add primitiveNeighborlist option

pyxtal_ff/descriptors/SO3.py

@@ -1,6 +1,6 @@
 from __future__ import division
 import numpy as np
-from ase.neighborlist import NeighborList
+from ase.neighborlist import NeighborList, NewPrimitiveNeighborList
 from optparse import OptionParser
 from scipy.special import sph_harm, spherical_in
 from ase import Atoms
@@ -18,9 +18,10 @@ class SO3:
         alpha: float, gaussian width parameter
         derivative: bool, whether to calculate the gradient of not
         weight_on: bool, if True, the neighbors with different type will be counted as negative
+        primitive: bool, use the asePrimitiveNeighborList
     '''
 
-    def __init__(self, nmax=3, lmax=3, rcut=3.5, alpha=2.0, derivative=True, stress=False, cutoff_function='cosine', weight_on=False):
+    def __init__(self, nmax=3, lmax=3, rcut=3.5, alpha=2.0, derivative=True, stress=False, cutoff_function='cosine', weight_on=False, primitive=False):
         # populate attributes
         self.nmax = nmax
         self.lmax = lmax
@@ -31,6 +32,7 @@ def __init__(self, nmax=3, lmax=3, rcut=3.5, alpha=2.0, derivative=True, stress=
         self._type = "SO3"
         self.cutoff_function = cutoff_function
         self.weight_on = weight_on
+        self.PrimitiveNeighborList = primitive
         return
 
     def __str__(self):
@@ -322,7 +324,10 @@ def build_neighbor_list(self, atom_ids=None):
             atom_ids = range(len(atoms))
 
         cutoffs = [self.rcut/2]*len(atoms)
-        nl = NeighborList(cutoffs, self_interaction=False, bothways=True, skin=0.0)
+        if self.PrimitiveNeighborList:
+            nl = NewPrimitiveNeighborList(cutoffs, self_interaction=False, bothways=True, skin=0.0)
+        else:
+            nl = NeighborList(cutoffs, self_interaction=False, bothways=True, skin=0.0)
         nl.update(atoms)
 
         center_atoms = []