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24
doc/compute_gyration.html
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@ -28,19 +28,22 @@
group of atoms, including all effects due to atoms passing thru
periodic boundaries.
</P>
<P>Rg is a measure of the size of the group of atoms, and is computed by
this formula
<P>Rg is a measure of the size of the group of atoms, and is computed as
the square root of the Rg^2 value in this formula
</P>
<CENTER><IMG SRC = "Eqs/compute_gyration.jpg">
</CENTER>
<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>A Rg^2 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. Note
that unlike the scalar Rg, each of the 6 values of the tensor is
effectively a "squared" value, since the cross-terms may be negative
and taking a sqrt() would be invalid.
</P>
<P>IMPORTANT NOTE: The coordinates of an atom contribute to Rg in
"unwrapped" form, by using the image flags associated with each atom.
@ -54,16 +57,15 @@ image</A> command.
<P><B>Output info:</B>
</P>
<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
length 6 (Rg^2 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 and vector values calculated by this compute are
"intensive". The scalar and vector values will be in distance
<A HREF = "units.html">units</A>, since they are the square root of values
represented by the formula above.
"intensive". The scalar and vector values will be in distance and
distance^2 <A HREF = "units.html">units</A> respectively.
</P>
<P><B>Restrictions:</B> none
</P>

24
doc/compute_gyration.txt
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@ -25,19 +25,22 @@ Define a computation that calculates the radius of gyration Rg of the
group of atoms, including all effects due to atoms passing thru
periodic boundaries.
Rg is a measure of the size of the group of atoms, and is computed by
this formula
Rg is a measure of the size of the group of atoms, and is computed as
the square root of the Rg^2 value in this formula
:c,image(Eqs/compute_gyration.jpg)
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.
A Rg^2 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. Note
that unlike the scalar Rg, each of the 6 values of the tensor is
effectively a "squared" value, since the cross-terms may be negative
and taking a sqrt() would be invalid.
IMPORTANT NOTE: The coordinates of an atom contribute to Rg in
"unwrapped" form, by using the image flags associated with each atom.
@ -51,16 +54,15 @@ image"_set.html command.
[Output info:]
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
length 6 (Rg^2 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 and vector values calculated by this compute are
"intensive". The scalar and vector values will be in distance
"units"_units.html, since they are the square root of values
represented by the formula above.
"intensive". The scalar and vector values will be in distance and
distance^2 "units"_units.html respectively.
[Restrictions:] none

22
doc/compute_gyration_molecule.html
View File

@ -38,8 +38,8 @@ compute 2 molecule gyration/molecule tensor
individual molecules. The calculation includes all effects due to
atoms passing thru periodic boundaries.
</P>
<P>Rg is a measure of the size of a molecule, and is computed by this
formula
<P>Rg is a measure of the size of a molecule, and is computed as the
square root of the Rg^2 value in this formula
</P>
<CENTER><IMG SRC = "Eqs/compute_gyration.jpg">
</CENTER>
@ -48,11 +48,14 @@ 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.
calculated, but a 6-element Rg^2 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. Note
that unlike the scalar Rg, each of the 6 values of the tensor is
effectively a "squared" value, since the cross-terms may be negative
and taking a sqrt() would be invalid.
</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
@ -87,9 +90,8 @@ section</A> for an overview of LAMMPS output
options.
</P>
<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>, since they are the square root of values
represented by the formula above.
"intensive". The vector and aray values will be in distance and
distance^2 <A HREF = "units.html">units</A> respectively.
</P>
<P><B>Restrictions:</B> none
</P>

22
doc/compute_gyration_molecule.txt
View File

@ -30,8 +30,8 @@ Define a computation that calculates the radius of gyration Rg of
individual molecules. The calculation includes all effects due to
atoms passing thru periodic boundaries.
Rg is a measure of the size of a molecule, and is computed by this
formula
Rg is a measure of the size of a molecule, and is computed as the
square root of the Rg^2 value in this formula
:c,image(Eqs/compute_gyration.jpg)
@ -40,11 +40,14 @@ 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.
calculated, but a 6-element Rg^2 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. Note
that unlike the scalar Rg, each of the 6 values of the tensor is
effectively a "squared" value, since the cross-terms may be negative
and taking a sqrt() would be invalid.
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
@ -79,9 +82,8 @@ section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
All the vector or array values calculated by this compute are
"intensive". The vector or array values will be in distance
"units"_units.html, since they are the square root of values
represented by the formula above.
"intensive". The vector and aray values will be in distance and
distance^2 "units"_units.html respectively.
[Restrictions:] none

19
doc/fix_nvt_sllod.html
View File

@ -56,9 +56,13 @@ periodic boundaries since that is consistent with maintaining the
velocity profile created by fix nvt/sllod. LAMMPS will give an
error if this setting is not consistent.
</P>
<P>The SLLOD equations of motion coupled to a Nose/Hoover thermostat are
discussed in <A HREF = "#Tuckerman">(Tuckerman)</A> (eqs 4 and 5), which is what is
implemented in LAMMPS in a velocity Verlet formulation.
<P>The SLLOD equations of motion, originally proposed by Hoover and Ladd
(see <A HREF = "#Evans">(Evans and Morriss)</A>), were proven to be identical to
Newton's equations of motion for all forms of homogeneous flow by
<A HREF = "#Daivis">(Daivis and Todd)</A>. As implemented in LAMMPS, they are
coupled to a Nose/Hoover chain thermostat in a velocity Verlet
formulation, closely following the implementation used for the <A HREF = "fix_nh.html">fix
nvt</A> command.
</P>
<P>Additional parameters affecting the thermostat are specified by
keywords and values documented with the <A HREF = "fix_nh.html">fix nvt</A>
@ -170,9 +174,12 @@ temp/deform</A>
</P>
<HR>
<A NAME = "Tuckerman"></A>
<A NAME = "Evans"></A>
<P><B>(Tuckerman)</B> Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys,
106, 5615 (1997).
<P><B>(Evans and Morriss)</B> Evans and Morriss, Phys Rev A, 30, 1528 (1984).
</P>
<A NAME = "Daivis"></A>
<P><B>(Daivis and Todd)</B> Daivis and Todd, J Chem Phys, 124, 194103 (2006).
</P>
</HTML>