* :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)
@@ -41,7 +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
@@ -54,7 +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
@@ -81,10 +83,27 @@ the dimension twice (array -> scalar). Thus a command that uses
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
@@ -112,7 +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
@@ -138,7 +157,7 @@ command.
.. _fixoutput:
Fixes that write output files
---------------------------------------------
-----------------------------
Several fixes take various quantities as input and can write output
