From 4805e1df2214fc7dfa7dc00fa9e5484d7c4bd262 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 13 Nov 2018 08:29:07 -0700 Subject: [PATCH] doc page additions for USER-PLUMED package --- doc/src/Build_extras.txt | 61 +++++++++++++++++++----------------- doc/src/Build_package.txt | 1 + doc/src/Packages_details.txt | 19 ++++++----- doc/src/Packages_user.txt | 3 ++ 4 files changed, 48 insertions(+), 36 deletions(-) diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index e4ab6b9541..3b685a44e3 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -41,11 +41,11 @@ 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, "USER-NETCDF"_#user-netcdf, +"USER-PLUMED"_#user-plumed, "USER-OMP"_#user-omp, "USER-QMMM"_#user-qmmm, "USER-QUIP"_#user-quip, @@ -719,47 +719,52 @@ USER-PLUMED package :h4,link(user-plumed) [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 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. +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. +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 +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: +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: +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 diff --git a/doc/src/Build_package.txt b/doc/src/Build_package.txt index f1aa4bb671..82833b867c 100644 --- a/doc/src/Build_package.txt +++ b/doc/src/Build_package.txt @@ -56,6 +56,7 @@ packages: "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, diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 4bc72f3147..fa9ad1bb95 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -89,6 +89,7 @@ as contained in the file name. "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, @@ -1205,14 +1206,16 @@ 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. +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 is written and maintained by -Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and -Gareth Tribello. +[Authors:] The "PLUMED library"_#PLUMED is written and maintained by +Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth +Tribello. + +:link(PLUMED,http://www.plumed.org) [Install:] @@ -1224,7 +1227,7 @@ extras"_Build_extras.html doc page. src/USER-PLUMED/README lib/plumed/README -"fix plumed "_fix_plumed.html +"fix plumed"_fix_plumed.html examples/USER/plumed :ul :line diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt index e1269b0d0c..07548fb643 100644 --- a/doc/src/Packages_user.txt +++ b/doc/src/Packages_user.txt @@ -62,6 +62,7 @@ Package, Description, Doc page, Example, Library "USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext "USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no "USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no +"USER-PLUMED"_Packages_details.html#PKG-USER-PLUMED, "PLUMED"_#PLUMED free energy library,"fix plumed"_fix_plumed.html, USER/plumed, ext "USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm_atom.html, n/a, no "USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext "USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no @@ -75,4 +76,6 @@ Package, Description, Doc page, Example, Library "USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, no "USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, no "USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext :tb(ea=c,ca1=l) + :link(MOFplus,https://www.mofplus.org/content/show/MOF-FF) +:link(PLUMED,http://www.plumed.org)