btype batom1 batom2
|
|
|
|
|
compute 1 all property/local atype aatom2
|
|
|
|
|
</PRE>
|
|
|
|
|
<P><B>Description:</B>
|
|
|
|
|
</P>
|
2009-12-19 02:41:14 +08:00
|
|
|
<P>Define a computation that stores the specified attributes as local
|
2011-08-26 01:01:01 +08:00
|
|
|
data so it can be accessed by other <A HREF = "Section_howto.html#howto_15">output
|
|
|
|
|
commands</A>. If the input attributes refer
|
|
|
|
|
to bond information, then the number of datums generated, aggregated
|
2009-12-19 02:41:14 +08:00
|
|
|
across all processors, equals the number of bonds in the system.
|
2009-12-22 07:01:36 +08:00
|
|
|
Ditto for pairs, angles, etc.
|
2009-12-18 01:28:50 +08:00
|
|
|
</P>
|
|
|
|
|
<P>If multiple input attributes are specified then they must all generate
|
|
|
|
|
the same amount of information, so that the resulting local array has
|
|
|
|
|
the same number of rows for each column. This means that only bond
|
|
|
|
|
attributes can be specified together, or angle attributes, etc. Bond
|
|
|
|
|
and angle attributes can not be mixed in the same compute
|
|
|
|
|
property/local command.
|
|
|
|
|
</P>
|
2009-12-22 08:22:16 +08:00
|
|
|
<P>If the inputs are pair attributes, the local data is generated by
|
|
|
|
|
looping over the pairwise neighbor list. Info about an individual
|
|
|
|
|
pairwise interaction will only be included if both atoms in the pair
|
2010-06-19 02:58:59 +08:00
|
|
|
are in the specified compute group. For <I>natom1</I> and <I>natom2</I>, all
|
|
|
|
|
atom pairs in the neighbor list are considered (out to the neighbor
|
|
|
|
|
cutoff = force cutoff + <A HREF = "neighbor.html">neighbor skin</A>). For <I>patom1</I>
|
|
|
|
|
and <I>patom2</I>, the distance between the atoms must be less than the
|
|
|
|
|
force cutoff distance for that pair to be included, as defined by the
|
|
|
|
|
<A HREF = "pair_style.html">pair_style</A> and <A HREF = "pair_coeff.html">pair_coeff</A>
|
|
|
|
|
commands.
|
2009-12-18 01:28:50 +08:00
|
|
|
</P>
|
2009-12-22 08:22:16 +08:00
|
|
|
<P>If the inputs are bond, angle, etc attributes, the local data is
|
|
|
|
|
generated by looping over all the atoms owned on a processor and
|
|
|
|
|
extracting bond, angle, etc info. For bonds, info about an individual
|
|
|
|
|
bond will only be included if both atoms in the bond are in the
|
|
|
|
|
specified compute group. Likewise for angles, dihedrals, etc.
|
2009-12-22 07:01:36 +08:00
|
|
|
</P>
|
2014-02-07 01:02:01 +08:00
|
|
|
<P>For bonds and angles, a bonds/angles that have been broken by setting
|
|
|
|
|
their bond/angle type to 0 will not be included. Bonds/angles that
|
|
|
|
|
have been turned off (see the <A HREF = "fix_shake.html">fix shake</A> or
|
|
|
|
|
<A HREF = "delete_bonds.html">delete_bonds</A> commands) by setting their bond/angle
|
|
|
|
|
type negative are written into the file. This is consistent with the
|
|
|
|
|
<A HREF = "compute_bond_local.html">compute bond/local</A> and <A HREF = "compute_angle_local.html">compute
|
|
|
|
|
angle/local</A> commands
|
|
|
|
|
</P>
|
2009-12-22 08:22:16 +08:00
|
|
|
<P>Note that as atoms migrate from processor to processor, there will be
|
|
|
|
|
no consistent ordering of the entries within the local vector or array
|
2009-12-18 01:28:50 +08:00
|
|
|
from one timestep to the next. The only consistency that is
|
|
|
|
|
guaranteed is that the ordering on a particular timestep will be the
|
2009-12-19 02:41:14 +08:00
|
|
|
same for local vectors or arrays generated by other compute commands.
|
|
|
|
|
For example, output from the <A HREF = "compute_bond_local.html">compute
|
|
|
|
|
bond/local</A> command can be combined with bond
|
|
|
|
|
atom indices from this command and output by the <A HREF = "dump.html">dump
|
|
|
|
|
local</A> command in a consistent way.
|
2009-12-18 01:28:50 +08:00
|
|
|
</P>
|
2010-06-19 02:58:59 +08:00
|
|
|
<P>The <I>natom1</I> and <I>natom2</I>, or <I>patom1</I> and <I>patom2</I> attributes refer
|
|
|
|
|
to the atom IDs of the 2 atoms in each pairwise interaction computed
|
2012-08-10 23:08:25 +08:00
|
|
|
by the <A HREF = "pair_style.html">pair_style</A> command. The <I>ntype1</I> and
|
|
|
|
|
<I>ntype2</I>, or <I>ptype1</I> and <I>ptype2</I> attributes refer to the atom types
|
|
|
|
|
of the 2 atoms in each pairwise interaction.
|
2009-12-22 07:56:43 +08:00
|
|
|
</P>
|
|
|
|
|
<P>IMPORTANT NOTE: For pairs, if two atoms I,J are involved in 1-2, 1-3,
|
|
|
|
|
1-4 interactions within the molecular topology, their pairwise
|
2011-04-12 03:49:41 +08:00
|
|
|
interaction may be turned off, and thus they may not appear in the
|
2009-12-22 07:56:43 +08:00
|
|
|
neighbor list, and will not be part of the local data created by this
|
2011-04-12 03:49:41 +08:00
|
|
|
command. More specifically, this may be true of I,J pairs with a
|
2009-12-22 07:56:43 +08:00
|
|
|
weighting factor of 0.0; pairs with a non-zero weighting factor are
|
|
|
|
|
included. The weighting factors for 1-2, 1-3, and 1-4 pairwise
|
|
|
|
|
interactions are set by the <A HREF = "special_bonds.html">special_bonds</A>
|
|
|
|
|
command.
|
|
|
|
|
</P>
|
2009-12-22 07:01:36 +08:00
|
|
|
<P>The <I>batom1</I> and <I>batom2</I> attributes refer to the atom IDs of the 2
|
|
|
|
|
atoms in each <A HREF = "bond_style.html">bond</A>. The <I>btype</I> attribute refers to
|
|
|
|
|
the type of the bond, from 1 to Nbtypes = # of bond types. The number
|
|
|
|
|
of bond types is defined in the data file read by the
|
2012-08-10 23:08:25 +08:00
|
|
|
<A HREF = "read_data.html">read_data</A> command.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The attributes that start with "a", "d", "i", refer to similar values
|
|
|
|
|
for <A HREF = "angle_style.html">angles</A>, <A HREF = "dihedral_style.html">dihedrals</A>, and
|
|
|
|
|
<A HREF = "improper_style.html">impropers</A>.
|
2009-12-18 01:28:50 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Output info:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>This compute calculates a local vector or local array depending on the
|
2009-12-19 02:41:14 +08:00
|
|
|
number of input values. The length of the vector or number of rows in
|
|
|
|
|
the array is the number of bonds, angles, etc. If a single input is
|
|
|
|
|
specified, a local vector is produced. If two or more inputs are
|
|
|
|
|
specified, a local array is produced where the number of columns = the
|
|
|
|
|
number of inputs. The vector or array can be accessed by any command
|
2011-08-26 01:01:01 +08:00
|
|
|
that uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
|
2009-12-18 01:28:50 +08:00
|
|
|
section</A> for an overview of LAMMPS output
|
|
|
|
|
options.
|
|
|
|
|
</P>
|
2010-01-24 07:20:05 +08:00
|
|
|
<P>The vector or array values will be integers that correspond to the
|
|
|
|
|
specified attribute.
|
|
|
|
|
</P>
|
2009-12-18 01:28:50 +08:00
|
|
|
<P><B>Restrictions:</B> none
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P><A HREF = "dump.html">dump local</A>, <A HREF = "compute_reduce.html">compute reduce</A>
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B> none
|
|
|
|
|
</P>
|
|
|
|
|
</HTML>
|
