diff --git a/doc/Section_commands.html b/doc/Section_commands.html index e8ed4df874..225e79fab2 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -347,10 +347,10 @@ each style or click on the style itself for a full description:
These are compute styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 06f29cbd6f..b340b1dad0 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -472,6 +472,7 @@ each style or click on the style itself for a full description: "erotate/sphere"_compute_erotate_sphere.html, "event/displace"_compute_event_displace.html, "group/group"_compute_group_group.html, +"gyration"_compute_gyration.html, "heat/flux"_compute_heat_flux.html, "ke"_compute_ke.html, "ke/atom"_compute_ke_atom.html, diff --git a/doc/compute.html b/doc/compute.html index 0a54ec677a..e245983a02 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -119,6 +119,7 @@ available in LAMMPS:
Syntax: +
+compute ID group-ID gyration ++
Examples: +
+compute 1 molecule gyration ++
Description: +
+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 +
+
+where M is the total mass of the group and Rcm is the center-of-mass +position of the group. +
+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 +"unwrapped" coordinates. See the Atoms section of the +read_data command for a discussion of image flags and +how they are set for each atom. You can reset the image flags +(e.g. to 0) before invoking this compute by using the set +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 this section for an overview of +LAMMPS output options. +
+The scalar value calculated by this compute is "intensive", meaning it +is independent of the number of atoms in the simulation. +
+Restrictions: none +
+Related commands: none +
+Default: none +
+ diff --git a/doc/compute_gyration.txt b/doc/compute_gyration.txt new file mode 100644 index 0000000000..8cd5b445e1 --- /dev/null +++ b/doc/compute_gyration.txt @@ -0,0 +1,59 @@ +"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 gyration command :h3 + +[Syntax:] + +compute ID group-ID gyration :pre + +ID, group-ID are documented in "compute"_compute.html command +gyration = style name of this compute command :ul + +[Examples:] + +compute 1 molecule gyration :pre + +[Description:] + +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 + +:c,image(Eqs/compute_gyration.jpg) + +where M is the total mass of the group and Rcm is the center-of-mass +position of the group. + +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 +"unwrapped" coordinates. See the Atoms section of the +"read_data"_read_data.html command for a discussion of image flags and +how they are set for each atom. You can reset the image flags +(e.g. to 0) before invoking this compute by using the "set +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 "this section"_Section_howto.html#4_15 for an overview of +LAMMPS output options. + +The scalar value calculated by this compute is "intensive", meaning it +is independent of the number of atoms in the simulation. + +[Restrictions:] none + +[Related commands:] none + +[Default:] none