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Merge pull request #609 from akohlmey/doc-changes-for-stable

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Final tweaks and doc changes for stable release
This commit is contained in:
Steve Plimpton
2017-08-09 17:37:35 -06:00
committed by GitHub
parent 691d1b730d 77a628e4ef
commit 7f437d7690
9 changed files with 180 additions and 113 deletions
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doc/src/Section_packages.txt
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@ -25,6 +25,17 @@ There are two kinds of packages in LAMMPS, standard and user packages:
"Table of standard packages"_#table_standard
"Table of user packages"_#table_user :ul
Either of these kinds of packages may work as is, may require some
additional code compiled located in the lib folder, or may require
an external library to be downloaded, compiled, installed, and LAMMPS
configured to know about its location and additional compiler flags.
You can often do the build of the internal or external libraries
in one step by typing "make lib-name args='...'" from the src dir,
with appropriate arguments included in args='...'. If you just type
"make lib-name" you should see a help message about supported flags
and some examples. For more details about this, please study the
tables below and the sections about the individual packages.
Standard packages are supported by the LAMMPS developers and are
written in a syntax and style consistent with the rest of LAMMPS.
This means the developers will answer questions about them, debug and
@ -34,7 +45,9 @@ LAMMPS.
User packages have been contributed by users, and begin with the
"user" prefix. If they are a single command (single file), they are
typically in the user-misc package. User packages don't necessarily
meet the requirements of the standard packages. If you have problems
meet the requirements of the standard packages. This means the
developers will try to keep things working and usually can answer
technical questions about compiling the package. If you have problems
using a feature provided in a user package, you may need to contact
the contributor directly to get help. Information on how to submit
additions you make to LAMMPS as single files or as a standard or user
@ -78,10 +91,10 @@ Package, Description, Doc page, Example, Library
"COMPRESS"_#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
"CORESHELL"_#CORESHELL, adiabatic core/shell model, "Section 6.6.25"_Section_howto.html#howto_25, coreshell, -
"DIPOLE"_#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
"GPU"_#GPU, GPU-enabled styles, "Section 5.3.1"_accelerate_gpu.html, WWW bench, int
"GPU"_#GPU, GPU-enabled styles, "Section 5.3.1"_accelerate_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
"GRANULAR"_#GRANULAR, granular systems, "Section 6.6.6"_Section_howto.html#howto_6, pour, -
"KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, WWW bench, -
"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
"MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
"MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
@ -90,7 +103,7 @@ Package, Description, Doc page, Example, Library
"MOLECULE"_#MOLECULE, molecular system force fields, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -
"MPIIO"_#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
"MSCG"_#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
"OPT"_#OPT, optimized pair styles, "Section 5.3.5"_accelerate_opt.html, WWW bench, -
"OPT"_#OPT, optimized pair styles, "Section 5.3.5"_accelerate_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"PERI"_#PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, -
"POEMS"_#POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
"PYTHON"_#PYTHON, embed Python code in an input script, "python"_python.html, python, sys
@ -101,8 +114,7 @@ Package, Description, Doc page, Example, Library
"SHOCK"_#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
"SNAP"_#SNAP, quantum-fitted potential, "pair snap"_pair_snap.html, snap, -
"SRD"_#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext
:tb(ea=c,ca1=l)
"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
[USER packages] :link(table_user),p
@ -118,7 +130,7 @@ Package, Description, Doc page, Example, Library
"USER-EFF"_#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
"USER-FEP"_#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
"USER-H5MD"_#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext
"USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, WWW bench, -
"USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"USER-LB"_#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
"USER-MEAMC"_#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
@ -126,7 +138,7 @@ Package, Description, Doc page, Example, Library
"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
"USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
"USER-NETCDF"_#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
"USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, WWW bench, -
"USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"USER-PHONON"_#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
"USER-QMMM"_#USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
"USER-QTB"_#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -
@ -136,8 +148,7 @@ Package, Description, Doc page, Example, Library
"USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
"USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext
:tb(ea=c,ca1=l)
"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
:line
:line
@ -364,9 +375,12 @@ GPU package :link(GPU),h4
[Contents:]
Dozens of pair styles and a version of the PPPM long-range Coulombic
solver optimized for NVIDIA GPUs. All such styles have a "gpu" as a
suffix in their style name. "Section 5.3.1"_accelerate_gpu.html gives
details of what hardware and Cuda software is required on your system,
solver optimized for GPUs. All such styles have a "gpu" as a
suffix in their style name. The GPU code can be compiled with either
CUDA or OpenCL, however the OpenCL variants are no longer actively
maintained and only the CUDA versions are regularly tested.
"Section 5.3.1"_accelerate_gpu.html gives details of what
hardware and GPU software is required on your system,
and details on how to build and use this package. Its styles can be
invoked at run time via the "-sf gpu" or "-suffix gpu" "command-line
switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS
@ -378,32 +392,41 @@ package, which has GPU-enabled styles.
[Install or un-install:]
Before building LAMMPS with this package, you must first build the GPU
library in lib/gpu from a set of provided C and Cuda files. You can
library in lib/gpu from a set of provided C and CUDA files. You can
do this manually if you prefer; follow the instructions in
lib/gpu/README. You can also do it in one step from the lammps/src
lib/gpu/README. Please note, that the GPU library uses MPI calls, so
you have to make certain to use the same MPI library (or the STUBS
library) settings as the main LAMMPS code. That same applies to the
-DLAMMPS_BIGBIG, -DLAMMPS_SMALLBIG, or -DLAMMPS_SMALLSMALL define.
You can also do it in one step from the lammps/src
dir, using a command like these, which simply invoke the
lib/gpu/Install.py script with the specified args:
make lib-gpu # print help message
make lib-gpu args="-m" # build GPU library with default Makefile.linux
make lib-gpu args="-i xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
make lib-gpu args="-i xk7 -p single -o xk7.single -m" # ditto, also build GPU library
make lib-gpu # print help message
make lib-gpu args="-b" # build GPU library with default Makefile.linux
make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
make lib-gpu args="-m mpi -p mixed -b" # build GPU library with mixed precision using settings in Makefile.mpi :pre
Note that this procedure starts with one of the existing
Makefile.machine files in lib/gpu. It allows you to alter 4 important
settings in that Makefile, via the -h, -a, -p, -e switches,
and save the new Makefile, if desired:
Note that this procedure through the '-m machine' flag starts with one of
the existing Makefile.machine files in lib/gpu. For your convenience,
machine makefiles for "mpi" and "serial" are provided, which have the
same settings as the corresponding machine makefiles in the main LAMMPS
source folder. In addition you can alter 4 important settings in that
Makefile, via the -h, -a, -p, -e switches, and also save a copy of the
new Makefile, if desired:
CUDA_HOME = where NVIDIA Cuda software is installed on your system
CUDA_HOME = where NVIDIA CUDA software is installed on your system
CUDA_ARCH = what GPU hardware you have (see help message for details)
CUDA_PRECISION = precision (double, mixed, single)
EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul
If the library build is successful, 2 files should be created:
lib/gpu/libgpu.a and lib/gpu/Makefile.lammps. The latter has settings
that enable LAMMPS to link with Cuda libraries. If the settings in
Makefile.lammps for your machine are not correct, the LAMMPS build
will fail.
If the library build is successful, at least 3 files should be created:
lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and lib/gpu/Makefile.lammps.
The latter has settings that enable LAMMPS to link with CUDA libraries.
If the settings in Makefile.lammps for your machine are not correct,
the LAMMPS build will fail, and lib/gpu/Makefile.lammps may need to
be edited.
You can then install/un-install the package and build LAMMPS in the
usual manner:
@ -499,11 +522,13 @@ in lib/kim/README. You can also do it in one step from the lammps/src
dir, using a command like these, which simply invoke the
lib/kim/Install.py script with the specified args.
make lib-kim # print help message
make lib-kim args="-b . none" # install KIM API lib with only example models
make lib-kim args="-b . Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
make lib-kim args="-b . OpenKIM" # install KIM API lib with all models
make lib-kim args="-a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver :pre
make lib-kim # print help message
make lib-kim args="-b " # (re-)install KIM API lib with only example models
make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
make lib-kim args="-b -a everything" # install KIM API lib with all models
make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver
make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location
make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
Note that in LAMMPS lingo, a KIM model driver is a pair style
(e.g. EAM or Tersoff). A KIM model is a pair style for a particular
@ -547,7 +572,7 @@ KOKKOS package :link(KOKKOS),h4
Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute
styles adapted to compile using the Kokkos library which can convert
them to OpenMP or Cuda code so that they run efficiently on multicore
them to OpenMP or CUDA code so that they run efficiently on multicore
CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their
style name. "Section 5.3.3"_accelerate_kokkos.html gives details of
what hardware and software is required on your system, and how to
@ -577,28 +602,28 @@ files for examples.
For multicore CPUs using OpenMP:
KOKKOS_DEVICES = OpenMP
KOKKOS_ARCH = HSW # HSW = Haswell, SNB = SandyBridge, BDW = Broadwell, etc
KOKKOS_ARCH = HSW # HSW = Haswell, SNB = SandyBridge, BDW = Broadwell, etc :pre
For Intel KNLs using OpenMP:
KOKKOS_DEVICES = OpenMP
KOKKOS_ARCH = KNL
KOKKOS_ARCH = KNL :pre
For NVIDIA GPUs using Cuda:
For NVIDIA GPUs using CUDA:
KOKKOS_DEVICES = Cuda
KOKKOS_ARCH = Pascal60,Power8 # P100 hosted by an IBM Power8, etc
KOKKOS_ARCH = Kepler37,Power8 # K80 hosted by an IBM Power8, etc
KOKKOS_ARCH = Kepler37,Power8 # K80 hosted by an IBM Power8, etc :pre
For GPUs, you also need these 2 lines in your Makefile.machine before
the CC line is defined, in this case for use with OpenMPI mpicxx. The
2 lines define a nvcc wrapper compiler, which will use nvcc for
compiling Cuda files or use a C++ compiler for non-Kokkos, non-Cuda
compiling CUDA files or use a C++ compiler for non-Kokkos, non-CUDA
files.
KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
CC = mpicxx
CC = mpicxx :pre
Once you have an appropriate Makefile.machine, you can
install/un-install the package and build LAMMPS in the usual manner.
@ -734,6 +759,12 @@ MEAM package :link(MEAM),h4
A pair style for the modified embedded atom (MEAM) potential.
Please note that the MEAM package has been superseded by the
"USER-MEAMC"_#USER-MEAMC package, which is a direct translation
of the MEAM package to C++. USER-MEAMC contains additional
optimizations making it run faster than MEAM on most machines,
while providing the identical features and USER interface.
[Author:] Greg Wagner (Northwestern U) while at Sandia.
[Install or un-install:]
@ -744,9 +775,10 @@ follow the instructions in lib/meam/README. You can also do it in one
step from the lammps/src dir, using a command like these, which simply
invoke the lib/meam/Install.py script with the specified args:
make lib-meam # print help message
make lib-meam args="-m gfortran" # build with GNU Fortran compiler
make lib-meam args="-m ifort" # build with Intel ifort compiler :pre
make lib-meam # print help message
make lib-meam args="-m mpi" # build with default Fortran compiler compatible with your MPI library
make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran)
make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :pre
The build should produce two files: lib/meam/libmeam.a and
lib/meam/Makefile.lammps. The latter is copied from an existing
@ -789,6 +821,9 @@ A variety of compute, fix, pair, dump styles with specialized
capabilities that don't align with other packages. Do a directory
listing, "ls src/MISC", to see the list of commands.
NOTE: the MISC package contains styles that require using the
-restrict flag, when compiling with Intel compilers.
[Install or un-install:]
make yes-misc
@ -902,9 +937,9 @@ University of Chicago.
Before building LAMMPS with this package, you must first download and
build the MS-CG library. Building the MS-CG library and using it from
LAMMPS requires a C++11 compatible compiler, and that LAPACK and GSL
(GNU Scientific Library) libraries be installed on your machine. See
the lib/mscg/README and MSCG/Install files for more details.
LAMMPS requires a C++11 compatible compiler and that the GSL
(GNU Scientific Library) headers and libraries are installed on your
machine. See the lib/mscg/README and MSCG/Install files for more details.
Assuming these libraries are in place, you can do the download and
build of MS-CG manually if you prefer; follow the instructions in
@ -912,15 +947,16 @@ lib/mscg/README. You can also do it in one step from the lammps/src
dir, using a command like these, which simply invoke the
lib/mscg/Install.py script with the specified args:
make lib-mscg # print help message
make lib-mscg args="-g -b -l" # download and build in default lib/mscg/MSCG-release-master
make lib-mscg args="-h . MSCG -g -b -l" # download and build in lib/mscg/MSCG
make lib-mscg args="-h ~ MSCG -g -b -l" # download and build in ~/mscg :pre
make lib-mscg # print help message
make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master
# with the settings compatible with "make serial"
make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master
# with the settings compatible with "make mpi"
make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release :pre
Note that the final -l switch is to create 2 symbolic (soft) links,
"includelink" and "liblink", in lib/mscg to point to the MS-CG src
dir. When LAMMPS builds it will use these links. You should not need
to edit the lib/mscg/Makefile.lammps file.
Note that 2 symbolic (soft) links, "includelink" and "liblink", will be created in lib/mscg
to point to the MS-CG src/installation dir. When LAMMPS is built in src it will use these links.
You should not need to edit the lib/mscg/Makefile.lammps file.
You can then install/un-install the package and build LAMMPS in the
usual manner:
@ -966,11 +1002,11 @@ make no-opt
make machine :pre
NOTE: The compile flag "-restrict" must be used to build LAMMPS with
the OPT package. It should be added to the CCFLAGS line of your
Makefile.machine. See Makefile.opt in src/MAKE/OPTIONS for an
example.
the OPT package when using Intel compilers. It should be added to
the CCFLAGS line of your Makefile.machine. See Makefile.opt in
src/MAKE/OPTIONS for an example.
CCFLAGS: add -restrict :ul
CCFLAGS: add -restrict for Intel compilers :ul
[Supporting info:]
@ -1039,9 +1075,10 @@ follow the instructions in lib/poems/README. You can also do it in
one step from the lammps/src dir, using a command like these, which
simply invoke the lib/poems/Install.py script with the specified args:
make lib-poems # print help message
make lib-poems args="-m g++" # build with GNU g++ compiler
make lib-poems args="-m icc" # build with Intel icc compiler :pre
make lib-poems # print help message
make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-poems args="-m icc" # build with Intel icc compiler :pre
The build should produce two files: lib/poems/libpoems.a and
lib/poems/Makefile.lammps. The latter is copied from an existing
@ -1151,9 +1188,10 @@ follow the instructions in lib/reax/README. You can also do it in one
step from the lammps/src dir, using a command like these, which simply
invoke the lib/reax/Install.py script with the specified args:
make lib-reax # print help message
make lib-reax args="-m gfortran" # build with GNU Fortran compiler
make lib-reax args="-m ifort" # build with Intel ifort compiler :pre
make lib-reax # print help message
make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
make lib-reax args="-m ifort" # build with Intel ifort compiler :pre
The build should produce two files: lib/reax/libreax.a and
lib/reax/Makefile.lammps. The latter is copied from an existing
@ -1370,15 +1408,15 @@ one step from the lammps/src dir, using a command like these, which
simply invoke the lib/voronoi/Install.py script with the specified
args:
make lib-voronoi # print help message
make lib-voronoi args="-g -b -l" # download and build in default lib/voronoi/voro++-0.4.6
make lib-voronoi args="-h . voro++ -g -b -l" # download and build in lib/voronoi/voro++
make lib-voronoi args="-h ~ voro++ -g -b -l" # download and build in ~/voro++ :pre
make lib-voronoi # print help message
make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++-<version>
make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++
make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6 :pre
Note that the final -l switch is to create 2 symbolic (soft) links,
"includelink" and "liblink", in lib/voronoi to point to the Voro++ src
dir. When LAMMPS builds it will use these links. You should not need
to edit the lib/voronoi/Makefile.lammps file.
Note that 2 symbolic (soft) links, "includelink" and "liblink", are
created in lib/voronoi to point to the Voro++ src dir. When LAMMPS
builds in src it will use these links. You should not need to edit
the lib/voronoi/Makefile.lammps file.
You can then install/un-install the package and build LAMMPS in the
usual manner:
@ -1420,7 +1458,8 @@ from the lammps/src dir, using a command like these, which simply
invoke the lib/atc/Install.py script with the specified args:
make lib-atc # print help message
make lib-atc args="-m g++" # build with GNU g++ compiler
make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
make lib-atc args="-m icc" # build with Intel icc compiler :pre
The build should produce two files: lib/atc/libatc.a and
@ -1437,8 +1476,10 @@ can either exist on your system, or you can use the files provided in
lib/linalg. In the latter case you also need to build the library
in lib/linalg with a command like these:
make lib-linalg # print help message
make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre
You can then install/un-install the package and build LAMMPS in the
usual manner:
@ -1478,9 +1519,10 @@ follow the instructions in lib/awpmd/README. You can also do it in
one step from the lammps/src dir, using a command like these, which
simply invoke the lib/awpmd/Install.py script with the specified args:
make lib-awpmd # print help message
make lib-awpmd args="-m g++" # build with GNU g++ compiler
make lib-awpmd args="-m icc" # build with Intel icc compiler :pre
make lib-awpmd # print help message
make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
make lib-awpmd args="-m icc" # build with Intel icc compiler :pre
The build should produce two files: lib/awpmd/libawpmd.a and
lib/awpmd/Makefile.lammps. The latter is copied from an existing
@ -1496,8 +1538,10 @@ these can either exist on your system, or you can use the files
provided in lib/linalg. In the latter case you also need to build the
library in lib/linalg with a command like these:
make lib-linalg # print help message
make lib-atc args="-m gfortran" # build with GNU Fortran compiler
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre
You can then install/un-install the package and build LAMMPS in the
usual manner:
@ -1590,9 +1634,11 @@ Restraints. A "fix colvars"_fix_colvars.html command is implemented
which wraps a COLVARS library, which implements these methods.
simulations.
[Authors:] Axel Kohlmeyer (Temple U). The COLVARS library was written
by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
Jerome Henin (LISM, CNRS, Marseille, France).
[Authors:] The COLVARS library is written and maintained by
Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA)
and Jerome Henin (LISM, CNRS, Marseille, France), originally for
the NAMD MD code, but with portability in mind. Axel Kohlmeyer
(Temple U) provided the interface to LAMMPS.
[Install or un-install:]
@ -1604,7 +1650,9 @@ which simply invoke the lib/colvars/Install.py script with the
specified args:
make lib-colvars # print help message
make lib-colvars args="-m g++" # build with GNU g++ compiler :pre
make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled :pre
The build should produce two files: lib/colvars/libcolvars.a and
lib/colvars/Makefile.lammps. The latter is copied from an existing
@ -1892,7 +1940,12 @@ Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP
packages, which have styles optimized for CPUs and KNLs.
You need to have an Intel compiler, version 14 or higher to take full
advantage of this package.
advantage of this package. While compilation with GNU compilers is
supported, performance will be suboptimal.
NOTE: the USER-INTEL package contains styles that require using the
-restrict flag, when compiling with Intel compilers.
[Author:] Mike Brown (Intel).
@ -1909,17 +1962,17 @@ For CPUs:
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
-fno-alias -ansi-alias -restrict $(OPTFLAGS)
-fno-alias -ansi-alias -restrict $(OPTFLAGS)
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
LIB = -ltbbmalloc -ltbbmalloc_proxy
LIB = -ltbbmalloc -ltbbmalloc_proxy :pre
For KNLs:
OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
-fno-alias -ansi-alias -restrict $(OPTFLAGS)
-fno-alias -ansi-alias -restrict $(OPTFLAGS)
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
LIB = -ltbbmalloc
LIB = -ltbbmalloc :pre
Once you have an appropriate Makefile.machine, you can
install/un-install the package and build LAMMPS in the usual manner.
@ -2224,11 +2277,15 @@ CPUs.
[Author:] Axel Kohlmeyer (Temple U).
NOTE: The compile flags "-restrict" and "-fopenmp" must be used to
build LAMMPS with the USER-OMP package, as well as the link flag
"-fopenmp". They should be added to the CCFLAGS and LINKFLAGS lines
of your Makefile.machine. See src/MAKE/OPTIONS/Makefile.omp for an
example.
NOTE: To enable multi-threading support the compile flag "-fopenmp"
and the link flag "-fopenmp" (for GNU compilers, you have to look up
the equivalent flags for other compilers) must be used to build LAMMPS.
When using Intel compilers, also the "-restrict" flag is required.
The USER-OMP package can be compiled without enabling OpenMP; then
all code will be compiled as serial and the only improvement over the
regular styles are some data access optimization. These flags should
be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine.
See src/MAKE/OPTIONS/Makefile.omp for an example.
Once you have an appropriate Makefile.machine, you can
install/un-install the package and build LAMMPS in the usual manner:
@ -2241,7 +2298,7 @@ make machine :pre
make no-user-omp
make machine :pre
CCFLAGS: add -fopenmp and -restrict
CCFLAGS: add -fopenmp (and -restrict when using Intel compilers)
LINKFLAGS: add -fopenmp :ul
[Supporting info:]
@ -2310,12 +2367,14 @@ without changes to LAMMPS itself.
Before building LAMMPS with this package, you must first build the
QMMM library in lib/qmmm. You can do this manually if you prefer;
follow the first two steps explained in lib/colvars/README. You can
follow the first two steps explained in lib/qmmm/README. You can
also do it in one step from the lammps/src dir, using a command like
these, which simply invoke the lib/colvars/Install.py script with the
these, which simply invoke the lib/qmmm/Install.py script with the
specified args:
make lib-qmmm # print help message
make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial")
make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi")
make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler :pre
The build should produce two files: lib/qmmm/libqmmm.a and
@ -2492,15 +2551,13 @@ follow the instructions in lib/smd/README. You can also do it in one
step from the lammps/src dir, using a command like these, which simply
invoke the lib/smd/Install.py script with the specified args:
make lib-smd # print help message
make lib-smd args="-g -l" # download and build in default lib/smd/eigen-eigen-*
make lib-smd args="-h . eigen -g -l" # download and build in lib/smd/eigen
make lib-smd args="-h ~ eigen -g -l" # download and build in ~/eigen :pre
make lib-smd # print help message
make lib-smd args="-b" # download and build in default lib/smd/eigen-eigen-...
make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3 :pre
Note that the final -l switch is to create a symbolic (soft) link
named "includelink" in lib/smd to point to the Eigen dir. When LAMMPS
builds it will use this link. You should not need to edit the
lib/smd/Makefile.lammps file.
Note that a symbolic (soft) link named "includelink" is created in
lib/smd to point to the Eigen dir. When LAMMPS builds it will use
this link. You should not need to edit the lib/smd/Makefile.lammps file.
You can then install/un-install the package and build LAMMPS in the
usual manner:

2
doc/src/Section_start.txt
View File

@ -909,7 +909,7 @@ src/MAKE/OPTIONS, which include the settings. Note that the
USER-INTEL and KOKKOS packages can use settings that build LAMMPS for
different hardware. The USER-INTEL package can be compiled for Intel
CPUs and KNLs; the KOKKOS package builds for CPUs (OpenMP), GPUs
(Cuda), and Intel KNLs.
(CUDA), and Intel KNLs.
Makefile.intel_cpu
Makefile.intel_phi

4
doc/src/accelerate_gpu.txt
View File

@ -62,7 +62,7 @@ respectively to your input script.
[Required hardware/software:]
To use this package, you currently need to have an NVIDIA GPU and
install the NVIDIA Cuda software on your system:
install the NVIDIA CUDA software on your system:
Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/0/information
Go to http://www.nvidia.com/object/cuda_get.html
@ -85,7 +85,7 @@ The GPU library is in lammps/lib/gpu. Select a Makefile.machine (in
lib/gpu) appropriate for your system. You should pay special
attention to 3 settings in this makefile.
CUDA_HOME = needs to be where NVIDIA Cuda software is installed on your system
CUDA_HOME = needs to be where NVIDIA CUDA software is installed on your system
CUDA_ARCH = needs to be appropriate to your GPUs
CUDA_PREC = precision (double, mixed, single) you desire :ul

2
doc/src/accelerate_kokkos.txt
View File

@ -113,7 +113,7 @@ To build with Kokkos support for CPUs, your compiler must support the
OpenMP interface. You should have one or more multi-core CPUs so that
multiple threads can be launched by each MPI task running on a CPU.
To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software
To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA software
version 7.5 or later must be installed on your system. See the
discussion for the "GPU"_accelerate_gpu.html package for details of
how to check and do this.

2
doc/src/suffix.txt
View File

@ -50,7 +50,7 @@ Intel(R) Xeon Phi(TM) coprocessors. :l
KOKKOS = a collection of atom, pair, and fix styles optimized to run
using the Kokkos library on various kinds of hardware, including GPUs
via Cuda and many-core chips via OpenMP or threading. :l
via CUDA and many-core chips via OpenMP or threading. :l
USER-OMP = a collection of pair, bond, angle, dihedral, improper,
kspace, compute, and fix styles with support for OpenMP

1
lib/atc/Makefile.mpic++ Symbolic link
View File

@ -0,0 +1 @@
Makefile.mpi

4
src/MEAM/pair_meam.cpp
View File

@ -47,6 +47,10 @@ static const char *keywords[] = {
PairMEAM::PairMEAM(LAMMPS *lmp) : Pair(lmp)
{
if (comm->me == 0)
error->warning(FLERR,"The pair_style meam command is unsupported. "
"Please use pair_style meam/c instead");
single_enable = 0;
restartinfo = 0;
one_coeff = 1;

4
src/REAX/pair_reax.cpp
View File

@ -46,8 +46,8 @@ using namespace LAMMPS_NS;
PairREAX::PairREAX(LAMMPS *lmp) : Pair(lmp)
{
if (comm->me == 0)
error->warning(FLERR,"The pair_style reax command will be deprecated "
"soon - users should switch to pair_style reax/c");
error->warning(FLERR,"The pair_style reax command is unsupported. "
"Please switch to pair_style reax/c instead");
single_enable = 0;
restartinfo = 0;

5
src/REPLICA/fix_neb.cpp
View File

@ -11,6 +11,11 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author for: Emile Maras (CEA, France)
new options for inter-replica forces, first/last replica treatment
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdlib.h>