jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7802 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2012-02-16 15:49:48 +00:00
parent 3ff9f1fa60
commit e546f9a54b
4 changed files with 48 additions and 10 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
doc/compute_pe_atom.html
View File

@ -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.
</P>
<P>The KSpace contribution is calculated using the method in
<A HREF = "#Heyes">(Heyes)</A> for the Ewald method and a related method for PPPM,
as specified by the <A HREF = "kspace_style.html">kspace_style pppm</A> command.
For PPPM, the calcluation requires 1 extra FFT each timestep that
per-atom stress is calculated.
</P>
<P>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</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Heyes"></A>
<P><B>(Heyes)</B> Heyes, Phys Rev B 49, 755 (1994),
</P>
</HTML>

11
doc/compute_pe_atom.txt
View File

@ -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),

18
doc/compute_stress_atom.html
View File

@ -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.
</P>
<P>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 <A HREF = "kspace_style.html">kspace_style pppm</A> command. Thus it
can significantly increase the cost of the PPPM calculation if it is
needed on a large fraction of the simulation timesteps.
<P>The KSpace contribution is calculated using the method in
<A HREF = "#Heyes">(Heyes)</A> for the Ewald method and a related method for PPPM,
as specified by the <A HREF = "kspace_style.html">kspace_style pppm</A> 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.
</P>
<P>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.
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Heyes"></A>
<P><B>(Heyes)</B> Heyes, Phys Rev B 49, 755 (1994),
</P>
</HTML>

17
doc/compute_stress_atom.txt
View File

@ -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),