Merge pull request #1204 from lammps/doc-plumed

src/USER-MOFFF/*      @hheenen

src/USER-MOLFILE/*    @akohlmey

src/USER-NETCDF/*     @pastewka

src/USER-PLUMED/*     @gtribello

src/USER-PHONON/*     @lingtikong

src/USER-PTM/*        @pmla

src/USER-OMP/*        @akohlmey

  endif()

endif()

if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)

if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE OR PKG_USER-PLUMED)

  find_package(LAPACK)

  find_package(BLAS)

  if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)

if(PKG_USER-PLUMED)

  find_package(GSL REQUIRED)

  set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")

  set(PLUMED_MODE_VALUES static shared runtime)

  set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})

  validate_option(PLUMED_MODE PLUMED_MODE_VALUES)

  string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)

  option(DOWNLOAD_PLUMED "Download Plumed (instead of using the system's one)" OFF)

  if(DOWNLOAD_PLUMED)

    include(ExternalProject)

    ExternalProject_get_property(plumed_build INSTALL_DIR)

    set(PLUMED_INSTALL_DIR ${INSTALL_DIR})

    list(APPEND LAMMPS_DEPS plumed_build)

    if(PLUMED_MODE STREQUAL "STATIC")

      add_definitions(-D__PLUMED_WRAPPER_CXX=1)

      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/plumed/obj/kernel.o

      ${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o ${GSL_LIBRARIES} ${CMAKE_DL_LIBS})

        "${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o" ${GSL_LIBRARIES} ${CMAKE_DL_LIBS} ${LAPACK_LIBRARIES})

    elseif(PLUMED_MODE STREQUAL "SHARED")

      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${CMAKE_DL_LIBS})

    elseif(PLUMED_MODE STREQUAL "RUNTIME")

      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so)

      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS})

    endif()

    set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")

  else()

    find_package(PkgConfig REQUIRED)

    pkg_check_modules(PLUMED plumed REQUIRED)

    if(PLUMED_MODE STREQUAL "STATIC")

      add_definitions(-D__PLUMED_WRAPPER_CXX=1)

      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)

    elseif(PLUMED_MODE STREQUAL "SHARED")

      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)

    elseif(PLUMED_MODE STREQUAL "RUNTIME")

      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel.so)

      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)

    endif()

    list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD})

  endif()

  include_directories(${PLUMED_INCLUDE_DIRS})

"USER-ATC"_#user-atc,

"USER-AWPMD"_#user-awpmd,

"USER-COLVARS"_#user-colvars,

"USER-PLUMED" _#user-plumed,

"USER-H5MD"_#user-h5md,

"USER-INTEL"_#user-intel,

"USER-MOLFILE"_#user-molfile,

"USER-NETCDF"_#user-netcdf,

"USER-PLUMED"_#user-plumed,

"USER-OMP"_#user-omp,

"USER-QMMM"_#user-qmmm,

"USER-QUIP"_#user-quip,

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

Before building LAMMPS with this package, you must first build PLUMED.

PLUMED can be built as part of the LAMMPS build or installed separately

from LAMMPS using the generic "plumed installation instructions"_plumedinstall.

:link(plumedinstall,http://plumed.github.io/doc-master/user-doc/html/_installation.html)

PLUMED can be linked into MD codes in three different modes: static,

shared, and runtime.  With the "static" mode, all required PLUMED code

is linked statically into the MD code. The MD code is then fully

independent from the PLUMED installation, but also you have to

rebuild/relink the MD code to update the PLUMED code inside it.  With

"shared" linkage mode, the MD code is linked to a shared library

containing the PLUMED code, preferably after it was installed in a

globally accessible location. This way the same installed PLUMED code

can be shared across multiple MD packages and can be updated, for as

long as the shared PLUMED library is ABI-compatible. The third linkage

mode is "runtime" which allows to switch the PLUMED kernel at runtime

between different variants through setting the PLUMED_KERNEL environment

varible, which has to point to the location of the libplumedKernel.so

dynamical shared object, which is then loaded at runtime. This is

particularly convenient for doing PLUMED development and comparing

multiple PLUMED versions without having to recompile the hosting MD

code. All three linkage modes are supported by LAMMPS on selected

operating systems (e.g. Linux) and using either CMake or traditional

make build. The "static" mode should be most portable, the "runtime"

mode support in LAMMPS makes the most assumptions about operating

system and compiler environment. If one mode does not work, try a

different one, or switch to a different build system, or consider

a global PLUMED installation or downloading it during building LAMMPS.

[CMake build]:

[Traditional make]:

-D DOWNLOAD_PLUMED=value   # download PLUMED for build, value = no (default) or yes

-D PLUMED_MODE=value       # Linkage mode for PLUMED, value = static (default), shared, or runtime :pre

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:

If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be

downloaded (the version of that is hardcoded to a vetted version of

PLUMED, usually a recent stable release version) and built inside the

CMake build directory.  If DOWNLOAD_PLUMED is set to "no" (the default),

CMake will try to detect an installed version of PLUMED and link to

that. For this to work, the PLUMED library has to be installed into a

location where the pkg-config tool can find it or the PKG_CONFIG_PATH

environment variable has to be set up accordingly.

make yes-user-plumed 

make machine :pre

The PLUMED_MODE setting determines the linkage mode of the PLUMED

library.  Allowed values are "static" (default), "shared", or "runtime".

For a discussion of PLUMED linkage modes, please see above.  When

enabling DOWNLOAD_PLUMED, the static linkage mode is recommended.

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:

[Traditional make]:

Before installing the USER-PLUMED package, first the PLUMED library

needs to be configured so that LAMMPS can find the right settings when

compiling and linking the LAMMPS executable itself. You can either

download and build PLUMED inside the LAMMPS plumed library folder or use

a previously installed PLUMED library and point LAMMPS to its

location. You also have to choose the linkage mode: "static" (default),

"shared" or "runtime".  For a discussion of PLUMED linkage modes, please

see above.

Download/compilation/configuration of the plumed library can be done

from the src folder through the following make args:

make lib-plumed                         # print help message

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

make lib-plumed args="-b"               # download and build PLUMED in lib/plumed/plumed2

make lib-plumed args="-p $HOME/.local"  # use existing PLUMED installation in $HOME/.local

make lib-plumed args="-p /usr/local -m shared"  # use existing PLUMED installation in

                                                # /usr/local and use shared linkage mode

:pre

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:

Note that 2 symbolic (soft) links, "includelink" and "liblink" are

created in lib/plumed to point into the location of the PLUMED build to

use and also a new file lib/plumed/Makefile.lammps is created with

settings suitable for LAMMPS to compile and link PLUMED in the desired

linkage mode. After this step is compleded, you can install the

USER-PLUMED package and compile LAMMPS in the usual manner:

make yes-user-plumed 

make machine :pre

make no-user-plumed

make machine :pre

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

usual way.  For shared linkage mode, libplumed.so must be found by the

LAMMPS executable, which on many operating systems means, you have to

set the LD_LIBRARY_PATH environment variable accordingly.

Support for the different linkage modes in LAMMPS varies for different

operating systems, using the static linkage is expected to be the most

portable, and thus set to be the default.

If you want to change the linkage mode, you have to re-run "make

lib-plumed" with the desired settings [and] do a reinstall if the

USER-PLUMED package with "make yes-user-plumed" to update the required

makefile settings with the changes in the lib/plumed folder.

:line

"USER-INTEL"_Build_extras.html#user-intel,

"USER-MOLFILE"_Build_extras.html#user-molfile,

"USER-NETCDF"_Build_extras.html#user-netcdf,

"USER-PLUMED"_Build_extras.html#user-plumed,

"USER-OMP"_Build_extras.html#user-omp,

"USER-QMMM"_Build_extras.html#user-qmmm,

"USER-QUIP"_Build_extras.html#user-quip,

"USER-NETCDF"_#PKG-USER-NETCDF,

"USER-OMP"_#PKG-USER-OMP,

"USER-PHONON"_#PKG-USER-PHONON,

"USER-PLUMED"_#PKG-USER-PLUMED,

"USER-PTM"_#PKG-USER-PTM,

"USER-QMMM"_#PKG-USER-QMMM,

"USER-QTB"_#PKG-USER-QTB,

[Install:] 

This package has "specific installation

instructions"_Build_extras.html#gpu on the "Build

instructions"_Build_extras.html#user-colvars on the "Build

extras"_Build_extras.html doc page.

[Supporting info:]

:line

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

USER-PLUMED package :link(PKG-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.

The fix plumed command allows you to use the PLUMED free energy plugin

for molecular dynamics to analyse and bias your LAMMPS trajectory on

the fly.  The PLUMED library is called from within the LAMMPS input

script by using the "fix plumed _fix_plumed.html command.

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

Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth

Tribello.

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

Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and

Gareth Tribello. 

:link(PLUMED,http://www.plumed.org)

[Install:]