From 9cd043e6825b1630df16bcbced68858db63aedff Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 6 Nov 2015 15:51:31 +0000 Subject: [PATCH] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14239 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/doc2/Manual.html.html | 4 +- doc/doc2/Section_commands.html | 15 ++-- doc/doc2/compute.html | 1 + doc/doc2/compute_hexorder_atom.html | 115 ++++++++++++++++++++++++++++ doc/doc2/compute_rdf.html | 7 +- 5 files changed, 131 insertions(+), 11 deletions(-) create mode 100644 doc/doc2/compute_hexorder_atom.html diff --git a/doc/doc2/Manual.html.html b/doc/doc2/Manual.html.html index 457f0160c6..c4c0509ea7 100644 --- a/doc/doc2/Manual.html.html +++ b/doc/doc2/Manual.html.html @@ -3,7 +3,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation

-

26 Oct 2015 version +

31 Oct 2015 version

Version info:

diff --git a/doc/doc2/Section_commands.html b/doc/doc2/Section_commands.html index 4e3e097fb2..6254a22fec 100644 --- a/doc/doc2/Section_commands.html +++ b/doc/doc2/Section_commands.html @@ -460,13 +460,14 @@ KOKKOS, o = USER-OMP, t = OPT. cluster/atomcna/atomcomcom/chunkcontact/atomcoord/atom damage/atomdihedral/localdilatation/atomdisplace/atomerotate/asphereerotate/rigid erotate/sphereerotate/sphere/atomevent/displacegroup/groupgyrationgyration/chunk -heat/fluximproper/localinertia/chunkkeke/atomke/rigid -msdmsd/chunkmsd/nongaussomega/chunkpairpair/local -pe (c)pe/atomplasticity/atompressure (c)property/atomproperty/local -property/chunkrdfreducereduce/regionslicesna/atom -snad/atomsnav/atomstress/atomtemp (ck)temp/aspheretemp/com -temp/chunktemp/deformtemp/partial (c)temp/profiletemp/ramptemp/region -temp/spheretitorque/chunkvacfvcm/chunkvoronoi/atom +heat/fluxhexorder/atomimproper/localinertia/chunkkeke/atom +ke/rigidmsdmsd/chunkmsd/nongaussomega/chunkpair +pair/localpe (c)pe/atomplasticity/atompressure (c)property/atom +property/localproperty/chunkrdfreducereduce/regionslice +sna/atomsnad/atomsnav/atomstress/atomtemp (ck)temp/asphere +temp/comtemp/chunktemp/deformtemp/partial (c)temp/profiletemp/ramp +temp/regiontemp/spheretitorque/chunkvacfvcm/chunk +voronoi/atom

These are additional compute styles in USER packages, which can be diff --git a/doc/doc2/compute.html b/doc/doc2/compute.html index 56709a891b..fc5922bd60 100644 --- a/doc/doc2/compute.html +++ b/doc/doc2/compute.html @@ -202,6 +202,7 @@ page.

  • gyration - radius of gyration of group of atoms
  • gyration/chunk - radius of gyration for each chunk
  • heat/flux - heat flux through a group of atoms +
  • hexorder/atom - bond orientational order parameter q6
  • improper/local - angle of each improper
  • inertia/chunk - inertia tensor for each chunk
  • ke - translational kinetic energy diff --git a/doc/doc2/compute_hexorder_atom.html b/doc/doc2/compute_hexorder_atom.html new file mode 100644 index 0000000000..309a13fbbc --- /dev/null +++ b/doc/doc2/compute_hexorder_atom.html @@ -0,0 +1,115 @@ + +
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
    + + + + + + +
    + +

    compute hexorder/atom command +

    +

    Syntax: +

    +
    compute ID group-ID hexorder/atom keyword values ... 
+
    +
    • ID, group-ID are documented in compute command + +
    • hexorder/atom = style name of this compute command + +
    • zero or more keyword/value pairs may be appended + +
    • keyword = degree + +
        n value = degree of order parameter 
+
      + +
    +

    Examples: +

    +
    compute 1 all hexorder/atom 
+compute 1 all hexorder/atom n 4 
+
    +

    Description: +

    +

    Define a computation that calculates qn the bond-orientational +order parameter for each atom in a group. The hexatic (n = 6) order +parameter was introduced by Nelson and Halperin as a way to detect +hexagonal symmetry in two-dimensional systems. For each atom, qn +is a complex number (stored as two real numbers) defined as follows: +

    +
    +
    +

    where the sum is over the n nearest neighbors +of the central atom. The angle theta +is formed by the bond vector rij and the x axis. theta is calculated +only using the x and y components, whereas the distance from the +central atom is calculated using all three +x, y, and z components of the bond vector. +Neighbor atoms not in the group +are included in the order parameter of atoms in the group. +

    +

    The optional keyword n sets the degree of the order parameter. +The default value is 6. For a perfect hexagonal lattice, +q6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3 +depends only on the orientation of the lattice relative to the x axis. +In an isotropic liquid, local neighborhoods may still exhibit +weak hexagonal symmetry, but because the orientational correlation +decays quickly with distance, the value of phi will be different for +different atoms, and |<q6>| << 1. +

    +

    The value of qn will be zero for atoms not in the +specified compute group. If the atom has less than n neighbors (within +the potential cutoff), then qn is set to zero. +

    +

    The neighbor list needed to compute this quantity is constructed each +time the calculation is performed (i.e. each time a snapshot of atoms +is dumped). Thus it can be inefficient to compute/dump this quantity +too frequently. +

    +

    IMPORTANT NOTE: If you have a bonded system, then the settings of +special_bonds command can remove pairwise +interactions between atoms in the same bond, angle, or dihedral. This +is the default setting for the special_bonds +command, and means those pairwise interactions do not appear in the +neighbor list. Because this fix uses the neighbor list, it also means +those pairs will not be included in the order parameter. One way +to get around this, is to write a dump file, and use the +rerun command to compute the order parameter for snapshots +in the dump file. The rerun script can use a +special_bonds command that includes all pairs in +the neighbor list. +

    +

    Output info: +

    +

    This compute calculates a per-atom array with 2 columns, giving the +real and imaginary parts of qn, respectively. +

    +

    These values can be accessed by any command that uses +per-atom values from a compute as input. See Section_howto +15 for an overview of LAMMPS output +options. +

    +

    The per-atom array contain pairs of numbers representing the +real and imaginary parts of qn, a complex number subject to the +constraint |qn| <= 1. +

    +

    Restrictions: none +

    +

    Related commands: +

    +

    compute coord/atom, compute centro/atom +

    +

    Default: +

    +

    The option default is n = 6. +

    +
    + + + +

    (Nelson) Nelson, Halperin, Phys Rev B, 19, 2457 (1979). +

    + diff --git a/doc/doc2/compute_rdf.html b/doc/doc2/compute_rdf.html index 9d9ce71e6b..e711008099 100644 --- a/doc/doc2/compute_rdf.html +++ b/doc/doc2/compute_rdf.html @@ -139,13 +139,16 @@ also numbers >= 0.0. since processors (in parallel) don't know about atom coordinates for atoms further away than that distance. If you want an RDF for larger distances, you can use the rerun command to post-process -a dump file. The definition of g(r) used by LAMMPS is only appropriate +a dump file and set the cutoff for the potential to be longer in the +rerun script. Note that in the rerun context, the force cutoff is +arbitrary, since you aren't running dynamics and thus are not changing +your model. The definition of g(r) used by LAMMPS is only appropriate for characterizing atoms that are uniformly distributed throughout the simulation cell. In such cases, the coordination number is still correct and meaningful. As an example, if a large simulation cell contains only one atom of type itypeN and one of jtypeN, then g(r) will register an arbitrarily large spike at whatever distance they -happen to be at, and zero everywhere else. coord(r) will show a step +happen to be at, and zero everywhere else. Coord(r) will show a step change from zero to one at the location of the spike in g(r).

    Related commands: