Merge pull request #744 from akohlmey/doc-update

HAS_VIRTUALENV = YES

endif

SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')

SOURCES=$(wildcard src/*.txt)

OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)

	@(\

		. $(VENV)/bin/activate ;\

		cp -r src/* $(RSTDIR)/ ;\

		sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\

		sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\

		echo "############################################" ;\

		doc_anchor_check src/*.txt ;\

		echo "############################################" ;\

	@(\

		. $(VENV)/bin/activate ;\

		cp -r src/* $(RSTDIR)/ ;\

		sphinx-build -j 8 -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\

		sphinx-build $(SPHINXEXTRA) -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\

		deactivate ;\

	)

	@mv  epub/LAMMPS.epub .

	@( \

		virtualenv -p $(PYTHON) $(VENV); \

		. $(VENV)/bin/activate; \

		pip install Sphinx==1.5.6; \

		pip install Sphinx; \

		pip install sphinxcontrib-images; \

		deactivate;\

	)

as 3d spheres, not 2d discs (circles), meaning their moment of inertia

will be the same as in 3d.  If you wish to model granular particles in

2d as 2d discs, see the note on this topic in "Section

6.2"_Section_howto.html#howto_2, where 2d simulations are disussed.

6.2"_Section_howto.html#howto_2, where 2d simulations are discussed.

:line

[Contents:]

Coarse-grained finite-size colloidal particles.  Pair stayle and fix

Coarse-grained finite-size colloidal particles.  Pair styles and fix

wall styles for colloidal interactions.  Includes the Fast Lubrication

Dynamics (FLD) method for hydrodynamic interactions, which is a

simplified approximation to Stokesian dynamics.

Note that 3 symbolic (soft) links, "includelink" and "liblink" and

"filelink", are created in lib/latte to point into the LATTE home dir.

When LAMMPS builds in src it will use these links.  You should 

also check that the Makefile.lammps file you create is apporpriate

also check that the Makefile.lammps file you create is appropriate

for the compiler you use on your system to build LATTE.

You can then install/un-install the package and build LAMMPS in the

[Contents:]

A "fix mscg"_fix_mscg.html command which can parameterize a

Mulit-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG

Multi-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG

library"_mscg_home.

:link(mscg_home,https://github.com/uchicago-voth/MSCG-release)

crystalline materials.  It includes many pair styles specific to these

systems, including for reactive DPD, where each particle has internal

state for multiple species and a coupled set of chemical reaction ODEs

are integrated each timestep.  Highly accurate time intergrators for

are integrated each timestep.  Highly accurate time integrators for

isothermal, isoenergetic, isobaric and isenthalpic conditions are

included.  These enable long timesteps via the Shardlow splitting

algorithm.

method.  Specifically, energy-conserving DPD (eDPD) that can model

non-isothermal processes, many-body DPD (mDPD) for simulating

vapor-liquid coexistence, and transport DPD (tDPD) for modeling

advection-diffuion-reaction systems. The equations of motion of these

advection-diffusion-reaction systems. The equations of motion of these

DPD extensions are integrated through a modified velocity-Verlet (MVV)

algorithm.

NOTE: The LAMMPS executable these steps produce is not yet functional

for a QM/MM simulation.  You must also build Quantum ESPRESSO and

create a new executable which links LAMMPS and Quanutm ESPRESSO

create a new executable which links LAMMPS and Quantum ESPRESSO

together.  These are steps 3 and 4 described in the lib/qmmm/README

file.

:link(quip,https://github.com/libAtoms/QUIP)

To use this package you must have the QUIP libAatoms library available

To use this package you must have the QUIP libAtoms library available

on your system.

[Author:] Albert Bartok (Cambridge University)

A "dump vtk"_dump_vtk.html command which outputs snapshot info in the

"VTK format"_vtk, enabling visualization by "Paraview"_paraview or

other visuzlization packages.

other visualization packages.

:link(vtk,http://www.vtk.org)

:link(paraview,http://www.paraview.org)

Read this first :h5,link(start_2_1)

If you want to avoid building LAMMPS yourself, read the preceeding

If you want to avoid building LAMMPS yourself, read the preceding

section about options available for downloading and installing

executables.  Details are discussed on the "download"_download page.

clean options).

The LMP_INC variable is used to include options that turn on ifdefs

within the LAMMPS code.  The options that are currently recogized are:

within the LAMMPS code.  The options that are currently recognized are:

-DLAMMPS_GZIP

-DLAMMPS_JPEG

usual place (under /usr/local), you also may not need to specify these

3 variables, assuming /usr/local is in your path.  On some large

parallel machines which use "modules" for their compile/link

environements, you may simply need to include the correct module in

environments, you may simply need to include the correct module in

your build environment, before building LAMMPS.  Or the parallel

machine may have a vendor-provided MPI which the compiler has no

trouble finding.

You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,

so the compiler and linker can find the needed FFT header and library

files.  Note that on some large parallel machines which use "modules"

for their compile/link environements, you may simply need to include

for their compile/link environments, you may simply need to include

the correct module in your build environment.  Or the parallel machine

may have a vendor-provided FFT library which the compiler has no

trouble finding.  See the src/MAKE/OPTIONS/Makefile.fftw file for an

The FFT_INC variable also allows for a -DFFT_SINGLE setting that will

use single-precision FFTs with PPPM, which can speed-up long-range

calulations, particularly in parallel or on GPUs.  Fourier transform

calculations, particularly in parallel or on GPUs.  Fourier transform

and related PPPM operations are somewhat insensitive to floating point

truncation errors and thus do not always need to be performed in

double precision.  Using the -DFFT_SINGLE setting trades off a little

also need to include -lfftw3f with the FFT_LIB setting, in addition to

-lfftw3.  For FFTW2, you also need to specify -DFFT_SIZE with the

FFT_INC setting and -lsfftw with the FFT_LIB setting (in place of

-lfftw).  Similarly, if FFTW2 has been preinstalled with an explicit

-lfftw).  Similarly, if FFTW2 has been pre-installed with an explicit

double-precision library (libdfftw.a and not the default libfftw.a),

then you can specify -DFFT_SIZE (and not -DFFT_SINGLE), and specify

-ldfftw to use double-precision FFTs.

If you use a command in a LAMMPS input script that is part of a

package, you must have built LAMMPS with that package, else you will

get an error that the style is invalid or the command is unknown.

Every command's doc page specfies if it is part of a package.  You can

Every command's doc page specifies if it is part of a package.  You can

type

lmp_machine -h :pre

[External libraries:]

Packages in the tables "Section 4"_Section_packages.html with an "ext"

in the last column link to exernal libraries whose source code is not

in the last column link to external libraries whose source code is not

included with LAMMPS.  You must first download and install the library

before building LAMMPS with that package installed.  E.g. the voronoi

package links to the freely available "Voro++ library"_voro_home2.  You

Obj_shared_foo.  This is so that each file can be compiled with the

-fPIC flag which is required for inclusion in a shared library.  The

build will create the file liblammps_foo.so which another application

can link to dyamically.  It will also create a soft link liblammps.so,

can link to dynamically.  It will also create a soft link liblammps.so,

which will point to the most recently built shared library.  This is

the file the Python wrapper loads by default.

numa Nm :pre

This option is only relevant when using pthreads with hwloc support.

In this case Nm defines the number of NUMA regions (typicaly sockets)

on a node which will be utilizied by a single MPI rank.  By default Nm

In this case Nm defines the number of NUMA regions (typically sockets)

on a node which will be utilized by a single MPI rank.  By default Nm

= 1.  If this option is used the total number of worker-threads per

MPI rank is threads*numa.  Currently it is always almost better to

assign at least one MPI rank per NUMA region, and leave numa set to

installed on a machine (e.g. your desktop), you can run on more

(virtual) processors than you have physical processors.

To run multiple independent simulatoins from one input script, using

To run multiple independent simulations from one input script, using

multiple partitions, see "Section 6.4"_Section_howto.html#howto_4

of the manual.  World- and universe-style "variables"_variable.html

are useful in this context.

is the total wall time for the section.  The {Performance} line is

provided for convenience to help predicting the number of loop

continuations required and for comparing performance with other,

similar MD codes.  The {CPU use} line provides the CPU utilzation per

similar MD codes.  The {CPU use} line provides the CPU utilization per

MPI task; it should be close to 100% times the number of OpenMP

threads (or 1 of no OpenMP). Lower numbers correspond to delays due

to file I/O or insufficient thread utilization.

Neighbor lists can be created in a different order :ulb,l

Bins used for sorting atoms can be oriented differently :l

The default stencil order for PPPM is 7. By default, LAMMPS will

calculate other PPPM parameters to fit the desired acuracy with

calculate other PPPM parameters to fit the desired accuracy with

this order :l

The {newton} setting applies to all atoms, not just atoms shared

between MPI tasks :l