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reformating RST file

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Steve Plimpton
2022-11-29 16:28:40 -07:00
parent 2d3630a31f
commit 0fc25a9942
1 changed files with 38 additions and 4 deletions
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doc/src/Developer_grid.rst
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@ -34,6 +34,9 @@ owned cells.
----------
Style commands
^^^^^^^^^^^^^^
Style commands which can define and use distributed grids include the
:doc:`compute <compute>`, :doc:`fix <fix>`, :doc:`pair <pair_style>`,
and :doc:`kspace <kspace_style>` styles. If you wish grid cell data
@ -78,6 +81,9 @@ define multiple data arrays for each grid it defines.
----------
Grid data allocation and access
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The simplest way for a command to allocate and access grid cell data
is to use the *create_offset()* methods provided by the Memory class.
Arguments for these methods can be values returned by the
@ -149,11 +155,12 @@ cells (the entire allocated grid).
----------
What follows are the public methods of the Grid3d class which a style
command can invoke. The Grid2d methods are similar; simply remove
arguments which refer to the z-dimension.
Grid class constructors
^^^^^^^^^^^^^^^^^^^^^^^
----------
The following sub-sections describe the public methods of the Grid3d
class which a style command can invoke. The Grid2d methods are
similar; simply remove arguments which refer to the z-dimension.
There are 2 constructors which can be used. They differ in the extra
i/o xyz lo/hi arguments:
@ -205,6 +212,9 @@ the second constructor.
----------
Grid class set methods
^^^^^^^^^^^^^^^^^^^^^^
The following methods affect how the Grid class computes which owned
and ghost cells are assigned to each processor. *Set_shift_grid()* is
the only method which influences owned cell assignement; all the rest
@ -288,6 +298,9 @@ simulation box.
----------
Grid class setup_grid method
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The *setup_grid()* method is called after the first constructor
(above) to partition the grid across processors, which determines
which grid cells each processor owns. It also calculates how many
@ -320,6 +333,9 @@ case.
----------
More grid class set methods
^^^^^^^^^^^^^^^^^^^^^^^^^^^
The following 2 methods can be used to override settings made by the
constructors above. If used, they must be called called before the
*setup_comm()* method is invoked, since it uses the settings that
@ -349,6 +365,9 @@ allows MSM to override the default values.
----------
Grid class get methods
^^^^^^^^^^^^^^^^^^^^^^
The following methods allow the caller to query the settings for a
specific grid, whether it created the grid or another command created
it.
@ -374,6 +393,9 @@ same as the "o" values returned by *setup_grid()*.
----------
Grid class owned/ghost communication
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If needed by the command, the following methods setup and perform
communication of grid data to/from neighboring processors. The
*forward_comm()* method sends owned grid cell data to the
@ -519,6 +541,9 @@ variants have this option.
----------
Grid class remap methods for load balancing
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The following methods are used when a load-balancing operation,
triggered by the :doc:`balance <balance>` or :doc:`fix balance
<fix_balance>` commands, changes the partitioning of the simulation
@ -598,6 +623,9 @@ and can then exit.
----------
Grid class I/O methods
^^^^^^^^^^^^^^^^^^^^^^
There are two I/O methods in the Grid classes which can be used to
read and write grid cell data to files. The caller can decide on the
precise format of each file, e.g. whether header lines are prepended
@ -708,6 +736,9 @@ one line to the output file.
----------
Style class grid access methods
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
A style command can enable its grid cell data to be accessible from
other commands. For example :doc:`fix ave/grid <fix_ave_grid>` or
:doc:`dump grid <dump>` or :doc:`dump grid/vtk <dump>`. Those
@ -786,6 +817,9 @@ array. Example code snippets with this logic were listed above,
----------
Final notes
^^^^^^^^^^^
Finally, here are two additional issues to pay attention to for
writing any style command which uses distributed grids via the Grid2d
or Grid3d class.