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