From 29eaf3f06091f314edc46d30e969eb15e179f327 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 10 Jan 2008 15:50:00 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1365 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/compute_pe_atom.html | 13 ++++++++++++- doc/compute_pe_atom.txt | 13 ++++++++++++- doc/compute_stress_atom.html | 4 ++-- doc/compute_stress_atom.txt | 4 ++-- doc/fix_shake.html | 3 ++- doc/fix_shake.txt | 3 ++- 6 files changed, 32 insertions(+), 8 deletions(-) diff --git a/doc/compute_pe_atom.html b/doc/compute_pe_atom.html index 89d4f3ea1d..bb562c6707 100644 --- a/doc/compute_pe_atom.html +++ b/doc/compute_pe_atom.html @@ -55,6 +55,13 @@ E.g. 1/4 of the dihedral energy to each of the 4 atoms. pairwise interactions between 1-4 atoms. The energy contribution of these terms is included in the pair energy, not the dihedral energy.

+

IMPORTANT NOTE: The per-atom energy does NOT include contributions due +to long-range Coulombic interactions (via the +kspace_style command). It's not clear this +contribution can easily be computed. There are also a few pair styles +for manybody potentials that are not yet instrumented to yield +per-atom energy. See the Restrictions below. +

Output info:

This compute calculates a scalar quantity for each atom, which can be @@ -62,7 +69,11 @@ accessed by any command that uses per-atom computes as input. See this section for an overview of LAMMPS output options.

-

Restrictions: none +

Restrictions: +

+

These pair styles do not yet tabulate per-atom energies to allow them +to work with this compute: airebo, +meam, and TIP4P.

Related commands:

diff --git a/doc/compute_pe_atom.txt b/doc/compute_pe_atom.txt index 2b4a6c83a2..b9ff81e734 100644 --- a/doc/compute_pe_atom.txt +++ b/doc/compute_pe_atom.txt @@ -52,6 +52,13 @@ 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. +IMPORTANT NOTE: The per-atom energy does NOT include contributions due +to long-range Coulombic interactions (via the +"kspace_style"_kspace_style.html command). It's not clear this +contribution can easily be computed. There are also a few pair styles +for manybody potentials that are not yet instrumented to yield +per-atom energy. See the Restrictions below. + [Output info:] This compute calculates a scalar quantity for each atom, which can be @@ -59,7 +66,11 @@ accessed by any command that uses per-atom computes as input. See "this section"_Section_howto.html#4_15 for an overview of LAMMPS output options. -[Restrictions:] none +[Restrictions:] + +These pair styles do not yet tabulate per-atom energies to allow them +to work with this compute: "airebo"_pair_airebo.html, +"meam"_pair_meam.html, and "TIP4P"_pair_lj.html. [Related commands:] diff --git a/doc/compute_stress_atom.html b/doc/compute_stress_atom.html index 08ae5055c9..d56ea7d8c8 100644 --- a/doc/compute_stress_atom.html +++ b/doc/compute_stress_atom.html @@ -112,8 +112,8 @@ xx, yy, zz, xy, xz, yz.

Restrictions:

-

These pair styles do not yet tabulate per-atom virial information to -allow them to work with this compute: airebo, +

These pair styles do not yet tabulate per-atom virials to allow them +to work with this compute: airebo, meam, and TIP4P.

Related commands: diff --git a/doc/compute_stress_atom.txt b/doc/compute_stress_atom.txt index d2defd723e..b2cf2f2c7c 100644 --- a/doc/compute_stress_atom.txt +++ b/doc/compute_stress_atom.txt @@ -108,8 +108,8 @@ xx, yy, zz, xy, xz, yz. [Restrictions:] -These pair styles do not yet tabulate per-atom virial information to -allow them to work with this compute: "airebo"_pair_airebo.html, +These pair styles do not yet tabulate per-atom virials to allow them +to work with this compute: "airebo"_pair_airebo.html, "meam"_pair_meam.html, and "TIP4P"_pair_lj.html. [Related commands:] diff --git a/doc/fix_shake.html b/doc/fix_shake.html index 87f875a803..ff5aaa606f 100644 --- a/doc/fix_shake.html +++ b/doc/fix_shake.html @@ -83,7 +83,8 @@ in the bond are in the group specified with the SHAKE fix.

The degrees-of-freedom removed by SHAKE bonds and angles are accounted for in temperature and pressure computations. Similarly, the SHAKE -contribution to the pressure virial is also accounted for. +contribution to the pressure of the system (virial) is also accounted +for.

Restart, fix_modify, output, run start/stop, minimize info:

diff --git a/doc/fix_shake.txt b/doc/fix_shake.txt index 075f5891df..302c43f27c 100644 --- a/doc/fix_shake.txt +++ b/doc/fix_shake.txt @@ -72,7 +72,8 @@ in the bond are in the group specified with the SHAKE fix. The degrees-of-freedom removed by SHAKE bonds and angles are accounted for in temperature and pressure computations. Similarly, the SHAKE -contribution to the pressure virial is also accounted for. +contribution to the pressure of the system (virial) is also accounted +for. [Restart, fix_modify, output, run start/stop, minimize info:]