diff --git a/doc/compute_group_group.html b/doc/compute_group_group.html index 794598e32..9323fe1bd 100644 --- a/doc/compute_group_group.html +++ b/doc/compute_group_group.html @@ -1,115 +1,117 @@ <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 group/group command </H3> <P><B>Syntax:</B> </P> <PRE>compute ID group-ID group/group group2-ID keyword value ... </PRE> <UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command <LI>group/group = style name of this compute command <LI>group2-ID = group ID of second (or same) group <LI>zero or more keyword/value pairs may be appended <LI>keyword = <I>pair</I> or <I>kspace</I> <PRE> <I>pair</I> value = <I>yes</I> or <I>no</I> <I>kspace</I> value = <I>yes</I> or <I>no</I> </PRE> </UL> <P><B>Examples:</B> </P> <PRE>compute 1 lower group/group upper compute 1 lower group/group upper kspace yes compute mine fluid group/group wall </PRE> <P><B>Description:</B> </P> <P>Define a computation that calculates the total energy and force interaction between two groups of atoms: the compute group and the specified group2. The two groups can be the same. </P> <P>If the <I>pair</I> keyword is set to <I>yes</I>, which is the default, then the the interaction energy will include a pair component which is defined as the pairwise energy between all pairs of atoms where one atom in the pair is in the first group and the other is in the second group. Likewise, the interaction force calculated by this compute will include the force on the compute group atoms due to pairwise interactions with atoms in the specified group2. </P> <P>If the <I>kspace</I> keyword is set to <I>yes</I>, which is not the default, and if a <A HREF = "kspace_style.html">kspace_style</A> is defined, then the the interaction energy will include a Kspace component which is the long-range Coulombic energy between all the atoms in the first group and all the atoms in the 2nd group. group. Likewise, the interaction force calculated by this compute will include the force on the compute group atoms due to long-range Coulombic interactions with atoms in the specified group2. </P> <P>This compute does not calculate any bond or angle or dihedral or improper interactions between atoms in the two groups. </P> <HR> <P>The pairwise contributions to the group-group interactions are calculated by looping over a neighbor list. The Kspace contribution to the group-group interactions require essentially the same amount of work (FFTs, Ewald summation) as computing long-range forces for the entire system. Thus it can be costly to invoke this compute too frequently. </P> <P>If you desire a breakdown of the interactions into a pairwise and Kspace component, simply invoke the compute twice with the appropriate yes/no settings for the <I>pair</I> and <I>kspace</I> keywords. This is no more costly than using a single compute with both keywords set to <I>yes</I>. The individual contributions can be summed in a <A HREF = "variable.html">variable</A> if desired. </P> <P>Thie <A HREF = "PDF/kspace.pdf">document</A> describes how the long-range group-group calculations are performed. </P> +<HR> + <P><B>Output info:</B> </P> <P>This compute calculates a global scalar (the energy) and a global vector of length 3 (force), which can be accessed by indices 1-3. These values can be used by any command that uses global scalar or vector 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>Both the scalar and vector values calculated by this compute are "extensive". The scalar value will be in energy <A HREF = "units.html">units</A>. The vector values will be in force <A HREF = "units.html">units</A>. </P> <P><B>Restrictions:</B> </P> <P>Not all pair styles can be evaluated in a pairwise mode as required by this compute. For example, 3-body and other many-body potentials, such as <A HREF = "pair_tersoff.html">Tersoff</A> and <A HREF = "pair_sw.html">Stillinger-Weber</A> cannot be used. <A HREF = "pair_eam.html">EAM</A> potentials only include the pair potential portion of the EAM interaction when used by this compute, not the embedding term. </P> <P>Not all Kspace styles support calculation of group/group interactions. The <I>ewald</I> and <I>pppm</I> styles do. </P> <P><B>Related commands:</B> none </P> <P><B>Default:</B> </P> <P>The option defaults are pair = yes and kspace = no. </P> </HTML> diff --git a/doc/compute_group_group.txt b/doc/compute_group_group.txt index 1197344af..6dfbdc318 100644 --- a/doc/compute_group_group.txt +++ b/doc/compute_group_group.txt @@ -1,105 +1,107 @@ "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 group/group command :h3 [Syntax:] compute ID group-ID group/group group2-ID keyword value ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l group/group = style name of this compute command :l group2-ID = group ID of second (or same) group :l zero or more keyword/value pairs may be appended :l keyword = {pair} or {kspace} :l {pair} value = {yes} or {no} {kspace} value = {yes} or {no} :pre :ule [Examples:] compute 1 lower group/group upper compute 1 lower group/group upper kspace yes compute mine fluid group/group wall :pre [Description:] Define a computation that calculates the total energy and force interaction between two groups of atoms: the compute group and the specified group2. The two groups can be the same. If the {pair} keyword is set to {yes}, which is the default, then the the interaction energy will include a pair component which is defined as the pairwise energy between all pairs of atoms where one atom in the pair is in the first group and the other is in the second group. Likewise, the interaction force calculated by this compute will include the force on the compute group atoms due to pairwise interactions with atoms in the specified group2. If the {kspace} keyword is set to {yes}, which is not the default, and if a "kspace_style"_kspace_style.html is defined, then the the interaction energy will include a Kspace component which is the long-range Coulombic energy between all the atoms in the first group and all the atoms in the 2nd group. group. Likewise, the interaction force calculated by this compute will include the force on the compute group atoms due to long-range Coulombic interactions with atoms in the specified group2. This compute does not calculate any bond or angle or dihedral or improper interactions between atoms in the two groups. :line The pairwise contributions to the group-group interactions are calculated by looping over a neighbor list. The Kspace contribution to the group-group interactions require essentially the same amount of work (FFTs, Ewald summation) as computing long-range forces for the entire system. Thus it can be costly to invoke this compute too frequently. If you desire a breakdown of the interactions into a pairwise and Kspace component, simply invoke the compute twice with the appropriate yes/no settings for the {pair} and {kspace} keywords. This is no more costly than using a single compute with both keywords set to {yes}. The individual contributions can be summed in a "variable"_variable.html if desired. Thie "document"_PDF/kspace.pdf describes how the long-range group-group calculations are performed. +:line + [Output info:] This compute calculates a global scalar (the energy) and a global vector of length 3 (force), which can be accessed by indices 1-3. These values can be used by any command that uses global scalar or vector values from a compute as input. See "this section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. Both the scalar and vector values calculated by this compute are "extensive". The scalar value will be in energy "units"_units.html. The vector values will be in force "units"_units.html. [Restrictions:] Not all pair styles can be evaluated in a pairwise mode as required by this compute. For example, 3-body and other many-body potentials, such as "Tersoff"_pair_tersoff.html and "Stillinger-Weber"_pair_sw.html cannot be used. "EAM"_pair_eam.html potentials only include the pair potential portion of the EAM interaction when used by this compute, not the embedding term. Not all Kspace styles support calculation of group/group interactions. The {ewald} and {pppm} styles do. [Related commands:] none [Default:] The option defaults are pair = yes and kspace = no.