Merge pull request #620 from amilumas/master

"dump vtk"_dump_vtk.html,

"group2ndx"_group2ndx.html,

"ndx2group"_group2ndx.html,

"temper/grem"_temper_grem.html :tb(c=3,ea=c)

"temper/grem"_temper_grem.html

"temper/npt"_temper_npt.html :tb(c=3,ea=c)

:line

   tad

   temper

   temper_grem

   temper_npt

   thermo

   thermo_modify

   thermo_style

tad.html

temper.html

temper_grem.html

temper_npt.html

thermo.html

thermo_modify.html

thermo_style.html

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Section_commands.html#comm)

:line

temper/npt command :h3

[Syntax:]

temper/npt  N M temp fix-ID seed1 seed2 pressure index :pre

N = total # of timesteps to run

M = attempt a tempering swap every this many steps

temp = initial temperature for this ensemble

fix-ID = ID of the fix that will control temperature and pressure during the run

seed1 = random # seed used to decide on adjacent temperature to partner with

seed2 = random # seed for Boltzmann factor in Metropolis swap

pressure = setpoint pressure for the ensemble

index = which temperature (0 to N-1) I am simulating (optional) :ul

[Examples:]

temper/npt 100000 100 $t nptfix 0 58728 1

temper/npt 2500000 1000 300 nptfix  0 32285 $p 

temper/npt 5000000 2000 $t nptfix 0 12523 1 $w :pre

[Description:]

Run a parallel tempering or replica exchange simulation using multiple

replicas (ensembles) of a system in the isothermal-isobaric (NPT)

ensemble.  The command temper/npt works like "temper"_temper.html but

requires running replicas in the NPT ensemble instead of the canonical

(NVT) ensemble and allows for pressure to be set in the ensembles.

These multiple ensembles can run in parallel at different temperatures

or different pressures.  The acceptance criteria for temper/npt is

specific to the NPT ensemble and can be found in references

"(Okabe)"_#Okabe2 and "(Mori)"_#Mori2.

Apart from the difference in acceptance criteria and the specification

of pressure, this command works much like the "temper"_temper.html

command. See the documentation on "temper"_temper.html for information

on how the parallel tempering is handled in general.

:line 

[Restrictions:]

This command can only be used if LAMMPS was built with the USER-MISC

package.  See the "Making LAMMPS"_Section_start.html#start_3 section

for more info on packages.

This command should be used with a fix that maintains the

isothermal-isobaric (NPT) ensemble.

[Related commands:]

"temper"_temper.html, "variable"_variable.html, "fix_npt"_fix_nh.html

[Default:] none

:link(Okabe2)

[(Okabe)] T. Okabe, M. Kawata, Y. Okamoto, M. Masuhiro, Chem. Phys. Lett., 335, 435-439 (2001).

:link(Mori2)

[(Mori)] Y. Mori, Y. Okamoto, J. Phys. Soc. Jpn., 7, 074003 (2010).