From a9ee5ac56a28de27d7dfc04fce30ff86e1c3e42f Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 25 Oct 2010 20:29:36 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5128 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/angle_coeff.html | 1 + doc/angle_coeff.txt | 1 + doc/angle_cosine_periodic.html | 70 ++++++++++++++++++++++++++++++++++ doc/angle_cosine_periodic.txt | 64 +++++++++++++++++++++++++++++++ doc/angle_style.html | 1 + doc/angle_style.txt | 1 + 6 files changed, 138 insertions(+) create mode 100644 doc/angle_cosine_periodic.html create mode 100644 doc/angle_cosine_periodic.txt diff --git a/doc/angle_coeff.html b/doc/angle_coeff.html index 71ec52e112..e7983c902f 100644 --- a/doc/angle_coeff.html +++ b/doc/angle_coeff.html @@ -69,6 +69,7 @@ specified by the associated angle_coeff command
  • angle_style class2 - COMPASS (class 2) angle
  • angle_style cosine - cosine angle potential
  • angle_style cosine/delta - difference of cosines angle potential +
  • angle_style cosine/periodic - DREIDING angle
  • angle_style cosine/squared - cosine squared angle potential
  • angle_style harmonic - harmonic angle
  • angle_style table - tabulated by angle diff --git a/doc/angle_coeff.txt b/doc/angle_coeff.txt index a164b6a661..b0ee2cf8d4 100644 --- a/doc/angle_coeff.txt +++ b/doc/angle_coeff.txt @@ -66,6 +66,7 @@ specified by the associated "angle_coeff"_angle_coeff.html command: "angle_style class2"_angle_class2.html - COMPASS (class 2) angle "angle_style cosine"_angle_cosine.html - cosine angle potential "angle_style cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential +"angle_style cosine/periodic"_angle_cosine_periodic.html - DREIDING angle "angle_style cosine/squared"_angle_cosine_squared.html - cosine squared angle potential "angle_style harmonic"_angle_harmonic.html - harmonic angle "angle_style table"_angle_table.html - tabulated by angle :ul diff --git a/doc/angle_cosine_periodic.html b/doc/angle_cosine_periodic.html new file mode 100644 index 0000000000..e8b3d464bf --- /dev/null +++ b/doc/angle_cosine_periodic.html @@ -0,0 +1,70 @@ + +
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
    + + + + + + +
    + +

    angle_style cosine/periodic command +

    +

    Syntax: +

    +
    angle_style cosine/periodic 
+
    +

    Examples: +

    +
    angle_style cosine/periodic
+angle_coeff * 75.0 1 6 
+
    +

    Description: +

    +

    The cosine/periodic angle style uses the following potential, which +is commonly used in the DREIDING force field, +particularly for organometallic systems where n = 4 might be used +for an octahedral complex and n = 3 might be used for a trigonal +center: +

    +
    +
    +

    where C, B and n are coefficients defined for each angle type. +

    +

    See (Mayo) for a description of the DREIDING force field +

    +

    The following coefficients must be defined for each angle type via the +angle_coeff command as in the example above, or in +the data file or restart files read by the read_data +or read_restart commands: +

    + +

    Note that the prefactor C is specified and not the overall force +constant K = C / n^2. When B = 1, it leads to a minimum for the +linear geometry. When B = -1, it leads to a maximum for the linear +geometry. +

    +

    Restrictions: +

    +

    This angle style can only be used if LAMMPS was built with the +"molecular" package (which it is by default). See the Making +LAMMPS section for more info on packages. +

    +

    Related commands: +

    +

    angle_coeff +

    +

    Default: none +

    +
    + + + +

    (Mayo) Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 +(1990). +

    + diff --git a/doc/angle_cosine_periodic.txt b/doc/angle_cosine_periodic.txt new file mode 100644 index 0000000000..63a8fc52cd --- /dev/null +++ b/doc/angle_cosine_periodic.txt @@ -0,0 +1,64 @@ +"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 + +angle_style cosine/periodic command :h3 + +[Syntax:] + +angle_style cosine/periodic :pre + +[Examples:] + +angle_style cosine/periodic +angle_coeff * 75.0 1 6 :pre + +[Description:] + +The {cosine/periodic} angle style uses the following potential, which +is commonly used in the "DREIDING"_Section_howto.html#4_4 force field, +particularly for organometallic systems where {n} = 4 might be used +for an octahedral complex and {n} = 3 might be used for a trigonal +center: + +:c,image(Eqs/angle_cosine_periodic.jpg) + +where C, B and n are coefficients defined for each angle type. + +See "(Mayo)"_#Mayo for a description of the DREIDING force field + +The following coefficients must be defined for each angle type via the +"angle_coeff"_angle_coeff.html command as in the example above, or in +the data file or restart files read by the "read_data"_read_data.html +or "read_restart"_read_restart.html commands: + +C (energy) +B = 1 or -1 +n = 1, 2, 3, 4, 5 or 6 for periodicity :ul + +Note that the prefactor C is specified and not the overall force +constant K = C / n^2. When B = 1, it leads to a minimum for the +linear geometry. When B = -1, it leads to a maximum for the linear +geometry. + +[Restrictions:] + +This angle style can only be used if LAMMPS was built with the +"molecular" package (which it is by default). See the "Making +LAMMPS"_Section_start.html#2_3 section for more info on packages. + +[Related commands:] + +"angle_coeff"_angle_coeff.html + +[Default:] none + +:line + +:link(Mayo) +[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 +(1990). diff --git a/doc/angle_style.html b/doc/angle_style.html index b1dce369e3..7ec349b11a 100644 --- a/doc/angle_style.html +++ b/doc/angle_style.html @@ -66,6 +66,7 @@ specified by the associated angle_coeff command
  • angle_style class2 - COMPASS (class 2) angle
  • angle_style cosine - cosine angle potential
  • angle_style cosine/delta - difference of cosines angle potential +
  • angle_style cosine/periodic - DREIDING angle
  • angle_style cosine/squared - cosine squared angle potential
  • angle_style harmonic - harmonic angle
  • angle_style table - tabulated by angle diff --git a/doc/angle_style.txt b/doc/angle_style.txt index 2e0e3a7304..aca79433e7 100644 --- a/doc/angle_style.txt +++ b/doc/angle_style.txt @@ -64,6 +64,7 @@ specified by the associated "angle_coeff"_angle_coeff.html command: "angle_style class2"_angle_class2.html - COMPASS (class 2) angle "angle_style cosine"_angle_cosine.html - cosine angle potential "angle_style cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential +"angle_style cosine/periodic"_angle_cosine_periodic.html - DREIDING angle "angle_style cosine/squared"_angle_cosine_squared.html - cosine squared angle potential "angle_style harmonic"_angle_harmonic.html - harmonic angle "angle_style table"_angle_table.html - tabulated by angle :ul