Added documentation describing PLUMED package installation

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USER-PLUMED package :link(USER-PLUMED),h4

[Contents:]

The fix plumed command allows you to use the plugin for molecular

dynamics PLUMED to analyse and bias your LAMMPS trajectory on the fly.

In practise PLUMED is called from within the lammps input script by using

the "fix plumed _fix_plumed.html command.

[Authors:] The PLUMED library is written and maintained by

Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and

Gareth Tribello. 

[Install or un-install:]

Before building LAMMPS with this package, you must first build 

PLUMED.  We recommending building PLUMED separately to LAMMPS using

the instructions that can be found at http://plumed.github.io/doc-master/user-doc/html/_installation.html.

Before compiling LAMMPS you can then install the fix plumed command

and compile LAMMPS in the usual manner:

make yes-user-plumed 

make machine :pre

Once this compilation completes you should be able to run LAMMPS in the usual

way.  When running LAMMPS with an input script that contains a fix

plumed command LAMMPS will try to call the PLUMED runtime library.  PLUMED

must therefore be available in your path if LAMMPS is compiled in this way.

On some machines it is not possible to call runtime libraries in the way described

above.  When compiling on these machines it is thus better to statically link 

PLUMED when compiling LAMMPS.  To do this you must either download a PLUMED

tarball from http://www.plumed.org/get-it or clone it using 

git clone https://github.com/plumed/plumed2.git.  If you download the tarball

unpack it in the /lib/plumed directory.  Similarly if you clone 

it clone it to the /lib/plumed directory as if there is a version of PLUMED within 

this directory LAMMPS will always try to statically link the version of PLUMED 

that this directory contains instead of dynamically linking the library.

Once you have downloaded PLUMED into /lib/plumed you must again build the code

here by following the instructions that can be found at

http://plumed.github.io/doc-master/user-doc/html/_installation.html.

You can statically link PLUMED manually and if you want to access the full 

range of PLUMED functionalities this is what you should do.  If you only want the

basic range of functionalities, however, (i.e. no user contributed modules) then 

you can download and compile PLUMED in one step from the lammps/src dir, using a 

command like like those below:

make lib-plumed                       # print help message

make lib-plumed  args="-b"            # download and build the latest stable version of PLUMED

These commands will simply invoke the lib/plumed/Install.py script with 

args specified.  Furthermore, once the script has completed you should 

have a compiled version of PLUMED.  With this built you can install/un-install

PLUMED and build LAMMPS in the usual manner:

make yes-user-plumed

make machine :pre

make no-user-plumed

make machine :pre

[Supporting info:]

src/USER-PLUMED/README

lib/plumed/README

"fix plumed "_fix_plumed.html

examples/USER/plumed :ul

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USER-DIFFRACTION package :link(USER-DIFFRACTION),h4

[Contents:]

#  Needs make yes-molecule

#        make yes-rigid

#        make yes-kspace

#        make yes-user-plumed    ( obviously )

#!/bin/bash

LAMMPS=../../../src/lmp_mpi