def calc_bondangle_append(self, bondangles, bond1, bond2, cutoff):
acc = 10 ** -6 # accuracy for angle calculation
# if both bonds are smaller than cutoff
if bond1.bondlength() < cutoff[0] and bond2.bondlength() < cutoff[1]:
preangle = (
calc.vecprod(bond1.bondvector(), bond2.bondvector())
/ calc.length(bond1.bondvector())
/ calc.length(bond2.bondvector())
)
# if angle is not 360 or 0
if preangle < 1 - acc:
bondangles.append(numpy.arccos(preangle) * 180.0 / numpy.pi)
def crystal_cut(self,point,normal): # plane=a*x+b*y+c*z+f=0
poplist=[]
#f =(-ax0-by0-cz0)
normal=calc.norm(normal)
f=(-calc.vecprod(normal,point))
# loop over molecules
for i in range(self.nmol()):
for j in range(0,self.mol[i].natoms()):
coo=self.mol[i].at()[j].Rcoord()
D=(calc.vecprod(normal,coo)+f)/calc.length(normal)
# if above plane remove
if D>0.0:
poplist.append(self.mol[i].id())
# rm double or tripple counts
poplist=sorted(list( set(poplist) ))
# pop molecules
for popi in range(0,len(poplist)):
self.rm_submol(poplist[popi])
print >> sys.stderr, ('... {:5d} molecules popped').format(len(poplist))
return