forked from lijiext/lammps
reformat recently changed paragraphs in the manual
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Axel Kohlmeyer
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4f00984bbc
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57204a0f66
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@ -735,66 +735,69 @@ from LAMMPS using the generic "plumed installation instructions"_plumedinstall.
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:link(plumedinstall,http://plumed.github.io/doc-master/user-doc/html/_installation.html)
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PLUMED can be linked into MD codes in three different modes: static,
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shared, and runtime. With the "static" mode, all the code that PLUMED requires
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is linked statically into LAMMPS. LAMMPS is then fully
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independent from the PLUMED installation, but you have to
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rebuild/relink it in order to update the PLUMED code inside it. With
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the "shared" linkage mode, LAMMPS is linked to a shared library
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that contains the PLUMED code. This library should preferably be installed in a
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globally accessible location. When PLUMED is linked in this way the same library
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can be used by multiple MD packages. Furthermore, the PLUMED library LAMMPS uses can be updated
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without the need for a recompile of LAMMPS for as
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long as the shared PLUMED library is ABI-compatible.
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shared, and runtime. With the "static" mode, all the code that PLUMED
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requires is linked statically into LAMMPS. LAMMPS is then fully
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independent from the PLUMED installation, but you have to rebuild/relink
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it in order to update the PLUMED code inside it. With the "shared"
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linkage mode, LAMMPS is linked to a shared library that contains the
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PLUMED code. This library should preferably be installed in a globally
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accessible location. When PLUMED is linked in this way the same library
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can be used by multiple MD packages. Furthermore, the PLUMED library
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LAMMPS uses can be updated without the need for a recompile of LAMMPS
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for as long as the shared PLUMED library is ABI-compatible.
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The third linkage
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mode is "runtime" which allows the user to specify which PLUMED kernel should be used at runtime
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by using the PLUMED_KERNEL environment
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variable. This variable should point to the location of the libplumedKernel.so
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dynamical shared object, which is then loaded at runtime. This mode of linking is
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particularly convenient for doing PLUMED development and comparing
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multiple PLUMED versions as these sorts of comparisons can be done without recompiling the hosting MD
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code. All three linkage modes are supported by LAMMPS on selected
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operating systems (e.g. Linux) and using either CMake or traditional
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make build. The "static" mode should be the most portable, while the "runtime"
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mode support in LAMMPS makes the most assumptions about operating
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system and compiler environment. If one mode does not work, try a
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different one, switch to a different build system, consider
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a global PLUMED installation or consider downloading PLUMED during the LAMMPS build.
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The third linkage mode is "runtime" which allows the user to specify
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which PLUMED kernel should be used at runtime by using the PLUMED_KERNEL
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environment variable. This variable should point to the location of the
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libplumedKernel.so dynamical shared object, which is then loaded at
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runtime. This mode of linking is particularly convenient for doing
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PLUMED development and comparing multiple PLUMED versions as these sorts
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of comparisons can be done without recompiling the hosting MD code. All
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three linkage modes are supported by LAMMPS on selected operating
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systems (e.g. Linux) and using either CMake or traditional make
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build. The "static" mode should be the most portable, while the
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"runtime" mode support in LAMMPS makes the most assumptions about
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operating system and compiler environment. If one mode does not work,
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try a different one, switch to a different build system, consider a
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global PLUMED installation or consider downloading PLUMED during the
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LAMMPS build.
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[CMake build]:
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When the "-D PKG_USER-PLUMED" flag is included in the cmake command you must ensure that
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GSL is installed in locations that are specified in your environment. There
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are then two additional commands that control the manner in which PLUMED is obtained and linked
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into LAMMPS.
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When the "-D PKG_USER-PLUMED" flag is included in the cmake command you
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must ensure that GSL is installed in locations that are specified in
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your environment. There are then two additional commands that control
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the manner in which PLUMED is obtained and linked into LAMMPS.
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-D DOWNLOAD_PLUMED=value # download PLUMED for build, value = no (default) or yes
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-D PLUMED_MODE=value # Linkage mode for PLUMED, value = static (default), shared, or runtime :pre
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If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
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downloaded (the version of PLUMED that will be downloaded is hard-coded to a vetted version of
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PLUMED, usually a recent stable release version) and built inside the
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CMake build directory. If DOWNLOAD_PLUMED is set to "no" (the default),
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CMake will try to detect and link to an installed version of PLUMED.
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For this to work, the PLUMED library has to be installed into a
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location where the pkg-config tool can find it or the PKG_CONFIG_PATH
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environment variable has to be set up accordingly. PLUMED should be installed
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in such a location if you compile it using the default make; make install commands.
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downloaded (the version of PLUMED that will be downloaded is hard-coded
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to a vetted version of PLUMED, usually a recent stable release version)
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and built inside the CMake build directory. If DOWNLOAD_PLUMED is set
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to "no" (the default), CMake will try to detect and link to an installed
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version of PLUMED. For this to work, the PLUMED library has to be
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installed into a location where the pkg-config tool can find it or the
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PKG_CONFIG_PATH environment variable has to be set up accordingly.
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PLUMED should be installed in such a location if you compile it using
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the default make; make install commands.
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The PLUMED_MODE setting determines the linkage mode for the PLUMED
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library. The allowed values for this flag are "static" (default), "shared", or "runtime".
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For a discussion of PLUMED linkage modes, please see above. When
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DOWNLOAD_PLUMED is enabled the static linkage mode is recommended.
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library. The allowed values for this flag are "static" (default),
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"shared", or "runtime". For a discussion of PLUMED linkage modes,
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please see above. When DOWNLOAD_PLUMED is enabled the static linkage
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mode is recommended.
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[Traditional make]:
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PLUMED needs to be installed before the USER-PLUMED package is installed
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so that LAMMPS can find the right settings when compiling and linking the LAMMPS executable.
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You can either download and build PLUMED inside the LAMMPS plumed library folder or use
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a previously installed PLUMED library and point LAMMPS to its
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location. You also have to choose the linkage mode: "static" (default),
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"shared" or "runtime". For a discussion of PLUMED linkage modes, please
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see above.
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so that LAMMPS can find the right settings when compiling and linking
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the LAMMPS executable. You can either download and build PLUMED inside
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the LAMMPS plumed library folder or use a previously installed PLUMED
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library and point LAMMPS to its location. You also have to choose the
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linkage mode: "static" (default), "shared" or "runtime". For a
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discussion of PLUMED linkage modes, please see above.
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Download/compilation/configuration of the plumed library can be done
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from the src folder through the following make args:
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@ -808,10 +811,10 @@ make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installati
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Note that 2 symbolic (soft) links, "includelink" and "liblink" are
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created in lib/plumed that point to the location of the PLUMED build to
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use. A new file lib/plumed/Makefile.lammps is also created with
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settings suitable for LAMMPS to compile and link PLUMED using the desired
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linkage mode. After this step is completed, you can install the
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USER-PLUMED package and compile LAMMPS in the usual manner:
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use. A new file lib/plumed/Makefile.lammps is also created with settings
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suitable for LAMMPS to compile and link PLUMED using the desired linkage
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mode. After this step is completed, you can install the USER-PLUMED
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package 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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@ -32,11 +32,10 @@ enhance the sampling of phase space.
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The documentation included here only describes the fix plumed command
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itself. This command is LAMMPS specific, whereas most of the
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functionality implemented in PLUMED will work with a range of
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MD codes, and when PLUMED is used as a stand alone code for analysis.
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The full "documentation for PLUMED"_plumeddocs is available online and
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included in the PLUMED source code. The PLUMED library development is
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hosted at
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functionality implemented in PLUMED will work with a range of MD codes,
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and when PLUMED is used as a stand alone code for analysis. The full
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"documentation for PLUMED"_plumeddocs is available online and included
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in the PLUMED source code. The PLUMED library development is hosted at
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"https://github.com/plumed/plumed2"_https://github.com/plumed/plumed2
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A detailed discussion of the code can be found in "(PLUMED)"_#PLUMED.
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@ -54,11 +53,12 @@ have been 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 way the plumed fix is implemented ensures that the minimum amount of information
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required is communicated. Furthermore, 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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time. The way the plumed fix is implemented ensures that the minimum
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amount of information required is communicated. Furthermore, PLUMED
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supports multiple, completely independent collective variables, multiple
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independent biases and multiple independent forms of analysis. There is
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thus really no restriction in functionality by only allowing only one
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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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