def test1():
datadir = resource_filename('sknano', 'data')
dirnames, fnames = listdir(datadir)
assert_true('__init__.py' in fnames)
assert_true('fullerenes' in dirnames)
assert_equal(dirnames, listdir_dirnames(datadir))
assert_equal(fnames, listdir_fnames(datadir))
def analyze_structure(rootdir=None, structure_file=None, **kwargs):
if rootdir is None or not os.path.isdir(rootdir):
rootdir = os.curdir
rundirs = \
listdir_dirnames(rootdir,
filterfunc=lambda name: name.startswith('run_'))
ion_coordination_counter = Counter()
graphene_coordination_counter = Counter()
for rundir in rundirs:
dumpdata = StructureReader.read(os.path.join(rundir, structure_file))
dumpdata.remap_atomattr_names({'c_atom_ke': 'ke'})
trj = dumpdata.trajectory
final_snapshot = trj[-1]
atoms = final_snapshot.atoms
atoms.mapatomattr('type', 'element', {1: 'C', 2: 'N'})
atoms.update_attrs()
ion = atoms.filtered(atoms.elements == 'N')[0]
graphene = atoms.filtered(atoms.elements == 'C')
ion_coordination_counter.update([ion.CN])
graphene_coordination_counter.update(graphene.coordination_numbers)
statstr = 'run statistics:\n'
statstr += 'rundir: {}\n'.format(rundir)
statstr += 'ion CN: {}\n'.format(ion.CN)
statstr += 'graphene CN counts: {}\n'.format(
Counter(graphene.coordination_numbers))
print(statstr)
print('final stats')
print('ion_coordination_counter: {}'.format(ion_coordination_counter))
print('graphene_coordination_counter: {}'.format(
graphene_coordination_counter))
def test1():
datadir = resource_filename('sknano', 'data')
dirnames, fnames = listdir(datadir)
assert_true('__init__.py' in fnames)
assert_true('fullerenes' in dirnames)
assert_equal(dirnames, listdir_dirnames(datadir))
assert_equal(fnames, listdir_fnames(datadir))
def analyze_structure(rootdir=None, structure_file=None, **kwargs):
if rootdir is None or not os.path.isdir(rootdir):
rootdir = os.curdir
rundirs = \
listdir_dirnames(rootdir,
filterfunc=lambda name: name.startswith('run_'))
ion_coordination_counter = Counter()
graphene_coordination_counter = Counter()
for rundir in rundirs:
dumpdata = StructureReader.read(os.path.join(rundir, structure_file))
dumpdata.remap_atomattr_names({'c_atom_ke': 'ke'})
trj = dumpdata.trajectory
final_snapshot = trj[-1]
atoms = final_snapshot.atoms
atoms.mapatomattr('type', 'element', {1: 'C', 2: 'N'})
atoms.update_attrs()
ion = atoms.filtered(atoms.elements == 'N')[0]
graphene = atoms.filtered(atoms.elements == 'C')
ion_coordination_counter.update([ion.CN])
graphene_coordination_counter.update(graphene.coordination_numbers)
statstr = 'run statistics:\n'
statstr += 'rundir: {}\n'.format(rundir)
statstr += 'ion CN: {}\n'.format(ion.CN)
statstr += 'graphene CN counts: {}\n'.format(
Counter(graphene.coordination_numbers))
print(statstr)
print('final stats')
print('ion_coordination_counter: {}'.format(ion_coordination_counter))
print('graphene_coordination_counter: {}'.format(
graphene_coordination_counter))
def load_fullerene_data():
"""Helper function to populate dict of fullerene data files."""
datadir = resource_filename('sknano', 'data/fullerenes')
fullerenes = \
listdir_dirnames(datadir, filterfunc=lambda name: name.startswith('C'))
fullerene_data = {}
for fullerene in fullerenes:
datapath = os.path.join('data', 'fullerenes', fullerene)
datadir = resource_filename('sknano', datapath)
fullerene_data[fullerene] = listdir_fnames(datadir)
return fullerene_data
def test2():
datadir = resource_filename('sknano', 'data')
filterfunc = lambda name: '_' not in name
dirnames, fnames = listdir(datadir, filterfunc=filterfunc,
filter_fnames=True, filter_dirnames=True)
assert_true('__pycache__' not in dirnames)
assert_true('__init__.py' not in fnames)
assert_equal(dirnames,
listdir_dirnames(datadir, filterfunc=filterfunc))
assert_equal(fnames,
listdir_fnames(datadir, filterfunc=filterfunc))
def load_fullerene_data():
"""Helper function to populate dict of fullerene data files."""
datadir = resource_filename('sknano', 'data/fullerenes')
fullerenes = \
listdir_dirnames(datadir, filterfunc=lambda name: name.startswith('C'))
fullerene_data = {}
for fullerene in fullerenes:
datapath = os.path.join('data', 'fullerenes', fullerene)
datadir = resource_filename('sknano', datapath)
fullerene_data[fullerene] = listdir_fnames(datadir)
return fullerene_data
def test2():
datadir = resource_filename('sknano', 'data')
filterfunc = lambda name: '_' not in name
dirnames, fnames = listdir(datadir,
filterfunc=filterfunc,
filter_fnames=True,
filter_dirnames=True)
assert_true('__pycache__' not in dirnames)
assert_true('__init__.py' not in fnames)
assert_equal(dirnames, listdir_dirnames(datadir, filterfunc=filterfunc))
assert_equal(fnames, listdir_fnames(datadir, filterfunc=filterfunc))