From a9318bc28e382ee433b42921c97fbefbc22165e8 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 22 Jun 2009 21:17:38 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2887 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 8 ++--- doc/Section_commands.txt | 1 + doc/fix.html | 2 +- doc/fix.txt | 1 + doc/fix_reax_bonds.html | 64 +++++++++++++++++++++++++++++++++++++++ doc/fix_reax_bonds.txt | 59 ++++++++++++++++++++++++++++++++++++ 6 files changed, 130 insertions(+), 5 deletions(-) create mode 100644 doc/fix_reax_bonds.html create mode 100644 doc/fix_reax_bonds.txt diff --git a/doc/Section_commands.html b/doc/Section_commands.html index f57d6f83c2..b553dd271c 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -322,10 +322,10 @@ of each style or click on the style itself for a full description: enforce2devaporatefreezegravitygyrationheatindentlangevin lineforcemsdmomentumnphnptnpt/aspherenpt/spherenve nve/aspherenve/limitnve/noforcenve/spherenvtnvt/aspherenvt/sllodnvt/sphere -orient/fccplaneforcepoemspourpress/berendsenprintrdfrecenter -rigidsetforceshakespringspring/rgspring/selftemp/berendsentemp/rescale -thermal/conductivitytmdttmviscosityviscouswall/granwall/lj126wall/lj93 -wall/reflectwiggle +orient/fccplaneforcepoemspourpress/berendsenprintrdfreax/bonds +recenterrigidsetforceshakespringspring/rgspring/selftemp/berendsen +temp/rescalethermal/conductivitytmdttmviscosityviscouswall/granwall/lj126 +wall/lj93wall/reflectwiggle

These are fix styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index e9a007064d..ef0ad89c7d 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -422,6 +422,7 @@ of each style or click on the style itself for a full description: "press/berendsen"_fix_press_berendsen.html, "print"_fix_print.html, "rdf"_fix_rdf.html, +"reax/bonds"_fix_reax_bonds.html, "recenter"_fix_recenter.html, "rigid"_fix_rigid.html, "setforce"_fix_setforce.html, diff --git a/doc/fix.html b/doc/fix.html index df432e4ce0..5772869ebd 100644 --- a/doc/fix.html +++ b/doc/fix.html @@ -150,7 +150,7 @@ list of fix styles available in LAMMPS:

  • press/berendsen - pressure control by Berendsen barostat
  • print - print text and variables during a simulation
  • rdf - compute radial distribution functions -
  • recenter - constrain the center-of-mass position of a group of atoms +
  • reax/bonds - write out ReaxFF bond information recenter - constrain the center-of-mass position of a group of atoms
  • rigid - constrain one or more clusters of atoms to move as a rigid body
  • setforce - set the force on each atom
  • shake - SHAKE constraints on bonds and/or angles diff --git a/doc/fix.txt b/doc/fix.txt index 8321fedcfe..8edef30c98 100644 --- a/doc/fix.txt +++ b/doc/fix.txt @@ -151,6 +151,7 @@ list of fix styles available in LAMMPS: Berendsen barostat "print"_fix_print.html - print text and variables during a simulation "rdf"_fix_rdf.html - compute radial distribution functions +"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information \ "recenter"_fix_recenter.html - constrain the center-of-mass position \ of a group of atoms "rigid"_fix_rigid.html - constrain one or more clusters of atoms to \ diff --git a/doc/fix_reax_bonds.html b/doc/fix_reax_bonds.html new file mode 100644 index 0000000000..aa60548fa8 --- /dev/null +++ b/doc/fix_reax_bonds.html @@ -0,0 +1,64 @@ + +
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
    + + + + + + +
    + +

    fix reax/bonds command +

    +

    Syntax: +

    +
    fix ID group-ID reax/bonds Nevery filename 
+
    + +

    Examples: +

    +

    fix 1 all reax/bonds 100 bonds.tatb +

    +

    Description: +

    +

    Write out the bond information computed by the ReaxFF potential +specified by pair_style reax. The bond information +is written to filename on timesteps that are multiples of Nevery, +including timestep 0. +

    +

    The format of the output file should be self-explantory. +

    +
    + +

    Restart, fix_modify, output, run start/stop, minimize info: +

    +

    No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various output +commands. No parameter of this fix can be +used with the start/stop keywords of the run command. +This fix is not invoked during energy minimization. +

    +

    Restrictions: +

    +

    This fix requires that the pair_style reax be +invoked. This fix is part of the "reax" package. It is only enabled +if LAMMPS was built with that package, which also requires the REAX +library be built and linked with LAMMPS. See the Making +LAMMPS section for more info. +

    +

    Related commands: +

    +

    pair_style reax +

    +

    Default: +

    +

    none +

    + diff --git a/doc/fix_reax_bonds.txt b/doc/fix_reax_bonds.txt new file mode 100644 index 0000000000..5e59485444 --- /dev/null +++ b/doc/fix_reax_bonds.txt @@ -0,0 +1,59 @@ +"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 + +fix reax/bonds command :h3 + +[Syntax:] + +fix ID group-ID reax/bonds Nevery filename :pre + +ID, group-ID are documented in "fix"_fix.html command +reax/bonds = style name of this fix command +Nevery = output interval in timesteps +filename = name of output file :ul + +[Examples:] + +fix 1 all reax/bonds 100 bonds.tatb + +[Description:] + +Write out the bond information computed by the ReaxFF potential +specified by "pair_style reax"_pair_reax.html. The bond information +is written to {filename} on timesteps that are multiples of {Nevery}, +including timestep 0. + +The format of the output file should be self-explantory. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. + +[Restrictions:] + +This fix requires that the "pair_style reax"_pair_reax.html be +invoked. This fix is part of the "reax" package. It is only enabled +if LAMMPS was built with that package, which also requires the REAX +library be built and linked with LAMMPS. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. + +[Related commands:] + +"pair_style reax"_pair_reax.html + +[Default:] + +none