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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3600 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2009-12-21 21:57:15 +00:00
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43
doc/compute_property_molecule.html
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@ -35,39 +35,18 @@
</P>
<P>Define a computation that stores the specified attributes as global
data so it can be accessed by other <A HREF = "Section_howto.html#4_15">output
commands</A>. If the input attributes refer to
bond information, then the number of datums generated, aggregated
across all processors, equals the number of bonds in the system.
commands</A> and used in conjunction with other
commands that generate per-molecule data, such as <A HREF = "compute_com_molecule.html">compute
com/molecule</A> and <A HREF = "compute_msd_molecule.html">compute
msd/molecule</A>.
</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>
<P>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.
</P>
<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
from one timestep to the next. The only consistency that is
guaranteed is that the ordering on a particular timestep will be the
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.
</P>
<P>The <I>batom1</I> and <I>batom2</I> attributes refer 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
<A HREF = "read_data.html">read_data</A> command. 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>.
<P>The <I>mol</I> attribute generates a list of molecule IDs in ascending
order for any molecule with one or more of its atoms in the specified
group. This list and ordering of molecule IDs will be consistent with
the ordering produced by other compute commands that generate
per-molecule datums. Thus this attribute can be used to produce
molecule IDs as labels for those datums when they are output to a
file, e.g. by the <A HREF = "fix_ave_time.html">fix ave/time</A> command.
</P>
<P><B>Output info:</B>
</P>

43
doc/compute_property_molecule.txt
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@ -27,39 +27,18 @@ compute 1 all property/molecule mol :pre
Define a computation that stores the specified attributes as global
data so it can be accessed by other "output
commands"_Section_howto.html#4_15. If the input attributes refer to
bond information, then the number of datums generated, aggregated
across all processors, equals the number of bonds in the system.
commands"_Section_howto.html#4_15 and used in conjunction with other
commands that generate per-molecule data, such as "compute
com/molecule"_compute_com_molecule.html and "compute
msd/molecule"_compute_msd_molecule.html.
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.
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.
Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array
from one timestep to the next. The only consistency that is
guaranteed is that the ordering on a particular timestep will be the
same for local vectors or arrays generated by other compute commands.
For example, output from the "compute
bond/local"_compute_bond_local.html command can be combined with bond
atom indices from this command and output by the "dump
local"_dump.html command in a consistent way.
The {batom1} and {batom2} attributes refer the atom IDs of the 2 atoms
in each "bond"_bond_style.html. The {btype} 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
"read_data"_read_data.html command. The attributes that start with
"a", "d", "i", refer to similar values for "angles"_angle_style.html,
"dihedrals"_dihedral_style.html, and "impropers"_improper_style.html.
The {mol} attribute generates a list of molecule IDs in ascending
order for any molecule with one or more of its atoms in the specified
group. This list and ordering of molecule IDs will be consistent with
the ordering produced by other compute commands that generate
per-molecule datums. Thus this attribute can be used to produce
molecule IDs as labels for those datums when they are output to a
file, e.g. by the "fix ave/time"_fix_ave_time.html command.
[Output info:]