From 674caeb3288d25c5e5d317f064542f4de2fecfa6 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 9 Jan 2009 00:14:52 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2357
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/Section_example.html |  1 +
 doc/Section_example.txt  |  1 +
 doc/Section_history.html |  1 -
 doc/Section_history.txt  |  1 -
 doc/Section_intro.html   | 28 +++++++++++++++++++++++-----
 doc/Section_intro.txt    | 28 +++++++++++++++++++++++-----
 doc/Section_start.html   |  1 +
 doc/Section_start.txt    |  1 +
 doc/compute.html         |  1 -
 doc/compute.txt          |  1 -
 doc/fix_wall_gran.html   |  7 ++++---
 doc/fix_wall_gran.txt    |  2 +-
 doc/pair_coeff.html      |  6 +++---
 doc/pair_coeff.txt       |  6 +++---
 doc/pair_style.html      |  6 +++---
 doc/pair_style.txt       |  6 +++---
 16 files changed, 67 insertions(+), 30 deletions(-)

diff --git a/doc/Section_example.html b/doc/Section_example.html
index 8514afb5d0..6e5843434c 100644
--- a/doc/Section_example.html
+++ b/doc/Section_example.html
@@ -45,6 +45,7 @@ Site</A>.
 <TR><TD >nemd</TD><TD >	  non-equilibrium MD of 2d sheared system</TD></TR>
 <TR><TD >obstacle</TD><TD > flow around two voids in a 2d channel</TD></TR>
 <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 >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 
diff --git a/doc/Section_example.txt b/doc/Section_example.txt
index ae472e0ad7..60a61f6061 100644
--- a/doc/Section_example.txt
+++ b/doc/Section_example.txt
@@ -41,6 +41,7 @@ min:	  energy minimization of 2d LJ melt
 nemd:	  non-equilibrium MD of 2d sheared system
 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
 rigid:    rigid bodies modeled as independent or coupled
 shear:    sideways shear applied to 2d solid, with and without a void :tb(s=:)
diff --git a/doc/Section_history.html b/doc/Section_history.html
index 5272e34c21..fb75631d1b 100644
--- a/doc/Section_history.html
+++ b/doc/Section_history.html
@@ -32,7 +32,6 @@ 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>bond creation potentials
 <LI>long-range point dipole solver
 <LI>torsional shear boundary conditions and temperature calculation
 <LI>charge equilibration
diff --git a/doc/Section_history.txt b/doc/Section_history.txt
index c1d9d3c8fc..e27bcb4a38 100644
--- a/doc/Section_history.txt
+++ b/doc/Section_history.txt
@@ -29,7 +29,6 @@ are being worked on; some haven't been implemented because of lack of
 time or interest; others are just a lot of work!
 
 NPT with changing box shape (Parinello-Rahman)
-bond creation potentials
 long-range point dipole solver
 torsional shear boundary conditions and temperature calculation
 charge equilibration
diff --git a/doc/Section_intro.html b/doc/Section_intro.html
index 46edaa4fc8..f56ebd4ba7 100644
--- a/doc/Section_intro.html
+++ b/doc/Section_intro.html
@@ -98,6 +98,21 @@ favorite interatomic potential, boundary condition, or atom type, see
 <A HREF = "Section_modify.html">this section</A>, which describes how you can add it to
 LAMMPS.
 </P>
+<P>General features: h4
+</P>
+<UL><LI>  runs on a single processor or in parallel
+<LI>  distributed-memory message-passing parallelism (MPI)
+<LI>  spatial-decomposition of simulation domain for parallelism
+<LI>  open-source distribution
+<LI>  highly portable C++
+<LI>  optional libraries needed: MPI and single-processor FFT
+<LI>  easy to extend with new features and functionality
+<LI>  in parallel, run one or multiple simulations simultaneously
+<LI>  runs from an input script
+<LI>  syntax for defining and using variables and formulas
+<LI>  syntax for looping over runs and breaking out of loops
+<LI>  run a series of simluations from one script 
+</UL>
 <H4>Kinds of systems LAMMPS can simulate: 
 </H4>
 <P>(<A HREF = "atom_style.html">atom style</A> command)
@@ -111,7 +126,7 @@ LAMMPS.
 <LI>  coarse-grained mesoscale models
 <LI>  ellipsoidal particles
 <LI>  point dipolar particles
-<LI>  hybrid systems 
+<LI>  hybrid combinations of these 
 </UL>
 <H4>Force fields: 
 </H4>
@@ -123,7 +138,8 @@ commands)
 <UL><LI>  pairwise potentials: Lennard-Jones, Buckingham, Morse,     Yukawa, soft, class 2 (COMPASS), tabulated
 <LI>  charged pairwise potentials: Coulombic, point-dipole
 <LI>  manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM),     Stillinger-Weber, Tersoff, AI-REBO
-<LI>  coarse-grain potentials: granular, DPD, GayBerne, REsquared, colloidal
+<LI>  coarse-grain potentials: DPD, GayBerne, REsquared, colloidal
+<LI>  mesoscopic potentials: granular, Peridynamics
 <LI>  bond potentials: harmonic, FENE, Morse, nonlinear, class 2,     quartic (breakable)
 <LI>  angle potentials: harmonic, CHARMM, cosine, cosine/squared,     class 2 (COMPASS)
 <LI>  dihedral potentials: harmonic, CHARMM, multi-harmonic, helix,     class 2 (COMPASS), OPLS
@@ -160,6 +176,7 @@ commands)
 <LI>  harmonic (umbrella) constraint forces
 <LI>  independent or coupled rigid body integration
 <LI>  SHAKE bond and angle constraints
+<LI>  bond breaking, formation, swapping
 <LI>  walls of various kinds
 <LI>  targeted molecular dynamics (TMD) and steered molecule dynamics (SMD) constraints
 <LI>  non-equilibrium molecular dynamics (NEMD)
@@ -171,10 +188,9 @@ commands)
 </P>
 <UL><LI>  velocity-Verlet integrator
 <LI>  Brownian dynamics
-<LI>  energy minimization via conjugate gradient relaxation
+<LI>  energy minimization via conjugate gradient or steepest descent relaxation
 <LI>  rRESPA hierarchical timestepping
-<LI>  parallel tempering (replica exchange)
-<LI>  run multiple independent simulations simultaneously 
+<LI>  parallel tempering (replica exchange) 
 </UL>
 <H4>Output: 
 </H4>
@@ -455,6 +471,8 @@ the list.
 
 
 <DIV ALIGN=center><TABLE  BORDER=1 >
+<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>
 <TR><TD >GROMACS pair potentials </TD><TD > Mark Stevens (Sandia)</TD></TR>
 <TR><TD >lmp2vmd tool </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt
index 5ff97a316e..982399b30c 100644
--- a/doc/Section_intro.txt
+++ b/doc/Section_intro.txt
@@ -95,6 +95,21 @@ favorite interatomic potential, boundary condition, or atom type, see
 "this section"_Section_modify.html, which describes how you can add it to
 LAMMPS.
 
+General features: h4
+
+  runs on a single processor or in parallel
+  distributed-memory message-passing parallelism (MPI)
+  spatial-decomposition of simulation domain for parallelism
+  open-source distribution
+  highly portable C++
+  optional libraries needed: MPI and single-processor FFT
+  easy to extend with new features and functionality
+  in parallel, run one or multiple simulations simultaneously
+  runs from an input script
+  syntax for defining and using variables and formulas
+  syntax for looping over runs and breaking out of loops
+  run a series of simluations from one script :ul
+
 Kinds of systems LAMMPS can simulate: :h4
 ("atom style"_atom_style.html command)
 
@@ -107,7 +122,7 @@ Kinds of systems LAMMPS can simulate: :h4
   coarse-grained mesoscale models
   ellipsoidal particles
   point dipolar particles
-  hybrid systems :ul
+  hybrid combinations of these :ul
 
 Force fields: :h4
 ("pair style"_pair_style.html, "bond style"_bond_style.html,
@@ -120,7 +135,8 @@ commands)
   charged pairwise potentials: Coulombic, point-dipole
   manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
     Stillinger-Weber, Tersoff, AI-REBO
-  coarse-grain potentials: granular, DPD, GayBerne, REsquared, colloidal
+  coarse-grain potentials: DPD, GayBerne, REsquared, colloidal
+  mesoscopic potentials: granular, Peridynamics
   bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \
     quartic (breakable)
   angle potentials: harmonic, CHARMM, cosine, cosine/squared, \
@@ -160,6 +176,7 @@ Ensembles, constraints, and boundary conditions: :h4
   harmonic (umbrella) constraint forces
   independent or coupled rigid body integration
   SHAKE bond and angle constraints
+  bond breaking, formation, swapping
   walls of various kinds
   targeted molecular dynamics (TMD) and steered molecule dynamics (SMD) constraints
   non-equilibrium molecular dynamics (NEMD)
@@ -170,10 +187,9 @@ Integrators: :h4
 
   velocity-Verlet integrator
   Brownian dynamics
-  energy minimization via conjugate gradient relaxation
+  energy minimization via conjugate gradient or steepest descent relaxation
   rRESPA hierarchical timestepping
-  parallel tempering (replica exchange)
-  run multiple independent simulations simultaneously :ul
+  parallel tempering (replica exchange) :ul
 
 Output: :h4
 ("dump"_dump.html, "restart"_restart.html commands) 
@@ -441,6 +457,8 @@ the list.
 
 :link(sjp,http://www.cs.sandia.gov/~sjplimp)
 
+Tersoff/ZBL potential : Dave Farrell (Northwestern U)
+peridynamics : Mike Parks (Sandia)
 fix smd for steered MD : Axel Kohlmeyer (U Penn)
 GROMACS pair potentials : Mark Stevens (Sandia)
 lmp2vmd tool : Axel Kohlmeyer (U Penn)
diff --git a/doc/Section_start.html b/doc/Section_start.html
index 89c9cecf3f..a3fbb214ca 100644
--- a/doc/Section_start.html
+++ b/doc/Section_start.html
@@ -297,6 +297,7 @@ typing "make package".
 <TR><TD >meam </TD><TD > modified embedded atom method (MEAM) potential</TD></TR>
 <TR><TD >molecule </TD><TD > force fields for molecular systems</TD></TR>
 <TR><TD >opt </TD><TD > optimized versions of a few pair potentials</TD></TR>
+<TR><TD >peri </TD><TD > Peridynamics model and potential</TD></TR>
 <TR><TD >poems </TD><TD > coupled rigid body motion</TD></TR>
 <TR><TD >xtc </TD><TD > dump atom snapshots in XTC format 
 </TD></TR></TABLE></DIV>
diff --git a/doc/Section_start.txt b/doc/Section_start.txt
index c037f44283..72c3ad65b8 100644
--- a/doc/Section_start.txt
+++ b/doc/Section_start.txt
@@ -291,6 +291,7 @@ manybody : metal, 3-body, bond-order potentials
 meam : modified embedded atom method (MEAM) potential
 molecule : force fields for molecular systems
 opt : optimized versions of a few pair potentials
+peri : Peridynamics model and potential
 poems : coupled rigid body motion
 xtc : dump atom snapshots in XTC format :tb(s=:)
 
diff --git a/doc/compute.html b/doc/compute.html
index a5e7195fa8..f094b1ca90 100644
--- a/doc/compute.html
+++ b/doc/compute.html
@@ -127,7 +127,6 @@ available in LAMMPS:
 <LI><A HREF = "compute_temp_asphere.html">temp/asphere</A> - temperature of aspherical particles
 <LI><A HREF = "compute_temp_com.html">temp/com</A> - temperature after subtracting center-of-mass velocity
 <LI><A HREF = "compute_temp_deform.html">temp/deform</A> - temperature excluding box deformation velocity
-<LI><A HREF = "compute_temp_dipole.html">temp/dipole</A> - temperature of point dipolar particles
 <LI><A HREF = "compute_temp_partial.html">temp/partial</A> - temperature excluding one or more dimensions of velocity
 <LI><A HREF = "compute_temp_ramp.html">temp/ramp</A> - temperature excluding ramped velocity component
 <LI><A HREF = "compute_temp_region.html">temp/region</A> - temperature of a region of atoms
diff --git a/doc/compute.txt b/doc/compute.txt
index 38e842bbec..9d5eba5bfd 100644
--- a/doc/compute.txt
+++ b/doc/compute.txt
@@ -124,7 +124,6 @@ available in LAMMPS:
 "temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
 "temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity
 "temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity
-"temp/dipole"_compute_temp_dipole.html - temperature of point dipolar particles
 "temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
 "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
 "temp/region"_compute_temp_region.html - temperature of a region of atoms
diff --git a/doc/fix_wall_gran.html b/doc/fix_wall_gran.html
index 3fbaac3a74..df492c9ec0 100644
--- a/doc/fix_wall_gran.html
+++ b/doc/fix_wall_gran.html
@@ -35,11 +35,12 @@
 
 <LI>args = list of arguments for a particular style 
 
-<LI>  <I>xplane</I> or <I>yplane</I> or <I>zplane</I> args = lo hi
+<PRE>  <I>xplane</I> or <I>yplane</I> or <I>zplane</I> args = lo hi
     lo,hi = position of lower and upper plane (distance units), either can be NULL)
   <I>zcylinder</I> args = radius
-    radius = cylinder radius (distance units)
-zero or more keyword/value pairs may be appended to args 
+    radius = cylinder radius (distance units) 
+</PRE>
+<LI>zero or more keyword/value pairs may be appended to args 
 
 <LI>keyword = <I>wiggle</I> or <I>shear</I> 
 
diff --git a/doc/fix_wall_gran.txt b/doc/fix_wall_gran.txt
index 488eea0af9..08e515452b 100644
--- a/doc/fix_wall_gran.txt
+++ b/doc/fix_wall_gran.txt
@@ -25,7 +25,7 @@ args = list of arguments for a particular style :l
   {xplane} or {yplane} or {zplane} args = lo hi
     lo,hi = position of lower and upper plane (distance units), either can be NULL)
   {zcylinder} args = radius
-    radius = cylinder radius (distance units)
+    radius = cylinder radius (distance units) :pre
 zero or more keyword/value pairs may be appended to args :l
 keyword = {wiggle} or {shear} :l
   {wiggle} values = dim amplitude period
diff --git a/doc/pair_coeff.html b/doc/pair_coeff.html
index 5b7c071ef4..ea9092ca61 100644
--- a/doc/pair_coeff.html
+++ b/doc/pair_coeff.html
@@ -105,9 +105,9 @@ the pair_style command, and coefficients specified by the associated
 <LI><A HREF = "pair_eam.html">pair_style eam/fs</A> - Finnis-Sinclair EAM
 <LI><A HREF = "pair_eam.html">pair_style eam/fs/opt</A> - optimized version of Finnis-Sinclair EAM
 <LI><A HREF = "pair_gayberne.html">pair_style gayberne</A> - Gay-Berne ellipsoidal potential
-<LI><A HREF = "pair_gran.html">pair_style gran/hertzian</A> - granular potential with Hertzian interactions
-<LI><A HREF = "pair_gran.html">pair_style gran/history</A> - granular potential with history effects
-<LI><A HREF = "pair_gran.html">pair_style gran/no_history</A> - granular potential without history effects
+<LI><A HREF = "pair_gran.html">pair_style gran/hertz/history</A> - granular potential with Hertzian interactions
+<LI><A HREF = "pair_gran.html">pair_style gran/hooke</A> - granular potential with history effects
+<LI><A HREF = "pair_gran.html">pair_style gran/hooke/history</A> - granular potential without history effects
 <LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb
 <LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm/implicit</A> - CHARMM for implicit solvent
 <LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long</A> - CHARMM with long-range Coulomb
diff --git a/doc/pair_coeff.txt b/doc/pair_coeff.txt
index 60913fed19..af62d62d44 100644
--- a/doc/pair_coeff.txt
+++ b/doc/pair_coeff.txt
@@ -101,9 +101,9 @@ the pair_style command, and coefficients specified by the associated
 "pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
 "pair_style eam/fs/opt"_pair_eam.html - optimized version of Finnis-Sinclair EAM
 "pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
-"pair_style gran/hertzian"_pair_gran.html - granular potential with Hertzian interactions
-"pair_style gran/history"_pair_gran.html - granular potential with history effects
-"pair_style gran/no_history"_pair_gran.html - granular potential without history effects
+"pair_style gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions
+"pair_style gran/hooke"_pair_gran.html - granular potential with history effects
+"pair_style gran/hooke/history"_pair_gran.html - granular potential without history effects
 "pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
 "pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
 "pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
diff --git a/doc/pair_style.html b/doc/pair_style.html
index 69ae43307b..8edb82b09e 100644
--- a/doc/pair_style.html
+++ b/doc/pair_style.html
@@ -107,9 +107,9 @@ the pair_style command, and coefficients specified by the associated
 <LI><A HREF = "pair_eam.html">pair_style eam/fs</A> - Finnis-Sinclair EAM
 <LI><A HREF = "pair_eam.html">pair_style eam/fs/opt</A> - optimized version of Finnis-Sinclair EAM
 <LI><A HREF = "pair_gayberne.html">pair_style gayberne</A> - Gay-Berne ellipsoidal potential
-<LI><A HREF = "pair_gran.html">pair_style gran/hertzian</A> - granular potential with Hertzian interactions
-<LI><A HREF = "pair_gran.html">pair_style gran/history</A> - granular potential with history effects
-<LI><A HREF = "pair_gran.html">pair_style gran/no_history</A> - granular potential without history effects
+<LI><A HREF = "pair_gran.html">pair_style gran/hertz/history</A> - granular potential with Hertzian interactions
+<LI><A HREF = "pair_gran.html">pair_style gran/hooke</A> - granular potential with history effects
+<LI><A HREF = "pair_gran.html">pair_style gran/hooke/history</A> - granular potential without history effects
 <LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb
 <LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm/implicit</A> - CHARMM for implicit solvent
 <LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long</A> - CHARMM with long-range Coulomb
diff --git a/doc/pair_style.txt b/doc/pair_style.txt
index f96bc89f84..953abfc80a 100644
--- a/doc/pair_style.txt
+++ b/doc/pair_style.txt
@@ -103,9 +103,9 @@ the pair_style command, and coefficients specified by the associated
 "pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
 "pair_style eam/fs/opt"_pair_eam.html - optimized version of Finnis-Sinclair EAM
 "pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
-"pair_style gran/hertzian"_pair_gran.html - granular potential with Hertzian interactions
-"pair_style gran/history"_pair_gran.html - granular potential with history effects
-"pair_style gran/no_history"_pair_gran.html - granular potential without history effects
+"pair_style gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions
+"pair_style gran/hooke"_pair_gran.html - granular potential with history effects
+"pair_style gran/hooke/history"_pair_gran.html - granular potential without history effects
 "pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
 "pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
 "pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb