correct section link descriptions

These are the accelerator packages

currently in LAMMPS, either as standard or user packages:

"GPU"_accelerate_gpu.html : for NVIDIA GPUs as well as OpenCL support

"USER-INTEL"_accelerate_intel.html : for Intel CPUs and Intel Xeon Phi

"KOKKOS"_accelerate_kokkos.html : for GPUs, Intel Xeon Phi, and OpenMP threading

"USER-OMP"_accelerate_omp.html : for OpenMP threading

"OPT"_accelerate_opt.html : generic CPU optimizations :tb(s=:)

"GPU Package"_accelerate_gpu.html with CUDA and OpenCL support for Nvidia GPUs and others :h5

"USER-INTEL Package"_accelerate_intel.html for Intel CPUs and Intel Xeon Phi :h5

"KOKKOS Package"_accelerate_kokkos.html for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading :h5

"USER-OMP Package "_accelerate_omp.html for OpenMP threading and generic CPU optimizations :h5

"OPT Package"_accelerate_opt.html generic CPU optimizations :h5

Inverting this list, LAMMPS currently has acceleration support for

three kinds of hardware, via the listed packages:

"pair_style lj/cut/opt"_pair_lj.html :ul

To see what accelerate styles are currently available, see

"Section_commands 5"_Section_commands.html#cmd_5 of the manual.  The

"Section 3.5"_Section_commands.html#cmd_5 of the manual.  The

doc pages for individual commands (e.g. "pair lj/cut"_pair_lj.html or

"fix nve"_fix_nve.html) also list any accelerated variants available

for that style.

This section describes the structure of a typical LAMMPS input script.

The "examples" directory in the LAMMPS distribution contains many

sample input scripts; the corresponding problems are discussed in

"Section_example"_Section_example.html, and animated on the "LAMMPS

"Section 7"_Section_example.html, and animated on the "LAMMPS

WWW Site"_lws.

A LAMMPS input script typically has 4 parts:

If there are other fixes that act immediately after the intitial stage

of time integration within a timestep (i.e. after atoms move), then

the command that sets up the dynamic group should appear after those

fixes.  This will insure that dynamic group assignements are made

fixes.  This will insure that dynamic group assignments are made

after all atoms have moved. :dd

{One or more respa levels compute no forces} :dt

13.1 Coming attractions :h4,link(hist_1)

The "Wish list link"_http://lammps.sandia.gov/future.html on the

LAMMPS WWW page gives a list of features we are hoping to add to

LAMMPS in the future, including contact names of individuals you can

email if you are interested in contributing to the developement or

would be a future user of that feature.

You can also send "email to the

developers"_http://lammps.sandia.gov/authors.html if you want to add

your wish to the list.

As of summer 2016 we are using the "LAMMPS project issue tracker

on GitHub"_https://github.com/lammps/lammps/issues for keeping

track of suggested, planned or pending new features. This includes

discussions of how to best implement them, or why they would be

useful. Especially if a planned or proposed feature is non-trivial

to add, e.g. because it requires changes to some of the core

classes of LAMMPS, people planning to contribute a new feature to

LAMMS are encouraged to submit an issue about their planned

implementation this way in order to receive feedback from the

LAMMPS core developers. They will provide suggestions about

the validity of the proposed approach and possible improvements,

pitfalls or alternatives.

Please see some of the closed issues for examples of how to

suggest code enhancements, submit proposed changes, or report

elated issues and how they are resoved. 

As an alternative to using GitHub, you may e-mail the

"core developers"_http://lammps.sandia.gov/authors.html or send

an e-mail to the "LAMMPS Mail list"_http://lammps.sandia.gov/mail.html

if you want to have your suggestion added to the list.

:line

6.27 "Drude induced dipoles"_#howto_27 :all(b)

The example input scripts included in the LAMMPS distribution and

highlighted in "Section_example"_Section_example.html also show how to

highlighted in "Section 7"_Section_example.html also show how to

setup and run various kinds of simulations.

:line

coefficients is done in the input data file via the

"read_data"_read_data.html command or in the input script with

commands like "pair_coeff"_pair_coeff.html or

"bond_coeff"_bond_coeff.html.  See "Section_tools"_Section_tools.html

"bond_coeff"_bond_coeff.html.  See "Section 9"_Section_tools.html

for additional tools that can use CHARMM or AMBER to assign force

field coefficients and convert their output into LAMMPS input.

stand-alone code could communicate with LAMMPS thru files that the

command writes and reads.

See "Section_modify"_Section_modify.html of the documentation for how

See "Section 10"_Section_modify.html of the documentation for how

to add a new command to LAMMPS.

(3) Use LAMMPS as a library called by another code.  In this case the

LAMMPS, pass it an input script to process, or execute individual

commands, all by invoking the correct class methods in LAMMPS.  From C

or Fortran you can make function calls to do the same things.  See

"Section_python"_Section_python.html of the manual for a description

"Section 11"_Section_python.html of the manual for a description

of the Python wrapper provided with LAMMPS that operates through the

LAMMPS library interface.

The files src/library.cpp and library.h contain the C-style interface

to LAMMPS.  See "Section_howto 19"_Section_howto.html#howto_19 of the

to LAMMPS.  See "Section 6.19"_Section_howto.html#howto_19 of the

manual for a description of the interface and how to extend it for

your needs.

Several programs included with LAMMPS as auxiliary tools can convert

native LAMMPS dump files to other formats.  See the

"Section_tools"_Section_tools.html doc page for details.  The first is

"Section 9"_Section_tools.html doc page for details.  The first is

the "ch2lmp tool"_Section_tools.html#charmm, which contains a

lammps2pdb Perl script which converts LAMMPS dump files into PDB

files.  The second is the "lmp2arc tool"_Section_tools.html#arc which

6.19 Library interface to LAMMPS :link(howto_19),h4

As described in "Section_start 5"_Section_start.html#start_5, LAMMPS

As described in "Section 2.5"_Section_start.html#start_5, LAMMPS

can be built as a library, so that it can be called by another code,

used in a "coupled manner"_Section_howto.html#howto_10 with other

codes, or driven through a "Python interface"_Section_python.html.

"variables"_variable.html to be used to define chunk IDs for each

atom.  This means you can write your own compute or fix to output a

per-atom quantity to use as chunk ID.  See

"Section_modify"_Section_modify.html of the documentation for how to

"Section 10"_Section_modify.html of the documentation for how to

do this.  You can also define a "per-atom variable"_variable.html in

the input script that uses a formula to generate a chunk ID for each

atom.