def update(self):
'''Rebuild or recompute the neighbor lists
Based on the changes of the atomic positions or due to calls to
``update_rcut`` and ``update_rmax``, the neighbor lists will be
rebuilt from scratch.
The heavy computational work is done in low-level C routines. The
neighbor lists array is reallocated if needed. The memory allocation
is done in Python for convenience.
'''
with log.section('NLIST'), timer.section('Nlists'):
assert self.rcut > 0
if self._need_rebuild():
# *rebuild* the entire neighborlist
if self.system.cell.volume != 0:
if self.system.natom / self.system.cell.volume > 10:
raise ValueError('Atom density too high')
# 1) make an initial status object for the neighbor list algorithm
status = nlist_status_init(self.rmax)
# The atom index of the first atom in pair is always at least
# nlow. The following status initialization avoids searching
# for excluded atom pairs in the neighbourlist build
status[3] = self.nlow
# 2) a loop of consecutive update/allocate calls
last_start = 0
while True:
done = nlist_build(self.system.pos, self.rcut + self.skin,
self.rmax, self.system.cell, status,
self.neighs[last_start:], self.nlow,
self.nhigh)
if done:
break
last_start = len(self.neighs)
new_neighs = np.empty((len(self.neighs) * 3) // 2,
dtype=neigh_dtype)
new_neighs[:last_start] = self.neighs
self.neighs = new_neighs
del new_neighs
# 3) get the number of neighbors in the list.
self.nneigh = nlist_status_finish(status)
if log.do_debug:
log('Rebuilt, size = %i' % self.nneigh)
# 4) store the current state to check in future calls if we
# need to do a rebuild or a recompute.
self._checkpoint()
self.rebuild_next = False
else:
# just *recompute* the deltas and the distance in the
# neighborlist
nlist_recompute(self.system.pos, self._pos_old,
self.system.cell, self.neighs[:self.nneigh])
if log.do_debug:
log('Recomputed')
def update(self):
'''Rebuild or recompute the neighbor lists
Based on the changes of the atomic positions or due to calls to
``update_rcut`` and ``update_rmax``, the neighbor lists will be
rebuilt from scratch.
The heavy computational work is done in low-level C routines. The
neighbor lists array is reallocated if needed. The memory allocation
is done in Python for convenience.
'''
with log.section('NLIST'), timer.section('Nlists'):
assert self.rcut > 0
if self._need_rebuild():
# *rebuild* the entire neighborlist
if self.system.cell.volume != 0:
if self.system.natom/self.system.cell.volume > 10:
raise ValueError('Atom density too high')
# 1) make an initial status object for the neighbor list algorithm
status = nlist_status_init(self.rmax)
# 2) a loop of consecutive update/allocate calls
last_start = 0
while True:
done = nlist_build(
self.system.pos, self.rcut + self.skin, self.rmax,
self.system.cell, status, self.neighs[last_start:]
)
if done:
break
last_start = len(self.neighs)
new_neighs = np.empty((len(self.neighs)*3)/2, dtype=neigh_dtype)
new_neighs[:last_start] = self.neighs
self.neighs = new_neighs
del new_neighs
# 3) get the number of neighbors in the list.
self.nneigh = nlist_status_finish(status)
if log.do_debug:
log('Rebuilt, size = %i' % self.nneigh)
# 4) store the current state to check in future calls if we
# need to do a rebuild or a recompute.
self._checkpoint()
self.rebuild_next = False
else:
# just *recompute* the deltas and the distance in the
# neighborlist
nlist_recompute(self.system.pos, self._pos_old, self.system.cell, self.neighs[:self.nneigh])
if log.do_debug:
log('Recomputed')
def update(self):
# Simply recompute distances, no need to rebuild
nlist_recompute(self.system.pos, self.system.pos, self.system.cell,
self.neighs[:self.nneigh])