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: </P> <DIV ALIGN=center><TABLE BORDER=1 > <TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD></TR> -<TR ALIGN="center"><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD></TR> -<TR ALIGN="center"><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD></TR> -<TR ALIGN="center"><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD></TR> -<TR ALIGN="center"><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A> +<TR ALIGN="center"><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD></TR> +<TR ALIGN="center"><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD></TR> +<TR ALIGN="center"><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD></TR> +<TR ALIGN="center"><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A> </TD></TR></TABLE></DIV> <P>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: <LI><A HREF = "compute_erotate_sphere.html">erotate/sphere</A> - rotational energy of spherical particles <LI><A HREF = "compute_event_displace.html">event/displace</A> - detect event on atom displacement <LI><A HREF = "compute_group_group.html">group/group</A> - energy/force between two groups of atoms +<LI><A HREF = "compute_gyration.html">gyration</A> - radius of gyration of group of atoms <LI><A HREF = "compute_heat_flux.html">heat/flux</A> - heat flux through a group of atoms <LI><A HREF = "compute_ke.html">ke</A> - translational kinetic energy <LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom diff --git a/doc/compute.txt b/doc/compute.txt index 0abdcf3233..e8a5cc8ed4 100644 --- a/doc/compute.txt +++ b/doc/compute.txt @@ -116,6 +116,7 @@ available in LAMMPS: "erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles "event/displace"_compute_event_displace.html - detect event on atom displacement "group/group"_compute_group_group.html - energy/force between two groups of atoms +"gyration"_compute_gyration.html - radius of gyration of group of atoms "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms "ke"_compute_ke.html - translational kinetic energy "ke/atom"_compute_ke_atom.html - kinetic energy for each atom diff --git a/doc/compute_gyration.html b/doc/compute_gyration.html new file mode 100644 index 0000000000..b3888a3729 --- /dev/null +++ b/doc/compute_gyration.html @@ -0,0 +1,64 @@ +<HTML> +<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> +</CENTER> + + + + + + +<HR> + +<H3>compute gyration command +</H3> +<P><B>Syntax:</B> +</P> +<PRE>compute ID group-ID gyration +</PRE> +<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command +<LI>gyration = style name of this compute command +</UL> +<P><B>Examples:</B> +</P> +<PRE>compute 1 molecule gyration +</PRE> +<P><B>Description:</B> +</P> +<P>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. +</P> +<P>Rg is a measure of the size of the group of atoms, and is computed by +this formula +</P> +<CENTER><IMG SRC = "Eqs/compute_gyration.jpg"> +</CENTER> +<P>where M is the total mass of the group and Rcm is the center-of-mass +position of the group. +</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 +"unwrapped" coordinates. See the Atoms section of the +<A HREF = "read_data.html">read_data</A> 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 <A HREF = "set.html">set +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#4_15">this section</A> for an overview of +LAMMPS output options. +</P> +<P>The scalar value calculated by this compute is "intensive", meaning it +is independent of the number of atoms in the simulation. +</P> +<P><B>Restrictions:</B> none +</P> +<P><B>Related commands:</B> none +</P> +<P><B>Default:</B> none +</P> +</HTML> 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