Loading doc/src/Build_extras.txt +57 −0 Original line number Diff line number Diff line Loading @@ -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, Loading Loading @@ -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 Loading doc/src/Packages_details.txt +28 −0 Original line number Diff line number Diff line Loading @@ -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:] Loading Loading
doc/src/Build_extras.txt +57 −0 Original line number Diff line number Diff line Loading @@ -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, Loading Loading @@ -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 Loading
doc/src/Packages_details.txt +28 −0 Original line number Diff line number Diff line Loading @@ -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:] Loading
