Commit 47b52ed2 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

Merge branch 'integration' into balance2

parents 08f0bf90 b97b9dd6

doc/.gitignore

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/html

doc/src/Manual.txt

+2 −2
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<!-- HTML_ONLY -->

<HEAD>

<TITLE>LAMMPS Users Manual</TITLE>

<META NAME="docnumber" CONTENT="22 Sep 2016 version">

<META NAME="docnumber" CONTENT="26 Sep 2016 version">

<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">

<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">

</HEAD>
@@ -21,7 +21,7 @@ 
<H1></H1>



LAMMPS Documentation :c,h3

22 Sep 2016 version :c,h4

26 Sep 2016 version :c,h4



Version info: :h4

doc/src/Section_commands.txt

+1 −0
Original line number Diff line number Diff line
@@ -501,6 +501,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. 
"bond/create"_fix_bond_create.html,

"bond/swap"_fix_bond_swap.html,

"box/relax"_fix_box_relax.html,

"cmap"_fix_cmap.html,

"controller"_fix_controller.html,

"deform (k)"_fix_deform.html,

"deposit"_fix_deposit.html,

doc/src/Section_example.txt

+3 −3
Original line number Diff line number Diff line
@@ -105,8 +105,8 @@ web site. 


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

you built LAMMPS with JPG support; see "Section start

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

you built LAMMPS with JPG support; see "Section

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

individually or turned into a movie or animated by tools like

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

"dump image"_dump_image.html doc page for more details.  E.g. this
@@ -136,5 +136,5 @@ The USER directory has a large number of sub-directories which 
correspond by name to a USER package.  They contain scripts that

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

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.

doc/src/Section_packages.txt

+54 −55
Original line number Diff line number Diff line
@@ -71,16 +71,16 @@ Package, Description, Author(s), Doc page, Example, Library 
"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, -

"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, -

"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, -

"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

"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, -

"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, -

"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
@@ -127,7 +127,6 @@ of the LAMMPS distribution. See the lib/package/README file for info 
on how to build the library.  If it is not listed as lib/package, then

it is a third-party library not included in the LAMMPS distribution.

See details on all of this below for individual packages.

p.s.: are we ever going to get commit messages from you? ;-)



:line
@@ -150,7 +149,7 @@ make 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

resquared"_pair_resquared.html,

"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf,
@@ -279,9 +278,8 @@ Contents: Compute and pair styles that implement the adiabatic 
core/shell model for polarizability.  The compute temp/cs command

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

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

core/shell capabilities.  See "Section howto

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

package.

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

for an overview of how to use the package.



To install via make or Make.py:
@@ -297,8 +295,8 @@ make machine :pre 


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



Supporting info: "Section howto

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

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

"compute temp/cs"_compute_temp_cs.html,

"pair_style born/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
@@ -335,7 +333,7 @@ GPU package :link(GPU),h5 


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

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,

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

also has GPU-enabled styles.
@@ -380,10 +378,11 @@ make machine :pre 


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



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

acclerate"_Section_accelerate.html, "Section accelerate

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

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

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

"Section 5.3"_Section_accelerate.html#acc_3,

"Section 5.3.1"_accelerate_gpu.html,

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,

examples/accelerate, bench/FERMI, bench/KEPLER
@@ -409,7 +408,7 @@ make 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

gran/hooke"_pair_gran.html, "pair_style

gran/hertz/history"_pair_gran.html, examples/pour, bench/in.chute
@@ -453,7 +452,7 @@ Contents: Dozens of atom, pair, bond, angle, dihedral, improper styles 
which run with the Kokkos library to provide optimization for

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

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

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

which also provide optimizations for the same range of hardware.
@@ -473,9 +472,8 @@ the KOKKOS_ARCH setting in Makefile.kokkos_cuda), Or, as illustrated 
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

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

system, you will need to read the "Section accelerate

kokkos"_accelerate_kokkos.html doc page for details of what

Makefile.machine settings are needed.

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

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



To install via make or Make.py for each of 3 hardware options:
@@ -495,11 +493,11 @@ make machine :pre 


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



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

acclerate"_Section_accelerate.html, "Section accelerate

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

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

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

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

"Section 5.3"_Section_accelerate.html#acc_3,

"Section 5.3.3"_accelerate_kokkos.html,

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

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

examples/accelerate, bench/FERMI, bench/KEPLER



:line
@@ -514,7 +512,7 @@ particle-mesh (PPPM), and multilevel summation method (MSM) solvers. 
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

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

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

tool has an "-fft" option which can insert these settings into your
@@ -536,12 +534,13 @@ make machine :pre 
Make.py -p ^kspace -a machine :pre



Supporting info: "kspace_style"_kspace_style.html,

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

6.7"_Section_howto.html#howto_7, "Section howto

6.8"_Section_howto.html#howto_8, "Section howto

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

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

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

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

"Section 6.7"_Section_howto.html#howto_7,

"Section 6.8"_Section_howto.html#howto_8,

"Section 6.9"_Section_howto.html#howto_9,

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

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

examples/peptide, bench/in.rhodo



:line
@@ -568,7 +567,7 @@ Make.py -p ^manybody -a machine :pre 


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,

examples/nb3d, examples/vashishta
@@ -700,9 +699,9 @@ Supporting info:"atom_style"_atom_style.html, 
"dihedral_style"_dihedral_style.html,

"improper_style"_improper_style.html, "pair_style

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

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

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

bench/in.chain, bench/in.rhodo

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

"Section 6.3"_Section_howto.html#howto_3,

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



:line
@@ -738,7 +737,7 @@ OPT package :link(OPT),h5 
Contents: A handful of pair styles with an "opt" in their style name

which are optimized for improved CPU performance on single or multiple

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,

which also have styles optimized for CPU performance.
@@ -763,10 +762,10 @@ make machine :pre 


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



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

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

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

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

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

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

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

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



:line
@@ -845,14 +844,14 @@ PYTHON package :link(PYTHON),h5 


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

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

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

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

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.



Building with the PYTHON package assumes you have a Python shared

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

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

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

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

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
@@ -950,7 +949,7 @@ REPLICA package :link(REPLICA),h5 
Contents: A collection of multi-replica methods that are used by

invoking multiple instances (replicas) of LAMMPS

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

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

in the package are nudged elastic band (NEB), parallel replica
@@ -973,7 +972,7 @@ make 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,

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

examples/tad
@@ -1148,13 +1147,13 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library 
"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-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-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-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-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-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, -, -
@@ -1353,12 +1352,12 @@ USER-DRUDE package :link(USER-DRUDE),h5 


Contents: This package contains methods for simulating polarizable

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

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

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

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

temp/drude"_compute_temp_drude.html, "pair thole"_pair_thole.html,
@@ -1432,7 +1431,7 @@ USER-INTEL package :link(USER-INTEL),h5 
Contents: Dozens of pair, bond, angle, dihedral, and improper styles

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

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

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

the KOKKOS, OPT, and USER-OMP packages, which also have CPU and
@@ -1440,7 +1439,7 @@ Phi-enabled styles. 


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

him directly if you have questions.
@@ -1532,7 +1531,7 @@ More information about each feature can be found by reading its doc 
page in the LAMMPS doc directory.  The doc page which lists all LAMMPS

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,

compute, pair, etc sections.
@@ -1609,7 +1608,7 @@ styles, and fix styles. 
 

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

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

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