def test_select_pairs():
"""Test selecting pairs with exclusions"""
pair = Pair('tail', 'tail', potential=mie(r, 1.0, 1.0))
alpha = 0.5
state_dir = get_fn('state0/')
state = State(k_B*T, state_dir=state_dir,
top_file=get_fn('2chains.hoomdxml'), name='state0')
rdf_filename = get_fn('state0/target-rdf.txt')
rdf = np.loadtxt(rdf_filename)
pair.add_state(state, rdf, alpha)
pair.select_pairs(state, exclude_up_to=3)
assert pair.states[state]['pair_indices'].shape[0] == 162
def init_state(state_number):
pair = Pair('0', '1', potential=mie(r, 1.0, 1.0))
topology_filename = get_fn('final.hoomdxml')
traj_filename = get_fn('state{0}/query.dcd'.format(state_number))
t = md.load(traj_filename, top=topology_filename)
pair_list = t.top.select_pairs('name "0"', 'name "1"')
rdf_filename = get_fn('state{0}/target-rdf.txt'.format(state_number))
rdf = np.loadtxt(rdf_filename)
alpha = 0.5
state_dir = get_fn('state{0}/'.format(state_number))
state = State(k_B*T, state_dir=state_dir,
top_file='sys.hoomdxml', name='state0')
pair.add_state(state, rdf, alpha, pair_list)
return pair, state, rdf
def test_select_pairs():
"""Test selecting pairs with exclusions"""
pair = Pair('tail', 'tail', potential=mie(r, 1.0, 1.0))
alpha = 0.5
state_dir = get_fn('state0/')
state = State(k_B * T,
state_dir=state_dir,
top_file=get_fn('2chains.hoomdxml'),
name='state0')
rdf_filename = get_fn('state0/target-rdf.txt')
rdf = np.loadtxt(rdf_filename)
pair.add_state(state, rdf, alpha)
pair.select_pairs(state, exclude_up_to=3)
assert pair.states[state]['pair_indices'].shape[0] == 162
def init_state(state_number):
pair = Pair('0', '1', potential=mie(r, 1.0, 1.0))
topology_filename = get_fn('final.hoomdxml')
traj_filename = get_fn('state{0}/query.dcd'.format(state_number))
t = md.load(traj_filename, top=topology_filename)
pair_list = t.top.select_pairs('name "0"', 'name "1"')
rdf_filename = get_fn('state{0}/target-rdf.txt'.format(state_number))
rdf = np.loadtxt(rdf_filename)
alpha = 0.5
state_dir = get_fn('state{0}/'.format(state_number))
state = State(k_B * T,
state_dir=state_dir,
top_file='sys.hoomdxml',
name='state0')
pair.add_state(state, rdf, alpha, pair_list)
return pair, state, rdf
def init_state(self, state_number):
pair = Pair("0", "1", potential=mie(r, 1.0, 1.0))
topology_filename = get_fn("final.hoomdxml")
traj_filename = get_fn(f"state{state_number}/query.dcd")
t = md.load(traj_filename, top=topology_filename)
pair_list = t.top.select_pairs('name "0"', 'name "1"')
rdf_filename = get_fn(f"state{state_number}/target-rdf.txt")
rdf = np.loadtxt(rdf_filename)
alpha = 0.5
state_dir = get_fn(f"state{state_number}/")
state = State(k_B * T,
state_dir=state_dir,
traj_file=traj_filename,
top_file="sys.hoomdxml",
name="state0")
pair.add_state(state, rdf, alpha, pair_list)
return pair, state, rdf
def test_select_pairs(self):
"""Test selecting pairs with exclusions"""
pair = Pair("tail", "tail", potential=mie(r, 1.0, 1.0))
alpha = 0.5
state_dir = get_fn("state0/")
state = State(
k_B * T,
state_dir=state_dir,
top_file=get_fn("2chains.hoomdxml"),
traj_file="query.dcd",
name="state0",
)
rdf_filename = get_fn("state0/target-rdf.txt")
rdf = np.loadtxt(rdf_filename)
pair.add_state(state, rdf, alpha)
pair.select_pairs(state, exclude_up_to=3)
assert pair.states[state]["pair_indices"].shape[0] == 162
def test_reload_query_trajectory():
state_dir = get_fn('state0/')
state = State(1.987e-3 * 500.0,
state_dir=state_dir,
top_file='sys.hoomdxml',
name='state0')
state.reload_query_trajectory()
assert (state.traj)
assert (state.traj.top)
def test_reload_query_trajectory():
state_dir = get_fn("state0/")
state = State(
1.987e-3 * 500.0,
state_dir=state_dir,
top_file="sys.hoomdxml",
traj_file="query.dcd",
name="state0",
)
state.reload_query_trajectory()
assert state.traj
assert state.traj.top
def test_is_exclusion():
top = md.load(get_fn('2chains.hoomdxml')).top
G = nx.Graph()
G.add_nodes_from([a.index for a in top.atoms])
bonds = [b for b in top.bonds]
bonds_by_index = [(b[0].index, b[1].index) for b in bonds]
G.add_edges_from(bonds_by_index)
tail_tail = top.select_pairs("name 'tail'", "name 'tail'")
assert is_1_n(tail_tail[0], 3, G)
assert is_1_n(tail_tail[0], 2, G)
assert is_1_n(tail_tail[0], 4, G)
assert is_1_n(tail_tail[2], 4, G)
assert not is_1_n(tail_tail[2], 3, G)
def test_select_pair_no_exclusions():
"""Test pair selection without exclusions"""
top = md.load(get_fn('2chains.hoomdxml')).top
pairs = top.select_pairs("name 'tail'", "name 'tail'")
assert pairs.shape[0] == 190
def test_select_pair_with_exclusions():
traj = md.load(get_fn('2chains.hoomdxml'))
pairs = traj.top.select_pairs("name 'tail'", "name 'tail'")
to_delete = find_1_n_exclusions(traj.top, pairs, 3)
pairs = np.delete(pairs, to_delete, axis=0)
assert pairs.shape[0] == 162
def test_find_1_n_exclusions():
top = md.load(get_fn('2chains.hoomdxml')).top
pairs = top.select_pairs("name 'tail'", "name 'tail'")
to_delete = find_1_n_exclusions(top, pairs, 3)
assert to_delete.shape[0] == 28
