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correct/update docs and parameter names for finding neighbor lists

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This commit is contained in:
Axel Kohlmeyer
2021-04-02 19:55:53 -04:00
parent 5583901b2c
commit 51212e62d9
2 changed files with 43 additions and 23 deletions
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64
python/lammps/core.py
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@ -1721,17 +1721,23 @@ class lammps(object):
# ------------------------------------------------------------------------- # -------------------------------------------------------------------------
def find_pair_neighlist(self, style, exact=True, nsub=0, request=0): def find_pair_neighlist(self, style, exact=True, nsub=0, reqid=0):
"""Find neighbor list index of pair style neighbor list """Find neighbor list index of pair style neighbor list
Try finding pair instance that matches style. If exact is set, the pair must Search for a neighbor list requested by a pair style instance that
match style exactly. If exact is 0, style must only be contained. If pair is matches "style". If exact is True, the pair style name must match
of style pair/hybrid, style is instead matched the nsub-th hybrid sub-style. exactly. If exact is False, the pair style name is matched against
"style" as regular expression or substring. If the pair style is a
hybrid pair style, the style is instead matched against the hybrid
sub-styles. If the same pair style is used as substyle multiple
types, you must set nsub to a value n > 0 which indicates the nth
instance of that sub-style to be used (same as for the pair_coeff
command). The default value of 0 will fail to match in that case.
Once the pair instance has been identified, multiple neighbor list requests Once the pair style instance has been identified, it may have
may be found. Every neighbor list is uniquely identified by its request requested multiple neighbor lists. Those are uniquely identified by
index. Thus, providing this request index ensures that the correct neighbor a request ID > 0 as set by the pair style. Otherwise the request
list index is returned. ID is 0.
:param style: name of pair style that should be searched for :param style: name of pair style that should be searched for
:type style: string :type style: string
@ -1739,44 +1745,58 @@ class lammps(object):
:type exact: bool, optional :type exact: bool, optional
:param nsub: match nsub-th hybrid sub-style, defaults to 0 :param nsub: match nsub-th hybrid sub-style, defaults to 0
:type nsub: int, optional :type nsub: int, optional
:param request: index of neighbor list request, in case there are more than one, defaults to 0 :param reqid: list request id, > 0 in case there are more than one, defaults to 0
:type request: int, optional :type reqid: int, optional
:return: neighbor list index if found, otherwise -1 :return: neighbor list index if found, otherwise -1
:rtype: int :rtype: int
"""
"""
style = style.encode() style = style.encode()
exact = int(exact) exact = int(exact)
idx = self.lib.lammps_find_pair_neighlist(self.lmp, style, exact, nsub, request) idx = self.lib.lammps_find_pair_neighlist(self.lmp, style, exact, nsub, reqid)
return idx return idx
# ------------------------------------------------------------------------- # -------------------------------------------------------------------------
def find_fix_neighlist(self, fixid, request=0): def find_fix_neighlist(self, fixid, reqid=0):
"""Find neighbor list index of fix neighbor list """Find neighbor list index of fix neighbor list
The fix instance requesting the neighbor list is uniquely identified
by the fix ID. In case the fix has requested multiple neighbor
lists, those are uniquely identified by a request ID > 0 as set by
the fix. Otherwise the request ID is 0 (the default).
:param fixid: name of fix :param fixid: name of fix
:type fixid: string :type fixid: string
:param request: index of neighbor list request, in case there are more than one, defaults to 0 :param reqid: id of neighbor list request, in case there are more than one request, defaults to 0
:type request: int, optional :type reqid: int, optional
:return: neighbor list index if found, otherwise -1 :return: neighbor list index if found, otherwise -1
:rtype: int :rtype: int
"""
"""
fixid = fixid.encode() fixid = fixid.encode()
idx = self.lib.lammps_find_fix_neighlist(self.lmp, fixid, request) idx = self.lib.lammps_find_fix_neighlist(self.lmp, fixid, reqid)
return idx return idx
# ------------------------------------------------------------------------- # -------------------------------------------------------------------------
def find_compute_neighlist(self, computeid, request=0): def find_compute_neighlist(self, computeid, reqid=0):
"""Find neighbor list index of compute neighbor list """Find neighbor list index of compute neighbor list
The compute instance requesting the neighbor list is uniquely
identified by the compute ID. In case the compute has requested
multiple neighbor lists, those are uniquely identified by a request
ID > 0 as set by the compute. Otherwise the request ID is 0 (the
default).
:param computeid: name of compute :param computeid: name of compute
:type computeid: string :type computeid: string
:param request: index of neighbor list request, in case there are more than one, defaults to 0 :param reqid: index of neighbor list request, in case there are more than one request, defaults to 0
:type request: int, optional :type reqid: int, optional
:return: neighbor list index if found, otherwise -1 :return: neighbor list index if found, otherwise -1
:rtype: int :rtype: int
"""
"""
computeid = computeid.encode() computeid = computeid.encode()
idx = self.lib.lammps_find_compute_neighlist(self.lmp, computeid, request) idx = self.lib.lammps_find_compute_neighlist(self.lmp, computeid, reqid)
return idx return idx

2
python/lammps/data.py
View File

@ -52,7 +52,7 @@ class NeighList:
def get(self, element): def get(self, element):
""" """
:return: tuple with atom local index, numpy array of neighbor local atom indices :return: tuple with atom local index, number of neighbors and ctypes pointer to neighbor's local atom indices
:rtype: (int, int, ctypes.POINTER(c_int)) :rtype: (int, int, ctypes.POINTER(c_int))
""" """
iatom, numneigh, neighbors = self.lmp.get_neighlist_element_neighbors(self.idx, element) iatom, numneigh, neighbors = self.lmp.get_neighlist_element_neighbors(self.idx, element)