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

doc/Section_commands.html

@@ -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_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_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_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_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_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

doc/Section_commands.txt

@@ -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,

doc/compute.html

@@ -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

doc/compute.txt

@@ -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

doc/compute_property_molecule.html

@@ -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>

doc/compute_property_molecule.txt

@@ -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