equal(cc[c, c], width, 1e-10)
# minimal box, ensure multiple of 4
h = .13
b = [2, 3, 4]
CO.minimal_box(b, h=h)
cc = CO.get_cell()
for c in range(3):
# print "cc[c,c], cc[c,c] / h % 4 =", cc[c, c], cc[c, c] / h % 4
for a in CO:
print(a.symbol, b[c], a.position[c], cc[c, c] - a.position[c])
assert (a.position[c] > b[c])
equal(cc[c, c] / h % 4, 0.0, 1e-10)
# connected atoms
assert (len(CO.find_connected(0, 1.1 * R)) == 2)
assert (len(CO.find_connected(0, 0.9 * R)) == 1)
H2O = Cluster(molecule('H2O'))
assert (len(H2O.find_connected(0)) == 3)
assert (len(H2O.find_connected(0, scale=0.9)) == 1)
# I/O
fxyz = 'CO.xyz'
fpdb = 'CO.pdb'
cell = [2., 3., R + 2.]
CO.set_cell(cell, scale_atoms=True)
barrier()
CO.write(fxyz)
barrier()
# minimal box, ensure multiple of 4
h = .13
b = [2, 3, 4]
CO.minimal_box(b, h=h)
cc = CO.get_cell()
for c in range(3):
# print "cc[c,c], cc[c,c] / h % 4 =", cc[c, c], cc[c, c] / h % 4
for a in CO:
print(a.symbol, b[c], a.position[c], cc[c, c] - a.position[c])
assert(a.position[c] > b[c])
equal(cc[c, c] / h % 4, 0.0, 1e-10)
# .............................................
# connected atoms
assert(len(CO.find_connected(0, 1.1 * R)) == 2)
assert(len(CO.find_connected(0, 0.9 * R)) == 1)
H2O = Cluster(molecule('H2O'))
assert (len(H2O.find_connected(0)) == 3)
assert (len(H2O.find_connected(0, scale=0.9)) == 1)
# .............................................
# I/O
fxyz='CO.xyz'
fpdb='CO.pdb'
cell = [2.,3.,R+2.]
CO.set_cell(cell, scale_atoms=True)
barrier()
CO.write(fxyz)
