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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2955 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2009-07-02 17:10:13 +00:00
parent a4eb700f97
commit 28fce3b01d
6 changed files with 46 additions and 14 deletions
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1
doc/Section_example.html
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@ -47,6 +47,7 @@ Site</A>.
<TR><TD >peptide</TD><TD > dynamics of a small solvated peptide chain (5-mer)</TD></TR>
<TR><TD >peri</TD><TD > Peridynamics example of cylinder hit by projectile</TD></TR>
<TR><TD >pour</TD><TD > pouring of granular particles into a 3d box, then chute flow</TD></TR>
<TR><TD >reax</TD><TD > simple example for ReaxFF force field</TD></TR>
<TR><TD >rigid</TD><TD > rigid bodies modeled as independent or coupled</TD></TR>
<TR><TD >shear</TD><TD > sideways shear applied to 2d solid, with and without a void
</TD></TR></TABLE></DIV>

1
doc/Section_example.txt
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@ -43,6 +43,7 @@ obstacle: flow around two voids in a 2d channel
peptide: dynamics of a small solvated peptide chain (5-mer)
peri: Peridynamics example of cylinder hit by projectile
pour: pouring of granular particles into a 3d box, then chute flow
reax: simple example for ReaxFF force field
rigid: rigid bodies modeled as independent or coupled
shear: sideways shear applied to 2d solid, with and without a void :tb(s=:)

12
doc/Section_history.html
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@ -31,11 +31,13 @@ GranFlow for granular materials.
are being worked on; some haven't been implemented because of lack of
time or interest; others are just a lot of work!
</P>
<UL><LI>NPT with changing box shape (Parinello-Rahman)
<LI>long-range point dipole solver
<LI>torsional shear boundary conditions and temperature calculation
<LI>charge equilibration
<LI>ReaxFF force field from Bill Goddard's group
<UL><LI>coupling to finite elements
<LI>new ReaxFF implementation (in addition to existing one)
<LI>stochastic rotation dynamics
<LI>Stokesian dynamics via fast lubrication dynamics
<LI>NPT with changing box shape (Parinello-Rahman)
<LI>long-range point-dipole solver
<LI>torsional shear boundary conditions and temperature calculation
</UL>
<HR>

10
doc/Section_history.txt
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@ -28,11 +28,13 @@ These are new features we'd like to eventually add to LAMMPS. Some
are being worked on; some haven't been implemented because of lack of
time or interest; others are just a lot of work!
coupling to finite elements
new ReaxFF implementation (in addition to existing one)
stochastic rotation dynamics
Stokesian dynamics via fast lubrication dynamics
NPT with changing box shape (Parinello-Rahman)
long-range point dipole solver
torsional shear boundary conditions and temperature calculation
charge equilibration
ReaxFF force field from Bill Goddard's group :ul
long-range point-dipole solver
torsional shear boundary conditions and temperature calculation :ul
:line

21
doc/Section_intro.html
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@ -192,6 +192,11 @@ commands)
<LI> rRESPA hierarchical timestepping
<LI> parallel tempering (replica exchange)
</UL>
<P>Diagnostics: h4
(<A HREF = "fix.html">fix</A> command, <A HREF = "compute.html">compute</A> command)
</P>
<P> see the various flavors of the fix and compute commands
</P>
<H4>Output
</H4>
<P>(<A HREF = "dump.html">dump</A>, <A HREF = "restart.html">restart</A> commands)
@ -208,9 +213,9 @@ commands)
<H4>Pre- and post-processing
</H4>
<P>Our group has also written and released a separate toolkit called
<A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which provides tools for doing setup, analysis,
<A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which provides tools for doing setup, analysis,
plotting, and visualization for LAMMPS simulations. Pizza.py is
written in <A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">the
written in <A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">the
Pizza.py WWW site</A>.
</P>
@ -246,10 +251,10 @@ section</A>. However, many people use other codes or
write their own tools for these tasks.
</P>
<P>As noted above, our group has also written and released a separate
toolkit called <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which addresses some of the listed
toolkit called <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which addresses some of the listed
bullets. It provides tools for doing setup, analysis, plotting, and
visualization for LAMMPS simulations. Pizza.py is written in
<A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW
<A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW
site</A>.
</P>
<P>LAMMPS requires as input a list of initial atom coordinates and types,
@ -471,6 +476,14 @@ the list.
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >compute heat/flux for Green-Kubo </TD><TD > Reese Jones (Sandia), Philip Howell (Siemens), Vikas Varsney (AFRL)</TD></TR>
<TR><TD >region cone </TD><TD > Pim Schravendijk</TD></TR>
<TR><TD >fix reax/bonds </TD><TD > Aidan Thompson (Sandia)</TD></TR>
<TR><TD >pair born/coul/long </TD><TD > Ahmed Ismail (Sandia)</TD></TR>
<TR><TD >fix ttm </TD><TD > Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)</TD></TR>
<TR><TD >fix box/relax </TD><TD > Aidan Thompson and David Olmsted (Sandia)</TD></TR>
<TR><TD >ReaxFF potential </TD><TD > Aidan Thompson (Sandia) and Hansohl Cho (MIT)</TD></TR>
<TR><TD >compute cna/atom </TD><TD > Wan Liang (Chinese Academy of Sciences)</TD></TR>
<TR><TD >Tersoff/ZBL potential </TD><TD > Dave Farrell (Northwestern U)</TD></TR>
<TR><TD >peridynamics </TD><TD > Mike Parks (Sandia)</TD></TR>
<TR><TD >fix smd for steered MD </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>

15
doc/Section_intro.txt
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@ -191,6 +191,11 @@ Integrators :h4
rRESPA hierarchical timestepping
parallel tempering (replica exchange) :ul
Diagnostics: h4
("fix"_fix.html command, "compute"_compute.html command)
see the various flavors of the fix and compute commands
Output :h4
("dump"_dump.html, "restart"_restart.html commands)
@ -211,7 +216,7 @@ plotting, and visualization for LAMMPS simulations. Pizza.py is
written in "Python"_python and is available for download from "the
Pizza.py WWW site"_pizza.
:link(pizza,http://www.cs.sandia.gov/~sjplimp/pizza.html)
:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
:link(python,http://www.python.org)
:line
@ -457,6 +462,14 @@ the list.
:link(sjp,http://www.cs.sandia.gov/~sjplimp)
compute heat/flux for Green-Kubo : Reese Jones (Sandia), Philip Howell (Siemens), Vikas Varsney (AFRL)
region cone : Pim Schravendijk
fix reax/bonds : Aidan Thompson (Sandia)
pair born/coul/long : Ahmed Ismail (Sandia)
fix ttm : Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)
fix box/relax : Aidan Thompson and David Olmsted (Sandia)
ReaxFF potential : Aidan Thompson (Sandia) and Hansohl Cho (MIT)
compute cna/atom : Wan Liang (Chinese Academy of Sciences)
Tersoff/ZBL potential : Dave Farrell (Northwestern U)
peridynamics : Mike Parks (Sandia)
fix smd for steered MD : Axel Kohlmeyer (U Penn)