making more links and anchors consistent and correct errors

If you uncomment the "dump image"_dump_image.html line(s) in the input

If you uncomment the "dump image"_dump_image.html line(s) in the input

script a series of JPG images will be produced by the run (assuming

script a series of JPG images will be produced by the run (assuming

you built LAMMPS with JPG support; see "Section start

you built LAMMPS with JPG support; see "Section

2.2"_Section_start.html for details).  These can be viewed

2.2"_Section_start.html#start_2 for details).  These can be viewed

individually or turned into a movie or animated by tools like

individually or turned into a movie or animated by tools like

ImageMagick or QuickTime or various Windows-based tools.  See the

ImageMagick or QuickTime or various Windows-based tools.  See the

"dump image"_dump_image.html doc page for more details.  E.g. this

"dump image"_dump_image.html doc page for more details.  E.g. this

correspond by name to a USER package.  They contain scripts that

correspond by name to a USER package.  They contain scripts that

illustrate how to use the command(s) provided in that package.  Many

illustrate how to use the command(s) provided in that package.  Many

of the sub-directories have their own README files which give further

of the sub-directories have their own README files which give further

instructions.  See the "Section packages"_Section_packages.html doc

instructions.  See the "Section 4"_Section_packages.html doc

page for more info on specific USER packages.

page for more info on specific USER packages.

"COMPRESS"_#COMPRESS, I/O compression, Axel Kohlmeyer (Temple U), "dump */gz"_dump.html, -, -

"COMPRESS"_#COMPRESS, I/O compression, Axel Kohlmeyer (Temple U), "dump */gz"_dump.html, -, -

"CORESHELL"_#CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "Section 6.6.25"_Section_howto.html#howto_25, coreshell, -

"CORESHELL"_#CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "Section 6.6.25"_Section_howto.html#howto_25, coreshell, -

"DIPOLE"_#DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, -

"DIPOLE"_#DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, -

"GPU"_#GPU, GPU-enabled styles, Mike Brown (ORNL), "Section accelerate"_accelerate_gpu.html, gpu, lib/gpu

"GPU"_#GPU, GPU-enabled styles, Mike Brown (ORNL), "Section 5.3.1"_accelerate_gpu.html, gpu, lib/gpu

"GRANULAR"_#GRANULAR, granular systems, -, "Section 6.6.6"_Section_howto.html#howto_6, pour, -

"GRANULAR"_#GRANULAR, granular systems, -, "Section 6.6.6"_Section_howto.html#howto_6, pour, -

"KIM"_#KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM

"KIM"_#KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM

"KOKKOS"_#KOKKOS, Kokkos-enabled styles, Trott & Moore (4), "Section 5"_accelerate_kokkos.html, kokkos, lib/kokkos

"KOKKOS"_#KOKKOS, Kokkos-enabled styles, Trott & Moore (4), "Section 5.3.3"_accelerate_kokkos.html, kokkos, lib/kokkos

"KSPACE"_#KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -

"KSPACE"_#KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -

"MANYBODY"_#MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -

"MANYBODY"_#MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -

"MEAM"_#MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam

"MEAM"_#MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam

"MC"_#MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -

"MC"_#MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -

"MOLECULE"_#MOLECULE, molecular system force fields, -, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -

"MOLECULE"_#MOLECULE, molecular system force fields, -, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -

"OPT"_#OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section accelerate"_accelerate_opt.html, -, -

"OPT"_#OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section 5.3.5"_accelerate_opt.html, -, -

"PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -

"PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -

"POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems

"POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems

"PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python

"PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python

Make.py -p ^asphere -a machine :pre

Make.py -p ^asphere -a machine :pre

Supporting info: "Section howto 6.14"_Section_howto.html#howto_14,

Supporting info: "Section 6.14"_Section_howto.html#howto_14,

"pair_style gayberne"_pair_gayberne.html, "pair_style

"pair_style gayberne"_pair_gayberne.html, "pair_style

resquared"_pair_resquared.html,

resquared"_pair_resquared.html,

"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf,

"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf,

core/shell model for polarizability.  The compute temp/cs command

core/shell model for polarizability.  The compute temp/cs command

measures the temperature of a system with core/shell particles.  The

measures the temperature of a system with core/shell particles.  The

pair styles augment Born, Buckingham, and Lennard-Jones styles with

pair styles augment Born, Buckingham, and Lennard-Jones styles with

core/shell capabilities.  See "Section howto

core/shell capabilities.  See "Section 6.26"_Section_howto.html#howto_26

6.26"_Section_howto.html#howto_26 for an overview of how to use the

for an overview of how to use the package.

package.

To install via make or Make.py:

To install via make or Make.py:

Make.py -p ^coreshell -a machine :pre

Make.py -p ^coreshell -a machine :pre

Supporting info: "Section howto

Supporting info: "Section 6.26"_Section_howto.html#howto_26,

6.26"_Section_howto.html#howto_26, "compute temp/cs"_compute_temp_cs.html,

"compute temp/cs"_compute_temp_cs.html,

"pair_style born/coul/long/cs"_pair_cs.html, "pair_style

"pair_style born/coul/long/cs"_pair_cs.html, "pair_style

buck/coul/long/cs"_pair_cs.html, pair_style

buck/coul/long/cs"_pair_cs.html, pair_style

lj/cut/coul/long/cs"_pair_lj.html, examples/coreshell

lj/cut/coul/long/cs"_pair_lj.html, examples/coreshell

Contents: Dozens of pair styles and a version of the PPPM long-range

Contents: Dozens of pair styles and a version of the PPPM long-range

Coulombic solver for NVIDIA GPUs.  All of them have a "gpu" in their

Coulombic solver for NVIDIA GPUs.  All of them have a "gpu" in their

style name.  "Section accelerate gpu"_accelerate_gpu.html gives

style name.  "Section 5.3.1"_accelerate_gpu.html gives

details of what hardware and Cuda software is required on your system,

details of what hardware and Cuda software is required on your system,

and how to build and use this package.  See the KOKKOS package, which

and how to build and use this package.  See the KOKKOS package, which

also has GPU-enabled styles.

also has GPU-enabled styles.

Make.py -p ^gpu -a machine :pre

Make.py -p ^gpu -a machine :pre

Supporting info: src/GPU/README, lib/gpu/README, "Section

Supporting info: src/GPU/README, lib/gpu/README,

acclerate"_Section_accelerate.html, "Section accelerate

"Section 5.3"_Section_accelerate.html#acc_3,

gpu"_accelerate_gpu.html, Pair Styles section of "Section commands

"Section 5.3.1"_accelerate_gpu.html,

3.5"_Section_commands.html#cmd_5 for any pair style listed with a (g),

Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5

for any pair style listed with a (g),

"kspace_style"_kspace_style.html, "package gpu"_package.html,

"kspace_style"_kspace_style.html, "package gpu"_package.html,

examples/accelerate, bench/FERMI, bench/KEPLER

examples/accelerate, bench/FERMI, bench/KEPLER

Make.py -p ^granular -a machine :pre

Make.py -p ^granular -a machine :pre

Supporting info: "Section howto 6.6"_Section_howto.html#howto_6, "fix

Supporting info: "Section 6.6"_Section_howto.html#howto_6, "fix

pour"_fix_pour.html, "fix wall/gran"_fix_wall_gran.html, "pair_style

pour"_fix_pour.html, "fix wall/gran"_fix_wall_gran.html, "pair_style

gran/hooke"_pair_gran.html, "pair_style

gran/hooke"_pair_gran.html, "pair_style

gran/hertz/history"_pair_gran.html, examples/pour, bench/in.chute

gran/hertz/history"_pair_gran.html, examples/pour, bench/in.chute

which run with the Kokkos library to provide optimization for

which run with the Kokkos library to provide optimization for

multicore CPUs (via OpenMP), NVIDIA GPUs, or the Intel Xeon Phi (in

multicore CPUs (via OpenMP), NVIDIA GPUs, or the Intel Xeon Phi (in

native mode).  All of them have a "kk" in their style name.  "Section

native mode).  All of them have a "kk" in their style name.  "Section

accelerate kokkos"_accelerate_kokkos.html gives details of what

5.3.3"_accelerate_kokkos.html gives details of what

hardware and software is required on your system, and how to build and

hardware and software is required on your system, and how to build and

use this package.  See the GPU, OPT, USER-INTEL, USER-OMP packages,

use this package.  See the GPU, OPT, USER-INTEL, USER-OMP packages,

which also provide optimizations for the same range of hardware.

which also provide optimizations for the same range of hardware.

below, you can use the Make.py script with its "-kokkos" option to

below, you can use the Make.py script with its "-kokkos" option to

choose which hardware to build for.  Type "python src/Make.py -h

choose which hardware to build for.  Type "python src/Make.py -h

-kokkos" to see the details.  If these methods do not work on your

-kokkos" to see the details.  If these methods do not work on your

system, you will need to read the "Section accelerate

system, you will need to read the "Section 5.3.3"_accelerate_kokkos.html

kokkos"_accelerate_kokkos.html doc page for details of what

doc page for details of what Makefile.machine settings are needed.

Makefile.machine settings are needed.

To install via make or Make.py for each of 3 hardware options:

To install via make or Make.py for each of 3 hardware options:

Make.py -p ^kokkos -a machine :pre

Make.py -p ^kokkos -a machine :pre

Supporting info: src/KOKKOS/README, lib/kokkos/README, "Section

Supporting info: src/KOKKOS/README, lib/kokkos/README,

acclerate"_Section_accelerate.html, "Section accelerate

"Section 5.3"_Section_accelerate.html#acc_3,

kokkos"_accelerate_kokkos.html, Pair Styles section of "Section

"Section 5.3.3"_accelerate_kokkos.html,

commands 3.5"_Section_commands.html#cmd_5 for any pair style listed

Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5

with a (k), "package kokkos"_package.html,

for any pair style listed with a (k), "package kokkos"_package.html,

examples/accelerate, bench/FERMI, bench/KEPLER

examples/accelerate, bench/FERMI, bench/KEPLER

:line

:line

Building with the KSPACE package requires a 1d FFT library be present

Building with the KSPACE package requires a 1d FFT library be present

on your system for use by the PPPM solvers.  This can be the KISS FFT

on your system for use by the PPPM solvers.  This can be the KISS FFT

library provided with LAMMPS, or 3rd party libraries like FFTW or a

library provided with LAMMPS, or 3rd party libraries like FFTW or a

vendor-supplied FFT library.  See step 6 of "Section start

vendor-supplied FFT library.  See step 6 of "Section

2.2.2"_Section_start.html#start_2_2 of the manual for details of how

2.2.2"_Section_start.html#start_2_2 of the manual for details of how

to select different FFT options in your machine Makefile.  The Make.py

to select different FFT options in your machine Makefile.  The Make.py

tool has an "-fft" option which can insert these settings into your

tool has an "-fft" option which can insert these settings into your

Make.py -p ^kspace -a machine :pre

Make.py -p ^kspace -a machine :pre

Supporting info: "kspace_style"_kspace_style.html,

Supporting info: "kspace_style"_kspace_style.html,

"doc/PDF/kspace.pdf"_PDF/kspace.pdf, "Section howto

"doc/PDF/kspace.pdf"_PDF/kspace.pdf,

6.7"_Section_howto.html#howto_7, "Section howto

"Section 6.7"_Section_howto.html#howto_7,

6.8"_Section_howto.html#howto_8, "Section howto

"Section 6.8"_Section_howto.html#howto_8,

6.9"_Section_howto.html#howto_9, "pair_style coul"_pair_coul.html,

"Section 6.9"_Section_howto.html#howto_9,

other pair style command doc pages which have "long" or "msm" in their

"pair_style coul"_pair_coul.html, other pair style command doc pages

style name, examples/peptide, bench/in.rhodo

which have "long" or "msm" in their style name,

examples/peptide, bench/in.rhodo

:line

:line

Supporting info: 

Supporting info: 

Examples: Pair Styles section of "Section commands

Examples: Pair Styles section of "Section

3.5"_Section_commands.html#cmd_5, examples/comb, examples/eim,

3.5"_Section_commands.html#cmd_5, examples/comb, examples/eim,

examples/nb3d, examples/vashishta

examples/nb3d, examples/vashishta

"dihedral_style"_dihedral_style.html,

"dihedral_style"_dihedral_style.html,

"improper_style"_improper_style.html, "pair_style

"improper_style"_improper_style.html, "pair_style

hbond/dreiding/lj"_pair_hbond_dreiding.html, "pair_style

hbond/dreiding/lj"_pair_hbond_dreiding.html, "pair_style

lj/charmm/coul/charmm"_pair_charmm.html, "Section howto

lj/charmm/coul/charmm"_pair_charmm.html,

6.3"_Section_howto.html#howto_3, examples/micelle, examples/peptide,

"Section 6.3"_Section_howto.html#howto_3,

bench/in.chain, bench/in.rhodo

examples/micelle, examples/peptide, bench/in.chain, bench/in.rhodo

:line

:line

Contents: A handful of pair styles with an "opt" in their style name

Contents: A handful of pair styles with an "opt" in their style name

which are optimized for improved CPU performance on single or multiple

which are optimized for improved CPU performance on single or multiple

cores.  These include EAM, LJ, CHARMM, and Morse potentials.  "Section

cores.  These include EAM, LJ, CHARMM, and Morse potentials.  "Section

accelerate opt"_accelerate_opt.html gives details of how to build and

5.3.5"_accelerate_opt.html gives details of how to build and

use this package.  See the KOKKOS, USER-INTEL, and USER-OMP packages,

use this package.  See the KOKKOS, USER-INTEL, and USER-OMP packages,

which also have styles optimized for CPU performance.

which also have styles optimized for CPU performance.

Make.py -p ^opt -a machine :pre

Make.py -p ^opt -a machine :pre

Supporting info: "Section acclerate"_Section_accelerate.html, "Section

Supporting info: "Section 5.3"_Section_accelerate.html#acc_3,

accelerate opt"_accelerate_opt.html, Pair Styles section of "Section

"Section 5.3.5"_accelerate_opt.html, Pair Styles section of

commands 3.5"_Section_commands.html#cmd_5 for any pair style listed

"Section 3.5"_Section_commands.html#cmd_5 for any pair style

with an (o), examples/accelerate, bench/KEPLER

listed with an (t), examples/accelerate, bench/KEPLER

:line

:line

Contents: A "python"_python.html command which allow you to execute

Contents: A "python"_python.html command which allow you to execute

Python code from a LAMMPS input script.  The code can be in a separate

Python code from a LAMMPS input script.  The code can be in a separate

file or embedded in the input script itself.  See "Section python

file or embedded in the input script itself.  See "Section

11.2"_Section_python.html" for an overview of using Python from

11.2"_Section_python.html#py-2 for an overview of using Python from

LAMMPS and for other ways to use LAMMPS and Python together.

LAMMPS and for other ways to use LAMMPS and Python together.

Building with the PYTHON package assumes you have a Python shared

Building with the PYTHON package assumes you have a Python shared

library available on your system, which needs to be a Python 2

library available on your system, which needs to be a Python 2

version, 2.6 or later.  Python 3 is not supported.  The build uses the

version, 2.6 or later.  Python 3 is not yet supported.  The build uses

contents of the lib/python/Makefile.lammps file to find all the Python

the contents of the lib/python/Makefile.lammps file to find all the Python

files required in the build/link process.  See the lib/python/README

files required in the build/link process.  See the lib/python/README

file if the settings in that file do not work on your system.  Note

file if the settings in that file do not work on your system.  Note

that the Make.py script has a "-python" option to allow an alternate

that the Make.py script has a "-python" option to allow an alternate

Contents: A collection of multi-replica methods that are used by

Contents: A collection of multi-replica methods that are used by

invoking multiple instances (replicas) of LAMMPS

invoking multiple instances (replicas) of LAMMPS

simulations. Communication between individual replicas is performed in

simulations. Communication between individual replicas is performed in

different ways by the different methods.  See "Section howto

different ways by the different methods.  See "Section

6.5"_Section_howto.html#howto_5 for an overview of how to run

6.5"_Section_howto.html#howto_5 for an overview of how to run

multi-replica simulations in LAMMPS.  Multi-replica methods included

multi-replica simulations in LAMMPS.  Multi-replica methods included

in the package are nudged elastic band (NEB), parallel replica

in the package are nudged elastic band (NEB), parallel replica

Make.py -p ^replica -a machine :pre

Make.py -p ^replica -a machine :pre

Supporting info: "Section howto 6.5"_Section_howto.html#howto_5,

Supporting info: "Section 6.5"_Section_howto.html#howto_5,

"neb"_neb.html, "prd"_prd.html, "tad"_tad.html, "temper"_temper.html,

"neb"_neb.html, "prd"_prd.html, "tad"_tad.html, "temper"_temper.html,

"run_style verlet/split"_run_style.html, examples/neb, examples/prd,

"run_style verlet/split"_run_style.html, examples/neb, examples/prd,

examples/tad

examples/tad

"USER-EFF"_#USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -

"USER-EFF"_#USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -

"USER-FEP"_#USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -

"USER-FEP"_#USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -

"USER-H5MD"_#USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md

"USER-H5MD"_#USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md

"USER-INTEL"_#USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, -

"USER-INTEL"_#USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section 5.3.2"_accelerate_intel.html, examples/intel, -, -

"USER-LB"_#USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -

"USER-LB"_#USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -

"USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, Tomas Oppelstrup & John Moriarty (LLNL), "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -, -

"USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, Tomas Oppelstrup & John Moriarty (LLNL), "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -, -

"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -

"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -

"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -

"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -

"USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE

"USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE

"USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_accelerate_omp.html, -, -, -

"USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -

"USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -

"USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -

"USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm

"USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm

"USER-QTB"_#USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -, -

"USER-QTB"_#USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -, -

Contents: This package contains methods for simulating polarizable

Contents: This package contains methods for simulating polarizable

systems using thermalized Drude oscillators.  It has computes, fixes,

systems using thermalized Drude oscillators.  It has computes, fixes,

and pair styles for this purpose.  See "Section howto

and pair styles for this purpose.  See "Section

6.27"_Section_howto.html#howto_27 for an overview of how to use the

6.27"_Section_howto.html#howto_27 for an overview of how to use the

package.  See src/USER-DRUDE/README for additional details.  There are

package.  See src/USER-DRUDE/README for additional details.  There are

auxiliary tools for using this package in tools/drude.

auxiliary tools for using this package in tools/drude.

Supporting info: "Section howto 6.27"_Section_howto.html#howto_27,

Supporting info: "Section 6.27"_Section_howto.html#howto_27,

src/USER-DRUDE/README, "fix drude"_fix_drude.html, "fix

src/USER-DRUDE/README, "fix drude"_fix_drude.html, "fix

drude/transform/*"_fix_drude_transform.html, "compute

drude/transform/*"_fix_drude_transform.html, "compute

temp/drude"_compute_temp_drude.html, "pair thole"_pair_thole.html,

temp/drude"_compute_temp_drude.html, "pair thole"_pair_thole.html,

Contents: Dozens of pair, bond, angle, dihedral, and improper styles

Contents: Dozens of pair, bond, angle, dihedral, and improper styles

that are optimized for Intel CPUs and the Intel Xeon Phi (in offload

that are optimized for Intel CPUs and the Intel Xeon Phi (in offload

mode).  All of them have an "intel" in their style name.  "Section

mode).  All of them have an "intel" in their style name.  "Section

accelerate intel"_accelerate_intel.html gives details of what hardware

5.3.2"_accelerate_intel.html gives details of what hardware

and compilers are required on your system, and how to build and use

and compilers are required on your system, and how to build and use

this package.  Also see src/USER-INTEL/README for more details. See

this package.  Also see src/USER-INTEL/README for more details. See

the KOKKOS, OPT, and USER-OMP packages, which also have CPU and

the KOKKOS, OPT, and USER-OMP packages, which also have CPU and

Supporting info: examples/accelerate, src/USER-INTEL/TEST

Supporting info: examples/accelerate, src/USER-INTEL/TEST

"Section 5"_Section_accelerate.html#acc_3

"Section 5.3"_Section_accelerate.html#acc_3

Author: Mike Brown at Intel (michael.w.brown at intel.com).  Contact

Author: Mike Brown at Intel (michael.w.brown at intel.com).  Contact

him directly if you have questions.

him directly if you have questions.

page in the LAMMPS doc directory.  The doc page which lists all LAMMPS

page in the LAMMPS doc directory.  The doc page which lists all LAMMPS

input script commands is as follows:

input script commands is as follows:

"Section 3"_Section_commands.html#cmd_5

"Section 3.5"_Section_commands.html#cmd_5

User-contributed features are listed at the bottom of the fix,

User-contributed features are listed at the bottom of the fix,

compute, pair, etc sections.

compute, pair, etc sections.

See this section of the manual to get started:

See this section of the manual to get started:

"Section 5"_Section_accelerate.html#acc_3

"Section 5.3"_Section_accelerate.html#acc_3

The person who created this package is Axel Kohlmeyer at Temple U

The person who created this package is Axel Kohlmeyer at Temple U

(akohlmey at gmail.com).  Contact him directly if you have questions.

(akohlmey at gmail.com).  Contact him directly if you have questions.

and bench/KEPLER dirs have input files and scripts and instructions

and bench/KEPLER dirs have input files and scripts and instructions

for running the same (or similar) problems using OpenMP or GPU or Xeon

for running the same (or similar) problems using OpenMP or GPU or Xeon

Phi acceleration options.  See the README files in those dirs and the

Phi acceleration options.  See the README files in those dirs and the

"Section accelerate"_Section_accelerate.html doc pages for

"Section 5.3"_Section_accelerate.html#acc_3 doc pages for

instructions on how to build LAMMPS and run on that kind of hardware.

instructions on how to build LAMMPS and run on that kind of hardware.

The bench/POTENTIALS directory has input files which correspond to the

The bench/POTENTIALS directory has input files which correspond to the

2.8 "Screen output"_#start_8

2.8 "Screen output"_#start_8

2.9 "Tips for users of previous versions"_#start_9 :all(b)

2.9 "Tips for users of previous versions"_#start_9 :all(b)

:line

:line

:line

2.1 What's in the LAMMPS distribution :h4,link(start_1)

2.1 What's in the LAMMPS distribution :h4,link(start_1)

This section has the following sub-sections:

This section has the following sub-sections:

"Read this first"_#start_2_1

2.2.1 "Read this first"_#start_2_1

"Steps to build a LAMMPS executable"_#start_2_2

2.2.1 "Steps to build a LAMMPS executable"_#start_2_2

"Common errors that can occur when making LAMMPS"_#start_2_3

2.2.3 "Common errors that can occur when making LAMMPS"_#start_2_3

"Additional build tips"_#start_2_4

2.2.4 "Additional build tips"_#start_2_4

"Building for a Mac"_#start_2_5

2.2.5 "Building for a Mac"_#start_2_5

"Building for Windows"_#start_2_6 :ul

2.2.6 "Building for Windows"_#start_2_6 :all(b)

:line

:line

files created when LAMMPS is built, for either all builds or for a

files created when LAMMPS is built, for either all builds or for a

particular machine.

particular machine.

 Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or

Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6

-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6

As explained above, any of these 3 settings can be specified on the

As explained above, any of these 3 settings can be specified on the

LMP_INC line in your low-level src/MAKE/Makefile.foo.

LMP_INC line in your low-level src/MAKE/Makefile.foo.

Building for a Mac :h5,link(start_2_5)

Building for a Mac :h5,link(start_2_5)

OS X is BSD Unix, so it should just work.  See the

OS X is a derivative of BSD Unix, so it should just work.  See the

src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.

src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.

:line

:line

we cannot provide support for those.

we cannot provide support for those.

With the so-called "Anniversary Update" to Windows 10, there is a

With the so-called "Anniversary Update" to Windows 10, there is a

Ubuntu subsystem available for Windows, that can be installed and

Ubuntu Linux subsystem available for Windows, that can be installed

then it can be used to compile/install LAMMPS as if you are running

and then used to compile/install LAMMPS as if you are running on a

on a Ubuntu Linux system.

Ubuntu Linux system instead of Windows.

As an alternative, you can download "daily builds" (and some older

As an alternative, you can download "daily builds" (and some older

versions) of the installer packages from

versions) of the installer packages from

This section has the following sub-sections:

This section has the following sub-sections:

"Package basics"_#start_3_1

2.3.1 "Package basics"_#start_3_1

"Including/excluding packages"_#start_3_2

2.3.2 "Including/excluding packages"_#start_3_2

"Packages that require extra libraries"_#start_3_3

2.3.3 "Packages that require extra libraries"_#start_3_3

"Packages that require Makefile.machine settings"_#start_3_4 :ul

2.3.4 "Packages that require Makefile.machine settings"_#start_3_4 :all(b)

Note that the following "Section 2.4"_#start_4 describes the Make.py

Note that the following "Section 2.4"_#start_4 describes the Make.py

tool which can be used to install/un-install packages and build the

tool which can be used to install/un-install packages and build the

files that enable a specific set of features.  For example, force

files that enable a specific set of features.  For example, force

fields for molecular systems or granular systems are in packages.

fields for molecular systems or granular systems are in packages.

"Section packages"_Section_packages.html in the manual has details

"Section 4"_Section_packages.html in the manual has details

about all the packages, including specific instructions for building

about all the packages, including specific instructions for building

LAMMPS with each package, which are covered in a more general manner

LAMMPS with each package, which are covered in a more general manner

below.

below.

For libraries with provided code, the sub-directory README file

For libraries with provided code, the sub-directory README file

(e.g. lib/atc/README) has instructions on how to build that library.

(e.g. lib/atc/README) has instructions on how to build that library.

This information is also summarized in "Section

This information is also summarized in "Section

packages"_Section_packages.html.  Typically this is done by typing

4"_Section_packages.html.  Typically this is done by typing

something like:

something like:

make -f Makefile.g++ :pre

make -f Makefile.g++ :pre

either build or use the package effectively.  These are the

either build or use the package effectively.  These are the

USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating

USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating

code performance on CPUs or other hardware, as discussed in "Section

code performance on CPUs or other hardware, as discussed in "Section

acclerate"_Section_accelerate.html. 

5.3"_Section_accelerate.html#acc_3. 

A summary of what Makefile.machine changes are needed for each of

A summary of what Makefile.machine changes are needed for each of

these packages is given in "Section packages"_Section_packages.html.

these packages is given in "Section 4"_Section_packages.html.

The details are given on the doc pages that describe each of these

The details are given on the doc pages that describe each of these

accelerator packages in detail:

accelerator packages in detail:

"USER-INTEL package"_accelerate_intel.html

5.3.1 "USER-INTEL package"_accelerate_intel.html

"KOKKOS package"_accelerate_kokkos.html

5.3.3 "KOKKOS package"_accelerate_kokkos.html

"USER-OMP package"_accelerate_omp.html

5.3.4 "USER-OMP package"_accelerate_omp.html

"OPT package"_accelerate_opt.html :ul

5.3.5 "OPT package"_accelerate_opt.html :all(b)

You can also look at the following machine Makefiles in

You can also look at the following machine Makefiles in

src/MAKE/OPTIONS, which include the changes.  Note that the USER-INTEL

src/MAKE/OPTIONS, which include the changes.  Note that the USER-INTEL

keyword is "t", not "-t".  Also note that each of the keywords has a

keyword is "t", not "-t".  Also note that each of the keywords has a

default setting.  Example of when to use these options and what

default setting.  Example of when to use these options and what

settings to use on different platforms is given in "Section

settings to use on different platforms is given in "Section

5.8"_Section_accelerate.html#acc_3.

5.3"_Section_accelerate.html#acc_3.

d or device

d or device

g or gpus

g or gpus

necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP

necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP

provides alternative methods via environment variables for binding

provides alternative methods via environment variables for binding

threads to hardware cores.  More info on binding threads to cores is

threads to hardware cores.  More info on binding threads to cores is

given in "this section"_Section_accelerate.html#acc_3.

given in "Section 5.3"_Section_accelerate.html#acc_3.

KOKKOS_ARCH=KNC enables compiler switches needed when compling for an

KOKKOS_ARCH=KNC enables compiler switches needed when compling for an

Intel Phi processor.

Intel Phi processor.