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@ -45,8 +45,7 @@ potentials: embedded atom method (EAM) potential files
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src: source files
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tools: pre- and post-processing tools :tb(s=:)
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Note that the "download page"_http://lammps.sandia.gov/download.html
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also has links to download
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Note that the "download page"_download also has links to download
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Windows exectubles and installers, as well as pre-built executables
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for a few specific Linux distributions. It also has instructions for
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how to download/install LAMMPS for Macs (via Homebrew), and to
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@ -655,15 +654,20 @@ are always included, plus optional packages. Packages are groups of
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files that enable a specific set of features. For example, force
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fields for molecular systems or granular systems are in packages.
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"Section packages"_Section_packages.html in the manual has details
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about all the packages, including specific instructions for building
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LAMMPS with each package, which are covered in a more general manner
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below.
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You can see the list of all packages by typing "make package" from
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within the src directory of the LAMMPS distribution. This also lists
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various make commands that can be used to manipulate packages.
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If you use a command in a LAMMPS input script that is specific to a
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particular package, you must have built LAMMPS with that package, else
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you will get an error that the style is invalid or the command is
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unknown. Every command's doc page specfies if it is part of a
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package. You can also type
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If you use a command in a LAMMPS input script that is part of a
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package, you must have built LAMMPS with that package, else you will
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get an error that the style is invalid or the command is unknown.
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Every command's doc page specfies if it is part of a package. You can
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also type
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lmp_machine -h :pre
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@ -695,9 +699,6 @@ Information on how to submit additions you make to LAMMPS as single
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files or either a standard or user-contributed package are given in
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"this section"_Section_modify.html#mod_15 of the documentation.
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Some packages (both standard and user) require additional auxiliary
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libraries when building LAMMPS. See more details below.
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:line
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[{Including/excluding packages:}] :link(start_3_2)
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@ -733,18 +734,18 @@ libraries (see below), and will also produce a smaller executable
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which may run a bit faster.
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When you download a LAMMPS tarball, these packages are pre-installed
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in the src directory: KSPACE, MANYBODY,MOLECULE. When you download
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LAMMPS source files from the SVN or Git repositories, no packages are
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pre-installed.
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in the src directory: KSPACE, MANYBODY,MOLECULE, because they are so
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commonly used. When you download LAMMPS source files from the SVN or
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Git repositories, no packages are pre-installed.
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Packages are included or excluded by typing "make yes-name" or "make
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no-name", where "name" is the name of the package in lower-case, e.g.
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name = kspace for the KSPACE package or name = user-atc for the
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USER-ATC package. You can also type "make yes-standard", "make
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no-standard", "make yes-std", "make no-std", "make yes-user", "make
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no-user", "make yes-all" or "make no-all" to include/exclude various
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sets of packages. Type "make package" to see the all of the
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package-related make options.
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no-user", "make yes-lib", "make no-lib", "make yes-all", or "make
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no-all" to include/exclude various sets of packages. Type "make
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package" to see all of the package-related make options.
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NOTE: Inclusion/exclusion of a package works by simply moving files
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back and forth between the main src directory and sub-directories with
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@ -766,11 +767,11 @@ files. Typing "make package-overwrite" will overwrite files in the
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package sub-directories with src files.
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Typing "make package-status" or "make ps" will show which packages are
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currently included. Of those that are included, it will list files
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that are different in the src directory and package sub-directory.
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Typing "make package-diff" lists all differences between these files.
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Again, type "make package" to see all of the package-related make
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options.
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currently included. For those that are included, it will list any
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files that are different in the src directory and package
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sub-directory. Typing "make package-diff" lists all differences
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between these files. Again, type "make package" to see all of the
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package-related make options.
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:line
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@ -805,7 +806,9 @@ where to find them.
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For libraries with provided code, the sub-directory README file
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(e.g. lib/atc/README) has instructions on how to build that library.
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Typically this is done by typing something like:
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This information is also summarized in "Section
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packages"_Section_packages.html. Typically this is done by typing
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something like:
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make -f Makefile.g++ :pre
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@ -820,12 +823,13 @@ directory:
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libpackage.a
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Makefile.lammps :pre
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The Makefile.lammps file will be a copy of the EXTRAMAKE file setting
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specified in the library Makefile.* you used.
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The Makefile.lammps file will typically be a copy of one of the
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Makefile.lammps.* files in the library directory.
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Note that you must insure that the settings in Makefile.lammps are
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appropriate for your system. If they are not, the LAMMPS build will
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fail.
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appropriate for your system. If they are not, the LAMMPS build may
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fail. To fix this, you can edit or create a new Makefile.lammps.*
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file for your system, and copy it to Makefile.lammps.
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As explained in the lib/package/README files, the settings in
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Makefile.lammps are used to specify additional system libraries and
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@ -860,79 +864,37 @@ the LAMMPS build will typically fail.
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A few packages require specific settings in Makefile.machine, to
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either build or use the package effectively. These are the
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USER-INTEL, KOKKOS, USER-OMP, and OPT packages. The details of what
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flags to add or what variables to define are given on the doc pages
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that describe each of these accelerator packages in detail:
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USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating
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code performance on CPUs or other hardware, as discussed in "Section
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acclerate"_Section_accelerate.html.
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A summary of what Makefile.machine changes are needed for each of
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these packages is given in "Section packages"_Section_packages.html.
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The details are given on the doc pages that describe each of these
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accelerator packages in detail:
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"USER-INTEL package"_accelerate_intel.html
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"KOKKOS package"_accelerate_kokkos.html
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"USER-OMP package"_accelerate_omp.html
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"OPT package"_accelerate_opt.html :ul
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Here is a brief summary of what Makefile.machine changes are needed.
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Note that the Make.py tool, described in the next "Section
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2.4"_#start_4 can automatically add the needed info to an existing
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machine Makefile, using simple command-line arguments.
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In src/MAKE/OPTIONS see the following Makefiles for examples of the
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changes described below:
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You can also look at the following machine Makefiles in
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src/MAKE/OPTIONS, which include the changes. Note that the USER-INTEL
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and KOKKOS packages allow for settings that build LAMMPS for different
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hardware. The USER-INTEL package builds for CPU and the Xeon Phi, the
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KOKKOS package builds for OpenMP, GPUs (Cuda), and the Xeon Phi.
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Makefile.intel_cpu
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Makefile.intel_phi
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Makefile.kokkos_omp
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Makefile.kokkos_cuda
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Makefile.kokkos_phi
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Makefile.omp :ul
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Makefile.omp
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Makefile.opt :ul
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For the USER-INTEL package, you have 2 choices when building. You can
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build with CPU or Phi support. The latter uses Xeon Phi chips in
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"offload" mode. Each of these modes requires additional settings in
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your Makefile.machine for CCFLAGS and LINKFLAGS.
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For CPU mode (if using an Intel compiler):
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CCFLAGS: add -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits
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LINKFLAGS: add -fopenmp :ul
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For Phi mode add the following in addition to the CPU mode flags:
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CCFLAGS: add -DLMP_INTEL_OFFLOAD and
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LINKFLAGS: add -offload :ul
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And also add this to CCFLAGS:
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-offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\"" :pre
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For the KOKKOS package, you have 3 choices when building. You can
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build with OMP or Cuda or Phi support. Phi support uses Xeon Phi
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chips in "native" mode. This can be done by setting the following
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variables in your Makefile.machine:
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for OMP support, set OMP = yes
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for Cuda support, set OMP = yes and CUDA = yes
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for Phi support, set OMP = yes and MIC = yes :ul
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These can also be set as additional arguments to the make command, e.g.
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make g++ OMP=yes MIC=yes :pre
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Building the KOKKOS package with CUDA support requires a Makefile
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machine that uses the NVIDIA "nvcc" compiler, as well as an
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appropriate "arch" setting appropriate to the GPU hardware and NVIDIA
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software you have on your machine. See
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src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine
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Makefile.
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For the USER-OMP package, your Makefile.machine needs additional
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settings for CCFLAGS and LINKFLAGS.
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CCFLAGS: add -fopenmp and -restrict
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LINKFLAGS: add -fopenmp :ul
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For the OPT package, your Makefile.machine needs an additional
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settings for CCFLAGS.
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CCFLAGS: add -restrict :ul
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Also note that the Make.py tool, described in the next "Section
|
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|
2.4"_#start_4 can automatically add the needed info to an existing
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|
machine Makefile, using simple command-line arguments.
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:line
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sjplimp