From e8fac9300b4d07fe75c8b3b3fdc94a9eb56e3d94 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 13 Jun 2012 16:02:51 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8272 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/compute_gyration.html | 21 ++++++++++++----- doc/compute_gyration.txt | 21 ++++++++++++----- doc/compute_gyration_molecule.html | 36 +++++++++++++++++++++++------- doc/compute_gyration_molecule.txt | 34 ++++++++++++++++++++-------- 4 files changed, 83 insertions(+), 29 deletions(-) diff --git a/doc/compute_gyration.html b/doc/compute_gyration.html index 79994c6dfc..a974a9898e 100644 --- a/doc/compute_gyration.html +++ b/doc/compute_gyration.html @@ -36,6 +36,12 @@ 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 command for a discussion of @@ -47,13 +53,16 @@ image 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 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 for an overview of LAMMPS output +options.

-

The scalar value calculated by this compute is "intensive". The -scalar value will be in distance units. +

The scalar and vector values calculated by this compute are +"intensive". The scalar and vector values will be in distance +units.

Restrictions: none

diff --git a/doc/compute_gyration.txt b/doc/compute_gyration.txt index 2cc818c5f5..6661fb439a 100644 --- a/doc/compute_gyration.txt +++ b/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 -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 diff --git a/doc/compute_gyration_molecule.html b/doc/compute_gyration_molecule.html index f74218009f..e3d49358cb 100644 --- a/doc/compute_gyration_molecule.html +++ b/doc/compute_gyration_molecule.html @@ -13,14 +13,23 @@

Syntax:

-
compute ID group-ID gyration/molecule 
+
compute ID group-ID gyration/molecule keyword value ... 
 

-