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updated as requested by @sjplimp

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Axel Kohlmeyer
2020-07-06 11:45:16 -04:00
parent 022252dde0
commit 47d77530e2
1 changed files with 22 additions and 24 deletions
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doc/src/Howto_output.rst
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@ -43,7 +43,7 @@ to output and the kind of data they operate on and produce:
.. _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
@ -56,7 +56,7 @@ bond distances.
.. _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
@ -88,24 +88,22 @@ or array.
Disambiguation
--------------
Some computes and fixes produce multiple kinds of data, e.g. a global
scalar and a global vector, or a global scalar and a per-atom vector
(i.e. one value per atom). Usually the context in which those are used
determines which datum is accessed. Example: if a compute provides both
a global scalar and a per-atom vector, the former will be used when
using ``c_ID`` in an equal-style variable, while the latter will be
referenced as ``c_ID`` in an atom-style variable. While atom-style
variables are otherwise also able to access global scalars, access to
the global scalar of the compute is not directly possible in this case.
This is resolved through first defining an equal-style variable that
accesses the scalar property and then access that equal-style variable
in the atom-style variable, which then may then also access the per-atom
property.
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
@ -133,7 +131,7 @@ intensive result.
.. _dump:
Dump file output
---------------------------
----------------
Dump file output is specified by the :doc:`dump <dump>` and
:doc:`dump_modify <dump_modify>` commands. There are several
@ -159,7 +157,7 @@ command.
.. _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>`,
@ -213,7 +211,7 @@ from normal thermodynamic or dump file output.
.. _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,
@ -240,7 +238,7 @@ output commands.
.. _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
@ -265,7 +263,7 @@ The output of this fix can be used as input to other output commands.
.. _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
@ -278,7 +276,7 @@ without the word "atom" or "local" produce global values.
.. _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
@ -290,7 +288,7 @@ describes them.
.. _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
@ -305,7 +303,7 @@ commands described in this section.
.. _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