def test_head_correction():
dr = 0.05
cutoff = 8
r = np.arange(0, 2.5, dr)
V_prev = mie(r, 1, 1)
V = mie(r, 2, 1)
V[:cutoff] = np.inf
linear_V = head_correction(r, np.copy(V), V_prev, "linear")
assert not np.isnan(linear_V).any() and not np.isinf(linear_V).any()
assert all(linear_V[cutoff:] == V[cutoff:])
exp_V = head_correction(r, np.copy(V), V_prev, "exponential")
assert not np.isnan(exp_V).any() and not np.isinf(exp_V).any()
assert all(exp_V[cutoff:] == V[cutoff:])
assert exp_V[0] > linear_V[0]
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_save_table_potential(self):
pair = Pair("A", "B", potential=mie(r, 1.0, 1.0))
pair.potential_file = tempfile.mkstemp()[1]
pair.save_table_potential(r, dr)
assert os.path.isfile(pair.potential_file)
def test_save_table_potential():
pair = Pair('A', 'B', potential=mie(r, 1.0, 1.0))
pair.potential_file = tempfile.mkstemp()[1]
pair.save_table_potential(r, dr)
assert os.path.isfile(pair.potential_file)
def test_tail_correction():
dr = 0.05
r = np.arange(0, 2.5, dr)
V = mie(r, 1, 1)
smooth_V = tail_correction(r, V, r_switch=2.25)
assert smooth_V[-1] == 0.0
def test_tail_correction():
dr = 0.05
r = np.arange(0, 2.5, dr)
V = mie(r, 1, 1)
smooth_V = tail_correction(r, V, r_switch=2.25)
assert smooth_V[-1] == 0.0