From e546f9a54b326ee46d58b1d4cfeeefa7da143f25 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 16 Feb 2012 15:49:48 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7802 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/compute_pe_atom.html | 12 ++++++++++++ doc/compute_pe_atom.txt | 11 +++++++++++ doc/compute_stress_atom.html | 18 +++++++++++++----- doc/compute_stress_atom.txt | 17 ++++++++++++----- 4 files changed, 48 insertions(+), 10 deletions(-) diff --git a/doc/compute_pe_atom.html b/doc/compute_pe_atom.html index 9496394e89..42704cf368 100644 --- a/doc/compute_pe_atom.html +++ b/doc/compute_pe_atom.html @@ -51,6 +51,12 @@ 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.

+

The KSpace contribution is calculated using the method in +(Heyes) for the Ewald method and a related method for PPPM, +as specified by the kspace_style pppm command. +For PPPM, the calcluation requires 1 extra FFT each timestep that +per-atom stress is calculated. +

As an example of per-atom potential energy compared to total potential energy, these lines in an input script should yield the same result in the last 2 columns of thermo output: @@ -81,4 +87,10 @@ stress/atom

Default: none

+
+ + + +

(Heyes) Heyes, Phys Rev B 49, 755 (1994), +

diff --git a/doc/compute_pe_atom.txt b/doc/compute_pe_atom.txt index 37c5ba7c6e..3d0a6f6697 100644 --- a/doc/compute_pe_atom.txt +++ b/doc/compute_pe_atom.txt @@ -48,6 +48,12 @@ 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. +The KSpace contribution is calculated using the method in +"(Heyes)"_#Heyes for the Ewald method and a related method for PPPM, +as specified by the "kspace_style pppm"_kspace_style.html command. +For PPPM, the calcluation requires 1 extra FFT each timestep that +per-atom stress is calculated. + As an example of per-atom potential energy compared to total potential energy, these lines in an input script should yield the same result in the last 2 columns of thermo output: @@ -77,3 +83,8 @@ The per-atom vector values will be in energy "units"_units.html. stress/atom"_compute_stress_atom.html [Default:] none + +:line + +:link(Heyes) +[(Heyes)] Heyes, Phys Rev B 49, 755 (1994), diff --git a/doc/compute_stress_atom.html b/doc/compute_stress_atom.html index b0bc2e4acd..71e7444d75 100644 --- a/doc/compute_stress_atom.html +++ b/doc/compute_stress_atom.html @@ -75,11 +75,13 @@ other atoms in the simulation, not just with other atoms in the group. pairwise interactions between 1-4 atoms. The virial contribution of these terms is included in the pair virial, not the dihedral virial.

-

The KSpace contribution to the per-atom stress requires 6 extra FFTs -each timestep that per-atom stress is calculated, if using the PPPM -solver via the kspace_style pppm command. Thus it -can significantly increase the cost of the PPPM calculation if it is -needed on a large fraction of the simulation timesteps. +

The KSpace contribution is calculated using the method in +(Heyes) for the Ewald method and a related method for PPPM, +as specified by the kspace_style pppm command. +For PPPM, the calcluation requires 6 extra FFTs each timestep that +per-atom stress is calculated. Thus it can significantly increase the +cost of the PPPM calculation if it is needed on a large fraction of +the simulation timesteps.

Note that as defined in the formula, per-atom stress is the negative of the per-atom pressure tensor. It is also really a stress*volume @@ -119,4 +121,10 @@ options.

Default: none

+
+ + + +

(Heyes) Heyes, Phys Rev B 49, 755 (1994), +

diff --git a/doc/compute_stress_atom.txt b/doc/compute_stress_atom.txt index 78dae4bda3..8e1d40d0a1 100644 --- a/doc/compute_stress_atom.txt +++ b/doc/compute_stress_atom.txt @@ -72,11 +72,13 @@ The "dihedral_style charmm"_dihedral_charmm.html style calculates pairwise interactions between 1-4 atoms. The virial contribution of these terms is included in the pair virial, not the dihedral virial. -The KSpace contribution to the per-atom stress requires 6 extra FFTs -each timestep that per-atom stress is calculated, if using the PPPM -solver via the "kspace_style pppm"_kspace_style.html command. Thus it -can significantly increase the cost of the PPPM calculation if it is -needed on a large fraction of the simulation timesteps. +The KSpace contribution is calculated using the method in +"(Heyes)"_#Heyes for the Ewald method and a related method for PPPM, +as specified by the "kspace_style pppm"_kspace_style.html command. +For PPPM, the calcluation requires 6 extra FFTs each timestep that +per-atom stress is calculated. Thus it can significantly increase the +cost of the PPPM calculation if it is needed on a large fraction of +the simulation timesteps. Note that as defined in the formula, per-atom stress is the negative of the per-atom pressure tensor. It is also really a stress*volume @@ -115,3 +117,8 @@ The per-atom array values will be in pressure*volume "compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html [Default:] none + +:line + +:link(Heyes) +[(Heyes)] Heyes, Phys Rev B 49, 755 (1994),