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Merge pull request #1063 from akohlmey/small-doc-fixes

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Fix some documentation issues
This commit is contained in:
Steve Plimpton
2018-08-20 13:39:59 -06:00
committed by GitHub
parent 2248bf12d5 4f37b46b10
commit 044141eb8f
6 changed files with 142 additions and 102 deletions
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2
doc/src/Manual_build.txt
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@ -81,7 +81,7 @@ sudo yum install python3-virtualenv :pre
Fedora (since version 22) :h4 Fedora (since version 22) :h4
sudo dnf install python3-virtualenv pre sudo dnf install python3-virtualenv :pre
MacOS X :h4 MacOS X :h4

5
doc/src/Packages_details.txt
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@ -382,6 +382,11 @@ switches"_Run_options.html. Also see the "GPU"_#PKG-GPU, "OPT"_#PKG-OPT,
have styles optimized for CPUs, KNLs, and GPUs. have styles optimized for CPUs, KNLs, and GPUs.
You must have a C++11 compatible compiler to use this package. You must have a C++11 compatible compiler to use this package.
KOKKOS makes extensive use of advanced C++ features, which can
expose compiler bugs, especially when compiling for maximum
performance at high optimization levels. Please see the file
lib/kokkos/README for a list of compilers and their respective
platforms, that are known to work.
[Authors:] The KOKKOS package was created primarily by Christian Trott [Authors:] The KOKKOS package was created primarily by Christian Trott
and Stan Moore (Sandia), with contributions from other folks as well. and Stan Moore (Sandia), with contributions from other folks as well.

52
doc/src/Packages_standard.txt
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@ -25,42 +25,42 @@ refers to the examples/USER/atc directory. The "Library" column
indicates whether an extra library is needed to build and use the indicates whether an extra library is needed to build and use the
package: package:
dash = no library no = no library
sys = system library: you likely have it on your machine sys = system library: you likely have it on your machine
int = internal library: provided with LAMMPS, but you may need to build it int = internal library: provided with LAMMPS, but you may need to build it
ext = external library: you will need to download and install it on your machine :ul ext = external library: you will need to download and install it on your machine :ul
Package, Description, Doc page, Example, Library Package, Description, Doc page, Example, Library
"ASPHERE"_Packages_details.html#PKG-ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, - "ASPHERE"_Packages_details.html#PKG-ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, no
"BODY"_Packages_details.html#PKG-BODY, body-style particles, "Howto body"_Howto_body.html, body, - "BODY"_Packages_details.html#PKG-BODY, body-style particles, "Howto body"_Howto_body.html, body, no
"CLASS2"_Packages_details.html#PKG-CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, - "CLASS2"_Packages_details.html#PKG-CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, n/a, no
"COLLOID"_Packages_details.html#PKG-COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, - "COLLOID"_Packages_details.html#PKG-COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, no
"COMPRESS"_Packages_details.html#PKG-COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys "COMPRESS"_Packages_details.html#PKG-COMPRESS, I/O compression, "dump */gz"_dump.html, n/a, sys
"CORESHELL"_Packages_details.html#PKG-CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, - "CORESHELL"_Packages_details.html#PKG-CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, no
"DIPOLE"_Packages_details.html#PKG-DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, - "DIPOLE"_Packages_details.html#PKG-DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, no
"GPU"_Packages_details.html#PKG-GPU, GPU-enabled styles, "Section gpu"_Speed_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int "GPU"_Packages_details.html#PKG-GPU, GPU-enabled styles, "Section gpu"_Speed_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
"GRANULAR"_Packages_details.html#PKG-GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, - "GRANULAR"_Packages_details.html#PKG-GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, no
"KIM"_Packages_details.html#PKG-KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext "KIM"_Packages_details.html#PKG-KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
"KOKKOS"_Packages_details.html#PKG-KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - "KOKKOS"_Packages_details.html#PKG-KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
"KSPACE"_Packages_details.html#PKG-KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, - "KSPACE"_Packages_details.html#PKG-KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, no
"LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext "LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, - "MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no
"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, - "MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no
"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int "MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
"MISC"_Packages_details.html#PKG-MISC, miscellanous single-file commands, -, -, - "MISC"_Packages_details.html#PKG-MISC, miscellanous single-file commands, n/a, no, no
"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, - "MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no
"MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, - "MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, n/a, no
"MSCG"_Packages_details.html#PKG-MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext "MSCG"_Packages_details.html#PKG-MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
"OPT"_Packages_details.html#PKG-OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - "OPT"_Packages_details.html#PKG-OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
"PERI"_Packages_details.html#PKG-PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, - "PERI"_Packages_details.html#PKG-PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, no
"POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int "POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
"PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys "PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys
"QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, - "QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, no
"REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int "REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
"REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, - "REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, no
"RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, - "RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, no
"SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, - "SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, n/a, no
"SNAP"_Packages_details.html#PKG-SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, - "SNAP"_Packages_details.html#PKG-SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, no
"SPIN"_Packages_details.html#PKG-SPIN, magnetic atomic spin dynamics, "Howto spins"_Howto_spins.html, SPIN, - "SPIN"_Packages_details.html#PKG-SPIN, magnetic atomic spin dynamics, "Howto spins"_Howto_spins.html, SPIN, no
"SRD"_Packages_details.html#PKG-SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, - "SRD"_Packages_details.html#PKG-SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, no
"VORONOI"_Packages_details.html#PKG-VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l) "VORONOI"_Packages_details.html#PKG-VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, n/a, ext :tb(ea=c,ca1=l)

58
doc/src/Packages_user.txt
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@ -32,7 +32,7 @@ refers to the examples/USER/atc directory. The "Library" column
indicates whether an extra library is needed to build and use the indicates whether an extra library is needed to build and use the
package: package:
dash = no library no = no library
sys = system library: you likely have it on your machine sys = system library: you likely have it on your machine
int = internal library: provided with LAMMPS, but you may need to build it int = internal library: provided with LAMMPS, but you may need to build it
ext = external library: you will need to download and install it on your machine :ul ext = external library: you will need to download and install it on your machine :ul
@ -40,35 +40,35 @@ ext = external library: you will need to download and install it on your machine
Package, Description, Doc page, Example, Library Package, Description, Doc page, Example, Library
"USER-ATC"_Packages_details.html#PKG-USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int "USER-ATC"_Packages_details.html#PKG-USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int "USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
"USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, - "USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no
"USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, - "USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, no
"USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, - "USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, no
"USER-COLVARS"_Packages_details.html#PKG-USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int "USER-COLVARS"_Packages_details.html#PKG-USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
"USER-DIFFRACTION"_Packages_details.html#PKG-USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, - "USER-DIFFRACTION"_Packages_details.html#PKG-USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, no
"USER-DPD"_Packages_details.html#PKG-USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, - "USER-DPD"_Packages_details.html#PKG-USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, no
"USER-DRUDE"_Packages_details.html#PKG-USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, - "USER-DRUDE"_Packages_details.html#PKG-USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, no
"USER-EFF"_Packages_details.html#PKG-USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, - "USER-EFF"_Packages_details.html#PKG-USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, no
"USER-FEP"_Packages_details.html#PKG-USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, - "USER-FEP"_Packages_details.html#PKG-USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, no
"USER-H5MD"_Packages_details.html#PKG-USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext "USER-H5MD"_Packages_details.html#PKG-USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, n/a, ext
"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - "USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, - "USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no
"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, - "USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no
"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, - "USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, no
"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, - "USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, - "USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, - "USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
"USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, - "USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no
"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext "USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext
"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext "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, - "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, - "USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no
"USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext "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, - "USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no
"USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext "USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
"USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, - "USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, no
"USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext "USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
"USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, - "USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, no
"USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, - "USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no
"USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, - "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, - "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, -, ext :tb(ea=c,ca1=l) "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)

119
doc/src/Speed_compare.txt
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@ -9,65 +9,108 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Comparison of various accelerator packages :h3 Comparison of various accelerator packages :h3
NOTE: this section still needs to be re-worked with additional KOKKOS
and USER-INTEL information.
The next section compares and contrasts the various accelerator The next section compares and contrasts the various accelerator
options, since there are multiple ways to perform OpenMP threading, options, since there are multiple ways to perform OpenMP threading,
run on GPUs, and run on Intel Xeon Phi coprocessors. run on GPUs, optimize for vector units on CPUs and run on Intel
Xeon Phi (co-)processors.
All 3 of these packages accelerate a LAMMPS calculation using NVIDIA All of these packages can accelerate a LAMMPS calculation taking
hardware, but they do it in different ways. advantage of hardware features, but they do it in different ways
and acceleration is not always guaranteed.
As a consequence, for a particular simulation on specific hardware, As a consequence, for a particular simulation on specific hardware,
one package may be faster than the other. We give guidelines below, one package may be faster than the other. We give some guidelines
but the best way to determine which package is faster for your input below, but the best way to determine which package is faster for your
script is to try both of them on your machine. See the benchmarking input script is to try multiple of them on your machine and experiment
with available performance tuning settings. See the benchmarking
section below for examples where this has been done. section below for examples where this has been done.
[Guidelines for using each package optimally:] [Guidelines for using each package optimally:]
The GPU package allows you to assign multiple CPUs (cores) to a single Both, the GPU and the KOKKOS package allows you to assign multiple
GPU (a common configuration for "hybrid" nodes that contain multicore MPI ranks (= CPU cores) to the same GPU. For the GPU package, this
CPU(s) and GPU(s)) and works effectively in this mode. :ulb,l can lead to a speedup through better utilization of the GPU (by
overlapping computation and data transfer) and more efficient
computation of the non-GPU accelerated parts of LAMMPS through MPI
parallelization, as all system data is maintained and updated on
the host. For KOKKOS, there is less to no benefit from this, due
to its different memory management model, which tries to retain
data on the GPU.
:ulb,l
The GPU package moves per-atom data (coordinates, forces) The GPU package moves per-atom data (coordinates, forces, and
back-and-forth between the CPU and GPU every timestep. The (optionally) neighbor list data, if not computed on the GPU) between
KOKKOS/CUDA package only does this on timesteps when a CPU calculation the CPU and GPU at every timestep. The KOKKOS/CUDA package only does
is required (e.g. to invoke a fix or compute that is non-GPU-ized). this on timesteps when a CPU calculation is required (e.g. to invoke
Hence, if you can formulate your input script to only use GPU-ized a fix or compute that is non-GPU-ized). Hence, if you can formulate
fixes and computes, and avoid doing I/O too often (thermo output, dump your input script to only use GPU-ized fixes and computes, and avoid
file snapshots, restart files), then the data transfer cost of the doing I/O too often (thermo output, dump file snapshots, restart files),
KOKKOS/CUDA package can be very low, causing it to run faster than the then the data transfer cost of the KOKKOS/CUDA package can be very low,
GPU package. :l causing it to run faster than the GPU package. :l
The GPU package is often faster than the KOKKOS/CUDA package, if the The GPU package is often faster than the KOKKOS/CUDA package, when the
number of atoms per GPU is smaller. The crossover point, in terms of number of atoms per GPU is on the smaller side. The crossover point,
atoms/GPU at which the KOKKOS/CUDA package becomes faster depends in terms of atoms/GPU at which the KOKKOS/CUDA package becomes faster
strongly on the pair style. For example, for a simple Lennard Jones depends strongly on the pair style. For example, for a simple Lennard Jones
system the crossover (in single precision) is often about 50K-100K system the crossover (in single precision) is often about 50K-100K
atoms per GPU. When performing double precision calculations the atoms per GPU. When performing double precision calculations the
crossover point can be significantly smaller. :l crossover point can be significantly smaller. :l
Both packages compute bonded interactions (bonds, angles, etc) on the Both KOKKOS and GPU package compute bonded interactions (bonds, angles,
CPU. If the GPU package is running with several MPI processes etc) on the CPU. If the GPU package is running with several MPI processes
assigned to one GPU, the cost of computing the bonded interactions is assigned to one GPU, the cost of computing the bonded interactions is
spread across more CPUs and hence the GPU package can run faster. :l spread across more CPUs and hence the GPU package can run faster in these
cases. :l
When using the GPU package with multiple CPUs assigned to one GPU, its When using LAMMPS with multiple MPI ranks assigned to the same GPU, its
performance depends to some extent on high bandwidth between the CPUs performance depends to some extent on the available bandwidth between
and the GPU. Hence its performance is affected if full 16 PCIe lanes the CPUs and the GPU. This can differ significantly based on the
are not available for each GPU. In HPC environments this can be the available bus technology, capability of the host CPU and mainboard,
case if S2050/70 servers are used, where two devices generally share the wiring of the buses and whether switches are used to increase the
one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide number of available bus slots, or if GPUs are housed in an external
full 16 lanes to each of the PCIe 2.0 16x slots. :l enclosure. This can become quite complex. :l
To achieve significant acceleration through GPUs, both KOKKOS and GPU
package require capable GPUs with fast on-device memory and efficient
data transfer rates. This requests capable upper mid-level to high-end
(desktop) GPUs. Using lower performance GPUs (e.g. on laptops) may
result in a slowdown instead. :l
For the GPU package, specifically when running in parallel with MPI,
if it often more efficient to exclude the PPPM kspace style from GPU
acceleration and instead run it - concurrently with a GPU accelerated
pair style - on the CPU. This can often be easily achieved with placing
a {suffix off} command before and a {suffix on} command after the
{kspace_style pppm} command. :l
The KOKKOS/OpenMP and USER-OMP package have different thread management
strategies, which should result in USER-OMP being more efficient for a
small number of threads with increasing overhead as the number of threads
per MPI rank grows. The KOKKOS/OpenMP kernels have less overhead in that
case, but have lower performance with few threads. :l
The USER-INTEL package contains many options and settings for achieving
additional performance on Intel hardware (CPU and accelerator cards), but
to unlock this potential, an Intel compiler is required. The package code
will compile with GNU gcc, but it will not be as efficient. :l
:ule :ule
[Differences between the two packages:] [Differences between the GPU and KOKKOS packages:]
The GPU package accelerates only pair force, neighbor list, and PPPM The GPU package accelerates only pair force, neighbor list, and (parts
calculations. :ulb,l of) PPPM calculations. The KOKKOS package attempts to run most of the
calculation on the GPU, but can transparently support non-accelerated
code (with a performance penalty due to having data transfers between
host and GPU). :ulb,l
The GPU package requires neighbor lists to be built on the CPU when using The GPU package requires neighbor lists to be built on the CPU when using
exclusion lists, hybrid pair styles, or a triclinic simulation box. :l exclusion lists, hybrid pair styles, or a triclinic simulation box. :l
The GPU package can be compiled for CUDA or OpenCL and thus supports
both, Nvidia and AMD GPUs well. On Nvidia hardware, using CUDA is typically
resulting in equal or better performance over OpenCL. :l
OpenCL in the GPU package does theoretically also support Intel CPUs or
Intel Xeon Phi, but the native support for those in KOKKOS (or USER-INTEL)
is superior. :l
:ule :ule

8
src/USER-COLVARS/fix_colvars.h
View File

@ -34,7 +34,6 @@ FixStyle(colvars,FixColvars)
#define LMP_FIX_COLVARS_H #define LMP_FIX_COLVARS_H
#include "fix.h" #include "fix.h"
#include <vector>
// forward declaration // forward declaration
class colvarproxy_lammps; class colvarproxy_lammps;
@ -77,13 +76,6 @@ class FixColvars : public Fix {
int num_coords; // total number of atoms controlled by this fix int num_coords; // total number of atoms controlled by this fix
tagint *taglist; // list of all atom IDs referenced by colvars. tagint *taglist; // list of all atom IDs referenced by colvars.
// TODO get rid of these
// std::vector<cvm::atom_pos> *coords; // coordinates of colvar atoms
// std::vector<cvm::rvector> *forces; // received forces of colvar atoms
// std::vector<cvm::rvector> *oforce; // old total forces of colvar atoms
// std::vector<cvm::real> *masses;
// std::vector<cvm::real> *charges;
int nmax; // size of atom communication buffer. int nmax; // size of atom communication buffer.
int size_one; // bytes per atom in communication buffer. int size_one; // bytes per atom in communication buffer.
struct commdata *comm_buf; // communication buffer struct commdata *comm_buf; // communication buffer