Added descriptions of static linking of PLUMED to README files

This directory contains links to the PLUMED library which is required

to use the PLUMED package and its fix plumed command in a

LAMMPS input script.  PLUMED should only be downloaded into this directory if 

you wish to statically link the library.  If you wish to link PLUMED as 

a dynamic library (as we recommend) then you can compile and build PLUMED

separately to LAMMPS.  To use PLUMED in conjuction with LAMMPS you then simply

need to ensure that the PLUMED library is in your path at runtime.

More info about the PLUMED library can be found at http://www.plumed.org.

You can type "make lib-plumed" from the src directory to see help on

how to download, build and statically link PLUMED via make commands, or you can

do the same thing by typing "python Install.py" from within this

directory.   Alternatively you can download and build PLUMED manually by following the instructions

below.

-----------------

Instructions:

1.  Download PLUMED either as a 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 unpack it in this /lib/plumed directory.

    Similarly if you clone it clone it to the /lib/plumed

    directory.

2.  Compile PLUMED from within its home directory.  In the 

    simplest cases this be done by issuing the commands

    % ./configure

    % make

    More detailed instructions can be found at

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

3.  There is no need to install PLUMED if you only wish

    to use it from LAMMPS.  You should thus only run 

    make install if you want to use PLUMED as a stand-alone

    code or from some other code.  To install it you can 

    run the following commands:

    a) install under the default /usr/local

       % sudo make install

    b) install under a user-writeable location by first

         changing the PREFIX variable when running the 

         configure command file, then

       % make install

-----------------

When these steps are complete you can build LAMMPS

with the PLUMED package installed:

% cd lammps/src

% make yes-user-plumed

% make mpi (or whatever target you wish)

    # This is for statically linking plumed2

    if ( test -e ../../lib/plumed/plumed2*/src/lib/Plumed.inc.static ) then  

       fname=`ls ../../lib/plumed/plumed2*/src/lib/Plumed.inc.static` 

       sed -i -e "4 i \

include $fname

" ../Makefile.package.settings

       sed -i -e '4 i \

include '$fname'

' ../Makefile.package.settings

       dname=`ls ../../lib/plumed/plumed2*/src/wrapper/Plumed.h`

       ln -s USER-PLUMED/$dname ../Plumed.h

    # This is for linking plumed2 as a runtime library  -- this is the default behavior

and maintained by Gareth Tribello (gareth.tribello@gmail.com).

PLUMED must instead be downloaded and compiled separately to LAMMPS.  This building 

and compiling of PLUEMD can be done before or after the building of LAMMPS as LAMMPS 

calls PLUMED as a dynamic library.  If you wish to use PLUMED with LAMMPS, however, 

you must run the command:

and compiling of PLUMED can be done before or after the building of LAMMPS as LAMMPS 

can call PLUMED as a dynamic library.  There is also the possibility to link PLUEMD 

statically.  In this case a copy of PLUMED must be downloaded into the lib/plumed 

directory.  This copy of PLUMED will then always be linked into the code at compile 

time. 

However you decide to link PLUMED (statically or dynamically) you must run the command:

make yes-user-plumed

before compiling LAMMPS.  Furthermore, you must ensure that PLUMED is in your 

before compiling LAMMPS in order to enable the module.   In addition, if you have chosen to 

link PLUMED dynamically you must ensure that PLUMED is in your 

PATH when running a LAMMPS calculation that takes advantage of PLUMED.  If 

PLUMED is not in the PATH an error will be returned whenever LAMMPS encounters 

the fix plumed command in its input.  To be clear, however, LAMMPS will run if 

it is compiled with fix-plumed enabled on inputs that do not contain a fix 

plumed command when PLUMED is not in the PATH.

PLUMED is linked as a runtime library and if PLUMED is not in the PATH an error will be returned whenever LAMMPS encounters 

the fix plumed command in its input.  To be clear, however, a LAMMPS executable that was dynamically linked with PLUMED will run 

even if PLUMED is not in the path if as long as the input does not contain a fix 

plumed command.

If you wish to statically link PLUMED you must download PLUMED to the /lib/plumed directory before compiling LAMMPS.  You can 

download a tar ball into that directory or you can clone the plumed2 repository from github there.  Once you have created a 

directory containing a distribution of PLUMED within /lib/plumed you then must build PLUMED within that directory by issuing 

the usual commands.  It is worth noting that we have provided a script that will download and build PLUMED for you with 

a minimal set of options.  To run this script you need to issue the following command:

make lib-plumed args="-b"

in the src directory. 

More info about the PLUMED library can be found at:

implemented within PLUMED.

There are also example scripts for using this package in the folder

examples/USER/colvars, as well as on the GitHub page for PLUMED.

examples/USER/plumed, as well as on the GitHub page for PLUMED.

Please contact Gareth Tribello (gareth.tribello@gmail.com) for questions

regarding this package.