git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8272 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/compute_gyration.html

@@ -36,6 +36,12 @@ this formula
 <P>where M is the total mass of the group, Rcm is the center-of-mass
 position of the group, and the sum is over all atoms in the group.
 </P>
+<P>A Rg tensor, stored as a 6-element vector, is also calculated by this
+compute.  The formula for the components of the tensor is the same as
+the above formula, except that (Ri - Rcm)^2 is replaced by (Rix -
+Rcmx) * (Riy - Rcmy) for the xy component, etc.  The 6 components of
+the vector are ordered xx, yy, zz, xy, xz, yz.
+</P>
 <P>IMPORTANT NOTE: The coordinates of an atom contribute to Rg in
 "unwrapped" form, by using the image flags associated with each atom.
 See the <A HREF = "dump.html">dump custom</A> command for a discussion of
@@ -47,13 +53,16 @@ image</A> command.
 </P>
 <P><B>Output info:</B>
 </P>
-<P>This compute calculates a global scalar (Rg).  This value can be used
+<P>This compute calculates a global scalar (Rg) and a global vector of
-by any command that uses a global scalar value from a compute as
+length 6 (Rg tensor), which can be accessed by indices 1-6.  These
-input.  See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
+values can be used by any command that uses a global scalar value or
-overview of LAMMPS output options.
+vector values from a compute as input.  See <A HREF = "Section_howto.html#howto_15">Section_howto
+15</A> for an overview of LAMMPS output
+options.
 </P>
-<P>The scalar value calculated by this compute is "intensive".  The
+<P>The scalar and vector values calculated by this compute are
-scalar value will be in distance <A HREF = "units.html">units</A>.
+"intensive".  The scalar and vector values will be in distance
+<A HREF = "units.html">units</A>.
 </P>
 <P><B>Restrictions:</B> none
 </P>

doc/compute_gyration.txt

@@ -33,6 +33,12 @@ this formula
 where M is the total mass of the group, Rcm is the center-of-mass
 position of the group, and the sum is over all atoms in the group.
 
+A Rg tensor, stored as a 6-element vector, is also calculated by this
+compute.  The formula for the components of the tensor is the same as
+the above formula, except that (Ri - Rcm)^2 is replaced by (Rix -
+Rcmx) * (Riy - Rcmy) for the xy component, etc.  The 6 components of
+the vector are ordered xx, yy, zz, xy, xz, yz.
+
 IMPORTANT NOTE: The coordinates of an atom contribute to Rg in
 "unwrapped" form, by using the image flags associated with each atom.
 See the "dump custom"_dump.html command for a discussion of
@@ -44,13 +50,16 @@ image"_set.html command.
 
 [Output info:]
 
-This compute calculates a global scalar (Rg).  This value can be used
+This compute calculates a global scalar (Rg) and a global vector of
-by any command that uses a global scalar value from a compute as
+length 6 (Rg tensor), which can be accessed by indices 1-6.  These
-input.  See "Section_howto 15"_Section_howto.html#howto_15 for an
+values can be used by any command that uses a global scalar value or
-overview of LAMMPS output options.
+vector values from a compute as input.  See "Section_howto
+15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+options.
 
-The scalar value calculated by this compute is "intensive".  The
+The scalar and vector values calculated by this compute are
-scalar value will be in distance "units"_units.html.
+"intensive".  The scalar and vector values will be in distance
+"units"_units.html.
 
 [Restrictions:] none
 

doc/compute_gyration_molecule.html

@@ -13,14 +13,23 @@
 </H3>
 <P><B>Syntax:</B>
 </P>
-<PRE>compute ID group-ID gyration/molecule 
+<PRE>compute ID group-ID gyration/molecule keyword value ... 
 </PRE>
 <UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command 
+
 <LI>gyration/molecule = style name of this compute command 
+
+<LI>zero or more keyword/value pairs may be appended 
+
+<LI>keyword = <I>tensor</I> 
+
+  <I>tensor</I> value = none
+
 </UL>
 <P><B>Examples:</B>
 </P>
 <PRE>compute 1 molecule gyration/molecule
+compute 2 molecule gyration/molecule tensor 
 </PRE>
 <P><B>Description:</B>
 </P>
@@ -37,6 +46,13 @@ formula
 position of the molecule, and the sum is over all atoms in the
 molecule and in the group.
 </P>
+<P>If the <I>tensor</I> keyword is specified, then the scalar Rg value is not
+calculated, but an Rg tensor is instead calculated for each molecule.
+The formula for the components of the tensor is the same as the above
+formula, except that (Ri - Rcm)^2 is replaced by (Rix - Rcmx) * (Riy -
+Rcmy) for the xy component, etc.  The 6 components of the tensor are
+ordered xx, yy, zz, xy, xz, yz.
+</P>
 <P>Rg for a particular molecule is only computed if one or more of its
 atoms are in the specified group.  Normally all atoms in the molecule
 should be in the group, however this is not required.  LAMMPS will
@@ -60,14 +76,18 @@ image</A> command.
 </P>
 <P><B>Output info:</B>
 </P>
-<P>This compute calculates a global vector of Rg values where the length
+<P>This compute calculates a global vector if the <I>tensor</I> keyword is not
-of the vector = Nmolecules.  These values can be used by any command
+specified and a global array if it is.  The length of the vector or
-that uses global vector values from a compute as input.  See <A HREF = "Section_howto.html#howto_15">this
+number of rows in the array is the number of molecules.  If the
+<I>tensor</I> keyword is specified, the global array has 6 columns.  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#howto_15">this
 section</A> for an overview of LAMMPS output
 options.
 </P>
-<P>The vector values calculated by this compute are "intensive".  The
+<P>All the vector or array values calculated by this compute are
-vector values will be in distance <A HREF = "units.html">units</A>.
+"intensive".  The vector or array values will be in distance
+<A HREF = "units.html">units</A>.
 </P>
 <P><B>Restrictions:</B> none
 </P>

doc/compute_gyration_molecule.txt

@@ -10,14 +10,19 @@ compute gyration/molecule command :h3
 
 [Syntax:]
 
-compute ID group-ID gyration/molecule :pre
+compute ID group-ID gyration/molecule keyword value ... :pre
 
-ID, group-ID are documented in "compute"_compute.html command
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
-gyration/molecule = style name of this compute command :ul
+gyration/molecule = style name of this compute command :l
+zero or more keyword/value pairs may be appended :l
+keyword = {tensor} :l
+  {tensor} value = none
+:ule
 
 [Examples:]
 
-compute 1 molecule gyration/molecule :pre
+compute 1 molecule gyration/molecule
+compute 2 molecule gyration/molecule tensor :pre
 
 [Description:]
 
@@ -34,6 +39,13 @@ where M is the total mass of the molecule, Rcm is the center-of-mass
 position of the molecule, and the sum is over all atoms in the
 molecule and in the group.
 
+If the {tensor} keyword is specified, then the scalar Rg value is not
+calculated, but an Rg tensor is instead calculated for each molecule.
+The formula for the components of the tensor is the same as the above
+formula, except that (Ri - Rcm)^2 is replaced by (Rix - Rcmx) * (Riy -
+Rcmy) for the xy component, etc.  The 6 components of the tensor are
+ordered xx, yy, zz, xy, xz, yz.
+
 Rg for a particular molecule is only computed if one or more of its
 atoms are in the specified group.  Normally all atoms in the molecule
 should be in the group, however this is not required.  LAMMPS will
@@ -57,14 +69,18 @@ image"_set.html command.
 
 [Output info:]
 
-This compute calculates a global vector of Rg values where the length
+This compute calculates a global vector if the {tensor} keyword is not
-of the vector = Nmolecules.  These values can be used by any command
+specified and a global array if it is.  The length of the vector or
-that uses global vector values from a compute as input.  See "this
+number of rows in the array is the number of molecules.  If the
+{tensor} keyword is specified, the global array has 6 columns.  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#howto_15 for an overview of LAMMPS output
 options.
 
-The vector values calculated by this compute are "intensive".  The
+All the vector or array values calculated by this compute are
-vector values will be in distance "units"_units.html.
+"intensive".  The vector or array values will be in distance
+"units"_units.html.
 
 [Restrictions:] none