Merge pull request #1028 from lammps/doc-reorg-intro-howto

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How to discussions :h2

These doc pages describe how to perform various tasks with LAMMPS,

both for users and developers.  The

"glossary"_http://lammps.sandia.gov website page also lists MD

terminology with links to corresponding LAMMPS manual pages.

The example input scripts included in the examples dir of the LAMMPS

distribution and highlighted on the "Examples"_Examples.html doc page

also show how to setup and run various kinds of simulations.

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.. toctree::

   Howto_github

   Howto_pylammps

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.. toctree::

   Howto_restart

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   Howto_output

   Howto_chunk

.. toctree::

   Howto_2d

   Howto_triclinic

   Howto_walls

   Howto_nemd

   Howto_granular

   Howto_spherical

   Howto_dispersion

.. toctree::

   Howto_temperature

   Howto_thermostat

   Howto_barostat

   Howto_elastic

   Howto_kappa

   Howto_viscosity

   Howto_diffusion

.. toctree::

   Howto_bioFF

   Howto_tip3p

   Howto_tip4p

   Howto_spc

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   Howto_body

   Howto_polarizable

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   Howto_drude

   Howto_drude2

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<!-- HTML_ONLY -->

"Using GitHub with LAMMPS"_Howto_github.html

"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html

"Using LAMMPS with bash on Windows"_Howto_bash.html

"Restart a simulation"_Howto_restart.html

"Visualize LAMMPS snapshots"_Howto_viz.html

"Run multiple simulations from one input script"_Howto_multiple.html

"Multi-replica simulations"_Howto_replica.html

"Library interface to LAMMPS"_Howto_library.html

"Couple LAMMPS to other codes"_Howto_couple.html :all(b)

"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html

"Use chunks to calculate system properties"_Howto_chunk.html :all(b)

"2d simulations"_Howto_2d.html

"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html

"Walls"_Howto_walls.html

"NEMD simulations"_Howto_nemd.html

"Granular models"_Howto_granular.html

"Finite-size spherical and aspherical particles"_Howto_spherical.html

"Long-range dispersion settings"_Howto_dispersion.html :all(b)

"Calculate temperature"_Howto_temperature.html

"Thermostats"_Howto_thermostat.html

"Barostats"_Howto_barostat.html

"Calculate elastic constants"_Howto_elastic.html

"Calculate thermal conductivity"_Howto_kappa.html

"Calculate viscosity"_Howto_viscosity.html

"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)

"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html

"TIP3P water model"_Howto_tip3p.html

"TIP4P water model"_Howto_tip4p.html

"SPC water model"_Howto_spc.html :all(b)

"Body style particles"_Howto_body.html

"Polarizable models"_Howto_polarizable.html

"Adiabatic core/shell model"_Howto_coreshell.html

"Drude induced dipoles"_Howto_drude.html

"Drude induced dipoles (extended)"_Howto_drude2.html :all(b)

"Manifolds (surfaces)"_Howto_manifold.html

"Magnetic spins"_Howto_spins.html

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"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS

Documentation"_ld - "LAMMPS Commands"_lc :c

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:link(lc,Section_commands.html#comm)

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2d simulations :h3

Use the "dimension"_dimension.html command to specify a 2d simulation.

Make the simulation box periodic in z via the "boundary"_boundary.html

command.  This is the default.

If using the "create box"_create_box.html command to define a

simulation box, set the z dimensions narrow, but finite, so that the

create_atoms command will tile the 3d simulation box with a single z

plane of atoms - e.g.

"create box"_create_box.html 1 -10 10 -10 10 -0.25 0.25 :pre

If using the "read data"_read_data.html command to read in a file of

atom coordinates, set the "zlo zhi" values to be finite but narrow,

similar to the create_box command settings just described.  For each

atom in the file, assign a z coordinate so it falls inside the

z-boundaries of the box - e.g. 0.0.

Use the "fix enforce2d"_fix_enforce2d.html command as the last

defined fix to insure that the z-components of velocities and forces

are zeroed out every timestep.  The reason to make it the last fix is

so that any forces induced by other fixes will be zeroed out.

Many of the example input scripts included in the LAMMPS distribution

are for 2d models.

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

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.

"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS

Documentation"_ld - "LAMMPS Commands"_lc :c

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:link(lc,Section_commands.html#comm)

:line

Barostats :h3

Barostatting means controlling the pressure in an MD simulation.

"Thermostatting"_Howto_thermostat.html means controlling the

temperature of the particles.  Since the pressure includes a kinetic

component due to particle velocities, both these operations require

calculation of the temperature.  Typically a target temperature (T)

and/or pressure (P) is specified by the user, and the thermostat or

barostat attempts to equilibrate the system to the requested T and/or

P.

Barostatting in LAMMPS is performed by "fixes"_fix.html.  Two

barosttating methods are currently available: Nose-Hoover (npt and

nph) and Berendsen:

"fix npt"_fix_nh.html

"fix npt/sphere"_fix_npt_sphere.html

"fix npt/asphere"_fix_npt_asphere.html

"fix nph"_fix_nh.html

"fix press/berendsen"_fix_press_berendsen.html :ul

The "fix npt"_fix_nh.html commands include a Nose-Hoover thermostat

and barostat.  "Fix nph"_fix_nh.html is just a Nose/Hoover barostat;

it does no thermostatting.  Both "fix nph"_fix_nh.html and "fix

press/berendsen"_fix_press_berendsen.html can be used in conjunction

with any of the thermostatting fixes.

As with the "thermostats"_Howto_thermostat.html, "fix npt"_fix_nh.html

and "fix nph"_fix_nh.html only use translational motion of the

particles in computing T and P and performing thermo/barostatting.

"Fix npt/sphere"_fix_npt_sphere.html and "fix

npt/asphere"_fix_npt_asphere.html thermo/barostat using not only

translation velocities but also rotational velocities for spherical

and aspherical particles.

All of the barostatting fixes use the "compute

pressure"_compute_pressure.html compute to calculate a current

pressure.  By default, this compute is created with a simple "compute

temp"_compute_temp.html (see the last argument of the "compute

pressure"_compute_pressure.html command), which is used to calculated

the kinetic component of the pressure.  The barostatting fixes can

also use temperature computes that remove bias for the purpose of

computing the kinetic component which contributes to the current

pressure.  See the doc pages for the individual fixes and for the

"fix_modify"_fix_modify.html command for instructions on how to assign

a temperature or pressure compute to a barostatting fix.

NOTE: As with the thermostats, the Nose/Hoover methods ("fix

npt"_fix_nh.html and "fix nph"_fix_nh.html) perform time integration.

"Fix press/berendsen"_fix_press_berendsen.html does NOT, so it should

be used with one of the constant NVE fixes or with one of the NVT

fixes.

Thermodynamic output, which can be setup via the

"thermo_style"_thermo_style.html command, often includes pressure

values.  As explained on the doc page for the

"thermo_style"_thermo_style.html command, the default pressure is

setup by the thermo command itself.  It is NOT the presure associated

with any barostatting fix you have defined or with any compute you

have defined that calculates a presure.  The doc pages for the

barostatting fixes explain the ID of the pressure compute they create.

Thus if you want to view these pressurse, you need to specify them

explicitly via the "thermo_style custom"_thermo_style.html command.

Or you can use the "thermo_modify"_thermo_modify.html command to

re-define what pressure compute is used for default thermodynamic

output.