Merge pull request #1180 from gtribello/master
Add natively supported PLUMED interface to LAMMPS
This commit is contained in:
Axel Kohlmeyer
@ -41,6 +41,7 @@ This is the list of packages that may require additional steps.
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"USER-ATC"_#user-atc,
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"USER-AWPMD"_#user-awpmd,
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"USER-COLVARS"_#user-colvars,
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"USER-PLUMED" _#user-plumed,
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"USER-H5MD"_#user-h5md,
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"USER-INTEL"_#user-intel,
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"USER-MOLFILE"_#user-molfile,
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@ -712,6 +713,62 @@ a corresponding Makefile.lammps.machine file.
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:line
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USER-PLUMED package :h4,link(user-plumed)
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[CMake build]:
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[Traditional make]:
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Before building LAMMPS with this package, you must first build
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PLUMED. We recommending building PLUMED separately to LAMMPS using
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the instructions that can be found at http://plumed.github.io/doc-master/user-doc/html/_installation.html.
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Before compiling LAMMPS you can then install the fix plumed command
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and compile LAMMPS in the usual manner:
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make yes-user-plumed
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make machine :pre
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Once this compilation completes you should be able to run LAMMPS in the usual
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way. When running LAMMPS with an input script that contains a fix
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plumed command LAMMPS will try to call the PLUMED runtime library. PLUMED
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must therefore be available in your path if LAMMPS is compiled in this way.
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On some machines it is not possible to call runtime libraries in the way described
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above. When compiling on these machines it is thus better to statically link
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PLUMED when compiling LAMMPS. To do this you must either download a PLUMED
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tarball from http://www.plumed.org/get-it or clone it using
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git clone https://github.com/plumed/plumed2.git. If you download the tarball
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unpack it in the /lib/plumed directory. Similarly if you clone
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it clone it to the /lib/plumed directory as if there is a version of PLUMED within
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this directory LAMMPS will always try to statically link the version of PLUMED
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that this directory contains instead of dynamically linking the library.
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Once you have downloaded PLUMED into /lib/plumed you must again build the code
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here by following the instructions that can be found at
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http://plumed.github.io/doc-master/user-doc/html/_installation.html.
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You can statically link PLUMED manually and if you want to access the full
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range of PLUMED functionalities this is what you should do. If you only want the
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basic range of functionalities, however, (i.e. no user contributed modules) then
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you can download and compile PLUMED in one step from the lammps/src dir, using a
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command like like those below:
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make lib-plumed # print help message
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make lib-plumed args="-b" # download and build the latest stable version of PLUMED
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These commands will simply invoke the lib/plumed/Install.py script with
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args specified. Furthermore, once the script has completed you should
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have a compiled version of PLUMED. With this built you can install/un-install
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PLUMED and build LAMMPS in the usual manner:
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make yes-user-plumed
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make machine :pre
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make no-user-plumed
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make machine :pre
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:line
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USER-H5MD package :h4,link(user-h5md)
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To build with this package you must have the HDF5 software package
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@ -1200,6 +1200,34 @@ examples/USER/colvars :ul
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:line
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USER-PLUMED package :link(USER-PLUMED),h4
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[Contents:]
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The fix plumed command allows you to use the plugin for molecular
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dynamics PLUMED to analyse and bias your LAMMPS trajectory on the fly.
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In practise PLUMED is called from within the lammps input script by using
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the "fix plumed _fix_plumed.html command.
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[Authors:] The PLUMED library is written and maintained by
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Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and
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Gareth Tribello.
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[Install:]
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This package has "specific installation
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instructions"_Build_extras.html#gpu on the "Build
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extras"_Build_extras.html doc page.
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[Supporting info:]
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src/USER-PLUMED/README
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lib/plumed/README
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"fix plumed "_fix_plumed.html
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examples/USER/plumed :ul
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:line
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USER-DIFFRACTION package :link(PKG-USER-DIFFRACTION),h4
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[Contents:]
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117
doc/src/fix_plumed.txt
Normal file
117
doc/src/fix_plumed.txt
Normal file
@ -0,0 +1,117 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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fix plumed command :h3
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[Syntax:]
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fix ID group-ID plumed keyword value ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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plumed = style name of this fix command :l
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keyword = {plumedfile} or {outfile} :l
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{plumedfile} arg = name of PLUMED input file to use (default: NULL)
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{outfile} arg = name of file on which to write the PLUMED log (default: NULL) :pre
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:ule
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[Examples:]
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fix pl all plumed all plumed plumedfile plumed.dat outfile p.log
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[Description:]
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This fix instructs LAMMPS to call the PLUMED library, which allows one
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to perform various forms of trajectory analysis on the fly and to also
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use methods such as umbrella sampling and metadynamics to enhance the
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sampling of phase space.
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The documentation included here only describes the fix plumed command.
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This command is LAMMPS specific whereas most of the functionality
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implemented in PLUMED will work with a range of MD codes and also when
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PLUMED is used as a stand alone code. The full documentation for PLUMED
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is available at "this website"_http://www.plumed.org/documentation
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The PLUMED library is developed at
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"https://github.com/plumed/plumed2"_https://github.com/plumed/plumed2 A
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detailed discussion of the code can be found in "(PLUMED)"_#PLUMED.
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There are some example scripts for using this package with LAMMPS in the
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examples/USER/plumed directory.
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:line
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The command to call PLUMED above is reasonably self explanatory. Within
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the input file for lammps the user is required to specify the input file
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for PLUMED and a file on which to output the PLUMED log. The user must
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specify both of these arguments every time PLUMED is to be used.
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Furthermore, the fix plumed command should appear in the LAMMPS input
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file after the relevant input paramters (e.g. the timestep) have been
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set.
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The {group-ID} entry is ignored. LAMMPS will always pass all the atoms
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to PLUMED and there can only be one instance of the plumed fix at a
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time. The plumed fix communicates the minimum amount of information
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required and the PLUMED supports multiple, completely independent
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collective variables, multiple independent biases and multiple
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independent forms of analysis. There is thus really no restriction in
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functionality by only allowing only one plumed fix in the LAMMPS input.
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The {plumedfile} keyword allows the user to specify the name of the
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PLUMED input file. Instructions as to what should be included in a
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plumed input file can be found in the "documentation for
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PLUMED"_http://www.plumed.org/documentation.
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The {outfile} keyword allows the user to specify the name of a file on
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which to output the PLUMED log. This log file normally just parots the
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information that is contained in the input file. The names of the files
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on which the results from the various analyses that have been performed
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using PLUMED will be specified by the user in the PLUMED input file.
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[Restart, fix_modify, output, run start/stop, minimize info:]
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When performing a restart of a calculation that involves PLUMED you must
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include a RESTART command in the PLUMED input file as detailed in the
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"PLUMED documentation"_http://www.plumed.org/documentation. When the
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restart command is found in the PLUMED input PLUMED will append to the
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files that were generated in the run that was performed previously.
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Furthermore, any history dependent bias potentials that were accumulated
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in previous calculations will be read in when the restart command is
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included in the PLUMED input.
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The "fix_modify"_fix_modify.html {energy} option is not supported by
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this fix.
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Nothing is computed by this fix that can be accessed by any of the
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"output commands"_Howto_output.html within LAMMPS. All the quantities
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of interest can be output by commands that are native to PLUMED,
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however.
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[Restrictions:]
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This fix is part of the USER-PLUMED package. It is only enabled if
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LAMMPS was built with that package. See the "Build
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package"_Build_package.html doc page for more info.
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There can only be one plumed fix active at a time. Since the interface
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communicates only the minimum amount of information and since the PLUMED
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module itself can handle an arbitrary number of analysis and biasing
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methods, this is not a limitation of functionality.
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[Related commands:]
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"fix smd"_fix_smd.html
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"fix colvars"_fix_colvars.html
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[Default:]
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The default options are plumedfile = NULL and outfile = NULL
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:line
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:link(PLUMED)
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[(PLUMED)] G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
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@ -117,6 +117,7 @@ Fixes :h1
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fix_phonon
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fix_pimd
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fix_planeforce
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fix_plumed
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fix_poems
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fix_pour
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fix_precession_spin
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@ -337,6 +337,7 @@ fix_orient.html
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fix_phonon.html
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fix_pimd.html
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fix_planeforce.html
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fix_plumed.html
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fix_poems.html
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fix_pour.html
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fix_precession_spin.html
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