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21
doc/compute_gyration.html
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@ -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
by any command that uses a global scalar value 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>This compute calculates a global scalar (Rg) and a global vector of
length 6 (Rg tensor), which can be accessed by indices 1-6. These
values can be used by any command that uses a global scalar value or
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
scalar value will be in distance <A HREF = "units.html">units</A>.
<P>The scalar and vector values calculated by this compute are
"intensive". The scalar and vector values will be in distance
<A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>

21
doc/compute_gyration.txt
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@ -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
by any command that uses a global scalar value from a compute as
input. See "Section_howto 15"_Section_howto.html#howto_15 for an
overview of LAMMPS output options.
This compute calculates a global scalar (Rg) and a global vector of
length 6 (Rg tensor), which can be accessed by indices 1-6. These
values can be used by any command that uses a global scalar value or
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
scalar value will be in distance "units"_units.html.
The scalar and vector values calculated by this compute are
"intensive". The scalar and vector values will be in distance
"units"_units.html.
[Restrictions:] none

36
doc/compute_gyration_molecule.html
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@ -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
<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
<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
of the vector = Nmolecules. These values can be used by any command
that uses global vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
<P>This compute calculates a global vector if the <I>tensor</I> keyword is not
specified and a global array if it is. The length of the vector or
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
vector values will be in distance <A HREF = "units.html">units</A>.
<P>All the vector or array values calculated by this compute are
"intensive". The vector or array values will be in distance
<A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>

34
doc/compute_gyration_molecule.txt
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@ -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
gyration/molecule = style name of this compute command :ul
ID, group-ID are documented in "compute"_compute.html command :ulb,l
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
of the vector = Nmolecules. These values can be used by any command
that uses global vector values from a compute as input. See "this
This compute calculates a global vector if the {tensor} keyword is not
specified and a global array if it is. The length of the vector or
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
vector values will be in distance "units"_units.html.
All the vector or array values calculated by this compute are
"intensive". The vector or array values will be in distance
"units"_units.html.
[Restrictions:] none