From 8077130fa243ba873637ad8ff92a3b4b03eb77ed Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 30 Nov 2007 23:59:23 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1200 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/compute_pe_atom.html | 67 ++++++++++++++++++++++++++++++++++++++++ doc/compute_pe_atom.txt | 62 +++++++++++++++++++++++++++++++++++++ 2 files changed, 129 insertions(+) create mode 100644 doc/compute_pe_atom.html create mode 100644 doc/compute_pe_atom.txt diff --git a/doc/compute_pe_atom.html b/doc/compute_pe_atom.html new file mode 100644 index 0000000000..6ba588bb2b --- /dev/null +++ b/doc/compute_pe_atom.html @@ -0,0 +1,67 @@ + +
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

compute pe/atom command +

+

Syntax: +

+
compute ID group-ID pe/atom keyword ... 
+
+ +

Examples: +

+
compute 1 all pe/atom
+compute 1 all pe/atom pair
+compute 1 all pe/atom pair bond 
+
+

Description: +

+

Define a computation that computes the per-atom potential energy for +each atom in a group. See the compute pe command if +you want the potential energy of the entire system. The per-atom +energies can be accessed as scalar values by any command that uses +per-atom computes, e.g. the dump custom command or fix +ave/spatial command or fix +ave/atom command. See this +section for an overview. +

+

The per-atom energy is calulated by the various pair, bond, etc +potentials defined for the simulation. If no extra keywords are +listed, then the potential energy is the sum of pair, bond, angle, +dihedral, and improper energy. If any extra keywords are listed, then +only those components are summed to compute the potential energy. +

+

Note that the energy of each atom is due to its interaction with all +other atoms in the simulation, not just with other atoms in the group. +

+

For an energy contribution produced by a small set of atoms (e.g. 4 +atoms in a dihedral or 3 atoms in a Tersoff 3-body interaction), that +energy is assigned in equal portions to each atom in the set. +E.g. 1/4 of the dihedral energy to each of the 4 atoms. +

+

The dihedral_style charmm style calculates +pairwise interactions between 1-4 atoms. The energy contribution of +these terms is included in the pair energy, not the dihedral energy. +

+

Restrictions: none +

+

Related commands: +

+

compute pe, compute +stress/atom +

+

Default: non +

+ diff --git a/doc/compute_pe_atom.txt b/doc/compute_pe_atom.txt new file mode 100644 index 0000000000..ace2cd1ec8 --- /dev/null +++ b/doc/compute_pe_atom.txt @@ -0,0 +1,62 @@ +"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 pe/atom command :h3 + +[Syntax:] + +compute ID group-ID pe/atom keyword ... :pre + +ID, group-ID are documented in "compute"_compute.html command +pe/atom = style name of this compute command +zero or more keywords may be appended +keyword = {pair} or {bond} or {angle} or {dihedral} or {improper} :ul + +[Examples:] + +compute 1 all pe/atom +compute 1 all pe/atom pair +compute 1 all pe/atom pair bond :pre + +[Description:] + +Define a computation that computes the per-atom potential energy for +each atom in a group. See the "compute pe"_compute_pe.html command if +you want the potential energy of the entire system. The per-atom +energies can be accessed as scalar values by any command that uses +per-atom computes, e.g. the "dump custom"_dump.html command or "fix +ave/spatial"_fix_ave_spatial.html command or "fix +ave/atom"_fix_ave_atom.html command. See "this +section"_Section_howto.html#4_15 for an overview. + +The per-atom energy is calulated by the various pair, bond, etc +potentials defined for the simulation. If no extra keywords are +listed, then the potential energy is the sum of pair, bond, angle, +dihedral, and improper energy. If any extra keywords are listed, then +only those components are summed to compute the potential energy. + +Note that the energy of each atom is due to its interaction with all +other atoms in the simulation, not just with other atoms in the group. + +For an energy contribution produced by a small set of atoms (e.g. 4 +atoms in a dihedral or 3 atoms in a Tersoff 3-body interaction), that +energy is assigned in equal portions to each atom in the set. +E.g. 1/4 of the dihedral energy to each of the 4 atoms. + +The "dihedral_style charmm"_dihedral_charmm.html style calculates +pairwise interactions between 1-4 atoms. The energy contribution of +these terms is included in the pair energy, not the dihedral energy. + +[Restrictions:] none + +[Related commands:] + +"compute pe"_compute_pe.html, "compute +stress/atom"_compute_stress_atom.html + +[Default:] none