def remove_unibonded(g,d=1.0,tol=0.01,use_fortran=use_fortran,iterative=False):
"""Removes from the geometry atoms with only one bond"""
sb = []
if g.dimensionality>0: use_fortran = False # only for 0d
if use_fortran: # use fortran routine
# array with true in right atoms
retain = clean_geometryf90.clean_geometry(g.r.transpose(),2)
sb = [] # remove this atoms
for i in range(len(retain)):
if not retain[i]: sb.append(i) # remove
gout = remove(g,sb) # remove those atoms
else: # use python routine
for i in range(len(g.r)):
r1 = g.r[i] # first position
nb = 0 # initialize
for direc in g.neighbor_directions(): # loop over directions
for r2 in g.replicas(d=direc): # loop over replicas
dr = r1-r2
if d-tol < dr.dot(dr) < d+tol: # if sirdt neighbor
nb += 1 # increase counter
if nb<2:
sb.append(i+0) # add to the list
gout = remove(g,sb) # remove those atoms
if iterative: # ensure that it hs the same number of atoms by calling again
if len(g.x) != len(gout.x): # call again
print("Iterative cleaning")
return remove_unibonded(gout,d=d,tol=tol,
use_fortran=use_fortran,iterative=iterative)
return gout # return the geometry
def remove_unibonded(g,d=1.0,tol=0.01,use_fortran=use_fortran,iterative=False):
"""Removes from the geometry atoms with only one bond"""
sb = []
if use_fortran: # use fortran routine
# array with true in right atoms
retain = clean_geometryf90.clean_geometry(g.r.transpose(),2)
sb = [] # remove this atoms
for i in range(len(retain)):
if not retain[i]: sb.append(i) # remove
gout = remove(g,sb) # remove those atoms
else: # use python routine
for i in range(len(g.r)):
r1 = g.r[i] # first position
nb = 0 # initialize
for r2 in g.r:
dr = r1-r2
if d-tol < dr.dot(dr) < d+tol: # if sirdt neighbor
nb += 1 # increase counter
if nb<2:
sb.append(i+0) # add to the list
gout = remove(g,sb) # remove those atoms
if iterative: # ensure that it hs the same number of atoms by calling again
if len(g.x) != len(gout.x): # call again
print("Iterative cleaning")
return remove_unibonded(gout,d=d,tol=tol,
use_fortran=use_fortran,iterative=iterative)
return gout # return the geometry
def remove_unibonded(g,d=1.0,tol=0.01,use_fortran=True):
"""Removes from the geometry atoms with only one bond"""
sb = []
if use_fortran: # use fortran routine
import clean_geometryf90
# array with true in right atoms
retain = clean_geometryf90.clean_geometry(g.r.transpose(),2)
sb = [] # remove this atoms
for i in range(len(retain)):
if not retain[i]: sb.append(i) # remove
return remove(g,sb) # remove those atoms
else: # use python routine
for i in range(len(g.r)):
r1 = g.r[i] # first position
nb = 0 # initialize
for r2 in g.r:
dr = r1-r2
if d-tol < dr.dot(dr) < d+tol: # if sirdt neighbor
nb += 1 # increase counter
if nb<2:
sb.append(i+0) # add to the list
return remove(g,sb) # remove those atoms
def remove_unibonded(g, d=1.0, tol=0.01, use_fortran=True):
"""Removes from the geometry atoms with only one bond"""
sb = []
if use_fortran: # use fortran routine
import clean_geometryf90
# array with true in right atoms
retain = clean_geometryf90.clean_geometry(g.r.transpose(), 2)
sb = [] # remove this atoms
for i in range(len(retain)):
if not retain[i]: sb.append(i) # remove
return remove(g, sb) # remove those atoms
else: # use python routine
for i in range(len(g.r)):
r1 = g.r[i] # first position
nb = 0 # initialize
for r2 in g.r:
dr = r1 - r2
if d - tol < dr.dot(dr) < d + tol: # if sirdt neighbor
nb += 1 # increase counter
if nb < 2:
sb.append(i + 0) # add to the list
return remove(g, sb) # remove those atoms