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Merge branch 'develop' into compute-efield-atom-wolf

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Axel Kohlmeyer
2023-01-03 10:51:33 -05:00
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doc/src/compute.rst
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@ -43,29 +43,38 @@ underscores.
----------
Computes calculate one of three styles of quantities: global,
per-atom, or local. A global quantity is one or more system-wide
values (e.g., the temperature of the system). A per-atom quantity is
one or more values per atom (e.g., the kinetic energy of each atom).
Per-atom values are set to 0.0 for atoms not in the specified compute
group. Local quantities are calculated by each processor based on the
atoms it owns, but there may be zero or more per atom (e.g., a list of
bond distances). Computes that produce per-atom quantities have the
word "atom" in their style (e.g., *ke/atom*\ ). Computes that produce
local quantities have the word "local" in their style
(e.g., *bond/local*\ ). Styles with neither "atom" or "local" in their
style produce global quantities.
Computes calculate one or more of four styles of quantities: global,
per-atom, local, or per-atom. A global quantity is one or more
system-wide values, e.g. the temperature of the system. A per-atom
quantity is one or more values per atom, e.g. the kinetic energy of
each atom. Per-atom values are set to 0.0 for atoms not in the
specified compute group. Local quantities are calculated by each
processor based on the atoms it owns, but there may be zero or more
per atom, e.g. a list of bond distances. Per-grid quantities are
calculated on a regular 2d or 3d grid which overlays a 2d or 3d
simulation domain. The grid points and the data they store are
distributed across processors; each processor owns the grid points
which fall within its sub-domain.
Note that a single compute can produce either global or per-atom or
local quantities, but not both global and per-atom. It can produce
local quantities in tandem with global or per-atom quantities. The
compute page will explain.
Computes that produce per-atom quantities have the word "atom" at the
end of their style, e.g. *ke/atom*\ . Computes that produce local
quantities have the word "local" at the end of their style,
e.g. *bond/local*\ . Computes that produce per-grid quantities have
the word "grid" at the end of their style, e.g. *property/grid*\ .
Styles with neither "atom" or "local" or "grid" at the end of their
style name produce global quantities.
Global, per-atom, and local quantities each come in three kinds: a
single scalar value, a vector of values, or a 2d array of values. The
doc page for each compute describes the style and kind of values it
produces (e.g., a per-atom vector). Some computes produce more than one
kind of a single style (e.g., a global scalar and a global vector).
Note that a single compute typically produces either global or
per-atom or local or per-grid values. It does not compute both global
and per-atom values. It can produce local values or per-grid values
in tandem with global or per-atom quantities. The compute doc page
will explain the details.
Global, per-atom, local, and per-grid quantities come in three kinds:
a single scalar value, a vector of values, or a 2d array of values.
The doc page for each compute describes the style and kind of values
it produces, e.g. a per-atom vector. Some computes produce more than
one kind of a single style, e.g. a global scalar and a global vector.
When a compute quantity is accessed, as in many of the output commands
discussed below, it can be referenced via the following bracket
@ -253,7 +262,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`pressure/uef <compute_pressure_uef>` - pressure tensor in the reference frame of an applied flow field
* :doc:`property/atom <compute_property_atom>` - convert atom attributes to per-atom vectors/arrays
* :doc:`property/chunk <compute_property_chunk>` - extract various per-chunk attributes
* :doc:`property/local <compute_property_local>` - convert local attributes to localvectors/arrays
* :doc:`property/grid <compute_property_grid>` - convert per-grid attributes to per-grid vectors/arrays
* :doc:`property/local <compute_property_local>` - convert local attributes to local vectors/arrays
* :doc:`ptm/atom <compute_ptm_atom>` - determines the local lattice structure based on the Polyhedral Template Matching method
* :doc:`rdf <compute_rdf>` - radial distribution function :math:`g(r)` histogram of group of atoms
* :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value