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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3599 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2009-12-21 21:43:10 +00:00
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6
doc/Section_commands.html
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@ -350,9 +350,9 @@ each style or click on the style itself for a full description:
<TR ALIGN="center"><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_molecule.html">gyration/molecule</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_molecule.html">msd/molecule</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
<TR ALIGN="center"><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_property_molecule.html">property/molecule</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
</TD></TR></TABLE></DIV>
<P>These are compute styles contributed by users, which can be used if

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doc/Section_commands.txt
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@ -485,6 +485,7 @@ each style or click on the style itself for a full description:
"pressure"_compute_pressure.html,
"property/atom"_compute_property_atom.html,
"property/local"_compute_property_local.html,
"property/molecule"_compute_property_molecule.html,
"rdf"_compute_rdf.html,
"reduce"_compute_reduce.html,
"reduce/region"_compute_reduce.html,

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doc/compute.html
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@ -193,6 +193,7 @@ available in LAMMPS:
<LI><A HREF = "compute_pressure.html">pressure</A> - total pressure and pressure tensor
<LI><A HREF = "compute_property_atom.html">property/atom</A> - convert atom attributes to per-atom vectors/arrays
<LI><A HREF = "compute_property_local.html">property/local</A> - convert local attributes to localvectors/arrays
<LI><A HREF = "compute_property_molecule.html">property/molecule</A> - convert molecule attributes to localvectors/arrays
<LI><A HREF = "compute_rdf.html">rdf</A> - radial distribution function g(r) histogram of group of atoms
<LI><A HREF = "compute_reduce.html">reduce</A> - combine per-atom quantities into a single global value
<LI><A HREF = "compute_reduce.html">reduce/region</A> - same as compute reduce, within a region

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doc/compute.txt
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@ -188,6 +188,7 @@ available in LAMMPS:
"pressure"_compute_pressure.html - total pressure and pressure tensor
"property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays
"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays
"property/molecule"_compute_property_molecule.html - convert molecule attributes to localvectors/arrays
"rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms
"reduce"_compute_reduce.html - combine per-atom quantities into a single global value
"reduce/region"_compute_reduce.html - same as compute reduce, within a region

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doc/compute_property_molecule.html Normal file
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@ -0,0 +1,90 @@
<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/molecule command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID property/molecule input1 input2 ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>property/molecule = style name of this compute command
<LI>input = one or more attributes
<PRE> possible attributes = mol
</PRE>
<PRE> mol = molecule ID
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all property/molecule mol
</PRE>
<P><B>Description:</B>
</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.
</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>
<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><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
</HTML>

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@ -0,0 +1,80 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute property/molecule command :h3
[Syntax:]
compute ID group-ID property/molecule input1 input2 ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
property/molecule = style name of this compute command :l
input = one or more attributes :l
possible attributes = mol :pre
mol = molecule ID :pre
:ule
[Examples:]
compute 1 all property/molecule mol :pre
[Description:]
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.
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.
[Output info:]
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 "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
options.
[Restrictions:] none
[Related commands:] none
[Default:] none