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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
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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:
Global/per-atom/local data Global/per-atom/local data
--------------------------------------- --------------------------
Various output-related commands work with three different styles of Various output-related commands work with three different styles of
data: global, per-atom, or local. A global datum is one or more data: global, per-atom, or local. A global datum is one or more
@ -56,7 +56,7 @@ bond distances.
.. _scalar: .. _scalar:
Scalar/vector/array data Scalar/vector/array data
------------------------------------- ------------------------
Global, per-atom, and local datums can each come in three kinds: a 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 single scalar value, a vector of values, or a 2d array of values. The
@ -88,24 +88,22 @@ or array.
Disambiguation Disambiguation
-------------- --------------
Some computes and fixes produce multiple kinds of data, e.g. a global Some computes and fixes produce data in multiple styles, e.g. a global
scalar and a global vector, or a global scalar and a per-atom vector scalar and a per-atom vector. Usually the context in which the input
(i.e. one value per atom). Usually the context in which those are used script references the data determines which style is meant. Example: if
determines which datum is accessed. Example: if a compute provides both a compute provides both a global scalar and a per-atom vector, the
a global scalar and a per-atom vector, the former will be used when former will be accessed by using ``c_ID`` in an equal-style variable,
using ``c_ID`` in an equal-style variable, while the latter will be while the latter will be accessed by using ``c_ID`` in an atom-style
referenced as ``c_ID`` in an atom-style variable. While atom-style variable. Note that atom-style variable formulas can also access global
variables are otherwise also able to access global scalars, access to scalars, but in this case it is not possible to do directly because of
the global scalar of the compute is not directly possible in this case. the ambiguity. Instead, an equal-style variable can be defined which
This is resolved through first defining an equal-style variable that accesses the global scalar, and that variable used in the atom-style
accesses the scalar property and then access that equal-style variable variable formula in place of ``c_ID``.
in the atom-style variable, which then may then also access the per-atom
property.
.. _thermo: .. _thermo:
Thermodynamic output Thermodynamic output
--------------------------------- --------------------
The frequency and format of thermodynamic output is set by the The frequency and format of thermodynamic output is set by the
:doc:`thermo <thermo>`, :doc:`thermo_style <thermo_style>`, and :doc:`thermo <thermo>`, :doc:`thermo_style <thermo_style>`, and
@ -133,7 +131,7 @@ intensive result.
.. _dump: .. _dump:
Dump file output Dump file output
--------------------------- ----------------
Dump file output is specified by the :doc:`dump <dump>` and Dump file output is specified by the :doc:`dump <dump>` and
:doc:`dump_modify <dump_modify>` commands. There are several :doc:`dump_modify <dump_modify>` commands. There are several
@ -159,7 +157,7 @@ command.
.. _fixoutput: .. _fixoutput:
Fixes that write output files Fixes that write output files
--------------------------------------------- -----------------------------
Several fixes take various quantities as input and can write output 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>`, 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: .. _computeoutput:
Computes that process output quantities 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 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, or local vector quantities as inputs and "reduce" them (sum, min, max,
@ -240,7 +238,7 @@ output commands.
.. _fixprocoutput: .. _fixprocoutput:
Fixes that process output quantities Fixes that process output quantities
-------------------------------------------------------- ------------------------------------
The :doc:`fix vector <fix_vector>` command can create global vectors as The :doc:`fix vector <fix_vector>` command can create global vectors as
output from global scalars as input, accumulating them one element at 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: .. _compute:
Computes that generate values to output Computes that generate values to output
----------------------------------------------------- ---------------------------------------
Every :doc:`compute <compute>` in LAMMPS produces either global or Every :doc:`compute <compute>` in LAMMPS produces either global or
per-atom or local values. The values can be scalars or vectors 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: .. _fix:
Fixes that generate values to output Fixes that generate values to output
---------------------------------------------- ------------------------------------
Some :doc:`fixes <fix>` in LAMMPS produces either global or per-atom or 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 local values which can be accessed by other commands. The values can
@ -290,7 +288,7 @@ describes them.
.. _variable: .. _variable:
Variables that generate values to output Variables that generate values to output
------------------------------------------------------- ----------------------------------------
:doc:`Variables <variable>` defined in an input script can store one or :doc:`Variables <variable>` defined in an input script can store one or
more strings. But equal-style, vector-style, and atom-style or more strings. But equal-style, vector-style, and atom-style or
@ -305,7 +303,7 @@ commands described in this section.
.. _table: .. _table:
Summary table of output options and data flow between commands Summary table of output options and data flow between commands
-------------------------------------------------------------------------- --------------------------------------------------------------
This table summarizes the various commands that can be used for This table summarizes the various commands that can be used for
generating output from LAMMPS. Each command produces output data of generating output from LAMMPS. Each command produces output data of