def buildPairs(self, rcut=5.0, molind_=None, nreal_=None): """ Returns the nonzero pairs, triples in self.x within the cutoff. Triples are non-repeating ie: no 1,2,2 or 2,2,2 etc. but unordered Args: rcut: the cutoff for pairs and triples Returns: pair matrix (npair X 2) triples matrix (ntrip X 3) """ pair = [] ntodo = self.natom if (nreal_ != None): ntodo = int(nreal_) pair = None if (self.alg==0): pair = Make_NListNaive(self.x,rcut,ntodo,int(self.DoPerms)) else: pair = Make_NListLinear(self.x,rcut,ntodo,int(self.DoPerms)) npairi = map(len,pair) npair = sum(npairi) p = None if (molind_!=None): p=np.zeros((npair,3),dtype = np.uint64) else: p=np.zeros((npair,2),dtype = np.uint64) pp = 0 for i in range(ntodo): for j in pair[i]: if (molind_!=None): p[pp,0]=molind_ p[pp,1]=i p[pp,2]=j else: p[pp,0]=i p[pp,1]=j pp = pp+1 del pair return p
def buildPairsAndTriples(self, rcut_pairs=5.0, rcut_triples=5.0, molind_=None, nreal_=None):
"""
Returns the nonzero pairs, triples in self.x within the cutoff.
Triples are non-repeating ie: no 1,2,2 or 2,2,2 etc. but unordered
Args:
rcut: the cutoff for pairs and triples
Returns:
pair matrix (npair X 2)
triples matrix (ntrip X 3)
"""
if (self.ele is None):
print("WARNING... need self.ele for angular SymFunc triples... ")
pair = []
tpair = [] # since these may have different cutoff
ntodo = self.natom
if (nreal_ != None):
ntodo = int(nreal_)
pair = None
tpair = None
if (self.alg==0):
pair = Make_NListNaive(self.x,rcut_pairs,int(ntodo),int(self.DoPerms))
tpair = Make_NListNaive(self.x,rcut_triples,int(ntodo),int(self.DoPerms))
else:
pair = Make_NListLinear(self.x,rcut_pairs,int(ntodo),int(self.DoPerms))
tpair = Make_NListLinear(self.x,rcut_triples,int(ntodo),int(self.DoPerms))
npairi = map(len,pair)
npair = sum(npairi)
npairi = map(len,tpair)
#ntrip = sum(map(lambda x: x*x if x>0 else 0, npairi))
ntrip = sum(map(lambda x: int(x*(x-1)/2) if x>0 else 0, npairi))
#print ("npair:", npair, " ntrip:", ntrip, " rcut_triples:", rcut_triples, " tpair", tpair, " ntodo:", int(ntodo), " self.DoPerms", int(self.DoPerms), " x:", self.x[:int(ntodo)], " pair:", pair)
p = None
t = None
if (molind_!=None):
p=np.zeros((npair,3),dtype = np.uint64)
t=np.zeros((ntrip,4),dtype = np.uint64)
else:
p=np.zeros((npair,2),dtype = np.uint64)
t=np.zeros((ntrip,3),dtype = np.uint64)
pp = 0
tp = 0
for i in range(ntodo):
for j in pair[i]:
if (molind_!=None):
p[pp,0]=molind_
p[pp,1]=i
p[pp,2]=j
else:
p[pp,0]=i
p[pp,1]=j
pp = pp+1
for j in tpair[i]:
for k in tpair[i]:
#if True:
if (k > j): # do not do ijk, ikj permutation
#if (k!=j):
if (molind_!=None):
t[tp,0]=molind_
t[tp,1]=i
if self.ele is not None and self.ele[j] > self.ele[k]: # atom will smaller element index alway go first
t[tp,2]=k
t[tp,3]=j
elif self.sort and j > k:
t[tp,2]=k
t[tp,3]=j
else:
t[tp,2]=j
t[tp,3]=k
else:
t[tp,0]=i
if self.ele is not None and self.ele[j] > self.ele[k]:
t[tp,1]=k
t[tp,2]=j
elif self.sort and j > k:
t[tp,1]=k
t[tp,2]=j
else:
t[tp,1]=j
t[tp,2]=k
tp=tp+1
del pair
del tpair
return p,t
def Update(self, x_, R2=10.0, R3=5.0):
"""
Update the lists of bodies and their coefficients.
Args:
x: A new position vector
R2: pair cutoff
R3: triples cutoff
"""
if (R2 < R3):
raise Exception("R3<R2 Assumption Violated.")
self.x = x_.copy()
for i in range(self.nf):
self.sings[i, :len(self.frags[i]), :] = self.x[
self.frags[i]].copy()
self.singz[i, :len(self.frags[i])] = self.z[self.frags[i]].copy()
centers = np.zeros((self.nf, 3))
for i in range(self.nf):
centers[i] = np.average(self.x[self.frags[i]], axis=0)
TwoBodyPairs = None
ThreeBodyPairs = None
#print "Number of Frags",self.nf
if (self.nf < 500):
TwoBodyPairs = Make_NListNaive(centers, R2, self.nf, int(False))
ThreeBodyPairs = Make_NListNaive(centers, R3, self.nf, int(False))
else:
TwoBodyPairs = Make_NListLinear(centers, R2, self.nf, int(False))
ThreeBodyPairs = Make_NListLinear(centers, R3, self.nf, int(False))
self.pairi = set()
self.tripi = set()
#print TwoBodyPairs
#print ThreeBodyPairs
for i in range(self.nf):
nnt = len(ThreeBodyPairs[i])
nnp = len(TwoBodyPairs[i])
if (nnp > 0):
for j in range(nnp):
if (j != None):
self.pairi.add(tuple(sorted([i, TwoBodyPairs[i][j]])))
if (nnt >= 2):
for j in range(nnt):
if (j != None):
for k in range(j + 1, nnt):
if (k != None):
if ThreeBodyPairs[i][k] in ThreeBodyPairs[
ThreeBodyPairs[i][j]]:
self.tripi.add(
tuple(
sorted([
i, ThreeBodyPairs[i][j],
ThreeBodyPairs[i][k]
])))
DistMatrix = Make_DistMat(self.x)
self.ntrip = len(self.tripi)
self.npair = len(self.pairi)
#print "num pairs", self.npair
#print "num trips", self.ntrip
self.pairi = map(list, self.pairi)
self.tripi = map(list, self.tripi)
#print "Pairs", self.pairi
#print "Trips", self.tripi
# Now generate the coeffs of each order and sum them.
self.singC = np.ones(self.nf)
self.pairC = np.ones(self.npair)
self.tripC = np.ones(self.ntrip)
self.singI = self.frags
self.pairI = []
self.tripI = []
self.pairs = np.zeros((self.npair, self.maxnatom, 3))
self.trips = np.zeros((self.ntrip, self.maxnatom, 3))
self.pairz = np.zeros((self.npair, self.maxnatom), dtype=np.uint8)
self.tripz = np.zeros((self.ntrip, self.maxnatom), dtype=np.uint8)
for trip_index, trip in enumerate(self.tripi):
i, j, k = trip[0], trip[1], trip[2]
self.tripI.append([self.frags[i] + self.frags[j] + self.frags[k]])
ni, nj, nk = len(self.frags[i]), len(self.frags[j]), len(
self.frags[k])
self.trips[trip_index, :ni, :] = self.x[self.frags[i]].copy()
self.trips[trip_index,
ni:(ni + nj), :] = self.x[self.frags[j]].copy()
self.trips[trip_index,
(ni + nj):(ni + nj +
nk), :] = self.x[self.frags[k]].copy()
self.tripz[trip_index, :ni] = self.z[self.frags[i]].copy()
self.tripz[trip_index, ni:(ni + nj)] = self.z[self.frags[j]].copy()
self.tripz[trip_index,
(ni + nj):(ni + nj +
nk)] = self.z[self.frags[k]].copy()
self.pairC[self.pairi.index(sorted([i, j]))] -= 1
self.pairC[self.pairi.index(sorted([j, k]))] -= 1
self.pairC[self.pairi.index(sorted([k, i]))] -= 1
self.singC[i] += 1
self.singC[j] += 1
self.singC[k] += 1
for pair_index, pair in enumerate(self.pairi):
i, j = pair[0], pair[1]
self.pairI.append([self.frags[i] + self.frags[j]])
ni, nj = len(self.frags[i]), len(self.frags[j])
self.pairs[pair_index, :ni, :] = self.x[self.frags[i]].copy()
self.pairs[pair_index,
ni:(ni + nj), :] = self.x[self.frags[j]].copy()
self.pairz[pair_index, :ni] = self.z[self.frags[i]].copy()
self.pairz[pair_index, ni:(ni + nj)] = self.z[self.frags[j]].copy()
self.singC[i] -= 1
self.singC[j] -= 1
return