diff --git a/doc/Manual.html b/doc/Manual.html index c9b671d11a..149dcb1aa6 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -1,478 +1,456 @@ - - - -LAMMPS Users Manual - - - - - - - - - -
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
+ + + + + + + + + LAMMPS Documentation — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+ + + - - -
- -

- -

LAMMPS Documentation -

-

31 Oct 2015 version -

-

Version info: -

-

The LAMMPS "version" is the date when it was released, such as 1 May + +

+
+
+ +
+ + + +
+
+
+ +

+

LAMMPS Documentation

+
+

10 Aug 2015 version

+
+
+

Version info:

+

The LAMMPS “version” is the date when it was released, such as 1 May 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a -feature, we release it immediately, and post a notice on this page of -the WWW site. Each dated copy of LAMMPS contains all the +feature, we release it immediately, and post a notice on this page of the WWW site. Each dated copy of LAMMPS contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run LAMMPS. It is also in the file src/version.h and in the LAMMPS directory name created when you unpack a tarball, and at the top of -the first page of the manual (this page). -

-
  • If you browse the HTML doc pages on the LAMMPS WWW site, they always -describe the most current version of LAMMPS. - -
  • If you browse the HTML doc pages included in your tarball, they -describe the version you have. - -
  • The PDF file on the WWW site or in the tarball is updated -about once per month. This is because it is large, and we don't want -it to be part of every patch. - -
  • There is also a Developer.pdf file in the doc +the first page of the manual (this page).

    +
      +
    • If you browse the HTML doc pages on the LAMMPS WWW site, they always +describe the most current version of LAMMPS.
      • +
    • If you browse the HTML doc pages included in your tarball, they +describe the version you have.
      • +
    • The PDF file on the WWW site or in the tarball is updated +about once per month. This is because it is large, and we don’t want +it to be part of every patch.
      • +
    • There is also a Developer.pdf file in the doc directory, which describes the internal structure and algorithms of -LAMMPS. -
    -

    LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel -Simulator. -

    -

    LAMMPS is a classical molecular dynamics simulation code designed to +LAMMPS.

    • +
+

LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel +Simulator.

+

LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely -under the terms of the GNU Public License (GPL). -

-

The primary developers of LAMMPS are Steve Plimpton, Aidan +under the terms of the GNU Public License (GPL).

+

The primary developers of LAMMPS are Steve Plimpton, Aidan Thompson, and Paul Crozier who can be contacted at -sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at -http://lammps.sandia.gov has more information about the code and its -uses. -

- - - - -
- -

The LAMMPS documentation is organized into the following sections. If +sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at +http://lammps.sandia.gov has more information about the code and its +uses.

+
+

The LAMMPS documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for useful information to add, please send an email to the developers so -we can improve the LAMMPS documentation. -

-

Once you are familiar with LAMMPS, you may want to bookmark this -page at Section_commands.html#comm since -it gives quick access to documentation for all LAMMPS commands. -

-

PDF file of the entire manual, generated by -htmldoc -

-

-

-
  1. -Introduction - - -
  2. Getting started - - -
  3. Commands - - -
  4. Packages - - -
  5. Accelerating LAMMPS performance - - -
  6. How-to discussions - - -
  7. Example problems - -
  8. Performance & scalability - -
  9. Additional tools - -
  10. Modifying & extending LAMMPS - - -
  11. Python interface - - -
  12. Errors - - -
  13. Future and history - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +we can improve the LAMMPS documentation.

+

Once you are familiar with LAMMPS, you may want to bookmark this page at Section_commands.html#comm since +it gives quick access to documentation for all LAMMPS commands.

+

PDF file of the entire manual, generated by +htmldoc

+
+ +
+
+
+
+

Indices and tables

+ +
+ + +
+
+ + +
+
+ +
+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/Manual.html.html b/doc/Manual.html.html index 457f0160c6..c4c0509ea7 100644 --- a/doc/Manual.html.html +++ b/doc/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/Manual.txt b/doc/Manual.txt index 5e6d3c285e..b0857e6c32 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation :c,h3 -31 Oct 2015 version :c,h4 +10 Aug 2015 version :c,h4 Version info: :h4 @@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands. .. toctree:: :maxdepth: 2 - :numbered: // comment + :numbered: Section_intro Section_start @@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands. Indices and tables ================== -* :ref:`genindex` // comment -* :ref:`search` // comment +* :ref:`genindex` +* :ref:`search` END_RST --> diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 8922902e94..dd77321061 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -838,9 +838,9 @@ KOKKOS, o = USER-OMP, t = OPT.

- - - + + + @@ -873,53 +873,60 @@ KOKKOS, o = USER-OMP, t = OPT.

gyration/chunk heat/flux +hexorder/atom improper/local inertia/chunk ke ke/atom -ke/rigid -msd +ke/rigid +msd msd/chunk msd/nongauss omega/chunk pair -pair/local -pe (c) +pair/local +pe (c) pe/atom plasticity/atom pressure (c) property/atom -property/local -property/chunk +property/local +property/chunk rdf reduce reduce/region slice -sna/atom -snad/atom +sna/atom +snad/atom snav/atom stress/atom temp (ck) temp/asphere -temp/com -temp/chunk +temp/com +temp/chunk temp/deform temp/partial (c) temp/profile temp/ramp -temp/region -temp/sphere +temp/region +temp/sphere ti torque/chunk vacf vcm/chunk -voronoi/atom + +voronoi/atom +  +  +  +  +  diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 6bbf013242..a31700043a 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -684,6 +684,7 @@ KOKKOS, o = USER-OMP, t = OPT. "gyration"_compute_gyration.html, "gyration/chunk"_compute_gyration_chunk.html, "heat/flux"_compute_heat_flux.html, +"hexorder/atom"_compute_hexorder_atom.html, "improper/local"_compute_improper_local.html, "inertia/chunk"_compute_inertia_chunk.html, "ke"_compute_ke.html, diff --git a/doc/compute.html b/doc/compute.html index b87801eec7..174e3a52e8 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -301,6 +301,7 @@ are given in the compute section of 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/compute.txt b/doc/compute.txt index 279ea046fb..90ff94e32a 100644 --- a/doc/compute.txt +++ b/doc/compute.txt @@ -197,6 +197,7 @@ page"_Section_commands.html#cmd_5. "gyration"_compute_gyration.html - radius of gyration of group of atoms "gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms +"hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6 "improper/local"_compute_improper_local.html - angle of each improper "inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk "ke"_compute_ke.html - translational kinetic energy diff --git a/doc/compute_hexorder_atom.html b/doc/compute_hexorder_atom.html new file mode 100644 index 0000000000..0b5d907723 --- /dev/null +++ b/doc/compute_hexorder_atom.html @@ -0,0 +1,286 @@ + + + + + + + + + + + compute hexorder/atom command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
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    +
    + +
    +

    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:

    +_images/hexorder.jpg +

    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, +*q*6 = 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 |<*q*6>| << 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.

    +
    +

    Warning

    +

    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
    +
    + +
    +

    Default

    +

    The option default is n = 6.

    +
    +

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

    +
    +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_rdf.html b/doc/compute_rdf.html index a2513f5403..ff301ee65a 100644 --- a/doc/compute_rdf.html +++ b/doc/compute_rdf.html @@ -251,13 +251,16 @@ 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).