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add a paragraph to the output howto explaining how ambiguity is resolved

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Axel Kohlmeyer
2020-07-06 11:13:23 -04:00
parent 14321d1fa0
commit 022252dde0
1 changed files with 26 additions and 5 deletions
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31
doc/src/Howto_output.rst
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@ -3,13 +3,15 @@ Output from LAMMPS (thermo, dumps, computes, fixes, variables)
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)
@ -81,6 +83,25 @@ 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 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.
.. _thermo:
Thermodynamic output