diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index d256a1afc8..e4ab6b9541 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -41,6 +41,7 @@ This is the list of packages that may require additional steps. "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, @@ -712,6 +713,62 @@ a corresponding Makefile.lammps.machine file. :line +USER-PLUMED package :h4,link(user-plumed) + +[CMake build]: + +[Traditional make]: + +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 + +:line + USER-H5MD package :h4,link(user-h5md) To build with this package you must have the HDF5 software package diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 031858e846..87f2493f93 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -1200,6 +1200,34 @@ examples/USER/colvars :ul :line +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:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/USER-PLUMED/README +lib/plumed/README +"fix plumed "_fix_plumed.html +examples/USER/plumed :ul + +:line + USER-DIFFRACTION package :link(PKG-USER-DIFFRACTION),h4 [Contents:]