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update neighbor list request developer notes

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Axel Kohlmeyer
2022-03-08 06:32:48 -05:00
parent 3b0a6ac840
commit 1296d6d938
1 changed files with 11 additions and 12 deletions
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doc/src/Developer_notes.rst
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@ -101,17 +101,16 @@ request that is a superset of the requested list. The neighbor list
build is then :doc:`processed in parallel <Developer_par_neigh>`.
The most commonly required neighbor list is a so-called "half" neighbor
list requested by a pair style, where each pair of atoms is listed only
once (except when then :doc:`newton command setting <newton>` for pair
is off; in that case pairs straddling sub-domains or periodic boundaries
will be listed twice). Thus these are the default settings when a
neighbor list request is created in:
list, where each pair of atoms is listed only once (except when the
:doc:`newton command setting <newton>` for pair is off; in that case
pairs straddling sub-domains or periodic boundaries will be listed twice).
Thus these are the default settings when a neighbor list request is created in:
.. code-block:: C++
void Pair::init_style()
{
neighbor->add_request(this, NeighConst::REQ_DEFAULT);
neighbor->add_request(this);
}
void Pair::init_list(int /*id*/, NeighList *ptr)
@ -126,7 +125,7 @@ The second argument contains a bitmask of flags that determines the kind
of neighbor list, i.e. a perpetual "half" neighbor list here.
To adjust a neighbor list request to the specific needs of a style
usually just a different additional request flag is needed. The :doc:`tersoff <pair_tersoff>` pair
an additional request flag is needed. The :doc:`tersoff <pair_tersoff>` pair
style, for example, needs a "full" neighbor list:
.. code-block:: C++
@ -162,7 +161,7 @@ For example with:
.. code-block:: C++
if (use_history) neighbor->add_request(this, NeighConst::REQ_SIZE|NeighConst::REQ_HISTORY);
if (use_history) neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_HISTORY);
else neighbor->add_request(this, NeighConst::REQ_SIZE);
In case a class would need to make multiple neighbor list requests with different
@ -176,7 +175,7 @@ done for example by the :doc:`pair style meam <pair_meam>`:
{
// [...]
neighbor->add_request(this, NeighConst::REQ_FULL)->set_id(1);
neighbor->add_request(this, NeighConst::REQ_DEFAULT)->set_id(2);
neighbor->add_request(this)->set_id(2);
}
void PairMEAM::init_list(int id, NeighList *ptr)
{
@ -191,7 +190,7 @@ internally by :doc:`Peridynamics pair styles <pair_peri>`:
.. code-block:: C++
neighbor->add_request(this, NeighConst::REQ_FULL|NeighConst::REQ_OCCASIONAL);
neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
It is also possible to request a neighbor list that uses a different cutoff
than what is usually inferred from the pair style settings (largest cutoff of
@ -201,9 +200,9 @@ all pair styles plus neighbor list skin). The following is used in the
.. code-block:: C++
if (cutflag)
neighbor->add_request(this,NeighConst::REQ_OCCASIONAL)->set_cutoff(mycutneigh);
neighbor->add_request(this, NeighConst::REQ_OCCASIONAL)->set_cutoff(mycutneigh);
else
neighbor->add_request(this,NeighConst::REQ_OCCASIONAL);
neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);
The neighbor list request function has a slightly different set of arguments
when created by a command style. In this case the neighbor list is