Merge pull request #2212 from akohlmey/compute-chunk-scalar

There are four basic kinds of LAMMPS output:

* :doc:`Thermodynamic output <thermo_style>`, which is a list

  of quantities printed every few timesteps to the screen and logfile.

* :doc:`Thermodynamic output <thermo_style>`, which is a list of

  quantities printed every few timesteps to the screen and logfile.

* :doc:`Dump files <dump>`, which contain snapshots of atoms and various

  per-atom values and are written at a specified frequency.

* Certain fixes can output user-specified quantities to files: :doc:`fix ave/time <fix_ave_time>` for time averaging, :doc:`fix ave/chunk <fix_ave_chunk>` for spatial or other averaging, and :doc:`fix print <fix_print>` for single-line output of

  :doc:`variables <variable>`.  Fix print can also output to the

  screen.

* Certain fixes can output user-specified quantities to files:

  :doc:`fix ave/time <fix_ave_time>` for time averaging,

  :doc:`fix ave/chunk <fix_ave_chunk>` for spatial or other averaging, and

  :doc:`fix print <fix_print>` for single-line output of

  :doc:`variables <variable>`.  Fix print can also output to the screen.

* :doc:`Restart files <restart>`.

A simulation prints one set of thermodynamic output and (optionally)

.. _global:

Global/per-atom/local data

---------------------------------------

--------------------------

Various output-related commands work with three different styles of

data: global, per-atom, or local.  A global datum is one or more

.. _scalar:

Scalar/vector/array data

-------------------------------------

------------------------

Global, per-atom, and local datums can each come in three kinds: a

single scalar value, a vector of values, or a 2d array of values.  The

scalar values as input can typically also process elements of a vector

or array.

.. _disambiguation:

Disambiguation

--------------

Some computes and fixes produce data in multiple styles, e.g. a global

scalar and a per-atom vector. Usually the context in which the input

script references the data determines which style is meant. Example: if

a compute provides both a global scalar and a per-atom vector, the

former will be accessed by using ``c_ID`` in an equal-style variable,

while the latter will be accessed by using ``c_ID`` in an atom-style

variable.  Note that atom-style variable formulas can also access global

scalars, but in this case it is not possible to do directly because of

the ambiguity.  Instead, an equal-style variable can be defined which

accesses the global scalar, and that variable used in the atom-style

variable formula in place of ``c_ID``.

.. _thermo:

Thermodynamic output

---------------------------------

--------------------

The frequency and format of thermodynamic output is set by the

:doc:`thermo <thermo>`, :doc:`thermo_style <thermo_style>`, and

.. _dump:

Dump file output

---------------------------

----------------

Dump file output is specified by the :doc:`dump <dump>` and

:doc:`dump_modify <dump_modify>` commands.  There are several

.. _fixoutput:

Fixes that write output files

---------------------------------------------

-----------------------------

Several fixes take various quantities as input and can write output

files: :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/histo <fix_ave_histo>`,

.. _computeoutput:

Computes that process output quantities

-----------------------------------------------------------

---------------------------------------

The :doc:`compute reduce <compute_reduce>` and :doc:`compute reduce/region <compute_reduce>` commands take one or more per-atom

or local vector quantities as inputs and "reduce" them (sum, min, max,

.. _fixprocoutput:

Fixes that process output quantities

--------------------------------------------------------

------------------------------------

The :doc:`fix vector <fix_vector>` command can create global vectors as

output from global scalars as input, accumulating them one element at

.. _compute:

Computes that generate values to output

-----------------------------------------------------

---------------------------------------

Every :doc:`compute <compute>` in LAMMPS produces either global or

per-atom or local values.  The values can be scalars or vectors or

.. _fix:

Fixes that generate values to output

----------------------------------------------

------------------------------------

Some :doc:`fixes <fix>` in LAMMPS produces either global or per-atom or

local values which can be accessed by other commands.  The values can

.. _variable:

Variables that generate values to output

-------------------------------------------------------

----------------------------------------

:doc:`Variables <variable>` defined in an input script can store one or

more strings.  But equal-style, vector-style, and atom-style or

.. _table:

Summary table of output options and data flow between commands

--------------------------------------------------------------------------

--------------------------------------------------------------

This table summarizes the various commands that can be used for

generating output from LAMMPS.  Each command produces output data of

**Output info:**

This compute calculates a per-atom vector, which can be accessed by

any command that uses per-atom values from a compute as input.  See

the :doc:`Howto output <Howto_output>` doc page for an overview of

This compute calculates a per-atom vector (the chunk ID), which can

be accessed by any command that uses per-atom values from a compute

as input.  It also calculates a global scalar (the number of chunks),

which can be similarly accessed everywhere outside of a per-atom context.

See the :doc:`Howto output <Howto_output>` doc page for an overview of

LAMMPS output options.

The per-atom vector values are unitless chunk IDs, ranging from 1 to

*Nchunk* (inclusive) for atoms assigned to chunks, and 0 for atoms not

belonging to a chunk.

belonging to a chunk.  The scalar contains the value of *Nchunk*.

Restrictions

""""""""""""

  if (narg < 4) error->all(FLERR,"Illegal compute chunk/atom command");

  peratom_flag = 1;

  scalar_flag = 1;

  extscalar = 0;

  size_peratom_cols = 0;

  create_attribute = 1;

  for (int i = 0; i < nlocal; i++) chunk[i] = ichunk[i];

}

/* ----------------------------------------------------------------------

   to return the number of chunks, we first need to make certain

   that compute_peratom() has been called.

------------------------------------------------------------------------- */

double ComputeChunkAtom::compute_scalar()

{

  if (invoked_peratom != update->ntimestep)

    compute_peratom();

  invoked_scalar = update->ntimestep;

  return (scalar = nchunk);

}

/* ----------------------------------------------------------------------

   set lock, so that nchunk will not change from startstep to stopstep

   called by fix for duration of time it requires lock

  void init();

  void setup();

  void compute_peratom();

  double compute_scalar();

  void set_arrays(int);

  double memory_usage();