changes for next patch, 2d disc options for spheres, fix external upgrade, bug...

are for 2d models.

NOTE: Some models in LAMMPS treat particles as finite-size spheres, as

opposed to point particles.  In 2d, the particles will still be

spheres, not disks, meaning their moment of inertia will be the same

as in 3d.

opposed to point particles.  See the "atom_style

sphere"_atom_style.html and "fix nve/sphere"_fix_nve_sphere.html

commands for details.  By default, for 2d simulations, such particles

will still be modeled as 3d spheres, not 2d discs (circles), meaning

their moment of inertia will be that of a sphere.  If you wish to

model them as 2d discs, see the "set density/disc"_set.html command

and the {disc} option for the "fix nve/sphere"_fix_nve_sphere.html,

"fix nvt/sphere"_fix_nvt_sphere.html, "fix

nph/sphere"_fix_nph_sphere.html, "fix npt/sphere"_fix_npt_sphere.html

commands.

:line

"neigh_modify"_neigh_modify.html exclude :ul

NOTE: By default, for 2d systems, granular particles are still modeled

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.

:line

6.7 TIP3P water model :link(howto_7),h4

cutoff.  The K values can be used if a flexible TIP3P model (without

fix shake) is desired.  If the LJ epsilon and sigma for HH and OH are

set to 0.0, it corresponds to the original 1983 TIP3P model

"(Jorgensen)"_#Jorgensen.

"(Jorgensen)"_#Jorgensen1.

O mass = 15.9994

H mass = 1.008

theta of HOH angle = 104.52 :all(b),p

These are the parameters to use for TIP3P with a long-range Coulombic

solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price for

solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price1 for

details:

O mass = 15.9994

These are the additional parameters (in real units) to set for O and H

atoms and the water molecule to run a rigid TIP4P model with a cutoff

"(Jorgensen)"_#Jorgensen.  Note that the OM distance is specified in

"(Jorgensen)"_#Jorgensen1.  Note that the OM distance is specified in

the "pair_style"_pair_style.html command, not as part of the pair

coefficients.

fully equilibrate the deformed cell before sampling the stress

tensor. Another approach is to sample the triclinic cell fluctuations

that occur in an NPT simulation. This method can also be slow to

converge and requires careful post-processing "(Shinoda)"_#Shinoda

converge and requires careful post-processing "(Shinoda)"_#Shinoda1

:line

[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909

(1990).

:link(Jorgensen)

:link(Jorgensen1)

[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem

Phys, 79, 926 (1983).

:link(Price)

:link(Price1)

[(Price)] Price and Brooks, J Chem Phys, 121, 10096 (2004).

:link(Shinoda)

:link(Shinoda1)

[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).

:link(MitchellFincham)

The source code for each of these codes is in the tools sub-directory

of the LAMMPS distribution.  There is a Makefile (which you may need

to edit for your platform) which will build several of the tools which

reside in that directory.  Some of them are larger packages in their

own sub-directories with their own Makefiles.

reside in that directory.  Most of them are larger packages in their

own sub-directories with their own Makefiles and/or README files.

"amber2lmp"_#amber

"binary2txt"_#binary

"ch2lmp"_#charmm

"chain"_#chain

"colvars"_#colvars

"createatoms"_#create

"createatoms"_#createtools

"drude"_#drude

"eam database"_#eamdb

"eam generate"_#eamgn

"eff"_#eff

"moltemplate"_#moltemplate

"msi2lmp"_#msi

"phonon"_#phonon

"polymer bonding"_#polybond

"polybond"_#polybond

"pymol_asphere"_#pymol

"python"_#pythontools

"reax"_#reax_tool

"restart2data"_#restart

"smd"_#smd

"vim"_#vim

"xmgrace"_#xmgrace

:line

drude tool :h4,link(drude)

The tools/drude directory contains a Python script called

polarizer.py which can add Drude oscillators to a LAMMPS

data file in the required format.

See the header of the polarizer.py file for details.

The tool is authored by Agilio Padua and Alain Dequidt: agilio.padua

at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr

:line

eam database tool :h4,link(eamdb)

The tools/eam_database directory contains a Fortran program that will

:line

polymer bonding tool :h4,link(polybond)

polybond tool :h4,link(polybond)

The polybond sub-directory contains a Python-based tool useful for

performing "programmable polymer bonding".  The Python file

:line

restart2data tool :h4,link(restart)

NOTE: This tool is now obsolete and is not included in the current

LAMMPS distribution.  This is because there is now a

"write_data"_write_data.html command, which can create a data file

from within an input script.  Running LAMMPS with the "-r"

"command-line switch"_Section_start.html#start_7 as follows:

lmp_g++ -r restartfile datafile

is the same as running a 2-line input script:

smd tool :h4,link(smd)

read_restart restartfile

write_data datafile

The smd sub-directory contains a C++ file dump2vtk_tris.cpp and

Makefile which can be compiled and used to convert triangle output

files created by the Smooth-Mach Dynamics (USER-SMD) package into a

VTK-compatible unstructured grid file.  It could then be read in and

visualized by VTK.

which will produce the same data file that the restart2data tool used

to create.

See the header of dump2vtk.cpp for more details.

IMPORTANT NOTE: LAMMPS' binary restart files are generally not portable

between platforms, compiler settings and LAMMPS versions. Changes in

the format itself are rare, but no effort is made to maintain backward

compatibility. Data files are mostly backward and forward portable,

if no features are used that exist in only one LAMMPS version.

This tool was written by the USER-SMD package author, Georg

Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics,

Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).

:line

The torque on the dipole can be obtained by differentiating the

potential using the 'chain rule' as in appendix C.3 of

"(Allen)"_#Allen:

"(Allen)"_#Allen1:

:c,image(Eqs/angle_dipole_torque.jpg)

[(Orsi)] Orsi & Essex, The ELBA force field for coarse-grain modeling of

lipid membranes, PloS ONE 6(12): e28637, 2011.

:link(Allen)

:link(Allen1)

[(Allen)] Allen & Tildesley, Computer Simulation of Liquids,

Clarendon Press, Oxford, 1987.

For the {sphere} style, the particles are spheres and each stores a

per-particle diameter and mass.  If the diameter > 0.0, the particle

is a finite-size sphere.  If the diameter = 0.0, it is a point

particle.

particle.  Note that by use of the {disc} keyword with the "fix

nve/sphere"_fix_nve_sphere.html, "fix nvt/sphere"_fix_nvt_sphere.html,

"fix nph/sphere"_fix_nph_sphere.html, "fix

npt/sphere"_fix_npt_sphere.html commands, spheres can be effectively

treated as 2d discs for a 2d simulation if desired.  See also the "set

density/disc"_set.html command.

For the {ellipsoid} style, the particles are ellipsoids and each

stores a flag which indicates whether it is a finite-size ellipsoid or

The {binning} styles perform a spatial binning of atoms, and assign an

atom the chunk ID corresponding to the bin number it is in.  {Nchunk}

is set to the number of bins, which can change if the simulation box

size changes.

size changes.  This also depends on the setting of the {units}

keyword; e.g. for {reduced} units the number of chunks may not change

even if the box size does.

The {bin/1d}, {bin/2d}, and {bin/3d} styles define bins as 1d layers

(slabs), 2d pencils, or 3d boxes.  The {dim}, {origin}, and {delta}