def generate(opts):
l = float(opts['Length'])
m = int(opts['m'])
n = int(opts['n'])
swnt = SWNTGenerator((m, n), Lz=l)
# need a better random temporary name
name = 'temp{}.xyz'.format(randrange(32768))
swnt.save(fname=name)
with open(name) as f:
xyzData = f.read()
os.remove(name)
return xyzData
def test4(self):
swnt = SWNTGenerator(n=10, m=5, nz=1)
bundle = \
SWNTBundleGenerator(n=10, m=5, nx=3, ny=3, nz=1,
bundle_packing='ccp')
assert_true(bundle.Natoms, bundle.Ntubes * swnt.Natoms)
assert_equal(bundle.Ntubes, len(set(bundle.mol_ids)))
def test3():
atoms = SWNTGenerator(n=20, m=0, nz=2).atoms
assert_equal(atoms.Natoms, 160)
atoms.assign_unique_ids()
atoms.update_attrs()
print(np.degrees(atoms.bonds.mean_length))
print(np.degrees(atoms.bonds.mean_angle))
atom0 = atoms[0]
atom0bonds = atom0.bonds
print("atom0: {}".format(atom0))
print("atom0.r: {}".format(atom0.r))
for NN in atom0.NN:
print("NN.r: {}".format(NN.r))
print(atom0bonds.atoms.Natoms)
print(atom0bonds.atoms.CM)
print("atoms.bonds.Nbonds: {}".format(atoms.bonds.Nbonds))
print("atoms.bonds.atoms.Natoms: {}".format(atoms.bonds.atoms.Natoms))
def test_structure_data(self):
fname = resource_filename('sknano', 'data/nanotubes/1005_5cells.data')
swnt = SWNTGenerator(n=10, m=5, nz=5)
swnt_atoms = swnt.atoms
swnt_atoms.compute_POAVs()
data = DATAReader(fname)
atoms = data.atoms
atoms.compute_POAVs()
assert_equals(swnt_atoms.Natoms, atoms.Natoms)
def test3(self):
new_swnt = SWNTGenerator((10, 10))
new_swnt.atoms.center_centroid()
test_swnt = \
XYZReader(resource_filename('sknano',
'data/nanotubes/1010_1cell.xyz'))
print(new_swnt.atoms.coords)
print(test_swnt.atoms.coords)
assert_true(np.allclose(new_swnt.atoms.coords, test_swnt.atoms.coords))
def test4():
atoms = SWNTGenerator(10, 5, nz=2).atoms
atoms.assign_unique_ids()
atoms.update_attrs()
atoms.center_centroid()
print(atoms.centroid)
bond = atoms.get_atom(atoms.Natoms // 2).bonds[0]
print(bond)
print('bond.atoms.coords:\n{}'.format(bond.atoms.coords))
bond_centroid = bond.centroid
print('bond.centroid: {}'.format(bond.centroid))
rot_axis = Vector(p0=[0, 0, bond_centroid.z], p=bond_centroid.p)
bond.rotate(angle=np.pi/2, axis=rot_axis)
print(bond)
print('bond.atoms.coords:\n{}'.format(bond.atoms.coords))
assert_true(np.allclose(bond_centroid, bond.centroid))
def test_generator_atoms():
from sknano.generators import SWNTGenerator
n, m = 5, 5
nz = 2
swnt = SWNTGenerator(n=n, m=m, nz=nz)
assert_equal(swnt.N, 2 * n)
assert_equal(swnt.Natoms, 2 * swnt.N * swnt.nz)
assert_equal(swnt.Natoms_per_unit_cell, 2 * swnt.N)
assert_equal(swnt.nz, nz)
assert_equal(swnt.Natoms_per_tube, swnt.Natoms_per_unit_cell * swnt.nz)
atoms = swnt.atoms
assert_equal(atoms.Natoms, swnt.Natoms_per_tube)
def test4():
atoms = SWNTGenerator(10, 5, nz=2).atoms
atoms.assign_unique_ids()
atoms.update_attrs()
atoms.center_centroid()
print(atoms.centroid)
bond = atoms.get_atom(atoms.Natoms // 2).bonds[0]
print(bond)
print("bond.atoms.coords:\n{}".format(bond.atoms.coords))
bond_centroid = bond.centroid
print("bond.centroid: {}".format(bond.centroid))
rot_axis = Vector(p0=[0, 0, bond_centroid.z], p=bond_centroid.p)
bond.rotate(angle=np.pi / 2, axis=rot_axis)
print(bond)
print("bond.atoms.coords:\n{}".format(bond.atoms.coords))
assert_true(np.allclose(bond_centroid, bond.centroid))
def test3():
atoms = SWNTGenerator(n=20, m=0, nz=2).atoms
assert_equal(atoms.Natoms, 160)
atoms.assign_unique_ids()
atoms.update_attrs()
print(np.degrees(atoms.bonds.mean_length))
print(np.degrees(atoms.bonds.mean_angle))
atom0 = atoms[0]
atom0bonds = atom0.bonds
print('atom0: {}'.format(atom0))
print('atom0.r: {}'.format(atom0.r))
for NN in atom0.NN:
print('NN.r: {}'.format(NN.r))
print(atom0bonds.atoms.Natoms)
print(atom0bonds.atoms.CM)
print('atoms.bonds.Nbonds: {}'.format(atoms.bonds.Nbonds))
print('atoms.bonds.atoms.Natoms: {}'.format(atoms.bonds.atoms.Natoms))
def test2():
atoms = SWNTGenerator(n=10, m=10, nz=3).atoms
atoms.assign_unique_ids()
atoms.update_attrs()
def test2():
atoms = SWNTGenerator(n=10, m=10, nz=3).atoms
atoms.assign_unique_ids()
atoms.update_attrs()
def test2(self):
swnt = SWNTGenerator(n=10, m=10, Lz=1.0, fix_Lz=True)
swnt.save()
self.tmpdata.append(swnt.fname)
swnt.save(structure_format='data')
self.tmpdata.append(swnt.fname)
def test1(self):
swnt = SWNTGenerator(n=10, m=10)
swnt.save()
self.tmpdata.append(swnt.fname)
swnt.save(structure_format='data')
self.tmpdata.append(swnt.fname)
