diff --git a/doc/Section_example.html b/doc/Section_example.html index d734fba6d8..c7070e85b7 100644 --- a/doc/Section_example.html +++ b/doc/Section_example.html @@ -32,8 +32,10 @@ Site.

+ + @@ -43,13 +45,14 @@ Site. + - + - - + +
colloid big colloid particles in a small particle solvent, 2d system
comb models using the COMB potential
crack crack propagation in a 2d solid
dipole point dipolar particles, 2d system
eim NaCl using the EIM potential
elastic zero temperature elastic constant tensor of silicon
ellipse ellipsoidal particles in spherical solvent, 2d system
flow Couette and Poiseuille flow in a 2d channel
melt rapid melt of 3d LJ system
micelle self-assembly of small lipid-like molecules into 2d bilayers
min energy minimization of 2d LJ melt
msst MSST shock dynamics
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
peri Peridynamic model of cylinder impacted by indenter
pour pouring of granular particles into a 3d box, then chute flow
prd parallel replica dynamics of a vacancy diffusion in bulk Si
reax simple example for ReaxFF force field
prd parallel replica dynamics of a vacancy diffusion in bulk Si
reax RDX and TATB models using the ReaxFF
rigid rigid bodies modeled as independent or coupled
shear sideways shear applied to 2d solid, with and without a void
@@ -65,17 +68,13 @@ lmp_linux < in.indent # run the problem 

../../tools/xmovie/xmovie -scale dump.indent
-

There is also a directory "couple" in the examples sub-directory, -which contains a stand-alone code umbrella.cpp that links LAMMPS as a -library. The README describes how to build the code. The code itself -runs LAMMPS on a subset of processors, sets up a LAMMPS problem -by invoking LAMMPS input script commands one at a time, does -a run, grabs atom coordinates, changes one atom position, puts -them back into LAMMPS, and does another run. +

There is also a COUPLE directory which has examples of how to link to +LAMMPS as a library and drive it from a wrapper program. See the +README file for more info.

-

This illustrates how an umbrella code could include new models and -physics while using LAMMPS to perform MD, or how the umbrella code -could call both LAMMPS and some other code to perform a coupled -calculation. +

There is also a USER directory which contains subdirectories of +user-provided examples for user packages. See the README files in +those directories for more info. See the doc/Section_start.html for +more info about user packages.

diff --git a/doc/Section_example.txt b/doc/Section_example.txt index 234198d380..3e7078c07c 100644 --- a/doc/Section_example.txt +++ b/doc/Section_example.txt @@ -28,8 +28,10 @@ Site"_lws. These are the sample problems in the examples sub-directories: colloid: big colloid particles in a small particle solvent, 2d system +comb: models using the COMB potential crack: crack propagation in a 2d solid dipole: point dipolar particles, 2d system +eim: NaCl using the EIM potential elastic: zero temperature elastic constant tensor of silicon ellipse: ellipsoidal particles in spherical solvent, 2d system flow: Couette and Poiseuille flow in a 2d channel @@ -39,13 +41,14 @@ meam: MEAM test for SiC and shear (same as shear examples) melt: rapid melt of 3d LJ system micelle: self-assembly of small lipid-like molecules into 2d bilayers min: energy minimization of 2d LJ melt +msst: MSST shock dynamics 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 +peri: Peridynamic model of cylinder impacted by indenter pour: pouring of granular particles into a 3d box, then chute flow -prd: parallel replica dynamics of a vacancy diffusion in bulk Si -reax: simple example for ReaxFF force field +prd: parallel replica dynamics of a vacancy diffusion in bulk Si +reax: RDX and TATB models using the ReaxFF rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void :tb(s=:) @@ -60,15 +63,11 @@ Running the simulation produces the files {dump.indent} and ../../tools/xmovie/xmovie -scale dump.indent :pre -There is also a directory "couple" in the examples sub-directory, -which contains a stand-alone code umbrella.cpp that links LAMMPS as a -library. The README describes how to build the code. The code itself -runs LAMMPS on a subset of processors, sets up a LAMMPS problem -by invoking LAMMPS input script commands one at a time, does -a run, grabs atom coordinates, changes one atom position, puts -them back into LAMMPS, and does another run. +There is also a COUPLE directory which has examples of how to link to +LAMMPS as a library and drive it from a wrapper program. See the +README file for more info. -This illustrates how an umbrella code could include new models and -physics while using LAMMPS to perform MD, or how the umbrella code -could call both LAMMPS and some other code to perform a coupled -calculation. +There is also a USER directory which contains subdirectories of +user-provided examples for user packages. See the README files in +those directories for more info. See the doc/Section_start.html for +more info about user packages. diff --git a/doc/Section_history.html b/doc/Section_history.html index dd0f264abc..8fe4156330 100644 --- a/doc/Section_history.html +++ b/doc/Section_history.html @@ -41,7 +41,6 @@ page on the LAMMPS WWW site for more details.
  • Triangulated particles
  • Stochastic rotation dynamics
  • Stokesian dynamics via fast lubrication dynamics -
  • NPT with changing box shape (Parinello-Rahman)
  • Long-range point-dipole solver
  • Per-atom energy and stress for long-range Coulombics
  • Long-range Coulombics via Ewald and PPPM for triclinic boxes diff --git a/doc/Section_history.txt b/doc/Section_history.txt index 4d22fa582d..6e17ca611d 100644 --- a/doc/Section_history.txt +++ b/doc/Section_history.txt @@ -38,7 +38,6 @@ Temperature accelerated dynamics Triangulated particles Stochastic rotation dynamics Stokesian dynamics via fast lubrication dynamics -NPT with changing box shape (Parinello-Rahman) Long-range point-dipole solver Per-atom energy and stress for long-range Coulombics Long-range Coulombics via Ewald and PPPM for triclinic boxes diff --git a/doc/Section_intro.html b/doc/Section_intro.html index 446109b3da..93db0021d1 100644 --- a/doc/Section_intro.html +++ b/doc/Section_intro.html @@ -173,7 +173,7 @@ commands)